Apr 09 2008

Intelligent Design Is Not Science

There – I said it. The meme lives.

In response to my blog post about Intelligent Design (ID), Jason Rosenhouse, who writes the excellent Evolution Blog, wrote an entry taking exception to the fact that I wrote that the primary scientific criticism of ID is that it is not science. He acknowledges that this claim is true – ID is not science – but he is concerned about framing the criticism of ID in this manner because it allows ID defenders to say that we are unfairly “expelling” ID from science. Rather he thinks we should focus on the specific claims of ID (irreducible complexity, etc) and explain scientifically why they are not valid. Below in my response which I posted in his comments.

Jason – Thanks for reviewing my blog post, but I must respectfully disagree with you. The fact that ID is not falsifiable and therefore not science is the primary scientific criticism of ID. All of the things you mentioned are also proper criticisms, but I think they are trumped by the fact that ID is not even science. Nowhere did I state that ID being not science should end the criticism.

Also – when ID proponents try to defend themselves on the very points you mention, they invariably wiggle out of criticism by creeping their position over to one that is not falsifiable. In the end, they always end up outside the arena of science defending an unfalsifiable version of ID. So your position is also a bit of a false dichotomy since – the points you mention and the unfalsifiable nature of ID are related in the way that I stated.

Further, I agree that we have to be mindful of how we state the case for evolution and against ID so as not to be easily exploited. However – the fact the ID is not science is not a point we should gloss over. It is an incredibly important point – we should fight over it and win. Keep in mind that ID was created for the very purpose of expanding the definition of science – this is actually THE fight. Everything else – while legitimate and important – is actually a distraction. Don’t get distracted.

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45 responses so far

45 Responses to “Intelligent Design Is Not Science”

  1. John Piereton 09 Apr 2008 at 6:16 pm

    Dr. Egnor has issued a “rebuttal”:

    http://www.evolutionnews.org/2008/04/is_intelligent_design_falsifia.html

    I’ve taken a whack at him:

    http://dododreams.blogspot.com/2008/04/navel-warfare.html

    But I’d be interested in your response (if you’re not tired of dealing with the clueless).

  2. richdieton 09 Apr 2008 at 6:20 pm

    I must agree that ID is *not* science in their ultimate claim and I don’t think that the incremental claims being falsifiable matters. If one link in their argument escapes falsifiability the rest of the claim’s status’ are irrelevant. The sentence “The earth orbits the sun and Jesus is magic” is a non-falsifiable compound claim.

    Further, I don’t see how it helps them one bit to be excluded from the appellation “science”. Science requires scientific hypothesis to test. Anything else is pure politics, AFAIC.

    Richard

  3. pecon 09 Apr 2008 at 7:15 pm

    “we should fight over it and win”

    Scientific contests aren’t “won” by “fighting.” If your theory is correct, you should be able to provide convincing evidence. If your adversary’s theory is wrong, you should be able to provide evidence against it.

    The fact that you are “fighting” Intelligent Design suggests that you oppose it for emotional, not scientific, reasons. If you were seeking to improve your understanding of nature, you would explore your adversaries’ claims to see if they contain any truth at all. Instead of fighting them off, as if these ideas were attacking and threatening you personally.

  4. Cannidaeon 09 Apr 2008 at 7:16 pm

    There is a tendancy lately to use the word “design” in tandem with evolution and it is a mistake. Once you call it bottom up “design” you are falling in to a trap and giving the ID’rs ammunition against your argument.

    While Evolution has the “Appearance of Design”, it is not in fact design. It is random mutations that lead either to no change, more robust life forms or extinction. I think in debate we dont bring up the point enough that evolution has killed more species then it actually allowed to survive. Do they purport that God has a grand design with a purpose for killing off huge quantities of random species ? I would be curious to hear if they do.

    I find the continued use of “darwinism” by the creationist camp (lets call ID by its real name) to be ridiculous. You can see they are being slimey in thier debate when they dont just call it evolution. We need to take them to task on it every time. There are no Darwinism degrees being handed out by universities.

