Sep 19 2016

Bacteria Evolving Resistance

Researchers at Harvard did a clever thing. They created a giant plate on which to grow bacteria, and included in the plate increasing concentrations of an antibiotic as you moved toward the center. They then plated bacteria on the outer edges and made a time-lapse video of the bacteria growing.

The end result was a video showing the evolution of progressive antibiotic resistance in the bacteria. You can actually see adaptive radiation, as the bacteria push up against the boundary to the next higher concentration of antibiotics, then multiple locations start to spawn new colonies spreading in the next zone.

The researcher made some more nuanced observations as well. For example, the bacterial grow slowed with new mutations, meaning they sacrificed something with the resistance mutation, but then they sped up again as they further evolved. Further, the most resistant bacteria were often not at the leading edge but were stuck behind less resistant bacteria.

The experiment resulted in an excellent visualization of evolution in process. Of course, this one piece of evidence does not “prove” something as complex and far ranging as the evolution of life on Earth. It is, however, a nice demonstration of evolution at work in a limited context.

Enter the Creationists

Creationists are evolution deniers. They deny, to varying degrees, the science of evolution. At the extreme end are those who believe in a recent creation and therefore deny evolution completely. But there are also those at the other end of the spectrum who acknowledge most of evolution but reserve one tiny slice that requires divine intervention. As long as they can demonstrate that there is one aspect of life that unguided evolution cannot explain, then they have proven God or whatever they imagine the “intelligent designer” to be.

Michael Behe occupies this latter end of the spectrum. In his recent book, The Edge of Evolution, he acknowledges common descent, a 4 billion year history of life on Earth. and even mutations and natural selection as the drivers of evolution.

But, he argues, some evolutionary developments were too unlikely to happen by chance and therefore required an intelligent designer to occasionally step in and make specific mutations or combinations of mutations happen by fiat. He is objectively wrong, and has been corrected numerous times by scientists, but that hasn’t stopped him.

Behe is now arguing that the recent Harvard study is not evidence for evolution, but is rather “devolution” because the acquired mutations do not create anything they just “break” existing enzymes.

Behe is wrong because there is no such thing as “devolution.” Evolution is simply heritable change, any change, and that change can create more complexity or more simplicity. Further, altering a protein does not “degrade” it – that notion is based on the false premise that there is a “correct” sequence of amino acids in any particular protein.

Evolution just makes proteins different. Proteins perform “better” or “worse” only in so much that they contribute to the survival and reproduction of the individual. If it is better for the survival of the organism for an enzyme to be slower, then the slower enzyme is better for that organism.

This is just one of the conceptual mistakes that Behe makes. Keep in mind that Behe has a narrative purpose to his motivated reasoning. He wants to arrive at the conclusion that random mutations and natural selection are not capable of creating life as we see it. Something else is required.

Here is his logic (as David Levin deconstructed very nicely here): creating complex structures that serve an adaptive purpose may require multiple simultaneous mutations. The probability of multiple simultaneous mutations is vanishingly small, so small that they are unlikely to occur at any significant rate over the span of life on Earth.

This is basically his irreducible complexity argument. It is wrong for two main reasons. The first is basically the lottery fallacy – considering the odds of John Smith winning the lottery by chance alone and concluding it could not have happened by chance. Rather, you should consider the odds that anyone would win the lottery. This is actually pretty good.

Behe looks at life on Earth and asks – what are the odds that this specific pathway or protein or whatever evolved by chance alone. He is failing to consider that there may have been billions of possible solutions or pathways down which that creature’s ancestors could have evolved. Species that failed to adapt either migrated to an environment in which they could survive, or they went extinct.

In other words, Behe should not be asking what the odds are that this bit of complexity evolved, but rather what are the odds that any complexity evolved. It is difficult to know the number of potential complexities that never evolved – that number may dwarf the odds of any one bit evolving.

Right there Behe’s entire premise is demolished, but he makes further mistakes. In his book he uses as a cornerstone of his argument the evolution of chloroquine resistance in the parasite that causes malaria. His big argument is that such resistance requires the simultaneous occurrence of two mutations. While this is very unlikely, the very short life cycle and great numbers of parasites means that it will happen occasionally by chance. Vertebrates, however, have a much slower life cycle and lower population numbers.

Therefore (and this is basically what the entire book is about) nothing more complex than chloroquine resistance could have evolved through Darwinian processes alone.

Casey Luskin, writing for the propaganda blog Evolution News and Views, proclaims that Behe has been proven right all along because a paper came out showing that chloroquine resistance does indeed require two mutations, although there are two possible forms of the second mutation (so he was only sort-of right). However, this misses the point entirely, as Luskin is famous for doing.

There are at least a couple of ways in which functions that require multiple mutations can occur through random processes. The first is when each mutation provides a small sequential advantage. This is what destroyed Behe’s examples of irreducible complexity, as simpler versions of structures can still function well enough to provide some survival advantage.

There is also the fact, although unrelated (as far as we know) to the current example of chloroquine resistance, that simpler structures could have served another purpose entirely and then were coopted to their current function. Simpler eyes still function as light receptors, and simpler wings could have served as displays, or for gliding or trapping prey.

The second way in which Behe’s logic fails that is directly related to the current example is that evolution involved more than natural selection. There is something called genetic drift – mutations happen and spread throughout populations without any selective pressure being involved at all. In fact, populations of parasites with one of the needed mutations have been identified. Then, within those subpopulations, just one more mutation is needed to confer resistance. This means that Behe was objectively wrong.

Therefore – you can have sequential mutation whenever one mutation confers any advantage, or simply through genetic drift.

There is, of course, also the now iconic example of Lenski’s bacteria that evolved over tens of thousands of generations to metabolize citrate as a food source. This required multiple sequential mutations that occurred by chance in some of the populations.

These are real world examples of multiple mutations occurring resulting in specific adaptive change. They disprove Behe’s thesis.

Conclusion

Evolutionary science is a robust discipline with many scientists around the world doing research and engaging with each other to figure out all the complexities and nuances of what is a very complex process that occurred over billions of years.

Creationists, even those who are trying to be scientifically respectable, like Behe, are simply not engaging with the community. They are making arguments that are logically and factually refuted, but they fail to adapt to valid criticism.

That is because they are not engaged in genuine science, but in motivated reasoning.

 

729 responses so far

729 Responses to “Bacteria Evolving Resistance”

  1. PrestonTon 19 Sep 2016 at 9:50 am

    I hope everyone is ready for the roadshow of cascading denialism so fervently thrust upon our plebeian intellects by ME.
    *grabs popcorn*

  2. bendon 19 Sep 2016 at 11:43 am

    Do you have a link to the Harvard experiment video?

  3. Lukas Xavieron 19 Sep 2016 at 12:00 pm

    This one: https://www.youtube.com/watch?v=plVk4NVIUh8

  4. hardnoseon 19 Sep 2016 at 1:13 pm

    It’s easy to argue against creationists and unscientific people like Behe. It would be much moire difficult to argue against a scientist who has no ideological agenda, such as http://www.thethirdwayofevolution.com/people/view/james-a-shapiro

    He has been studying adaptation in bacteria and has found that they modify their own DNA in response to environmental challenges such as antibiotics. He has been studying what he calls “natural genetic engineering,” the mechanisms cells use to modify their DNA.

    You can’t accuse Shapiro of being a creationist, or of motivated reasoning. He is just reporting the evidence he has found.

    I really wish Steve Novella would stop focusing on the easy targets, and look at what is really going on in evolution science.

    (And I really hope there won’t be another thousand comments with feeble arguments against Shapiro, and others, who are making these observations).

  5. hardnoseon 19 Sep 2016 at 1:17 pm

    And by the way, why does anyone need more proof that bacteria adapt to antibiotics? This video has nothing to do with the controversies about what causes evolution.

  6. SFinksteron 19 Sep 2016 at 1:50 pm

    By Behe’s logic, the glass of water in front of me is impossible. I mean, what are the chances that, of the ~10^80 atoms of hydrogen in the universe, these specific ~16×10^24 atoms of hydrogen all got together in the same place at the same time to form the water that now sits in front of me?

  7. Steven Novellaon 19 Sep 2016 at 2:10 pm

    It is silly to ask why I am not writing about something else. Fallacy of relative privation.
    In any case, I’ll get around to Shapiro. For now, how’s this: https://whyevolutionistrue.wordpress.com/2012/12/02/james-shapiro-gets-evolution-wrong-again/

    “Shapiro still hasn’t provided a credible alternative theory of how adaptive features of an organism arise. “Natural genetic engineering” certainly can’t. And until he provides a credible theory, he will be a voice crying out in the wilderness, thinking himself a paradigm-changer but sounding more like a crank.”

  8. hardnoseon 19 Sep 2016 at 3:02 pm

    “Shapiro still hasn’t provided a credible alternative theory of how adaptive features of an organism arise.”

    It is not necessary to provide an alternative. Shapiro says the current theory is wrong. That is the point. He does not pretend to know more than he knows. He does not try to go beyond the evidence.

    The whyevolutionistrue website is a great resource if you only care about ideology, not science.

  9. Banzai Otison 19 Sep 2016 at 3:07 pm

    Seriously cool video! Would be interesting to see it repeated with other types of gradients. Maybe a decreasing ratio of a food source that the wild type can metabolize to one it can’t? (inspired by Lenski, obviously) Or temperature, acidity, etc.?

    Also, for anyone needing more evidence that a handful of neurologica commenters can’t seem accept that the entire world doesn’t revolve around their pet issues:

    “And by the way, why does anyone need more proof that bacteria adapt to antibiotics? This video has nothing to do with the controversies about what causes evolution.”

  10. Steven Novellaon 19 Sep 2016 at 3:53 pm

    First, Shaprio is making claims for his so-called “natural genetic engineering” – so he is making claims to knowledge that go beyond the evidence. There is no evidence for his proposed alternative.

    Second, he (and you) are simply wrong about natural selection and random mutations There is plenty of evidence that these are sufficient to explain evolutiionary changes. The bottom line is that the recent discoveries about the regulatory functions of DNA is all compatible with natural selection and does not even imply natural genetic engineering, let alone prove it.

    You can keep calling it ideology all you want. It’s just name-calling when you have nothing to back it up.

  11. hammyrexon 19 Sep 2016 at 3:56 pm

    Shapiro mostly gets ignored because his research is still in the 1980s as far as actual evidence. There’s still no actual evidence of directed evolution or teleology – the smoking guns his theory-of-everything desperately needs to differentiate itself from the more mundane conclusions drawn from the actual empirical evidence.

    This is part of why expertise is important. It doesn’t privilege you to evidence, but it does help in understanding when a discovery is and is not actually novel. For someone with no understanding of biology but starts immediately jerking off the moment they hear “information theory” in a body of work, yeah, Shaprio is amazing. But his hypothesis has been a hypothesis for like 25? years now hasn’t really progressed much.

    To be blunt, it doesn’t get discussed much because it’s not necessarily a noteworthy observation that evolutionary theory would create mechanisms that take advantage of… evolution. I.e., having systems that respond to severe environmental stress begin hypermutating to produce more variety is fascinating… and yet not unexpected.

  12. hardnoseon 19 Sep 2016 at 4:20 pm

    [First, Shaprio is making claims for his so-called “natural genetic engineering” – so he is making claims to knowledge that go beyond the evidence. There is no evidence for his proposed alternative.]

    Obviously you have not read Shapiro’s articles. You cannot get unbiased information from a website like whyevolutionistrue.

  13. bachfiendon 19 Sep 2016 at 4:22 pm

    Hardnose,

    Shapiro provides absolutely no support for your opinion that there’s a direction in evolution. That’s there’s an innate tendency towards increasing complexity and intelligence in biological systems. Natural genetic engineering could be 100% correct (it probably isn’t), and provide for an organism’s current needs, but it can’t provide for an organism’s future needs, which would be necessary for there to be a direction in evolution.

    You’re just completely confused. You claim that ‘natural variation within populations and natural selection’ isn’t the ’cause’ of evolution whereas everyone agrees with you – it’s a mechanism of evolution. You’re setting up a straw man argument.

    You completely derailed a previous thread causing it to accumulate over 1,000 comments with multiple comments, often 3 or 4 in sequence, from you.

    You’ve now returned to your claim that since we don’t know everything about evolution, we know nothing about evolution.

    Systems science doesn’t support your worldview. Shapiro doesn’t support your worldview. Just leave it off. Better still, just everyone ignore hardnose in the hope he’ll just go away.

  14. hardnoseon 19 Sep 2016 at 5:44 pm

    bachfiend,

    I will just say it once more and I will not continue repeating the same things hundreds of times like I did before. You won’t ever understand any of this, but I am saying it AGAIN here, at the beginning of this thread, for anyone else who was lucky enough to miss it the first five hundred times.

    Shapiro says that the current status quo theory about the cause of evolution is not true. He provides evidence. That is all I am saying. The theory loved by Dawkins, Coyne, etc., is wrong. All of you who are devoted to that theory, which claims to explain evolution, are devoted to a theory that is wrong. In the opinion of Shapiro and many others, and I happen to agree with them.

    Shapiro does NOT claim to understand the cause of evolution. YOU claim to know the cause of evolution. The whole point of everything I have been wasting my time posting has been to explain that.

    I never said Shapiro’s research supports my personal philosophy, whatever that is. This argument has been about SCIENCE, and about REAL SKEPTICISM.

    So if you still can’t get it, then go on and continue to think you know things that you don’t know, and no one knows, if that makes you happy. But I will not continue trying to reason with an irrational person.

  15. KillCurveon 19 Sep 2016 at 6:09 pm

    Behe’s irreducible complexity argument also ignores the role of gene duplications in allowing genomic sequences to acquire mutations. I’ve seen him in a live debate once, he isn’t even a particularly engaging pseudo-scholar.

  16. bachfiendon 19 Sep 2016 at 8:38 pm

    Hardnose,

    I’ll break my suggestion just once by responding to you again. There’s no doubt about the ’cause’ of evolution. Even Shapiro doesn’t disagree. The argument is about the exact mechanism of evolution.

    The cause of evolution is a changing environment of a population of organisms. The environment includes not just climate, but also other organisms – competitors, predators and prey.

    If the population’s environment changes, and there’s natural variation within the population with some variants better adapted to survive and reproduce, then that population will evolve. Or it will migrate (or rather its range of distribution will shift into regions where the environment is more conducive to survival) or more likely it will go extinct.

    If there’s an argument, then it’s about the mechanism. Natural genetic engineering could be true, and provide new variation upon which natural selection would then work. Your favoured directed mutations, instead of random mutations, could also be true, but impossible to prove. As I’ve noted many times (and you refuse to acknowledge), to test directed mutation you would need to detect all the mutations occurring in real time. And to find that some beneficial mutations occur at a higher than expected frequency. But mutations are detected some time after they’ve occurred. It’s impossible to distinguish between directed mutations with increased frequency of beneficial ones and random mutations and natural selection winnowing out the non-beneficial ones.

    You’re not arguing on the basis of science or evidence. You’re arguing that we don’t know everything, hence we don’t know anything. You’re the illogical one. And a persistent troll.

  17. hardnoseon 19 Sep 2016 at 8:40 pm

    I am not answering the same things AGAIN backfiend. You won’t read the things you are blathering about, so your opinions are worthless.

  18. bachfiendon 19 Sep 2016 at 9:11 pm

    Hardnose,

    I’ve read Shapiro’s book. It’s only 147 pages long and not difficult to understand. I’m not impressed by it. You refuse to read it.

    You’re still very, very, very confused. You don’t know the difference between ’cause’ and ‘mechanism’. The cause of evolution is known. There’s argument about some details of the mechanism. Shapiro may be correct (he probably isn’t). You are definitely 100% wrong. There’s no evidence for direction in evolution or directed mutation.

    Your opinions are completely worthless, so go away and stop trolling on this blog. Go and comment on ‘Evolutionnews’ where your opinions would fit better.

  19. hardnoseon 19 Sep 2016 at 9:26 pm

    You aren’t the boss here, so give up.

  20. bachfiendon 19 Sep 2016 at 10:05 pm

    Hardnose,

    I mightn’t be the boss here, but you’re certainly the resident troll, and a remarkably persistent one with extremely ignorant and stupid opinions. Your opinions are absolutely worthless. You don’t know the definitions of what you are criticising. You’re setting up straw men which don’t actually exist.

  21. steve12on 19 Sep 2016 at 10:53 pm

    Bachfiend:

    I think the funniest part of the Mike Pence / Evolution post debacle was the halfway point at which The Troll’s furious googling revealed the existence of James Shapiro to him (for the first time in his life) and he IMMEDIATELY became a devotee.

    He’s just so transparently full of shit. I don’t even think he believes he’s fooling anyone with this routine.

  22. bachfiendon 19 Sep 2016 at 11:33 pm

    Steve12,

    I was bemused by that too. How he managed to almost seamlessly transition from systems science to natural genetic engineering with a slight detour via epigenetics. And all the time denying that he’d ever claimed that there’s an innate tendency to increasing complexity and intelligence in biological systems, that gorillas are extremely intelligent, that intelligence has no survival value, that humans had stopped evolving a long time before the agricultural revolution and that human brains are unchanged since prehistoric times.

  23. PrestonTon 20 Sep 2016 at 1:47 am

    As far as HN’s much beleaguered point of directionality to evolution, are there any examples of organisms evolving to states of lower intelligence? Can one intuit scenarios where less intelligence would be a beneficial trait for an organism? Conversely, is there any logic to the notion that intelligence per se bestows advantages otherwise not afforded?

    The one I can think of offhand is if there were metabolic constraints of the environment that would preclude a well developed brain, but I’m having trouble thinking about the actual circumstances of such a reality. Maybe something like the movie Pandorum?

  24. bachfiendon 20 Sep 2016 at 3:38 am

    Preston,

    Brains are expensive to build and expensive to run. The human brain for example accounts for 2% of body weight but consumes 20% of body energy at rest (although you shouldn’t restrict yourself to just humans).

    In conditions of plenty, it pays to get rid of brain mass (and intelligence) because the energy required to build a brain and run it are better put into other activities, such as reproducing. Parasites have smaller brains than their free living relatives.

    It’s more of an advantage having larger brains and more intelligence in conditions where resources are scarce. The New Caledonian crow (which is one of the most intelligent birds around with amazing problem solving abilities) lives on an island with few resources.

    Humans aren’t more intelligent than they need to be. They’re only just as intelligent as they need to be. It’s a mistake to assert that humans living in a hunter-gatherer lifestyle have unused intelligence. Having to hunt your food and to know which plants are edible, and which methods of preparation are necessary if they’re toxic, takes a lot of brain power.

  25. hardnoseon 20 Sep 2016 at 9:11 am

    “Having to hunt your food and to know which plants are edible, and which methods of preparation are necessary if they’re toxic, takes a lot of brain power.”

    Yes it sure does. That explains why rabbits are so brilliant.

  26. Steven Novellaon 20 Sep 2016 at 9:22 am

    What was likely a very important factor for humans was that we live in cooperative groups. We use coordinated activity to hunt, for example. We have complex social structures where the ability to communicate and to infer someone else’s mental state is a huge advantage. Then, of course, we also started using tools. Bipedalism freed up our hands to manipulate the environment.

    None of this, of course, applies to rabbits. Offering that as a counter example is very telling.

  27. hammyrexon 20 Sep 2016 at 11:09 am

    If humans are so smart, why we still got rabbits?

  28. Lukas Xavieron 20 Sep 2016 at 12:31 pm

    On the subject of rabbits vs. humans, there are several points that impact on intelligence. For example, variety of diet. If you stick to a small selection of foodstuffs, you don’t need that much intelligence. You learn the few types that are good and stick to them. The more omnivorous a species is, the more benefit they gain from being able to recognize specific foods.

    Also, there’s litter size and generation time. The fewer children you have and the more time you invest in them, the more important it becomes to avoid poisoning them. On the other hand, losing a single rabbit from a litter is a negligible cost, whereas the cost of growing a larger brain is higher (since it would lengthen gestation and reduce litter size).

    For a rabbit, the cost of growing the brain would be high, whereas the benefit gained would be minor. A group of smart rabbits would likely end up out-bred by their dumber cousins. The opposite is true of humans.

  29. hardnoseon 20 Sep 2016 at 12:34 pm

    “What was likely a very important factor for humans was that we live in cooperative groups. We use coordinated activity to hunt, for example. We have complex social structures where the ability to communicate and to infer someone else’s mental state is a huge advantage.”

    There are many other cooperative hunting species, such as wolves. They can’t use weapons, but obviously their hunting is a complex social activity and requires communication.

    You seem to be unaware that living in cooperative groups is extremely common throughout nature. Of course, people who know nothing about other species assume that humans invented social living.

  30. Lukas Xavieron 20 Sep 2016 at 12:46 pm

    @hardnose
    I’m not sure what point you think you’re making. Wolves are, after all, rather intelligent creatures. It seems to me that your example is reinforcing Steven’s point, not refuting it.

  31. Steven Novellaon 20 Sep 2016 at 12:56 pm

    HN – As Lukas said, I fully expected you to make that very point, because it is the easy place to go to if you are engaged in motivated reasoning. The gratuitous and silly dig is also classic HN.

    As Lukas said, cooperative predators tend to be very smart. Birds that live in environments with scarce food resources develop incredible problem solving skills. Other social animals, like other primates, are also very smart.

    Our ancestors had a lifestyle that hit most of the factors that contribute to intelligence – social group, cooperative hunting, omnivores, scarce resources, and then tool use and language.

    Factors that would benefit from greater intelligence are associated with higher intelligence. You don’t have a point to make.

  32. steve12on 20 Sep 2016 at 1:30 pm

    Is this an actual discussion about whether selection pressures have an effect on the phenotypes of living things? Really?

    The idea that traits “progress” in a given “direction” even if selection pressures are pushing them the other way is so breathtakingly stupid that one doesn’t know how to react.

  33. hardnoseon 20 Sep 2016 at 3:50 pm

    Random mutations and natural selection does not account for the intelligence seen throughout nature, even in “simple” organisms like bacteria. That is what recent evolution research has been showing, as explained by James Shapiro.

    Science is going beyond the simplistic theory that claims to explain how and why life evolved. Dawkins, Coyne, “skeptics” at this blog, are clinging to obsolete ideas.

  34. steve12on 20 Sep 2016 at 4:03 pm

    So the evidence for the theory that Dr. The Troll has been proffering for several years HE just found out about a few weeks ago. That’s nice.

    And now he thinks it’s the New Paradigm of biology.

    Can’t make this shit up.

  35. bachfiendon 20 Sep 2016 at 4:36 pm

    We should stop trying to educate the Troll. He still doesn’t get the point that ‘random mutations and natural selection’ aren’t the ’cause’ of evolution, or anything in evolution – such as intelligence. It’s just a mechanism.

    When he demonstrates that he’s learnt the difference between ’cause’ and ‘mechanism’, then we ought to respond to him again.

    It’s a mistake to think that intelligence has no survival value, a mistake made by no less than Alfred Wallace, who thought that hunter gatherers such as the Australian Aborigine were too intelligent for their lifestyle – that their brains were too large.

    And I think of the Burke and Wills expedition which attempted to cross the Australian continent from south to north in around 1860 and on their return starved to death on Coopers Creek despite the local Aborigines attempting to help them and being chased off for their pains (one member of their party accepted their help, survived and was later found by a search party).

    They starved in the midst of plenty. The Aborigines had a rich source of plant foods available, many of which had to be prepared – such as ground into flour, soaked in water and baked – because they’re very toxic raw. Knowing which foods are available and how they need to be prepared takes a lot of intelligence.

  36. BillyJoe7on 20 Sep 2016 at 5:21 pm

    “And now he thinks it’s the New Paradigm of biology”

    …before he has even read the book!
    (Then again most christians have never read the bible either)

  37. BillyJoe7on 20 Sep 2016 at 5:30 pm

    …and notice how he went back on automatic with his “random mutation and natural selection is not the cause of evolution” after he got absolutely slaughtered over his comparison of rabbits to humans.

  38. hardnoseon 20 Sep 2016 at 5:41 pm

    Rabbits know what plants to eat, as do other herbivores, without having brains capable of advanced mathematics. Human intelligence did not evolve so that we could figure out what plants to eat.

  39. hardnoseon 20 Sep 2016 at 5:42 pm

    “He still doesn’t get the point that ‘random mutations and natural selection’ aren’t the ’cause’ of evolution, or anything in evolution – such as intelligence. It’s just a mechanism.”

    You don’t know what the word “cause” means.

  40. Bill Openthalton 20 Sep 2016 at 6:33 pm

    hardnose —
    Rabbits don’t have the complex, long-lasting societies humans have. Human consciousness and language (awareness of one’s internal state and the protocol to exchange that information with other humans) are necessary for the long-term cooperation humans exhibit. Humans also developed ways to record language, because better working societies are evolutionary advantageous for its members, and record-keeping allows for better planning and cooperation.

  41. RickKon 20 Sep 2016 at 6:42 pm

    Guys, please don’t let’s not do this again. We are at 40 comments, spinning the same exasperating circles that will just take us to another string of 1000 pointless posts.

    Bach said “We should stop trying to educate the Troll”. Yes! Bach, in all those years where you almost single-handedly kept Comments alive on Egnorsnce, did you ever once feel you made progress educating Egnor? There is really no point to this. If you crush every point hardnose puts forward, he’ll just change the topic. It’s the contrarianism that motivates him, not the consistency or integrity of his views.

    It just pains me to see us all give him exactly what he wants.

  42. hardnoseon 20 Sep 2016 at 7:09 pm

    “Rabbits don’t have the complex, long-lasting societies humans have. Human consciousness and language (awareness of one’s internal state and the protocol to exchange that information with other humans) are necessary for the long-term cooperation humans exhibit. Humans also developed ways to record language, because better working societies are evolutionary advantageous for its members, and record-keeping allows for better planning and cooperation.”

    The Homo Sapiens brain had already evolved long before written language, and long before human society became complex. Primitive hunter/gatherers were/are just as intelligent as we are.

    The complexity of human society and technology came along AFTER the human brain had evolved.

  43. hardnoseon 20 Sep 2016 at 7:10 pm

    What bachfiend lacks in knowledge he makes up for with extreme stubbornness and dogmatism.

  44. bachfiendon 20 Sep 2016 at 7:24 pm

    Hardnose appears to have adopted the tactics of Michael Egnor. When he doesn’t have facts and logic on his side he resorts to insults.

    I wonder whether it’s true that modern humans are becoming less intelligent than their hunter gatherer ancestors, as is often claimed, with the crutch provided by modern technology? Written language and the Internet allowing us not to have to reason, instead being able to find predigested facts, often selected to fit our preconceptions.

    I’m beginning to not only think that it’s true, but also that hardnose is its perfect demonstration.

  45. mumadaddon 20 Sep 2016 at 7:40 pm

    RickK: “Guys, please don’t let’s not do this again.”

    We should all wear virtual tee shirts with the slogan ‘Je suis Arnold.’

    #solidarity

    😀

  46. mumadaddon 20 Sep 2016 at 7:43 pm

    Ps that was not sarcasm directed at rick (on case it came off that way), but agreement. Hn is an attention whore, don’t let’s keep being his John.

  47. arnieon 20 Sep 2016 at 8:30 pm

    By golly, I think I finally detect progress toward letting HN Troll and his nonsense die on the vine by ignoring him (after a rational response or two when he first “enters” a string) rather than compulsively and fruitlessly feeding him almost endlessly. I’m encouraged. And I am not knocking the quality of what you guys are writing. It has often been educational for me. But it also often becomes quickly counterproductive shortly after HN enters the conversation.

  48. arnieon 20 Sep 2016 at 8:35 pm

    BTW, our hosts frequently sets an excellent example on how to respond to HN a time or two or three with science based responses exposing HN’s nonsense followed by simply responding no more, i.e., not continuing participating in the feeding-the-troll phase of the string.

  49. arnieon 20 Sep 2016 at 8:36 pm

    I meant “host”, singular, not plural

  50. hardnoseon 20 Sep 2016 at 8:47 pm

    But none of you ever provide scientific evidence for your Dawkinism. It just has to be true because … because … it’s simple and it explains everything.

    Natural genetic engineering is a fact, not a theory someone dreamed up.

  51. PrestonTon 20 Sep 2016 at 9:38 pm

    bachfiend,

    I appreciate your comment. It doesn’t quite answer what I’m trying to understand– let me try again to ask:

    Do you imagine a circumstance where once a certain level of intelligence is reached that less intelligence would be selected for by the environment to the degree that those less intelligent individuals are more fit?

    I understand that the definition of intelligence applied is key to the question. For example, say two groups diverge significantly enough genetically as to be different species, one developing a more social/emotional intelligence while another adapts a more logical/rational tendencies (assuming those could somehow adapt independently at the level of the brain).

    I understand the rabbit example, but I’m specifically asking about what one may refer to as ‘de’evolution (although I recognize that’s a meaningless term and begs the question).

    The simplest way I can think to ask: could humans evolve to be less intelligent?

  52. chikoppion 20 Sep 2016 at 9:50 pm

    Heh!

    😉

  53. chikoppion 20 Sep 2016 at 10:07 pm

    I think the question of selection for less sophisticated intelligence would be difficult to answer.

    The historical data we have on species is morphological, genetetic, and geographic. To assess intelligence we’d need behavioral data. We could look at cranial size, but that’s not a measure of intellect (human brains have shrunk to a degree).

    There are cases of species losing sense organs, such as eyeless fish. I would assume the loss of a sense would correspond to a degradation or loss of the associated brain function. That’s not the same as a measure of intelligence, but it would be an example of reduced brain capability due to selection.

    Could humans evolve to be less intelligent? We may have a better handle on that question following the upcoming Presidential debate.

  54. steve12on 21 Sep 2016 at 12:06 am

    Preston:

    “The simplest way I can think to ask: could humans evolve to be less intelligent?”

    Yes. There’s theoretically almost an infinite number of ways this could happen across many different facets of intelligence. I think it’s highly unlikely, however, that we could become MUCH less intelligent because the ability to abstract the world in such a way that it can be novelly recombined and simulated is incredibly powerful. This ability (et al. obviously) is so powerful and flexible / adaptive that it’s difficult to think of a selection pressure selecting against it. But not impossible.

    Most scenarios that I can think of would likely involve some non-selection mechanisms acting first, like drift, following some cataclysm:

    http://evolution.berkeley.edu/evolibrary/article/bottlenecks_01

    The easiest possibility is that the allele frequency left-over by chance renders the average in the population less intelligent than before the event.

    Now, however a further dumbing is even easier. The lowered genetic diversity can make the population less robust in adapting to new conditions, like maybe the ones that created the cataclysm in the first place. In this case, some specialized adaptation may be more important than intelligence, and could be preserved even if it means the population as a whole gets dumber.

    Imagine a scenario as Bachfiend conjured above, where high quality food (especially protein) is scarce. Low quality food is relatively easy to get, requiring no special skills like hunting. Now imagine a mutation that somehow reduces brain size (makes the brain develop slower, work slower but metabolically more efficiently, whatever). This individual has more energy, is more robust, and out-competes for mates. The easy to get lo- quality food actually suits him better! He’s not a LOT dumber than his contemporaries, but the energy he’s saving offsets this.

    This variant spreads through the population, which is small enough now that the mean of the population gets pulled further into Dumbland, and fairly quickly (evolutionarily anyway).

  55. bachfiendon 21 Sep 2016 at 1:58 am

    Preston,

    The only way I could imagine humans evolving to be less intelligent would be if society developed so that there was no struggle for survival. If everyone had android servants and androids did all the work necessary. And if selection for partners shifted towards the less intelligent as being the desired partners (although, it should be noted that intelligence isn’t entirely genetic – it’s more like 50% nature, 50% nurture). Something along the lines of the Eloi and the Morlocks in HG Wells’ novel ‘the Time Machine’.

    The only reasonable example I can think of intelligence being selected against is in parasites, and it’s not actually intelligence that’s being selected against, it’s actually selection for individuals which genetically put more resources into reproducing rather than developing a larger CNS.

    The point is that the less intelligent may turn out to be (reproductively) more fit if they have more offspring which manage to survive to reproductive age and which then proceed to have more offspring themselves. Which would happen only in states of plenty with no competitors, a very unusual state of conditions.

  56. Bill Openthalton 21 Sep 2016 at 4:36 am

    bachfiend —
    The real problem is that it’s hard to measure the average intelligence of a species. It’s already neigh impossible to gauge and compare the intelligence of two individuals — is someone with a PhD in mathematics but who cannot iron his shirts more or less intelligent than a goldsmith?
    Intelligence, consciousness, empathy etc. are words that describe behaviours. There is no absolute scale of intelligence where, for example, understanding the basic theorem of calculus ranks higher than being able to change a tap. And by the time we no longer do calculus or replace taps, we’re certainly not going to worry about being less intelligent than our ancestors 🙂 .

  57. bachfiendon 21 Sep 2016 at 5:54 am

    Bill,

    I completely agree, which is why I referred in previous comments to the intelligence of parasites. And of birds. I recently read a book ‘the Intelligence of Bees’ (actually in German ‘die Intelligenz der Bienen’ by Randolf Menzel) which discusses how intelligent honey bees are.

    I’d personally define intelligence as being the ability to form a useful mental model of the external world and to be able to react meaningfully to it bringing benefit to the organism. Being able to perform calculus shouldn’t be a defining feature of intelligence – or at least I hope it shouldn’t be; I did calculus to the final year of high school achieving a distinction pass, but then realised after 6 months university that I’d forgotten all of it.

  58. Bill Openthalton 21 Sep 2016 at 6:08 am

    bachfiend —
    Hab’s auch gelesen — ausgezeichnet.

  59. BillyJoe7on 21 Sep 2016 at 7:43 am

    “Hab’s auch gelesen — ausgezeichnet.”

    I don’t know any German but it’s similar to Dutch, of which I can read a smattering.
    I’m guessing the translation is: Have you also read it – ?

    (Dutch translation: heb je ook gelezen)

  60. bachfiendon 21 Sep 2016 at 7:56 am

    BillyJoe,

    Actually it’s short for ‘ich habe es auch gelesen’ meaning ‘I’ve also read it’.

  61. BillyJoe7on 21 Sep 2016 at 8:03 am

    ah, yes…Ik heb het ook gelezen

  62. Bill Openthalton 21 Sep 2016 at 8:42 am

    BillyJoe7 —
    Een Australiër die Nederlands kent? What’s going on Down Under?

  63. steve12on 21 Sep 2016 at 9:13 am

    “The real problem is that it’s hard to measure the average intelligence of a species”

    I should have specified in my example above that I was avoiding this issue and treating “intelligence” as a monlithic trait (like g). I don’t agree that it should be, but some level of simplification was required in order to work out an idealized example to answer Preston’s question.

  64. Steven Novellaon 21 Sep 2016 at 9:18 am

    For the record, Lenski’s experiments alone provide compelling evidence for both random mutations and natural selection. He followed colonies for tens of thousands of generations, saved them, and then re-ran older generations forward again to see what happens. Seriously – it is worth fully absorbing his experiments and their implications.

  65. PrestonTon 21 Sep 2016 at 10:07 am

    Interesting conversation, thanks guys! I must admit that when I graduated in bioengineering I had ideas similar to HN insofar as I believed there was a directionality in evolution as it relates to intelligence. It actually wasn’t until I starting listening to the SGU a few years ago that I started to understand just how tricky it is to divorce what seems to be or what ought to be from what is.

    Cheers everyone

    – P

  66. Bill Openthalton 21 Sep 2016 at 11:07 am

    PrestonT —

    I must admit that when I graduated in bioengineering I had ideas similar to HN insofar as I believed there was a directionality in evolution as it relates to intelligence.

    Was that despite the education, or because of the education?

  67. hardnoseon 21 Sep 2016 at 12:51 pm

    “Lenski’s experiments alone provide compelling evidence for both random mutations and natural selection.”

    The experiments provide evidence for natural selection — but natural selection is an obvious fact that does not need more evidence. How do you think these experiments showed that the mutations were random?

  68. BillyJoe7on 21 Sep 2016 at 5:21 pm

    Bill: “Een Australiër die Nederlands kent? What’s going on Down Under?”

    My family migrated to Australia from the Netherlands when I was two years of age.
    (Lots of flies here but none as bad as the one buzzing just over my head 😉 )

  69. RCon 21 Sep 2016 at 5:30 pm

    “The only way I could imagine humans evolving to be less intelligent would be if society developed so that there was no struggle for survival.”

    There hasn’t been any real struggle for survival for humanity as a species for quite a while.

    I think people are way overthinking this question – there’s a pretty clear trend towards people with higher education levels reproducing at a lower rate than those of lower education levels.

    If there’s a correlation between general intelligence and education level (which I suspect there is) – then we’re already evolving to be less intelligence

  70. bachfiendon 21 Sep 2016 at 6:49 pm

    RC,

    I think you’re going down the fallacious track popularised by Nicholas Wade in ‘a Troublesome Inheritance’. Intelligence, however it’s defined, is probably around 50% nature and 50% nurture. Of the 50% that’s nature (genetic if you like), intelligence depends on many genes of small effect, not as single genes of either dominant or recessive effect.

    So, a very intelligent (or very unintelligent parent) doesn’t have children who are very intelligent (or very unintelligent) or just of average intelligence. They tend to have children of intermediate intelligence. They illustrate ‘the regression to the mean’.

    The relationship between intelligence, education level and number of children is also tenuous. In developing countries, the easiest way of decreasing the birth rate is to educate the women.

    I wouldn’t agree that there’s no struggle for existence within humanity. Even in rich developed countries, there are people who are doing it tough. In this morning’s edition of the Age I read an interesting article by the economics editor referring to a study in which people are asked to imagine having to find $3000 for an emergency, and then doing an IQ test. The poor who struggle from day to day financially suffered a 13 point drop in IQ on average. The rich, who don’t have day to day financial worries, showed no drop in IQ scores on average.

  71. Bill Openthalton 21 Sep 2016 at 7:03 pm

    RC —
    I would be amazed if there is a strong correlation between intelligence (whatever that is) and education level. The correlation would be between certain aptitudes and the education level one attains. Depending on the circumstances, specific aptitudes are more or less useful (e.g. mental arithmetic, a skill and aptitude that’s no longer contributing to academic success).
    In any case, it’s living in a complex society that determines brain power, and our societies continue to become larger and more complex. Specific aptitudes are mere side-effects of humanity’s social skills.

  72. Bill Openthalton 21 Sep 2016 at 7:07 pm

    bachfiend —
    That only proves humans don’t perform well when stressed, and that people have different stress triggers. It also proves IQ tests don’t measure intelligence. But we already knew that.

  73. Steven Novellaon 21 Sep 2016 at 7:14 pm

    HN – they had multiple colonies of the same strain of bacteria. The needed mutations for citrate metabolism occurred in some lines but not others, and after different numbers of generations, and when they went back to older generations and ran them again, different things happened. Mutations occurred at random over time and in different lines, including running the same lines again. Mutations occurred at random, and at a rate that matched random chance.

  74. hardnoseon 21 Sep 2016 at 8:53 pm

    “Mutations occurred at random over time and in different lines, including running the same lines again. Mutations occurred at random, and at a rate that matched random chance.”

    It doesn’t say that in the article you linked.

  75. bachfiendon 21 Sep 2016 at 9:12 pm

    Steve,

    I’m not actually certain that that’s true about the citrate metabolism. It’s been argued that it was an artefact of the subculturing method. If E. coli are given more time before subculturing, then apparently they regularly show the ability to metabolise citrate. It seems to have more to do with the length of time necessary to turn on genes instead of the length of time necessary to generate new mutations within genes.

    Meaning that mutations within genes resulting in beneficial changes within the gene products are actually rare, which would be an argument against directed mutations, which should have resulted in multiple and early beneficial changes. And that the main genetic alteration in evolution are changes, mutations in some perhaps most cases, in the regulatory portions of the genome determining when and where genes are activated producing gene products.

  76. bachfiendon 21 Sep 2016 at 9:29 pm

    Hardnose,

    ‘It doesn’t say that in the article you linked’.

    Where exactly did Steven Novella link to an article on the Lenski et al experiment. You’re not making stuff up, are you? But anyway. Lenski’s results provide absolutely no evidence for directed mutations with natural genetic engineering. If you were keeping score, on the basis of the Lenski experiment, it would be ‘random mutations’, with selection 1, ‘directed mutations’ 0.

    I’ve broken my rule about not responding to you, yet again, but I don’t count laughing at you as responding.

  77. hardnoseon 21 Sep 2016 at 9:36 pm

    “Where exactly did Steven Novella link to an article on the Lenski et al experiment.”

    In the first line of this post.

    “Lenski’s results provide absolutely no evidence for directed mutations with natural genetic engineering.”

    Steve N just said the research showed the beneficial mutations were random.

  78. RCon 21 Sep 2016 at 10:00 pm

    Hardnose’s above post is a perfect example of why honest conversation with him is impossible.

    The two statements:

    “…provide absolutely evidence for directed…”

    and

    “… the research showed the beneficial mutations were random”

    are nowhere even close to the same thing.

    He either doesn’t understand basic logical language constructs, or he’s deliberately being dishonest and obtuse.

  79. hardnoseon 21 Sep 2016 at 10:22 pm

    bachfiend said there was no evidence for directed mutations. That is very different from what Steve N said, that the evidence showed the mutations were random.

    I was showing that backfiend and Steve N are saying different things about the same research.

    At least from reading that article, it did not seem like they were even looking at whether the mutations were random or not.

  80. bachfiendon 21 Sep 2016 at 10:55 pm

    RC,

    You’ve stolen my thunder. I just spent 10′ on a PC trying to find whether Steve Novella had ever linked to an article on the Lenski experiment providing absolutely no evidence for directed mutations (I wondered whether there might not have been some artefact of iPads causing links not be be displayed).

    But no – I’d actually made the comment, not Steve. And it was my opinion anyway – Lenski’s experiment showed that beneficial mutations in E. coli are actually rare, consistent with them being random and mostly non-beneficial. And not consistent with mutations being directed and beneficial, which is the same as saying that Lenski’s results provide absolutely no evidence of directed mutations.

    And as I’ve often pointed out to hardnose (and he persistently refuses to admit, so I no longer point it out to him), it’s impossible on practical grounds to show that some mutations might be directed, that they might be beneficial, that they might occur at a higher frequency than chance, unless it’s possible to detect all the mutations occurring in real time, and finding that some mutations occur at a higher frequency than other ones, and that these mutations later cause some benefit (because obviously benefit is only proved with the elapse of time).

    It’s impossible to distinguish between directed non-random beneficial mutations from non-directed random mutations with natural selection winnowing out the more frequent non-beneficial ones. But Lenski’s results provide no evidence that if directed non-random beneficial mutations occur that they’re any more frequent than rare and almost a miracle. Not significant if they happen.

    Hardnose is either dishonest or delusional. On second thoughts, I agree with you. Humans are becoming less intelligent, and people like hardnose are pulling down the average. They would not have survived in less civilised times, and would have been culled by natural selection.

  81. BillyJoe7on 22 Sep 2016 at 6:34 am

    Swatting the fly:

    “By 1968, Operation Hardnose was being marginalized by use of other intelligence systems, such as air- and ground-based electronic sensors. Also, with the advent of the AC-130 Spectre gunship, which both generated its own targets as well as struck them, there was little use for Hardnose spotting enemy vehicles. Hardnose faded into insignificance after that”

  82. Steven Novellaon 22 Sep 2016 at 9:07 am

    The Lenski study did not specifically conclude that mutations are random, because that was not the point of the study, but it is clearly in the data. The “beneficial” mutations were rare and random. Most strains did not develop them, and the strains that did developed them unpredictably.

    There was no evidence in that vast data of directed or non-random mutations.

    There is other evidence that mutations are essentially random. Although, to be clear, they are not mathematically random, they are chaotic. There are hotspots (likely as a consequence of DNA repair), and there are environmental influences on the rate of mutations. So when and where the mutations occur are not truly random but are constrained and influenced by internal and external factors. However, which mutations occur and their effects appear to be completely random, and that is what we mean.

    The Lenski experiments support this. Mutational effects are random, not directed or predictable.

  83. hardnoseon 22 Sep 2016 at 10:02 am

    Right, it was not the point of the study to see if beneficial mutations are random, and your conclusion that they are random is philosophical, not scientific.

    Shapiro claims that there is conclusive evidence for natural genetic engineering, and he is an expert in the evolution of bacterial resistance.

    If you only read about Shapiro’s research at the whyevolutionistrue website, you will have no idea what he actually says.

  84. PrestonTon 22 Sep 2016 at 10:20 am

    @Bill O,
    I took several courses on evolutionary biology, but to my memory directionality was never discussed. Generally though, in my experience, engineering is an interesting interplay between using science to discover what is true and manipulating that to mold the world into what ought to be– there’s a certain reality distortion field that makes that possible, so I’ve always allowed for a certain flexibility in my thinking that I’ve further honed from over time with stuff like the SGU.

    What I’m still trying to square in this discussion is SN’s point: “… Mutational effects are random, not directed or predictable.” (which is obvious to me), and thinkers like David Christian: https://www.ted.com/talks/david_christian_big_history?language=en
    where central to his thesis is the argument that the universe has evolved from the simple to the more complex, and the more complex something becomes the more stringent the conditions to maintain that complexity (i.e. ‘goldilocks conditions’ for life, metabolic necessities of a brain).

    The other thought dovetailing with David Christian’s point are the admittedly out there arguments that the universe is ‘programmable’ (https://en.wikipedia.org/wiki/Programming_the_Universe), that entropy acts on ‘bits’ of the universe the way a processor executes binary, processing itself to higher states of entropy and chaos, and from those states of chaos comes the complex order we observe in natural phenomena (https://en.wikipedia.org/wiki/Fractal). Big Bang–> pure energy –> leptons/quarks–> atoms –> [gravity] –> stars –> iron –> rocky planets –> liquids –> molecules –> templates for molecules (RNA/DNA) = long term response to environment –> cell + metabolism –> asexual reproduction –> sexual reproduction –> nerve nets = short term response to environment –> ganglia –> brains –> social structures (packs, prides, herds) –> tools –> language –> writing –> etc, each layer building complexity on the last.

    Yada yada yada all aboard the woo woo train. However many reaches of logic you just read there I think underpins a general idea that many people (including HN and at times myself) perceive something of a higher order going on, something that is hard to see from the vantage point of our consciousness. To analogize, maybe in our understanding of biology we’re at the point of Newtonian mechanics and kinematics of motion which are accurate in most cases, but the page long equations of general relativity open the kimono of the universe a bit more and represent a higher order of understanding that we have yet to achieve in our other projects.

  85. PrestonTon 22 Sep 2016 at 10:23 am

    ^^ by ‘molecules’ I meant complex organics

  86. Bill Openthalton 22 Sep 2016 at 11:07 am

    PrestonT —
    We do indeed seem to be in the presence of stuff that’s eager to combine. If it wasn’t the case, we wouldn’t be able to make that observation. As for entropy acting on ‘bits’ of the universe, in thermodynamics, entropy is a measure of the disorder in a system, thus it cannot act on anything, let alone process itself. Fractals are a mathematical concept that can be used to model irregular natural objects, but that doesn’t mean the natural object is produced by a process that has anything in common with the modeling process.

    The problem with Lloyd’s analogy “the universe is a quantum computer” is that it introduces an idea of purpose — if the universe is a computer, someone must have built it. This type of view is expected from a professor of mechanical engineering (which is all about building things for a purpose).

    Your progression uses a human-centered definition of “complex”. There is no reason to assume that sexual reproduction is more complex than star formation, unless you assume humans to be the pinnacle of complexity.

    Our understanding of the world is shaped by what we are, a gregarious ape that has discovered how to build societies more complex than those of ants and termites. One of the things we do is to try and find a nicely structured story to explain what we observe. We see agency and purpose where there is none. This might have a social value, but it skews or perception of the natural world.

  87. Bill Openthalton 22 Sep 2016 at 11:09 am

    … skews OUR perception …

  88. hardnoseon 22 Sep 2016 at 11:12 am

    “However many reaches of logic you just read there I think underpins a general idea that many people (including HN and at times myself) perceive something of a higher order going on, something that is hard to see from the vantage point of our consciousness. To analogize, maybe in our understanding of biology we’re at the point of Newtonian mechanics and kinematics of motion which are accurate in most cases, but the page long equations of general relativity open the kimono of the universe a bit more and represent a higher order of understanding that we have yet to achieve in our other projects.”

    Yes, many of us are thinking that.

  89. PrestonTon 22 Sep 2016 at 1:04 pm

    @Bill O
    “The problem with Lloyd’s analogy “the universe is a quantum computer” is that it introduces an idea of purpose — if the universe is a computer, someone must have built it.”

    I can’t speak for Lloyd, but I don’t perceive that idea as imparting some purpose to the universe itself, merely just a description of the directionality of time and its effect on observable matter measured in entropy.

    “Your progression uses a human-centered definition of “complex”. There is no reason to assume that sexual reproduction is more complex than star formation, unless you assume humans to be the pinnacle of complexity.”

    Forgive my self-serving steel manning a bit here, but I think it’s a reasonable statement that the human brain is the most complex formation that we know of in the universe by any reasonable interpretation of complexity I’ve implied. Sure, stars have more mass and by that very fact have certain ‘complexity’ that makes them difficult to model deterministically at the micro level (perhaps like the waves of the ocean); however, reactions are more homogenized throughout, and the system is able to be modeled stochastically without losing the ethos of our understanding of it. There are fewer dependencies in the system and the conditions needed for something called a star to form are simpler– a lot of atoms near in each other (in relative terms), where many of them are hydrogen. On the other hand, the conditions required to spawn and support a brain seem exponentially more complex, as does the system itself.

    In more absolute terms, life couldn’t exist before stars because the elements needed to form the organic molecules upon which life is scaffolded couldn’t exist before supernovae. Life itself does appear to have some notion of directionality, albeit a meandering one, and that directionality is dependent on a narrowing set of constraints– temperature, radiation, metabolic necessities, etc. So while random mutation and natural selection form the engine of evolution, there does appear to be a road, and the road appears to generally go somewhere. I don’t mean this as implication of purpose or deity, and I’m not saying life couldn’t or doesn’t backtrack like Sisyphus and his boulder, but “life finds a way” and that way seems to favor brains at the physical level and increasing levels of consciousness/real-time decision making at the meta level.

    Thoughts?

  90. chikoppion 22 Sep 2016 at 1:09 pm

    [hardnose] Right, it was not the point of the study to see if beneficial mutations are random, and your conclusion that they are random is philosophical, not scientific.

    Shapiro claims that there is conclusive evidence for natural genetic engineering, and he is an expert in the evolution of bacterial resistance.

    NGE is a suite of mechanisms. Those mechanisms still produce genomic and phenotypic variability. Shapiro clearly states that it is the role of selection to determine which, if any, of the outcomes of NGE variation produced will be beneficial, adopted, or propagated.

    Random Mutations (variability) + Selection = Evolution

    [Shapiro] “In terms of generating completely novel genome components, such as exons, introns and regulatory sites, the NGE examples described in Sections 2, 3 and 4 provide rapid means of producing innovations, which can be tested immediately by selection for adaptive utility. If they provide adaptive added value, they will be retained, amplified and dispersed by further cell fusion and NGE activities, as we have seen in Sections 2 and 4. If the novelties are not beneficial, they will be lost or maintained in an unselected fashion.”

    Beneficial or not beneficial as determined by selection.

  91. chikoppion 22 Sep 2016 at 1:15 pm

    [PrestonT] So while random mutation and natural selection form the engine of evolution, there does appear to be a road, and the road appears to generally go somewhere.

    What would it look like if the ‘road’ didn’t appear to go somewhere?

  92. hardnoseon 22 Sep 2016 at 1:31 pm

    “Shapiro clearly states that it is the role of selection to determine which, if any, of the outcomes of NGE variation produced will be beneficial, adopted, or propagated.”

    Obviously you never read any of the hundreds of comments where I corrected your misunderstanding.

    Natural selection is not being questioned. Shapiro, and any scientific person, knows that natural selection obviously happens.

    What you can’t seem to get is that, according to Shapiro’s research, natural selection is NOT THE CAUSE of evolution. Shapiro explicitly says this.

    NGE generates variations. There is no guarantee that everything NGE generates will be beneficial. This is not a magic process. But it is NOT random and purposeless either.

    If you don’t read what Shapiro wrote, instead of some misleading misinterpretation on a Dawkinist website, it makes no sense for you to criticize his ideas.

  93. PrestonTon 22 Sep 2016 at 2:18 pm

    @chikoppi,

    Interesting question. For clarity, I’m using ‘road’ metaphorically and not with the implication of purpose. I guess the simplest answer (although a cop-out) is that consciousness wouldn’t have formed to ask that question.

    Maybe another way to look at is the increasing ability of an organism to add layers of abstraction onto its model of the environment in the service of real-time decision making. Based on those models, the ability to intuit the future with some accuracy in a given time frame bestows benefits general and powerful enough as to preserve that feature indefinitely, regardless of the metabolic disadvantages that may come with it. The environment then selects for continual improvements to these traits, such as the formation of the pre-frontal cortex. Major environmental changes and extinction events may set that progression back, but the suggestion here is that the push will always be in that direction. In due time the environment, so long as those defining narrow conditions of temperature and radiation return, will again select for these features.

    Directionality in HN’s explanation is an obvious overreach because it ascribes agency where there is none. Conversely, claiming no directionality whatsoever seems to contradict what we observe in our own evolution and would seem to preclude intelligent life existing elsewhere, whose existence seems to rest on the same principles of the evolution of life towards general intelligence.

    Seems like a parallel to our own specie’s quest to create an AGI. Hard, not impossible, only a matter of time, provided we don’t nuke ourselves first.

  94. PrestonTon 22 Sep 2016 at 2:37 pm

    @chikoppi,

    Just realized I rambled but didn’t answer your question.

    “What would it look like if the ‘road’ didn’t appear to go somewhere?”