    In the Argument:

    Can you prove that evolution happens – Yes, science

    Can you prove that there is a God creating everything – No, not science

    They will always lose. We can not let them high jack us into using thier terminology. Keep the argument on the facts and pick your speech carefully and it will all be good = )

  5. Cannidaeon 09 Apr 2008 at 9:02 pm

    I believe that the “fight” in question, is the attack on our education system to teach creationism as science. you can debate the hell out of it with words, but ID is in court trying to force non scientific teaching into the science classroom. That is a fight, and it is one we have to win if we hope to advance as humans.

  6. weingon 09 Apr 2008 at 9:27 pm

    “That is a fight, and it is one we have to win if we hope to advance as humans.”
    I would agree with the above but would change “humans” to “Americans”. If this country screws up, others will just laugh their asses off at us and will gladly take up the torch. There was a time, not too long ago, when the Islamic world carried the light of science and civilization.

  7. Zacfon 09 Apr 2008 at 11:43 pm

    ID doesn’t stand for Intelligent Design. It stands for Intellectual Dishonesty.

  8. badrabbion 10 Apr 2008 at 12:02 am

    Cannidae;

    I have over the past few blogging days come to respect you a great deal. So it is with affection that I want to gently quibble with your following statement:

    “While Evolution has the “Appearance of Design”, it is not in fact design.”

    That there is design in living organisms is glaringly obvious. One look at every organ system, be it the heart, liver, immune system etc. cries out that there is a very high order design. To use an overused cliche, a single cell is perhaps more complex and more designed than a 747 Boeing Airliner.

    The question is whether the design is ‘top down’, ie. intelligent, or bottom up, of the variety advocated by proponents of Evolution theory.

    There is no doubt – at least in my mind – that there is bottom up design, ie. Evolutionary change occurring every day. All organisms react to environmental pressures and random mutations do occasionally lead to changes in allele frequencies.

    The question is whether ALL design is driven by random mutation and natural selection. Proponents of Evolution theory seem to claim that every organism past or present came about as a result of Evolutionary processes. Is this true?

    Maybe!

    I submit that proponents of Evolution, in order to deal once and for all with ID people, must prove 3 things:

    1. That random mutations and natural selection can lead to changes in allele frequencies. (I think that scientific evidence clearly shows this).

    2. That random mutations and natural selection routinely (by this word I mean frequently on a temporal scale) lead to speciation. Here again, I think that there is some evidence but by no means is the scientific evidence solid. Examples of observed speciation, to my knowledge, are scant at best.

    3. That random mutation and natural selection must account for ALL speciation, both in the past and in the present. Here, the data is least impressive. I grant that the task of proving all speciation being Evolutionary is especially difficult. I also grant that there is a legitimate argument to be made for reasonable inference (if you have some ducks quacking in a room, it is a reasonable inference to assume that the silent ducks also quack).

    On the whole, I think that Evolutionary theory is strong. However, in order to defeat ID proponents, it is necessary to provide more evidence of the second and third variety.

  9. Chris Nobleon 10 Apr 2008 at 2:47 am

    John Pieret writes: “D r. Egnor has issued a “rebuttal”:”

    Egnor just reiterates Phillip Johnsons parody where he claims that ID can be falsified by “proving” Darwinism.
    http://www.pbs.org/wgbh/nova/id/defense-id.html

    Holy False Dichotomies Batman !

    Egnor presumably thinks that Drawinism can only be falsified by “proving” ID.

  10. Clavainon 10 Apr 2008 at 4:55 am

    badrabbi said

    “The question is whether ALL design is driven by random mutation and natural selection. Proponents of Evolution theory seem to claim that every organism past or present came about as a result of Evolutionary processes. Is this true? maybe!”

    its just natural selection, there is also Artificial Selection, Sexual selection etc..

    about the definition of design

    Design doesn’t always need a designer, right ?

    Isn’t that the whole reason why “Intelligent Design” has the word “Intelligent” in it ?

  11. badrabbion 10 Apr 2008 at 8:50 am

    Clavain;

    Agreed. Other than natural selection, there are other forms of selection as well.

    “Intelligent” design, as far as I know, refers to design by a being who purposefully designed living organisms. Thus, for example, breeding of dogs to obtain variety is a form of intelligent design.

    And I agree that design doesn’t always need an intelligent designer. Rocks, for example, seem to be shaped very intricately and appear complex and beautiful, but are not intelligently designed.

    I hope I have clarified things a bit.