    Refactoring: What would we observe if there wasn’t any directionality to the evolution of intelligence?

    As far as I know, Cnideria is the first to evolve simple nerve nets, the advantage being it could respond to immediate changes in the environment, as opposed to waiting for the very slow genetic changes that don’t benefit the survival of the individual. Move towards good things and away from bad things, and make that decision as instantly as a transistor gate on a processor = a generally good thing.

    Zoom in on that trait– the ability to respond to immediate changes in the environment continues to increase in sophistication over time and corresponds to a more complex nervous system.

    So I guess what you wouldn’t see is that: you wouldn’t see a progression of sophistication in the responses of organisms to environmental stimuli. Nerve nets would have been a sufficient enough adaptation, and more complex structures would have been selected against because of the metabolic necessities and whatever else.

    Life evolves into environmental niches– extremophiles exist in thermal vents where other things can’t, but when you look at relatively temperate environments, the ability to sustain complexity is higher. As long as that ability is present, life evolves to fill them, and increasing intelligence is generally selected for in these environments.

    That was my attempt to answer your question, although you asked the trillion dollar question so I’m sure I’m missing something.

  95. RCon 22 Sep 2016 at 2:37 pm

    “NGE generates variations. There is no guarantee that everything NGE generates will be beneficial. This is not a magic process. But it is NOT random and purposeless either.”

    How exactly are they different from being random? What purpose does each mutation have?

    You can’t just say “It has purpose” without being able to specify that purpose.

  96. PrestonTon 22 Sep 2016 at 2:40 pm

    And by sustaining complexity I mean that the environment must be able to support the biological structures. If it’s too hot, the chemical or radiative environment too harsh, the delicate bonds that form complex biomolecules don’t happen, limiting the types of life that can exist there.

  97. chikoppion 22 Sep 2016 at 2:45 pm

    What you can’t seem to get is that, according to Shapiro’s research, natural selection is NOT THE CAUSE of evolution. Shapiro explicitly says this.

    1) Genetic mechanisms and errors in transcription/repair cause variation in the genome.
    2) Genetic mechanisms can also increase the likelihood of variation in response to environmental factors.
    3) The mutations produced present a range of possibilities.
    4) Those variations MAY or MAY NOT be beneficial.
    5) Selection determines which IF ANY will be adopted and propagated.

    Does the above describe Modern Synthesis or does it describe Shapiro’s position?

  98. chikoppion 22 Sep 2016 at 2:47 pm

    Crap. Trying again…

    [hardnose] What you can’t seem to get is that, according to Shapiro’s research, natural selection is NOT THE CAUSE of evolution. Shapiro explicitly says this.

    1) Genetic mechanisms and errors in transcription/repair cause variation in the genome.
    2) Genetic mechanisms can also increase the likelihood of variation in response to environmental factors.
    3) The mutations produced present a range of possibilities.
    4) Those variations MAY or MAY NOT be beneficial.
    5) Selection determines which IF ANY will be adopted and propagated.

    Does the above describe Modern Synthesis or does it describe Shapiro’s position?

  99. chikoppion 22 Sep 2016 at 3:09 pm

    @PrestonT

    It wasn’t meant as a trick question. 🙂

    [PrestonT] So I guess what you wouldn’t see is that: you wouldn’t see a progression of sophistication in the responses of organisms to environmental stimuli. Nerve nets would have been a sufficient enough adaptation, and more complex structures would have been selected against because of the metabolic necessities and whatever else.

    Plants? Fungi? Bacteria? Increasing sophistication of intelligence doesn’t seem to be the only survival trick in town—nor even favored by the dominant evolutionary branches.

    I think you’re right that life evolves into available niches. Descendants increasingly bear the scars of evolutionary predecessors, meaning they possess an increasing accumulation of selected traits. Greater diversification and complexity seems like an inevitable outcome of populations evading extinction.

  100. hardnoseon 22 Sep 2016 at 3:12 pm

    “Does the above describe Modern Synthesis or does it describe Shapiro’s position?”

    The Modern Synthesis and Shapiro’s position are in opposition, as Shapiro has stated. The Modern Synthesis says that potentially beneficial genetic mutations are accidents, errors. Shapiro says that the potentially beneficial genetic mutations result from the natural genetic engineering mechanisms in cells, and are NOT accidents or errors.

    I have explained this to you several times.

    In both the Modern Synthesis and in Shapiro’s position natural selection occurs. That is not relevant. The two theories are in opposition. According to Dawkins, for example, natural selection is the organizing force of evolution. According to Shapiro, natural selection is NOT the organizing force of evolution.

    I hope you got it this time.

  101. hardnoseon 22 Sep 2016 at 3:13 pm

    “Directionality in HN’s explanation is an obvious overreach because it ascribes agency where there is none.”

    No, I have never ascribed agency. I have said, many times, that the cause of evolution is NOT KNOWN.

  102. PrestonTon 22 Sep 2016 at 4:19 pm

    @chikoppi,

    “Plants? Fungi? Bacteria? Increasing sophistication of intelligence doesn’t seem to be the only survival trick in town—nor even favored by the dominant evolutionary branches.”

    Definitely not saying intelligence is the only game in town. The base of a pyramid allows the top to exist and by definition is larger. There’s more bacterial biomass than anything, and the strategies that allow these less complex organisms to thrive represent the first rungs on a tall ladder that seems to end with humans.

    I feel like there’s a bit of talking past each other here. What I’m trying to wrap my head around is what appears to be directionality of evolution to favor increasing complexity– more complex structures and dependencies– especially as they relate to the formation of traits that enhance real-time information processing and increasingly sophisticated strategies for an organism to preserve its future. You bring up plants and fungi and bacteria as if these are answers to my question which tells me I’m not explaining myself well enough or you’re not being charitable to the ideas I’m attempting to grapple with here.

    Phototaxis and chemotaxis are strategies that fall somewhere on the spectrum of intelligence. Pack hunting is another, and it’s more complicated. Division of labor appeared to be a game changer, as was writing.

    I guess what I’m saying is that when intelligence can evolve, it does. The local maximum is humanity, and if all life on Earth were wiped out except for the extremophiles, intelligence would evolve again to the level of complexity that new environment could support.

  103. hardnoseon 22 Sep 2016 at 4:32 pm

    “The base of a pyramid allows the top to exist and by definition is larger.”

    I tried to explain that to them here many times.

    “or you’re not being charitable to the ideas I’m attempting to grapple with here.”

    They aren’t. They don’t want to understand.

    According to systems biology, which has been around since at least the early 20th century, natural open systems evolve towards greater complexity. No one has an explanation for why, but we can see that it does happen.

    It is important to remember that natural systems are OPEN.

  104. PrestonTon 22 Sep 2016 at 4:59 pm

    There’s nuances here that I’m totally missing in what I’m presenting. Evolution is radiative, and what I’m saying could be interpreted as ALL life moving towards greater complexity. I don’t mean to say that at all.

    I don’t have any answers, I’m just noting the peculiarity about the universe itself moving to states of complexity via entropy, and that intelligent life exists as a by-product of that process in conditions that can support greater molecular complexity.

    And so on.

    HN, while we may have facets of agreement, I’ve learned time and time again that my own mind is subject to biases that are difficult for me to trace, and it’s a life-long process to uncover and neutralize these biases. I sense resistance from you in that respect. If there’s one thing I’ve learned from following this blog and SGU, if we grasp too hard on what seems to be true, we might miss what actually is true.

    I’m open to having my mind changed, and I’m patient to try and lay out my thoughts.

  105. RickKon 22 Sep 2016 at 5:12 pm

    PrestonT

    Do you think life has a road, or is “complexity” just another dimension through which life can radiate out from its humble beginnings?

  106. bachfiendon 22 Sep 2016 at 5:14 pm

    Golly, this thread is at risk of spiralling completely out of control, all due to hardnose, and his persistent trolling and his refusal to face facts. It’s in danger of achieving the 1000+ comments of the previous thread on evolution.

    Hardnose persists in claiming that the cause of evolution is not known, whereas the cause of evolution is known. Evolution is caused by a changing environment of a population, which includes climate and other populations – competitors, predators and prey.

    The demonstration mentioned in this thread illustrates it nicely – the antibiotic concentration gradient increasing towards the centre of the plate represents a changing environment for the bacteria growing towards the centre of the plate, which causes them to evolve.

    The mechanism of evolution is natural variation within populations (which could be due to random mutations, Shapiro’s natural genetic engineering or even hardnose’s directed non-random mutations) acted upon by selection (most importantly natural, but it could also be sexual, or even just chance in small populations due to the founder effect or neutral drift).

    Lenski’s decades long experiment doesn’t show much about evolution – the culture medium used at the beginning of the experiment is exactly the same as the culture medium used currently, so the E coli’ environment hasn’t changed. What is being investigated is the ability of the bacteria to develop adaptations that will allow them to divide faster and for longer before hitting the limits of the environment, as its resources are depleted. The initial inoculum in each new flask will double 6 or 7 times before reaching the limit and then stop dividing for most of the day.

    A new variant that can divide more rapidly or more often that its competitors will form a increasing proportion of the bacterial population at the end of each day’s growth phase and have a greater chance of being inoculated into the next day’s flask. Most of the bacteria in each flask don’t survive, and the ones that do survive is just a matter of chance – just a matter of how many of each variant is present at the end of the growth phase each day.

    The study wasn’t looking at whether mutations occurring were random or not. No study can do that. To determine whether mutations are random or non-random, it would be necessary to detect all the mutations occurring in real time, not just the ones that have survived the experimental setup at the end of a day or even after 1 or 2 years of the experiment. It would be necessary to find ALL the mutations occurring and determining whether there are some possible mutations which occur at a higher frequency than chance suggesting that mutations are non-random. Or not.

    What the study did show was that mutations are actually rare. Just one strain developed the ability to metabolise citrate within the 6 or 7 generations of each day’s growth. Apparently, the E. coli strain used has the ability to metabolise citrate if it’s given enough time, much more than the 24 hours of the experimental protocol. Citrate apparently isn’t a favoured energy source, and it takes extra time for the regulatory portions of the bacterial genome to be switched on so that the genes concerned with metabolising citrate can be activated and start to produce the necessary enzymes and transport molecules.

    Presumably a mutation occurred in the regulatory portions of the genome allowing the genes to be activated much earlier. And this mutation was actually very rare, occurring in just one strain after tens of thousands of generations.

    It’s evidence that mutations are random and non-directed subject to selection, not that they’re non-random and directed (due to Shapiro’s natural genetic engineering?).

    Hardnose doesn’t like the current model of evolution because it’s simple. That’s its advantage – it is simple.

    The cause of evolution is a changing environment acting on a population.

    The mechanism of evolution is natural variation within a population acted upon by selection (most importantly natural).

    This is exactly what everyone has been telling hardnose explicitly and implicitly for years.

    Hardnose is incapable or unwilling to recognise the difference between ’cause’ and ‘mechanism’. The cause of evolution is known. The argument is about the mechanism. Shapiro could be 100% correct, but it wouldn’t make hardnose’s delusion that there’s direction in evolution true, that there’s an innate tendency towards increasing complexity and intelligence in biological systems.

    Please stop feeding the Troll.

    Hardnose

  107. RCon 22 Sep 2016 at 5:29 pm

    @hn

    “. The Modern Synthesis says that potentially beneficial genetic mutations are accidents, errors.”

    The Modern Synthesis says no such thing.

  108. BillyJoe7on 22 Sep 2016 at 5:51 pm

    Preston,

    “I guess what I’m saying is that when intelligence can evolve, it does”

    I’m sorry but you don’t have a good grasp of modern evolutionary theory if that is your conclusion.
    If the environment changes such that the evolution of intelligence would increase the chances of survival in that changed environment, then intelligence will evolve. If not, it won’t.
    Intelligence is not primary, it is secondary. The change in the environment is primary.

    “The local maximum is humanity, and if all life on Earth were wiped out except for the extremophiles, intelligence would evolve again to the level of complexity that new environment could support”

    No.
    It’s not a matter of intelligence evolving to the level of complexity that new environment could support.
    The environment is primary.
    If that changed environment favours the evolution of intelligent organisms, then intelligence will evolve. If not, it won’t. In other words, the environment is the driver for the evolution of intelligence (whenever it does evolve), not the limiting condition for intelligence as you have concluded.
    That was the point about bacteria, fungi, and plants.

  109. hardnoseon 22 Sep 2016 at 6:01 pm

    “HN, while we may have facets of agreement, I’ve learned time and time again that my own mind is subject to biases that are difficult for me to trace, and it’s a life-long process to uncover and neutralize these biases. I sense resistance from you in that respect.”

    No, I am completely aware of what they believe here. I read about evolution theory from all the usual angles, and I understand the theory promoted by, especially, Dawkins. And all the currently popular mainstream evolution theories are very similar. The most important idea in all of them is the idea that genetic mutations are always accidents/errors.

    That centrally important idea is contradicted by Shapiro’s, and others, research.

    backfiend says the cause of evolution is known, because he does not understand the theories or the controversies. He says it doesn’t matter if genetic mutations are random or engineered by the cell. It only matters if you care about the central controversy.

    If you don’t care, fine, but stop arguing about nothing.

  110. hardnoseon 22 Sep 2016 at 6:03 pm

    BillyJoe7 thinks he knows all about it. But all he does is mindlessly follow Dawkins.

  111. hardnoseon 22 Sep 2016 at 6:03 pm

    PrestonT,

    The trouble is, you are using common sense and observing reality. They don’t like that here. You are supposed to follow dogmatic authoritarian leaders.

  112. hardnoseon 22 Sep 2016 at 6:06 pm

    If Shapiro is correct, then Dawkins is wrong, and Steve Novella is wrong.

    backfiend seems to have an inability to think rationally. His goal is to feel that he is correct and I am wrong, and he has no interest in listening or comprehending.

  113. RickKon 22 Sep 2016 at 6:06 pm

    Bach, you should probably read the details of the Lenski experiment. It took over 30,000 generations before one of the 12 populations evolved the ability to consume citrate. And the critical beneficial mutation built on some random, neutral mutations that in themselves provided no benefit. I’m not sure what you’re talking about when you say one strain developed the ability to metabolize citrate after 6 or 7 generations each day.

    The fact that this highly beneficial mutation happened only in one population, and only as a result of previous neutral genetic drift, is of course evidence that the mutations were random. And the fact that the entire population then evolved to have this new ability was an example of evolution through random variation guided by natural selection.

  114. hardnoseon 22 Sep 2016 at 6:09 pm

    Novella stated in his recent comment that the Lenski experiments demonstrate that beneficial genetic mutations happen by chance.

    The Lenski experiments do not show that, were not even intended to show that.

    I am not promoting an ideology or a particular theory of evolution. I am saying that Novella’s statement is wrong. I am saying that the CAUSE of evolution is not known.

    backfiend, in case you somehow don’t know — a CAUSE is what makes something happen, and a MECHANISM is what makes something happen. It is possible for something to have MORE THAN ONE CAUSE. Some causes are more important than others. All this is incomprehensible to you because you somehow got through the education system without ever learning how to think rationally.

  115. chikoppion 22 Sep 2016 at 6:17 pm

    [PrestonT] What I’m trying to wrap my head around is what appears to be directionality of evolution to favor increasing complexity– more complex structures and dependencies– especially as they relate to the formation of traits that enhance real-time information processing and increasingly sophisticated strategies for an organism to preserve its future.

    My first observation is that organic ‘complexity’ started at a degree scale of 1 (the least possibly complex). Over time, were any variation in complexity possible, organisms would necessarily become more complex.

    Second, more complex is not necessarily favored by evolution. It wasn’t the ‘most complex’ organisms that survived the Permian Extinction event. There are also ample examples of traits being lost (simplified), including limbs and organs. Less complex species can wipe out more complex species or more easily survive when the environment changes drastically.

    Third, considering a given environment we would expect to see a diverse range of complexity among organisms as the biosphere adapts to exploit all potential niches over time. Isn’t that what we see now?

    Fourth, as I suggested earlier, survivors carry forward the evolutionary adaptations of their predecessors. The longer and more diverse a branch of evolution becomes, and the more traits exist to be inherited, the more complexity is likely to be found.

    In short, the fact that there ‘is’ a diversity of complexity doesn’t mean that evolution ‘favors’ increasing complexity. It’s just one of the possible outcomes.

  116. chikoppion 22 Sep 2016 at 6:50 pm

    [hardnose] The Modern Synthesis says that potentially beneficial genetic mutations are accidents, errors.

    Strawman.

    Genetic mechanisms (transcription, repair, epigenic functions, etc.), sometimes triggered by environmental factors, sometimes not, produce variability in the genome.

    Is that ‘accidental?’ Are those variabilities ‘errors?’ Does that sentence differ at all from the following?

    Genetic mechanisms (natural genetic engineering), sometimes triggered by environmental factors, sometimes not, produce variability in the genome.

    [hardnose] a CAUSE is what makes something happen, and a MECHANISM is what makes something happen.

    So “cause” and “mechanism” are interchangeable in your lexicon? Good. Then we’re done here.

    If: CAUSE = MECHANSIM

    The CAUSE of evolution is: Random (agnostic) Mutation + Selection

    1) Genetic mechanisms create variation in the genome.
    2) Genetic mechanisms can also increase the likelihood of variation in response to environmental factors.
    3) The variable mutations produced present a range of possibilities.
    4) Those variations MAY or MAY NOT be beneficial.
    5) Selection determines which IF ANY will be adopted and propagated.

    Finally, everybody agrees.

  117. Bill Openthalton 22 Sep 2016 at 6:53 pm

    PrestonT —
    The pyramid you’re seeing exists only in your mind, as a manageable model of life on Earth. There is no pyramid with humans on top in the real world.
    The same is true for any perceived directionality. Periods of favourable circumstances lead to many life forms, and these can engage in evolutionary competitions resulting in extreme features, such has size, speed, armour and intelligence. When such a period ends, there is a massive reduction in diversity, and the next cyclus leads to another outcome. Dinosaurs were huge, mammals are intelligent. Whatever will arise after the next meteorite or Deccan flats is anyone’s guess.

  118. bachfiendon 22 Sep 2016 at 7:00 pm

    Hardnose,

    I’ll try just one more time.

    The ’cause’ of the Earth orbiting around the Sun is the fact that the Earth has mass and the Sun has mass. The ‘mechanism’ of the Earth orbiting the Sun is that masses attract by a gravitational force mediated by a hypothetical boson ‘graviton’. Or masses curve space-time according to General Relativity so that masses move through space-time in a straight line. There’s more than one possible mechanism.

    The ’cause’ of evolution is changing environments. The ‘mechanism’ of evolution, the simplest and almost certainly the most probable, is natural variation within populations and selection, responding to changing environments.

    More complicated suggested mechanisms, such as General Relativity explaining planetary orbits, need to be supported by observations, which General Relativity passed with flying colours.

    There’s very little evidence for NGE. And even less for your directed mutations.

    You really need to learn the difference between ’cause’ and ‘mechanism’. They’re not synonyms. Or in your case, I’ll note that that means that they’re not the same thing. Or would you prefer if I use just words of one syllable?

  119. hardnoseon 22 Sep 2016 at 7:38 pm

    “There’s very little evidence for NGE.”

    So Shapiro is either lying or delusional?

  120. bachfiendon 22 Sep 2016 at 8:30 pm

    Hardnose,

    He’s just mistaken. Being mistaken in science isn’t a bad thing.

  121. PrestonTon 22 Sep 2016 at 9:42 pm

    @RickK
    “Do you think life has a road, or is “complexity” just another dimension through which life can radiate out from its humble beginnings?”

    No idea, but what a juicy thought.

    @BillyJoe7
    “I’m sorry but you don’t have a good grasp of modern evolutionary theory if that is your conclusion.
    If the environment changes such that the evolution of intelligence would increase the chances of survival in that changed environment, then intelligence will evolve. If not, it won’t.
    Intelligence is not primary, it is secondary. The change in the environment is primary.”

    I’ll be the first to say that I don’t have nearly as good a grasp as people who study this for a living. I just spent 4 years in college studying how to manipulate biology and as a hobbyist before and after, so my interest is in squaring what seems to be with what is through conversations like this, not in devoting my life to investigating it. Although I do sense a bit of dogmatism here in your definition of ‘environment.’ It seems to consist of everything in the background except other life which discounts greatly the competitive advantage intelligence imparts against other life to maximize position in any given environment. Also, I apologize if my understanding isn’t as deep or profound as yours, but you don’t have to be a snarky asshole about it. I’m just trying to learn here.

    @chikoppi,

    “Second, more complex is not necessarily favored by evolution. It wasn’t the ‘most complex’ organisms that survived the Permian Extinction event. There are also ample examples of traits being lost (simplified), including limbs and organs. Less complex species can wipe out more complex species or more easily survive when the environment changes drastically.”

    I already made concessions here– life drifting in directions of complexity and drastic environmental changes that reset the clock are different things, and I’m talking about the former. Traits being lost is interesting. I’ve seen examples of limbs and sense organs, a more interesting find for me would be an organism with a well developed brain that’s an ancestor of an organism with a significantly less developed one (not just smaller) or the total lack of one. Are there any examples of this?

    “In short, the fact that there ‘is’ a diversity of complexity doesn’t mean that evolution ‘favors’ increasing complexity. It’s just one of the possible outcomes.”

    Yeah totally agreed. I’m not saying ALL life goes that way, I’m wondering if some life will always go that way, given the time and environmental conditions.

    I think I agree with your other points.

    @ Bill O,

    “When such a period ends, there is a massive reduction in diversity, and the next cyclus leads to another outcome. Dinosaurs were huge, mammals are intelligent. Whatever will arise after the next meteorite or Deccan flats is anyone’s guess.”

    That’s a really interesting point. I wonder what would have happened if a meteorite didn’t give mammals the chance to dominate. Would sentient dinosaurs have evolved? As they competed with each other, would more complex social structures amongst smaller species have evolved to compete with the larger, etc?

  122. bachfiendon 22 Sep 2016 at 10:30 pm

    Preston,

    I went back and looked at BillyJoe’s comment and he doesn’t seem to be excluding other life as being part of the environment (if I’m wrong about this, perhaps he’ll correct me?).

    I regard the environment to include everything, including competitors, predators and prey. Lenski’s decades long study doesn’t show much evolution, because the culture medium is the same, there’s no predators or prey, and the only competitors are bacteria of exactly the same strain, and the only way they can outcompete their competitors is to divide faster and longer. The study was looking at whether it happened, how often and how rapidly. And surprise – it does happen.

    I can’t think of a single case of a species with a well developed brain losing its brain completely. But I can think of plenty of species with well developed brains going completely extinct. Being intelligent is such an obvious survival aid, but it may not be enough. There were at least 5 species of Homo living within the past 50,000 years and 4 of them have gone extinct; Homo erectus, Homo neanderthalensis, Homo denisova and Homo florenensis. And they were all intelligent. They certainly lost their well developed brains because they also lost the surrounding bodies.

    It’s a mistake to think that a species which is well defined in the fossil record ever evolves into a new species, which would also include a species with a well developed brain evolving into one without. A species which is common and widespread enough to have left fossils in the geological record will usually have small reproductively and geographically localised subpopulations, and it’s in these subpopulations in which formation of new species occurs. The original species may persist. Or it may go extinct. And usually does.

    This is the lesson of Punctuated Equilibrium, which doesn’t actually state that evolution can ever occur rapidly in geological time – merely that it’s usual to see one species being replaced by another in the geological column.

    As I’ve previously noted, the only examples of species losing intelligence occurs in parasites. There are free living nematodes, and there are parasitic intestinal nematodes. The parasitic ones don’t require even the minimal intelligence of their free living cousins, which have to earn their living. And their long term survival, on evolution basis, depends on their hosts not going extinct.

  123. bachfiendon 22 Sep 2016 at 10:43 pm

    Also, I’ve just noticed a few typo’s such as ‘Deccan flats’. I read it several times before realising – it’s ‘Deccan traps’ (they sound much the same, aren’t obviously wrong and seem to make more sense – I’ve certainly done the same in the past). Traps comes from the Swedish word for stairs (similar to the German word ‘Treppe’) and refers to its physical appearance.

  124. BillyJoe7on 23 Sep 2016 at 12:34 am

    Preston,

    “Although I do sense a bit of dogmatism here in your definition of ‘environment.’ It seems to consist of everything in the background except other life which discounts greatly the competitive advantage intelligence imparts against other life to maximize position in any given environment”

    Your sense of my definition of environment is wrong, as any one here can affirm from past discussions.
    Also I have no idea what made you think so.

    “Also, I apologize if my understanding isn’t as deep or profound as yours, but you don’t have to be a snarky asshole about it. I’m just trying to learn here”

    Your sense of my intentions is also wrong.
    And if you’re trying to learn it’s not a good idea to start name calling those trying to help (yes, that was my intention, sorry if I came across differently)

  125. steve12on 23 Sep 2016 at 1:42 am

    Preston:

    “I’ve seen examples of limbs and sense organs, a more interesting find for me would be an organism with a well developed brain that’s an ancestor of an organism with a significantly less developed one (not just smaller) or the total lack of one. Are there any examples of this?”

    Why is this more interesting to you? Would it provide more evidence for something than the loss of limbs or senses would?

  126. PrestonTon 23 Sep 2016 at 2:46 am

    @bachfiend,

    Thanks for the info!

    ” There were at least 5 species of Homo living within the past 50,000 years and 4 of them have gone extinct; Homo erectus, Homo neanderthalensis, Homo denisova and Homo florenensis”

    Do we know why they went extinct?

    @BillyJoe7,

    Please accept my apologies. Startup life has me very sleep deprived the past week. This is a very interesting topic for me for many reasons and for a long time, so sometimes my own reality distortion field gets me in trouble.

    @steve12,

    Well yeah because that would be a pretty big nail in the coffin for any notion of directionality to increasing brain function. Extinction events caused by sudden environmental changes are one thing, but if in a relatively stable background environment there were examples of life evolving to lower states of information processing then that would be really interesting.

    Thank you all for engaging with me. I’ve been a long time lurker on SN’s blog and it’s comment sections, so I’ve read each of your writings now for awhile and it’s fun for it to finally be two way.

  127. bachfiendon 23 Sep 2016 at 5:51 am

    Preston,

    No one knows why any of the Homo species on the very twiggy branch of human evolution went extinct. Was it competition from other Homo species? Was it climate change? Apparently Homo sapiens almost went extinct around 75,000 years ago with the global cooling from the eruption of Toba in Sumatra.

    Actually we don’t know how intelligent any of the extinct Homo species were. It’s assumed that since they’re Homo species, then they were also intelligent.

    We have a fairly good idea of the social life of Homo neanderthalensis. We know that Homo erectus were probably tool makers and fire users. We know Homo denisova only on the basis of the DNA retrieved from a finger bone, and it would be difficult to reconstruct the whole individual from that, let alone their social life and intelligence. Homo florensis is known from fossils washed into a cave which gives no indication of social life or intelligence.

    I’m probably committing the hardnose fallacy in assuming that there’s an innate tendency to increasing intelligence and that later species, such as Homo florensis, are more intelligent than earlier ones.

  128. hardnoseon 23 Sep 2016 at 9:11 am

    “I’m probably committing the hardnose fallacy in assuming that there’s an innate tendency to increasing intelligence and that later species, such as Homo florensis, are more intelligent than earlier ones.”

    I must have explained this to you at least fifty times by now. The system overall increases in complexity. That is perfectly obvious to any member of the homo sapiens species that has not yet lost its brain.

    There is no reason to think an individual species will evolve towards increasing intelligence. I have explained to you that our species has not become more intelligent since prehistoric times. You thought that was ridiculous, because you know nothing about anthropology.

  129. chikoppion 23 Sep 2016 at 10:38 am

    The “prehistoric period” is about 6,000 years ago. Not much time on the scale of evolution or the history of our species. There is controversy about what has happened to Homo Sapiens intelligence during that period, with some claiming evidence we’ve become smarter, others that we’ve lost our intellectual edge.

    Homo Sapiens is about 200,000 years old. During that time there is evidence our ‘intelligence’ has evolved.

    [Wikipedia] Around 80–100,000 years ago, three main lines of Homo sapiens diverged, bearers of mitochondrial haplogroup L1 (mtDNA) / A (Y-DNA) colonizing Southern Africa (the ancestors of the Khoisan/Capoid peoples), bearers of haplogroup L2 (mtDNA) / B (Y-DNA) settling Central and West Africa (the ancestors of Niger–Congo and Nilo-Saharan speaking peoples), while the bearers of haplogroup L3 remained in East Africa.

    The “Great Leap Forward” leading to full behavioral modernity sets in only after this separation. Rapidly increasing sophistication in tool-making and behaviour is apparent from about 80,000 years ago, and the migration out of Africa follows towards the very end of the Middle Paleolithic, some 60,000 years ago. Fully modern behaviour, including figurative art, music, self-ornamentation, trade, burial rites etc. is evident by 30,000 years ago. The oldest unequivocal examples of prehistoric art date to this period, the Aurignacian and the Gravettian periods of prehistoric Europe, such as the Venus figurines and cave painting (Chauvet Cave) and the earliest musical instruments (the bone pipe of Geissenklösterle, Germany, dated to about 36,000 years ago).

  130. steve12on 23 Sep 2016 at 10:55 am

    Preston:

    “Well yeah because that would be a pretty big nail in the coffin for any notion of directionality to increasing brain function. Extinction events caused by sudden environmental changes are one thing, but if in a relatively stable background environment there were examples of life evolving to lower states of information processing then that would be really interesting.”

    Why would brains be any different in re: to direction than sense organs or limbs?

  131. steve12on 23 Sep 2016 at 11:00 am

    “hardnoseon 23 Sep 2016 at 9:11 am”

    The Troll MAD!!!! The TROLL SMASH!!!!

  132. hardnoseon 23 Sep 2016 at 11:10 am

    “Homo Sapiens is about 200,000 years old. During that time there is evidence our ‘intelligence’ has evolved.”

    You don’t know the difference between cultural and biological evolution.

  133. hardnoseon 23 Sep 2016 at 11:13 am

    PrestonT,

    James Shapiro is a molecular biologist who has been studying bacterial adaptaion/evolution for decades. He has found plentiful and conclusive evidence that beneficial mutations are directed, NOT accidental. You can read about his “natural genetic engineering” ideas.

    Shapiro’s theory is in direct opposition to neo-Darwinism/modern synthesis, which says that all beneficial mutations are accidental.

    You can decide for yourself, don’t mindlessly believe the unthinking status quo defenders here.

  134. Steven Novellaon 23 Sep 2016 at 11:19 am

    HN – you don’t make actual arguments, you just make the same assertions over and over again. You apparently can’t tell the difference.

    As Rick pointed out in the comment right before yours, the Lenski experiments absolutely provide evidence that beneficial mutations arise at random. This was explained to you several times, and you just deny it, without making any counterargument.

    The Lenski experiments followed multiple cultures of bacteria over decades for tens of thousands of generations, including saving generations and then rerunning them. This is a vast amount of experimental data. No one paper is going to analyze or describe is all.

    The core question Lenski was asking is – could the bacteria evolve to eat citrate if given enough time and opportunity? The answer was yes. Could then evolve this trait even if it requires multiple mutations? The answer was also yes.

    He wasn’t asking specifically, “are mutations random,” but that is entirely irrelevant, the experiments still provide evidence that they are. You can analyze large data sets and ask many questions, even if that was not the original question of the researchers. This is done all the time.

    Only one of the 12 colonies evolved to eat citrate, and only after genetic drift provided a necessary mutation to allow it to happen. In colonies without this favorable drift, they never evolved to eat citrate. When you go back to older generations without the favorable mutation, they don’t evolve to eat citrate. When you go back and run colonies that have the needed mutation, they do evolve to eat citrate, but after different numbers of generations.

    This is all exactly what you would predict if mutations were occurring essentially at random. This is not what you would predict if there were some force producing needed mutations.

    Now, I predict you will not address this argument or this evidence. You will simply repeat your limited set of assertions and then call people names.

  135. Steven Novellaon 23 Sep 2016 at 11:42 am

    To expand on this a bit, for those who are interested, there is an entire field of experimental evolution, of which the Lenski experiments are just one example.

    Here is a discussion of the findings so far: http://glanglab.com/Genomics2014.pdf

    I suggest reading the whole thing, but note this line: “Phenotypic evolution, therefore, may be predictable despite the inherent randomness of genotypic evolution. ”

    The randomness of genotypic evolution is another way of saying that mutations are random.
    Phenotypes are predictable in that they are under selective pressure, but how new traits evolve to meet that selective pressure is unpredictable.

    This is the most direct evidence we have looking at the actual occurrence of mutations. They are random for direction and effect. What is not random is the frequency and location on the genome of mutations. Here there are hotspots and feedbacks. That is not controversial.

  136. hardnoseon 23 Sep 2016 at 12:02 pm

    So you deny that Shapiro has found evidence for natural genetic engineering?

  137. steve12on 23 Sep 2016 at 12:22 pm

    I don’t know Steve…

    A perfectly sound alternative interpretation of Lenski’s data is that the Conscious Universe (i.e., NOT God!) was too busy directing mutations that would lead to human intelligence to give Lenski’s bacteria the mutations they needed to eat citrate, as was befitting their destiny. So they had to wait for a random mutation.

    I mean, it’s a Conscious Universe – not magic!

  138. steve12on 23 Sep 2016 at 12:25 pm

    It’s sweetly ironic to see Dr. The Troll, of all people, resort to appeal to authority.

    Like mulled wine on a brisk fall night, it’s warm and satisfying in my belly.

  139. PrestonTon 23 Sep 2016 at 12:53 pm

    @steve12,
    “Why would brains be any different in re: to direction than sense organs or limbs?”

    The implicit assumption I’m orbiting is that once a certain level of brain function is reached, any environment would consistently select for those traits and ones built on top, barring extinction events caused by sudden environmental shifts. As your line of questioning is alluding, I’m fallaciously begging the question that adaptations of the nervous system hold some privileged place in evolution. So, my assumptions here are that changes to limbs and sense organs are subordinate to the adaptations of the CNS controlling it.

    Now that this conversation has been going on for a few days, I guess what I’m doing is softly claiming once a brain is sufficiently developed, competitive pressures with other life leads to a runaway sophistication of those brains; whether those creatures evolve fins, legs, or wings is less relevant than the abilities of their nervous systems. Extinction events have been brought up multiple times, and in the cases of sudden environmental changes like that all bets are off, but if we assume as a thought experiment a relatively stable environment where the major competitive pressures were resource competition with other life, then may the best nervous system win.

    I’m aware that this is fallacious; looking to replace this mental model with one more accurate, but so far I’m hung up on it. Probably because as humans our brains are evolved to a point where we have the intelligence to break the bonds of nature pretty much entirely, and it seems like there’s no going back for us unless we kill ourselves. We’ll only get smarter (collectively), more connected, more resistant to any given environment, more ‘selected’ for. The image stuck in my head is a graph where the x-axis is age of life as we know it and the y-axis is some nebulously defined ‘level of consciousness’– the graph is up and to the right and will continue to go that way barring an extinction event we can’t avoid. And say we do go extinct, I think even if it took a few more billion years, that graph would repeat itself either on Earth or somewhere else. Is intelligence an emergent property of the universe? Is it inevitable? Those are the itchy questions for me. I think it is, but hey what do I know?!

  140. chikoppion 23 Sep 2016 at 1:23 pm

    [hardnose] You don’t know the difference between cultural and biological evolution.

    Oh…right. So no archeological evidence could possibly be applicable then (not enough Scottsmen, I guess).

    Recent Acceleration of Human Adaptive Evolution, Hawks, Wang, Cochran, Moyzis
    https://www.researchgate.net/publication/5761823_Recent_Acceleration_of_Human_Adaptive_Evolution

    The new genetic adaptations, some 2,000 in total, are not limited to the well-recognized differences among ethnic groups in superficial traits such as skin and eye color. The mutations relate to the brain, the digestive system, life span, immunity to pathogens, sperm production, and bones—in short, virtually every aspect of our functioning.

    Scanning genomes in the haplotype map for these clues, the researchers discovered that 7 percent of human genes fit the profile of a recent adaptation, with most of the change happening from 40,000 years ago to the present.

    “The clearest example of that is malaria,” Hawks says. “The disease is about 35,000 years old, with the most lethal form of it just 5,000 years old.” Yet in sub-Saharan Africa and other regions where it is endemic, “people have already developed 25 new genes that protect against malaria, including the Duffy blood type, an entirely new blood group,” he notes. More recently, HIV resistance has appeared due to a genetic mutation now found in 10 percent of Europeans. Scientists speculate that the variant may have originally evolved as a protection against smallpox.

    Some genes that appear to have been recently selected, Moyzis and his collaborators suggest, influence the function and development of the brain. Other fast-changing genes—roughly 100—are associated with neurotransmitters, including serotonin (a mood regulator), glutamate (involved in general arousal), and dopamine (which regulates attention). According to estimates, fully 40 percent of these neurotransmitter genes seem to have been selected in the past 50,000 years, with the majority emerging in just the past 10,000 years.

    Stronger evidence that natural selection has continued to shape the brain in recent epochs comes from studies of DRD4, a mutation in a neurotransmitter receptor that Moyzis, Wang, and many others have linked to attention-deficit/hyperactivity disorder (ADHD). Children diagnosed with ADHD are twice as likely to carry the variant gene as those without the diagnosis. DRD4 makes a receptor in the brain less effective in bonding to dopamine, which might explain why Ritalin, which increases the amount of dopamine in the space between neurons, is often helpful in treating the problem.

  141. chikoppion 23 Sep 2016 at 2:37 pm

    [hardnose] So you deny that Shapiro has found evidence for natural genetic engineering?

    “NGE” is a catch-all phrase Shapiro coined that refers to any genetic mechanism that manipulates DNA. He didn’t “discover” these mechanisms.

    [Shapiro] For me, NGE is shorthand to summarize all the biochemical mechanisms cells have to cut, splice, copy, polymerize and otherwise manipulate the structure of internal DNA molecules, transport DNA from one cell to another, or acquire DNA from the environment.

  142. hardnoseon 23 Sep 2016 at 2:46 pm

    [“NGE” is a catch-all phrase Shapiro coined that refers to any genetic mechanism that manipulates DNA. He didn’t “discover” these mechanisms.]

    He found evidence for it, I said. The fact is that NGE is known to happen.

    So how does Lenski’s experiment contradict the observed fact of NGE? It doesn’t.

  143. hardnoseon 23 Sep 2016 at 2:49 pm

    “It’s sweetly ironic to see Dr. The Troll, of all people, resort to appeal to authority.”

    There is nothing illogical about pointing out that an expert has found evidence for something, from decades of research.

    Do you think Steve Novella, or any of you here, know more about evolution than James Shapiro?

    That’s fine if you disagree with his evidence, but you would have to explain why you disagree. None of you have explained. You just say he is wrong, and give no reason.

    Now THAT is illogical.

  144. chikoppion 23 Sep 2016 at 3:46 pm

    [chikoppi] “NGE” is a catch-all phrase Shapiro coined that refers to any genetic mechanism that manipulates DNA. He didn’t “discover” these mechanisms.

    [hardnose] He found evidence for it, I said. The fact is that NGE is known to happen.
    So how does Lenski’s experiment contradict the observed fact of NGE? It doesn’t.

    I’m not sure how to explain this to you.

    “NGE” refers to a collection of known genetic mechanisms. Shapiro didn’t discover them OR find evidence for them. He lumped them together as a group and claimed that, together, these mechanisms are the ones most responsible for generating genetic variability.

    NGE is not itself a mechanism. It is a theoretical model.

    [Shapiro] In summary, NGE encompasses a set of empirically demonstrated cell functions for generating novel DNA structures. These functions operate repeatedly during normal organism life cycles and also in generating evolutionary novelties, as abundantly documented in the genome sequence record.

    Here is where Shapiro himself cites the mechanisms he incorporates into his model and the individuals who were actually responsible for the research:

    http://shapiro.bsd.uchicago.edu/ExtraRefs.MolecularMechanismsNaturalGeneticEngineering.shtml

  145. BillyJoe7on 23 Sep 2016 at 4:07 pm

    Preston,

    Thanks for your apology.
    But read your last post again and see how you’ve done what you said I was doing in my post – you imagine a scenario where the environment is stable but the brain evolves because of competition from other organisms. You seem to have forgotten that the “environment” includes other organsims. I understand that, in that particular post, by stable environment, you mean excluding catastrophic change in the physical environment that leads to an extinction event, or more precisely, an environment where the only change is competition between life forms. But then your argument loses its force because it is based on an equivocation of the word “environment”. You need to use that word consistently. If you do, then the consistent conclusion is that intelligence is selected for in the type of environmental change that you envisioned, and as a direct result of that environmental change. In other words, environmental change is still the driver. Intelligence does not increase on its own by some sort of innate tendency (or by The Hand of God; or by The Conscious Universe!).

  146. steve12on 23 Sep 2016 at 4:08 pm

    Peeston:

    “Now that this conversation has been going on for a few days, I guess what I’m doing is softly claiming once a brain is sufficiently developed, competitive pressures with other life leads to a runaway sophistication of those brains; whether those creatures evolve fins, legs, or wings is less relevant than the abilities of their nervous systems.”

    I see where you’re coming from. I don’t think there is runaway sophistication, but a human brain wasn’t going to come out of a foot. The brain is the most complicated thing we know of, and condifering the structural specialization of it, it was going to evolve from a structure that was also complicated and similar in many respects. It is certainly redolent of a direction even though, as you rightly point out, there isn’t one.

    “Extinction events have been brought up multiple times, and in the cases of sudden environmental changes like that all bets are off, but if we assume as a thought experiment a relatively stable environment where the major competitive pressures were resource competition with other life, then may the best nervous system win.”

    They certainly convey a huge advantage, at least for megafauna. For us, we’re slow, hairless weakling babies (in the neoteny sense) with small litters, difficulty birthing, and no physical weaponry yet we rule this little rock. For now. A few changes in the environment and we’re toast, brains or no.

    “Is intelligence an emergent property of the universe? Is it inevitable? Those are the itchy questions for me. I think it is, but hey what do I know?!”

    I tend to say no considering just based on the state of the evidence. But maybe in a Drake equation sense, it is all but inevitable. Intelligence (i’ll be broad) is more sort of a flexible strategy that’s not dependent on any absolute type of physical environment. Maybe for all intents and purposes it is!

  147. steve12on 23 Sep 2016 at 4:28 pm

    P-R-eston!!!

    Apologies! That looks like some sort of purpose misspelling – I assure you it is not!

  148. PrestonTon 23 Sep 2016 at 4:56 pm

    @BillyJoe7,
    “But then your argument loses its force because it is based on an equivocation of the word “environment”. You need to use that word consistently. If you do, then the consistent conclusion is that intelligence is selected for in the type of environmental change that you envisioned, and as a direct result of that environmental change. In other words, environmental change is still the driver. Intelligence does not increase on its own by some sort of innate tendency (or by The Hand of God; or by The Conscious Universe!).”

    Yeah I can agree with all of that. Slight nuance + question– if a non catastrophic environment consistently selects for greater intelligence, what’s the difference between “environment as the primary driver” and an “innate tendency” for intelligence to develop under said ‘stable’ conditions?

    @steve12,
    “A few changes in the environment and we’re toast, brains or no.”
    Do you think at some point we will have innovated ourselves into some measure of permanent durability? Genetic engineering + spacefaring tech + bioprinting + nanotech etc suggest a future where we’re practically immortal with population centers in every conceivable environment.

  149. BillyJoe7on 23 Sep 2016 at 5:39 pm

    Preston,

    “…if a non catastrophic environment consistently selects for greater intelligence, what’s the difference between “environment as the primary driver” and an “innate tendency” for intelligence to develop under said ‘stable’ conditions?”

    For a start, we know exactly what we mean when we say that changes in the environment drive evolutionary change (through selection amongst random mutations). In other words, there is a well defined mechanism. But we don’t have a clear idea of what is meant by an innate tendency for intelligence to increase. In other words, we can’t even come up with a plausible mechanism by which there is an innate tendency for intelligence to increase, let alone one suported by evidence.

  150. chikoppion 23 Sep 2016 at 6:19 pm

    Yeah I can agree with all of that. Slight nuance + question– if a non catastrophic environment consistently selects for greater intelligence, what’s the difference between “environment as the primary driver” and an “innate tendency” for intelligence to develop under said ‘stable’ conditions?

    I believe you should rethink this a bit.

    Homo Sapiens shares the same environment as the majority of terrestrial fauna. Intelligence is one of the traits that can provide a selection benefit. Other traits, in the absence of increasing intelligence, have proven equally beneficial if not more so (in the same environment).

    The tuatara (a lizard-like creature which is the last known species of the Rhynchocephalia order) has been around for roughly 200 million years. Although it has undergone evolutionary change, it has not developed increasingly sophisticated intelligence (however that might be defined).

    I think you might be over-anthropomorphizing.

  151. Bill Openthalton 23 Sep 2016 at 8:38 pm

    bachfiend —
    Re Deccan flats, I had just been listening to “From the Cape Flats with love” by the South African stand-up comedian Marc Lottering, so the Deccan Traps morphed into the Deccan Flats. A nice brain fart.

  152. bachfiendon 23 Sep 2016 at 9:04 pm

    Bill,

    Yes, but I actually read ‘Deccan flats’ several times and it made perfect sense to me. In the same way that I thought it was ‘one foul swoop’ instead of ‘one fell swoop’ for years (although, nowadays I use ‘one fowl swoop’ instead so as to conjure a mental picture of a chook perched in a tree just waiting to inflict terrible retribution on on a transgressor).

  153. hardnoseon 23 Sep 2016 at 10:03 pm

    [“NGE” refers to a collection of known genetic mechanisms. Shapiro didn’t discover them OR find evidence for them. He lumped them together as a group and claimed that, together, these mechanisms are the ones most responsible for generating genetic variability.]

    I have no idea what you are arguing about or why. I never said he discovered them. He found evidence for them, and many others found evidence for them. There is no doubt that they exist.

    And of course you have no logical arguments against these scientific facts.

    And Lenski’s experiment did nothing to show that all mutations are random. There are random and semi-random elements in some mutation-generators. But there is absolutely no reason to say all mutations are accidents and errors.

    And no one here has any good arguments for their belief that adaptive mutations are all entirely random.

    Instead, you would rather generate evidence-free speculations on how intelligence evolved by accident. That is the kind of discussion you would normally see at the philosophy blogs, where fantasy is mistaken for reality.

    Here we have real science showing that the popular theory about the cause of evolution is at least partially wrong. And all you care about is defending your rigid beliefs.

    And when neo-Darwinism devotees occasionally have to admit that NGE is real, and obviously has a role in evolution, they always fall back on evidence-free philosophizing, and claim that the evolution of NGE was caused by accidents and selection. NOT because there is any evidence for that, but because their theory MUST be true.

  154. bachfiendon 23 Sep 2016 at 10:32 pm

    Sigh… hardnose has returned yet again with his evidence free philosophical ponderings about evolution, confusing ’cause’ with ‘mechanism’ and thinking that ‘natural variation and selection’ is ‘accident’, despite it being anything ‘but’.

    There are very good reasons for thinking that intelligence is eminently capable of being selected for, and is anything other than not an accident. Though, there’s no evidence that it’s deliberately created or maintained by a conscious agent, whether a deity or the universe as a whole.

  155. Niche Geekon 23 Sep 2016 at 11:25 pm

    HN: “There are random and semi-random elements in some mutation-generators. But there is absolutely no reason to say all mutations are accidents and errors.”

    If I accept your premiss, how does Shapiro tell a random mutation from a semi-random mutation? You’ve acknowledged that some mutations are accidents and some errors so there must be a way to tell them apart.

  156. chikoppion 24 Sep 2016 at 2:05 am

    [hardnose] I have no idea what you are arguing about or why. I never said he discovered them. He found evidence for them, and many others found evidence for them. There is no doubt that they exist.

    No sh*t. Genetic mechanisms that cause variation in the genome is a foundational premise of modern synthesis and universally accepted. Naturally occurring horizontal gene transfer has been known about since the 1950s.

    And of course you have no logical arguments against these scientific facts.

    Nope.

    And Lenski’s experiment did nothing to show that all mutations are random. There are random and semi-random elements in some mutation-generators. But there is absolutely no reason to say all mutations are accidents and errors.

    As has been explained repeatedly, no one says this. You are the one who labeled them “accidents and errors.” There are genetic mechanisms that cause variation. Some are influenced or activated by environmental triggers. Sometimes molecular or chemical effects cause an otherwise stable process to produce variable results. The end result in all cases is variation that can be acted upon by selection. Again, a foundational premise of modern synthesis.

    And no one here has any good arguments for their belief that adaptive mutations are all entirely random. Instead, you would rather generate evidence-free speculations on how intelligence evolved by accident. That is the kind of discussion you would normally see at the philosophy blogs, where fantasy is mistaken for reality.

    What we have is a wealth of evidence for 1) how a genome varies due to identified mechanisms, 2) how selection (non-randomly) determines which, if any, of those variations will persist to be propagated throughout a population. What we don’t have is any evidence that evolutionary processes follow a pre-determined course.

    Here we have real science showing that the popular theory about the cause of evolution is at least partially wrong. And all you care about is defending your rigid beliefs.

    ‘Cause?’ Meaning ‘mechanism?’ Which? Agnostic variation? No, Shapiro states that NGE produces both beneficial and non-beneficial results. Selection? No, he also states that the output of NGE is immediately subject to selective determination.

    And when neo-Darwinism devotees occasionally have to admit that NGE is real, and obviously has a role in evolution, they always fall back on evidence-free philosophizing, and claim that the evolution of NGE was caused by accidents and selection. NOT because there is any evidence for that, but because their theory MUST be true.

    What is the alternative origin of any genetic mechanism if not variation and selection? What evidence exists for said origin?

  157. Steven Novellaon 24 Sep 2016 at 7:10 am

    HN – It always feels like we are talking past each other. Stop for one minute from repeating your silly accusations that we are all ideologues and try to grasp what we are actually saying.

    Common ground:
    – The location and frequency of mutations is not random. There are genetic mechanisms that contribute to mutations, increasing the frequency and creating hotspots on the genome. As far as we can tell, these serve the purpose of generating variation when and where it is needed.

    – There are epigenetic factors that can respond to environmental situations by making specific changes to the genome, but so far the specific changes found act more like a toggle than any permanent change to the genome. It’s a way for a population to alter a function to meet an immediate need, but does not result in evolutionary change (other than as above, generating more variation).

    – Natural selection ultimately acts on any variation to preserve what works.

    Disputed ground:

    Where we seem to disagree, and it’s hard to tell because you are terrible at making your specific position clear, is whether or not the specific mutational changes that occur are random or guided in some way. (It’s also possible they are non-random but non-guided – an A may turn to a T more often than a T to an A, but that is inconsequential for our purposes).

    My position aligns with that of the scientific consensus – there is no evidence for any mechanism by which the specific mutations that occur are guided in any way, move toward any predetermined or specific end, or are anything other than completely random. There is also no evidence that the specific mutations that occur are guided or non-random.

    The evidence we do have, especially from experimental evolutionary biology, is consistent with mutational effects being random.

    There is no physical mechanism by which a cell could know that it needs to change a C to a G in a specific location of a gene to result in the substitution of a specific amino acid, that will have a beneficial effect on the properties of the resulting protein.

    When cellular mechanisms promote mutations, the cells are essentially just rolling the dice over and over and letting natural selection sort out the results.

    This is the scientific consensus. It is consistent with the existing evidence and our knowledge of possible mechanisms.

    If you disagree with any part of this – then state exactly why you do, and give us reasons and evidence, not just assertions and insults.

  158. bachfiendon 24 Sep 2016 at 5:14 pm

    Steven,

    Hardnose’s position is even less defensible. He disagrees with the standard accepted theory (model) of evolution. That the CAUSE of evolution is a changing environment (which includes climate, competitors, predators and prey) acting on a reproductively isolated population, and the MECHANISM of evolution is natural variation within a population and selection.

    Hardnose confuses ’cause’ with ‘mechanism’. He disagrees that natural variation within a population and selection can cause evolution, and in that he’s almost completely correct. No one disagrees with him to any great extent, but it’s irrelevant.

    What hardnose objects to is the idea that evolution depends on accidents, on chance. Well, there is some chance involved. The environment is largely unpredictable. Mutations are random. Small populations may show neutral drift and the founder effect, and the variants that come to dominate may not actually the best adapted variants available. But there’s no chance involved with selection acting on variation within populations – almost always the best adapted wins. Not that there might have better solutions available, but selection and evolution has to manage with the variations available, not the ones that are theoretically possible.

    Evolution is contingent. Most people would agree with Gould that if the tape of life were to be rerun, completely different species would result. I suspect hardnose wants to agree with Simon Conroy Morris that if the tape of life were rerun, humans, or something similar, were inevitable.

    Hardnose likes the idea of beneficial non-random directed mutations. As I’ve pointed out to him many times, it’s impossible to distinguish random non-directed mutations with selection winnowing out the non-beneficial ones from beneficial non-random directed mutations, because obviously you only detect the mutations after a period of time (as with Lenski’s experiment). What Lenski’s study does show is that mutations in his system are very rare (which makes some sense – each day there’s 6 to 7 doublings of the inoculum in each flask before the end of the growth phase – if a mutation occurs in a single bacterium at the start of the day, then the new variant with the new mutation will be present in only around 128 daughter bacteria – provided it’s not a lethal mutation – and then in the next day 99% of the bacteria are discarded leaving just 1% to be recultured, meaning that there may be 0, 1 or 2 of the variant at the start of the day and 0, 128 or 256 of the variant at the end of the day. Assuming the new variant is able to double 7 times instead of 6). The new variant will take many days, if ever, to dominate a flask.

    Hardnose loves linking to secondary sources instead of primary sources. In the previous thread he linked to a news article discussing a study which hardnose claimed showed that mutations aren’t random. The researchers actually studied mitochondria in a variety of tissues from 2 individuals at post mortem and found that the mitochondria from muscle, kidneys and liver had mutations in the mitochondrial DNA controlling the rate of replication of the DNA, which is exactly what would be expected if mutations are random subjected to selection. The mutant mitochondria (which are symbiotic bacteria) had the ability to proliferate more than the original mitochondria, and came to dominate numerically after perhaps many years. Just like the E. coli in Lenski’s study. The mutation in the mitochondria was beneficial to the mitochondria and were selected. Any deleterious mutation in mitochondria are just eliminated by selection.

  159. hardnoseon 24 Sep 2016 at 6:12 pm

    I have explained my position here many times, but it gets drowned in avalanches of irrelevant nonsense (see the comment above this one, for example).

    As I have said, evolution research is not finished, and evolution has not yet been explained. That also happens to be Shaprio’s position.

    Neo-Darwinists, such as Dawkins and Coyne, believe that evolution has been explained. Like Steve Novella, they are certain that all beneficial genetic mutations are accidents/errors.

    But since we know that natural genetic engineering does occur, it is not reasonable to assume mutations are never a purposeful response to environmental stress.

    We know that cells have the ability to modify their DNA, and we know that they use these abilities. Why on earth would anyone feel certain that these abilities are never used for the cell’s advantage, and for the advantage of its descendants?

    It is highly unscientific to deny that something happens, just because you don’t understand how it happens.

    A truly scientific, skeptical, approach demands that we refrain from thinking we know the answer to things we do not yet understand.

  160. ccbowerson 24 Sep 2016 at 7:04 pm

    “But since we know that natural genetic engineering does occur, it is not reasonable to assume mutations are never a purposeful response to environmental stress.”

    “Purpose” is your own interpretation of what happens, and is a very fuzzy concept for this topic. How would mutation occurring with a “purpose” differ from mutation that occurs without “purpose?” Do you have specific examples? If not, what are you arguing about?

    “Like Steve Novella, they are certain that all beneficial genetic mutations are accidents/errors.”

    It is not about certainty, but a fairly straightforward interpretation of the evidence. We know that mutations do occur essentially at random (I think you would agree that this type of mutation occurs), do you have evidence that they occur in a directed fashion? If you have evidence of specific mutations that purposefully (whatever that means) created what are they? If you don’t, what are you arguing about?

    Hundreds of words arguing why everyone else is wrong, yet none to explain how/why you are correct.

  161. hardnoseon 24 Sep 2016 at 7:10 pm

    “Hundreds of words arguing why everyone else is wrong, yet none to explain how/why you are correct.”

    I am correct in saying that evolution is not understood. You are incorrect in saying that evolution is understood.

  162. Bill Openthalton 24 Sep 2016 at 7:49 pm

    hardnose —

    Why on earth would anyone feel certain that these abilities are never used for the cell’s advantage, and for the advantage of its descendants.

    Because cells don’t have minds capable of understanding the concepts of self, advantage and descendent, let alone have the knowledge of their genome and the effects of manipulating specific genes. It’s just too far-fetched to ever take seriously.
    Do you also believe ants build faster than light spaceships? We have as much evidence for this as for your claims about cells, and it is about as likely. But hell, it would be fun if it were true.

  163. bachfiendon 24 Sep 2016 at 8:20 pm

    Hardnose,

    You still don’t understand that the cause of evolution is the changing environment of a reproductively isolated population. If the population’s environment isn’t changing, then there’s no evolution (save for neutral genetic drift). Populations evolve to the environment that currently exists, and that’s where the selection comes in.

    Populations can’t evolve to suit environments that don’t currently exist. Selection can’t favour variations better adapted to future currently non-existent conditions. They can’t evolve to suit future environments. To simplify it for you – the dodo on Mauritius couldn’t evolve the power of flight in the early 17th century so as to adapt for the arrival of Dutch and English sailors. Evolution doesn’t have foresight. If the environment changes too much, then the population just goes extinct, which is the history of 99.9% of species on Earth.

    There’s no direction in evolution. The universe doesn’t exist to create you. You’re committing the lottery fallacy, thinking that current state of affairs was the pre-ordained aim. You’re just an accident. Live with it.

    We do understand evolution. You refuse to understand evolution because of your ideological blinkers.

  164. bachfiendon 24 Sep 2016 at 8:52 pm

    And to illustrate hardnose’s ideological blinkers, in his very first comment on the previous thread on evolution on August 5 he wrote “‘The mechanism of this change is natural selection acting on essentially random variation’. That is NOT part of the theory of evolution. That is Neo-Darwinism” (actually it’s part of evolution ever since Darwin, in all its revisions. And finishes with ‘Your motivation? To support materialism/atheism. You never admit this, and pretend not to see it. You are committed to an ideology and cannot see beyond it’.

    If hardnose disagrees with the mechanism of evolution then by his argument he’s supporting non-materialism/theism. For ideological reasons (actually worldview reasons, but then again hardnose has enormous problems with the meaning of words and concepts).

  165. hardnoseon 24 Sep 2016 at 8:58 pm

    “For ideological reasons (actually worldview reasons, but then again hardnose has enormous problems with the meaning of words and concepts).”

    I was just having the same thought about you.

  166. bachfiendon 24 Sep 2016 at 9:33 pm

    Hardnose,

    If you think that selection can chose variations to suit organism’s future needs, not to adapt to current conditions, then you need to demonstrate that it actually occurs. You need to provide the evidence that it actually occurs. You pride yourself (wrongly as it turns out) to be evidence.

    There’s absolutely no evidence for your delusion.

    You confuse current state with preordained target. You’re committing the lottery fallacy. Or to put it differently, the sharpshooter fallacy. Imagine someone has a large barn with one wall composed of a thick iron plate. And affixes a wooden target on it. And then fires 100 arrows at it at random. And someone comes along and sees one arrow stuck in the middle of the target, and claims that the archer must have been an expert – ignoring all the arrows on the ground in front of the barn. And embedded in tree trunks to either side of the barn. And in innocent passers by on the other side of the barn.

    I don’t accept Darwinian evolution for worldview reasons. I accept it because it’s the best and most economical explanation.

  167. bachfiendon 24 Sep 2016 at 9:36 pm

    Oops,

    The last sentence of the first paragraph in the comment above should have read …evidence based’. Hardnose’s pigheadedness is just exasperating.

  168. hardnoseon 24 Sep 2016 at 9:46 pm

    Genetic mutations may not be randomly generated, but bachfiend’s comments obviously are.

  169. bachfiendon 24 Sep 2016 at 10:33 pm

    Hardnose,

    No – you’re describing your randomly generated comments. You’re stupid, ignorant, illogical, evidence-free, meschugge, of low IQ…. You’re a typical internet Troll.

  170. steve12on 24 Sep 2016 at 10:46 pm

    “Do you think at some point we will have innovated ourselves into some measure of permanent durability? Genetic engineering + spacefaring tech + bioprinting + nanotech etc suggest a future where we’re practically immortal with population centers in every conceivable environment.”

    Permanent? No. I think that’s way too much of an overreach. I think there are certainly structures like brains that confer a sufficiently flexible survival advantage that they aren’t likely to be selected against.

    But evolution is more than mutation and selection. I brought up genetic drift above in my example of how a lowering in intelligence humans can occur to highlight this point. There are all kinds of cataclysms that could make brains completely irrelevant and just kill us. Life on the bottom of the ocean, e.g. (say, we lose the magnetosphere or something) is suddenly the most fit life on the planet. Our brains are useless against radiation. Good bye. And that’s just one example.

    As far as the tech angle, sure anything is possible I guess. But I have no reason to think that we’ll technologically create de facto invulnerability anytime soon. I don’t buy that sort of Kurzweil notion that we can extrapolate limitless technological advancement in any particular area based on some unitary non linear rate of change.

    I’ll believe in those technologies when we’re in some reasonable distance to attainment, and I don’t think that we are.

  171. ccbowerson 24 Sep 2016 at 10:52 pm

    “I am correct in saying that evolution is not understood. You are incorrect in saying that evolution is understood.”

    Where did I say that? I didn’t. Stop arguing against strawmen to avoid making your own argument. Stay on topic.

    Where is your evidence for ‘purpose’ in specific mutations? What is the evidence for directed mutations? We have evidence that mutations appear random; where is there evidence to the contrary?

    People are willing to engage in the details of your arguments. I will not when we can’t get past the initial stages of establishing ANY evidence for your position . Put up or shut up.

  172. Steve Crosson 24 Sep 2016 at 10:57 pm

    This whole stupid argument is about the phrase “Natural Genetic Engineering”. HN (and apparently Shapiro) feel that for engineering to occur, then there must be an engineer. Which is probably technically true. But that simply illustrates Shapiro’s ideological bias in the first place when he decided to rename a bunch of already known cellular mechanisms as NGE.

    Hardnose, read Shapiro’s book. It’s only about $20 and very short. And it is mostly references to OTHER PEOPLE’S WORK. None of this stuff is secret or even very new. Shapiro has just taken current knowledge and reached some conclusions that hardly anyone else takes seriously.

    As has already been pointed out dozens of times, Shapiro even acknowledges the fact that NS is necessary to sort out which mutations are beneficial, but then does not seem to realize that fact pretty much invalidates his whole point about NGE playing a primary role as a guiding force. Especially since Shapiro is unable to provide any plausible (or even possible) mechanism for his beliefs. He is simply JAQing off (just asking questions) because as long as he believes there is mystery then he can fill in the blanks any way he wants.

    Shapiro doesn’t have any evidence — he just has opinions. And he tries to pick and choose other people’s work that he can twist to support his own beliefs. Around here, we call that the Hardnose Technique .

  173. steve12on 24 Sep 2016 at 11:00 pm

    This recent exchange really goes to my point that he is purposefully trolling is.

    Here, Steve does a really good job of boiling things down to the points of contention:
    # Steven Novella on 24 Sep 2016 at 7:10 am

    Any person who was arguing in good faith would have replied to that post and moved the conversation forward.

    Dr. TheTroll responds here.

    # hardnoseon 24 Sep 2016 at 6:12 pm

    He ignores just about all of Steve’s post. Really? Totally on purpose. Totally in bad faith.

    This guys is some sort of F*ing weirdo that gets off on the attention or the feeding of some delusions of grandeur that he’s bested the experts.

    What a little freak.

  174. ccbowerson 25 Sep 2016 at 12:13 am

    Over a thousand comments on the Mike Pence Evolution post. I can’t engage his nonsense this much.

    If we are going to engage him, let’s stick to substance, demand evidence for his nonsense arguments, and keep him on the topic. Respect your time and stop playing his game. If HN is a fool, what do you call those of us who constantly engage a fool in his nonsense?

    Despite many threads about directed mutations he has provided no evidence that is better explained by a “purposeful” mutation hypothesis than is already explained by what is mainstream modern evolutionary theory.

    Still waiting on that evidence, and all he does is responds “I am correct in saying that evolution is not understood.”

    So to the extent that we have gaps in knowledge, that is evidence for your nonsense? Again, where is the evidence that is best explained by your directed mutations?

  175. BillyJoe7on 25 Sep 2016 at 12:13 am

    HN: “Why on earth would anyone feel certain that these abilities are never used for the cell’s advantage, and for the advantage of its descendants”

    BO: “Because cells don’t have minds capable of understanding the concepts of self, advantage and descendent, let alone have the knowledge of their genome and the effects of manipulating specific genes. It’s just too far-fetched to ever take seriously”

    This has been put to him at least three times now but he never responds and won’t again – unless my saying so makes him finally respond!

    Cells would need to have a fairly perfect knowledge of their own genomes. They would need to know which genes do what. They would need to know which changes would be beneficial, and which changes would be detrimental so that they can select the beneficial ones. They would have to have the ability to direct the correct mutation to the correct part of the genome. And, of course, in order to select the correct mutation, they would have the ability to sense the change in the environment to which they are creating beneficial mutations.

    Either that or he is using the words “purposeful” and “directed” metaphorically and, if that’s the case, there is actually nothing to explain and we merely need to remind ourselves that cells can’t actually do all those things listed in the above paragraph. We don’t actually mean that cells purposefully direct mutations in their genomes.

  176. BillyJoe7on 25 Sep 2016 at 12:17 am

    Perhaps we should all stop posting and force him to respond to SN’s last post.
    We are giving him too much to pick and choose from.

  177. BillyJoe7on 25 Sep 2016 at 1:10 am

    And here I am defeating my own suggestion…

    I don’t have a lot of spare time, and I’m presently quarter way through a 600 page book on cancer (if anyone is interested, it is “The Emperor of All Maladies” by Siddhartha Mukherjee, an impressive first book by an oncologist which is essentially an easy to read – and really well written – account of the history of the treatment of cancer), but I’ve decided to read again that damn annoying book by James Shapiro “Evolution: A View from the 21st Century”. It’s annoying because it talks about all the advances in understanding that have accumulated over the past fifty years as if it is all undiscovered and new; and it presumes what will “inevitably” be discovered over the course of the present century (as if anyone could actually know); and it completely mischaracterises Modern Evolutionary Theory (see below).

    Here is James Shapiro at the end of his introduction to his book:
    “…the conventional view of evolution [is] as a selection-biased random walk through the limitless space of possible DNA configurations”
    I’m not sure if that was ever the case, but it certainly has not been for at least three decades.

  178. BillyJoe7on 25 Sep 2016 at 1:59 am

    James Shapiro in “Proofreading DNA Replication”:

    Firstly he falsely claims that proofreading is not part of the conventional approach to evolutionary change! Then he says that when an error occurs in DNA replication, DNA polymerase senses the distortion in the structure of the growing double helix and polymerization is halted. Clearly the word “senses” is a metaphor. In truth, the distortion simply results in the DNA polymerase being unable to continue (as a result of basic physics and chemistry).

    The point is that if we clearly understand that the processes being described in his book are mechanical processes based on underlying principles of physics and chemistry, then there really is no room for “purpose” and “direction” except as mere metaphors for what is actually mechanistic cause and effect. My impression is that some people lose sight of that fact which leads them to the erroneous conclusion that something “extra” is required – God for some, The Conscious Universe for others, who knows what for James Shapiro.

  179. BillyJoe7on 25 Sep 2016 at 2:15 am

    …and again:

    “Proteins…recognize specific types of mismatches [between the template DNA and the new DNA strand] and direct the error excision and replacement process”

    The highlighted words are just metaphors for what happens mechanistically.

  180. BillyJoe7on 25 Sep 2016 at 2:31 am

    Well you would think so, but here is James Shapiro’s explanation using yet another metaphor:

    “We can think of this….proofreading process as equivalent to a quality control system in human manufacturing. Like human quality control systems, it is based on surveillance and correction (cognitive processes) rather than mechanical precision”

    It may not be precise – 1 error in 10^5 for the polymerase, and 1 error in 10^9 after proofreading – but it is still mechanical. It may be “like” a “cognitive process”, but it is actually a mechanical process.

    Ok, I’ll finish now, otherwise I’m never going to finish this damn book.

  181. bachfiendon 25 Sep 2016 at 5:52 am

    Hardnose is a John Hampden of the Internet. In case you don’t know the history, John Hampden made the life of Alfred Wallace (the co-discover of natural selection as a mechanism of speciation) a misery for some 21 years, in an attempt to prove that John Hampden’s ideas were correct.

    John Hampden wasn’t stalking Alfred Wallace in connection with evolution. He was a flat Earth believer. He wagered that no one would be able to prove that the Earth was round. Wallace took up the bet, proved that the Earth was round and unleashed the pychopathic hate campaign of Hampden, only ended by his all too delayed death.

    Wallace should never taken up the bet, since everyone sensible at the time knew that the Earth was round. In the same way that we should ignore our little narcistic Internet Troll hardnose with his similarly delusional idea that mutations are non-random. And that evolution has a direction.

  182. ccbowerson 25 Sep 2016 at 7:42 am

    “We are giving him too much to pick and choose from.”

    Yes. Spending time arguing evolutionary mechanisms allow him to revert to “evolution is not fully understood.” No matter what is said by others, we have his incredulity to counter, and he is really not going to let that change.

    “And here I am defeating my own suggestion…”

    Thanks for the book suggestion, and your comments on the Shapiro book are useful, as I doubt I will get around to reading that.

  183. hardnoseon 25 Sep 2016 at 9:36 am

    “Shapiro even acknowledges the fact that NS is necessary to sort out which mutations are beneficial, but then does not seem to realize that fact pretty much invalidates his whole point about NGE playing a primary role as a guiding force.”

    I have explained this probably hundreds of times by now, but you just can’t seem to get it. Natural selection is a fact. It is impossible to deny natural selection, because it is something that absolutely has to happen.

    But there is a big difference between acknowledging that NS really does happen, and claiming (as Dawkins does) that NS is the organizing force of evolution.

    Selection, whether natural or artificial, will always sort things out. That is saying nothing about what causes the variations that will be selected from.

    You can create variations with artificial genetic engineering, and you can sort them out with artificial selection. Does the fact that you sorted them out with artificial selection invalidate the fact that you created them with artificial genetic engineering?

    The whole controversy centers on what is the cause of beneficial mutations. There may be many different causes and explanations. A lot of research has been done and some of it has found directed mutations, while some has found random mutations. This research is ongoing.

    Dawkins, Lenski, etc., believe that all beneficial mutations are accidents/errors. However it is known that cells do have the ability to modify their DNA.

    You are worried that natural genetic engineering assumes that cells have some kind of “intelligence.” But cells do all kinds of complicated things to maintain their survival, and the survival of the organism or colony they may belong to. Why doesn’t that get you worried that cells might be intelligent?

    Whatever you feel a need to believe is irrelevant. All that counts, in a controversy like this, is scientific observations and data.

  184. Steve Crosson 25 Sep 2016 at 11:23 am

    Hardnose: “I have explained this probably hundreds of times by now …”

    You have explained nothing!

    You (and Shapiro) have made evidence-free assertions and are simply interpreting the available evidence far differently than the vast majority of actual experts. Unless you can provide evidence (and prove you actually understand it) that counters Steve Novella’s excellent summation, then you are simply an ideologue and a troll.

    Asserting that something is true simply because Shapiro says it is, is NO different than asserting something is true because the bible or any other “holy” book says so.

    I agree with the many others who have said that they will not continue to engage you unless you provide meaningful evidence and are willing to rationally and logically discuss it. That is how we determine what we know in the first place. Your constant refrain of “we don’t know everything” is meaningless bullshit which does nothing to weaken what we actually DO KNOW. And what we DO KNOW is that the laws of physics, chemistry and logic strongly indicate that your hypothesis is so wildly implausible as to be safely considered impossible — UNLESS you can provide good evidence to the contrary. Extraordinary claims require extraordinary evidence.

    As others have said, put up or shut up. It is pointless to try to have a discussion with a child who wants to believe in Santa Claus.

  185. steve12on 25 Sep 2016 at 11:40 am

    Kudos to BJ7 for reading Shapiro’s book.

    I read Dr. TheTroll’s response above, and I’m sure I see that same errors as everyone else. But this is the thing: the more your reply boxes him in a corner, the more likely he is to either not reply or obfuscate.

    He’s just going to live in the margins of what we mean by “random” and “intelligence”.

    Seriously. How much of his schtick is based on refusal to define terms or acknowledge distinctions in terminology? Steve already granted:

    “The location and frequency of mutations is not random. There are genetic mechanisms that contribute to mutations, increasing the frequency and creating hotspots on the genome. As far as we can tell, these serve the purpose of generating variation when and where it is needed.”

    Dr.The Troll ran like Usain Bolt from this because it would mean that this nonsense would GO somewhere. He won’t acknowledge the “in respect to what” part of discussing what random means in the the context of the Modern Synthesis. And this refusal started 1000 (!!!!!) comments ago. 1000 comments and this ass hole is still dodging this?

    He’s a little liar that will continue to derail and needle while refusing to engage for the purpose of assuaging some sickness in his personality-disorder addled psyche. And right now, he runs this blog. That’s just what has happened now.

    Enough is enough. He’s been given every opportunity to stop lying.

    I vote for ban (not that we actually vote on this, I know :))

  186. hardnoseon 25 Sep 2016 at 12:07 pm

    “The location and frequency of mutations is not random. There are genetic mechanisms that contribute to mutations, increasing the frequency and creating hotspots on the genome. As far as we can tell, these serve the purpose of generating variation when and where it is needed.”

    That is the point I have been trying to make, and that is the kind of thing Shapiro has been saying.

    If the variations were accidents/errors, as Dawkins claims, they would not occur “when and where” they are needed.

  187. Steve Crosson 25 Sep 2016 at 12:18 pm

    Shorter hardnose: “I can’t back up any of my claims with evidence so I’m going to try to baffle you with bullshit.”

  188. chikoppion 25 Sep 2016 at 12:35 pm

    If the variations were accidents/errors, as Dawkins claims, they would not occur “when and where” they are needed.

    Are you claiming Dawkins denies that genetic mechanisms which produce site-specific variation have environmental triggers? Because that claim would be truly and exceptionally ignorant.

  189. mumadaddon 25 Sep 2016 at 12:35 pm

    “If the variations were accidents/errors, as Dawkins claims, they would not occur “when and where” they are needed.”

    Hilarious! He’s talked himself round in a circle. Always tilting at windmills…

    I vote ban too. This has become ridiculous.

  190. hardnoseon 25 Sep 2016 at 12:50 pm

    “The location and frequency of mutations is not random. There are genetic mechanisms that contribute to mutations, increasing the frequency and creating hotspots on the genome. As far as we can tell, these serve the purpose of generating variation when and where it is needed.”

    “there is no evidence for any mechanism by which the specific mutations that occur are guided in any way, move toward any predetermined or specific end, or are anything other than completely random.”

    Steve N’s position seems a little confusing. He states that mutations occur where and when they are needed, and then he states that the “specific mutations” are completely random.

    So he agrees that the location of mutations is not random, but is related to the needs of the cell at a particular time.

    However, he thinks that the actual change, at a particular location at a particular time, is unrelated to the needs of the cell.

    That may be true, or not. It seems he is going beyond what is currently known.

    But let’s say he is right, and the timing and location of mutations are purposeful (not random accidents or errors), but the actual changes are random. In other words, there is a predetermined set of possibilities, but the selection from that set is random.

    That would mean that beneficial mutations are NOT accidents/errors. It would mean that, although there may be a random (or semi-random) component in the process, the process overall is relevant to the cells’ needs at the moment.

    Of course, it may turn out that as evolution research progresses, more cases of directed mutation will be found. And in that case, the consensus would eventually change.

    But even if Steve N’s assumptions turn out to be correct, strict neo-Darwinism, as expressed by Dawkins, etc., would be wrong.

    Dawkins says that genetic mutations are never in any way a response to environmental stress, and in no way serve the purposes of the cell. He says beneficial mutations are always the result of accidents/errors.

    In my opinion, some degree of randomness is probably involved, but there is also purpose.

    We can see combinations of randomness and purpose throughout nature, and also in our human lives.

    A plant’s seeds are scattered randomly by the wind — some land in good soil and are able to grow, while others may land on rocks or in salt water, and die.

    But you would never say the whole process of generating seeds is random and purposeless.

  191. Willyon 25 Sep 2016 at 1:12 pm

    hn: “But you would never say the whole process of generating seeds is random and purposeless.”

    Bad analogy.

    Of course, the process of generating and spreading seeds as we know it today is NOT “random and purposeless”; however, the mutations that led to the processing of generating and spreading seeds was indeed random and purposeless. The chicken and the egg, kind of, except the purposelessness came first for sure.

  192. Steve Crosson 25 Sep 2016 at 1:15 pm

    To repeat, shorter hardnose: “I can’t back up any of my claims with evidence so I’m going to try to baffle you with bullshit (so I can pretend I was right all along).”

    Pretty much everyone agrees that very sophisticated mechanisms have evolved to create variations in the genome which are then acted upon by Natural Selection. Even Dawkins, which you would know if you actually read (and understood) him. But I guess that is too much to ask if you can’t even bother to read your own idol’s book. You’re arguing against a straw man of your own imagination.

    You still haven’t provided any evidence in support of your extremely implausible guided evolution BS.

  193. chikoppion 25 Sep 2016 at 1:59 pm

    [hardnose] Dawkins says that genetic mutations are never in any way a response to environmental stress, and in no way serve the purposes of the cell. He says beneficial mutations are always the result of accidents/errors.

    No. He does not say that.

    Environmental factors can influence the rate of site-specific variability by activating specific genetic mechanisms.

    To produce variability the mechanism in question must lack absolute fidelity, that is, given one set of inputs it must produce a range of outputs. Otherwise, there would be no variability and no mutations.

    An example would be DNA repair mechanisms, which sometimes restore the strand to the initial pre-damage state and sometimes alter it due to the deletion of nucleotides. This is equally true for the mechanisms lumped into Shapiro’s NGE model. Horizontal transfer mechanisms produce variable (non-deterministic) results (in part because they rely upon the aforementioned DNA repair mechanisms).

    Whether or not the variability introduced produces a product that is ultimately beneficial is determined by selection.

  194. bachfiendon 25 Sep 2016 at 3:58 pm

    If hardnose is claiming that it’s possible for a cell to have mechanisms that alter its DNA in such a way as to provide increased variability at a time when it’s necessary to have increased variability – when the cell’s environment is changing – then I don’t have too much problem in accepting that it might be feasible.

    I don’t think that the evidence is there though. And even if – the changes have to undergo selection to winnow out the deleterious changes leaving the beneficial ones.

    But if hardnose is persisting in his opinion that cells can change their DNA to meet future needs, to adapt to conditions not currently existing, that changes in DNA are directed, then he’s just wrong. There’s no evidence to support that claim.

    He still wants his innate propensity of increasing complexity and intelligence in biological systems. Systems science doesn’t support it. NGE doesn’t provide a mechanism. There’s no evidence that there’s a tendency to increasing complexity and intelligence anyway.

  195. hardnoseon 25 Sep 2016 at 4:12 pm

    The conversation here gets into an infinite loop:

    1. Someone says the genetic mutations that turn out to be beneficial were generated randomly.

    2. I show evidence that cells can modify their DNA in response to environmental pressures.

    3. Someone says that, even if the mutations are not entirely random, they are still subject to natural selection, and therefore natural selection is true.

    4. I say that I agree natural selection is true, every scientific person agrees that natural selection is true.

    5. I say that the controversy is about whether beneficial mutations result entirely from accidents/errors.

    6. Someone says there is no evidence for that.

    JUMP TO LINE 2

  196. Steve Crosson 25 Sep 2016 at 4:34 pm

    Repeating yet again:

    Shorter hardnose: “I can’t back up any of my claims with evidence so I’m going to try to baffle you with bullshit (so I can pretend I was right all along).”

    Until you actually provide evidence for your belief that something other than NS is the guiding force for evolution, then no matter how many times you try to repeat the loop, you’ll still be wrong.

  197. BillyJoe7on 25 Sep 2016 at 4:48 pm

    hardnose,

    The problem is that you are still attacking straw man versions of the modern synthesis; you still do not understand what is meant by the word “random” (note: when you put what SN said in your own words, you are WRONG. He is NOT saying that); you refuse to accept that words like “purpose” and “direction” are anthropomorphisms; and you have still not supplied any evidence or a possible mechanism for purposeful directed mutation assuming that you are NOT using these words as mere anthropomorphisms (and if you aren’t there is actually NO argument – you are simply agreeing with the modern synthesis without realizing it)

    In other words, the problem is one of your own creation.

  198. BillyJoe7on 25 Sep 2016 at 4:51 pm

    aren’t = are

  199. chikoppion 25 Sep 2016 at 4:57 pm

    1. Someone says the genetic mutations that turn out to be beneficial were generated randomly.
    2. I show evidence that cells can modify their DNA in response to environmental pressures.
    3. Someone says that, even if the mutations are not entirely random, they are still subject to natural selection, and therefore natural selection is true.
    4. I say that I agree natural selection is true, every scientific person agrees that natural selection is true.
    5. I say that the controversy is about whether beneficial mutations result entirely from accidents/errors.
    6. Someone says there is no evidence for that.

    It’s your language.

    1) genetic mechanisms can be influenced by environmental factors to introduce variability*
    2) whether or not any of the resulting variations are beneficial is determined by selection
    3) selection determines which, if any, heritable mutations (traits) are propagated throughout a population

    *mutations also occur in the course of normal DNA function

    In other words:

    1) Random mutation (processes that introduce non-deterministic variability)
    2) Selection
    3) Evolution

  200. hardnoseon 25 Sep 2016 at 5:33 pm

    chikoppi,

    You are making the unwarranted assumption that the generated mutations are just as likely to be detrimental as beneficial. Shapiro strongly disagrees with that.

    (No, I don’t idolize Shapiro, I am referring to him in this debate, as one biologist who currently challenges neo-Darwinism).

    It is well known that cells have complex machinery for reading, correcting, and modifying their DNA.
    Some researchers have found that mutations can be directed — in other words, they are more likely to be beneficial than detrimental. Other researchers deny this.

    It is NOT scientific to decide, at this time, that mutations can never be directed. It is NOT scientific to say that beneficial mutations are always randomly generated.

    There is still an awful lot of uncertainty in evolution research.

  201. hardnoseon 25 Sep 2016 at 5:37 pm

    Also:

    When a neo-Darwinist does admit that cells can modify their DNA, they always claim that these natural engineering mechanisms evolved according to neo-Darwinist principles.

    In other words, NGE evolved by random mutations and selection.

    Well, sure, you can always say that, if you are a devout neo-Darwinist. But you would have absolutely no scientific reason for that belief.

  202. BillyJoe7on 25 Sep 2016 at 5:38 pm

    hardnose,

    “1. Someone says the genetic mutations that turn out to be beneficial were generated randomly.”

    After all this time you still do not understand, or refuse to understand, what is meant by the word “random” as used by evolutionary biologists.

    “2. I show evidence that cells can modify their DNA in response to environmental pressures”

    Firstly, you have not shown any evidence at all, you have simply stated it as a fact. But that is besides the point because…nobody disagrees that there are constraints – physical, chemical, epigenetic.

    “3. Someone says that, even if the mutations are not entirely random…”

    Within the constaints of physics, chemistry and the epigentic mechanisms (that have been built into the genome by the same processes), the mutations are random. If you throw a coin, you can’t get an apple pie, but it’s random as to whether you throw a head or a tail.

    “4. I say that I agree natural selection is true…”

    You are doing your best to minimise the vital importance of natural selection. Without naturtal selection evolution cannot occur. Period.

    “5. I say that the controversy is about whether beneficial mutations result entirely from accidents/errors.”

    You still don’t understand that having contraints does not mean that mutations are not random. You can’t throw a die and get a 7, but it is still random as to whehter you throw a 6.

    “6. Someone says there is no evidence for that.”

    There is no evidence that within the contraints of physics, chemistry and the epigentic mechanisms (that have been built into the genome by the same processes), mutations are not random as to whether they are beneficial. That is the entire point. And, if you do not disagree with that point then you do not disagree with the modern synthesis, merely with your straw man version of it.

    But I’m interested – where does that leave your “puposeful” and “directed” except as anthropomorphisms, and if do agree that they are anthropomorhpisms, what is your argment exactly.

  203. BillyJoe7on 25 Sep 2016 at 5:48 pm

    hardnose,

    “When a neo-Darwinist does admit that cells can modify their DNA…”

    They don’t “admit” it, they’ve know it for over 50 years!

    “…they always claim that these natural engineering mechanisms evolved according to neo-Darwinist principles”

    How else?
    There is no other mechanism.
    There is no other plausible or possible mechanism.

    “In other words, NGE evolved by random mutations and selection”

    That’s right.
    Imagine the first ever mutation. Within the constraints of physics and chemistry and the availabilty of the necessary ingredients in the environment, and before any epigenetic mechanism had evolved, the mutations were random and the selection was natural. Therefore, epigentic mechanism must have arisen through random mutation and natural selection, and these epigentic mechanisms then acted as further constraints on those random mutations on which natural selection could act.
    There is no other possible or plausible mechanism.

  204. Bill Openthalton 25 Sep 2016 at 6:02 pm

    BillyJoe7 —
    The problem lies in the active tone of the sentence

    “2. I show evidence that cells can modify their DNA in response to environmental pressures”

    The cells do not modify their DNA, the DNA is modified by natural processes. The cell is not endowed with agency as suggested by the active voice, but exactly that is what hardnose apparently believes — the cell is a homunculus. It’s like this recent headline from nj.com: “Girl, 17, critical after car crashes into tree in Whiting”. The car didn’t decide to crash into a tree, and neither does a cell decide to change its DNA. The car was crashed into the tree, and the cell’s DNA was changed by the environmental pressure. The language is the problem.

  205. BillyJoe7on 25 Sep 2016 at 6:08 pm

    hardnose,

    “You are making the unwarranted assumption that the generated mutations are just as likely to be detrimental as beneficial. Shapiro strongly disagrees with that.”

    No, he does not. He is saying that there are constraints to random mutation. He agrees that the mutations that do occur within these constraints are random with respect to whether or not they are beneficial, and that natural selection selects the beneficial mutations. He has been quoted here numerous times saying exactly that.

    “It is well known that cells have complex machinery for reading, correcting, and modifying their DNA”

    All of which act as constraints within which mutations are random as to whether or not they are beneficial.

    “Some researchers have found that mutations can be directed — in other words, they are more likely to be beneficial than detrimental.”

    Example please, because this is getting pretty tiring.

    “It is NOT scientific to decide, at this time, that mutations can never be directed. It is NOT scientific to say that beneficial mutations are always randomly generated.”

    But it IS scientific to arrive at a position based on the totality of the evidence that exists at the present time. And that position is that evolution occurs by a process of random mutation and natural selection, and that there is no evidence or mechanism for direction and purpose in evolution except as short hand metaphors or anthropomorphisms for what are purely mechanistic processes.

    There is still an awful lot of uncertainty in evolution research.

  206. BillyJoe7on 25 Sep 2016 at 6:17 pm

    Bill,

    That is what I mean by his use of metaphors/anthropomorphisms as if they are the real thing
    I’m trying to get him to state clearly whether he is using them as metaphors or if he really believes cells do things purposefully.

    “The cell is a homunculus”

    That thought entered my mind yesterday but then I forget about it.
    For the words “purpose” and “direct” not to be metaphors, the cell would have to be a homunculus!
    The whole idea is ridiculous on its face.

  207. hardnoseon 25 Sep 2016 at 7:09 pm

    Coyne’s definition of neo-Darwinism:

    “There is only one going theory of evolution, and it is this: organisms evolved gradually over time and split into different species, and the main engine of evolutionary change was natural selection.”

    Shapiro criticizes that theory, and claims that natural selection is NOT the main engine of evolutionary change.

    Coyne believes that mutations that turn out to be beneficial (are later selected for) are accidents/errors. In other words, they are random with respect to the needs of the cell.

    Shapiro believes that beneficial mutations can result from natural genetic engineering mechanisms within cells. They are NOT random, but are related to the needs of the cell. Some randomness may be involved, but the mutations are triggered by environmental stress and are related to the cell’s adaptive needs.

    Based on everything I had learned about evolution in the past, I agree with Shapiro and I disagree with Coyne.

  208. chikoppion 25 Sep 2016 at 7:19 pm

    I was about to reply, but BillyJoe7 said pretty much what I was about to.

    (P.S. Where do I get some of those coins that turn into apple pie?)

    The benefit of mutations in evolution is to produce variation in a population.

    If a mutation doesn’t appear until it is needed then it is already too late.

    Take the Harvard video referenced in this article. The vast majority of bacteria perished when encountering the higher concentration of antibiotic. Those that didn’t were the ones that already had atypical resistance. We know the needed variation wasn’t manufactured in response to the environment, because any bacteria that encountered the barrier without already having the variant gene(s) were killed.

    This mechanism of variation and selection doesn’t even require DNA.

    The same process is observed in non-cellular structures such a prions. Prions are folded protein strands. They don’t have DNA. They are just complex molecules. Prions replicate by binding to other proteins and causing them to adopt the same shape. Because the replication process is imperfect (constrained but non-deterministic) it creates variation. For this reason populations of prions “evolve” due to selective pressures, developing traits like drug resistance.

  209. hardnoseon 25 Sep 2016 at 7:35 pm

    “If a mutation doesn’t appear until it is needed then it is already too late.”

    It is known that bacteria can increase their mutation rate in response to stress. So the mutations are created when they are needed, and can result in adaptation.

  210. hardnoseon 25 Sep 2016 at 7:42 pm

    “If a mutation doesn’t appear until it is needed then it is already too late.”

    It is also known that bacteria can communicate with each other. So bacteria might be warned about an antibiotic before they encounter it.

  211. chikoppion 25 Sep 2016 at 7:50 pm

    [hardnose] Shapiro believes that beneficial mutations can result from natural genetic engineering mechanisms within cells. They are NOT random, but are related to the needs of the cell. Some randomness may be involved, but the mutations are triggered by environmental stress and are related to the cell’s adaptive needs.

    First, everybody believes that things like horizontal gene transfer and the other known mechanisms Shapiro lumps into his NGE model can produce mutations that may ultimately prove beneficial. This is a non-statement.

    Second, these mechanisms produce variation, NOT specific outcomes.

    [Shapiro] “In terms of generating completely novel genome components, such as exons, introns and regulatory sites, the NGE examples described in Sections 2, 3 and 4 provide rapid means of producing innovations, which can be tested immediately by selection for adaptive utility. If they provide adaptive added value, they will be retained, amplified and dispersed by further cell fusion and NGE activities, as we have seen in Sections 2 and 4. If the novelties are not beneficial, they will be lost or maintained in an unselected fashion.”

    If you are trying to say that environmental factors may stimulate site-specific genetic variation (that may or may not prove beneficial to the specific needs of the organism), then you would have it essentially correct.

    The question of whether variation or selection is more responsible for evolutionary outcomes is philosophical and largely irrelevant. Both are equally indispensable to the evolutionary process.

  212. chikoppion 25 Sep 2016 at 7:58 pm

    [hardnose] It is also known that bacteria can communicate with each other. So bacteria might be warned about an antibiotic before they encounter it.

    True dat! (So good you said it twice?) 🙂

    Dying bacteria might release a chemical that acts activates any number of responses in the colony, such as increased rate of cell division. The result would be an increase in the rate at which genetic variations were produced, which would improve the likelihood that some cells would be equipped to survive the threat.

  213. hardnoseon 25 Sep 2016 at 8:33 pm

    Shapiro: “the NGE examples described in Sections 2, 3 and 4 provide rapid means of producing innovations, which can be tested immediately by selection for adaptive utility. If they provide adaptive added value, they will be retained, amplified and dispersed by further cell fusion and NGE activities, as we have seen in Sections 2 and 4. If the novelties are not beneficial, they will be lost or maintained in an unselected fashion.”

    We have been through this already. Yes, Shapiro says here that the innovations will be tested by natural selection. He does NOT say that the innovations are random, unrelated to the problem the bacteria are facing.

    Random mutations are MUCH more likely to be harmful than helpful. They are highly unlikely to address the problem the organism is facing.

    So why would NGE mechanisms create random mutations? It is already known that they can determine the location of the mutations, so we know they are not completely random.

    It is a mistake to interpret that quote as Shapiro being in agreement with neo-Darwinism.

  214. bachfiendon 25 Sep 2016 at 9:13 pm

    Hardnose,

    No one would be arguing with you if you didn’t have the nonsensical idea that the universe is conscious. Or that there’s an innate tendency to increasing complexity and intelligence in biological systems. That evolution has aims and goals.

    And as I’ve noted to you many times, it’s impossible to distinguish between non-random directed beneficial mutations from random non-directed mutations with the beneficial mutations favoured by natural selection.

    You don’t detect new mutations in real time. For each beneficial mutation that spreads throughout a population (including of bacteria) and becomes detectable, there could have been a hundred or a thousand lethal mutations which are immediately removed before detection. How would you detect a beneficial mutation in a single bacterium in a flask full of other bacteria, until it has reproduced numerous times and formed a significant fraction of the bacteria?

    Beneficial mutations are preferentially detected because they preferentially survive, not because they’re preferentially produced.

    You’re committing the sharpshooter fallacy. Counting the hits and ignoring the misses (which aren’t detectable anyway).

  215. hardnoseon 25 Sep 2016 at 9:43 pm

    We know that mutation rates can increase in response to stress, and we know that the location of mutations is not necessarily random.

    Why would we go from knowing that, to deciding that all mutations are random?

    We also know that cells purposefully modify their DNA.

    There is absolutely no reason for sticking to neo-Darwinism, in spite of what is scientifically known.

  216. bachfiendon 25 Sep 2016 at 10:11 pm

    Hardnose,

    As usual you retreat into irrelevance. Even if mutations increase in number due to stress and their location isn’t random, being localised to specific sites in the genome, you still can’t get to any of the mutations that occur being non-random in nature. The mutations still have to be tested by natural selection, as Shapiro notes, to pick out the beneficial ones to be amplified by survival and reproduction.

    Why would anyone assume that if the first two assertions are true, that the third is also true, that mutations are directed, somehow?

    And that still doesn’t get you to direction in evolution. Adaptation to current needs can’t predict future conditions.

  217. chikoppion 25 Sep 2016 at 10:19 pm

    [hardnose] Random mutations are MUCH more likely to be harmful than helpful. They are highly unlikely to address the problem the organism is facing.

    See my reply above (25 Sep 2016 at 1:59 pm) regarding the necessity of non-deterministic processes in producing mutations.

    Also, citation needed regarding your above claim.

    So why would NGE mechanisms create random mutations? It is already known that they can determine the location of the mutations, so we know they are not completely random.

    No. They can’t “determine the location of the mutations.” Environmental factors can impact the rate at which variability is introduced to gene sequences. It doesn’t target specific nucleotides, nor does it determine what sequence will be adopted in the case of horizontal transfer. It has the effect of making gene sequences less stable.

    We can agree that it is more likely a beneficial mutation may occur in a population if a particular gene sequence is subject to an increased rate of variation. But the individual instances of variation are non-directional.

    High-variability makes a population more robust by providing more options for selection to act upon.

  218. ccbowerson 25 Sep 2016 at 10:41 pm

    “Some researchers have found that mutations can be directed — in other words, they are more likely to be beneficial than detrimental.”

    This is like the “people are saying” Trumpism. Who are “some researchers” and what is their evidence? Or is that a vague statement to dodge any substance to your position.

    “It is NOT scientific to decide, at this time, that mutations can never be directed. It is NOT scientific to say that beneficial mutations are always randomly generated.”

    Nice reversal of the argument and burden of proof. It is well established that random mutations occur, but it is not established that directed nonrandom beneficial mutations occur.

    People aren’t “deciding” that they don’t occur, they have no reason to believe that they do occur without good evidence. But feel free to actually engage the topic any day now and provide some evidence for your position. Perhaps you are waiting until your one millionth word to do this. You are getting close.

  219. hardnoseon 25 Sep 2016 at 10:46 pm

    “Even if mutations increase in number due to stress and their location isn’t random, being localised to specific sites in the genome, you still can’t get to any of the mutations that occur being non-random in nature. The mutations still have to be tested by natural selection, as Shapiro notes, to pick out the beneficial ones to be amplified by survival and reproduction.”

    We have gone over exactly the same things so many times.

    You seem to think something has to be either entirely random or entirely non-random, with no possibilities in between.

    Shapiro says the mutations are tested by natural selection. So what? I have told you over and over the natural selection is going to happen. That has nothing to do with whether or not the mutations are random, or partly random, or not random.

    The cell does not know exactly what mutations will allow it to survive and antibiotic, so there is an element of randomness. But the cell seems to create certain types of mutations in response to certain types of problems. So there is an element of non-randomness.

    We do not have all the information, no one understands exactly how bacteria adapt to antibiotics, etc.

    But we can see that there obviously is an element of non-randomness.

    Natural selection is NOT the driving engine of evolution. That is what Shapiro says, that is what I believe.

    Dawkins says that natural selection is the ONLY driver of evolution. And he says that the principles of evolution are known, there is no controversy.

    Dawkins is wrong, that is what Shapiro says, that is what I am saying here. We have good scientific reasons for thinking that Dawkins is wrong.

  220. hardnoseon 25 Sep 2016 at 10:50 pm

    And Shapiro is not coming to this controversy as a supporter of any particular ideology or philosophy.

    Dawkins, on the other hand, is a devout atheist whose mission is to stamp out religion. So he is emotionally and ideologically motivated to see things a certain way.

    Ideologies and passionate beliefs interfere with unbiased scientific reasoning.

  221. Steve Crosson 25 Sep 2016 at 10:52 pm

    hardnose,

    Watch the video again and then try to answer one question: Why aren’t the bacteria advancing in a much straighter line?

    After all, there are literally millions of individual cells reaching each demarcation line at pretty much the same time. If they really can intelligently respond to the current needs of the cell, then it sure isn’t apparent. Even if they can only improve the odds of a beneficial mutation for the current situation to perhaps 1 in 10, or even 1 in a 100, then there would have to be a LOT of simultaneous successful adaptations. There would be so many (thousands) that it would be difficult or impossible for the human eye to tell them apart and the line would appear to be smooth.

    Instead, we see only a handful of successful lines that occur at varying times and have varying levels of success. Which is exactly what you would expect to see if the successful adaptations were simply the luck of the draw, i.e. random, un-guided, non-engineered, etc.

    This fact, along with the Lenski experiments and the ton of other evidence which has been presented in this and the Mike Pence thread, is the reason that most people question Shapiro’s beliefs. That could change of course if he actually did provide evidence instead of speculation. But so far, neither he nor you has ever presented anything to even slightly call into question the mountain of evidence against you.

  222. Steve Crosson 25 Sep 2016 at 10:56 pm

    hardnose:

    And Shapiro is not coming to this controversy as a supporter of any particular ideology or philosophy.

    Just because he says it, doesn’t mean it’s true.

    Ideologies and passionate beliefs interfere with unbiased scientific reasoning.

    Which is exactly the problem that you and apparently Shapiro have.

  223. bachfiendon 25 Sep 2016 at 11:35 pm

    Hardnose,

    You accuse me of thinking that mutations have to be all random or all non-random, with no middle ground. You do have reading problems don’t you?

    That’s exactly what I was stating. Mutations could increase in number due to stress and they could be non-random in location, but that doesn’t mean that they’re non-random in nature. I conceded the middle ground.

    Also, no one thinks that natural selection is the driving engine of evolution. You’re setting up a straw man argument. Natural selection is a ‘purifying’ force, getting rid of the ‘unfit’, including the previously ‘fit’, the ones adapted to the environment, which has subsequently changed.

    Natural selection doesn’t create the fit. It just gets rid of the unfit.

    The driving engine of evolution is a changing environment as the demonstration of bacterial growth on a giant agar plate with an increasing gradient of antibiotic concentration. The environment for the bacteria is changing as they grow towards increasing antibiotic concentrations.

    Natural selection on its own without a changing environment will do very little, as Lenski’s experiment demonstrated. Only 1 out of 12 lines of E. coli managed to evolve the ability to use citrate after tens of thousands of generations. And that’s only because of competition for scarce resources in an artificial environment.

  224. chikoppion 26 Sep 2016 at 12:09 am

    [hardnose] Natural selection is NOT the driving engine of evolution. That is what Shapiro says, that is what I believe. Dawkins says that natural selection is the ONLY driver of evolution. And he says that the principles of evolution are known, there is no controversy. Dawkins is wrong, that is what Shapiro says, that is what I am saying here. We have good scientific reasons for thinking that Dawkins is wrong.

    What you have is word-salad. “Driving engine” is a meaningless and subjective adjective.

    Genetic processes result in mutations via variation (which is definitionally non-deterministic).

    Selection determines which, if any, of those options are useful, heritable, or propagated.

    The one does not work without the other. Change in one organism is not evolution. Evolution requires a change in the heritable traits of a population.

  225. bachfiendon 26 Sep 2016 at 3:30 am

    Hardnose,

    And I used ‘driving engine’ of evolution only because you used the term. I assume that you were embarrassed to use the word ’cause’, and you were just do your usual trick of changing terms.

    Let’s do some calculations. The reading (and transcription) error rate in bacteria such as E. coli is between one in a million and one in a hundred million base pairs. E. coli has more than 5 million base pairs in its genome. Assuming a transcription error rate of one in a hundred million, there’s a 5% chance there will be at least one error (or mutation) in one daughter bacterium from a division. And a much lower chance of 2 or more mutations.

    With a one in a million transcription error (mutation) rate, the chance of one mutation is 99.5%, two – 99% and 10 around 95%.

    Assume the mutation rate increases when the bacterium is under stress. And the mutations occur in ‘hot’ spots, where mutations have the most effect. There’d be a 95% chance of at least 10 mutations in the ‘hot’ spots. And a very significant chance of very large numbers of mutations.

    If the mutations are directed non-random and beneficial, then why didn’t Lenski’s study show all the 12 lines of E. coli developing the ability to metabolise citrate in a short time instead of just one, and that only after tens of thousands of generations? And why don’t bacteria rapidly and uniformly develop antibiotic resistance instead of what transpired in the demonstration discussed by Steve Novella.

    Mutations may increase when the cell is under stress. They may occur in critical ‘hot’ spots. But there’s no evidence that they’re anything but random in nature – deleterious, neutral or (rarely) beneficial accounting for the rarity of beneficial mutations in both studies.

  226. SteveAon 26 Sep 2016 at 7:24 am

    HN: “Dawkins, on the other hand, is a devout atheist whose mission is to stamp out religion. So he is emotionally and ideologically motivated to see things a certain way.”

    Again with the ‘it’s just Dawkins’ talk.

    What about the tens of thousands of biologists and geneticists who’d pour equal scorn on your deluded thinking. Do you think they’re all hell-bent on tearing down your theist/ID fantasies. Or would that sound like some kind of crazy conspiracy?

    Oh, and “he is emotionally and ideologically motivated” – projection much?

  227. hardnoseon 26 Sep 2016 at 10:02 am

    “Mutations could increase in number due to stress and they could be non-random in location, but that doesn’t mean that they’re non-random in nature. I conceded the middle ground.”

    Ok, cells seem to be able to increase the rate of mutations and to select the location. Most evolution researchers, including Shapiro, would probably accept that. (Not Dawkins, probably, but let’s forget about fanatics for now).

    But we do not know if cells have strategies that increase the percentage of potentially beneficial mutations.

    Some researchers have found evidence for directed mutations, others have not. Lenski did not (however, maybe cells don’t have good strategies for dealing with that particular challenge, we don’t know).

    We do know that mutations can be partially directed — at least in quantity and location. We also know, or assume, there is an element of randomness. We do not know to what degree mutations are random, or non-random, in various scenarios. The research is not finished.

    Let’s assume for right now that cells are only able to increase the rate and location of mutations. We agree that research has shown that. Even if that is all cells can do (and they can probably do a lot more, but forget that for now) — even if that is all they can do, then beneficial mutations are NOT entirely the result of chance.

    We all agree that there is some degree of direction involved. We just don’t know exactly how much is directed, vs. random.

    This means that natural selection is NOT the driver, cause, engine, mechanism, of evolution/adaptation. As Shapiro says, natural selection happens AFTER cells have engineered the potentially beneficial mutations.

    An environmental challenge is one element, bacteria increasing their rate of certain types of mutations is one element. Individuals that succeed in meeting the challenge survive, and the rest die — that is natural selection. NS is a necessary part of the process, but that is saying nothing. NS simply means that some attempts succeed and others fail.

    This type of contest is seen throughout nature (and human civilization also).

  228. chikoppion 26 Sep 2016 at 10:15 am

    There are still so many fallacious statements in that post, but you’ve at least modified your position as a result of the conversation. I’ll credit you with that.

  229. Willyon 26 Sep 2016 at 10:35 am

    hn–EVERYONE thinks natural selection happens AFTER change has occurred.

  230. Steve Crosson 26 Sep 2016 at 12:13 pm

    I’m going to keep repeating this as long as necessary — so, probably forever.

    Shorter hardnose: “I can’t back up any of my claims with evidence so I’m going to try to baffle you with bullshit (so I can pretend I was right all along).”

    We all agree that there is some degree of direction involved.

    No we don’t! Only you, Shapiro and a few other outliers believe that there is any direction to evolution. You have never provided one bit of evidence to support that contention.

    The ONLY thing that we agree on is that more variation equals greater opportunity for a beneficial mutation to occur. The more often you roll a pair of dice, the more likely it is that you will eventually get “snake eyes”. There is no change at all in the randomness of the process, and there certainly is no evidence for any kind of direction or guidance.

    You’ve ignored my challenge about the video, but it is a perfect example of your mistake. If individual cells really were able to respond to their environment, then why don’t they?

    As the video makes clear, out of millions of cells supposedly making intelligent/directed changes to their own genome, only a very, very few actually succeed in creating a beneficial mutation. If there is a direction, it is clearly going the wrong way.

    We may not know everything about evolution yet, but we know enough to know that there is no evidence for any kind of direction or goal.

  231. hardnoseon 26 Sep 2016 at 12:51 pm

    Lenski’s experiment involves a particular kind of challenge. Maybe the strain of bacteria in the experiment have a hard time in that scenario.

    Other research has found bacteria doing a very good job of adapting to challenges such as antibiotics. And we know all too well how easily bacteria can become resistant.

  232. Sylakon 26 Sep 2016 at 12:52 pm

    Bacteria can evolved resistance to anti-biotic and humans can develops resistance to facts ( e have nice example here), but can we evolved a resistance to hardnose? Because WOW, that a persistent infections to my brains, I can feel my neurons blowing up when I read is circular motivated reasoning.

    Anyway, that video was awesome, Dr Novella post was right on the point. Nothing else to be added.

  233. hardnoseon 26 Sep 2016 at 1:00 pm

    “EVERYONE thinks natural selection happens AFTER change has occurred.”

    Well it couldn’t possibly come before. But Dawkins, Coynes, etc., consider NS to be the driver, the organizing force of evolution. It comes after the changes, but since the changes are random (unrelated to the needs of the organism), they are not the organizing force, and it’s the actions of NS that organizes them.