  12. Taylor Con 10 Apr 2008 at 10:01 am

    I think its pretty obvious that we are designed. If you find a watch out in a field, you would think it was designed. All the supplies are around it, but things don’t put themselves together. We are much more intricate than watches, and all the materials are around us… you know where im going.

  13. Cannidaeon 10 Apr 2008 at 11:03 am

    The word design is an easy word to split hairs on and that is why I suggest not using it. Design implies concious intent. We dont talk about Galactic design, solar design or earth design.They are also the complex results of random events guided by natural laws of the universe and we shouldn’t talk about evolutionary design either.

    As for re-branding creationism as Intellegent + Design it is a phrase that flows nicely off the tongue. It is slick marketing.

    Cold Icecream
    Fast Racecar
    Falling Rain
    Intellegent Design

    None of the 4 above need the qualifier in front of them. it is already understood that Icecream is cold, racecars are fast, rain falls and design implies concious intent.

    I respectfully maintain my original position

    Taylor C

    Your argument may be valid, that we are designed by a creator, however it is faith not science and you can not prove or disprove it.

    You are also commiting a logical fallacy “I can not imagine any other way so any other way is not possible” If you opened your mind to what is out there in genetic research, you may find yor position changing.

    The realm of religion explaining the order of the universe has been and is being pushed back at an astonishing pace by people not satisfied with the answer “God did it” and “That is the platform of the church and you do not question the church” and the world is a better place for it.

    Weing

    Short term I agree, but long term all of humanity. Maybe not so long term with the rate the world is changing.

    Zacf

    /Two Thumbs Up !!

  14. DevilsAdvocateon 10 Apr 2008 at 12:08 pm

    Dr. Novella:

    “It [that ID is unfalsifiable, therefore unscientific] is an incredibly important point – we should fight over it and win.”

    It has been ‘fought’ over and science ‘won’. Long time ago. I hope continuing to conduct a debate won long ago doesn’t serve to legitimize ID. I also hope we haven’t set as our goal for having ‘won’ the complete change in belief among IDiots. That’s not going to happen, obviously. Pro-science advocates universally acknowledge the IDiots to be proselytizing rather than debating, pretending to debate solely to keep their agenda alive. It seems to me continuing to provide them publicity and a stage is inconsistent with the acknowledgement they aren’t seriously debating the science of anything.

  15. Cannidaeon 10 Apr 2008 at 4:11 pm

    Taylor

    this should help with your project

    http://en.wikipedia.org/wiki/Abiogenesis

    I like the way you are going about it, becoming intimate with the strengths and weakness’ of both sides of the debate.

    For myslef, I find it much easier to buy into evolution and life arising spontaneously out of favorable conditions on earth then the god hypothesis.

    You point to origin of first cells which science at least makes a compelling attempt to explain but as yet I have seen no compelling theories of where god might have come from. To use your own argument, God did not just put himself together.

  16. Cannidaeon 10 Apr 2008 at 4:15 pm

    nicely written BlackCat. you hit the points I missed completly = )

  17. daedalus2uon 10 Apr 2008 at 4:31 pm

    Which is more likely, that something of finite complexity occurred (abiogenesis) or that something of infinite complexity occurred (the occurance of God)?

    Nothing about cells is infinite, you simply can’t get an infinite regression to try and explain the occurance of cells.

  18. Taylor Con 10 Apr 2008 at 9:03 pm

    Alright. Both my papers are on the evolution of the eye, how would you explain it and if you were creationists how would you try to disprove it?

  19. Taylor Con 10 Apr 2008 at 9:05 pm

    black cat, i never claimed to know alot about evolution. stop trying to make me look retarded =)

  20. rochabillon 10 Apr 2008 at 10:00 pm

    I perhaps couldn’t be more torn in two by these two points of view. I suppose I do have to lean in favor of the idea that we must be cautious of how we attack ID if attack is the correct word. As stated by both sides, ID is most defiantly NOT science. . . However, this stance does give the appearance of not allowing them to have a legitimate voice in the scientific community. Though, in my opinion, no such voice is deserved. This has to do only with manner in which we present ourselves and which presentation is most effective. And to that end, I am convinced that giving the appearance that we are allowing what they have to say IS science and then allowing the preponderance of evidence to quell these absurd ideas. If we had no need to placate to the ignorant we would be better served by Dr. Novella’s presentation that ID is not science, because it isn’t. It is quite painful sitting atop this fence by the way.