    Dawkins says that evolution is NOT random, even though he says all genetic mutations are entirely random. His reasoning is that NS is non-random.

    NS is something people like Dawkins can always fall back on to explain anything. Creationists can always fall back on God as an explanation, for Dawkins it’s NS. Same kind of concept.

  234. ccbowerson 26 Sep 2016 at 1:51 pm

    “Creationists can always fall back on God as an explanation, for Dawkins it’s NS. Same kind of concept.”

    Yeah. Same exact concept. Except that is different in almost every way, like the existence of overwhelming evidence for NS. Or natural versus supernatural. Or coherent versus incoherent, etc.

    You like to bring up individuals as surrogates for arguments themselves, so you can argue strawmen and mischaracterizations. Lame and boring.

    Show me some mutations that are best explained by directed or nonrandom mutations, rather than random mutation followed by NS. Of course beneficial traits should be more likely to persist in either senario, but one predicts that the mutations that form are random with respect to survival, while the other one (the one you are promoting) predicts mutations should form that are preferentially beneficial.

    We are still waiting for anything but strawmen, dodging, and special pleading.

  235. Steve Crosson 26 Sep 2016 at 1:51 pm

    Lenski’s experiment involves a particular kind of challenge. Maybe the strain of bacteria in the experiment have a hard time in that scenario.

    Textbook example of the logical fallacy known as Special Pleading.

    Other research has found bacteria doing a very good job of adapting to challenges such as antibiotics. And we know all too well how easily bacteria can become resistant.

    Because there are trillions thus dramatically increasing the possibility of a random mutation occurring which turns out to be beneficial — as is clearly demonstrated in the video!

    Dawkins says that evolution is NOT random, even though he says all genetic mutations are entirely random. His reasoning is that NS is non-random.

    Of course NS is non-random — it couldn’t be otherwise. The laws of physics and chemistry determine which organisms (and which mutations) are best suited to survive in any given environment.

  236. hardnoseon 26 Sep 2016 at 3:11 pm

    “the existence of overwhelming evidence for NS.”

    Because NS by definition has to be true. It is not a meaningful concept.

    And there is NO evidence for Dawkins’ claim, that NS is the driving force of evolution.

  237. hardnoseon 26 Sep 2016 at 3:12 pm

    “Of course NS is non-random — it couldn’t be otherwise. The laws of physics and chemistry determine which organisms (and which mutations) are best suited to survive in any given environment.”

    I never said otherwise. I said Dawkins considers NS to be the non-random ORGANIZING FORCE of evolution.

    NS is not random, NS is always true, NS is an empty concept.

  238. Steve Crosson 26 Sep 2016 at 4:26 pm

    I said Dawkins considers NS to be the non-random ORGANIZING FORCE of evolution.

    Still waiting for you to provide some actual evidence of an alternative ORGANIZING FORCE of evolution.

    Endless repetition of evidence-free assertions by either you or Shapiro =/= Evidence.

  239. BillyJoe7on 26 Sep 2016 at 4:26 pm

    In his last dozen posts, hn has descended into almost total incoherence, and it is impossible to respond in any meaningful way to incoherence, so that’s not a bad strategy when your argument has completely failed and you want to create the appearance of still being in the game. His other strategy is to avoid like the plague responding to any posts that destroy his position, and he has increasingly made use of this strategy. The combination make it not worth reading what he has to say, not worth responding to what he says, and a complete waste of time trying to educate him. The only reason left is to educate the fence-sitters who read this blog, but they have surely lost interest long ago in the mind numbing stupidly of his ramblings.

  240. arnieon 26 Sep 2016 at 4:44 pm

    IMO, BillyJoe7 put it succintly and very correctly. And it doesn’t matter anymore if HN “has the last word”. At this point, no one will be educated nor likely to be influenced by his incoherent nonsense. Thank you BJ7.

  241. ccbowerson 26 Sep 2016 at 4:47 pm

    “In his last dozen posts, hn has descended into almost total incoherence…”

    This is because the comments have been leaner and not delving into irrelevant details and side arguments. This is precisely how we should always engage HN on these topics, to avoid giving him troll food by sticking to the substance.

    At some points it almost appears that he has learned something enough to narrow his arguments, but of course I’m sure after some time has past we will be back to square 1.

  242. ccbowerson 26 Sep 2016 at 4:50 pm

    “Because NS by definition has to be true. It is not a meaningful concept.”

    Hahaha. If NS is not meaningful, how did it revolutionize science?

  243. bachfiendon 26 Sep 2016 at 4:52 pm

    Hardnose,

    I’ve pointed out to you many times, and you’ve always refused to respond, it’s impossible to distinguish between non-random directed beneficial mutations and random non-directed mutations with the beneficial ones being left because the harmful ones have been eliminated by selection unless you can detect all the mutations occurring in real time. Which is not possible.

    A researcher who sets up an experimental study in which bacteria are placed under some stress and then comes back later and finds that bacteria with mutations form a larger than expected proportion of the total number of bacteria alive at that point of time in the study (if the rate of mutation was fixed at a certain rate), that the mutations which occurred were located at specific points along the bacterial genome rather than being randomly scattered along its length and that they’re generally beneficial, she’s NOT justified in claiming that her experiment indicates that the rate of mutation increases with stress, that there’s hot spots for mutation in the bacterial genome and that mutation is directed towards beneficial ones because the mutations which are detected are beneficial.

    An alternative explanation is that:

    Lethal mutations are eliminated immediately, leaving just the beneficial ones, giving the appearance of direction towards beneficial mutations.
    Mutations in critical parts of the bacterial genome are generally lethal, and are eliminated immediately leaving just mutations in certain less critical parts of the genome, such as the regulatory areas or less critical enzyme genes, giving the appearance of ‘hot’ spots for mutation in the genome.
    The normal bacteria without mutations could die out more quickly, in response to the stress, than the bacteria with beneficial mutations, which are able to divide more often (owing to the loss of competition) giving the impression that the mutation rate has increased.

    The only way of distinguishing between the two possibilities, and it’s not definitive just highly suggestive, is to compare the rate at which beneficial mutations occur.

    With non-random directed beneficial mutations, particularly if they’re increased in rate and localised at hot spots in the genome due to NGE, then beneficial mutations should occur often and early.

    With random non-directed mutations, with the non-beneficial ones being removed by selection, then beneficial mutations should occur later and infrequently.

    And what did we find with the Lenski study? Possibility number 2 – only one strain out of 12 evolved the ability to metabolise citrate, and that only after tens of thousanands of generations, highly suggestive that mutations aren’t directed towards benefit and that they’re random.

    You think the bacteria in Lenski’s weren’t under the right kind of stress? The bacteria in each flask at the start of each day represented 1/100 of the bacteria in the flask at the end of the previous day, and were presented with a new pristine environment and were able to divide 6 or 7 times before all the available sugars were consumed leaving them to starve for the rest of the day. Dividing 6 or 7 times would only take 2 or 3 hours, leaving the bacteria to starve for over 20 hours of the day. And yet – there’s this lovely rich resource of delicious citrate just waiting to be used, if the bacteria develop just 2 mutations. If they develop the necessary two mutations, then they would have a marvellous new source of energy to divide and come to dominate.

    NGE with increased mutation rate in ‘hot’ spots should do the job nicely. The bacteria are under stress. They’re starving. They need the citrate for energy. Just 2 mutations would do it. Non-random directed mutations should easily do it.

    Does it happen?

    NO. You get exactly the result expected if mutations are random.

  244. Bill Openthalton 26 Sep 2016 at 6:02 pm

    hardnose —

    Lenski’s experiment involves a particular kind of challenge. Maybe the strain of bacteria in the experiment have a hard time in that scenario.

    A textbook example of special pleading.

  245. hardnoseon 26 Sep 2016 at 6:09 pm

    “Hahaha. If NS is not meaningful, how did it revolutionize science?”

    Not everyone thinks it revolutionized science. It revolutionized science for some, by causing them to fall into a sort of black logic hole.

  246. ccbowerson 26 Sep 2016 at 7:11 pm

    “Not everyone thinks it revolutionized science”

    Look at our understanding of life before and after natural selection. It takes serious motivated reasoning to deny its incredible impact. In retrospect it may seem obvious, but that is only true after understanding the body of knowledge that resulted from the insights from natural selection and evolution more broadly.

  247. hardnoseon 26 Sep 2016 at 7:39 pm

    “Look at our understanding of life before and after natural selection.”

    It has certainly had a big impact. Unfortunately, it is nonsense.

    Natural selections says that organisms that do not die will survive and will probably reproduce.

    How could that not be true??

    Natural selection supposedly explains how accidental mutations cause evolution. It sounds good, to some people, but it is NOT scientific. A scientific theory is based on evidence.

    We KNOW that natural selection happens, and we KNOW that evolution happens.

    We do NOT know that beneficial mutations are accidents.

    We know that cells have sophisticated mechanisms (NGE) for reading, repairing, and modifying their DNA.

    We have NO REASON to assume that NGE has no role in evolution.

    We have NO REASON to assume beneficial mutations are accidents.

  248. hardnoseon 26 Sep 2016 at 7:41 pm

    MORE RESEARCH IS NEEDED.

    Dogmatic statements of faith are not helpful.

  249. Steve Crosson 26 Sep 2016 at 8:05 pm

    We have NO REASON to assume that NGE has no role in evolution.

    We have NO REASON to assume that THOR has no role in producing lightning — except for a complete lack of supporting evidence or plausibility.

  250. bachfiendon 26 Sep 2016 at 8:28 pm

    Hardnose,

    As usual, and like all typical Internet Trolls, you refuse to address the point I was making in my last comment.

    We have NO reason to believe that NGE has any role in evolution. Even in the limited cases of bacteria developing resistance to antibiotics or E. coli developing the ability to metabolise citrate in Lenski’s setup, it fails its predictions.

    We have plenty of reasons to believe that beneficial mutations are accidents. It fits all the data we have, including the fact that the natural history of species ever living is that at least 99.9% of them have gone extinct. The result of a changing environment on a species is that it either evolves, migrates or goes extinct. Usually goes extinct. Evolving into a new species is actually very rare and is largely confined to small localised reproductively isolated populations.

    There’s no direction in mutations allowing anything more than a very tiny proportion of species to survive change. And that only temporarily.

    And even if NGE provides a mechanism allowing a cell to adapt to currently existing changed environmental conditions, it can’t allow a cell to adapt to future environmental conditions, if your preference for direction in evolution, for there to be an innate tendency for increasing complexity and intelligence in biological systems, to be true.

    Leave it off. You’re just wrong with your core beliefs. NGE, even if it were to be true, doesn’t help you at all.

  251. ccbowerson 26 Sep 2016 at 8:39 pm

    “It has certainly had a big impact. Unfortunately, it is nonsense…We know that cells have sophisticated mechanisms (NGE) for reading, repairing, and modifying their DNA…MORE RESEARCH IS NEEDED.”

    So NS is nonsense? How do you think that sophisticated mechanisms for DNA reading and repair arose?

    Then you top it off with an appeal to future evidence, as if that will vindicate you. But hey, I guess if your position is not compatible with available evidence, then what else can you do but to make up a future in which you are right today?

  252. chikoppion 27 Sep 2016 at 12:42 am

    We KNOW that natural selection happens, and we KNOW that evolution happens.

    We do NOT know that beneficial mutations are accidents.

    We know that cells have sophisticated mechanisms (NGE) for reading, repairing, and modifying their DNA.

    We have NO REASON to assume that NGE has no role in evolution.

    We have NO REASON to assume beneficial mutations are accidents.

    We have CONFIRMATION that not only are “sophisticated genetic mechanisms” not required, but even DNA isn’t necessary for evolution to occur. Remember the prions (above, 25 Sep 2016 at 7:19 pm)?

    All that is needed is 1) replication with variation, 2) selective pressure.

    I think it would be helpful were you to stop thinking in terms of “beneficial mutations” and “non-beneficial” mutations. No change to the phenotype is intrinsically beneficial. The important factor is variation within a population. It is variation that allows a population to survive and adapt.

  253. hardnoseon 27 Sep 2016 at 9:40 am

    “So NS is nonsense? How do you think that sophisticated mechanisms for DNA reading and repair arose?”

    No one knows how NGE evolved. You are using NS as an explanation for everything.

  254. Steve Crosson 27 Sep 2016 at 3:02 pm

    No one knows how NGE evolved.

    Actually, the conceptual framework of NGE evolved from the anthropomorphic fever dreams of James Shapiro when he decided (without evidence) that an entire class of complicated cellular mechanisms (discovered by other people) were somehow deserving of a fancy name which seemed to imbue them with agency — while neglecting to provide evidence.

    The reason that almost all scientists tend to use NS as an explanation is because it is the ONLY mechanism to date which has ANY evidence AT ALL — and that evidence is copious.

  255. hardnoseon 27 Sep 2016 at 3:06 pm

    NGE mechanisms are known to exist. I can’t understand how you can deny that.

  256. BillyJoe7on 27 Sep 2016 at 3:30 pm

    Well, what a perfect example of hn’s inability to understand what he reads.
    And the irony – he “can’t understand” how Steve can deny something that he is not denying!

  257. Steve Crosson 27 Sep 2016 at 3:32 pm

    Reading comprehension is a wonderful thing. You should try it sometime.

    I SAID the mechanisms exist. It is Shapiro’s characterization of them as “engineering” which is the misleading and totally unsubstantiated part.

  258. Steve Crosson 27 Sep 2016 at 3:38 pm

    It should be obvious but my last comment was directed to HN. BJ7 snuck a comment in the middle while I was typing.

  259. bachfiendon 27 Sep 2016 at 4:01 pm

    Hardnose,

    If NGE exists, and I’ve provided arguments that it doesn’t in relation to the parts where there’s supposed to be accelerated mutations in ‘hot’ spots, then it’s still subject to natural selection. And NGE doesn’t provide any mechanism for directed mutations, which you desperately want to exist.

    You still refuse to respond to my arguments.

    Evolution is CAUSED by a changing environment. It’s MECHANISM is natural variation (which could be due to NGE or random mutations) acted upon by selection (predominantly natural).

    I don’t know how many times I have to repeat myself before it gets through your thick creationist Internet Troll skull. You know nothing about evolution. Your ignorance is breathtaking.

    If natural selection exists on the Internet you would have been banned long ago, at least from all evidence based blogs. You would have been forced to sites such as Evolution News.

  260. BillyJoe7on 27 Sep 2016 at 5:11 pm

    Certainly Jerry Coyne would have booted him after his first post. He has zero tolerance of creationists andf new-agers like our little friend here.

  261. BillyJoe7on 27 Sep 2016 at 5:27 pm

    Steve Cross: “It should be obvious but my last comment was directed to HN”
    I wouldn’t bet on it being obvious to hn. 😉

  262. hardnoseon 27 Sep 2016 at 5:44 pm

    “Evolution is CAUSED by a changing environment. It’s MECHANISM is natural variation (which could be due to NGE or random mutations) acted upon by selection (predominantly natural).”

    No matter how many times you repeat that, it will still be stupid.

  263. hardnoseon 27 Sep 2016 at 5:45 pm

    Coyne and Dawkins are crusaders.

  264. bachfiendon 27 Sep 2016 at 7:51 pm

    Hardnose,

    What’s actually stupid is that I actually think that I can inform an extremely ignorant person as to the facts. I’m extremely surprised that a person who claims to have a PhD degree can be so ill-informed. And who thinks that contradiction is argument. And is extremely doctrinaire, unwilling to consider whether the science he accepts, such as Shapiro’s NGE, is valid or not.

    As I’ve said. Your’e an ignorant, creationist Internet Troll. You’re illogical. You deserve to be banned. You’re a waste of space. You’re not worth the electrons this blog is printed with.

  265. BillyJoe7on 28 Sep 2016 at 7:19 am

    Another stratedy hn uses is to copy comments we’ve made about him and paste them into his own comments about us. He is not original in that, though, because Climate deniers have been using that stratedy for ages. So neither his comments nor his stratedy are original.

  266. Steve Crosson 28 Sep 2016 at 8:27 am

    Another stratedy hn uses is to copy comments we’ve made about him and paste them into his own comments about us.

    Perfect example of the cargo cult mentality. To an unsophisticated mind:

    If something sounds like science, then it must be just as good as science.

    If something sounds logical, then it must be logical.

    If a character flaw applies to hardnose, then it must apply to everyone else.

    Pretty much sums up HN’s life story in three statements.

  267. ccbowerson 28 Sep 2016 at 11:30 am

    And the whole strategy of doing the above is to create a false equivalency, to make it seem like supported scientific consensus is no better than his otherwise preferred nonsense.

  268. Steve Crosson 28 Sep 2016 at 11:56 am

    ccbowers,

    True enough, but I honesty don’t think that hardnose realizes that the two sides are NOT equivalent. He has made it clear that he doesn’t understand science, logic or his own cognitive biases.

    At least when the media engages in false equivalence (e.g. Trump vs. Clinton all too often recently), they tend to do it out of a misguided sense of “fairness” and the desire to appear unbiased.

    In hardnose’s case, I think he is both a True Believer and the typical Internet Troll.

  269. mumadaddon 28 Sep 2016 at 12:21 pm

    If you can’t beat ’em, troll ’em.

  270. hardnoseon 28 Sep 2016 at 12:21 pm

    You really can’t support your idea that all beneficial mutations are accidents/errors, either with scientific evidence or logic.

    Easier to criticize me personally.

  271. Kabboron 28 Sep 2016 at 12:45 pm

    Of course I can. My mutation is that I have telekinesis, whereas my daughter only has telekinetic control over metal objects. That is a clear step down to me. My mother and father had floramancy (plant control) and flight respectively, so my mutation is clearly random. Argument solved.

  272. hardnoseon 28 Sep 2016 at 2:12 pm

    We know that bacteria can communicate with each other, and we know that bacteria can adapt to antibiotics. And we know they are able to purposely modify their DNA.

    If you are able to put all that together, you can see that beneficial mutations mostly likely can be directed and adaptive.

    If you are unable to put all that together, then your brain has been warped by indoctrination.

  273. steve12on 28 Sep 2016 at 2:49 pm

    Steve Cross:

    Great comment re: the cargo cult. Feynman is perfect here, and this goes beyond Dr. TheTroll.

    People who embrace pseudoscience LOVE Richard Feynman. Always ready with the quotes. Their same shallow take on science (the Universe, really) is their take on Feynman.

    “He wasn’t this stodgy scientist who was skeptical of new ideas (they think), he was open minded and whimsical! And he admonished scientists not to fool themselves into a false sense of the depth of their understanding!”

    Translation: He would believe MY bullshit!

    I always laugh because Feynman didn’t believe ANYTHING!!! He was the most skeptical person on Earth!

    But that didn’t mean throwing his hands up postmodern style, as many interpret it, to reflexively reject consensus science because consensus science is incomplete.

  274. hardnoseon 28 Sep 2016 at 3:27 pm

    And we also know that the rate and locations of mutations can change in response to environmental stress.

    It is pretty far-fetched to continue insisting that all beneficial mutations must be accidents/errors.

  275. bachfiendon 28 Sep 2016 at 4:43 pm

    Hardnose,

    I’ve pointed out to you why the idea that bacteria can increase the mutation rate in response to stress, in ‘hot’ spots and in directed beneficial ways is fallacious.

    As I’ve pointed out many times, in different words, that mutations don’t announce themselves with flashing lights. If they’re ‘beneficial’ they don’t signal it with waving flags. Mutations in bacteria to be detected have to be present in multiple copies – many millions in fact. So the original bacterium with the new mutation has to divide at least 32 times, over at least 10 hours, before it’s detectable, so already there’s some selection involved – the lethal mutations are already eliminated. And that also means that mutations in critical regions of the genome will also be eliminated too, leaving just mutations in less critical regions such as the regulatory areas, giving the impression that there are ‘hot’ spots. And if the mutations are beneficial, then perhaps the non-mutated bacteria die faster in response to the stress giving the false impression that the mutation rate is increased.

    To prove that bacteria under stress can increase their mutation rate, in ‘hot’ spots and in a non-random directed ‘beneficial’ way, it would be necessary to detect ALL mutations in real time, which is impossible to do, even in theory let alone in practice.

    The only way of distinguishing between the two possibilities – random non-directed mutations with the non-‘beneficial’ ones removed by natural selection and non-random directed ‘beneficial’ mutations – would be to put bacteria under stress and discover how frequently ‘beneficial’ mutations occur.

    ‘Random mutations’ would predict they’d occur late and infrequently. ‘Non-random mutations’ would predict they’d occur frequently and early.

    And what actually happens? They occur late and infrequently, so the evidence is that mutations are random and non-directed.

    And even if mutations were non-random and directed – in order to adapt bacteria to current changed conditions – it doesn’t support your delusion that there is direction in evolution one little tiny bit. That there’s an innate tendency to increasing complexity and intelligence in biological systems.

    That remains as wrong as it always has been.

  276. Steve Crosson 28 Sep 2016 at 5:03 pm

    steve12,

    My favorite Feynman quote is:

    The first principle is that you must not fool yourself, and you are the easiest person to fool.

    Unfortunately, most people ** cough – hardnose – cough ** seem to believe that it only applies to everyone else except themselves.

  277. ccbowerson 28 Sep 2016 at 5:19 pm

    “He has made it clear that he doesn’t understand science, logic or his own cognitive biases.”

    Yes, I remember in a probiotic post a few months ago, he basically argued that his personal experiences trumped well controlled research. He was declaring that subluxations were real and chiropractic works, based upon his experience. And that experienced trumps real evidence to the contrary. He thinks that cognitive biases and logical errors are things that only happen to others.

  278. ccbowerson 28 Sep 2016 at 5:44 pm

    “At least when the media engages in false equivalence (e.g. Trump vs. Clinton all too often recently), they tend to do it out of a misguided sense of “fairness” and the desire to appear unbiased.”

    We usually refer to this behavior as “false balance,” when applied to the media, which carries with it the intent you describe and aspects that are specific to media and journalism. False equivalence is broader and may not carry a particular implied intent or context.

    In one sense, I agree that HN may not realize to what extent he is doing this, but, at the same time, I have a hard time buying this because he is being constantly told this is the case. Plus, the amount of motivated reasoning and dishonest arguments are just too frequent. Hence the true believer and troll duality.

  279. hardnoseon 29 Sep 2016 at 12:25 pm

    We know that bacteria can communicate with each other, and we know that bacteria can adapt to antibiotics. And we know they are able to purposely modify their DNA.

    And we also know that the rate and locations of mutations can change in response to environmental stress.

    It is pretty far-fetched to continue insisting that all beneficial mutations must be accidents/errors.

  280. Steve Crosson 29 Sep 2016 at 2:03 pm

    ccbowers:

    In one sense, I agree that HN may not realize to what extent he is doing this, but, at the same time, I have a hard time buying this because he is being constantly told this is the case. Plus, the amount of motivated reasoning and dishonest arguments are just too frequent. Hence the true believer and troll duality.

    Sorry if I wasn’t clear. I’m pretty sure that hardnose knows exactly what he is doing, or at least he thinks he does. Just like the cargo cult tribes, HN is simply imitating actions without understanding them in the hopes that they will produce his desired results.

    After receiving gifts and more advanced technology from early explorers, some primitive island tribes continued to clear airplane runways, build bamboo “control towers” and simulated “radios” in the vain hope that more visitors would arrive bearing more fabulous gifts.

    Similarly, hardnose thinks he understands science and logic, but can’t tell the difference between real science and pseudoscience (e.g. subluxations, etc.). He continually raises the same debunked “arguments” in the mistaken belief that they are “just as good as” real science and logic.

    Case in point: HN has repeated his last comment verbatim multiple times. He doesn’t have the knowledge (or the wit) to realize that his “argument” has been thoroughly debunked multiple times and in multiple ways.

    Exactly like the primitive cargo cult native tribes (or Einstein’s definition of insanity), hardnose continually makes the same mistakes because he is unwilling or unable to learn from his mistakes.

  281. hardnoseon 29 Sep 2016 at 2:37 pm

    Nothing I said has been debunked. Even Steve Novella accepts that the rate and location of mutations can vary in response to environmental stress.

    If you can’t accept that, then YOU don’t understand science or logic.

  282. Steve Crosson 29 Sep 2016 at 3:34 pm

    We know that bacteria can communicate with each other, and we know that bacteria can adapt to antibiotics. And we know they are able to purposely modify their DNA.
    And we also know that the rate and locations of mutations can change in response to environmental stress.
    It is pretty far-fetched to continue insisting that all beneficial mutations must be accidents/errors.

    Starting with something that is generally agreed upon, but then adding something that is NOT accepted (“purposely”), does NOT make your conclusion valid.

    Like I said, no understanding of science or logic. Many people have explained in several different ways why your conclusion is illogical and unsupported by any evidence. But, just like the unsophisticated primitive cargo cult tribes, you can’t understand your mistake and continue to post the same nonsense that you believe “is just as good as science”.

    Pro Tip: If Shapiro’s hypothesis actually was scientific or logical (or at least had some persuasive evidence), then 25 years is plenty of time for the rest of the world to have noticed. They don’t give Nobel Prizes for upholding the status quo — they give them to people who upset the applecart. It’s not like Shapiro is shy or afraid of self promotion. Everyone has noticed — they’re just not impressed.

  283. hardnoseon 29 Sep 2016 at 3:39 pm

    So you think Shapiro doesn’t understand science or logic?

  284. Steve Crosson 29 Sep 2016 at 3:46 pm

    “So you think Shapiro doesn’t understand science or logic?”

    Seems pretty obvious that he doesn’t if he hasn’t been able to make a persuasive case or find compelling evidence in over a quarter century.

  285. bachfiendon 29 Sep 2016 at 4:22 pm

    Hardnose quotes:

    ‘And by the way, why does anyone need more proof that bacteria adapt to antibiotics? This video has nothing to do with the controversies about what causes evolution’ (September 19)

    ‘Shapiro claims that there is conclusive evidence for natural genetic engineering, and he is an expert in the evolution of bacterial resistance’. (September 22).

    If Shapiro’s expertise is in bacterial resistance, then it’s of no value in settling the so-called controversies of evolution according to hardnose.

    Hardnose is just an ignorant increasingly desperate creationist Internet Troll who is just repeating arguments he doesn’t understand and refusing to consider counter arguments.

    As I’ve noted many times, even if bacteria under stress increase mutations in ‘hot’ spots in the genome in a non-random directed ‘beneficial’ manner (which I’ve argued is actually wrong – anyone who argues that it happens is just falling for the sharpshooter fallacy), it doesn’t assist hardnose in his delusion that there’s:

    Direction in evolution.

    That there’s an innate tendency towards increasing complexity and intelligence in biological systems.

    Both of these delusions of hardnose remain just as fallacious as they always were.

  286. BillyJoe7on 29 Sep 2016 at 4:36 pm

    James Shapiro has not subjected his ideas to peer review (where they would have been tested by scientists with expertise in evolutionary biology, genetics, and microbiology), preferring instead to present them untested direct to the general public (who have no expertise and insufficient scientific background to understand why he is wrong). This is a sure sign that he does not have the courage of his convictions. Of course his peers have reviewed him in any case and almost uniformly found his ideas without foundation. In particular, that he does not understand modern evolutionary theory and attacks a misinformed straw man version of it (ie his argument against the central dogma), and that he extrapolates wildly beyond the facts, strong in the conviction that the future will vindicate him by supplying the missing evidence and mechanism for his fanciful ideas.

  287. BillyJoe7on 29 Sep 2016 at 4:39 pm

    …hardnose, on the other hand, understands neither modern evolutionary theory, nor James Shapiro.

  288. hardnoseon 29 Sep 2016 at 9:53 pm

    “James Shapiro has not subjected his ideas to peer review”

    Proof of your dishonesty and/or ignorance. You didn’t even bother to search for any of his articles.

    https://www.ncbi.nlm.nih.gov/pubmed/?cmd=Search&term=James+A.+Shapiro

  289. BillyJoe7on 29 Sep 2016 at 10:49 pm

    The illogic of James Shapiro.

    “Once formed, symbiogenetic organisms have to succeed in the struggle for existence. But nothing about their origins involves Natural Selection”

    Here he dismisses natural selection by saying that it plays no role in the origin of symbiogenetic organisms. But of course it doesn’t! That is not the role of natural selection! The origin of symbiogenetic organisms – the merger of two organisms into one – is a mutation event! Of course natural selection plays no role there. The role of natural selection is to select the symbiogenetic organisms that have reproductive advantage and to select the mutations within the respective genomes of the merged organisms that change the character of the symbiosis to reproductive advantage.

    The original merger – the original mutation – is actually neutral. Further mutations that improve the symbiosis between the two merged organisms to reproductive advantage are the ones that come to predominate in their environment. That is natural selection. And that is why natural selection is essential to evolution. James Shapiro has never been able to explain away this inconvenient fact. And he has never been able to provide an alternative mechanism. And that fact alone is what relegates his role in the development of evolutionary theory to an irrelevant side show.

  290. BillyJoe7on 29 Sep 2016 at 11:04 pm

    hn, you are referring to publication peer review. I Was referring to the broader process of pursuading your peers of the value of your ideas. He is not engaged in that process. He circumvents this process and brings his discredited ideas direct to an non-discerning public.

  291. hardnoseon 29 Sep 2016 at 11:18 pm

    “Here he dismisses natural selection by saying that it plays no role in the origin of symbiogenetic organisms.”

    You actually think he doesn’t understand natural selection???

  292. hardnoseon 29 Sep 2016 at 11:20 pm

    What Shapiro is saying is extremely relevant to the central evolution controversy.

    Saying natural selection is essential to evolution is just stubborn stupidity. We all know that natural selection can’t not happen.

    The important question is what causes the variations that are selected from.

    You INSIST they are accidents/errors.

    Shapiro, and others, have found conclusive evidence that the are NOT accidents/errors.

  293. BillyJoe7on 29 Sep 2016 at 11:55 pm

    hn: “You actually think he doesn’t understand natural selection???”

    Not only do I think it, I have clearly demonstrated it, and you have yet to refute it.

    More correctly, he doesn’t recognise it when it’s staring him in the face – as I just demonstrated!
    I challenge you to copy my post and refute it line by line.
    You can’t do it and you know it, otherwise you would have done so already.

  294. BillyJoe7on 29 Sep 2016 at 11:58 pm

    …and you still clearly do not understand the meaning of “random” in the phrase “random mutation”. And in this you have become wilfully ignorant.

  295. bachfiendon 30 Sep 2016 at 12:14 am

    Hardnose,

    Mutations could be ‘NOT accidents/errors’, but it still doesn’t assist you in your delusion that there’s direction in evolution. That there’s an innate tendency towards increasing complexity and intelligence in biological systems.

    In that you remain completely ignorant and delusional.

    And anyway – I’ve pointed out that anyone who thinks that mutations are non-random, directional and ‘beneficial’ is committing the sharpshooter fallacy.

    I’ll explain it to you as an analogy in the hope that it will finally penetrate your thick creationist Internet Troll skull.

    Suppose you have an archer shooting arrows at a target mounted on the side of a large barn. And most of his arrows are standard in weight and well balanced, but he also has a smaller number of heavier arrows of variable weight some of which are well balanced, but others are poorly balanced. And there’s a gusty wind blowing between the archer and the target.

    The standard well balanced arrows are organisms (say, bacteria) with no mutations. The heavier arrows are organisms with mutations. The well balanced ones are the ones with mutations in the ‘hot’ spots. The unbalanced ones are the ones in mutations in non-‘hot’ spots and the very heavy ones (the ones the archer’s bow isn’t powerful enough to allow the archer to reach the target with them) are the organisms with immediately lethal mutations.

    The arrows which hit the target are the organisms which are present when the researcher comes back to see what happened due to the changed environment, the gusty side wind.

    And what will she find in the target? A smaller percentage of standard well balanced arrows than originally shot (because the gusty wind blew more of these arrows of course), a larger percentage of heavier well balanced arrows (because the heavier arrows were less likely to be blown off course), a lower percentage of unbalanced heavier arrows (because occasionally the wind gusts blew them onto target) and no very heavy arrows (because they all landed at the archer’s feet).

    Result; decreased percentage ‘no mutations’ [which results in the false impression that the mutation rate has increased] increased ‘mutations in ‘hot’-spots (regulatory and non-critical genes), decreased ‘mutations in non-‘hot’-spots (critical genes) and none due to immediately lethal mutations. Counting up the number of mutations, there’d be a disproportionate number of ‘beneficial’ ones and also no lethal ones [which results in the false impression that there’s direction in mutation too].

    There’s just too many ‘unknowns’ to determine whether mutations are random or not. It’s not known what the original mutation rate was. Mutations can’t be detected in real time. They have to be present in numerous copies, meaning that already there’s some selection involved. And it’s also not known where they occurred, whether they were in regulatory or non-critical genes or elsewhere. It’s just not possible, not even in theory, let alone in practice, to detect mutations as they occur.

    The only way of distinguishing between random non-directional mutations with selection from non-random directional ‘beneficial’ mutations is to see what happens to a population under stress.

    ‘Random mutations’ predicts the adaptations will occur late and infrequently.

    ‘Non-random mutations’ predicts the adaptations will occur early and frequently.

    And what do we see? Adaptations occurring late and infrequently, such as in Lenski’s one out of 12 lines of E. coli being able to use citrate, and only after tens of thousands of generations.

    But anyway. You remain an ignorant creationist Internet Troll who’s just wasting our time.

  296. hardnoseon 30 Sep 2016 at 9:52 am

    “And that is why natural selection is essential to evolution. James Shapiro has never been able to explain away this inconvenient fact. And he has never been able to provide an alternative mechanism. And that fact alone is what relegates his role in the development of evolutionary theory to an irrelevant side show.”

    Every aspect of that statement is completely wrong. You are not capable of understanding what Shapiro has said. Either that, or you did not read any of it.

  297. Kabboron 30 Sep 2016 at 10:52 am

    The abridged version of the bachfiend arrow analogy:

    1. take 1000 arrows
    2. fire them at a target
    3. The 100 arrows that hit closest to the bull’s eye are replicated: 5 exact copies, 5 with slight variances
    repeat steps 2 and 3

    You eventually end up with a great set of arrows for your target.

    Then you can change your target and repeat the experiment. The arrows will change to match the target. These are some smart arrows.

  298. Steve Crosson 30 Sep 2016 at 12:13 pm

    Hardnose,

    “Every aspect of that statement is completely wrong.” Why?

    “You are not capable of understanding what Shapiro has said.” Prove that you do understand him.

    Explain why, in detail exactly why Shapiro is right and almost everyone else is wrong.

    I’m betting you won’t even try and if you do, you’ll fail abysmally. You have repeatedly demonstrated that your reading comprehension is absurdly bad.

  299. hardnoseon 30 Sep 2016 at 3:12 pm

    I have explained it many times already. It is obvious and should not need to be explained.

    Evolution involves generation of variations and selection among variations. No one disagrees with that. Shapiro agrees with that. It can’t be otherwise.

    If mutations are always accidents/errors, then natural selection has an all-important role in the process. Dawkins describes natural selection as the organizing force of evolution. He says that organisms appear designed because natural selection “designs” them.

    However, if mutations are directed or partially directed, the role of natural selection is much less important. It happens, because it can’t not happen. Organisms that survive survive. Organisms that survive longer are more likely to reproduce more. How could that not be true?

    In Dawkins’ explanation of evolution, ALL mutations are accidents/errors. But they have no organizing or designing role. That is entirely up to natural selection.

    In Shapiro’s explanation of evolution, beneficial mutations result from deliberate actions of the cell. These “directed” or “adaptive” mutations are the organizing force of evolution. Natural selection, in this scenario, is NOT the designing, organizing force of evolution. Natural selection happens, but it is much less important than in neo-Darwinism.

    Directed mutations might have an element of randomness, but they are NOT accidents/errors. It is very possible for something to be directed, and yet have an element of randomness.

    If you can turn off your rigid black and white thinking for a moment, you might be able to see this.

  300. Steve Crosson 30 Sep 2016 at 4:37 pm

    hardnose,

    Yet again, you’ve managed to display your poor reading comprehension. I didn’t ask for an explanation of what Shapiro believes..

    This is the challenge: “Explain why, in detail exactly why Shapiro is right and almost everyone else is wrong.”

    You accused us of not understanding Shapiro, but you have not given any evidence that YOU understand him. I doubt you’ve even read his book yet.

    Unless you understand Shapiro’s evidence well enough to explain and defend it to others, then you have no good reason to accept his judgment as superior to the majority of established experts. You agree with him purely because of your ideology.

    What is Shapiro’s evidence that beneficial mutations are directed and why is that evidence more persuasive to you than the evidence provided by the majority of experts?

    If you can’t answer that, then you are simply a true believer who has no interest in evidence or truth.

    And before you go off on another tangent because of another comprehension failure, the question about the relative importance of NS is completely irrelevant until directed mutations are proven to be real.

    So, to repeat, what specifically is Shapiro’s evidence that mutations can be directed (beneficially) and why is it more persuasive than all of the evidence that indicates otherwise?

  301. BillyJoe7on 30 Sep 2016 at 4:51 pm

    hardnose,

    “In Shapiro’s explanation of evolution, beneficial mutations result from deliberate actions of the cell. These “directed” or “adaptive” mutations are the organizing force of evolution. Natural selection, in this scenario, is NOT the designing, organizing force of evolution. Natural selection happens, but it is much less important than in neo-Darwinism”

    Firstly, you’ve introduced the word “adaptive” for the first time.
    I’m pretty sure you don’t understand the context in which this word is generally used.
    Secondly, you give it as an alternative to “directed”.
    Does that mean you are shying away from that loaded word?
    Thirdly, you have the word “directed” in scare quotes for the first time.
    Does that mean you are now agreeing that using that word is merely an anthropomorphism?
    Finally, you have now avoided the use of the word purposeful altogether.
    Are you now backing away from using that word to describe the actions of bacteria?

    On the other hand, you are still using the word directed without scare quotes.
    Does that mean you are sticking with the literal interpretation of that word?
    Do you really think bacteria direct there DNA to produce mutations that are more likely to be beneficial.
    (I was going to say “purposefully direct their mutations…” but you’ve not used that word here.)
    If so, how exactly do they do this without having superhuman powers of perception and intellect?
    What is Shapiro’s mechanism whereby bacteria direct their DNA to produce beneficial mutations?
    What would such a mechanism even look like?

    The fact is, it is natural selection that has resulted in bacteria acquiring those epigenetic mechanisms (Shapiro’s NGE). It really is the only game in town and it’s perfectly capable of doing the job along with random mutations – meaning random with respect to whether or not they are beneficial for the organism. Those epigenetic mechanisms constrain the range of mutations that can occur, and produce hot spots and cold spots in the genome, but the mutations that actually occur are random with respect to whether or not they are beneficial to the organism. This is the pivotal point that you are missing.

  302. BillyJoe7on 30 Sep 2016 at 5:11 pm

    …along with the fact that those epigenetic mechanisms (Shapiro’s NGEs) got there by the same process of random mutation and natural selection!

  303. bachfiendon 30 Sep 2016 at 5:25 pm

    Hardnose,

    You remain completely ignorant of evolution.

    I’ll repeat it once more.

    The CAUSE of evolution is a changing environment affecting a reproductively isolated population. Such as bacteria being exposed to a new antibiotic. E. coli in a flask being exposed to an environment with depletion of its preferred sugars leaving just citrate as in Lenski’s study. Drought on the Galápagos Islands causing the predominant food source to be larger tougher seeds for seed eating Darwin finches.

    The MECHANISM of evolution is natural variation within reproductively populations and selection (mainly natural).

    You’ve changed ‘mechanism’ to ‘organising force’, but it still the same. If the environment isn’t changing then there’s no evolutionary change, or not much save for neutral drift.

    Shapiro gives emphasis to mutations because NGE is (barely) plausible in single cell bacteria. A single mutation in a bacterium has an immediate effect on the bacterium’s survival and ability to grow, and almost immediately is reproduced and passed onto daughter bacteria potentially allowing it to dominate.

    Mutations in bacteria could be non-random and directed in response to stress and not random and non-directed, with natural selection acting if there’s some sort of stress present or not. I don’t think that it’s plausible though – non-random directed mutations should produce early and frequent adaptations to stress in bacteria, instead of what we actually see – late and infrequent adaptations.

    NGE is completely implausible in multicellular organisms. Humans and mice contain more than 20,000 genes. Any feature you wish to consider – intelligence, beak size in Darwin finches, whatever – is due to the combined action of many genes of small effect. Natural variation within multicellular organisms, particularly in mammals, birds, etc, is largely due to the particularly combination of variants of many genes of small effect, not due to new mutations within single genes.

    If Shapiro’s NGE was to be plausible in multicellular organisms, that a single non-random directed mutation in a single gene in response to stress could produce a needed adaptation to the stress – for example larger stronger beaks in seed eating Darwin finches in order to crack the larger tougher seeds predominating in a drought – then you’d have to surmise that it’s possible for a drought to cause mutations within the cells destined to become the bird’s beak within the chick embryo within the egg, in which case the mutation wouldn’t be passed onto future bird generations. Or the drought would have had to produce a mutation in the gonads of the adult breeding birds leading to a larger inheritable beak in their offspring.

    I can’t even imagine a way in which the stress of a drought could produce directed non-random mutations within cells tucked away within chick embryos in an egg or in gonads of adult birds.

    In evolutionary biology, environmental change is a given. As is natural variation due to the effects of many genes of small effect. Natural selection is the sieve determining which natural variants will dominate in response to which particular changed environment. Larger strong beaks in Darwin finches during droughts due to a predominance of genes for large beaks in order to crack the preponderant larger tougher seeds. Smaller weaker beaks during non-drought periods due to a predominance of genes for smaller beaks because the preponderant smaller less tough seeds are easier to crack by any bird (and large beaks are more expensive to build and maintain).

    Mutations aren’t all that important in complex multicellular organisms compared to bacteria. And big mutations in important genes are punished almost immediately by natural selection since they’re almost always lethal. Mutations might lead to some increased variation within populations, if they’re small and non-lethal, but they’re not the only, or even main, cause of variation, particularly in humans or mice.

    And it’s the natural variation within populations that’s acted upon by natural selection in response to a changing environment that causes evolutionary change. It’s the changing environment that causes the evolutionary change.

    And it still doesn’t make your delusions that there’s direction in evolution, that it has aims and goals, that there’s an innate tendency towards increasing complexity and intelligence in biological systems any less wrong.

    You still remain an ignorant creationist Internet Troll. You’ve wasted too much of my time.

  304. BillyJoe7on 30 Sep 2016 at 5:39 pm

    hardnose,

    “If mutations are always accidents/errors…”

    You really must stop.
    This is our position:
    Mutations are constrained by physics, chemistry, and epigenetics, but the mutations that do occur are random with respect to whether or not the are beneficial for the organism.
    And those epigenetic mechanisms got there by the same process.

    “…then natural selection has an all-important role in the process”

    Again please stop.
    It is random mutation and natural selection.
    Not one or the other, but both together.

    “However, if mutations are directed or partially directed…”

    When you say mutations are “directed” do you simply mean that the mutations are “constrained”?
    – constrained by those epigenetic mechanismS (NGEs)?
    If so, please use the less loaded word.
    If not, please explain the mechanism by which mutations are (partially) directed to be beneficial.

    “…the role of natural selection is much less important”

    Do you simply mean that, because epigentics constrains the types of mutations that can occur and that, therefore, there are fewer mutations and that, therefore, there is less work for natural selection to do. Is that what you are saying?
    If not, please explain what you ARE saying.
    Even then, how can it be less important if it is actually ESSENTIAL in order for evolution to occur.

  305. hardnoseon 30 Sep 2016 at 6:48 pm

    “The fact is, it is natural selection that has resulted in bacteria acquiring those epigenetic mechanisms (Shapiro’s NGE).”

    (NGE involves directly modifying DNA, which is not the same thing as epigenetics.)

    When you call something a “fact,” there should be some kind of evidence for it.

    “It really is the only game in town and it’s perfectly capable of doing the job along with random mutations”

    How the hell could you, or anyone, possibly know that? And I don’t care if Dawkins says NS is the only game in town. That doesn’t mean it’s true.

  306. Steve Crosson 30 Sep 2016 at 7:12 pm

    Hardnose,

    When you call something a “fact,” there should be some kind of evidence for it.

    Exactly. You’ve said many times that according to Shapiro, “directed” mutations are a fact.

    Still waiting for your explanation of Shapiro’s evidence and why it is so compelling.

  307. bachfiendon 30 Sep 2016 at 7:17 pm

    Hardnose,

    You still refuse to address my criticisms of your delusions.

    You’re pretty ignorant with limited reading comprehension, so I’ll make it simple and short.

    Environmental CHANGE CAUSES evolutionary CHANGE in populations by the MECHANISM of natural variation within a reproductively isolated population acted upon by selection (predominantly natural).

    Shapiro’s NGE might be a plausible mechanism for producing increased natural variation within ‘simple’ singlecelled bacteria, as a result of increased mutations, but it’s not a plausible mechanism for producing increased variation within ‘complex’ multicellular organisms such as Darwin finches. Or simpler hardnoses.

    The role of mutations in multicellular organisms in evolution is overrated.

  308. bachfiendon 01 Oct 2016 at 5:24 am

    We’ve pandered to hardnose’s delusions for far too long.

    Shapiro’s natural genetic engineering might be a plausible mechanism for generation variation in simple prokaryotic organisms (I don’t think so, for the reasons I’ve provided in more than several comments) but it’s completely implausible for complex eukaryotic cells, let alone multicellular eukaryotes.

    The degree of genetic complexity is vastly different between prokaryotes and eukaryotes. A prokaryote such as E. coli has several thousand genes and a genome of around 6 million base pairs. A eukaryote such as Homo sapiens has over 20,000 genes and a genome of 3 billion base pairs (ten times the genes and a genome 500 times larger). Each gene consists mostly of introns, which have to be spliced out of the mRNA before its translated into protein. Most of the genome consists of junk DNA (unless the religiously motivated creationists are right, and it’s mostly functional – although they aren’t).

    The prokaryotic genome is much simpler. And much better ‘designed’, something an engineer would take pride in. The eukaryotic genome is nothing anyone would be proud to accept as having ‘designed’.

    Environmental change could produce non-random directed mutations in prokaryotes, because they’d cause effects which produce immediate effects, to be acted upon by selection to winnow out deleterious mutations, and also immediately be replicated by division of the bacteria containing the mutations increasing its frequency in the population.

    Environmental change can’t produce non-random directed mutations in multicellular eukaryotes. How could it produce mutations in the developing foetus or the germ cells within gonads hidden away in larger organisms?

    I find the idea that there’s hot spots for mutation within the genome suspect too. I don’t think that there’s any evidence that it happens. Unless it is possible to detect all the mutations occurring in real time (which is not possible) and finding that there are segments which infrequently develop mutations, then it’s not possible to show that hot spots occur, segments of the genome with increased mutations.

    A lot of nonsense is written about Punctuated Equilibrium, in which one species is replaced abruptly by another in the geological column. The idea that it indicates that evolutionary change can sometimes happen rapidly in geological time, consistent with mutations in hot spots, is just fallacious.

    It just indicates that one population can be replaced by another population rapidly in geological time in response to environmental change. Species don’t evolve. It’s populations that evolve. A species needs to be widespread and common for it to have a good chance of the rare process of fossilisation yielding fossils of it in the geological column.

    A widespread species will often have geographically and reproductively isolated subpopulations. Small populations evolve more rapidly than large populations, because they tend to be geographically restricted and subject to a more uniform environment causing a uniform selective pressure pushing all the population in the same direction. Evolutionary change is still slow and gradual, and because this population is small and restricted, it’s not represented as fossils in the geological column to show the slow changes occurring.

    And then there’s a sudden climate change event causing the extinction of the common widespread population which disappears abruptly from the geological column. And if the new changed climate suits the evolved subpopulation it becomes common and widespread and its fossils then abruptly appear in the geological column.

    No rapid evolution. Just rapid replacement. Not due to increased genetic changes. Due to slow gradual genetic changes in small populations.

  309. Steve Crosson 01 Oct 2016 at 12:25 pm

    We’ve pandered to hardnose’s delusions for far too long.

    True enough . It is pretty obvious that hardnose is primarily a troll with zero interest in learning or changing his mind about anything.

    OTOH, I very much enjoy reading the detailed explanations from bachfiend, chikoppi and many others. It is always good to hear new perspectives or even just to get a refresher on things you might already know.

    On the Gripping Hand (sorry, SF nerd joke/allusion), it is also obvious that HN really cares about this particular issue and (similar to Donald Trump) he can’t stand the thought of being proven wrong about anything.

    I think it is only fair that we troll him just as hard as he is trying to troll us. HN’s SOP is always the same. He constantly repeats the same Cut&Paste “sound bite” assertions and never presents the (supposedly strong) underlying evidence. In essence, hardnose engages in a never-ending Appeal to Authority in spite of the fact that his “authorities” are clear outliers.

    Currently, we wind up doing all the work. There are many very strong well-reasoned positions in both this and the Mike Pence thread, but HN either ignores them completely or dismisses them without evidence. There is no guarantee that he even reads them other than perhaps to skim for phrases that he can then parrot back out of context.

    I suggest that we all try to hold firm to the Hitchen’s Principle: ”That which can be asserted without evidence can be dismissed without evidence. In other words, force hardnose to engage on the specific details of his evidence and be able to defend it against the opposing point of view.

    Make hardnose prove that it is reasonable to accept Shapiro’s directed mutations claim before we are even willing to debate the corollary if Shapiro is right, then NS is less important hypothesis. The burden of proof should be entirely on hardnose and Shapiro since they clearly hold the outlier position (and a particularly implausible one at that).

    In other words, rub his nose in the fact that the ONLY reason that hardnose accepts Shapiro’s beliefs is because of ideology. If I’m wrong, and if HN actually is capable of understanding the nitty-gritty and can coherently explain the evidence, then perhaps we will all learn something.

    In any event, that is the only possible way that hardnose will be able to “win” the argument. Unlike HN, I’m sure that almost all of us would willingly change our minds if the evidence is good. But it has to be actual evidence and not just constant repetition of other people are saying.

  310. mumadaddon 01 Oct 2016 at 2:31 pm

    Or, just ignore him. You will see that his posts don’t change. Quite funny to watch him try needle people into a response.

    Je suis Arnie

    #solidarity

  311. mumadaddon 01 Oct 2016 at 2:48 pm

    Seriously, so much work, so much effort, has gone into this thread. What percentage do you think hn has contributed? How long does it take him to type out a couple of sentences asserting that you’re wrong, that the entire edifice of evolutionary science is about to crumble because undemonstrated effects caused by impossible forces?

    I don’t mean to devalue the contributions you’ve all made. They were mostly excellent. And, sincerely, it’s not like I don’t like a good argument myself, but this is not one of those. In real life, you might encounter people who are blatantly wrong about something, and want to discuss the issue in the hopes of convincing them and because you find the topic worthwhile, but you would surely walk away of the realised that person was mentally deficient, had no understanding of what you were discussing, or was just trying to wind you up for their own satisfaction.

  312. mumadaddon 01 Oct 2016 at 2:50 pm

    you would surely walk *if you* realised…

  313. Steve Crosson 01 Oct 2016 at 3:17 pm

    “Or, just ignore him.”

    Lots of people have said that, including me on occasion, but sometimes that is easier said than done. Hardnose may be a troll, but he can be pretty good at it. Besides, many of us seem to be unable to leave obvious nonsense unchallenged — regardless of how likely it is that said nonsense could confuse or mislead any newcomers to the blog.

    Also, it’s obvious that hardnose NEEDS to believe he is “winning”. Notice how often he tries to “have the last word”. At least if we always try to make it clear that he is unwilling or unable to answer specific questions regarding the crux of the issue, then it will be that much more difficult for him to pretend that he won.

    As I said, the burden of proof should be on hardnose and he should have to do most of the work. It’s worth a try anyway. He has been pulling the same stunts for years and there are always some people (including me all too often) that are willing to feed the troll. As long as he feels that we are puting more effort into it than he is, hardnose will be satisfied. If we can reverse that inequality, then perhaps he won’t find the game so enjoyable any more.

    I propose that we collectively pull an Eliza. In other words, just keep saying “Tell me more” until HN provides evidence and is willing to discuss specific details. Just refuse to waste our time on any unsupported assertions or appeals to authority.

    Instead of many different people wasting time explaining why directed mutations are extremely unlikely and implausible, we should insist that HN provide his evidence first. After all, he is the outlier with the burden of proof. If he is not willing to do that, then ignore him but at least it will obvious that he is the one who failed the test and there will be no wiggle room for him to pretend he won.

  314. Steve Crosson 01 Oct 2016 at 3:22 pm

    mumudadd,

    I was typing (and thinking about) my last comment while you were posting yours. In general I agree with everything you said, but I still think my 3:17 comment is the best approach to dealing with hardnose.

  315. mumadaddon 01 Oct 2016 at 6:50 pm

    Steve Cross,

    Nobody’s going to stumble across any thread on this blog and think hn is right because his two sentence denialist rubbish was left unchallenged.

    They might start to wonder when otherwise sane people lead hn into the weeds… dignify his shit with detailed responses, and feed him content for a thousand plus comment thread where he just keeps. on. repeating. crap.. with no acknowledgement of, or engagement with, any evidence or argument that has been presented.

    He is trolling you big time, and you’ve convinced yourselves that your responses are somehow for the betterment public knowledge. They aren’t. You’re doing loads of work and nobody but hn cares.

  316. mumadaddon 01 Oct 2016 at 7:00 pm

    “You’re doing loads of work and nobody but hn cares”

    I realise that’s fallacious; Obviously I care, as does everyone who’s tried to throw cold water over hn dominated threads.

    Je suis Arnie.

    #solidarity

  317. mumadaddon 01 Oct 2016 at 7:02 pm

    I think the appropriate response to hn is to either ignore him totally or take the piss viciously.

  318. Steve Crosson 01 Oct 2016 at 8:20 pm

    Mumadadd,

    Well, as I said, I pretty much agree with you, but it doesn’t seem realistic to suggest ignoring him. Past history seems to have proven that there will always be at least a few people responding (and yes, I admit to being one of them all too often).

    As I see it, the situation hasn’t changed materially for years. I have been reading for a long time even though I never really had much time to comment until relatively recently. Hardnose has had plenty of time to refine his Trollish bag of tricks and he knows which buttons to push.

    But, during the same time, I think most of us have learned which of HN’s buttons are pushable. He will never admit it but I think it is clear that he hates to be proven wrong and he likes to pretend he is not an ideologue.

    I think it is time to fight fire with fire, and start trolling the troll. All the while making sure that he is the one wasting time and energy instead of us. I could be wrong, but I suspect that if no one ever took his bait, a lot of the fun would go out of his game. Instead of spending a lot of time creating a reasonable, comprehensive rebuttal to his nonsense, everyone (at least those who can’t ignore him and feel compelled to reply) should simply (and very briefly) point out that the vast majority of experts and evidence disagree with him, and unless hardnose is willing to explain his new evidence in persuasive and specific detail, then there is no need to continue the conversation. In essence: “You’re wrong hardnose until you are willing and able to prove otherwise!”

    As I said, I agree that ignoring would be the optimum choice, but since that never seems to be 100% successful, then perhaps we can control the discussion in our favor instead of his. Now, we’ll see if I can follow my own advice. 🙂

  319. BillyJoe7on 02 Oct 2016 at 1:26 am

    There has been some suggestion, from what I have read elsewhere about Shapiro, that he has been blinded by his primary interest in microbiology into seeing evolution as something that happens at the level of individual microbes instead of in a population.

    That could explain his dismissal of natural selection as an important/essential element in evolution. He sees evolution as a bacteria with a beneficial mutation passing it onto the next generation. He doesn’t see the competition between bacteria with a mutation and those without the mutation or with a different mutation, with only the bacteria with a beneficial mutation surviving and perhaps ultimately coming to predominate in the population of bacteria.

    A mutation cannot come to predominate in a population except via natural selection.

  320. BillyJoe7on 02 Oct 2016 at 1:41 am

    From my own perspective, having read his book twice now, he seems to be oblivious to natural selection even when it is actually implied in what he writes – when it staring him right in the face. This is especially true when he talks about HGT and hybridization. He sees these two processes as evolution in action rather than a mutation event on which natural selection must act in order for it to succeed at a population level.

    He also has a habit of referring to his adversaries as traditionalists, conventionalists, and evolutionists, and only occasionally neo-Darwinists. You have to wonder if he is confusing modern evolutionary theory with an uneducated layman’s understanding of evolution. Certainly, if his criticisms are about modern evolutionary theory, he has erected massive straw men and strewn them all over his book.

  321. ccbowerson 02 Oct 2016 at 9:17 am

    “Instead of many different people wasting time explaining why directed mutations are extremely unlikely and implausible, we should insist that HN provide his evidence first. After all, he is the outlier with the burden of proof. ”

    This has been, more or less, my approach for some time now. I will point out his fallacious arguments, and demand evidence for his claims, but unless he really engages with evidence or substantive discussion, I will not get dragged into the weeds. Perhaps if he came up with something new I might get dragged in for a little while, but I’m not staying there. I just don’t have that much free time to waste on nonsense.

  322. ccbowerson 02 Oct 2016 at 9:25 am

    “You have to wonder if he is confusing modern evolutionary theory with an uneducated layman’s understanding of evolution.”

    I can see how this would appeal to a commenter on this blog.

    Is the Shapiro book worth reading? Is there anything compelling in it with regards to evidence? Because without that, his argument would be basically an “argument from incredulity.” That a certain level of complexity requires more elaborate explanation. At least, that seems to be the case from afar.

  323. hardnoseon 02 Oct 2016 at 1:29 pm

    You have all consistently and deliberately missed the central point I have been making.

    I do NOT claim to have an explanation for evolution.

    Extreme neo-Darwinists like Dawkins and Coyne, and most of you here, claim to have an explanation for how and why evolution happens. Their theory says that all mutations that turn out to be beneficial are accidents and errors. Their theory says that cells do NOT modify their DNA in response to environmental changes.

    I have NOT said there is an alternative theory that explains evolution. I have been saying that your theory is WRONG.

    There is no evidence for your theory, as most of you have reluctantly admitted. But then you turn things around and criticize me for not having a theory. It is impossible to get you to see that some things are not currently known. There is no advantage in pretending to know something you do not know.

    Shapiro doesn’t claim to have an alternate theory either. He has been observing bacterial adaptation and analyzing the DNA record and has made interesting observations. He has decided that the foundation of neo-Darwinism is wrong, and I agree with him.

  324. hardnoseon 02 Oct 2016 at 1:36 pm

    I think you all would have to agree that processes are constantly going on within cells that are purposeful. The purpose is to keep the cells alive.

    You can’t possibly believe that these processes are random.

    Bacteria, for example, are constantly involved in purposeful activities, with the goal of staying alive. You know that, it is a fact.

    But when the environment changes and bacteria must adapt or die, you deny there could be anything purposeful in their adaptive response.

  325. hardnoseon 02 Oct 2016 at 1:44 pm

    “He [Shapiro sees evolution as a bacteria with a beneficial mutation passing it onto the next generation. He doesn’t see the competition between bacteria with a mutation and those without the mutation or with a different mutation, with only the bacteria with a beneficial mutation surviving and perhaps ultimately coming to predominate in the population of bacteria.”

    Of course he knows that! Why should he waste time saying something that obviously has to be true?

    Natural selection is something that can’t not happen. As a supposed explanation for evolution, it is a concept that contains no meaning.

    Shaprio knows that some bacteria adapt successfully, while others fail to adapt and die. It goes without saying.

    I don’t understand how you misunderstood him so profoundly.

  326. ccbowerson 02 Oct 2016 at 2:19 pm

    “I have NOT said there is an alternative theory that explains evolution. I have been saying that your theory is WRONG.”

    You show a profound lack of understanding of epistemology and science. Modern evolutionary theories have incredible explanatory power, and have made many predictions over time that we later have found evidence for.

    If you are going to make the case that current theories are incorrect, you would need to show specific observations and evidence that are incompatible with current theories (which you have NOT done) and provide a theory that explains the data better (otherwise you are just an unjustified naysayer). If there is no better explanation, then you have no legitimate complaint.

    But we know that you ARE just naysayer. You have shown this over and over again over the years. You need to wedge a gap for your pet belief of inserting purpose in everything in the universe.

  327. hardnoseon 02 Oct 2016 at 3:41 pm

    “Modern evolutionary theories have incredible explanatory power, and have made many predictions over time that we later have found evidence for.”

    Again, you are confusing evidence for evolution with evidence for neo-Darwinism.

  328. bachfiendon 02 Oct 2016 at 4:05 pm

    Hardnose,

    As an ignorant creationist Internet troll you persist in getting what the theory of evolution actually is completely wrong. The theory is that the cause of evolutionary change is environmental change affecting a reproductively isolated population (no environmental change, no evolutionary change usually, save for neutral drift). The mechanism is natural variation within a population and selection (most importantly natural).

    The argument is about the mechanism. Non-random directed beneficial mutations might possibly be plausible in bacterial prokaryotes (but there’s no evidence for it – adaptations should occur early and frequently instead of late and infrequently – as is observed – if it’s true), but it’s completely implausible in multicellular eukaryotes such as mammals, reptiles and birds with their germ cells hidden away in gonads inside bodies and their developing embryos hidden away in bodies or eggs.

    And Shapiro’s NGE provides no support for your delusion that there’s direction in evolution. That there’s an innate tendency to increasing complexity and intelligence in biological systems.

    It goes without saying that you’re profoundly ignorant, lack logic skills and just persist in repeating the same fallacious statements over and over again.

    You’re repeating nonsense doesn’t make it true.

  329. hardnoseon 02 Oct 2016 at 4:12 pm

    “it’s completely implausible in multicellular eukaryotes such as mammals, reptiles and birds with their germ cells hidden away in gonads inside bodies”

    You are ignoring the fact that cells can communicate.

    “You’re repeating nonsense doesn’t make it true.”

    Just what I was thinking about you.

  330. BillyJoe7on 02 Oct 2016 at 4:26 pm

    ccbowers,

    The book is worth reading if you’re interested in the details of DNA regulation, but you’ll have to put up with his annoying habit of creating straw man versions of modern evolutionary theory (though he never calls it that) and his obvious blindness to natural selection, though he does largely restrict this to the introductions and/or conclusions to his chapters. He certainly does have a very detailed knowledge of what he calls natural genetic engineeering if you’re interested in that level of detail.

  331. bachfiendon 02 Oct 2016 at 4:30 pm

    Hardnose,

    How exactly do cells communicate? In particular with the cells within an avian egg separated from the environment by a hard shell and the bodies of their nesting parents?

    You’ve asserted that it’s a fact that cells communicate. Tell me how, and how it bears any connection to how non-random directed mutations could plausibly occur in multicellular eukaryotes in producing evolutionary change?

    You’re assertion rich and evidence poor. And nothing you’ve written assists your delusions about direction in evolution.

    Random mutations and natural selection isn’t the cause of evolution. It’s a mechanism of evolution, and not the only one. Why do you persist in denying this obvious fact (besides pigheadedness and profound ignorance)?

  332. BillyJoe7on 02 Oct 2016 at 4:48 pm

    I see hn is back at square one asking all the same questions that have already been answered many times before and making all the same claims that he still is unable to back up with evidence or mechanism and that have been destroyed many times over with evidence and logic. And he still doesn’t understand that science is not about kidding yourself that you have destroyed a commonly held theory, but by offering up a competing theory. Without that, you are not actually doing science.

  333. BillyJoe7on 02 Oct 2016 at 5:08 pm

    Bachfiend,

    You are right of course. Shapiro has been blinded by his study of bacteria which is his primary specialty. Even if what he says is true for bacteria, it can’t be true for muticellular oraganisms. But he really has no excuse. His errors have been pointed out to him many times over the years since his book came out and whenever he writes an article in HuffPo but, instead of learning from them, he digs in further. The problem is that he misinforms the public like our little friend here who is incapable of seeing beyond what he has written.

  334. hardnoseon 02 Oct 2016 at 6:13 pm

    “science is not about kidding yourself that you have destroyed a commonly held theory, but by offering up a competing theory. Without that, you are not actually doing science.”

    That’s just crazy. You can’t criticize a bad idea, unless you have a better alternative?

    Sometimes no one knows why something happens. That doesn’t mean we have to accept a theory that has no evidence, just so we can feel like we understand.

  335. Steve Crosson 02 Oct 2016 at 8:02 pm

    Hardnose:

    That’s just crazy. You can’t criticize a bad idea, unless you have a better alternative?

    No, you can’t. For starters, you don’t get to call it a bad idea when it fits a mountain of available evidence and has great explanatory power.

    The only way to successfully criticize a widely accepted theory to offer a better theory that fits the evidence just as well or better and also has equal or better explanatory and predictive capability. That is the way science works, and this has been explained to you many times. You’re either stupid or lying.

    Almost all genuine experts in the field agree that there is a mountain of evidence in support of the modern theory of evolution. Unless you can provide counter evidence and and prove that practically everyone is mistaken, then you are just an ignorant crank.

    FYI, simply parroting another ignorant crank IS NOT COUNTER EVIDENCE. Unless you are personally able to explain in specific detail why you (and Shapiro) are correct, then the majority of the world will continue to regard you as just another one of a multitude of ignorant cranks who have no evidence for their beliefs.

  336. bachfiendon 02 Oct 2016 at 8:55 pm

    Hardnose,

    But we do understand WHY evolutionary change happens. Evolutionary change happens because the environment of a reproductively isolated population changes.

    We also understand HOW the evolutionary change in reproductively isolated populations happens. The natural variations present within reproductively isolated populations is acted upon by selection (mainly natural) to alter the relative frequencies within the natural variants present.

    The natural variation within populations could be generated by non-random directed beneficial mutations within bacterial prokaryotes (although I’ve provided reasons why it’s completely fallacious to imagine that it happens with a major flaw in logical thinking).

    The evidence is consistent that mutations are random and non-selected, and are sorted out by natural selection.

    Non-random directed mutations just doesn’t work in multicellular eukaryotes including birds and mammals. You haven’t provided any reasoning as to how it could work, unless you’re thinking of your bizarre delusional belief in a conscious universe?

    It’s all very simple really. Perhaps too simple for a simple fellow such as you? You want the ‘secret’ of life to be inexplicable to fit your worldview.

  337. BillyJoe7on 02 Oct 2016 at 11:41 pm

    Nope, science demands you that you provide an alternative theory. It is insufficent to simply think that you have demolished the old theory because you could be wrong about that…as has been amply and repeatedly shown to be the case here.

  338. SteveAon 03 Oct 2016 at 7:13 am

    hardnose: “But when the environment changes and bacteria must adapt or die, you deny there could be anything purposeful in their adaptive response.”

    That’s right, when the local pH rises beyond what’s comfortable, the bacterium all look up what to do in their little user manuals and change their genomes accordingly. Or do they hold a meeting and take a vote on the appropriate changes to make? Or do they all commune with a higher intelligence that will guide their actions?

    Or if none of the above, then what?

    Actually, don’t bother answering on my account. I doubt I’ll be visiting this thread again.

  339. hardnoseon 03 Oct 2016 at 8:34 am

    “Almost all genuine experts in the field agree that there is a mountain of evidence in support of the modern theory of evolution.”

    They agree that their is a mountain of evidence FOR EVOLUTION.

  340. hardnoseon 03 Oct 2016 at 8:36 am

    “The evidence is consistent that mutations are random and non-selected, and are sorted out by natural selection.”

    There is NO evidence that mutations are random. If there is evidence, why hasn’t anyone here shown any examples?

  341. hardnoseon 03 Oct 2016 at 8:42 am

    “The only way to successfully criticize a widely accepted theory to offer a better theory that fits the evidence just as well or better and also has equal or better explanatory and predictive capability.”

    There is a widely accepted theory of evolution that is illogical, implausible, and lacks evidence. It has been accepted for reasons that are not scientific.

    There is absolutely no reason to accept a theory that has NO EVIDENCE, just because we do not yet have an alternate explanation.

  342. hardnoseon 03 Oct 2016 at 11:52 am

    And by the way, how widely accepted is it really? Aside from people who love Dawkins and believe everything he says. Do you really think most biologists agree with Dawkins and Coyne that evolution has been figured out?

  343. BillyJoe7on 03 Oct 2016 at 4:21 pm

    Wrong – evolution by random mutation and natural selection.
    Wrong – there is a mountain of evidence for random mutation.
    Wrong – the modern theory of evolution is totally plausible, logical and evidential.
    Wrong – there is no reasom to accept a theory that has no evidence and no mechanism.
    Wrong – all evolutionary biologists accept the modern theory of evolution except a few fringe dwellers.

    Score: 0

    Go back to grade 1.

  344. hardnoseon 03 Oct 2016 at 4:52 pm

    “Wrong – evolution by random mutation and natural selection.”

    So you finally agree it’s wrong.

  345. hardnoseon 03 Oct 2016 at 4:54 pm

    “Wrong – there is a mountain of evidence for random mutation.”

    Of course there are occasional errors. Of course there is evidence for that.

    But there is no evidence that advantageous mutations are, or have been, generally random errors.

  346. bachfiendon 03 Oct 2016 at 5:02 pm

    Hardnose,

    As I’ve pointed out to you on numerous occasions, the only way of distinguishing random non-directed mutations with the beneficial ones winnowed out by natural selection from non-random directed beneficial mutations would be to be able to detect all the mutations in real time.

    This isn’t possible, not even in theory, let alone in practice. For a mutation to be detected, it has to have survived and been replicated so that there’s millions of copies, so already there’s selection in action.

    The evidence for random mutations and against non-random mutations is the predictions they make. With random non-directed mutations, adaptations to change should be late and infrequent. With non-random directed beneficial mutations, adaptations to change should be early and frequent.

    And what sort of adaptations do we see? Late and infrequent, consistent with random non-directed mutations.

    I know that it’s difficult for a motivated ignoramus such as you to understand, but the broad strokes of evolution has actually been ‘figured out’. Evolutionary change is largely CAUSED by a changing environment affecting a reproductively isolated population. The MECHANISM of the evolutionary change in reproductively isolated populations is mainly natural variation within the population and natural selection.

    The arguments are about the details. Shapiro’s NGE could be a cause of natural variation within populations, although there’s no evidence that it’s plausible, not even for bacterial prokaryotes let alone multicellular eukaryotes.

    There’s absolutely no support for your delusion, except in religiously motivated creationists, that there’s direction in evolution. That there’s an innate tendency towards increasing complexity and intelligence in biological systems.

    You’re just wasting our time. You’re an ignorant creationist Internet troll who refuses to answer anyone’s arguments as to why your opinions are delusional, instead just carping about trivia.

  347. hardnoseon 03 Oct 2016 at 6:24 pm

    “Shapiro’s NGE could be a cause of natural variation within populations, although there’s no evidence that it’s plausible, not even for bacterial prokaryotes let alone multicellular eukaryotes.”

    Of course there is evidence that it’s plausible. Why would bacteria not use their abilities to survive?

  348. hardnoseon 03 Oct 2016 at 6:37 pm

    “There’s absolutely no support for your delusion, except in religiously motivated creationists, that there’s direction in evolution. That there’s an innate tendency towards increasing complexity and intelligence in biological systems.”

    You keep repeating that, but I never said there was evidence for it. I said many times that the reasons for life, and evolution, are not known scientifically.

    And your deep hatred for religion is obvious in that comment. You are obviously a follower of Dawkins, who thinks that religion has been disproved by science.

    I don’t think science can tell us anything about religion. I think real scientists are either agnostic, or, if they are religious, keep their beliefs out of their scientific opinions.

    Dawkins is a devout believer in atheism, and he misuses science to support his faith.

  349. Steve Crosson 03 Oct 2016 at 7:29 pm

    hardnose:

    I said many times that the reasons for life, and evolution, are not known scientifically.

    For Anything, if the cause is unknown, then it effectively occurs randomly — by definition.

    The only way to prove something is not random is to discover the cause. Since you deny that has happened, then you have just admitted that you are completely wrong.

    You are an ignorant, illogical cretin that couldn’t use logic to prove a tautology was true.

  350. bachfiendon 03 Oct 2016 at 7:33 pm

    Hardnose,

    You persist in being an ignorant creationist Internet troll. You persist in not responding to any of the arguments destroying your misconceptions concerning evolution.

    I don’t hate religion. I don’t even hate religious scientists. I just dislike those who bring their religious beliefs into science. As I’ve noted, creationists such as you want to see direction in evolution (if they accept evolution that is). They want to believe that humans were the goal of evolution.

    There’s no evidence that this is the case. Evolution doesn’t have direction. There’s no aims or targets.

    For a book that’s worth reading I recommend ‘Evolution and Belief. Confessions of a Religious Paleontologist by Robert Asher. It’s very good. So good in fact that Stephen Meyer devoted several pages to criticising it in ‘Darwin’s Doubt’.

    You don’t have any evidence for your delusions. You’re just wasting our time with your stupid questions such as ‘why would bacteria not use their abilities to survive?’ What abilities? How about programmed cell death in bacteria? This is death by suicide analogous to the programmed cell death (apoptosis) in eukaryotes, using genes which are conserved across prokaryotes and eukaryotes. Why would bacteria commit suicide actively using genes instead of surviving?

    You’re profoundly ignorant about the science you reject. Your opinions and thoughts are absolutely worthless. You’re too ignorant to realise how ignorant you are. And you’re far too quick to ascribe motives to your critics.

  351. Steve Crosson 03 Oct 2016 at 7:40 pm

    “And you’re far too quick to ascribe motives to your critics.”

    In fairness, if bacteria have motives, then critics probably do too. 😉

  352. hardnoseon 03 Oct 2016 at 7:57 pm

    “For Anything, if the cause is unknown, then it effectively occurs randomly — by definition.”

    That statements shows that you don’t bother to think. Things happen for a reason, whether we know the cause or not.

    The idea that beneficial mutations are errors is a hypothesis.

    We never assume something happened accidentally just because we don’t know why it happened.

    That would be insane.

  353. Steve Crosson 03 Oct 2016 at 9:58 pm

    I was hoping you would take the bait.

    Things happen for a reason, whether we know the cause or not.

    Prove it. That is your evidence free assertion.

    Even if we assume that most things appear to have a cause (although not necessarily some significant metaphysical reason), there is still no discernible difference between random chance and an unknown cause.

    Until you KNOW the cause, it is childishly foolish to make any assumptions. Between quantum uncertainty and chaos theory, we know that some things will always be beyond our ability to predict and thus effectively random.

    You anthropomorphize everything when you casually use words like “reason” and “accident”. That is called “begging the question” and it is a very common logical fallacy. You are assuming that your starting conditions are already proven, but you have not yet demonstrated them to be true.

    The idea that beneficial mutations are errors is a hypothesis.
    We never assume something happened accidentally just because we don’t know why it happened.
    That would be insane.

    This has been refuted numerous times. Re-read the thread and try not to be so stupid.

    Bottom line: you’ve provided no evidence for your mistaken beliefs. No one is likely to believe that an ignorant layman is more likely to be correct than the opinion of experts. You don’t have the knowledge or expertise to even know if Shapiro is correct or not. You’re just an ignorant ideologue.

  354. BillyJoe7on 03 Oct 2016 at 11:35 pm

    Just a note for our illiterate friend…

    WRONG refers to your answers
    The other bit is the correct answer.
    Go back to grade 1.

  355. hardnoseon 04 Oct 2016 at 10:56 am

    “Until you KNOW the cause, it is childishly foolish to make any assumptions.”

    That is what I have been saying.

    Since the cause of advantageous genetic mutation is not, in general, known, it is irrational to make the assumption these mutations are always accidents or errors.

    And knowing the extensive mechanisms cells use for modifying their DNA (for which there is conclusive evidence), it is irrational to assume these mechanisms are never used for adapting to environmental changes.

  356. Kabboron 04 Oct 2016 at 12:53 pm

    The summary of the positions here:

    Everyone else: Show me that the mutations are not random.

    hardnose: Show me that the mutations are not not random.

    While we are at it, let’s give our concrete photographic evidence that there is no big foot.

  357. Steve Crosson 04 Oct 2016 at 1:04 pm

    Nice try.

    Since all available evidence supports the idea that mutations are random with respect to the needs of the organism, we are justified in assuming you are wrong until you actually provide some evidence.

  358. Steve Crosson 04 Oct 2016 at 1:06 pm

    Just to be clear, my comment is directed at hardnose’ idiocy.

  359. hardnoseon 04 Oct 2016 at 7:14 pm

    “Since all available evidence supports the idea that mutations are random with respect to the needs of the organism, we are justified in assuming you are wrong until you actually provide some evidence.”

    You have NO EVIDENCE that the mutations are random. You think it’s the null hypothesis, because you have no idea what null hypothesis means.

    You are extremely confused.

  360. bachfiendon 04 Oct 2016 at 8:22 pm

    Hardnose,

    You persist in being extremely confused. You don’t have the faintest idea what the null hypothesis is. You have the hypothesis that mutations are non-random directed and beneficial to the needs of the organism. The null hypothesis is therefore that mutations are random non-directed and neutral to the needs of the organism (including both beneficial and non-beneficial ones).

    To test your hypothesis, you need to show that the mutations observed occur in a distribution not consistent with mutations being random.

    Which I have noted on many occasions (and which you refuse to acknowledge) is impossible to do in theory, let alone in practice. It would be necessary to detect ALL the mutations as they occur in real time.

    But that’s not possible. For a mutation to be detected, it has to exist in many copies – perhaps millions. So the mutation has to have survived and been replicated many times, immediately removing lethal mutations in critical parts of the organism’s genome from ever being detected.

    The null hypothesis can’t even be started to be tested, because the full distribution of all mutations occurring can’t be determined. Already, of the mutations capable of being detected there is an excess of ‘beneficial’ mutations.

    It’s such an obvious point, I wonder how anyone remotely intelligent could fail to understand it.

    The only way, without detecting all mutations in real time, to distinguish ‘random non-directed mutations, with selection winnowing out the deleterious mutations’ from ‘non-random directed beneficial mutations’ is to consider the predictions the predictions the rival hypotheses would make.

    ‘Random mutations’ would predict that adaptations to a changed environment occur late and infrequently.

    ‘Directed mutations’ would predict that they’d occur early and frequently.

    And what do we observe when we test the two predictions?

    They occur late and infrequently. Only one out of 12 lines of E. coli in Lenski’s study managed to develop the ability to metabolise citrate, and only after tens of thousands of generations, despite the ability to metabolise citrate being of enormous benefit to bacteria living in an otherwise energy poor and sugar deficient environment for much of the time.

    The evidence supports the hypothesis that mutations are random and non-directed. Beneficial mutations are late occurring and infrequent.

    As usual, I expect that you’ll ignore this argument against your delusion, just like all Internet trolls do.

  361. Steve Crosson 04 Oct 2016 at 8:50 pm

    You have NO EVIDENCE that the mutations are random. You think it’s the null hypothesis, because you have no idea what null hypothesis means.

    Yet another example of an endless line of evidence free statements.

    You have NO EVIDENCE that there is no evidence that the mutations are random. When you can prove that, then we can talk about the rest of your allegations.

  362. hardnoseon 04 Oct 2016 at 9:09 pm

    “You have NO EVIDENCE that there is no evidence that the mutations are random.”

    Are you trying to see how ridiculous and irrational you can be?

    You are claiming to know how and why life evolved. I don’t claim to know. If you wanted to defend your belief, you would provide some evidence for it.

  363. Steve Crosson 04 Oct 2016 at 9:32 pm

    Almost all experts agree that there is a mountain of evidence in support of the modern theory of evolution. If you disagree, then prove them wrong — with evidence.

    “You are claiming to know how and why life evolved.”

    Another lie. No one claims to know “why” life evolved or even if there is a “why”. Regarding “how”, no one claims to know how life got started. But once it did, the mountain of available evidence supports the current theory about how the huge diversity of life evolved over billions of years.

    If you think they’re wrong, then prove it with some evidence.

  364. hardnoseon 04 Oct 2016 at 9:43 pm

    “Almost all experts agree that there is a mountain of evidence in support of the modern theory of evolution.”

    There is a mountain of evidence to support evolution. Natural selection has to be true, no evidence needed.

    There is NO evidence for Dawkins’ theory that natural selection is the only organizing force of evolution.

    There is NO evidence that adaptive mutations are always accidents or errors.

    You know all this, but you stubbornly pretend not to know.

  365. Steve Crosson 04 Oct 2016 at 9:55 pm

    There is NO evidence for Dawkins’ theory that natural selection is the only organizing force of evolution.
    There is NO evidence that adaptive mutations are always accidents or errors.

    Wrong. All the available evidence fully supports the existing theory. If you have some evidence that proves something else exists, then present it.

  366. hardnoseon 04 Oct 2016 at 10:05 pm

    “All the available evidence fully supports the existing theory.”

    WHAT EVIDENCE?

  367. Steve Crosson 04 Oct 2016 at 10:12 pm

    “WHAT EVIDENCE?”

    Your refusal to read, try to understand or accept the evidence is not my fault. The majority of experts agree that the evidence is persuasive.

    You’re the outlier. It is up to you to try to prove the majority is wrong.

  368. hardnoseon 04 Oct 2016 at 10:14 pm

    “Your refusal to read, try to understand or accept the evidence is not my fault. The majority of experts agree that the evidence is persuasive.

    You’re the outlier. It is up to you to try to prove the majority is wrong.”

    I see. You believe in a theory that you have no evidence for, because you think the majority of experts believe in it.

    And you consider yourself a skeptic?

  369. Steve Crosson 04 Oct 2016 at 10:47 pm

    “And you consider yourself a skeptic?”

    Yes, yes I do … because I’ve read and understood the evidence before I reached a conclusion.

    You should try it sometime.

  370. Steve Crosson 04 Oct 2016 at 10:49 pm

    BTW, if you ever did provide some actual evidence, I would read it too, and factor it into my conclusion. I read Shapiro’s stuff and found it very weak. Have you even read his book yet?

    Still waiting for some good evidence to support your contentions.

  371. bachfiendon 05 Oct 2016 at 6:00 am

    Hardnose,

    As expected, you have refused yet again to answer my argument against the validity of your multiple delusions.

    You’re ignorant about evolution. Your opinions of no weight. You’re just wasting our time.

  372. Kabboron 05 Oct 2016 at 8:05 am

    It is like hardnose is looking at a car and proclaiming that humans can’t have made it. There must be some other outside force that made the car. Not that there is any evidence of such, it is a simple argument from incredulity.

    The current theory provides everything a scientific theory should. It accounts for what we see in nature, and provides predictive power. There is a chance it is not be the complete picture, but until we find evidence that it is not the complete picture we should treat it as such. That does not mean we stop researching.

    Much like Newtonian physics, we use it until such a time as it proves that it needs to be modified. Asserting that it is wrong before we have evidence that it is wrong is a waste of your time and ours.

  373. hardnoseon 05 Oct 2016 at 8:53 am

    “I’ve read and understood the evidence”

    Where are you hiding that evidence Cross? Why is it being kept secret?

    Dawkins’ clever trick is to show a ton of evidence for evolution, then use natural selection to explain evolution, and pretend there is evidence for his explanation.

    And you all fall for it.

  374. hardnoseon 05 Oct 2016 at 8:54 am

    I do NOT meant to imply Dawkins is deceptive. He genuinely believes in his fanatical cause.

  375. Steven Novellaon 05 Oct 2016 at 11:38 am

    “There is NO evidence for Dawkins’ theory that natural selection is the only organizing force of evolution.
    There is NO evidence that adaptive mutations are always accidents or errors.”

    Wow, you’re still flogging those straw men. Incredible. I know you’re hopeless, but for those playing name that logical fallacy:

    The accepted consensus (not Dawkin’s theory) is that natural selection is a major organizing force in evolution. There is copious evidence for natural selection. It is not the only force in evolution, there is also, for example, genetic drift.

    But notice how you frame what is essentially a negative claim as if the burden of proof is on scientists. “There is NO evidence that NS is the ONLY force.” In other words, you are saying that scientists have to prove the negative that there is no other force in evolution. Science doesn’t work that way. Rather, if you think there is another force that is not yet known, then you need to propose a coherent hypothesis, figure out how to test it, and then test it.

    Same goes for mutations. “There is NO evidence that mutations are ALWAYS errors” is the same as saying, you have to prove the negative that there are no non-random mutations. That is just BS.

    There is evidence for natural selection, and that it is a major force in evolution. There is also evidence that genetic drift is also a major force in evolution. There is NO evidence for any top-down designing force in evolution, nor any plausible mechanism. That is a much better way to state the current consensus.

    There is evidence that mutations are mostly spontaneous, but that the location and timing of mutations are not random because they are affected by a host of cellular mechanisms and environmental factors that create mutation “hotspots”.

    There is evidence that the specific mutations and their effects are entirely unguided. There is no force, or design, or intelligence, or even cellular algorithm that “knows” to change an A to a G at one specific place in one specific gene because the resulting protein with have some net adaptive effect on the organism. There is no plausible mechanism for this, and no evidence that it happens.

    Stop asking scientists to prove negatives, and stop attacking silly strawmen. It is truly tiresome.

  376. hardnoseon 05 Oct 2016 at 2:21 pm

    “There is evidence that the specific mutations and their effects are entirely unguided.”

    You are wrong. If you are thinking of Lenski’s experiment, that is only one researcher and the evidence is not at all conclusive or convincing.

    Evidence for natural selection being the primary organizing force of evolution does not exist. You believe it because you like the theory.

    I have stated here repeatedly that there is still no good explanation for evolution. I can’t provide evidence for a nonexistent theory.

    You believe there is a good explanation, but you think it does not require any evidence.

  377. steve12on 05 Oct 2016 at 3:20 pm

    “I have stated here repeatedly that there is still no good explanation for evolution.”

    OK, we’ve got it. Nobody knows. Thanks! Buh-Bye!

  378. bachfiendon 05 Oct 2016 at 5:35 pm

    Hardnose,

    As I’ve noted on numerous occasions, you’re just wasting our time. You’re a typical Internet troll. You ought to be banned (Steve – is this possible on your blog?)

    You keep changing the words you use without changing your non-existent argument. Now you declare that there’s no explanation for evolution instead of no cause.

    There’s a perfectly good explanation for evolution. The environment of a reproductively isolated population changes which causes, or explains if you like, evolutionary change within the population predominantly by the mechanism of natural selection acting on natural variation within the population.

    If you now think that there’s no good explanation for evolution then why did you link to Shapiro’s website, in your very first comment on this thread, which ‘promises’ to do just that?

    You claim that there’s no evidence that mutations are random – which is the null hypothesis, the negative hypothesis – so where is your evidence that mutations are non-random and directed?

    You shouldn’t return until you’ve capable of answering this question.

    You are completely delusional in thinking that evolution has a direction. That there’s an innate tendency to increasing complexity and intelligence in biological systems.

  379. hardnoseon 05 Oct 2016 at 7:02 pm

    What makes you think your opinions have any value bachfiend?

  380. bachfiendon 05 Oct 2016 at 8:30 pm

    Hardnose,

    My opinions have value, whereas yours don’t, because I follow the evidence. I don’t rely on secondary sources (which are often misleading) as you do. I attempt to go back and read the primary source on which the news article or blog post or whatever is based. And I’m often surprised (but not shocked) to discover that the secondary source is wrong, and has misinterpreted the primary source. Or that the primary source, even worse, is wrong too.

    Your opinions are completely evidence free. You refuse to provide any evidence whatsoever that mutations are non-random directed and beneficial. Or that evolution has direction. Or that there’s an innate tendency to increasing complexity and intelligence in biological systems.

    You refuse to answer questions or address arguments.

    You’re an ignorant creationist Internet troll. Your opinions on evolution are worthless because you’re ignorant and completely clueless about evolution and almost all science. Let alone statistics and logic.

  381. hardnoseon 06 Oct 2016 at 8:46 am

    “You claim that there’s no evidence that mutations are random – which is the null hypothesis, the negative hypothesis”

    That is absolutely not true. You don’t know what “null hypothesis” means.

  382. bachfiendon 06 Oct 2016 at 9:55 am

    Hardnose,

    You remain completely clueless, as shown by your ignorance concerning the null hypothesis. You have absolutely no idea what the null hypothesis is. Go away and look it up.

    But as I’ve noted on many occasions (which you’ve never acknowledged), to distinguish between random and non-random mutations it would be necessary to detect all mutations as they occur in real time. For any mutation to be detected it has to survive and be replicated many times producing perhaps millions of copies, so already there’s selection of beneficial mutations.

    It’s not possible to detect all mutations, both in theory and in practice.

    Statistics really can’t be applied to distinguishing between random and non-random mutations. Not all the mutations can ever be detected, and there’s a bias involved in the ones which are missed.

    They can only be distinguished by the predictions they make.

    ‘Random mutations’ predicts late and infrequent adaptations to stress.

    ‘Non-random mutations’ predicts early and frequent adaptations to stress.

    And what do we see? Late and infrequent adaptations to stress consistent with mutations being random.

    I still ask you – what evidence do you have that mutations are non-random directed and beneficial? You’re the one making the extraordinary claim, and hence you should be the one providing the evidence, if there is any.

  383. steve12on 06 Oct 2016 at 11:24 am

    Dr. TheTroll: A Challenge / Question:

    (Since there’s no hope of shunning at this point…)

    Let’s be experimentally generative instead of arguing the literature.

    “You don’t know what “null hypothesis” means.”

    Obviously you do. You have a science PhD and advanced knowledge of evolutionary biology so this should be easy and a useful alternative to this circular discussion.

    Please describe an experiment that would test your ideas re mutation. You are not shackled by our current technology; you may invent technologies that do not yet exist so long as you do not use the technology to obscure experimental description / details (e.g., “I invented an answer machine that says mutations are directed!)

    As is customary, please phrase the hypotheses: H^0 (the null hypothesis) and H^1 (the research / alternative hypothesis).

    We don’t need to agree or disagree re: any result here. We are merely discussing whether the setup of the experiment is sound.

    So let’s have some creative fun!

  384. hardnoseon 06 Oct 2016 at 1:19 pm

    “You have absolutely no idea what the null hypothesis is.”

    You think “null hypothesis” means the phenomenon under investigation happened by accident.

    You are WRONG, that is NOT the definition.

    You have never done inferential statistics, obviously.

  385. hardnoseon 06 Oct 2016 at 1:27 pm

    “Please describe an experiment that would test your ideas re mutation.”

    I am really tired of telling you that I DO NOT have a theory of evolution.

    There is NO scientific or logical reason to accept your theory that all mutations are accidents. That idea has been popularized and you accepted it without any skepticism.

  386. steve12on 06 Oct 2016 at 1:28 pm

    So is that a “no” Dr. TheTroll?

    Are you actually going to turn down a chance to take the discussion in a new and potentially useful direction to instead continue this repetitive back and forth?

    Really?

  387. steve12on 06 Oct 2016 at 1:51 pm

    “I am really tired of telling you that I DO NOT have a theory of evolution.”

    So you don’t know the difference b/w theory and hypothesis. Hmmm….

    I asked for a HYPOTHETICAL experiment that would test whether mutations were guided or not. And I gave you the freedom to no technological constraints.

    Now please define H^0 and H^1 and give me you experiment. No theory of evolution required. This is almost a technical exercise – why are you refusing?

  388. steve12on 06 Oct 2016 at 2:08 pm

    Dr. TheTroll:

    I’ll give you a hint, even though a real scientist like yourself doesn’t need it.

    H^0 or H^1 that are vague and not in relationship to your hypothetical experiment are not useful. Statements like “Mutations are guided” are essentially incorrect.

    I’ll use an example that I’ve used here several times: the effects of sugar on aggressive behavior in kids.
    I’m going to give 10 kids kids a cup of sugar (active treamtment) and 10 kids a cup of Stevia (placebo). This is my IV. Then, I’m going to have RA’s count the number of times Sugar Group kids strike another kid (Sug Strikes) and the number of times Stevia kids strike another kid (StevStrikes).

    H^0: SugStrikes=StevStrikes
    H^1: SugStrikes>StevStrikes

    Notice that I did not say:
    H^0: Sugar doesn’t cause aggresiveness
    H^1: Sugar doesn cause aggresiveness

    OK, your turn.

  389. steve12on 06 Oct 2016 at 2:10 pm

    “Statements like “Mutations are guided” are essentially incorrect.”

    I mean incorrect as an answer to this specific challenge. I’m leaving aside the actual truth of the statement for now while we build our experiment.

  390. hardnoseon 06 Oct 2016 at 3:44 pm

    I have no idea what you are asking. I know how to design experiments. I am not a molecular biology researcher, and never said I was.

    I know what “null hypothesis” means.

  391. steve12on 06 Oct 2016 at 3:53 pm

    “I have no idea what you are asking.”

    What part don’t you understand?

    You don’t have to be a molecular biology researcher to come up with a hypothetical experiment! And you don’t have to know anything technical because I gave you licence to make up technology. You can do this experiment on any level you like, and any theory you want to use is fine. You can make that up too.

    In essence, you have free reign.

    So on you go. What hypothetical experiment can you design that would test your hypothesis that mutations are guided?

    I can think of 10 off the top of my head!

  392. steve12on 06 Oct 2016 at 3:54 pm

    “…you don’t have to know anything technical…”

    I mean technical re: molecular biology. You do have to understand research design, if for no other reason than to be methodologically consistent with the hypothetical constraints that YOU are allowed to invent.

  393. steve12on 06 Oct 2016 at 4:05 pm

    If you’re stuck, may I gently suggest that you think of the Lenski experiment? I can think of a few variants of that experiment that could be pretty clean tests of your hypothesis…

  394. hardnoseon 06 Oct 2016 at 4:44 pm

    “What hypothetical experiment can you design that would test your hypothesis that mutations are guided?”

    I never said I had a hypothesis. I said YOUR theory has NO evidence.

    I never said mutations are guided. I said Shaprio has found conclusive evidence that cells modify their DNA. The word “guided” is not mentioned. It is not controversial.

    Cells do all kinds of things with the purpose of staying alive, or keeping the organism or colony they belong to alive. It is only reasonable to think they would modify their DNA with the purpose of adapting to adverse conditions.

  395. hardnoseon 06 Oct 2016 at 4:46 pm

    Epigenetic research has already shown that genetic modifications can be inherited.

    There is no reason to deny that other kinds of genetic modifications, aside from epigenetics, might be inherited.

  396. BillyJoe7on 06 Oct 2016 at 4:55 pm

    …same old same old word games with no balls

  397. hardnoseon 06 Oct 2016 at 5:01 pm

    “Recent work shows that [bacterial] adaptive resistance requires epigenetic inheritance”

    https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4363326/

  398. hardnoseon 06 Oct 2016 at 5:02 pm

    More nails in the coffin of your Dawkinism.

  399. steve12on 06 Oct 2016 at 5:05 pm

    Dr. TheTroll:

    “I never said I had a hypothesis. I said YOUR theory has NO evidence.”

    HAHAHAHAHAHAHAHA!!!!! What a FRAUD!!!!

    Do you know what ‘hypothetical’ means? Make one up then! You keep saying that mutations are guided / non random – you might try one of those.

    **What’s really happening here**
    I’m challenging you to actually PROVE you know what you’re talking about. You can’t find a HuffPo piece to get you out of this.

    You CANNOT design a hypothetical experiment. You DO NOT know how. You DO NOT really know what a null hypothesis is. Like my kids in methods, you sort of have the concept, but not really,

    PUT UP OR STFU!!!

    Give me you experiment DOCTOR!

    HAHAHAHAHAHAHA! I broke you ! HAHAHAHAHAH

  400. steve12on 06 Oct 2016 at 5:08 pm

    BJ7:

    “…same old same old word games with no balls”

    Indeed. Afraid to stake himself to anything considering that he’s lied all this while about his credentials, and he CANNOT DO IT.

    GIVE US THE EXPERIMENT!!!!
    GIVE US THE EXPERIMENT!!!!
    GIVE US THE EXPERIMENT!!!!

    #BROKE_DrTheTroll

  401. mumadaddon 06 Oct 2016 at 5:39 pm

    And this is another clear example of where everyone should either keep hn on point or sit back and say nothing.

  402. mumadaddon 06 Oct 2016 at 5:39 pm

    Ps. Nice work, steve12. Entertaining too.

  403. mumadaddon 06 Oct 2016 at 5:45 pm

    Epigenetics! Right then, no reason to assume that mutations aren’t random with respect to reproductive success!

    I win! You deluded fools…

  404. hardnoseon 06 Oct 2016 at 5:54 pm

    “You CANNOT design a hypothetical experiment. You DO NOT know how. You DO NOT really know what a null hypothesis is. Like my kids in methods, you sort of have the concept, but not really”

    No I am not obediently doing your stupid homework assignments, for no credit. I am not your kid in methods.

    I know exactly what a null hypothesis is. backfiend doesn’t even know how to look it up on wikipedia.

  405. steve12on 06 Oct 2016 at 5:55 pm

    I aim to please Mumadadd.

    I just think it’s unbelievable that a scientist can’t come up with a hypothetical experiment even when they’re allowed magical technologies and hypothetical premises.

    I gave the guy everything but goddamn fairy dust, including a template.

    This is an exercise I’ve given to undergrads in intro research methods, but the Good Doctor won’t even take a stab.

    #FAIL
    #BROKE_DrTheTroll

  406. bachfiendon 06 Oct 2016 at 5:58 pm

    Hardnose,

    Another one of your quotes:

    ‘And by the way, why does anyone need more proof that bacteria adapt to antibiotics? This video has nothing to do with the controversies about what causes evolution’.

    If your statement is true (it isn’t by the way, it isn’t even not ‘not wrong’), then the fact that bacteria can dial up and dial down their resistance to an antibiotic when it’s present or not also has nothing to do with evolution either.

    You did read the paper didn’t you? Or did you just read the title? The bacteria dialling up or dialling down their antibiotic resistance have started already being antibiotic resistant because of their original genetics. Producing unnecessary gene products, whether it’s one for resistance to an antibiotic or the ability to metabolise a given sugar, incurs costs, so bacteria have evolved the ability to dial up genes when necessary and dial down genes when not needed, whether the antibiotic is present or not, or the particular sugar is present or not.

    Antibiotics aren’t a novel threat to bacteria. Bacteria have been engaged in chemical warful long before human pharmaceutical companies came along thinking they’d won the war against our bacteria masters.

    Bacteria obviously have evolved the ability to modulate their metabolism. It’s a well known phenomenon and certainly not a surprise.

    OK – what does the null hypothesis mean? Define it specifically. Stating that you know what it means doesn’t count.

    I don’t think that it means that the phenomenon under investigation, such as mutations, happened by accident. Mutations obviously have a cause, whether ionising radiation, misreading errors in replication, mutagenenic chemicals, free radical damage, whatever… The null hypothesis just states that the phenomenon under investigation occurs randomly in respect to a second phenomenon. That there’s no correlation between the two phenomena.

    And then you do your experiment and obtain your results. If the results show that there is a correlation, that it’s not random, then the null hypothesis is rejected. And it may, just may mind you, indicate that there’s causation involved. That one phenomenon might have caused the other. That environmental stress might cause increased mutations.

    It doesn’t prove it though. And as I’ve noted on numerous occasions, AND WHICH YOU PERSIST IN REFUSING TO ADDRESS, it’s impossible to show that mutations are either random or non-random unless all the mutations occurring can be detected in real time, which is impossible both in theory and in practice.

    You’re an ignorant creationist Internet troll. You’re just wasting our time.

  407. steve12on 06 Oct 2016 at 5:58 pm

    OH, IT’S GETTIN’ GOOD!!!!!

    “No I am not obediently doing your stupid homework assignments, for no credit. I am not your kid in methods.
    I know exactly what a null hypothesis is. backfiend doesn’t even know how to look it up on wikipedia.”

    So you could do it, you just don’t feel like it?

    What a loser!!!! Oh, Oh, Oh – how I love this. 1400 posts, but now he’s got cold fingers.

    BWAHAHAHAHA!!!!!

    #BROKE_DrTheTroll

  408. Steve Crosson 06 Oct 2016 at 6:03 pm

    I know exactly what a null hypothesis is. backfiend doesn’t even know how to look it up on wikipedia.

    Hate to tell you this, but it is obvious to the rest of the world that your entire “expertise” is solely from Wikipedia. Dozens of people have already explained that your understanding of the null hypothesis is superficial and mostly wrong.

  409. mumadaddon 06 Oct 2016 at 6:05 pm

    Ah, bachfiend, do you really think that detailed explanations are the best bet here?

  410. Steve Crosson 06 Oct 2016 at 6:07 pm

    hardnose, you can’t even prove that you understand how to tell good evidence from bad. That is the challenge that steve12 has put to you. It is a simple challenge really. He has certainly given enough hints and provided exceedingly generous constraint. Any high school science student should be able to do it easily. If you actually had half the qualifications you claim to have, you could have done it in your sleep.

    The fact that you can’t do it proves beyond all doubt that you are just an ideologue. You don’t have the skills to tell if Shapiro is right or wrong and you just believe him because you want to. You are just a fraud — and a stupid one at that.

    Your most recent “proof” (about epigenetics) makes that clear yet again. It has nothing to do with proving “intent”, “guidance”, or “direction”.

  411. steve12on 06 Oct 2016 at 6:09 pm

    BTW, DrTheTroll – I know you’re never going to do this. You couldn’t if you wanted to because you don’t have the chops. It’s that simple. It’s like me doing a backflip. I can try all I want – I’m incapable.

    But watching you squirm so obviously avoiding answering my question IS the answer. It answers that you’re understanding of these issues is HuffPo deep, that you lied about having a PhD, and that you are nothing but a religious weirdo with personality issues vying for some sort of freak-O attention.

    and I. f*cking. love. it.

    #BROKE_DrTheTroll

  412. mumadaddon 06 Oct 2016 at 6:13 pm

    This is how it happens. Bachfiend just fed hn a load of content he can work on until everyone forgets this and focuses on his latest two sentence assertion.

    (No offence, bachfiend, your content is great, but you lack troll management skills.)

  413. Steve Crosson 06 Oct 2016 at 6:15 pm

    “Ah, bachfiend, do you really think that detailed explanations are the best bet here?”

    Well, I enjoy them and appreciate the work. But sadly, it is way beyond obvious that hardnose couldn’t understand even simpler explanations — even if he was open-minded enough to try. It took me a long time to realize it, but HN is a lot stupider than I thought possible.

    I mean, really … steve12 couldn’t have made it any more obvious if he wrote TRAP in flashing letters and Dr. Oblivious comes off looking like a bigger fool than I could have imagined.

  414. steve12on 06 Oct 2016 at 6:15 pm

    Sh!t!

    I forgot that DrTheTroll can just go to the HuffPo “Hypothetical Experiments that Could Show That Mutations Are Guided” section!

    Oh wait…

  415. Steve Crosson 06 Oct 2016 at 6:22 pm

    Ha Ha !!!

    Just read “your understanding of these issues is HuffPo deep”. Ouch !!

    That is even more insulting than “Wikipedia deep”.

  416. Steve Crosson 06 Oct 2016 at 6:30 pm

    I forgot that DrTheTroll can just go to the HuffPo “Hypothetical Experiments that Could Show That Mutations Are Guided” section!

    As Shapiro’s scientific journal of choice, they probably do have a section like that.

    Speaking of Shapiro, if hardnose had actually read his book (or even understood the articles he claimed to have read), he could simply have regurgitated some Shapiro nonsense. But NOPE — hardnose falls head first into the trap and then decides to keep on digging.

  417. hardnoseon 06 Oct 2016 at 6:39 pm

    “I just think it’s unbelievable that a scientist can’t come up with a hypothetical experiment even when they’re allowed magical technologies and hypothetical premises.”

    I am not good at following your orders and I am not interested in your stupid assignments.

  418. hardnoseon 06 Oct 2016 at 6:48 pm

    “I don’t think that it means that the phenomenon under investigation, such as mutations, happened by accident. Mutations obviously have a cause, whether ionising radiation, misreading errors in replication, mutagenenic chemicals, free radical damage, whatever…”

    You said mutations are not accidents. You said mutations obviously have a cause. Then you said the cause is damage or errors (accidents). A chain of pure nonsense.

    “The null hypothesis just states that the phenomenon under investigation occurs randomly in respect to a second phenomenon. That there’s no correlation between the two phenomena.”

    You’re a random BS machine.

  419. Steve Crosson 06 Oct 2016 at 6:51 pm

    Just keep digging hardnose. You’ll get out of that hole in about 8000 miles.

  420. hardnoseon 06 Oct 2016 at 6:54 pm

    Dawkins has a passionate ideological agenda. He makes confident claims and provides no evidence at all to support them. He uses clever tricks to distract so you don’t notice that giant hole in his logic.

    And so far no one here has even tried to defend Dawkins. Instead you get all infantile and insult me, hoping anyone who reads this will be stupid enough to think that means you won the argument.

    You did not win the argument. You have not even tried.

  421. hardnoseon 06 Oct 2016 at 6:55 pm

    And no, I don’t take orders from anyone here and I don’t do your assignments.

  422. hardnoseon 06 Oct 2016 at 7:00 pm

    We were taking about the idea that natural selection is the organizing force in evolution/adaptation, and that genetic mutations are always unrelated to the needs of the organism or species.

    There is absolutely no way that could be considered the null hypothesis.

    No matter what random idiocy bachfiend generates, you will defend whatever he says.

    Because making sense and understanding is not your goal here.

  423. Steve Crosson 06 Oct 2016 at 7:14 pm

    hardnose,

    You’re not fooling anyone — except possibly yourself.

    Just keep digging. FYI, the farther underground you get, the hotter it is. Drink plenty of liquids.

  424. bachfiendon 06 Oct 2016 at 7:23 pm

    Hardnose,

    Aw gawd, you really are stupid aren’t you? You have this hypothesis that mutations, somehow, are non-random directed and beneficial to the needs of the organism in response to some environmental stress. By definition, the null hypothesis, the one you’re hoping to disprove, is that mutations are random and non-directed.

    Once you’ve disproved the null hypothesis then you’ve demonstrated that in your experimental set up that there’s a correlation between the two phenomena you’re examining, that there’s a linkage somehow between mutations and environmental stress.

    It doesn’t prove that there’s a causal relationship though. There might be a third phenomenon causing the other two. Or the direction of the causal relationship, if there is one that is. Or your experimental method could be flawed and you’re just producing bogus results.

    I don’t feel the need to defend Richard Dawkins. He’s perfectly capable of defending himself.

    I’m criticising you and your delusional ideas that evolution has a direction with aims and goals. And that there’s an inherent tendency for increasing complexity and intelligence in biological systems (except apparently not in hardnoses). And that the universe is conscious.

    I’m attacking your bullshit, and your idiotic creationist Internet trolling.

    You’re just wasting our time. You ought to be banned.

  425. Steve Crosson 06 Oct 2016 at 7:50 pm

    hardnose:

    Instead you get all infantile and insult me, hoping anyone who reads this will be stupid enough to think that means you won the argument.

    People will look at the evidence to decide who wins.

    Since you haven’t provided any, it is not looking good for your side.

  426. hardnoseon 06 Oct 2016 at 7:59 pm

    I asked you to provide evidence for your theory, many times, but you never did. I said many times that evolution has not been explained. You claim to have an explanation for evolution, but you have no evidence for it.

    That is why this has been going in endless circles.

    backfiend’s gibberish is just more senseless distraction from the whole point.

  427. Steve Crosson 06 Oct 2016 at 8:21 pm

    I never said mutations are guided. I said Shaprio has found conclusive evidence that cells modify their DNA. The word “guided” is not mentioned. It is not controversial.

    You’ve said many, many times that mutations are not random. Care to explain how that is different than guided.