  21. Cannidaeon 10 Apr 2008 at 10:01 pm

    is it fair of me to highjack things off wikipedia instead of typing them all out ??

    http://en.wikipedia.org/wiki/Evolution_of_the_eye

    I would have a hard time trying to disprove moutains of scienintific evidence which is why I stand firmly in the camp of evolution. I think there are some standard arguments that the eye is irreducibly (sp?) complex from the ID side but when you go through them they seem intellectually dishonest to me. Almost as though they are bending the truth on purpose, whether maliciously or through blind adherance to ideology is hard to tell sometimes.

    an example of the ID argument against the evolution of the eye:

    http://www.discovery.org/scripts/viewDB/index.php?command=view&id=1416

    It is a lot reading and too sum it up in my own words;

    Scientist go to school for many years to learn the scientific method and how it is applied, they choose which little niche they want to specialize in and then spend many more years, decades, entire lifteimes worth of work in many cases learning about thier subject in insanely minute detail. they take all the facts in to consideration, write up thier best summaries of how things work, step into the fire of peer review where other scientists criticize their work and tell them where there are holes and where they made mistakes. Back to the drawing board to narrow things down even further repeating that process many times. finally they have a working theory with no bugs in it that anyone (including all the experts on the subject and many many more people with familiarity of the subject) can find.

    We have a theory. Eureka!!

    ID proponet comes a long with very limited knowledge, twisted logic and an ideological (sp?) agenda and says the scientist mountiain of work is useless gibberish.

    Who will you believe.

    If you choose science, HOW DOES ANYONE BUT YOU BENEFIT? Scientist are not asking for 10% of your income in tithes.

  22. themightylearton 10 Apr 2008 at 10:30 pm

    ID = Idiotus Desperatus

    There! And no I don’t know a lick of Latin, I just made that up.

  23. Cannidaeon 10 Apr 2008 at 10:52 pm

    what is with the super long moderator check ?

  24. weingon 10 Apr 2008 at 11:05 pm

    Taylor,

    You are asking the impossible. Creationism is not science and cannot be disproved. Creationists are not scientists and are not capable of disproving evolution. Scientists would disprove evolution by, for example, finding fossil evidence of a modern human dating 1.2 million years ago, fossils of modern horses dating to the eocene, etc.

  25. badrabbion 11 Apr 2008 at 12:17 am

    TheBlackCat;

    As usual, your posts are outstanding. I continue to learn a great deal from you.

    I agree that ‘temporal scale’ should be measured in generations rather than time. I also agree that ‘speciation’ is a difficult definition.

    Would it be satisfactory, for the purpose of this discussion, to define speciation as the development of new functional systems from an ancestor species? Thus, for example, a bacterium that develops sensitivity to light from ancestor bacteria lacking this ability would be considered a speciation event. I know that this is not a strict definition of speciation, but I think that such a development would be convincing evidence of speciation, at least to me.

    Speaking more broadly, by a speciation event, I am talking about genetic change in a species such that new genetic information is introduced in the gene pool of the species.

    Again, taking bacteria as examples, I often hear of antibiotic resistance as demonstration of evolution. However, when I inspect the mechanism of bacterial resistance, it turns out that in nearly all cases, antibiotic resistance is conferred on a bacterium by its loss of a given functional protein. That is, bacteria lose a given functional gene that makes non-functional a previously functional protein which fortuitously causes antibiotic resistance.

    More impressive, though, would be to see a bacterium ‘invent’ a novel way to fight a given antibiotic. If, for example, a bacterium produced a whole new protein to envelope the antibiotic molecule (not unlike what our immune systems do), I would be impressed.

    Of course, my being impressed is not a criterion for proving evolution, but such evidence would be nice!

  26. badrabbion 11 Apr 2008 at 12:24 am

    As I read my own post, I realized that I was less than clear. Let me try another example:

    If it were shown that a given species of rat, having lived in caves for millions of years, has lost its sight, I think we would all call this ‘evolution’. If this rat ancestor rat possessed x amount of genetic information, after evolving, it now possesses

  27. badrabbion 11 Apr 2008 at 12:29 am

    L
    As I read my own post, I realized that I was less than clear. Let me try another example:

    If it were shown that a given species of rat, having lived in caves for millions of years, has lost its sight, I think we would all call this ‘evolution’. If this rat ancestor rat possessed x amount of genetic information, after evolving, it now possesses

  28. rochabillon 11 Apr 2008 at 9:54 am

    I changed my mind. My loathing has outwieghed my compassion for the misguided. Allowing them to continue beliveing what they are preaching is actually science is detremental to our cause.