    Cells do all kinds of things with the purpose of staying alive, or keeping the organism or colony they belong to alive. It is only reasonable to think they would modify their DNA with the purpose of adapting to adverse conditions.

    You’ve just used purpose to describe the actions of cells. How is that different than “intent” or “guidance”?

    Regardless of whether or not you understand the meaning of the words “theory” or hypothesis”, you clearly have an OPINION. We’d just like to know on what evidence you are basing that opinion.

    Everyone, including Shapiro, agrees that NS plays a role in evolution. You’ve even admitted that many times. There is a ton of evidence to support that fact in spite of your self-contradictory comments about lack of evidence.

    The ONLY question on the table is whether there are additional factors in play. Absent any good evidence for those additional factors, most experts have concluded that there may not be anything else required. In any event, it is bad practice to assume additional complications unnecessarily — Occam’s Razor and all that.

    There’s PLENTY of evidence that Natural Selection is an important factor in evolution — by your own admission. Now, if you’ll just provide some evidence in support of your “extra stuff”, then we can move forward.

  428. mumadaddon 07 Oct 2016 at 6:24 am

    Apologies to Steve C and bachfiend if my last few comments directed to you have come across at all pissy. It’s not born of frustration at you, but of my perception that hn is getting what he wants and you’re doing all the work while he merely pokes at you. However, I do realise that people may want to carry on the thread for reasons other than pest control, so I’ll can the criticism. And, I should reiterate, the content of your posts has been top notch.

  429. bachfiendon 07 Oct 2016 at 6:39 am

    Hardnose,

    Evolution has been explained many times to you. You’re just too stupid to understand it. Ignorant creationist Internet trolls such as you ought to be banned from this blog, in the same way that Jerry Coyne would have banned you from his blog ages ago (perhaps you have been?)

    Perhaps Steve Novella should start a thread discussing your psychopathology?

  430. Steve Crosson 07 Oct 2016 at 6:52 am

    mumadadd,

    No offense taken. Anyway, I fully agree with you that the goal should always be to make him work harder than we do — or at least to point out HN’s childish contradictions so clearly that he can’t even pretend to rebut them.

    Personally, I’ve really enjoyed bachfiend’s repeated taunting. It’s obvious that he is getting under HN’s skin when hardnose can only resort to pretending they don’t make sense. Either hardnose realizes that he can’t counter backfiend’s arguments (possible) or else he is genuinely too stupid to understand bach’s logic (more probable).

  431. Steve Crosson 07 Oct 2016 at 7:00 am

    bach,

    “Perhaps Steve Novella should start a thread discussing your psychopathology?”

    As entertaining (and deserved) as that might be, Dr. N would never sanction it because it is clearly unethical.

    We’ll just have to content ourselves with pointing out HN’s childish contradictions and woeful ignorance, and then laughing at his inability to respond intelligently.

  432. steve12on 07 Oct 2016 at 8:20 am

    Dr.TheTroll, Phd,MD,OBS,BS

    “I am not good at following your orders and I am not interested in your stupid assignments.”

    It’s stupid to ask someone what WOULD constitute a dispositive experimental result in a scientific discussion? WHAT?!?!? Only a non-scientist would consider this an “assignment”. A scientist would just answer the question.

    No, you are UNABLE to answer. And you used null in that same sufficiently-vague-as-to-be- meaningless manner again above.

    GIVE ME YOUR IDEALIZED EXPERIMENT!
    GIVE ME YOUR IDEALIZED EXPERIMENT!
    GIVE ME YOUR IDEALIZED EXPERIMENT!

    Come on Dr.TheTroll you f*cking COWARD! You talk all this sh!t but now you refuse to talk???

    COWARD
    COWARD
    COWARD

  433. steve12on 07 Oct 2016 at 8:29 am

    To All,

    Dr. TheTroll as maintained that the evidence that mutations are random w/ respect to outcome is lacking. We are going on 1500 posts with this!

    So I’m asking him: what experimental evidence WOULD BE sufficient for him to conclude that they were in fact random with respect to outcome? (I actually made it even looser).

    After all of the circular nonsense, I think it’s downright inappropriate for him to contend that this is an “assignment” and refuses to answer! So, echoing Mumaddad, I ask everyone here to suspend discussion with Dr. The Troll until he ANSWERS THE Q and gives us his hypothetical experiment.

    It’s one thing to contend that the phenomena isn’t real – it’s quite another to out and out refuse to answer what evidence you WOULD find compelling!

    It’s a very legitimate Q and he has no right to continue in the discussion w/o answering it.

  434. steve12on 07 Oct 2016 at 8:33 am

    *has maintained*

  435. hardnoseon 07 Oct 2016 at 9:35 am

    “Everyone, including Shapiro, agrees that NS plays a role in evolution. You’ve even admitted that many times. There is a ton of evidence to support that fact in spite of your self-contradictory comments about lack of evidence.”

    You know, this is getting really ridiculous. Natural selection plays a role because IT HAS TO. It is true by definition. It is not a scientific concept!

  436. hardnoseon 07 Oct 2016 at 9:36 am

    Dawkins, and others, say natural selection is the organizing force of evolution. THAT is what needs evidence. There is NO evidence for it.

  437. hardnoseon 07 Oct 2016 at 9:37 am

    Dawkins has built his preaching career and his New Atheist movement on an idea that has NO evidence.

  438. hardnoseon 07 Oct 2016 at 9:58 am

    If Coyne would have banned me, that’s because he represents an ideological movement.

    The fact that you want me banned from this blog means my comments are a threat to your ideology.

  439. bachfiendon 07 Oct 2016 at 10:05 am

    Hardnose,

    Besides the fact that there’s plenty of evidence that natural variation within reproductively isolated populations together with natural selection is the main cause of evolutionary change in response to a changing environment, there’s absolute no evidence whatsoever for your delusions that evolution has direction with aims and goals. That there’s an inherent tendency to increasing complexity and intelligence in biological systems. That the universe is conscious.

    You remain an extremely ignorant creationist Internet troll who’s incapable of rubbing together his two neurons and coming up with a coherent idea, let alone answer any of the questions you’ve been asked.

    You’re a one trick pony, capable of repeating only the same meaningless statements.

    Rather sad and pitiful really.

  440. Steve Crosson 07 Oct 2016 at 10:18 am

    hardnose:

    Natural selection plays a role because IT HAS TO. It is true by definition. It is not a scientific concept!

    For years, you’ve demonstrated that you have no understanding of science — AT ALL.

    Prove me wrong. Answer steve12’s challenge. You can’t, because you don’t even understand the basics.

  441. steve12on 07 Oct 2016 at 10:39 am

    Dr. TheTroll:

    # hardnose on 07 Oct 2016 at 9:35 am
    # hardnose on 07 Oct 2016 at 9:36 am
    # hardnose on 07 Oct 2016 at 9:37 am
    # hardnose on 07 Oct 2016 at 9:58 am

    Hmmm.. that’s a really weird experiment that you’re proposing. I definitely do not understand the H^0 or the H^1.

    I have no idea what would be sufficient evidence in your eyes that mutations are guided, random or otherwise.

    Can you provide some clarity here so that we have a sense of what evidence would be sufficient?

  442. steve12on 07 Oct 2016 at 10:45 am

    Dr. TheTroll:

    You’ve been coming here for years telling us that the Universe works very differently than we think it does.

    Why will you not provide us with some prospective methods to demonstrate how you could show us that?

    So you’re a PhD scientist with definitive opinions about how the scientific establishment is wrong, but all you can do is repeat “I don’t know / We don’t know?”

    You’re a PhD scientist with 0 potential ideas for how to show that you’re right? Even if allowed almost no constraints on instrumentation and technology?

    Please explain how this can be.

  443. hardnoseon 07 Oct 2016 at 12:23 pm

    There is evidence for natural selection. Natural selection is an obvious fact that must true. There is evidence for it, but there is no need for evidence for natural selection, since it is an inevitable truth.

    There is NO evidence that natural selection is the organizing force of evolution.

  444. hardnoseon 07 Oct 2016 at 12:27 pm

    Dawkins tricks his followers, and probably himself, into thinking evidence for natural selection is evidence that natural selection is the driving, organizing, force of evolution.

  445. hardnoseon 07 Oct 2016 at 12:32 pm

    “You’re a PhD scientist with 0 potential ideas for how to show that you’re right? Even if allowed almost no constraints on instrumentation and technology?”

    That is just stupid. Research on this is being done by molecular biologists. If I had an idea for an experiment to decide if adaptive mutations are accidents or not, that would prove nothing. The experiment would have to be done.

    All you are doing is trying to distract from your inability to show evidence for your opinion.

  446. steve12on 07 Oct 2016 at 12:39 pm

    “The experiment would have to be done.”

    HA HA HA HA HA !!!!!!!

    You’re a scientist and you never thought of a hypothetica experiment that you couldn’t actually do or would be difficult to do?

    First you didn’t understand the question. Then the question was arbitrarily re-interpreted as an “assignment” to give you an excuse so as not to answer it. Now the thing that every scientist ever does all the time is “stupid”.

    Oh, this is rich!

    YOU CANNOT DOT IT!!! AND I LOVE IT!!!!

    How about this Dr. TheTroll:

    I’ll further loosen the constraints of my question.

    Do you have ANY experiments that you have EVER thought of to test ANY of your assertions that you’ve made here?

    ANY!!!

    It’s OK if there’s no current technology available, and you need to invent some.

    Please communicate the experiment to us in scientific form so that it can properly discussed.

    ANY AT ALL!

  447. steve12on 07 Oct 2016 at 12:44 pm

    I’ve never asked a grad student, postdoc, or lab director what their “dream” experiment would be and got any of these responses

    1. I don’t understand
    2. I don’t do your assignments!
    3. None, because experiment would have to be done. I don’t idly think about experiments – in only do them
    4. This is stupid

    HA HA HA HA HA!!!!

    I love Dr.TheTroll now!

  448. steve12on 07 Oct 2016 at 12:45 pm

    Remember Dr. TheTroll:

    ANY experiment. ANY experiment at all on anything (not just evo) with no constraints but the scientific method.

    ANY???

    Come on ya COWARD!

  449. Steve Crosson 07 Oct 2016 at 12:46 pm

    What’s the matter hardnose?

    Can’t find any HuffPo articles on performing basic science experiments?

  450. hardnoseon 07 Oct 2016 at 12:51 pm

    And the research I have been reading includes plenty of experiments that demonstrate directed mutations. Obviously you’re too lazy to actually read the research.

  451. Steve Crosson 07 Oct 2016 at 1:03 pm

    hardnose,

    You’ve read exactly zero research that actually demonstrates directed mutations.

    That’s why Shapiro is still an outlier opinion and considered to be a quack.

    You don’t know enough science to understand the research, and you sure as hell couldn’t tell the difference between a meaningful experiment and a worthless one.

    Either admit this, or else meet steve12’s challenge. You can’t meet it and we all know that.

  452. steve12on 07 Oct 2016 at 1:24 pm

    “And the research I have been reading includes plenty of experiments that demonstrate directed mutations. Obviously you’re too lazy to actually read the research”

    HA HA HA!

    You can’t do it, can you? You’re a PhD scientist who can’t name ONE EXPERIMENT that you’ve ever even THOUGHT of?

    Not ONE?!?!?!?!? About ANYTHING?!?!?!?

    For chrissakes. Have the decency to yourself to take whatever remnant of dignity you have left and leave. Or go away for a week and call a friend who’s a scientist to get an experimental idea then come back with it and say you were on vacation.

    Anything is better than this pathetic display you’re subjecting us all to.

    I actually am starting to feel bad for you.

  453. hardnoseon 07 Oct 2016 at 2:59 pm

    There is extensive literature, beginning with Cairns in 1988 and continuing to the present, on the question of whether adaptive mutations are directed or not. The researchers do not all agree. This is still an open question and an active area of research.

    Demanding that someone who is not a molecular biologist design an experiment to resolve the question once and for all demonstrates your complete ignorance of the scientific process.

    The fact remains that Dawkins has no evidence whatsoever for his certainty that adaptive mutations are accidents.

    And it is recognized, as Steve Novella admits, that rates of adaptive mutations can increase in response to environmental stress, and that specific DNA locations can be targeted. That strongly suggests that there is at least an element of direction in adaptive mutations.

  454. chikoppion 07 Oct 2016 at 3:55 pm

    [hardnose] And it is recognized, as Steve Novella admits, that rates of adaptive mutations can increase in response to environmental stress, and that specific DNA locations can be targeted. That strongly suggests that there is at least an element of direction in adaptive mutations.

    No.

    The rate of VARIATION can increase and GENE SEQUENCES may be targeted.

    A gene sequence may include anywhere from 1K to 1M or more base pairs. To produce a deterministic result in the phenotype a genetic mechanism would need to selectively, predictively, and precisely edit a specific handful of nucleotides within the gene sequence. Further, to produce an emergent trait the mechanism would likely have to coordinate across multiple gene sequences. Further still, the mechanism itself would have to exist a priori in order to be triggered when needed.

    No mechanism does this. All known mechanisms function by making sequences more variable by introducing instability (yes, even those in Shapiro’s collection of mechanisms).

    There is no evidence for “directed mutations.” Variability is not a bug, it is a feature. Variability makes a population more diverse, and evolution occurs in populations, not individual organisms.

  455. Steve Crosson 07 Oct 2016 at 4:16 pm

    Demanding that someone who is not a molecular biologist design an experiment to resolve the question once and for all demonstrates your complete ignorance of the scientific process.

    Hey moron, steve12 said ANY experiment, just to prove you understand basic science.

    No reading comprehension at all!!!!

    Not to mention the fact that if you don’t have a pretty damn good understanding of molecular biology and science, then there is no way in hell that you are qualified to judge Shapiro’s work or any other evidence on this subject.

    You are just a fraud and a particularly stupid one at that. You can’t even lie well.

  456. BillyJoe7on 07 Oct 2016 at 4:34 pm

    chikoppi,

    Thanks again for your eloquent and succinct demolition of the Shapiro pipe dream.
    It’s all played out and confirmed in miniature by how the immune system reacts to invading pathogens.
    But, of course, your post will be either misunderstood or ignored, or responded to with meaningless gibberish.

  457. bachfiendon 07 Oct 2016 at 5:31 pm

    Hardnose,

    As I keep on pointing out to you, and you persist in not acknowledging, mutations can’t be recognised in real time, not even in theory let alone in practice. Mutations to be detected have to be in millions of copies, after surviving and being replicated many times.

    Already there’s selection involved. The lethal and severely deleterious mutations have already been eliminated leaving mostly neutral and beneficial mutations.

    Whatever experiment you set up which is just looking at the mutations you can detect will just detect the random mutations which are beneficial and not in critical regions of the genome – vital genes – giving the false impression that mutations are non-random, directed and beneficial, occurring in hot spots (anywhere else in the genome that’s not critical).

    Not all the mutations occurring in real life, or in experiments mimicking real life such as Lenski’s study,are ever detectable.

    The experiments looking at whether mutations are directed are very artificial, taking an organism which is a mutant and seeing how long it takes for it to back-mutate to normal. A mutant strain of E. coli for example which is unable to metabolise lactose for example, plating it out on a plate with lactose being the only energy source and waiting to see how long it takes to backmutate to being able to utilise lactose and grow.

    The parent mutant strain isn’t able to grow, so any colonies which form on the plate are backmutants, so it’s a easy task of counting the number of back mutations occurring, and how rapidly.

    But it still doesn’t detect all the mutations occurring. No experiment can do so, not in theory, let alone in practice. And it’s a highly artificial setup.

    As I’ve noted many times: the only way to distinguish ‘random non-directed mutations with the beneficial ones winnowed out by natural selection’ and ‘non-random directed beneficial mutations’ is by the predictions they make, similar to the way that Einsteinian physics was shown to be more correct than Newtonian physics. Einstein predicted that the sun causes a certain angle of deflection of light from a distant star during a solar eclipse larger than the value calculated using Newtonian physics, due to the curving of space-time. And when the observations were made in 1919, Einstein’s prediction was confirmed, meaning that General Relativity was supported.

    ‘Random mutations’ predicts that adaptations to stress will be late and infrequent.

    ‘Directed mutations’ predicts that adaptations to stress will be early and frequent.

    And what do we see? Late and infrequent adaptations. Random mutations.

  458. steve12on 07 Oct 2016 at 7:08 pm

    “Demanding that someone who is not a molecular biologist design an experiment to resolve the question once and for all ”

    The more you twist, the more I love it. Clearly I figured this question would resolve the question once and for all. Clearly.

    And I said ANY experiment.

    ANY!!!!!

    YOU ARE UNABLE.

    HA HA HA HA HA HA!!!!!!

    #BrokeTheTroll

  459. steve12on 07 Oct 2016 at 7:09 pm

    Missed Steve C’s post…mine is redundant

  460. steve12on 07 Oct 2016 at 7:10 pm

    YOU ARE A SCIENTIST!

    GIVE US A HYPOTHETICAL EXPERIMENT!

  461. mumadaddon 07 Oct 2016 at 7:33 pm

    ‘Directed mutations’ predicts that adaptations to stress will be early and frequent.

    Does it not also predict:

    – no genetic drift
    – low extinction rate
    – low rate of fatal recessive traits
    – low rate of deleterious recessive traits

    All of this can and has been quantified…

  462. mumadaddon 07 Oct 2016 at 7:45 pm

    Hang on, I forgot that some mutations are random, but some aren’t. So I guess it’s impossible to tell which ones are random and which aren’t.

    Hold on, I have an expert on hand.

    http://theness.com/neurologicablog/index.php/mike-pence-does-not-understand-evolution/#comment-196122

    Random means unrelated to the needs of the organism.

    Non-random means related to the needs of the organism.

    That is your answer mumadadd, stop asking.

    Wait till I tell Richard Dawkins, he is gonna FREAK OUT!!!

  463. mumadaddon 07 Oct 2016 at 7:57 pm

    Hoisted by my own petard…

    Sorry, Steve12.

  464. bachfiendon 07 Oct 2016 at 8:33 pm

    Mumadadd,

    Yes, non-random directed beneficial mutation theory does predict all of those phenomena you mention.

    Genetic disease, such as Duchenne muscular dystrophy, should be unknown in humans.

    Oh, sorry, I forgot. The Fall explains human genetic disease. Mutations are directed, but by God. God really just hates humans sometimes.

  465. hardnoseon 07 Oct 2016 at 10:56 pm

    “Genetic disease, such as Duchenne muscular dystrophy, should be unknown in humans.”

    It is really unbelievably stupid to think that anyone has suggested that mistakes can never happen. I said it is very possible that adaptive mutations are not all errors. You interpret that to mean there should never be any genetic errors.

    You aren’t making even the slightest effort to think logically.

  466. hardnoseon 07 Oct 2016 at 11:00 pm

    “And I said ANY experiment.”

    I have no idea what it is you are demanding. You obviously can’t admit you don’t have evidence for your faith, so you create asinine distractions.

    Adaptive mutations are being researched, and have been for decades. Just read some of the research if you want to know about it.

  467. Steve Crosson 07 Oct 2016 at 11:19 pm

    I have no idea what it is you are demanding.

    It’s Official! Hardnose finally admits he doesn’t understand basic science and couldn’t describe even a simple experiment to attempt to validate his fraudulent persona.

    What a doofus !!!

  468. hardnoseon 07 Oct 2016 at 11:52 pm

    One strategy they have used for determining if mutations are directed or random is to see if the adaptive mutation occurred before or after the environmental stress began.

    If it occurred before the stress, it was “random,” if it occurred after the stress it may have been directed.

    Cairns, for example, has published this kind of research.

  469. hardnoseon 07 Oct 2016 at 11:56 pm

    Another strategy has been to see if the DNA reverts to its previous state when the stress is removed. If it does, that suggests the mutation was directed.

  470. hardnoseon 08 Oct 2016 at 12:25 am

    “A basic principle of genetics is that the likelihood that a particular mutation occurs is independent of its phenotypic consequences. The concept of adaptive mutation seemed to challenge this principle with the discoveries of mutations stimulated by stress, some of which allow adaptation to the stress. The emerging mechanisms of adaptive genetic change cast evolution, development and heredity into a new perspective, indicating new models for the genetic changes that fuel these processes.”

    http://www.nature.com/nrg/journal/v2/n7/full/nrg0701_504a.html

  471. steve12on 08 Oct 2016 at 12:28 am

    “It’s Official! Hardnose finally admits he doesn’t understand basic science and couldn’t describe even a simple experiment to attempt to validate his fraudulent persona.”

    HA HA HA ! Right?

    Me: Describe any hypothetical experiment
    Dr.TheTroll: “I have no idea what it is you are demanding.”

    Which of the words is tripping ya up there kid? Is it “hypothetical”? “any”? “experiment”?

    I’m happy to define any of them for you – just say the word.

    How pathetic is this? He’s actually playing dumb that he doesn’t understand. What’s next Dr.TheTroll? You gonna say you don’t speak English to try and get out of this?

    HA HA HA!

    You’re a scientist who can’t describe a hypothetical experiment. Do you honestly think anyone would ever believe that?

    You’re a disgrace. You’re a weirdo sittinging in your basement pretending to be a scientist. Just stop it.

  472. hardnoseon 08 Oct 2016 at 12:37 am

    A hypothetical experiment to see if genetic mutations are random?

    As I already said, this research has been going on for decades.

  473. hardnoseon 08 Oct 2016 at 12:38 am

    Did you mean any kind of experiment? Having nothing to do with what we have been arguing about? You don’t make any sense.

  474. bachfiendon 08 Oct 2016 at 3:15 am

    So hardnose is now linking to a 2001 abstract concerning ‘directed’ mutations. Not the full paper, which he wouldn’t be able to understand, and also very old research – if it can be understood as such.

    And now he reckons he can distinguish between ‘random’ and ‘directed’ mutations based on whether the mutation occurred before or after the ‘stress’.

    Which begs the question as to how he’d detect the mutations when they’re in low frequency in a large population before there’s been any natural selection amplifying the number of organisms containing the mutation in question.

    When a mutation occurs, the cell containing it doesn’t signal its presence by a flashing light or waving a flag. The mutation announces its presence by its effects – causing the cell to die or stop reproducing (in which case it won’t be detected), not doing much at all with neutral mutations causing normal reproduction (in which case, the mutation may or may not be detected) or causing the cell to thrive with beneficial mutations (which will almost certainly be detected).

    If we didn’t have mammalian fossils from the Mesozoic (and there aren’t many, mainly just teeth and bone fragments), he’d be arguing that the K-P event (whether due to the Chicxulub impact or the Indian Deccan traps volcanic eruption) caused the evolution of the mammals, based on the absence of fossils before and the abundance of fossils after the K-P event.

    And mutations in very low number are extremely difficult to detect, unless you know exactly which mutations you’re looking for(which excludes all unknown mutations, whether random or directed) and have specific markers for the mutations (which are available for many known human genetic diseases).

    Obviously to everyone except hardnose it would be extremely difficult and expensive to sequence the genomes of many individual organisms in a large population in order to detect unknown ‘random’ or even ‘directed’ mutations arising before a ‘stress’ – and even then it’s probable that many mutations would be missed completely, particularly since they’d be present in very small numbers.

    Hardnose isn’t particularly practical. Or logical. He has a peculiarly idiosyncratic idea as to what’s possible or not in practice.

  475. mumadaddon 08 Oct 2016 at 3:20 am

    “One strategy they have used for determining if mutations are directed or random is to see if the adaptive mutation occurred before or after the environmental stress began.

    If it occurred before the stress, it was “random,” if it occurred after the stress it may have been directed.”

    Wow… Just, wow. I’m going to test psychopath posters by having supposed psychics predict the outcome of a coin flip; when they get it right, that’s psychic powers, when they don’t, it isn’t.

  476. mumadaddon 08 Oct 2016 at 3:21 am

    Frigging phone:

    “Wow… Just, wow. I’m going to test *psychic powers* by having supposed psychics predict the outcome of a coin flip; when they get it right, that’s psychic powers, when they don’t, it isn’t.”

    I think my phone had a Freudian slip!

  477. Steve Crosson 08 Oct 2016 at 9:57 am

    Wow … just Wow!

    Every post hardnose makes gets more wrong and more ridiculous.

    Hey hardnose. Shouldn’t you be going to work pretty quick? Those burgers aren’t gonna flip themselves.

    Your parents are gonna kick you out of the basement if you lose one more job.

  478. hardnoseon 08 Oct 2016 at 10:30 am

    This conversation has disintegrated into idiocy. My comments are rational, your replies are insane. Maybe intentionally insane. Your goal is obviously to get me to stop posting sensible scientific criticisms of Dawkins’ theory.

    Novella won’t ban me, because he tolerates rational criticism, even if he doesn’t like it.

  479. Steve Crosson 08 Oct 2016 at 10:35 am

    Hardnose: “Your goal is obviously to get me to stop posting sensible scientific criticisms of Dawkins’ theory.”

    Except that Dr. Novella (a real doctor) has made it quite clear that your “criticisms” are neither rational or scientific.

    Seriously, don’t be late for work. Remember to smile when you ask “Would you like fries with that?”

    And don’t forgot it is October already — push all of the Pumpkin flavored crap.

  480. steve12on 08 Oct 2016 at 10:52 am

    The sweet, sweet smell of victory….

    “A hypothetical experiment to see if genetic mutations are random?”

    “Did you mean any kind of experiment? Having nothing to do with what we have been arguing about? You don’t make any sense.”

    This is SO, SO great. Dr.TheTroll is literally going down the “no hable ingles” road.
    “¿Qué quiere decir ‘hypothetical’ muchacho?”

    He’s the Black Knight form the Holy Grail. I’ve lopped off all of his limbs with this question, but he insists he’s won. First h doesn’t take assignments, not he doesn’t understand.

    I LOVE THIS. The squirming. The lying.

    It’s over Johnny. It’s over.

    GIVE US YOUR HYPOTHETICAL EXPERIMENT OR STFU
    GIVE US YOUR HYPOTHETICAL EXPERIMENT OR STFU
    GIVE US YOUR HYPOTHETICAL EXPERIMENT OR STFU

    #BrokeTheTroll

  481. steve12on 08 Oct 2016 at 10:53 am

    “And don’t forgot it is October already — push all of the Pumpkin flavored crap.”

    BWA HA HA HA!

  482. steve12on 08 Oct 2016 at 11:06 am

    Please everyone, I encourage you to ask Dr.TheTroll for some hypothetical experiment that WOULD make his point every single time you interact with him on any topic. You can just add it in after whatever else you’d like to say to him.

    This is a perfectly legitimate Q for anyone. As a scientist, he should easily be able to answer.

  483. grabulaon 08 Oct 2016 at 11:48 am

    hardnose isn’t a scientist, he’s claimed that dozens of times and then shown a stunning lack of understanding when it comes to even basic science. Getting into the woods with him is just getting lost. Arguing with him is just giving him something to do to entertain himself.

  484. hardnoseon 08 Oct 2016 at 12:34 pm

    I will ignore the immature stupidity and I will continue posting rational criticisms of Dawkinism. Some of you here have obviously been off your meds too long.

  485. grabulaon 08 Oct 2016 at 12:39 pm

    stupidity is using words like dawkinism and not understanding basic evolution but insisting on arguing about it anyway.

  486. hardnoseon 08 Oct 2016 at 12:41 pm

    “Selection-induced mutations are nonrandom mutations that occur as specific and direct responses to environmental challenges and primarily in nondividing cells under conditions of intense prolonged selection. Selection-induced mutations have been shown to occur at six loci in Escherichia coli, but their existence has not previously been demonstrated in any eukaryotic organism. Here it is shown that selection-induced mutations occur at the HIS4 locus in the eukaryotic microorganism Saccharomyces cerevisiae.”

    https://www.ncbi.nlm.nih.gov/pubmed/1584764

  487. mumadaddon 08 Oct 2016 at 12:42 pm

    Nobody talks about Dawkins more than hn; if not for him the name would never be uttered. He’s obsessed for some reason.

  488. Steve Crosson 08 Oct 2016 at 12:49 pm

    Nobody talks about Dawkins more than hn; if not for him the name would never be uttered. He’s obsessed for some reason.

    Probably because it was one of the first books about evolution that hardnose read that he wasn’t smart enough to understand.

  489. Steve Crosson 08 Oct 2016 at 12:59 pm

    hardnose isn’t a scientist, he’s claimed that dozens of times and then shown a stunning lack of understanding when it comes to even basic science.

    Everyone has known that for years — except hardnose.

    Steve12 proposed an extremely simple challenge in the hopes that even hardnose would finally recognize that he was out of his depth.

    No such luck. Clearly, hardnose is patient zero on the Dunning-Kruger spectrum.

  490. BillyJoe7on 08 Oct 2016 at 1:29 pm

    “Nobody talks about Dawkins more than hn; if not for him the name would never be uttered”

    And I’ll bet he has read not a single one of Richard Dawkins’ books.

    On the other hand, his hero James Shapiro has managed to write a whole book criticising modern evolutionary theory without once referencing Stephen Gould. Can you imagine that? A book criticising modern evolutionary theory without a single reference to Stephen Gould! And not a single mention of genetic drift! It’s as if he has never heard of either!

    (I imagine hn reading this and thinking…Stephen who?…genetic what? :D)

  491. BillyJoe7on 08 Oct 2016 at 1:30 pm

    …for some reason the laughing emoticon no longer works 🙁

  492. chikoppion 08 Oct 2016 at 1:33 pm

    Hardnose quote-mined the abstract of a 2001 paper that is behind a paywall (so the actual research isn’t available).

    I’d like to point out how inane this abstract statement actually is:

    A basic principle of genetics is that the likelihood that a particular mutation occurs is independent of its phenotypic consequences.

    Fair enough, as stated. However, the frequency of the mutation rate is not unrelated. As the rate of mutation increases in a population the likelihood of any particular (possible) mutation occurring also increases.

    The concept of adaptive mutation seemed to challenge this principle with the discoveries of mutations stimulated by stress, some of which allow adaptation to the stress.

    “[D]iscoveries of mutations stimulated by stress.” In other words, an increase in the rate of mutation within a population due to environmental factors. This isn’t a “discovery.” Environmental mutagens have been explicitly studied since the 1920’s. Disease and reproductive rates are also common environmentally-influenced factors that impact the rate of mutation.

    “[S]ome of which allow adaptation to the stress.” And the majority of which, don’t, are actually detrimental or entirely unrelated to the extant adaptive need of the organism. And sometimes no sufficient adaptation occurs and the population is eradicated due the the environmental stress factor.

    Increased variability within a population, as stimulated by environmental factors, is not evidence of “directed mutation.”

    If a die is rolled once per minute that chance of a “6” occurring in 1:6.

    If a die is rolled 10 times per minute the chance of a “6” occurring is 10×1:6.

    Both scenarios are equally random. Neither scenario is going to result in a “7” being rolled.

    The emerging mechanisms of adaptive genetic change cast evolution, development and heredity into a new perspective, indicating new models for the genetic changes that fuel these processes.

    No, they don’t.

    The abstract not only presented no evidence, but it was based on faulty premises.

    As an aside, I’ve noticed this is a common tactic of the ID cranks. They attempt to conflate (or merely confuse) the outcome that occurs in a population with the individual mutation events that occur within individual organisms.

    “See, the population adapted, so the cell “knew” it needed that mutation.” All while ignoring the Petri dishes filled with the 99% of organisms that perished or the experiments in which the entire population was eradicated.

    The fact that a “beneficial” mutation exists within a population that allows it to adapt to an environmental challenge is not evidence for “directed” mutation. Variation is something that occurs only on the level of populations. Actual mutations occur within individual organisms. Don’t attempt to observe population dynamics and then erroneously apply those dynamics to individual mutation events.

  493. hardnoseon 08 Oct 2016 at 3:45 pm

    “Steve12 proposed an extremely simple challenge in the hopes that even hardnose would finally recognize that he was out of his depth.”

    Biologists have been researching this for decades and have not found a simple answer. So I guess you think all those biologists are out of their depth.

    Just continue being morons. Everyone reading this blog will learn to ignore you.

  494. hardnoseon 08 Oct 2016 at 3:47 pm

    “Nobody talks about Dawkins more than hn”

    Dawkins is the most well-known leader of the “natural selection explains it all” cult. I suppose you want a complete list of every evolutionary biologist who agrees with Dawkins, every time I say anything about evolution.

  495. grabulaon 08 Oct 2016 at 3:51 pm

    Hardnose sez: “I suppose you want a complete list of every evolutionary biologist who agrees with Dawkins, every time I say anything about evolution.”

    How about just an indication you understand the subject to which you speak?

  496. hardnoseon 08 Oct 2016 at 3:53 pm

    “not a single mention of genetic drift”

    The explanatory power of genetic drift is even weaker than natural selection. Natural selection supposedly explains the evolution of complex traits and behaviors, although this claim lacks evidence and is unscientific. Does it seem likely to any of you retards that genetic drift would do a better job than natural selection? I don’t see why Shapiro should bother mentioning it.

  497. grabulaon 08 Oct 2016 at 4:08 pm

    “…although this claim lacks evidence and is unscientific”

    holy crap dude, you are so out of your depth.

  498. grabulaon 08 Oct 2016 at 4:09 pm

    It always amazes me how woo types can take a complex idea, boil it down to something inaccurate and over simplified and then use their supposed new understanding to force a strawman.

  499. mumadaddon 08 Oct 2016 at 4:55 pm

    Phew, got away without answering Steve12’s challenge. Think I got away with it.

  500. mumadaddon 08 Oct 2016 at 5:05 pm

    C’mon, design an experiment!

    Do mice like cheese?

    When mice eat cheese, is it because they like it?

    I’ve already given too much away, but run with that — design an experiment to test whether mice likeep cheese.

    I know: when mice eat cheese it’s because they like it, and when they don’t it’s because they don’t. So it’s impossible to tell

  501. mumadaddon 08 Oct 2016 at 5:10 pm

    For some reason my phone’s autocorrect thinks I’ve started a new word every time I hit backspace (but only ever when posting on this blog), hence typos such as ‘likeep’. Sorry about that. Corrected version below.

    C’mon, design an experiment!

    Do mice like cheese?

    When mice eat cheese, is it because they like it?

    I’ve already given too much away, but run with that — design an experiment to test whether mice like cheese.

    I know: when mice eat cheese it’s because they like it, and when they don’t it’s because they don’t. So it’s impossible to tell

  502. chikoppion 08 Oct 2016 at 5:38 pm

    This constant erroneous quote-mining is an embarrassment.

    [hardnose] “Selection-induced mutations are nonrandom mutations that occur as specific and direct responses to environmental challenges and primarily in nondividing cells under conditions of intense prolonged selection. Selection-induced mutations have been shown to occur at six loci in Escherichia coli, but their existence has not previously been demonstrated in any eukaryotic organism. Here it is shown that selection-induced mutations occur at the HIS4 locus in the eukaryotic microorganism Saccharomyces cerevisiae.” https://www.ncbi.nlm.nih.gov/pubmed/1584764

    First, this paper was published in 1992.

    Second, the research is based on a paper by John Cairns (The Origin of Mutants, 1988).

    I’m posting a lengthy quotation from an excellent blog post on the subject (by Adrea Bottaro, 2004). I SUGGEST YOU READ IT IN ITS ENTIRETY.

    http://www.talkreason.org/articles/Heresy.cfm

    Within a few years, evidence accumulated for non-teleological models of mutation. By 1998, essentially everyone in the field, including Cairns and his closest collaborators, agreed that the original observation did not reflect “directed” mutations, which by that time had been re-baptized with the less loaded term “adaptive mutations” [5, 6]. Nevertheless, several interesting features of bacterial biology had been discovered in the process. One alternative model for the observations proposes that starved bacteria enter a “hypermutable” state , either by virtue of a specific genetic “rescue” program, or as a result of breakdown of normal cellular control mechanisms [7]. In this state, high levels of mutations are introduced throughout the bacterial genome, but selection for specific mutants makes it appear as if the environmental conditions preferentially targeted mutations to the selected gene. Importantly, this mechanism has relevance for the onset of bacterial resistance to antibiotic drugs, and possibly to certain cellular states involved in cancer development [5]. In another novel mechanism which has been observed, a multiplication of the copies of the crippled gene (“amplification”) is first favorably selected because it leads to a small but detectable increase in its product’s minimal activity [8]. This massive gene amplification makes for better chances of mutation, and when these occur the extra gene copies become a burden, and are eliminated by selection. The final result is the appearance of highly targeted mutations. Research on all these mechanisms is actively ongoing [9].

    Cairns today is Professor of Microbiology at the Radcliffe Infirmary, one of the medical teaching hospitals of Oxford University, and remains a recognized leading authority in mutation genetics. His 1988 article is one of the highest cited papers in the field, and has spawned an entire new area of study.

    Perhaps, if ID advocates stopped dedicating most of their efforts to political pamphlets and challenges to grade school education standards, and attempted some real scholarship, their complaints could be taken more seriously. With the advent of the internet, avenues for disseminating unorthodox scientific results outside of any imaginary or real “censorship” system are more abundant than ever, and it’s a safe bet that ID advocates, who even edit their own electronic journal, would have published them if they had any. Given however their deafening scientific silence, they might as well claim that the dog ate all their manuscripts.

    I’ll let Dr. Cairns have the last word:

    [Scientific] truth is quite unlike the verdict of a court of law, because it does not depend on advocacy. [10]

    Acknowledgements
    I would like to thank Dr. John Cairns for kindly replying to my e-mails, and sharing his thoughts on the adaptive mutation controversy and scientific fairness in general.

  503. bachfiendon 08 Oct 2016 at 5:46 pm

    Hardnose,

    You still don’t get it.

    The cause of evolution is changed environmental conditions acting on a reproductively isolated population.

    The mechanism of evolution is natural variation within reproductively isolated populations acted upon by selection (predominantly natural) in response to changed environmental conditions.

    Natural selection does nothing unless the environment changes. And it does nothing if there’s no genetic variation within the population. A non-variable reproductively isolated population subjected to a sufficiently changed environment will go extinct- the history of 99.9% of species ever living on Earth.

    Now your’e citing a 1992 paper, which is very old, with the title ‘Selection-induced mutations occur in yeast’.

    Do you notice something? ‘Selection-induced’ maybe? Despite the author’s caveats regarding whether the research is true, and whether back mutation of mutated genes back to the original gene is non-random (which needs verification by other researchers using the same and different methods in the subsequent 24 years), selection seems to be doing a pretty good job in this very artificial non-real world situation of a mutant mutating back to a non-mutant.

    Neutral drift only gets motioned in evolution because occasionally in very small populations natural variation is lost just by chance. It’s about the only chance in evolution besides the environmental change.

  504. mumadaddon 08 Oct 2016 at 5:59 pm

    chikoppi — thanks for your cool-headed and incisive responses to the papers cited by hn. 🙂

  505. hardnoseon 08 Oct 2016 at 6:03 pm

    “design an experiment to test whether mice likeep cheese.”

    mumadadd, why are you such a dope? He asked for an experiment to resolve the controversy over whether adaptive mutations can be directed or not. The research has been going on for decades with no simple answer.

    Showing once again a complete ignorance of how science works.

  506. mumadaddon 08 Oct 2016 at 6:09 pm

    “He asked for an experiment to resolve the controversy over whether adaptive mutations can be directed or not.”

    I really just want to throw this down again.

    http://theness.com/neurologicablog/index.php/bacteria-evolving-resistance/#comment-206478

    How about this Dr. TheTroll:

    I’ll further loosen the constraints of my question.

    Do you have ANY experiments that you have EVER thought of to test ANY of your assertions that you’ve made here?

    ANY!!!

    It’s OK if there’s no current technology available, and you need to invent some.

    Please communicate the experiment to us in scientific form so that it can properly discussed.

    ANY AT ALL!

    hn, we know that mice eat cheese, but how could we find out if it’s because they like to eat cheese?

    This is as simple as it gets. I almost want to give you a bunch of clues to set you off in the right direction, just so we can get to you defining the null.

  507. hardnoseon 08 Oct 2016 at 6:13 pm

    Here’s an experiment:

    We hook up mumadadd to electrodes, and he gets a shock each time he says something inane.

    We do this on successive days, to see if his idiocy decreases at all.

  508. steve12on 08 Oct 2016 at 6:13 pm

    Dr. The Troll:

    “Biologists have been researching this for decades and have not found a simple answer. So I guess you think all those biologists are out of their depth.”

    So we went from “I don’t take assignments” to “I don’t understand” now we’re on “The experiment won’t actually settle the science”.

    Any more excuses?

    I’ll say this for the sake of the those who don’t want to go back through the thread.

    The point of a hypothetical experiment with loosened constraints is not to have an experiment that will solve the problem. It’s to try and look at what evidence COULD or WOULD be answer the Q. It’s an idealization. What would it mean if experiment X were to come out with result Y?

    This is a useful exercise that scientist do ALL THE TIME.

    Declining to engage in the exercise because it won’t settle the question, or because it’s immature, or whatever is LAUGHABLE.

    Dr. TheTroll, you’ve been arguing the same thing over and over and over.

    Why not try something else if it could push the conversation along? Why not muse about what evidence WOULD be dispositive since you say that evidence is lacking?

    You keep saying “we don’t know” . Well, what would allow us to know? That’s an initial step scientists take all the time.

    SO WHAT’S THE PROBLEM??????

    If you’re scientist, GIVE US A HYPOTHETICAL EXPERIMENT. ANYTHING.

    YOU. CANNOT. DO. IT.

    because…

    YOU. ARE. NOT. A. SCIENTIST.

    You are a lying sack of shit.

    Prove me wrong….

    #BrokeTheTroll

  509. steve12on 08 Oct 2016 at 6:14 pm

    GIVE US A HYPOTHETICAL EXPERIMENT!
    GIVE US A HYPOTHETICAL EXPERIMENT!
    GIVE US A HYPOTHETICAL EXPERIMENT!

  510. steve12on 08 Oct 2016 at 6:17 pm

    “hn, we know that mice eat cheese, but how could we find out if it’s because they like to eat cheese?”

    Good one Mumadadd! He couldn’t put that in any formal scientific form either.

  511. hardnoseon 08 Oct 2016 at 6:33 pm

    “You are a lying sack of shit.”

    Moderators — are you paying attention at all?

  512. mumadaddon 08 Oct 2016 at 6:35 pm

    “Moderators — are you paying attention at all?”

    hn, are you paying attention at all? Have you forgotten which forum you’re trolling right now?

  513. hardnoseon 08 Oct 2016 at 6:42 pm

    According to the wikipedia summary, the controversy has not been resolved:

    “The hypothesis of directed mutagenesis was first proposed in 1988[4] by John Cairns, of Harvard University[5] who was studying Escherichia coli that lacked the ability to metabolize lactose. He grew these bacteria in media in which lactose was the only source of energy. In doing so, he found that the rate at which the bacteria evolved the ability to metabolize lactose was many orders of magnitude higher than would be expected if the mutations were truly random. This inspired him to propose that the mutations that had occurred had been directed at those genes involved in lactose utilization.[6]

    Later support for this hypothesis came from Susan Rosenberg, then at the University of Alberta, who found that an enzyme involved in DNA recombinational repair, recBCD, was necessary for the directed mutagenesis observed by Cairns and colleagues in 1989.

    The directed mutagenesis hypothesis was challenged in 2002, when John Roth and colleagues showed that the phenomenon was due to general hypermutability due to selected gene amplification, and was thus a standard Darwinian process. Later research published in 2006 by Jeffrey D. Stumpf, Anthony R. Poteete, and Patricia L. Foster, however, concluded that amplification could not account for the adaptive mutation and that “mutants that appear during the first few days of lactose selection are true revertants that arise in a single step”.

    https://en.wikipedia.org/wiki/Directed_mutagenesis

  514. steve12on 08 Oct 2016 at 6:49 pm

    “You are a lying sack of shit.”
    Moderators — are you paying attention at all?”

    You lie about what you’ve said when someone shows you to be wrong.
    You lie about what others have said to try and invalidate our arguments.
    You lie about your scientific credentials.

    What part did I get wrong? Are you offended by my salty language? Tough shit.

    GIVE US A HYPOTHETICAL EXPERIMENT!
    GIVE US A HYPOTHETICAL EXPERIMENT!
    GIVE US A HYPOTHETICAL EXPERIMENT!

  515. mumadaddon 08 Oct 2016 at 7:02 pm

    “According to the wikipedia summary, the controversy has not been resolved”

    Um, the bit you quoted wasn’t the summary, but around two thirds of the whole page, and actually titled ‘Recent Studies’.

    In fact, aside from 6 references, this is the entirety of the page that you didn’t quote in the ‘summary’:

    Directed mutagenesis, also known as directed mutation, is a hypothesis proposing that organisms can respond to environmental stresses through directing mutations to certain genes or areas of the genome.
    History

    The Russian ichthyologist Lev Berg proposed directed mass mutations as the main mechanism for evolution in his anti-Darwinian book Nomogenesis; or, Evolution Determined by Law (1922).[1] Early studies of “directed mutation” were performed by German geneticists. Richard Goldschmidt in 1929 due to his experiments on drosophila through exposure to elevated temperatures had claimed to have produced evidence for directed mutation. Viktor Jollos (1887-1941) in the 1930s had also carried out experiments on drosophila and written that his results had confirmed Goldschmidt’s work which was evidence for direct mutation in contrast to natural selection. However, later American geneticists were unable to replicate these experiments.[2][3]

  516. hardnoseon 08 Oct 2016 at 7:08 pm

    “E. coli bacteria exposed to three common antibiotics were more likely to develop antibiotic resistance following low-level antibiotic exposure than after exposure to high concentrations that would kill the bacteria or inhibit their growth, according to a timely article in Microbial Drug Resistance, a peer-reviewed journal published by Mary Ann Liebert, Inc.”

    http://phys.org/news/2011-06-coli-bacteria-resistance-exposure-antibiotics.html#nRlv

    If adaptive mutations were always random, then this should not happen.

  517. hardnoseon 08 Oct 2016 at 7:10 pm

    “You are a lying sack of shit.”

    You need to be banned.

  518. mumadaddon 08 Oct 2016 at 7:16 pm

    http://theness.com/neurologicablog/index.php/review-of-probiotics/#comment-143698

    “And mumadadd, unfortunately you won’t believe me but I’ll tell you anyway. I know the cause and cure for insomnia. You have some vertebrae slightly out of place. It causes restless muscles, especially in the legs. I get that once in a while, and fix it the same way I fix allergy symptoms. The reason you don’t always have insomnia is that those vertebrae are not always out of place.”

  519. mumadaddon 08 Oct 2016 at 7:18 pm

    http://theness.com/neurologicablog/index.php/review-of-probiotics/#comment-143695

    “I know for an absolute fact that chiropractic can work for allergies. I am sure no big agency or drug company has ever studied this. No, not every chiropractic technique works for every allergy patient. You can only find this out by trial end error. It is a fact I have experienced repeatedly.”

  520. hardnoseon 08 Oct 2016 at 7:25 pm

    No, mumadadd, you didn’t deserve any helpful advice from me.

  521. mumadaddon 08 Oct 2016 at 7:27 pm

    Nor did I get any.

  522. hardnoseon 08 Oct 2016 at 7:47 pm

    Some people believe in chiropractic, yoga, etc., others don’t. It has nothing to do with the evolution controversy.

  523. steve12on 08 Oct 2016 at 7:48 pm

    “You are a lying sack of shit.”
    You need to be banned.

    Oh no? Are you getting mad at me? Little butthurt?

    Kind of like when you’re arguing a point with someone and they suddenly change the argument just when you prove them wrong?

    Or when someone purposefully misrepresents what you say so that they can never be proven wrong?

    Or when someone selectively responds only to the post that give them rhetorical advantage, while ignoring the ones that are inconvenient for their point?

    All of that is tantamount to lying. The curse words are for flare. Tough shit.

  524. hardnoseon 08 Oct 2016 at 7:48 pm

    The fact that there still is an evolution controversy has blown some of your minds, and regrettably seems to have caused at least one nervous breakdown. Such is the insane power of ideology.

  525. steve12on 08 Oct 2016 at 7:52 pm

    So anyway Dr. TheTroll:

    When are you going to give us that hypothetical experiment?

    Do remember to put it in formal scientific form.

    It can be about evolution…but it doesn’t have to be. I think it can greatly improve out sense of what kind of evidence would be sufficient in making some headway toward answering this question.

  526. steve12on 08 Oct 2016 at 7:54 pm

    “The fact that there still is an evolution controversy has blown some of your minds, and regrettably seems to have caused at least one nervous breakdown. Such is the insane power of ideology.”

    Hmmm… Such an odd experimental desig…. Wait a second! That’s not an experiment at all!

    PLEASE give us you hypothetical experiment!

    I mean, it’s not like you’re a liar and can’t devise one, right?

  527. hardnoseon 08 Oct 2016 at 8:01 pm

    I already described the mumadadd experiment. You aren’t paying attention! Stay after class.

  528. steve12on 08 Oct 2016 at 8:06 pm

    Leave the humor to me…

    Experiment please…

  529. mumadaddon 08 Oct 2016 at 8:14 pm

    Ah, the mumadadd experiment. Wait a sec.

  530. mumadaddon 08 Oct 2016 at 8:15 pm

    We hook up mumadadd to electrodes, and he gets a shock each time he says something inane.

    We do this on successive days, to see if his idiocy decreases at all.

  531. mumadaddon 08 Oct 2016 at 8:17 pm

    Okay, let’s go.

    Start by defining ‘inane’ and ‘idiocy’ and describe how they are measured.

  532. Steve Crosson 08 Oct 2016 at 8:32 pm

    And make sure you define the null hypothesis in this experiment.

    And explain how and why you could blind the experiment.

  533. Steve Crosson 08 Oct 2016 at 8:34 pm

    Oh, and here’s a good idea. Let’s run the same experiment on hardnose. I’m sure we will get exponentially more data points.

  534. mumadaddon 08 Oct 2016 at 8:49 pm

    Let’s just start with me. I want to see how idiotic I am! Actually I don’t have much time tonight, I have a specialist coming over to realign my Chakras.

  535. steve12on 08 Oct 2016 at 8:50 pm

    “Ah, the mumadadd experiment. Wait a sec.”

    Ha! Actually leave the humor to Mumaddad…

    This could be an experiment. Single subject so manip only one variable. Operationalize idiocy as…score on the WAIS? The WAIS has equivalent forms (I think), so we could do a before and after shocking (T1 and T2) w/o administering the same test.

    I never designed a single subject study before. I may have to do some reading….

    H^0: T1 WAIS score = T2 WAIS score
    H^1: T1 WAIS score < T2 WAIS score

    You obviously have to use a nonparametric test to compare T1 and T2. Could you use a Wilcoxan? OR would you simply use a binomial?

    Kind of a boring experiment considering I said we could do anything.

    Sorry about all of the shock Mumaddad…

  536. mumadaddon 08 Oct 2016 at 9:07 pm

    “Sorry about all of the shock Mumaddad…”

    Yeah, why would you do that to me — I thought we were friends!

  537. steve12on 08 Oct 2016 at 9:25 pm

    Not personal!!!!! It’s for science! (SCIENCE!)

  538. mumadaddon 08 Oct 2016 at 9:34 pm

    Steve12,

    Wait, you forgot to operationalise ‘inane’. I think maybe some sort of word association game with the answers fed to a panel of randomly selected volunteers; they each press a button when they think the answer is dumb, and you have a threshold of say 65% for a hit. Then the shock.

  539. bachfiendon 09 Oct 2016 at 5:27 am

    Hardnose is surprised that E. coli exposed to low concentrations of antibiotics develop more antibiotic resistance than if exposed to high concentrations of antibiotics that either kill them (obviously a dead bacterium is not capable of developing resistance – but it’s probably too difficult an idea for hardnose to grasp) or stop them multiplying (which basically gives their host time to eliminate them by natural defences).

    He further thinks that this isn’t supposed to happen if adaptive mutations were always random. Actually, it’s precisely what is expected. And anyway – antibiotic resistance isn’t always due to new mutations. There’s natural variation for resistance to antibiotics within any bacterial species. An infection with E. coli will often contain bacteria ranging from completely sensitive to the antibiotics given to completely resistant to whatever antibiotics are given in tolerable doses.

    Antibiotics need to be given in sufficiently high dose for long enough to eradicate as many of the bacteria being treated, leaving a sufficiently small number of bacteria to be dealt by the host’s immune system. Giving low doses of antibiotics just removes the sensitive bacteria reducing competition for the resistant ones, which then thrive.

    It’s such an obvious point illustrating hardnose’s ignorance, and demonstrates why we don’t need to take seriously his assertion that there’s a controversy regarding evolution. There’s no controversy. Just discussion concerning the details.

  540. hardnoseon 09 Oct 2016 at 8:22 am

    Here’s another experiment:

    Two groups of people, 20 in each.

    One group brushes with Crest, the other uses Brand X.

    After one month, see which group has fewer cavities.

    Dependent measure: number of cavities.

    Null hypothesis: Crest is crap.

  541. hardnoseon 09 Oct 2016 at 8:32 am

    “Hardnose is surprised that E. coli exposed to low concentrations of antibiotics develop more antibiotic resistance than if exposed to high concentrations of antibiotics”

    I wasn’t surprised. When exposed to a lethal environmental stress, the only bacteria that survive are the ones who already had the adaptive mutation. But if the stress is not lethal, bacteria have a chance to generate adaptive mutations.

    That is how some researchers have interpreted this. But bachfiend, as we know, is the world’s leading expert on evolution so of course he knows better.

  542. bachfiendon 09 Oct 2016 at 11:16 am

    Hardnose,

    You remain incredibly ignorant. Your suggested experiment to compare Crest toothpaste versus brand X is 1. Ridiculously short (how many people develop cavities after just one month?). 2. Ridiculously small (to compare efficacy of toothpaste in preventing dental decay you’d need thousands of subjects to detect the small effects likely to be present). 3. The null hypothesis, if there was one, would be that brushing your teeth with any toothpaste is no better than brushing with none. Or not brushing at all. Actually it would need a control group.