  29. Taylor Con 11 Apr 2008 at 10:33 am

    Badrabbi, your example isnt showing progressive evolution. First of all, it is MICRO evolution. Second, loss of vision does not benefit the rat in any way, isn’t evolution all about species changing and growing for what will be best?

  30. Cannidaeon 11 Apr 2008 at 11:09 am

    Taylor, after many hours my reply to you finally passed moderation, it up a ways as a result if you want to check it out it has links both to the evolution of the eye and arguments against it.

    Also, evolution doesnt have to change a species for the better. Many species over specialize for thier environment and then become extinct. in the recent news (yesterday) a frog was found that has no lungs, respirates soley through its skin and must have fast flowing cold water to survive. Very few are left as the evironment that it can survive in is being destroyed.

    As for the rat that evolved to lose it eyes example, there are fish that live in caves in total darkness that no longer have eyes.

  31. DevilsAdvocateon 11 Apr 2008 at 11:17 am

    Let’s just say a certain level of willful ignorance is impervious to learning, by *design*, yuk, yuk.

    This reminds me of UFO believers, where they hold up an “unexplained” case, demand you explain it, you explain it, and they drop it only to hold up another “unexplained” case. There are always unexplained cases, of course, and this dance goes on forever.

    On the internet alone are mountains and mountains of articles, stories, illustrations, and other treatments of these very basic ID “unexplained” cases. Mountains more are found in libraries and bookstores. It is so prevalent, one must go out of one’s way to avoid it (hence “willful ignorance”). Just like with the Ufools, they are totally explained, but IDiots have decided to ignore those explanations and take some perverse pleasure in asking about it over and over, I guess hoping to meet someone somewhere who can’t or won’t bother to do their reesearch for them so they can have a brief but satisfying ‘Aha!’ moment.

    Then comes my recommendation to address such people with a smile, a nod, and just walk away.

  32. badrabbion 11 Apr 2008 at 12:59 pm

    TheBlackCat;

    I hope your comments were not directed at me.

    I am sorry, my last post was cut off in the middle. I tried again to repost and again it was cut off exactly at the same place.

    My point regarding the rat that lost its eyes through evolution was that in this case evolution resulted in a net loss of genetic information (maybe). What I was saying was that I would be more comfortable in finding examples where evolution resulted in an increase in genetic information, leading to phynotypic variation.

    Said another way, are there examples that can be found where through mutation or other mechanisms of evolution, such that the result is a net gain of genetic information?

    And please do not lose patience. I am not sold on the idea of ID. Far from it. I also do not think I am an IDiot. I am more inclined to believe in Evolution theory. I do have questions, though, whose answers seem to be lost in the vitreol of ID/Evolution debate. Both sides seem to hate one another and in the cross fire, people like me who really want to know what is going on get cought in the middle.

  33. mindmeon 11 Apr 2008 at 5:16 pm

    A classic example of a mutation that has led to a gain in information and produced a novel adaptation is the nylon bug:

    http://www.nmsr.org/nylon.htm

    For others see here:

    http://www.gokorea.info/evo/evo.htm#_Toc183420381

    It would be really odd to geneticists who have been claiming this happens for decades but could point to no such examples. I sure hope as scientists make this claim in their papers a peer reviewer would once say “hey, could you footnote an example of such?”

    See here as well:

    http://www.gokorea.info/evo/evo.htm#_Toc184917173

    “Along the lineage leading to modern humans we infer the gain of 689 genes and the loss of 86 genes since the split from chimpanzees”

    Let me ask you, what would you, BR, what would you accept as evidence of a mutation that results in a gain of genetic information?

  34. DevilsAdvocateon 11 Apr 2008 at 5:44 pm

    Excellent post, Black Cat.

  35. badrabbion 12 Apr 2008 at 1:38 am

    BlackCat;

    I read your example of the Nylonase gene. In reviewing the literature, both of the creationists and the evolutionists, the following were clear:

    1. There is a novel gene that seems to enable Flavibacterium to digest Nylon. This gene appears to have evolved from a frame shift mutation and duplication. The location of the gene is somewhat unusual in that it occurs in a location with repeating DNA sequence which is fortunate in that stop codons are not created there. All this, more or less, is Chinese to me, but I accept that Nylonase is a novel protein that seems to have been evolved by natural selection.

    2. Creationists appear to have desperately attempted to invalidate this enzyme as an example of evolution. They seem to have made a big deal that the gene was created inside a plasmid, which as I understand, is essentially a virus living inside a bacterium. I am not certain why evolution inside a plasmid does not count as evolution. So I accept that Creationists are wrong on this issue.

    As an aside, if BlackCat can explain why there is a big deal made re the plasmid issue, I would be grateful.

    I am comfortable with nylonase serving as an example of a beneficial mutation.

    Are there more examples?

    Is there an estimate as to how many beneficial evolutionary events (such as the development of Nylonase) we can expect over a given time period?

  36. badrabbion 12 Apr 2008 at 1:59 am

    mindme;

    With all due respect, I was not able to grok your links. The abstracts you site are too vague.

    Your link re nylonase was very interesting, and I accept it as a legitimate example of net info gain by Evolutionary mechanisms.

  37. mindmeon 12 Apr 2008 at 8:20 am

    BR

    Your question about how many beneficial mutations we should expect is kind of a vague question. There are good estimates of the mutation rate. Sure. How many produce novel mutations that lead to survival is a hard one to answer. Remember, evolution is not about the organism getting better and developing new features all the time. If the niche the organism lives in is unchanging and there is no nearby niche that’s unexploited, novel mutations would have little effect. They are only beneficial if they give the creature a better chance than the rest of the species of passing on genes. If I can produce as many children without wings as you can produce with wings, humans aren’t going to evolve wings.

    However if the environment changed, either rapidly or slowly, then novel mutations would come into play. Lets say, for example, rising ocean leaves brought the sea closer to a group of animals that had always been landlocked. The sea is a source of new food. Let’s say a genetic mutation in rats produces bits of webbing between their little claws. The mutation has always been there, it pops up randomly in the population, but was of no survival benefit. These kinds of things are common. Even in humans we’ve noticed some silly differences. Some people can roll their tongue, some can’t. Some people have dangly earlobes, some don’t. Some people have single eyelids, some people have double eyelids. These little differences don’t confer any survival advantage but if suddenly our food source became scarce and a nearby food sourced was easy to exploit by people would could roll their tongues, that odd little mutation is going to go from being a funny thing you can do in a pub to something that lets you live.

    Anyway, any rat with the random mutation of the webbing would have a slight advantage in getting at food in the shallow water. A rat without the webbing might miss meals and die. The rat with the webbing would get a meal and live and pass on these gene. The gene would become more common in that population. Other mutations might also occur. Rats with more webbing and less fur would have an advantage. Rats with nostrils pointing more up and back could swim farther…

    Think about this. A dolphin looks a lot more like a shark than it looks like a rat. A creationist would make a prediction that a dolphin and shark should be more genetically similar. Both are hairless, both have fins, both have teeth. God would surely re-use the genes. This is their argument for why man and chimps are so genetically similar. God is just making use of what works. But an evolutionist would go, no a dolphin evolved from a mammal and a shark is a fish. A dolphin should actually share more genes with a rat. Ah. A testable hypothesis. And if it didn’t, that would present a very large problem for evolution. Guess what? A dolphin and rat are much more genetically similar than a shark and a dolphin.

    Anyway, don’t think evolution has any goal in mind of producing X Men. If a species is getting three squares a day, it’s going to continue being that species. If a new food source appears next door, some of that species might evolve to exploit that new food source and become a whole new species.

  38. badrabbion 12 Apr 2008 at 9:44 am

    Mindme;

    Thanks for the comment. Your explanation of dolphin/shark vs. dolphin/bat is compelling.

    I also agree with your explanation of the vagueness of classifying a given mutation as ‘beneficial’. Of course, a trait can be either beneficial or harmful given the circumstances. I understand that.

    For the purpose of this discussion, I had limited the definition of a ‘beneficial’ evolutionary event to a mutation (or other evolutionary mechanism) that gives rise to a net increase of information in the gene pool. Thus, for example, the Nylonase gene BlackCat and you offered is a perfect in that it meets that definition.