    You also have a profound misconception about bacteria. E. coli isn’t a homogenous species. There are thousands of types. The size of its genome can vary by up to 30% just because one of the survival mechanisms of bacteria is to divide as rapidly as possible with often the bacterial chromosome not being completely replicated before the bacterium divides leaving one daughter short of a number of genes. If the missing genes aren’t necessary for its current environment – then good, it can divide faster in future and thrive.

    Giving inadequate ones of antibiotics to E. coli infections nicely illustrates evolution in action.

    Evolution is caused by environmental change (in this case a low concentration of antibiotics) acting on a population of E. coli, which has natural variation within the population, ranging from completely sensitive to resistant to the antibiotics. Selection kills off the sensitive and less resistant bacteria leaving the more resistant bacteria to thrive.

    There may not necessarily be new mutations. In fact there probably won’t be. Giving inadequate doses of antibiotics in infections leads to resistant infections because treatment hasn’t killed off the more resistant bacteria, which then multiply to produce a recurrent infection composed of bacteria with greater innate resistance.

    Which are these ‘some researchers’ who have have interpreted inadequate antibiotic treatment leading to resistant infections to be the result of new mutations? As I have noted to you on numerous occasions, cells don’t signal that they’ve developed a new mutation by flashing lights or waving flags. It’s impossible to determine when a mutation has occurred when the mutation is in low number in a large population.

    And don’t forget – microorganisms have been engaged in chemical warfare of offence and defence with naturally occurring antibiotics for hundreds of millions of years.

  543. hardnoseon 09 Oct 2016 at 11:31 am

    “The null hypothesis, if there was one, would be that brushing your teeth with any toothpaste is no better than brushing with none. Or not brushing at all. Actually it would need a control group.”

    Proving once again that you know nothing about science. The control group uses Brand X. The null hypothesis is that Crest is no better than Brand X.

  544. hardnoseon 09 Oct 2016 at 11:43 am

    “There may not necessarily be new mutations. In fact there probably won’t be. Giving inadequate doses of antibiotics in infections leads to resistant infections because treatment hasn’t killed off the more resistant bacteria”

    Will the nonsense here ever dry up?

    How the hell would you know if there would be new mutations?

    And giving ADEQUATE does of antibiotics ALSO leads to resistance because the more resistant bacteria were not killed.

    Lethal environmental stress leaves only the bacteria that already had the adaptive mutation.

    Non-lethal stress POSSIBLY gives bacteria a chance to generate adaptive mutations.

    Notice I said “possibly.” Unlike you, I don’t read my own preferences into scientific data.

  545. hardnoseon 09 Oct 2016 at 12:05 pm

    “In-host increased mutability is a general situation that may affect several different bacterial genes. However, regulation of mutability also has a gene-specific component. It has been pointed out that bacteria have two different sets of genes: housekeeping genes, which are relevant for basic bacterial metabolism and structure and that mutate at an expected low frequency, and contingency genes (52), which are important for bacterial adaptability to changing environments and that are highly mutable. Indeed, very high rates of mutation may indicate not a real mutation but, rather, some programmed recombination event.”

    http://aac.asm.org/content/44/7/1771.full

  546. Steve Crosson 09 Oct 2016 at 12:33 pm

    Holy Shit hardnose,

    When are you going to realize that almost all of your “evidence” proves us right and you wrong?

    We’ve been saying for weeks that increased variability is real and is a distinct survival advantage. It does NOT mean that any guidance or direction is involved. It simply means that organisms with built-in variability will be naturally selected more often than those that are less able to rapidly adapt to changing environments.

    Until you can prove that organisms know how to make the correct mutations rather than just a selection, you’ve done nothing except provide more evidence that the modern synthesis is correct.

  547. steve12on 09 Oct 2016 at 12:42 pm

    >Here’s another experiment:
    >Two groups of people, 20 in each.
    >One group brushes with Crest, the other uses Brand X.
    >After one month, see which group has fewer cavities.
    >Dependent measure: number of cavities.
    >Null hypothesis: Crest is crap.

    First think I get from google is real similar to your example:
    https://www.ugrad.cs.ubc.ca/~cs444/lectures/444-05_experiment_I_worksheet.pdf

    And the null is incorrect. You get closer here:
    “The null hypothesis is that Crest is no better than Brand X.”

    Closer, but no. What happens if it’s worse? We avoid this vagueness by expressing our H^0 and H^1 mathematically. You should know that.

    Your null needs to be falsified statistically by your H^1 (# of cavities in Group A < than the # in Group B).

    Therefore, the null must be that the # of cavities in Group A (Crest) = (EQUALS, this is essential) the # of cavities in group B (Brand X).

    If you were a scientist you wouldn't talk about the null like this for a defined experiment.

  548. steve12on 09 Oct 2016 at 12:43 pm

    So essentially, Dr. The Troll stole a boring experiment on line and still screwed it up.

    So funny…

  549. steve12on 09 Oct 2016 at 12:44 pm

    What test would you run to see if A < B?

  550. Steve Crosson 09 Oct 2016 at 1:00 pm

    hardnose,

    I’m genuinely curious. Exactly who is it that you think you are fooling? It has probably been years since anyone here took your “knowledge” seriously. When you bother to provide “evidence”, at least 90% of the time it says the exact opposite of what you think it does or else it is completely irrelevant to the subject at hand. The rest of the time, it is either very old (and subsequently proven wrong) or else extremely weak to begin with and not accepted as meaningful by anyone except a few outliers or cranks.

    Every single time you comment, you reveal your ignorance of basic science and logic. More often than not, you fail at simple reading comprehension. Literally no one here believes your ‘qualifications”. At this stage, it is really hard to believe that you are even fooling yourself into believing that you are fooling us at all.

    If you do think you are fooling anyone, then I feel sorry for you. That is just sad and pathetic. You spend a lot of time trying (and failing) to support your preconceptions. If you spent the same time seeking genuine knowledge with an open mind, then you might actually have a chance to become as smart as you would like to be.

    Besides, even if every single one of your beliefs should happen to be completely true, you will still NEVER convince anyone else until you do the hard work of learning basic science and logic and how to identify meaningful evidence (and design legitimate experiments).

  551. hardnoseon 09 Oct 2016 at 1:39 pm

    “We’ve been saying for weeks that increased variability is real and is a distinct survival advantage. It does NOT mean that any guidance or direction is involved. It simply means that organisms with built-in variability will be naturally selected more often than those that are less able to rapidly adapt to changing environments.”

    Right. Instead of saying “God did it” we can say “Natural selection did it.”

    If you could pull your head out of your ass for one minute you would see that this verifies what Shapiro has been saying.

  552. hardnoseon 09 Oct 2016 at 1:40 pm

    “Dr. The Troll stole a boring experiment on line and still screwed it up.”

    The Crest experiment was from a TV ad in the 1960s or 70s.

    Continue to demonstrate the vast array of subjects of which you know nothing.

  553. hardnoseon 09 Oct 2016 at 1:42 pm

    “What happens if it’s worse? We avoid this vagueness by expressing our H^0 and H^1 mathematically. You should know that.”

    Oh how impressive. Moron (sorry to keep using that word but I can’t think of a better description).

    The experiment is to see if Crest is BETTER than Brand X. The T test would be one-tailed.

  554. Steve Crosson 09 Oct 2016 at 1:57 pm

    We asked for a scientific experiment — NOT advertising smoke and mirrors.

    The fact that you don’t know the difference speaks volumes.

  555. Steve Crosson 09 Oct 2016 at 1:59 pm

    Right. Instead of saying “God did it” we can say “Natural selection did it.”

    We all know that NS exists and has a real effect on the world. Even you have admitted that. You just can’t provide evidence for anything else.

    Nor can you even describe one simple legitimate science experiment.

    What a loser.

  556. BillyJoe7on 09 Oct 2016 at 4:32 pm

    hn: “We don’t know”.

    Yes we do.

    We know that there is no possible/plausible mechanism for directed/adaptive mutation.
    We know that the ordinary process of random mutation and natural selection are perfectly capable of explaining evolution regardless of whether or not there are hot spots in the genome.

    Therefore directed/adaptive mutation is excluded by ockham’s razor.

    James Shapiro’s opinion bleeds to death on this razor.
    That is why evolutionary biologist now ignore him completely and why he writes for free for huffpo.
    I hope hn suffers a similar fate after this thread.

  557. bachfiendon 09 Oct 2016 at 5:49 pm

    Hardnose,

    You keep getting evolution wrong. We don’t say ‘natural selection did it’. We say that ‘the changing environment acting on a variable population did it’.

    Also you persist in misunderstanding how antibiotics work in infections. The aim is to kill or or stop most of the bacteria from dividing (antibiotics are often considered to be bactericidal- kills bacteria, or bacteristatic – stops bacteria from dividing, although there’s overlap between the two) giving the host time to mount an immune defence.

    The aim is to reduce the number of bacteria the host has to fight. The host isn’t defenceless. It can usually cope quite well against a small number of the surviving resistant bacteria, provided there aren’t large numbers of surviving less resistant bacteria for the host to fight against too. Particularly since, as demonstrated in the video discussed by Steve Novella’s thread above, resistant bacteria are often less fit in other ways than sensitive bacteria.

    Giving adequate amounts of bacteria reduces the number of bacteria to be overcome. Giving inadequate amounts of antibiotics might lead to symptomatic relief and the appearance of cure, but there still remains a number of resistant bacteria the host’s immune system hasn’t got rid of. Which can then multiply causing a recurrent infection more resistant on average, because the more resistant bacteria in the variable population have survived, that the original infection. Which then requires large doses of antibiotics (or different ones) to cure.

    Bacteria could develop new mutations for antibiotic resistance during a short course of antibiotic treatment. Or there could be a small number of bacteria existing with old mutations for antibiotic resistance due to previous antibiotic exposure (and which hadn’t lost the resistance in the meantime because there are reduced fitness problems with being antibiotic resistant).

    But how would you know whether the mutations are new or old? I’d asked you for the names of ‘some researchers’ who believe that the only mechanism of developing antibiotic resistance is new mutations.

    And anyway. The most alarming mechanism of bacteria acquiring new antibiotic resistance doesn’t involve new mutations. It involves the transfer of plasmids containing antibiotic resistance genes from other bacteria, often not even of the same species, resulting in resistance to more than one antibiotic developing in one hit. Which is favoured with antibiotic treatment too.

    Only you could take a news article for lay people which makes the very sensible suggestion that if you take antibiotics in sufficiently high dose and for sufficiently long enough to cure the infection and read in to it that resistance to antibiotics only develops as a result of new mutations.

  558. steve12on 09 Oct 2016 at 5:54 pm

    “The experiment is to see if Crest is BETTER than Brand X. The T test would be one-tailed.”

    HA HA HA HA HA!

    Uhhhhh, no. You have a short memory Dr. TheTroll.

    Let’s see what your experiment was (however ill-defined it may have been):
    >Here’s another experiment:
    >Two groups of people, 20 in each.
    >One group brushes with Crest, the other uses Brand X.
    >After one month, see which group has fewer cavities.
    >Dependent measure: number of cavities.
    >Null hypothesis: Crest is crap.

    Pay special attention to line #4:
    “After one month, see which group has fewer cavities.”

    Does this sound like you’re testing a directional hypothesis? No, it doesn’t.

    So what’s the real problem?
    YOU never specified the hypotheses because YOU didn’t specify your H^0 and H^1 in mathematical form, as I pointed out. We specify EVERYTHING that we can in science. Had you specified your H^0 and H^1 (i.e., had you known HOW to do that), it would have been obvious.

    Thanks for pointing out exactly WHY you can’t simply SAY that your null hypothesis is “Crest is crap”, or some such.

    You should never have tried to propose an experiment. You have no idea how to do it.

    #FAIL

    #BokeTheTroll

  559. steve12on 09 Oct 2016 at 5:56 pm

    “The Crest experiment was from a TV ad in the 1960s or 70s.
    Continue to demonstrate the vast array of subjects of which you know nothing.”

    I cede this point. I do no know TV commercials from before I was born.

    I DO however know how to do scientific research, and YOU do not.

    I’ll take my skill set over yours.

    #BrokeTheTroll

  560. hardnoseon 10 Oct 2016 at 12:29 am

    “We know that the ordinary process of random mutation and natural selection are perfectly capable of explaining evolution”

    How do you know that, with no evidence?

  561. hardnoseon 10 Oct 2016 at 12:34 am

    “In-host increased mutability is a general situation that may affect several different bacterial genes. However, regulation of mutability also has a gene-specific component. It has been pointed out that bacteria have two different sets of genes: housekeeping genes, which are relevant for basic bacterial metabolism and structure and that mutate at an expected low frequency, and contingency genes (52), which are important for bacterial adaptability to changing environments and that are highly mutable. Indeed, very high rates of mutation may indicate not a real mutation but, rather, some programmed recombination event.”

    http://aac.asm.org/content/44/7/1771.full

  562. steve12on 10 Oct 2016 at 12:54 am

    Dr. TheTroll:

    So am I to assume that because you had some trouble with that simple toothpaste experiment, you’re not going to propose any hypothetical experiments re: guided mutations?

  563. bachfiendon 10 Oct 2016 at 2:58 am

    Hardnose the troll,

    So now you’re linking to a full article published in 2000, so congratulations on citing a review article in a respectable journal which is almost up to date for you, being just 16 years old.

    Instead of just ‘cut and pasting’ a paragraph from it, how about discussing the review article to demonstrate that you actually understand it, unlikely though that is.

  564. chikoppion 10 Oct 2016 at 2:59 am

    [hardnose] http://aac.asm.org/content/44/7/1771.full

    I’m curious, what is it you think this article says?

    Because you either didn’t read it, or you do not understand the theory you claim to be arguing against.

  565. bachfiendon 10 Oct 2016 at 5:40 am

    Chikkopi,

    That’s exactly what I was wondering.

    I suspect that he just randomly selects an old paper and chooses any random section. At least the reference (52) was recent (1998) to the date the review article was published (2000).

    One of the reference authors was a certain R Lenski who seems strangely familiar.

  566. Steve Crosson 10 Oct 2016 at 7:57 am

    Like I’ve said many times, hardnose’s “evidence” rarely says what he thinks it does. He is obviously doing simple keyword searches and then cut&pasting whatever he finds that he THINKS will support his case. Or, more accurately, what he HOPES will support it. Pretty sure there is no actual thinking involved.

    Hardnose is too ignorant, uneducated, and just plain stupid to understand what his “research” really means.

    The ultimate poster child for the Dunning Kruger effect.

  567. hardnoseon 10 Oct 2016 at 10:26 am

    “Adaptive mutation.The mutation process has classically been studied in actively dividing bacteria (33, 35), as it was assumed that mutations occur as the consequence of errors during the DNA replication process. However, more recent work has demonstrated that mutation also occurs in nondividing cells (22, 36, 64,69). These mutation events are the basis of the so-called adaptive mutation (or stress-induced mutagenesis) (63). A special feature of stress-induced mutagenesis is the fact that the mutation rate can increase over time by several orders of magnitude for cells under starvation conditions (50, 69).”

    http://aac.asm.org/content/44/7/1771.full

  568. hardnoseon 10 Oct 2016 at 10:27 am

    “Analysis of several model systems have demonstrated that stress-enhanced bacterial mutation is a regulated phenomenon.”

  569. steve12on 10 Oct 2016 at 10:51 am

    Dr. TheTroll:

    Lemme get this straight:

    You take the challenge re: experimental design. You botch it. Now you just wanna ignore how it ended?

    I don’t think so….

    You’re a PhD scientist who can’t design an experiment comparing 2 toothpaste brands?

    HA HA HA HA HA HA !!!!!

    PLEASE explain this Doc! Are you a little upset that in the same post where you called me a “moron” I showed you that you were actually the one that was wrong?

    Bit of advice: save your insults for when you KNOW you’re right, lest you be made to look like an IDIOT.

    HA! So great. Took the bait and I reeled ya in.

    #BrokeTheTroll

  570. Steve Crosson 10 Oct 2016 at 10:53 am

    Continually repeating the same “evidence” that does NOT help your case, AT ALL, merely reinforces the fact that you don’t have any idea what you are talking about.

    You need to learn the basics.

    Start with designing and describing any simple but REAL scientific experiment as steve12 challenged. Until you learn the simple stuff, you’ll never have a prayer of finding and understanding evidence that might actually support your point of view.

  571. Steve Crosson 10 Oct 2016 at 10:56 am

    I’m sure it is clear to everyone except possibly/probably hardnose, but my comment about “Continually repeating the same “evidence” was directed at hardnose.

    Repeating something three times doesn’t have any magical effect except in the fairy tale world he lives in.

  572. hardnoseon 10 Oct 2016 at 11:25 am

    There is lots of recent research on antibiotic resistance, since it is a medically important topic.

    So don’t worry, I will keep you informed, as time permits, of evidence supporting Shapiro’s ideas.

    (Even though I am retired I am involved in things and can’t spend unlimited time here trying to de-program you).

  573. chikoppion 10 Oct 2016 at 11:43 am

    [hardnose] “Adaptive mutation.The mutation process has classically been studied in actively dividing bacteria (33, 35), as it was assumed that mutations occur as the consequence of errors during the DNA replication process. However, more recent work has demonstrated that mutation also occurs in nondividing cells (22, 36, 64,69). These mutation events are the basis of the so-called adaptive mutation (or stress-induced mutagenesis) (63). A special feature of stress-induced mutagenesis is the fact that the mutation rate can increase over time by several orders of magnitude for cells under starvation conditions (50, 69).”

    Yes, I read the article.

    What do you think is relevant? We already know mutations occur in cells during stages other than replication. We also know that environmental factors can impact the rate of mutations caused by genetic mechanisms. We’ve been over and over these factors ad nauseam.

  574. chikoppion 10 Oct 2016 at 11:45 am

    Grrr…text correction!

    [hardnose] “Adaptive mutation.The mutation process has classically been studied in actively dividing bacteria (33, 35), as it was assumed that mutations occur as the consequence of errors during the DNA replication process. However, more recent work has demonstrated that mutation also occurs in nondividing cells (22, 36, 64,69). These mutation events are the basis of the so-called adaptive mutation (or stress-induced mutagenesis) (63). A special feature of stress-induced mutagenesis is the fact that the mutation rate can increase over time by several orders of magnitude for cells under starvation conditions (50, 69).”

    Yes, I read the article.

    What do you think is relevant? We already know mutations occur in cells during stages other than replication. We also know that environmental factors can impact the rate of mutations caused by genetic mechanisms. We’ve been over and over these factors ad nauseam.

  575. Steve Crosson 10 Oct 2016 at 11:56 am

    There is lots of recent research on antibiotic resistance

    Of course there is, but none of it shows any evidence for guidance or direction.

    I will keep you informed, as time permits, of evidence supporting Shapiro’s ideas.

    No need. We’ll hear about long before you do. If any genuine evidence ever does appear, it will be a very significant discovery. It will necessarily appear on the real science sites first.

    It is impossible for the cranks and ideologues to get confused and misinterpret something before they’ve even heard of it. By the time you read your looney-tunes version, we will already know about the real science.

  576. steve12on 10 Oct 2016 at 12:08 pm

    “Dr.” TheTroll

    So you think if you ignore me I’ll go away? Fat chance…

    YOU FAILED THE CHALLENGE. And did so in such a way that revealed you lied.

    So now it’s simply not possible that you’re a PhD scientist. NOT POSSIBLE.

    LIAR.

    #BrokeTheTroll

  577. hardnoseon 10 Oct 2016 at 12:49 pm

    Somebody, please, get steve12 his tranquilizers.

  578. Steve Crosson 10 Oct 2016 at 12:56 pm

    Why???

    Everyone deserves a victory lap when they win — especially when it is such a thorough, utterly lopsided win. It’s not his fault that you were trivially easy to outwit. He was fighting a battle with an unarmed man.

  579. steve12on 10 Oct 2016 at 1:08 pm

    “Somebody, please, get steve12 his tranquilizers.”

    Ya know, people do say that I have a lot of energy.

    You, on the other hand are an inveterate liar who’s angry that I bested and exposed you.

    #BrokeTheTroll

  580. steve12on 10 Oct 2016 at 1:10 pm

    Steve C:

    “It’s not his fault that you were trivially easy to outwit.”

    Yeah, only so much credit I can take on this one…

  581. Steve Crosson 10 Oct 2016 at 2:56 pm

    “Yeah, only so much credit I can take on this one…”

    Don’t feel bad. Not your fault that an unarmed man challenged you to a battle of wits.

    And, although the judges couldn’t award any extra points for difficulty, they gave you (and mumadadd) full marks for technical excellence (and humor).

    My sides still hurt from laughing so hard.

  582. steve12on 10 Oct 2016 at 4:12 pm

    Yeah – Some of Mumaddad’s comments were killing me…

  583. hardnoseon 10 Oct 2016 at 4:31 pm

    I have no idea what steve12 thinks he won. I have evidence and logic but he has provided nothing of value.

    Why doesn’t steve12 describe his experiment that would conclusively decide if adaptive mutations are accidents or not?

    I’ll give him an hour, that should be plenty of time.

  584. BillyJoe7on 10 Oct 2016 at 4:53 pm

    I’m pretty sure the little guy is determined to have a sort of pyrrhic victory by posting the last comment in this thread, so I’m not sticking around for lavatory roll.

    So, congratulations and thanks to bachfiend, steve12, Steve Cross, and chikoppi (whose posts elicited not a single response from our little contrarian!). All of you have deepened my understanding of evolutionary theory.

  585. BillyJoe7on 10 Oct 2016 at 4:55 pm

    …sorry, I forgot mumadadd!
    Congratulations to mumadadd for his persistence in the face of intransigence! 🙂

  586. steve12on 10 Oct 2016 at 5:09 pm

    Dr. TheTroll

    “I have no idea what steve12 thinks he won. ”

    Yeah ya do.

    I won the point of showing conclusively that you are not a scientist.

    And let me be clear – this doesn’t matter. You don’t have to be a PhD to have a valid viewpoint or to be very educated about different topics in science, etc. We’re not right because some of us are scientists or because our evidence is from scientists or any of that. We’re right because of the EVIDENCE and reasonable interpretation thereof.

    YOU on the other hand try to enhance the impact of your argument by saying that you are trained as a scientist. It helps nor hurts your arguments; they’re inane and uneducated contrarianism sprinkled with lies. That would be true if you had 20 PhDs (note: you have 0).

    I just got tired of your duplicitous “arguing style” complete with lies about your credentials. So I set out to show that you are a lying sack of shit.

    I succeeded.

    “Why doesn’t steve12 describe his experiment that would conclusively decide if adaptive mutations are accidents or not?”

    Oh, how clever sir! I declare! Your rouse has turned the tables on me!

    How’s this. If you post yours, I will fix it and then give you a real one. But since I asked first, and you’re the fake scientist, I await yours good sir.

    But I’ll do you a solid and post a hint in my next reply 🙂

  587. steve12on 10 Oct 2016 at 5:17 pm

    And now my HINT! Pay close attention!

    Remember I told you earlier that it would be easy to modify Lenski’s experiment? And you know how you’re really only good with toothpaste-themed research?

    I’m thinking that your God that directs evolution likes Crest toothpaste better than the leading brand, right? I know mine does. In a poll, 11 out of 10 guiders of evolution agree on this.

    So what about the bacteria, ha? Think THEY might learn to eat CREST but not the leading brand? See where I’m going Doctor???

    Are ya smellin’ my Petri Dish, if ya know what I’m sayin’?

    You’re welcome.

  588. steve12on 10 Oct 2016 at 5:23 pm

    Kudos to you BJ7!

    You, et al. (don’t want to name anyone because I WILL forget folks) really brought up a lot of studies I hadn’t read before.

    This is the best counterpoint to my suggestion that conversing with Dr. TheTroll is a waste.

    I brought nothing this time really. I was just a dick honestly….

  589. hardnoseon 10 Oct 2016 at 6:27 pm

    “If you post yours, I will fix it and then give you a real one. But since I asked first, and you’re the fake scientist, I await yours good sir.”

    I explained that there is a controversy, and a lot of research has been done, and there has not yet been a definite conclusion. But you are more interested in being a dick head than having a rational debate.

    So now, because you “asked first” that means you do not have to explain how you can prove that adaptive mutations are accidents.

    I have already shown good evidence that you are wrong. You have not shown any evidence for your opinion.

    You need to think adaptive mutations are accidents, and nature is stupid, and DNA is mostly junk, etc., etc., because that somehow lets you feel superior. Real intelligence is only found in human brains, but not all brains, only the ones that adore Dawkins.

  590. Steve Crosson 10 Oct 2016 at 6:52 pm

    Real intelligence is only found in human brains, but not all brains, only the ones that adore Dawkins.

    Well, if you say so. I think “adore” is a bit strong. It’s more accurate to say that most of us merely agree that Dawkins is mostly right about evolution and the modern synthesis.

    But you’re absolutely right that intelligence is NOT found in all brains — only the ones that adore/accept Dawkins.

    By your own admission, that leaves you out.

  591. hardnoseon 10 Oct 2016 at 7:01 pm

    It is true I do not belong to your Dawkins club. And it is true that means I can’t be intelligent, according to you. And the great majority of humanity can’t be intelligent, according to you. And that allows you to feel special and superior.

    I am glad you at least admitted that all of you who want me banned are devoted members of the Dawkins tribe. And tribes need to stick together so they can feel superior. And they try to get rid of “contrarians” who don’t buy their mythology.

    And that is what is going on here. You see yourselves as highly evolved and superior, but in reality you are just being a primitive tribe.

  592. hardnoseon 10 Oct 2016 at 7:05 pm

    And I have been trying to fight irrational tribalism with reason and evidence. It might seem hopeless, but maybe someone reading this thread has stopped to think that maybe Dawkins is not all-knowing. Maybe Dawkins does not know the secret of how everything got to be here.

    There is a gaping hole in his logic. And I can’t help seeing it. There is a trick in his reasoning, which even Dawkins probably is not conscious of. But it is a trick.

  593. hardnoseon 10 Oct 2016 at 7:09 pm

    There is conclusive evidence for evolution.
    There is conclusive evidence for natural selection.
    Therefore, natural selection explains evolution.

    BIG OBVIOUS LOGICAL ERROR. At the heart of the modern synthesis.

    Only a small minority has fallen for it. But that minority is very loud, very egotistical, and very confident.

  594. steve12on 10 Oct 2016 at 7:41 pm

    BJ7, prophet:

    “I’m pretty sure the little guy is determined to have a sort of pyrrhic victory by posting the last comment in this thread, so I’m not sticking around for lavatory roll.”

  595. hardnoseon 10 Oct 2016 at 8:09 pm

    https://en.wikipedia.org/wiki/Masatoshi_Nei#New_evolutionary_concepts

    “Nei has long maintained the view that the driving force of evolution is mutation including any types of DNA changes (nucleotide changes, chromosomal changes, and genome duplication) and natural selection is merely a force eliminating less fit genotypes (theory of mutation-driven evolution)”

  596. hardnoseon 10 Oct 2016 at 8:10 pm

    https://www.amazon.com/Mutation-Driven-Evolution-Masatoshi-Nei/dp/0199661731

    “The theory asserts, perhaps somewhat controversially, that the driving force behind evolution is mutation, with natural selection being of only secondary importance.”

  597. steve12on 10 Oct 2016 at 8:31 pm

    Those are weird sounding experiments. I don’t think that they’ll work.

    remember: think toothpaste

  598. chikoppion 10 Oct 2016 at 9:05 pm

    Just stop. It’s obvious you don’t have any idea what you’re even arguing about anymore and no one gives a rat’s ass what adjectives are applied to which factors of evolution.

    All you’re doing now is quote-mining random crap from web search because you think you like the way the words sound.

    To quote the great orange muppet and our soon to be commandeerer in chief: “Very, very terrible! So bad you won’t believe it, folks. Sad.”

  599. grabulaon 10 Oct 2016 at 10:17 pm

    so Dr. Hardnose last few pieces of evidence are a wiki page and an excerpt from a book on amazon.

    BTW it’s been a while but if i remember correctly he claimed his science background came from some homeopathic training or some such woo.

  600. Mr Qwertyon 11 Oct 2016 at 4:28 am

    It is a bit sad at this point. Reminds me of a friends father who in the recent years started losing his grips with reality – really, really nice guy but there’s little point getting into any kind of explaining anymore, the capacity to reason has left the building.

  601. hardnoseon 11 Oct 2016 at 9:25 am

    Evidence has been increasing that natural selection is NOT the cause of evolution. Some researchers are now questioning neo-Darwinism, the modern synthesis and the central dogma. Some are rejecting its fundamental concepts.

    Dawkins seems to be unaware of developmental evolution, systems biology, etc. Coyne stubbornly rejects it all. Dawkins and Coyne are only interested in defending the status quo, they have no desire to learn.

  602. chikoppion 11 Oct 2016 at 10:54 am

    Yawn.

  603. hardnoseon 11 Oct 2016 at 12:27 pm

    “Masatoshi Nei has been a major contributor to the field of molecular
    evolution. In this important book, he argues for, among other things,
    the end of “beanbag genetics,” finding the mathematical formulations
    that describe the effects of selection and drift on single genes
    wanting. He casts serious doubt on natural selection as the primary
    driving force in evolution, arguing instead that mutation is the major
    determinant of evolutionary change.”

    http://jhered.oxfordjournals.org/content/106/4/420.full.pdf

  604. hardnoseon 11 Oct 2016 at 12:29 pm

    “evolution by omnipotent natural selection is similar to creationism, in which natural selection is replaced by God.”

    Well that’s cool, a respected evolution researcher says exactly what I said.

  605. hardnoseon 11 Oct 2016 at 12:30 pm

    “When it comes to his criticisms of “beanbag genetics,” Nei is not a naive iconoclast”

  606. hardnoseon 11 Oct 2016 at 12:36 pm

    Nei does not deny the existence of natural selection. Indeed, he
    points out that purifying selection operates on most genes and recognizes
    the role of selective sweeps of single nucleotide polymorphisms
    in populations. But he does not see natural selection as a creative
    force in evolution, dismissing that kind of thinking as teleological.

  607. chikoppion 11 Oct 2016 at 12:45 pm

    Yawn!

  608. hardnoseon 11 Oct 2016 at 12:56 pm

    http://www.cell.com/ajhg/fulltext/S0002-9297(13)00516-8

    “Masatoshi Nei has been one of the major figures in evolutionary genetics since the latter third of the 20th century. He has personally contributed enormously to what we know today and remembers with awe-inspiring detail what others have said. When such an oracle speaks, we should listen carefully.”

    “Nei challenges the widely if often reflexively held view that natural selection is the fine-tuning process that accounts for the traits of organisms. This classical Darwinian view holds that there is always enough standing genomic variation that, when the environment changes, a species can adapt to it. However, through the years prominent geneticists, including Nei, have argued that mutation rather than selection is the driver of evolution.”

  609. steve12on 11 Oct 2016 at 1:00 pm

    “Yawn!”

    Yeah, really. The only fun thing to watch is when you ignore him he says even crazier things to provoke a response.

    I’ll only respond to an experiment at this point. Or to mock.

    I’m so glad my ego doesn’t require me to feel “special” like this, like I’m smarter than everyone else or any of that. Sounds like a rough existence actually

  610. hardnoseon 11 Oct 2016 at 1:21 pm

    You said Shapiro is an outlier (although he isn’t). You certainly cannot say that about Nei.

    You have lost this argument, so give up. Insulting me is not a rational response. You have no rational response.

    It is a fact that Dawkins and Coyne stand for a theory that is increasingly being challenged by respected evolution researchers.

  611. chikoppion 11 Oct 2016 at 2:19 pm

    What argument?

    Genetic variation delimits what change is possible and selection+drift determines what change is actual. That’s the consensus theory. Apply any adjectives to those factors you like. One does not exist without the other.

    You aren’t fooling anyone. You desperately want to assert that evolution is guided, meaning that it has a pre-destined course or outcome. You know that’s an irrational position, so you flail about in an attempt to impugn what you (often mistakenly) perceive to be the consensus theory.

    No one cares. Even if we found out everything we think we know about genetics and evolution (they are not synonymous) were false, it wouldn’t help you one bit. Nothing in the litany of quote-mined google results you’ve subjected us to even remotely suggests guided evolution.

    When evidence exists that the consensus theory should change then the consensus theory will change. Your opinion and my opinion is 100% irrelevant to that outcome. Until the scientific community comes to that conclusion the current theory remains the correct theory, as it reflects our best explanatory understanding of the facts.

  612. hardnoseon 11 Oct 2016 at 2:40 pm

    According to Nei, everything you have been saying about evolution is wrong.

  613. hardnoseon 11 Oct 2016 at 2:42 pm

    “When evidence exists that the consensus theory should change then the consensus theory will change. Your opinion and my opinion is 100% irrelevant to that outcome. Until the scientific community comes to that conclusion the current theory remains the correct theory, as it reflects our best explanatory understanding of the facts.”

    The consensus has been changing, while you weren’t paying attention. Dawkins is becoming obsolete.

  614. hardnoseon 11 Oct 2016 at 2:49 pm

    “You desperately want to assert that evolution is guided, meaning that it has a pre-destined course or outcome.”

    That is absolutely false. Jerk.

  615. steve12on 11 Oct 2016 at 3:11 pm

    “Jerk.”

    Uh oh!!!! Dr. TheTroll is angry!

  616. chikoppion 11 Oct 2016 at 3:27 pm

    According to X…

    Don’t care.

    The consensus has been changing…

    Really? In what factual way has the consensus changed? Not vagaries, not snatches of quotations, not nebulous statements. In what tangible, factual way has the consensus understanding of evolution changed that is a departure from anything I have said in this forum?

    That is absolutely false…

    I’m glad to hear it. If you are now on record as not believing that evolution is a guided, directed, or pre-destined process I hereby retract my prior statement with all appropriate apologies. I’m not sure how you’ll square that position with your visceral aversion to the phrases “non-directed mutations” and “accidents and errors,” but that’s not my row to hoe.

  617. steve12on 11 Oct 2016 at 4:01 pm

    But that’s the game chikoppi

    Mutations are guided, they’re not, and we don’t know
    I don’t know what materialism is – but I’m against it.
    I’ll go 1500 posts about random mutations – but I’ll refuse to define random.

    What kind of sick person does this shit? I think we’re all guilty of the worst en masse attribution error of all time in thinking that some small part of this guy is well intended, or wants an ernest exchange, simply because we are and do.

    Why would any sane person engage in this…whatever this is… deliberately? What would be the purpose of such an encounter? Where you lie, obfuscate, ignore, and straw-man anonymously?

    I call it trolling. But truth is it’s much weirder. His is in a class by himself, I must say.

    I’d love to meet Dr. TheTroll actually. Part of me is fascinated truth be told.

    You near Boston Troll Boy?

  618. hardnoseon 11 Oct 2016 at 4:14 pm

    “In what tangible, factual way has the consensus understanding of evolution changed that is a departure from anything I have said in this forum?”

    You could READ what I posted. Nei, who is much more knowledgeable about current evolution research than Dawkins, says that Dawkins is WRONG. He says that natural selection is NOT the organizing force of evolution.

    You have all insisted that Dawkins is RIGHT, that evolution is explained by natural selection.

    Nei says approximately the same thing as Shapiro. They do not try to explain what causes the mutations that lead to evolution and adaptation, because that is unknown.

    But they have found plenty of evidence that Dawkins is WRONG. And YOU are WRONG.

    WRONG WRONG WRONG WRONG WRONG.

    But you can’t admit it.

  619. chikoppion 11 Oct 2016 at 5:06 pm

    I have never once cited Dawkins. Not once. Stop trying to invoke him as a strawman.

    I don’t know what “the organizing force of evolution” means. I know what variation is, I know what a mutation is, I know how mutagenic processes can be induced by environmental factors, I know how epigenetics can regulate gene expression, I know how selection and propagation function…all according to the consensus theory.

    In what factual way do you think the consensus theory has changed? Don’t just repeat a phrase that you think is proof of something. Actually articulate the distinction.

  620. Bill Openthalton 11 Oct 2016 at 5:18 pm

    619 replies and still going strong. hardnose is a very effective troll, I must admit. Could he be the re-incarnation of Rev. Don Kool who used to troll the Unix groups on Usenet?

  621. Steve Crosson 11 Oct 2016 at 5:28 pm

    Bill O,

    More likely one of Donald Trump’s (no doubt many) illegitimate children. Hardnose has definitely got the narcissistic need to always be right and he definitely has a habit of lying repeatedly even though his lies are easily proved wrong.

  622. bachfiendon 11 Oct 2016 at 5:37 pm

    Hardnose,

    You still don’t understand evolution. The cause of evolution (the driving force) is environmental change acting on a reproductively isolated population. If there’s enough natural variation within the reproductively isolated population, then the mechanism of natural selection will cause the relative frequencies of natural variants to change n response to the environmental change.

    If there is sufficient natural variation within the population, and the environmental change is severe enough, then it will go extinct – the history of 99.9% of all species ever living on Earth.

    Natural selection doesn’t cause anything. It’s just a mechanism. It determines what survives.

    Nei talks about RARE constraint breaking mutations. Rare, rare, rare,… I don’t know what he’s talking about(nor do you apparently relying as you usually do on Wikipedia and book reviews), but I suppose one example he might be thinking about is the formation of eukaryotes 2 billion years ago from the fusion of a eubacterium and an Archaea bacterium, which was apparently unique (although Nick Lane in ‘the Vital Question’ provides tantalising evidence that t might have almost happened a second time recently).

    Rare constraint breaking mutations still have to survive natural selection though. And rare doesn’t imply that they’re non-random or directed either.

    It actually sounds more like random non-directed mutations with the deleterious mutations being eliminated by natural selection. Which is precisely what I’ve been claiming all the time. There’s no evidence that mutations can ever be non-random and directed because if they were, then why are beneficial mutations so rare.? Why are adaptations late and infrequent instead of early and frequent?

  623. hardnoseon 11 Oct 2016 at 5:40 pm

    “In what factual way do you think the consensus theory has changed?”

    READ what I posted. A real expert says that Dawkins, neo-Darwinism, the modern synthesis, is wrong. There is no consensus theory. There is a controversy.

    I have explained this all so damned carefully it does not seem possible you still don’t get it.

    I have been citing experts who say that natural selection is NOT the organizing force of evolution. Dawkins, Coyne, say that it is.

    These experts are saying that evolution is caused by mutations. The mutations are not accidental. You don’t get it, you are so brainwashed you are not able to think logically.

  624. hardnoseon 11 Oct 2016 at 6:02 pm

    “It actually sounds more like random non-directed mutations with the deleterious mutations being eliminated by natural selection. Which is precisely what I’ve been claiming all the time.”

    Nei is a leading expert on evolution. bachfiend is NOT an expert, he only thinks he is.

    You are not capable of reading I guess.

    What you just said here is neo-Darwinism. That is exactly what Nei says is WRONG.

    I don’t know how to explain things to people who are determined not to think, and will not read.

  625. hardnoseon 11 Oct 2016 at 6:05 pm

    Dawkins, Coyne, etc., say that adaptive mutations are always accidental. Therefore, they say the organizing, driving, force of evolution is natural selection.

    Nei (and Shapiro, and others) says that natural selection is NOT the organizing, driving, force of evolution.

    So what is? The mutations themselves drive evolution, according to Nei. That means adaptive mutations cannot be merely accidental.

    The logic is simple. Anyone should be able to get this.

  626. chikoppion 11 Oct 2016 at 7:16 pm

    [hardnose] Dawkins, Coyne, etc., say that adaptive mutations are always accidental. Therefore, they say the organizing, driving, force of evolution is natural selection.

    Nei (and Shapiro, and others) says that natural selection is NOT the organizing, driving, force of evolution.

    So what is? The mutations themselves drive evolution, according to Nei. That means adaptive mutations cannot be merely accidental.

    There’s that word again. “Accidental.”

    Define “accidental” as you use it in this context (I think you’re about to directly contradict Shapiro).

    What is the difference between an “accidental” mutation and a “non-accidental” mutation?

  627. hardnoseon 11 Oct 2016 at 7:18 pm

    Nei: “If you say evolution occurs by natural selection, it looks scientific compared with saying God created everything. Now they say natural selection created everything, but they don’t explain how. If it’s science, you have to explain every step. That’s why I was unhappy. Just a replacement of God with natural selection doesn’t change very much. You have to explain how.”

    http://discovermagazine.com/2014/march/12-mutation-not-natural-selection-drives-evolution

    As I have been trying to tell you.

  628. hardnoseon 11 Oct 2016 at 7:21 pm

    “My position is mutation creates variation, then natural selection may or may not operate, it may or may not choose the good variation and eliminate the bad one, but natural selection is not the driving force.”

    In direct contradiction of what Dawkins and Coyne believe.

  629. hardnoseon 11 Oct 2016 at 7:30 pm

    Nei: “… any time a scientific theory is treated like dogma, you have to question it. The dogma of natural selection has existed a long time. Most people have not questioned it. Most textbooks still state this is so. Most students are educated with these books.”

  630. hardnoseon 11 Oct 2016 at 7:30 pm

    Nei: “You have to question dogma. Use common sense. You have to think for yourself, without preconceptions. That is what’s important in science.”

    I like this guy!

  631. hardnoseon 11 Oct 2016 at 8:35 pm

    There IS a controversy. Evolution has NOT been explained.

    Dawkins and Coyne are dogmatic, unwilling to change their minds when evidence changes. Not interested in keeping up with new research.

  632. chikoppion 11 Oct 2016 at 8:41 pm

    Uh-huh.

    What is the difference between an “accidental” mutation and a “non-accidental” mutation?

  633. hardnoseon 11 Oct 2016 at 9:01 pm

    “What is the difference between an “accidental” mutation and a “non-accidental” mutation?”

    How many times have we already been through this?

    The central premise of neo-Darwinism is that the genetic mutations that lead to evolution, after being processed by natural selection, are caused by accidents and errors. They are NOT the driving force of evolution. The driving force is natural selection.

    Shapiro and Nei, for example, believe that the central premise of neo-Darwinism is wrong. They both say that natural selection is NOT the driving force of evolution.

    Dawkins says adaptive mutations are not related to the cell’s, or the organism’s needs. Since they are “random,” there must be something to sort out the good from the bad. And that is natural selection.

    There is no evidence for what Dawkins claims.

    So what IS the driving force? No one seems to know.

    The important point here is that Nei, a leader in evolution research, says that natural selection cannot be the organizing, driving, force of evolution.

    Dawkins depends on natural selection because he has a very simple theory, and he wants that theory to be true.

    But as Nei says, there is no evidence for the natural selection theory. Yes, natural selection does happen, but we have no evidence for the idea that it can explain evolution.

    So if we are honest, and if we are scientific skeptics, we have to consider rejecting simple Dawkins’s theory. And we have to live with the fact that we do not know the cause of evolution.

  634. hardnoseon 11 Oct 2016 at 9:07 pm

    I am coming from the perspective of systems biology, which I learned about in the early 1980s. It had already been around for a long time.

    What I have read recently about Nei’s ideas, and Shapiro’s ideas, agree with what I had learned from systems biology. That natural systems evolve towards greater complexity. Nei and Shaprio might not be familiar with systems biology, but their ideas support it.

    Now, I am sure you will forget what I said about complexity. It is not individual organisms or species that increase in complexity. Obviously, that is not the case. But the overall system of life on earth has obviously increased in complexity.

    That is what Nei has been observing.

  635. chikoppion 11 Oct 2016 at 10:30 pm

    So much mischaracterization.

    [hardnose] The central premise of neo-Darwinism is that the genetic mutations that lead to evolution, after being processed by natural selection, are caused by accidents and errors.

    [hardnose] Dawkins says adaptive mutations are not related to the cell’s, or the organism’s needs. Since they are “random,” there must be something to sort out the good from the bad. And that is natural selection.

    1) Are you claiming that either Shapiro or Nei are making the assertion that mutations are directed, i.e. that genetic mechanisms produce specific changes to the genome that provide the organism with a needed trait in response to changing environmental needs?

    2) If you are NOT claiming that, then what distinguishes an “accidental” mutation from a “non-accidental” mutation?

    [Shapiro] The opponents of evolution are trying to confuse and mislead the public and the Texas school board textbook review committee. They have taken a real scientific debate and made it appear as a challenge to the legitimacy of evolution science itself.

    […] There is much that remains to be learned about the evolutionary process. Many problems remain without known solutions. But the sources of genome variation, including rapid changes throughout the genome, are no longer mysterious. We can describe how dozens of them occur in detail, down to the level of individual phosphodiester linkages in novel DNA structures.

    [Weiss, reviewing Nei] Nei challenges the widely if often reflexively held view that natural selection is the fine-tuning process that accounts for the traits of organisms. This classical Darwinian view holds that there is always enough standing genomic variation that, when the environment changes, a species can adapt to it. However, through the years prominent geneticists, including Nei, have argued that mutation rather than selection is the driver of evolution. The reasoning is basically that at any given time the complex integration of genomic mechanisms has been molded by eons of adaptive selection and cannot be changed much without being harmful. Major phenotypic change can arise only after the occurrence of rare “constraint-breaking” mutations that escape the established mold.

    Nei expresses his view by tracing the history of ideas on selection and mutation as new knowledge of genes and their mechanisms has accumulated. Comparative sequence analysis clearly shows that the amino acid code of most genes is constrained relative to less clearly functional parts of the genome. Because developmental processes involve many interacting genes, a mutation of large effect is most likely to disrupt the system—for example, to cause serious disease. But genomic data have also shown that more substantial mutations, such as redundancy generated by gene duplication, that can enable new function to evolve do occasionally arise.

    [hardnose] And we have to live with the fact that we do not know the cause of evolution.

    It seems Shapiro and Nei would disagree. They each claim to know how new traits emerge and Nei claims that genetic mechanisms are the result of selection.

  636. chikoppion 11 Oct 2016 at 10:32 pm

    Argh! Damn html tags!

    I’m sure you can figure out what’s from who in the above. I’m not going to repost a corrected version.

  637. steve12on 11 Oct 2016 at 11:43 pm

    Dr. TheTroll:

    “So what IS the driving force? No one seems to know.”

    OK, then we’re at a dead end. There’s no more evidence – the science just isn’t there yet.

    So at this point we can only speculate. So let’s do that!.

    What hypothetical experiment or series of experiments might fill in this gap? When you’re dealing with the frontier in science, it’s always instructive to ask what evidence could shed light on your situation without the limits of current technology or methods.

    I can’t see any reason why you wouldn’t do this given that you’ve shown that the limit of knowledge has been reached. That means there’s no more point to posting snippets from the literature.

    I await your experiment.

  638. bachfiendon 12 Oct 2016 at 3:50 am

    Hardnose,

    So, we’ve finally returned after all this time to your central delusions that evolution has direction. That it has aims and targets. That there’s an innate tendency to increasing complexity and intelligence in biological systems.

    The book review of Nei’s book that you linked to made much the same point. Nei appears to believe that there is an innate tendency to complexity in Life – ignoring the fact that bacteria, yeasts and protozoa just persist in remaining simple and not complex after billions of years of evolution.

    Rare constraint breaking mutations most certainly don’t mean that they’re non-random and directed. For all we know, there could have been thousands of constraint breaking mutations, which just didn’t succeed and subsequently disappeared.

    There’s no way of knowing.

    It’s a mistake and a sign of illogical thinking to regard the current situation to be anything other than an accident. To imagine that humans capable of thinking about such questions was somehow pre-ordained.

    If the K-P event (whether due to the Chicxulub bolide impact or the Indian Deccan traps eruption), then certainly humans ntelligent enough to ponder the meaning of life wouldn’t have evolved.

    Or perhaps I should have written that humans not intelligent enough to avoid these circular arguments you so prefer wouldn’t have evolved.

  639. SteveAon 12 Oct 2016 at 7:50 am

    I was surprised to see this thread is still going, so thought I’d dip back in.

    Not at all surprised to see Hardnose repeating his own confused, misunderstood BS, but very amused to find that a new cornerstone of his argument is Mr Nei, another scientist who Googled into his consciousness only a couple of days ago, but who is now treated as an all-knowing guru of genetics – a champion of truth beating down the demonic Dawkins, who, as we all know, is virtually the only person in the whole world who still holds a Darwinian view of evolution. Honest, it’s just him and his henchman Coyne…

    (Btw, Nei is a talented researcher who’s done a lot of important work, but in his advanced years he appears to have his sights set on a ‘legacy’ so is pushing his ideas a little beyond what’s sensible, imo. Though, in any event, none of Nei’s work supports Hardnose’s preposterous arguments in any way. A fact that only helps to underline his idiocy.)

    To answer Steve12’s questions:

    “What kind of sick person does this shit? I think we’re all guilty of the worst en masse attribution error of all time in thinking that some small part of this guy is well intended, or wants an ernest exchange, simply because we are and do.

    Why would any sane person engage in this…whatever this is… deliberately? What would be the purpose of such an encounter? Where you lie, obfuscate, ignore, and straw-man anonymously?”

    I would argue that Hardnose is essentially on an evangelical mission. He’s a proselytizer trying to confound the diehard sceptical readers of the blog by pointing out the ‘holes’ in our blindly-held cherished theories. In doing so he helps to bolster his own belief (to sum up: evolution is wrong = god is real = I’m not going to die) and might also save some souls for Jesus, or whoever.

    I always thought that Sonic (a previous troll with an MO similar to Hardnose) was on this same mission, and it might not be a coincidence that when Sonic ‘left’, Hardnose stepped to the fore.

    Anyway, food for thought.

    Thanks to Steve12, chikoppi, bachfiend et al for continuing to call out HN on his crap.

  640. hardnoseon 12 Oct 2016 at 8:42 am

    “Nei appears to believe that there is an innate tendency to complexity in Life – ignoring the fact that bacteria, yeasts and protozoa just persist in remaining simple and not complex after billions of years of evolution.”

    He is NOT ignoring that. I explained this to you many times already. The system overall has obviously increased in complexity. More complex organisms cannot exist without the simpler organisms.

  641. hardnoseon 12 Oct 2016 at 8:44 am

    “It’s a mistake and a sign of illogical thinking to regard the current situation to be anything other than an accident. To imagine that humans capable of thinking about such questions was somehow pre-ordained.”

    No one f-cking said it was pre-ordained.

  642. hardnoseon 12 Oct 2016 at 8:56 am

    Nei has pointed out that there is NO EVIDENCE for the neo-Darwinist idea that natural selection is the driving force of evolution. That is what I have been saying here.

    Nei and Shapiro do NOT claim to know what the driving force of evolution is. They have been studying the mechanisms involved. They do not have the arrogance to think they have it all figured out.

    My central argument here has been that there is NO evidence for the idea that natural selection explains evolution.

    I have shown you that some real experts are saying the same thing.

    You have lost the argument, but won’t admit it.

    Real skeptics want to know what the evidence shows, and will listen to rational arguments. Most of you who have been commenting on this thread are NOT real skeptics. You are true believers and devoted followers of Dawkins and Coyne.

  643. SteveAon 12 Oct 2016 at 9:10 am

    Hardnose: “My central argument here has been that there is NO evidence for the idea that natural selection explains evolution.”

    Wrong and wrong.

    Wrong, because there is plenty of evidence that natural selection is pretty much all that’s needed. It’s just that you don’t understand it, or even make much of an effort to do so. And you have failed to provide any convincing evidence to the contrary, or even attempted to explain how convincing evidence might be derived. Remember that experiment you were asked to describe? Still working on that are we?

    Also wrong, because that is not your central argument. Your central argument is that evolution has a “driving force” (your own phrase).

    So is the man behind the wheel deaf, blind and dumb (in which case his actions are best described as random). Or is he driving with a purpose?

    Which one? Care to put your cards on the table?

  644. hardnoseon 12 Oct 2016 at 10:53 am

    “there is plenty of evidence that natural selection is pretty much all that’s needed.”

    There is NONE. And a leading evolution researcher, Nei, says the same thing I have been saying here. There is NO evidence that natural selection can explain evolution.

  645. hardnoseon 12 Oct 2016 at 10:54 am

    There is evidence for evolution, there is evidence for natural selection. There is NO evidence that natural selection is the driving force, or the organizing force, or the cause, of evolution.

    So far, none of you have been capable of understanding that simple logic.

  646. hardnoseon 12 Oct 2016 at 11:19 am

    “Remember that experiment you were asked to describe? Still working on that are we?”

    That is pure idiocy. Experts have been working on this for decades, and they do not have a simple experiment. No I am not working on your stupid assignments that do not make any sense. I am showing what some highly qualified evolution researchers have found.

  647. chikoppion 12 Oct 2016 at 11:56 am

    Stop trying to stuff words in their mouths.

    [hardnose] Nei and Shapiro do NOT claim to know what the driving force of evolution is. They have been studying the mechanisms involved. They do not have the arrogance to think they have it all figured out.

    [Shapiro] The key issue, from my perspective, is: Where do functional adaptive innovations come from in evolution? Do they come from cellular activities that restructure the genome (natural genetic engineering), or do novelties arise as a consequence of natural selection optimizing fitness over time? While you clearly believe that natural selection is the creative agent, you do not acknowledge that a controlled, signal-responsive process of genome change is the alternative innovative process that I suggest. “Perhaps natural genetic engineering plays a more important role than natural selection” is what I wrote in the blog.

    [Shapiro] There is much that remains to be learned about the evolutionary process. Many problems remain without known solutions. But the sources of genome variation, including rapid changes throughout the genome, are no longer mysterious. We can describe how dozens of them occur in detail, down to the level of individual phosphodiester linkages in novel DNA structures.

    [Weiss, reviewing Nei] Nei challenges the widely if often reflexively held view that natural selection is the fine-tuning process that accounts for the traits of organisms. This classical Darwinian view holds that there is always enough standing genomic variation that, when the environment changes, a species can adapt to it. However, through the years prominent geneticists, including Nei, have argued that mutation rather than selection is the driver of evolution.