    The nylonase gene clearly arose from a region of DNA that made another protein, mutated to produce a gene whose protein product actually had a novel function. This is, unquestionably a mutation that produced a net increase in gene pool information.

    The question is whether these kinds of examples are ubiquitous or rare in nature of laboratory. So I would appreciate more examples.

  39. TheBlackCaton 12 Apr 2008 at 11:19 am

    As an aside, if BlackCat can explain why there is a big deal made re the plasmid issue, I would be grateful.

    Bacteria have many things significantly different from eukaryotes (like us). One of those is how their DNA is partitioned. Our DNA is broken into sections called chromosomes. These are linear regions of DNA that form dense objects during cell duplication. Bacteria, on the other hand, have much of their core DNA contained in usually one, ring-shaped structure of DNA. That is, there are no ends of the DNA strand. However, they also have a large amount of DNA in much smaller ring-shaped DNA fragments called plasmids. These usually only have one or a few genes. What is useful about them is that they can be shared amongst bacteria, even widely different populations. This allows them to spread new and mutated genes rapidly through the population. It serves a similar purpose to sexual reproduction in many plants and animals, that it is it allows for new combinations of genes. Evolution in these genes is still very much evolution, there are no grounds for creationists to complain about it. The advantage, for studying science, is that the genes can be spread very rapidly through a population. I am not aware of a mechanism to actually pick beneficial genes, I think the sharing of plasmid is either random or complete (in that they share all their plasmids). I am not sure about that, however.

    As for additional examples, I already provided one: the evolution of novel sugar digesting enzymes after the first ones were intentionally destroyed. I should point out that such examples would not be all that common in modern organisms. Organisms have been living with each other for billions of years. The evolution of novel biochemical pathways would often require the presence of new chemical in the environment that the organism does not presently have the pathways necessary to handle. That is not a common occurrence, the most notable recent one being the evolution of ethyl alcohol synthesis by yeast and even that is an ancient occurrence. Considering this I am a bit surprised by the number of examples I am aware of.

    Another example is actually in corn. A specific breed of corn evolved, from scratch, from non-protein coding regions of DNA, a gated ion channel. You could think of a gated ion channel as a door, a very specific door that only lets specific things through. Further, the door is only open when it receives a certain chemical signal. What is more it is made up of several identical proteins that fit together to form the channel. So it really needs 5 things: 2 very specific binding sites that allow instances of the protein to link up, a third very specific binding site that binds to the signaling molecules and when it does so substantially changes the structure of the group of proteins so they can let the ion through, the ion-selective channel that must have a very specific size, shape, and set of electrical properties, and a trans-membrane domain that causes it to embed it itself in a cell membrane. This evolved from scratch within the last hundred years or so, and in an organism with complexity comparable to humans.

    Another example is the HIV protein VPU. It has undergone a number of radical changes since HIV first infected humans in the early 1900′s. This includes gaining the ability to form an ion channel (not gated, but it still requires 4 of the 5 parts I listed), additional specific binding sites, large changes in overall structure, and splitting into several different variants that are specialized for different tasks. It appears to be largely responsible for the wide variation in virulence of different HIV strains.

    And as for resistance, you are simply incorrect. Resistance, both in bacteria, plants, animals, and fungi, very often involves the evolution of novel enzymes to break down the toxic compound into harmless ones. This is found in bacterial resistance as well as insect resistance (such as blowflies) Other examples, such as in malaria, have the organism develop resistance by developing a mechanism to expel the toxin before it reaches dangerous levels.

  40. badrabbion 13 Apr 2008 at 2:19 am

    BlackCat;

    Thanks for your explanation of plasmids. College has been a while, and I think I had confused a plasmid with a phage.

    Regarding bacteria re-evolving enzymes to digest sugar, I would appreciate some specifics. Which bacteria? What study? I did a google search under “bacteria evolving carbohydrates enzymes” yielded 226,000 hits. I followed some of the links. It is simply amazing to find the details to which the evolution of individual enzymes are worked out.

    However, I was not able to find your specific example of re-evolving the sugar digestion enzymes.

  41. badrabbion 13 Apr 2008 at 6:04 pm

    Mindme;

    The answer to your question is ‘absolutely’!