    Neither is arguing that there is any “mystery.” What BOTH are arguing is that large-scale mutation events are necessary (or at least more responsible) for the emergence of new phenotype traits and speciation rather than incremental change guided by selection.

    BOTH agree that mutations are the results of non-deterministic processes, what you attempt to dismissively label “accidents and errors.” Nei specifically cites gene duplication, which is a replication error, as a mutation which enables major phenotypic change.

  648. steve12on 12 Oct 2016 at 1:16 pm

    Dr. TheTroll:

    “That is pure idiocy.”

    HA HA HA!!!! Oh boy. You are outdoing yourself, do you know that kid?

    Hypothetical experiments and brainstorming experimental approaches is “idiocy”???

    HA!!!!!!!!

    The guy who says we know nothing about anything is ALSO against moving toward FINDING OUT???

    Oh, that is good.

    “Experts have been working on this for decades, and they do not have a simple experiment.”

    I said experiment or (series of experiments) with NO TECHNICAL CONSTRAINTS. Real reseachers have MANY constraints. E.G., if you wanna put the same bacteria on two different PLANETS (we’ll call one Crest and the other BrandX) with different conditions and come back in a billion years, you can do that. You can DO whatever you want.

    It’s an EXERCISE in BRAINSTORMING you buffoon. But because I insist that you state it in a formal scientific way, you can’t participate, especially after the toothpaste fiasco.

    “No I am not working on your stupid assignments that do not make any sense. I am showing what some highly qualified evolution researchers have found.”

    Of course you’re not – you’re incapable!

    HA HA HA!!!!

    #BrokeTheTroll

  649. hardnoseon 12 Oct 2016 at 1:29 pm

    The Crest TV commercial is often used as an example in intro to research methods classes. But you are too bone-headed ignorant to get the joke.

  650. Steve Crosson 12 Oct 2016 at 1:39 pm

    hardnose,

    Every single time you open your mouth, you highlight your ignorance, lack of education and inability to think clearly. The Crest thing is a stupidly unfunny joke and a lame attempt to deflect attention from the fact you can’t meet steve12’s challenge.

    You often reference Wikipedia. You can do yourself a big favor and save even more embarrassment if you look up the following terms:

    [Confirmation Bias]

    It is obvious that you are ONLY searching for evidence that agrees with your current beliefs. You are making no effort at all to try to understand the other side of the question. You can’t even give an accurate description of the modern synthesis because you have never even tried to find out what it is or what evidence supports it.

    [Cherry Picking]

    You ONLY look for statements and phrases that you think will support your beliefs. And you can’t even do that well. It’s obvious that you don’t have the education or critical thinking skills to even understand your own “evidence”. Almost without exception, every single thing you post either says the opposite of what you believe it says or else is not related at all to the topic.

    [Argument from Ignorance]

    You continually claim that there is no evidence for the modern synthesis with the implication that your beliefs are more plausible. WRONG. Even IF there was no evidence in support of the modern synthesis, it still wouldn’t mean that Shapiro or Nei or anyone else is correct. The only thing that would prove them correct is supporting evidence — which you have often admitted does not exist.

  651. hardnoseon 12 Oct 2016 at 1:42 pm

    “Neither is arguing that there is any “mystery.” What BOTH are arguing is that large-scale mutation events are necessary (or at least more responsible) for the emergence of new phenotype traits and speciation rather than incremental change guided by selection.”

    They are not talking about any mysteries. They also are not claiming to explain why evolution happens. BOTH are saying that evolution cannot be explained by natural selection. That is what I have been saying, and what most of you here have been denying.

    “BOTH agree that mutations are the results of non-deterministic processes, what you attempt to dismissively label “accidents and errors.” Nei specifically cites gene duplication, which is a replication error, as a mutation which enables major phenotypic change.”

    You are so completely wrong. I never said mutations result from deterministic processes, and I never said Shapiro or Nei said that. Shapiro says that cells can modify their DNA in response to environmental challenges. You leave out everything important from your statements.

    You are not capable of reading and processing information accurately chikoppi. You are just not capable of it.

  652. hardnoseon 12 Oct 2016 at 1:45 pm

    “Even IF there was no evidence in support of the modern synthesis, it still wouldn’t mean that Shapiro or Nei or anyone else is correct.”

    There is no evidence that natural selection explains evolution. That’s what I have been saying, and that is what Nei and Shapiro have both said.

    I have been saying that over and over in all these hundreds of comments, but you don’t get it. And I have shown that a leading expert says the same thing, and you still can’t get it.

  653. steve12on 12 Oct 2016 at 1:54 pm

    Speaking of the toothpaste thing….

    Ya know, Dr. TheTroll, I never got a reply to my correction of the now infamous toothpaste experiment here:

    # steve12on 09 Oct 2016 at 5:54 pm

    Why?

  654. steve12on 12 Oct 2016 at 1:57 pm

    I get it: when things aren’t breaking your way you just ignore. Kind of how you review the literature.

    Well, what passes for the literature for you: HuffPo science and Discovery magazine, pop-science for held-back fourth graders

  655. chikoppion 12 Oct 2016 at 2:53 pm

    [hardnose] They are not talking about any mysteries. They also are not claiming to explain why evolution happens. BOTH are saying that evolution cannot be explained by natural selection. That is what I have been saying, and what most of you here have been denying.

    Here is what you claimed…

    [hardnose] Nei and Shapiro do NOT claim to know what the driving force of evolution is. They have been studying the mechanisms involved. They do not have the arrogance to think they have it all figured out.

    Nei (as reported by Weiss) expressly claims to know that the “driving force” of evolution is mutation and immediately thereafter provides his rationale for making that claim.

    Shapiro openly mocks the idea that genetic processes that result in novel traits are not well understood. He does NOT claim to “not know why evolution happens,” but rather speculates that “perhaps natural genetic engineering plays a more important role than natural selection.”

    [hardnose] You are so completely wrong. I never said mutations result from deterministic processes, and I never said Shapiro or Nei said that. Shapiro says that cells can modify their DNA in response to environmental challenges. You leave out everything important from your statements.

    You have repeatedly derided modern synthesis by suggesting that it relies on mutations produced from “accidents and errors.” You have repeatedly insinuated that Nei, Shapiro, or both disagree with the mechanistic principles of modern synthesis. They do not. The mechanisms they cite are the same mechanisms. If the mutations that modern syntheses recognizes are “accidents and errors” then so too are those cited by Nei and Shapiro.

    YOU attempt to construct an argument for a position by insinuating facts that do not exist and making willful mischaracterizations of both the position you are arguing against and the quote-mined parcels you profer up.

    To reiterate my prior statement…

    Neither is arguing that there is any “mystery.” What BOTH are arguing is that large-scale mutation events are necessary (or at least more responsible) for the emergence of new phenotype traits and speciation rather than incremental change guided by selection.”

    That’s it. Modern synthesis recognizes these mechanisms and mutation events. They are part of the theory. The question being debated is 1) whether or not such events are necessary for phenotype change, 2) whether incremental phenotype change is possible without such events, and (assuming the answer to 2 is ‘yes’) 3) what is the relative contribution of large-scale mutation vs. incremental change guided by selection.

  656. hardnoseon 12 Oct 2016 at 3:37 pm

    “Nei (as reported by Weiss) expressly claims to know that the “driving force” of evolution is mutation and immediately thereafter provides his rationale for making that claim.”

    He says mutations cause evolution, but he does not say what causes mutations.

  657. hardnoseon 12 Oct 2016 at 3:39 pm

    You are brainless chikoppi and you consistently miss the point.

    If natural selection is not the organizing force of evolution, then something else is. And no one knows what that is.

    Dawkins and Coyne claim to know what the organizing force of evolution is. But there is no evidence for their claim.

    So shut up.

  658. BillyJoe7on 12 Oct 2016 at 4:12 pm

    hardnose lecturing chikoppi is like an ant lecturing Einstein.

    So, so funny 😀

    http://i0.kym-cdn.com/entries/icons/original/000/015/725/url-3-10tjli1.jpeg

  659. Steve Crosson 12 Oct 2016 at 4:20 pm

    hardnose,

    Some facts:

    You have NO idea what the modern synthesis actually says, and couldn’t understand it if you did.

    ALL of your evidence fully supports the modern synthesis and is actually PART of it.

    NONE of your evidence supports direction, guidance, non-randomness, increased complexity or any other of your weasel word definitions.

    NONE of us here are gullible or stupid enough to make the same mistakes interpreting evidence that you do.

    This has been true for years and is extremely unlikely to change in the future. If it is really that important for your self image to pretend that you are right, then you will have much better luck if you find a web site with lower standards of evidence. Find one that accepts subluxations, big foot, ancient aliens and stuff like that. You’ll fit right in and your ego will finally be stroked.

  660. Steve Crosson 12 Oct 2016 at 4:27 pm

    BJ7,

    I think you are being unfair to ants. They are capable of some pretty amazing engineering feats.

    Not to mention the song about the ant and the rubber tree plants (which probably most of you are too young to remember).

  661. chikoppion 12 Oct 2016 at 4:37 pm

    [hardnose] He says mutations cause evolution, but he does not say what causes mutations.

    Are you seriously claiming that Nei, a molecular biologist, doesn’t claim to know how genetic mutations occur? His entire book is premised on the evidence that he knows how genetic mutations occur. Again, Shapiro mocked someone who tried to insinuate that molecular processes in genetics were not well understood.

    Yes, both Nei and Shapiro claim to know, in exacting detail, what causes mutations. That is the premise of their field and foundation of their argument(s).

    [hardnose] If natural selection is not the organizing force of evolution, then something else is. And no one knows what that is. Dawkins and Coyne claim to know what the organizing force of evolution is. But there is no evidence for their claim.

    Nei claims to know. In fact, you just said: “he says mutations cause evolution.”

    Here, let me help you with more correct language:

    [Weiss, on Nei] However, through the years prominent geneticists, including Nei, have argued that mutation rather than selection is the driver of evolution. The reasoning is basically that at any given time the complex integration of genomic mechanisms has been molded by eons of adaptive selection and cannot be changed much without being harmful. Major phenotypic change can arise only after the occurrence of rare “constraint-breaking” mutations that escape the established mold.

    So is Nei wrong to claim he knows that “mutation rather than selection is the driver of evolution?”

    He makes that assertion because he claims to know what causes mutations, especially that he claims to know what causes the types of mutations responsible for “major phenotypic change.”

    [hardnose]So shut up.

    Just imagine my dismay.

  662. BillyJoe7on 12 Oct 2016 at 4:41 pm

    Yes, I’m sorry, I apologise to the ants, they are like Einstein compared with our little pipsqueak here

  663. Steve Crosson 12 Oct 2016 at 4:48 pm

    Ants are certainly much better at understanding and dealing with reality.

  664. steve12on 12 Oct 2016 at 5:10 pm

    Can you imagine how stazy (not sure if he’s stupid or crazy, but I actually think the latter) you have to be to argue that NS doesn’t contribute much to evolution?

    Yes, there’s the lab evidence in every organism that we can test this with in relatively small time periods.

    But it also has-to-be for the simplest of reasons:

    1. Genes get passed on from progenitor to progeny
    2. You can only fuck if you’re alive
    3. Time goes in one direction, so 1&2 are iterative and cumulative.

    This idiot is essentially arguing about these points!

    But this is the beauty of out resident Troll. He flip-flops on NS like Trump re: the Iraq War. He’ll say”Of course NS impacts evolution!”. But then he’ll say it doesn’t, then he’ll tell Chikoppi to “shut up” for arguing that the only debate is the relative contribution of the forces.

    It’s all so stupid.

  665. steve12on 12 Oct 2016 at 5:11 pm

    Can you imagine how stazy (not sure if he’s stupid or crazy, but I actually think the latter) you have to be to argue that NS doesn’t contribute much to evolution?

    Yes, there’s the lab evidence in every organism that we can test this with in relatively small time periods.
    But it also has-to-be for the simplest of reasons:

    1. Genes get passed on from progenitor to progeny
    2. You can only f^ck if you’re alive
    3. Time goes in one direction, so 1&2 are iterative and cumulative.

    This idiot is essentially arguing about these points!

    But this is the beauty of out resident Troll. He flip-flops on NS like Trump re: the Iraq War. He’ll say”Of course NS impacts evolution!”. But then he’ll say it doesn’t, then he’ll tell Chikoppi to “shut up” for arguing that the only debate is the relative contribution of the forces.
    It’s all so stupid.

  666. chikoppion 12 Oct 2016 at 5:41 pm

    Eh. To be fair, both Shapiro and Nei have interesting observations.

    Shapiro’s position is much softer than Nei. He just says, ‘Look, there are these mechanisms capable of producing significant mutations. Might they not be a greater contributor to the emergence of new traits than a process of incremental steps over time?’

    Nei takes a far more inflexible position. He pretty much says significant changes to the phenotype can’t happen unless they happen all at once. That doesn’t necessarily result in speciation, but it would be the origin of any trait that requires change in more than a single gene sequence.

    Yes, Nei does identify the mechanisms or causes of these types of mutations.

    When either of these guys talk about ‘natural selection’ they’re referring to it in the classical sense of a slow accumulation of mutations within a population leading to the emergence of a new trait. I don’t think either denies natural selection occurs, they just question how probable it is that novel traits could arise by a culumulative process (Shapiro: ‘somewhat,’ Nei: ‘not at all.’)

    Both of them acknowledge the role of ‘selection’ acting upon individual mutations. Shapiro flat-out states that the mutations resulting from NGE are immediately subject to selection. Nei states that only upon rare occasion is a significant mutation not harmful to the organism, which is again ‘selection’ determining which mutations survive to contribute to evolutionary processes.

  667. hardnoseon 12 Oct 2016 at 5:43 pm

    I have been saying that there is no evidence for the idea that natural selection is the driving force of evolution.

    I have found expert researchers who say the same thing.

    That is what this whole argument has been about.

    You can’t see it. It is just incredible that you can’t see something that obvious and simple.

    Dawkins and Coyne, and Lenski and Novella, and all of you, cannot show any evidence that natural selection is the driving force of evolution. You just believe it, for no real reason.

    I have been very patiently trying to explain it to you. But you are not able to think logically.

  668. bachfiendon 12 Oct 2016 at 5:49 pm

    I’ve always regarded ‘the driving force of evolution’ to be environmental change ( which includes climate change and alterations in other species – competitors, predators and prey).

    So this morning I decided to google ‘driving force of evolution’ (actually I Yahoo’d it, because I’m currently in Beijing, and the Chinese for some reason don’t like google) and the first hit was for an article from 2010 in which Liverpool researchers provide evidence that the driving force is the interaction between species, for example bacteria and their viruses, that’s the ‘driving force’ as an illustration of the Red Queen Hypothesis.

    Which sort of agrees with my definition.

    So, evolution is perfectly well explained by:

    The cause (or driving force) of evolution is environmental change, acting on

    Natural variation within populations, which may be increased by mutations,

    And with natural selection winnowing out the deleterious variants and favouring the ‘fitter’ ones.

    There’s no real controversy concerning the basic cause or mechanisms of evolution.

    There’s no good current explanation for major evolutionary changes, such as the formation of the first eukaryote 2 billion years ago or the first multicellular eukaryote around 700 million years ago. The first primitive fusion of a eubacterium and an Archaea bacterium to form the first eukaryote had to provide some sort of advantage over prokaryotes, but what it was and where it arose, and under which conditions, is a mystery.

    I wonder if it’s one of Nei’s rare constraint breaking mutations? Forming eukaryotes certainly does seen rare. There were bacteria for at least 1.8 billion years before it happened. And it apparently happened just once(although there are tantalising hints that it may have happened on more than one occasion, as discussed in Nick Lane’s ‘the Vital Question’)

  669. bachfiendon 12 Oct 2016 at 5:56 pm

    Hardnose,

    ‘I have been saying that there is no evidence that natural selection is the driving force of evolution’.

    Agreed. Natural selection isn’t the driving force of evolution. It’s a mechanism.

    You persist in constructing a straw man argument no one actually accepts.

    You’re extremely tiresome. And boring.

  670. hardnoseon 12 Oct 2016 at 7:58 pm

    “There’s no real controversy concerning the basic cause or mechanisms of evolution.”

    There are real controversies.

    You said the basic cause is a changing environment. But what you are really saying is the same thing Dawkins says. The environment changes, and individuals that happen by chance to have the right mutations survive better and reproduce more.

    That is just another way of saying that natural selection is the driving, or organizing, force.

    But there is no evidence that evolution happens that way. Nei and Shapiro both deny that natural selection is an important force in evolution.

    Dawkins says that life on earth appears to have been designed, and that it cannot be the result of chance. I agree with him on that point. He says that although mutations happen by chance, natural selection imposes order and design. He has no evidence for this opinion, but it has been widely accepted anyway.

    Other evolutionary biologists disagree with Dawkins. But if natural selection is not the organizing force, then what is? Why does life appear designed if it evolved by chance?

    Shapiro leaves that question open. He observes intelligent processes going on in cells, but he doesn’t speculate on where that intelligence came from.

    Nei doesn’t seem to address the problem. He feels certain that natural selection is unimportant, and that mutation drives evolution.

    So there definitely is controversy and confusion.

    And most of the world is completely unaware of the depth and importance of this controversy. The public evolution debates don’t usually go anywhere near it.

    When Steve Novella posts about evolution, he only considers neo-Darwinism vs Christian creationism. Christian creationism is naive and easy to demolish. But neo-Darwinism is, in a very different way, also a naive over-simplification.

    Nei says that Christian creationists and neo-Darwinists are very similar. Creationists say “God did it,” and neo-Darwinists say “Natural selection did it.” Neither can provide evidence or logic to back up their belief.

    But what does Nei think causes the mutations that he says cause evolution? Does he agree with the neo-Darwinists that they are accidents? But that would be saying that life on earth is simply a product of random accidents. Even Dawkins the atheist thinks that is impossible.

    Systems biology says that natural systems evolve toward greater complexity. They do not pretend to know why. Nei believes that life has evolved towards greater complexity (the system overall, not every species). So maybe Nei has been influenced by systems biology. Don’t know yet.

  671. Steve Crosson 12 Oct 2016 at 8:42 pm

    hardnose,

    Don’t be coy. Everyone here knows that the ONLY reason you are insisting that there is something special in place of or in addition to NS is because you are trying to support your own pet theory of guided evolution/smart universe nonsense. There is no point in pretending you don’t have an agenda.

    You have no interest in an honest discussion and you certainly don’t care about (and wouldn’t understand) the details as long as there is enough uncertainty for you to believe in your magical hypothesis.

  672. bachfiendon 12 Oct 2016 at 9:11 pm

    Hardnose,

    Just because Richard Dawkins says something doesn’t make it necessarily wrong.

    It’s common sense that the driving force of evolution is environmental change.

    You’ve now gone and introduced a new term ‘organising force’ and equated it to ‘driving force’. I’ll accept ’cause’ and ‘driving force’ to be synonyms, but ‘organising force’ isn’t a synonym for either. As an analogy, the ‘driving force’ of a car is its motor. The ‘organising force’ is its gears and steering wheel.

    Natural selection is two steps away from the driving force of evolution- environmental change. Regardless of whether the natural variation in populations is due to random or non-random mutations (and mutation carries a lot of emotional baggage implying that it’s usually not to be desired; genetic change would be a better term), natural selection still doesn’t become a driving force of evolution.

    If you think that systems biology states that natural systems evolve towards greater complexity then either 1. Systems biology is wrong or 2. Your interpretation of systems biology is wrong.

    Based on your past performance, I’d pick possibility (2).

  673. chikoppion 12 Oct 2016 at 9:38 pm

    Why does life appear designed if it evolved by chance?

    Sharpshooter fallacy. (I wish I could make this text blink!)

    What would life look like if it didn’t appear designed? We only see the remains of the carnage. All the mutations that didn’t work, all the species that didn’t adapt, all the random evolutionary mishaps, those get erased. They weren’t “designed.” We’re here because we’re decendents of the <1% of random evolutionary "accidents and errors" that survived.

    This is the same fallacy that drives the illusion of "intelligence" in nature. What Shapiro refers to as "intelligent" mechanisms are, unsurprisingly, those mechanisms that usually work. Why would genomic mechanisms that didn’t work persist or proliferate? Who is counting the genetic mishaps that mangle DNA and never get replicated?

    Nei comes right out and says that genomic mechanisms are the product of selection (meaning the untold number of “accidents and errors” that didn’t successfully compete or replicate were deleted).

    [hardnose] But what does Nei think causes the mutations that he says cause evolution? Does he agree with the neo-Darwinists that they are accidents?

    Yes. In that context of usage, yes. Nei states 1) that the mechanisms which regulate genes are the product of selection, 2) that mutations of “large effect” are most likely to be harmful, 3) that substantial mutations which are not harmful occur “occasionally” in the data (for which he specifically cites the example of a replication error).

    [Weiss, reviewing Nei] The reasoning is basically that at any given time the complex integration of genomic mechanisms has been molded by eons of adaptive selection and cannot be changed much without being harmful. Major phenotypic change can arise only after the occurrence of rare “constraint-breaking” mutations that escape the established mold.

    […] Because developmental processes involve many interacting genes, a mutation of large effect is most likely to disrupt the system—for example, to cause serious disease. But genomic data have also shown that more substantial mutations, such as redundancy generated by gene duplication, that can enable new function to evolve do occasionally arise.

    [hardnose] Systems biology says that natural systems evolve toward greater complexity.

    Closed systems increase in entropy. OPEN systems will increase in courseness (decrease in entropy) so long as the energy input is greater than heat lost from the system. This is thermodynamics and it’s not a mystery.

    Take away radiation from the sun and watch how fast “organic complexity” falls.

    But there is no evidence that evolution happens that way. Nei and Shapiro both deny that natural selection is an important force in evolution.

    I debated adding this last bit, because I see no substantive conflict between traits that emerge gradually and those that result from large-scale mutations. Both are ultimately the result of non-deterministic processes and subject to selection. But you keep asking, so here you go…

    New Evidence That Natural Selection Is A General Driving Force Behind The Origin Of Species
    https://www.sciencedaily.com/releases/2006/02/060224090021.htm

    Parallel Speciation by Natural Selection
    https://www.jstor.org/stable/2463062?seq=1#page_scan_tab_contents

    Evidence for evolution in response to natural selection in a contemporary human population
    http://www.pnas.org/content/108/41/17040.full

    Natural selection on protein-coding genes in the human genome
    http://www.nature.com/nature/journal/v437/n7062/abs/nature04240.html

    Evidence for natural selection in the HAVCR1 gene: high degree of amino-acid variability in the mucin domain of human HAVCR1 protein.
    https://www.ncbi.nlm.nih.gov/pubmed/15889130

    Evidence that natural selection maintains genetic variation for sleep in Drosophila melanogaster
    http://bmcevolbiol.biomedcentral.com/articles/10.1186/s12862-015-0316-2

    Testing Natural Selection with Genetics: Biologists working with the most sophisticated genetic tools are demonstrating that natural selection plays a greater role in the evolution of genes than even most evolutionists had thought
    https://www.scientificamerican.com/article/testing-natural-selection/

    Isolating a Role for Natural Selection in Speciation: Host Adaptation and Sexual Isolation in Neochlamisus bebbianae Leaf Beetles
    http://www.jstor.org/stable/2411347?seq=1#page_scan_tab_contents

    Divergent natural selection drives the evolution of reproductive isolation in an Australian wildflower
    http://onlinelibrary.wiley.com/doi/10.1111/evo.12994/full

  674. chikoppion 12 Oct 2016 at 9:42 pm

    Crap. I just posted a reply and because it contained a number of links it got stuck in moderation.

    If it doesn’t appear by tomorrow I’ll repost without the links.

  675. BillyJoe7on 12 Oct 2016 at 11:38 pm

    You could copy your original post and paste into two or more separate posts ensuring none of them contains more than three links. If you wait till tomorrow no one will see it because the conversation will have moved on.

  676. Steve Crosson 13 Oct 2016 at 8:27 am

    I think we need some new moderation rules:

    1). Anything chikoppi posts goes up immediately.

    2). Anything hardnose posts with more than three words goes into moderation for a few decades to see if his future science ever comes true.

  677. hardnoseon 13 Oct 2016 at 8:55 am

    chikoppi, thanks for posting evidence for natural selection, we really needed that. After I said about a thousand times THERE IS EVIDENCE FOR NATURAL SELECTION.

    There is NO evidence for the neo-Darwinist claim that natural selection is the organizing force (or whatever you want to call it today, I am using Dawkin’s term) of evolution.

  678. Steve Crosson 13 Oct 2016 at 9:20 am

    Hardnose,

    You are mind-bogglingly stupid. Even if you didn’t read or can’t understand chikoppi’s links, the titles alone make it clear that there is a LOT of evidence that NS is an organizing and guiding force of evolution.

    Your only play is to claim that the evidence is wrong. Only an idiot would deny the existence of something right under his nose.

    So go ahead. Let’s see your evidence that everyone chikoppi referenced is wrong. This should be fun. You haven’t got the faintest idea of what Shapiro or Nei is really saying. I can hardly wait to hear your interpretation of chikoppi’s links.

  679. mumadaddon 13 Oct 2016 at 9:57 am

    hn,

    I’m about to blow your mind… Richard Dawkins actually has his own website, AND it has a comments section.

    If you’re so bent on arguing with Richard Dawkins perhaps you should go haunt that site.

  680. bachfiendon 13 Oct 2016 at 11:08 am

    Hardnose,

    ‘Driving force of evolution’ is most certainly NOT the same as ‘organising force of evolution’.

    Your desperate attempt to make them equivalent terms is just another example of your obfuscation.

    Environmental change is the driving force of evolution. It’s the cause.

    Natural selection is a mechanism of evolution. It’s a guiding force of evolution directing the course of evolution along the paths leading to increased reproductive success.

    There’s plenty of evidence that natural selection is an important guiding force of evolution (I suppose it could also be described as an ‘organising force’). Even you agree that natural selection exists and favours adaptive changes.

    Natural selection doesn’t cause anything. It’s not a driving force of evolution.

  681. hardnoseon 13 Oct 2016 at 11:33 am

    “is a LOT of evidence that NS is an organizing and guiding force of evolution.”

    Why does Nei say that there isn’t any? People often think evidence for NS is the same thing as evidence that NS is the organizing guiding force of evolution. It is not the same thing at all.

  682. hardnoseon 13 Oct 2016 at 11:36 am

    “Environmental change is the driving force of evolution. It’s the cause.”

    You don’t understand causality at all. I explained this already. There can be multiple causes. Some causes can be necessary, others can be sufficient. It is ridiculous to insist there is only one cause of evolution. You are probably the only one who says it.

  683. hardnoseon 13 Oct 2016 at 11:37 am

    “Natural selection doesn’t cause anything. It’s not a driving force of evolution.”

    According to Dawkins and Coyne, it is.

  684. steve12on 13 Oct 2016 at 11:46 am

    I know Dr. The Troll didn’t need to be destroyed re: content, but holy shit:
    # chikoppi on 12 Oct 2016 at 9:38 pm

    But honestly, Dr. TheTroll, your response is why everyone hates you rather than just disagree with you.

    You have changed your position on natural selection over the course of this thread (and the one before)1000 times. Natural selection is whatever you need it to be to in order for you to gain rhetorical advantage at the moment.

    THIS is why everyone thinks you’re a dick. THIS is why I call you a liar.

  685. Steve Crosson 13 Oct 2016 at 11:53 am

    I would accuse hardnose of playing semantic word games, but he’s not that smart. He has never been able to clearly define what he means by any of the words he throws around, except to insist that they always mean whatever he thinks will best support his point.

    Regardless of what we call it, Natural Selection is a significant and necessary component of evolution. Without something actively removing harmful or less successful mutations/variations from the gene pool, there could be no possibility of the appearance of design. All variation would be reincorporated into the genome and diversity could not happen.

    Even Nei’s dramatic changes must survive the filter of NS. In any event, there is no reason to care what ANYONE’s opinion is on NS. It is a Red Herring.

    The ONLY thing that will support hardnose’s basic premise is actual evidence that mutations are NOT random! No one except hardnose has ever claimed that, and hardnose has never been able to provide one bit of evidence to support it.

  686. steve12on 13 Oct 2016 at 12:11 pm

    Steve C.

    “I would accuse hardnose of playing semantic word games, but he’s not that smart. He has never been able to clearly define what he means by any of the words he throws around, except to insist that they always mean whatever he thinks will best support his point.”

    I actually disagree with this. I’m not saying he’s brilliant or anything, and he obviously is ignorant of this literature (et al.), but I see clear intent in his changing goal posts, leaving terms vague, etc.

    As just one (of many) examples, go back to his refusal to define “materialism” for literally years. He only defined it when people started ignoring him, and then stopped using the term in accordance w/ his own definition as soon as people paid attention again.

    That’ s not borne of dim wit, that’s being a dick.

  687. Steve Crosson 13 Oct 2016 at 12:15 pm

    “That’ s not borne of dim wit, that’s being a dick.”

    Why not both?

    There’s plenty of evidence in support of both propositions.

  688. steve12on 13 Oct 2016 at 12:33 pm

    Fair enough, they’re not mutually exclusive!

  689. hardnoseon 13 Oct 2016 at 2:39 pm

    “The ONLY thing that will support hardnose’s basic premise is actual evidence that mutations are NOT random! No one except hardnose has ever claimed that”

    Shapiro says they are not random. He disagrees with neo-Darwinism, and said so explicitly.

    As far as I know, Nei doesn’t say if he thinks they are random or not. But he does say that natural selection is not important. So if mutations were random and natural selection is not important, evolution would be a mostly random process. And that is not probable, or even possible. Even Dawkins would say it would not be possible for a completely, or mostly, random process to result in the evolution that has occurred.

    Evolutionary biologists have to be careful what they say, because they don’t want to be accused of supporting intelligent design.

  690. Steve Crosson 13 Oct 2016 at 3:21 pm

    Let’s start with the stupidest comment first:

    Evolutionary biologists have to be careful what they say, because they don’t want to be accused of supporting intelligent design.

    LOTS of people (e.g. Behe, Egnor) would happily support intelligent design — IF they could ever find any proof. In addition, every other sane researcher would just as readily accept credit for any Nobel worthy, paradigm shifting discovery, regardless of what it was.

    Shapiro says they are not random. He disagrees with neo-Darwinism, and said so explicitly.

    Shapiro says that cells have mechanism in place to help ensure that mutations are not completely random (and thus unrecognizable as DNA), but he freely admits (and this quote has been pointed out to you many times) that NS is required to determine which mutations are successful — because they are random with respect to the needs of the host.

    Shapiro disagrees with his straw man (and incorrect) version of the modern synthesis.

    As far as I know, Nei doesn’t say if he thinks they are random or not. But he does say that natural selection is not important. So if mutations were random and natural selection is not important, evolution would be a mostly random process. And that is not probable, or even possible. Even Dawkins would say it would not be possible for a completely, or mostly, random process to result in the evolution that has occurred.

    Which proves you don’t understand what either of them is saying. Nei explicitly says that NS is needed to weed out the unsuccessful mutations. Dawkins explicitly says that NS is what gives the appearance of design.

    Back to the point. Regardless of what you or anyone else thinks, NS is real and it plays a role. The ONLY question is whether it is all that is necessary or just some of it.

    Still waiting for actual proof that mutations are directed somehow. This NS smokescreen is just a particularly pathetic argument from ignorance.

  691. bachfiendon 13 Oct 2016 at 5:27 pm

    Hardnose,

    Care to link to anything where Jerry Coyne or Richard Dawkins has specifically stated that they believe that natural selection is ‘a driving force’ of evolution? Or are you just making stuff up again, putting words into other people’s mouths, confabulatimg as usual.

    I know Richard Dawkins has referred to natural selection as a ‘guiding force’. I doubt that Jerry Coyne would have used ‘driving force’ either.

  692. hardnoseon 13 Oct 2016 at 10:53 pm

    “he [Shapiro] freely admits (and this quote has been pointed out to you many times) that NS is required to determine which mutations are successful — because they are random with respect to the needs of the host.”

    Shapiro NEVER says adaptive mutations are random with respect to the needs of the host. How could you possibly interpret anything he said that way?

    And we all know NS happens. I have said this so many times. Shapiro and Nei know that NS happens. But they don’t consider it important. It just happens because it necessarily has to happen.

  693. hardnoseon 13 Oct 2016 at 10:55 pm

    “Nei explicitly says that NS is needed to weed out the unsuccessful mutations. Dawkins explicitly says that NS is what gives the appearance of design.”

    You do not understand Shapiro or Nei at al.

  694. hardnoseon 13 Oct 2016 at 10:57 pm

    “Back to the point. Regardless of what you or anyone else thinks, NS is real and it plays a role. The ONLY question is whether it is all that is necessary or just some of it.”

    That question is of CENTRAL importance. Dawkins thinks NS is all-important. Nei and Shapiro think it does not in any way explain evolution.

    The question is at the center of the whole evolution controversy, and you try to minimize it. Because you don’t understand any of this.

  695. bachfiendon 14 Oct 2016 at 3:36 am

    Hardnose,

    This is getting tedious. You keep on claiming that the conventional wisdom regarding evolution is that natural selection is the cause of evolution. That it is the driving force of evolution. That it ‘explains’ evolution.

    And you persist in claiming that it’s wrong because you want mutations to be non-random, directed and beneficial to the needs of the organism, so as to eliminate the degree of chance and contingency involved in evolution.

    No one believes that natural selection is the cause of evolution. It’s a mechanism of evolution. It’s a guiding force of evolution, not a driving force.

    I’ve challenged you to provide evidence that either Richard Dawkins or Jerry Coyne believe that natural selection is a driving force of evolution, and you haven’t done so.

    You further state that you believe that Shapiro and Nei play down the role of natural selection in evolution, despite all the evidence to the contrary in their writings. With again, the straw man argument that neither ‘thinks’ natural selection explains evolution.

    Which is true enough. Natural selection doesn’t explain evolution, but it certainly severely constrains it. And not explaining evolution doesn’t mean that natural selection isn’t very important, as Richard Dawkins believes.

  696. Steve Crosson 14 Oct 2016 at 9:59 am

    “he [Shapiro] freely admits (and this quote has been pointed out to you many times) that NS is required to determine which mutations are successful — because they are random with respect to the needs of the host.”
    Shapiro NEVER says adaptive mutations are random with respect to the needs of the host. How could you possibly interpret anything he said that way?

    hardnose,

    You really are dense. IF the mutations/variations WEREN’T “random with respect to the needs of the host”, there would be NO NEED for Natural Selection. Your hypothesized guided/directed/smart mutation would be all that is necessary.

    But, as I have said repeatedly, the relative importance of NS is irrelevant to the question at hand. Even if NS played no roll at all, it still doesn’t mean that your particular hypothesis is automatically true. Until you have evidence for one specific explanation, it could be anything at all.

    So let’s hear your evidence!!

    You’ve already failed to meet steve12’s challenge, so let’s make it even easier. You have already claimed that there is evidence for directed mutations, so show us the evidence. You don’t have to design an experiment. Simply point out one of the already existing experiments that prove the existence of directed mutations.

    This should be drop-dead simple. Find a supporting experiment and explain why it is good evidence. No need to do all the hard work of design. All that will already be done. Just explain the null hypothesis, whether they have proven or disproven it, and the level of statistical significance.

    Like I said, easy-peasy. No design work needed at all. Just a simple explanation of an experiment that supports your hypothesis and why we should believe it.

    You can do that easily, right? Because if you can’t, then it proves conclusively that either no evidence exists or else you are incapable of understanding if it is reasonable to accept it as good evidence.

    Prove you actually know what you are talking about.

    #BrokeTheTroll #ShowYourEvidence

  697. hardnoseon 14 Oct 2016 at 12:42 pm

    If it was so easy, someone would have done it. Obviously. The research has been going on for decades. It is an extremely complex problem, both scientifically and philosophically.

  698. hardnoseon 14 Oct 2016 at 12:52 pm

    If you believe adaptive mutations are non-directed (“random”), then it follows that natural selection is the creative, organizing, force of evolution. That is exactly what Dawkins says.

    But some leading researchers believe natural selection is an unimportant factor in evolution.

    If you combine the idea that adaptive mutations are “random” with the idea that natural selection is NOT important, the conclusion is that evolution is a “random”, accidental, process.

    I don’t see how anyone can believe that evolution happened by chance. No amount of time would be adequate for that to happen. It is not mathematically possible. That is why Dawkins is so emphatic about saying natural selection is the guiding, organizing, factor.

    Yes, I do believe nature has some kind of intelligence. Because that is what the evidence indicates. I am NOT a Christian, I do not have any particular religious beliefs. I am only looking at the evidence.

    The evidence is confusing and most people misunderstand the terminology. The question of what caused life to evolve is still very much open.

  699. Steve Crosson 14 Oct 2016 at 1:32 pm

    If it was so easy, someone would have done it. Obviously. The research has been going on for decades. It is an extremely complex problem, both scientifically and philosophically.

    But wait!! You’ve said earlier that Shapiro had evidence of non-random mutations. Is that not true?

    Yes, I do believe nature has some kind of intelligence. Because that is what the evidence indicates.

    But you are completely unable to point to one single experiment or any evidence at all that supports your belief.

    Sad, very sad … pathetic really. It’s heartbreaking to encounter a victim of Cranial Anal Inversion Syndrome. C.A.I.S. is a cruel disease that robs its victims of the ability to use reason or logic. We need more research to find the cure.

    #BrokeTheTroll #ShowYourEvidence #HelpCureCAIS

  700. hardnoseon 14 Oct 2016 at 1:38 pm

    https://www.theguardian.com/science/2008/feb/09/darwin.dawkins1

    Dawkins quote:

    “Darwin’s big idea explains all of life”

    Dawkins’ description of Darwin’s theory:

    “Given sufficient time, the non-random survival of hereditary entities (which occasionally miscopy) will generate complexity, diversity, beauty, and an illusion of design so persuasive that it is almost impossible to distinguish from deliberate intelligent design.”

    “… the denominator in the explanatory equation is spectacularly small and simple: natural selection, the non-random survival of genes in gene pools”

  701. BillyJoe7on 14 Oct 2016 at 2:13 pm

    Fail, fail, and fail.

    Nowhere in those three quotes does Darwin say that natural selection is the “driving force” of evolution.

  702. BillyJoe7on 14 Oct 2016 at 2:28 pm

    Darwin’s lesson for science in general:

    “There remain deep questions, in physics and cosmology, that await their Darwin. Why are the laws of physics the way they are? Why are there laws at all? Why is there a universe at all? Once again, the lure of “design” is tempting. But we have the cautionary tale of Darwin before us. We’ve been through all that before. Darwin emboldens us – difficult as it is – to seek genuine explanations: explanations that explain more than they”

    So where is your alternative explanation that does not require at least as much explanation as that which it is trying to explain? The Intelligent Designer and The Conscious/Intelligent Universe are both in that category. They both require more explanation than that which they are trying to explain.

  703. Steve Crosson 14 Oct 2016 at 2:35 pm

    hardnose,

    When you don’t actually know the cause of something, you don’t get to just make stuff up. That’s how we wound up with thousands of mutually incompatible religions, homeopathy, chiropractic, etc.

    You are assuming agency but you don’t actually know the cause. That is literally no different than inventing Thor to try to explain lightning. You’re just guessing. And that is all you are doing unless you are able to confirm or disprove your guess/hypothesis with an actual experiment.

    And that is all that Shapiro or Nei or anyone else can do unless they support their speculation with experimental evidence.

    It really doesn’t matter if you believe your hypothesis makes sense (It doesn’t, but that’s a side issue). Even if it did, many, many (probably most) beliefs were once thought to make sense — until we discovered the real cause.

    You may feel that NS/environment/mutations are insufficient to explain evolution, and lots of people (religious or otherwise) agree with you. But, at least for now, there is no evidence for anything else.

    So, until and unless you can provide some evidence, all you are doing is repeating your opinion. You’re welcome to it, but no one cares.

    #BrokeTheTroll #ShowYourEvidence #HelpCureCAIS

  704. hardnoseon 14 Oct 2016 at 4:43 pm

    “So where is your alternative explanation that does not require at least as much explanation as that which it is trying to explain? The Intelligent Designer and The Conscious/Intelligent Universe are both in that category. They both require more explanation than that which they are trying to explain.”

    The “natural selection did it” theory lacks evidence. The evidence we have is that natural selection occurs (how could it not?), but we have no evidence that NS explains evolution.

    An alternative to the “NS did it” theory is “Everything just came together by chance.” I think you have to admit THAT is not scientific or mathematically plausible.

    Another alternative theory is that the universe is made out of information. No, that theory is not simple, and is admittedly way beyond our comprehension.

    So at this moment we don’t have a nice simple comprehensible explanation. As I have said many times at this blog, if we are real skeptics, sometimes we have to admit there is something we do not know.

    Is it scientific to accept an explanation just because it’s simple and you like it? That is why Dawkins accepts the “NS did it” theory.

    Nei is a mainstream evolutionary biologist, and he says neo-Darwinism is just as unscientific as creationism.

  705. BillyJoe7on 14 Oct 2016 at 4:59 pm

    Nope.
    Unless you come up with a better explanation, you’re not doing science, you’re just pissing in the wind.

    (And, by the way, if you have a theory that is “way beyond our comprehension”, you don’t have a theory)

  706. Steve Crosson 14 Oct 2016 at 5:06 pm

    hardnose,

    None of this blather makes your nonsense more likely to be true.

    Most experts think that plenty of evidence supports the modern synthesis.

    You have a wacky belief with ZERO evidence. Deal with it. Go get your subluxations adjusted. Maybe that will cure your CAIS.

  707. chikoppion 14 Oct 2016 at 6:44 pm

    [hardnose] The “natural selection did it” theory lacks evidence. The evidence we have is that natural selection occurs (how could it not?), but we have no evidence that NS explains evolution.

    An alternative to the “NS did it” theory is “Everything just came together by chance.” I think you have to admit THAT is not scientific or mathematically plausible.

    It isn’t “just” selection. It is selection acting upon a variable replicator. It also isn’t “just” chance. It is an initial set of (extremely basic) constraints that are delimited by chemistry, physics, and the environment (availability of chemical components and heat).

    Here’s an experiment that tests those premises in which a minimal chemical replicator is artificially constructed and tested in laboratory conditions:

    Self-Replicating Chemicals Evolve Into Lifelike Ecosystem
    https://www.wired.com/2009/01/replicatingrna/

    [hardnose] Another alternative theory is that the universe is made out of information. No, that theory is not simple, and is admittedly way beyond our comprehension.

    Great. Test it. Construct the theory in a manner that is falsifiable under experimental conditions. To simply say “it must be X because I can’t think of any other reason” is not sufficient. We’ve all heard that a million times over when dealing with apologetics.

  708. bachfiendon 14 Oct 2016 at 9:12 pm

    Hardnose,

    You can’t have it both ways. You can’t have adaptive radiations being random and natural selection being non-important.

    Either adaptive mutations are non-random and natural selection isn’t important, or adaptive mutations are random and natural selection is very important.

    You’re still committing the sharpshooter fallacy – thinking that the current state of Life on Earth with all its current panoply of species has to be explained precisely by a theory for the theory to be valid.

    The precise species existing depends very much on chance, not accident. And numerous extinction events, including the K-P event 65 MYA. At least 99.9% of all species ever living have gone extinct, despite ‘non-random, directed beneficial mutations’ (if they exist, which I doubt).

    The current range of living species might be extremely improbable, but there’s almost an infinite number of different ones possible.

    And as noted on many occasions, Richard Dawkins doesn’t state that natural selection is a driving or creative force. It’s a guiding force. The variations upon which it acts, according to how well they’re fitted to the environment, are created by other mechanisms.

    Natural selection doesn’t ‘explain’ evolution – it’s not the cause of evolution – but it certainly strongly determines where it’s going to go.

  709. hardnoseon 14 Oct 2016 at 11:07 pm

    “Unless you come up with a better explanation, you’re not doing science, you’re just pissing in the wind.”

    No you are wrong, you do not understand science.

    If there is a theory that has no evidence, we do not have to accept it just because we don’t have a better theory.

  710. hardnoseon 14 Oct 2016 at 11:15 pm

    “You have a wacky belief with ZERO evidence.”

    My “wacky” belief is that we don’t know the cause of evolution.

    I think it’s far wackier to believe something when you have no evidence for it.

  711. BillyJoe7on 15 Oct 2016 at 12:42 am

    What’s far wackier is to continually deny the evidence and mechanism for the modern theory of evolution and pump for one without evidence or mechanism and that is “way beyond our comprehension”.

  712. bachfiendon 15 Oct 2016 at 3:22 am

    Hardnose,

    We do know the cause of evolution (and environmental change does include more than one sort of change). It’s extremely ignorant of you to persist in repeating the same fallacious claim.

    And we have plenty of evidence that natural selection is a very important guiding force in evolution.

    You’re attempting to overthrow a well established theory without showing that it’s false. Or that there’s a better theory available.

  713. JJ Borgmanon 15 Oct 2016 at 7:11 am

    Some of us can benefit from this: http://undsci.berkeley.edu/article/howscienceworks_19

    and this: http://www.dictionary.com/browse/semantics

    I am stunned by the willful ignorance displayed on this thread…you know who you are. I suppose there is a reason for keeping comments open, but I think it should be closed. I hypothesize it’s a matter of hit-counts, but lack enough information to theorize that that is the case.

    A disturbing feature of this discourse is the co-mingling of origin-of-life vs evolution-of-life. It is a hip-check to relevant topical conversation. In addition, it should come as no surprise that there is a tremendous amount of non-intelligent affect at work in biology. There is simply reaction. Chemical reaction. It is easy to admit that we do not know how the laws of physics and chemistry were implemented. It is a joy to explore the possibilities. I’m glad people commit their life’s work to that endeavor.

    However, being largely ignorant in these areas, I tend to agree with the “experts”. And ignore the “cranks”. To be Popeyesque: I know what I know and that’s all that I know.

  714. Steve Crosson 15 Oct 2016 at 8:35 am

    hardnose:

    My “wacky” belief is that we don’t know the cause of evolution.
    I think it’s far wackier to believe something when you have no evidence for it.

    Umm … we all believe you when you say that you don’t know the cause of evolution — it’s obvious. But no one really cares. You would simply be one more ignorant person out of billions.

    Nope. Your wacky belief is that “nature has some kind of intelligence. Because that is what the evidence indicates.”

    But you’ve NEVER been able to demonstrate one single shred of this supposed evidence. Therefore, by your own definition, your belief is wacky.

  715. steve12on 15 Oct 2016 at 10:02 am

    Dr. TheTroll:

    “So at this moment we don’t have a nice simple comprehensible explanation. As I have said many times at this blog, if we are real skeptics, sometimes we have to admit there is something we do not know.”

    OK, so (per usual) your whole point is that “we don’t know”.

    So let me get this straight:
    You can post, essentially, “we don’t know, we don’t know, we don’t know” over and over and over, but you refuse to speculate about what type of evidence could lead to knowing?????

    What possible excuse do you have for yourself.

    I ask again: what hypothetical experiment or experiments might lead to settling this?

  716. steve12on 15 Oct 2016 at 10:14 am

    If you set aside everything else, the way he moves the goal posts around re: the definition and role of NS is enough evidence to show that he’s a deliberate liar.

    Add to that that he ignores half the posts!

    Can anyone really think they won a debate by simply refusing to acknowledge the best evidence against them by pretending they didn’t say it?

    It’s just so stupid.

  717. Steve Crosson 15 Oct 2016 at 10:44 am

    JJ Borgman,

    Great link about howscienceworks. It identifies (and explains) pretty much every misconception that hardnose has ever had.

    Now, if only he would read, understand and take it to heart.

  718. BillyJoe7on 15 Oct 2016 at 10:28 pm

    “Great link about howscienceworks”

    Except that there is an error regarding special relativity. 🙁

    “…a person speeding away from Earth in a spacecraft will perceive the distance of the spacecraft’s travel and the elapsed time of the trip to be different than would a person sitting at Cape Canaveral”

    This is actually incorrect as well as being incorrectly stated.
    In the frame of reference of Cape Canaveral, the spacecraft is moving away at speed X, and, in the frame of reference of the spacecraft, Cape Canaveral is moving away at speed X. And the observations that are made about space and time in both frames of reference will be identical.

  719. BillyJoe7on 16 Oct 2016 at 1:09 am

    Don’t get me wrong – in the generalities that website is excellent, but the details are sometimes inaccurate. Above I outlined its inaccuracy in explaining special relativity.
    Here is the website’s inaccurate low down on acupuncture:

    http://undsci.berkeley.edu/article/acupuncture

    In fact, acupuncture is not useful for anything – it is simply an elaborate placebo that “seems” to work for a couple of highly subjective symptoms. But objective tests of these subjective symptoms demonstrate that there is no effect beyond placebo.

  720. mumadaddon 19 Oct 2016 at 6:53 pm

    Aah, evolutionary theory: if we don’t know anything then we don’t know that…

    🙂

  721. hardnoseon 20 Oct 2016 at 6:08 pm

    Too bad none of you were capable of following my logic on this very important topic.

    Why is it important you wonder. Because your theory says that nature cannot possibly be intelligent.

    Why does that matter? Because if you are right, and there is no intelligence in nature, then it should be possible for scientists to understand nature completely, to control it and improve it.

    That would be nice, right? Yes of course, but suppose you are wrong. Then scientists’ attempts to improve on nature might backfire in surprising ways. Maybe in ways that we do not like very much.

    Technology has progressed greatly, making it possible for scientists to “improve” on nature with genetic engineering, for example. Since they believe that nature evolved by an essentially random process (plus natural selection, blah blah blah), then messing with it should not cause any catastrophes. It’s a mess to begin with, after all, a product of chance.

    But if nature is intelligent, and exquisitely complex, then you want to think twice before trying to improve it. You might consider that things are there for a reason, not a haphazard pile of junk.

    Regulatory DNA is an example of something that was considered random junk not long ago. There is still lots of other stuff in DNA that is considered random junk.

    The two philosophies (nature is mindless random garbage vs nature is intelligent) are at odds.

    The general non-scientistific public usually assumes nature is intelligent, and that is one reason most non-scientists are worried about GMOs.

    Our society is deeply divided along various lines, but the nature is intelligent vs the nature is mindless divide is fundamental, and underlies many of the current controversies.

  722. hardnoseon 20 Oct 2016 at 6:10 pm

    And you are all mystified as to why the public often distrusts science.

  723. chikoppion 20 Oct 2016 at 6:55 pm

    [hardnose] And you are all mystified as to why the public often distrusts science.

    No. Not really. It’s generally for some irrational reason like conflating the existence of basic physical laws that govern the interaction of molecules with a sign of disembodied intelligence. That, and a general lack of science literacy combined with a psychological need to invent quasy-mystical notions in an attempt to make sense of a complex world. It’s no surprise that people prefer simplistic narratives and feel threatened when contradicted.

    Besides, it’s obvious that things evolve the way they do because of the transdimensional alien ghosts. No, I can’t prove they’re real, but it makes sense guys! Lots of people believe in ghosts, so it’s totally a valid theory! Some scientists are researching it. You don’t know…what if you’re wrong?!

  724. Steve Crosson 20 Oct 2016 at 7:48 pm

    chikoppi,

    Best.Mike.Drop. Ever.

  725. bachfiendon 20 Oct 2016 at 11:37 pm

    Well, hardnose has gone completely mad and achieved the maximum points for illogical thinking.

    Surely if ‘nature is intelligent’ then it would be capable of pushing back against ill considered human attempts to control it? A cosmic intelligence would surely be capable of righting the damage reckless humans inflict on nature?

    Nature is ‘exquisitely complex’, meaning that it’s extremely difficult ‘for scientists to understand nature completely, to control it and improve it’, but it doesn’t mean that it is ‘intelligent’. Not being able to understand all the details of nature actually means that the precautionary principle kicks it – any suggested intervention in nature has to be considered carefully before proceeding. Actions have a very unfortunate habit of having very unpleasant unexpected consequences, because nature is complex and chaotic, with numerous interconnections between its various elements.

    Hardnose is committing ‘the Lord of the Flies’ fallacy. He imagines that scientists without the delusion that nature is intelligent will behave as badly and as destructively as the children marooned on an island without responsible adults in the novel.

    Natural selection results in apparent design in nature, not a haphazard arrangement of its parts. It gives the illusion of intelligence. Which doesn’t mean that it’s not intelligible.

  726. BillyJoe7on 21 Oct 2016 at 5:33 am

    This thread was about as dead as hn’s brain until mumadadd resurrected it.
    I’m going to have him for breakfast.

  727. JJ Borgmanon 21 Oct 2016 at 6:53 am

    hardnose,

    Your logic is not hard to follow…it cannot be done. Your logic flows about as smoothly as the early versions of Garmin. Many routes it offered didn’t exist or were on mountain fire passes untraversable by any normal means of transport. Your last post launches sideways on ridiculous assertions about the position of current evolutionary theory. I’m no expert, but your assertions are not only illogical, but also adamantly transparent.

    You are in a rut. Take down your shingle.

  728. steve12on 21 Oct 2016 at 10:13 am

    “The two philosophies (nature is mindless random garbage vs nature is intelligent) are at odds.”

    At least Dr. TheTroll is fair in his assessment of others’ arguments.

    “That would be nice, right? Yes of course, but suppose you are wrong. Then scientists’ attempts to improve on nature might backfire in surprising ways. Maybe in ways that we do not like very much.”

    Aren’t you just plagiarizing ‘Godzilla’ here?

    “it’s obvious that things evolve the way they do because of the transdimensional alien ghosts”

    Dr.TheTroll can go on and on about Godzilla all he wants, but we all know the transdimensional alien ghosts are the REAL organizing force behind evolution.

    Thanks Chikoppi!

  729. mumadaddon 21 Oct 2016 at 5:12 pm

    BJ7,

    “I’m going to have him for breakfast.”

    If you promise me you won’t use me as a condiment I’ll tell you exactly what I go with.

    PS. Sorry, just checked in, was a bit smashed and thought I’d have a little cheeky last word.

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