    I am in the process of reading about BlackCat’s examples. My source of antibiotic resistance being about loss of function rather that developing “novel enzymes” is as follows:

    http://www.trueorigin.org/bacteria01.asp

    Pay particular attention to table I in the middle of the page.

    If the above article and more like it prove to be wrong, then, yes of course I would be more skeptical. If on the other hand, I am unable to verify the presence of these “novel enzymes”, then I would be more skeptical about creationist claims.

    I have no agenda here beyond getting at the truth.

  42. badrabbion 13 Apr 2008 at 6:51 pm

    Ok, regarding insect resistance, this is an exceedingly difficult subject to investigate for a lay person such as I. My understanding, having read a number of articles on the subject is as follows:

    Some insects display a remarkable ability to become resistant to pesticides. The mechanisms for such resistance, best as I can tell, are summarized by:

    1. Mutations that lead to an over-expression of pre-existing enzymes that hydrolyze the pesticides. A given estrase which already exists inside an insect is over expressed 50-100 fold so that this estrase sequesters and destroys the pesticide.

    2. Mutations occur, such that the target protein of the pesticide changes in shape, making the pesticide less efficient. Here, the target protein also becomes less efficient in doing what it was supposed to do in the first place.

    3. There is already a pre-selection! I do not pretend to understand this mechanism, but according to this link (http://www.abc.net.au/science/news/stories/s1642457.htm), 70 year old insects, which could not have possibly been exposed to the pesticide nevertheless have the prerequisites of resistance.

    4. There is a novel mutation of the estrase gene such that the estrase enzyme becomes more efficient at neutralization of the pesticide. I am still trying to understand this (I do not have subscriptions to the full text articles).

    It seems that mechanisms 1 and 2 do not really serve as examples of ‘beneficial’ mutations in that they confer a loss of a mechanism rather than a net gain of information.

    Mechanism 3, granted that it is bizarre, actually gives credence to creationist claims.

    Mechanism 4 is what I think BlackCat was hinting at. I am trying to get more information about it.

  43. mindmeon 13 Apr 2008 at 8:45 pm

    BR

    That table sort of reminds me of Harun Yahya’s fishing lures prove there is no evolution:

    http://forbiddenmusic.wordpress.com/2008/01/09/atlas-of-creation-by-harun-yahya/

    I’ve seen creationists make this argument many times. There has been no evolution. Evolutionists say evolution takes place over great periods of time. So then they show several dozen 100 million year old fossils next to photos of ostensibly living modern examples and say “they’re identical! there has been no evolution!”

    So, yeah, odd that all these fossils show no evolution. Shouldn’t these fish and plants have evolved? But they haven’t!

    The problem with this is two fold.

    One, it’s a strawman. Creationists confuse “change happens over time” with “change always happens over time”. Not everything changes. As noted above, if a species is in a stable niche and getting three squares a day, there are no selective pressures.

    Two, it’s cherry picking. They are merely cataloging examples of species that haven’t changed much. This is predicted by evolution and not at all fatal to the theory.

    To wit, the table is cherry picking. Sure of the many ways bacteria acquire resistance, loss is one way. So it looks impressive, cataloging only the examples of resistance through loss.

  44. weingon 13 Apr 2008 at 11:15 pm

    It’s been a while since I took microbiology, but I don’t recall that bacteria developing resistance to an antibiotic caused it to lose something. This is a simple example. A penicillinase producing bacteria will be resistant to penicillin. We can and do alter the structure of the penicllin molecule and come up with other antibiotics of the penicllin family that do not fit to the active site of the penicllinase and the pencillin derivative is not inactivated, the bacteria cannot make a cell wall as it divides and dies. Due to random mutations, the three dimensional structure of the penicllinase will vary from bacteria to bacteria. In some of these penicillinases, the active site that the penicllin derivative fits into will be a better fit and the penicllin derivative will be inactivated and that bacteria will be able to build a cell wall and survive. Its progeny will be resistant to the action of the new penicillin. There is no loss of anything for the bacteria to acquire this resistance.

  45. [...] We state that it is not even wrong – it is simply not asking a teastable scientific question. I discuss in detail here why ID is not science. This distinction is perhaps too subtle for Egnor. To further demonstrate his [...]

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