Sep 01 2009

Evolving Mice

Evolution deniers (and deniers in general) often support their denial with the baseless assertion that there is no evidence for evolution, or for some aspect of evolution, like natural selection. It’s easy to make this claim if you are just ignorant of the evidence, or don’t care about factual accuracy. More sophisticated deniers are well aware of the evidence, they just rationalize some trivial excuse to dismiss it.

It amazes me to this day that creationists can say with a straight face that there are no transitional fossils, when such fossil evidence is regularly pulled from the ground, and numerous dramatic examples (or at least their replicas) fill our museums. In a pinch they say, for example, that Archeopteryx is not a transitional species from dinosaur to bird, it’s just a bird that happened to have teeth, and a long tail, and claws, and lacked certain flight adaptations. Although at other times they might say it was just a dinosaur with feathers. This is denial by labeling.

There is also evidence for the ability of mutation and natural selection to produce adaptive changes in a population.  The most elegant and detailed of this kind of evidence is now the research of Richard Lenski, who followed thousands of generations of bacteria in the lab, showing how they made a series of mutations that resulted in their ability to thrive on citrate as a new food source. Answers in Genesis has a typically incoherent rationalization, based upon their own ignorance of evolutionary theory:

Many evolutionists state that the bacteria are experiencing “adaptive evolution.” However, this is not evolution but rather adaptation. Molecules-to-man evolution requires an increase in information and functional systems. Instead, these bacteria are likely experiencing a loss of information and functional systems as has been observed in other mutant bacteria in Lenski’s lab. While these changes are beneficial in the lab environment, they do not lead to a net gain that moves bacteria in an upward evolutionary direction.

I wonder how they conclude that they are “likely” experiencing a loss of information. They are just making this up. And, it’s not even relevant. You see the century-old misconceptions in this nonsense – that evolution must be constantly “upward”. Also we see the common denialist strategy of acknowledging evidence but then dismissing it because of what it is not. AIG admits this is evidence of adaptation, but it is not evidence of increased complexity. This is irrelevant on every level – evolution does not require an increase in complexity, and adaptation is a critical component of evolution.These bacteria put together three randomly occurring mutations in order to evolve a new trait that adapted them to a new environment.

Now scientists report on a new stunning example of random mutations spreading through a population as an adaptation to a new environment. Dr Catherine Linnen of Harvard University and colleagues studied a population of deer mice living in the sand dunes of Nebraska. Deer mice are normally dark colored for optimal camouflage against dark soil. However, the mice living in the sand dunes are sandy colored. This provided an excellent research opportunity, as the sand dunes are known to be a recent geological feature – about 8-15 thousand years old.

What this means is that within that time frame dark colored deer mice moved into the sand dunes and must have later developed their light sandy-colored coats. Further, light-colored coats is not a variety that already exists in the deer mice population. In some cases, a species may already contain the genetic diversity to adapt to a number of environments, and those variations that are most adaptive will simply predominate in each particular environment. But no new mutations or traits are required.

In this case, Linnen discovered that the light-colored fur was the result of a single gene, named Agouti, that first appeared in wild deer mice populations only 4,000 years ago, and then rapidly predominated in the sand dune population. Essentially, the mice had to wait for a light-colored mutation to appear at random, but once it did it was heavily selected for.

This is a very nice evolutionary story. It demonstrates the appearance of a new mutation providing raw material for natural selection.

And, of course, the evolution-deniers are already busy downplaying and butchering this new bit of science. One creation site writes:

New Scientist noted that the mutation consisted of a single amino acid deletion within one gene known to be responsible for coat color in many mammals.  So if natural selection did anything, it deleted something; it did not invent something new (certainly not a new protein or enzyme from scratch).  Calling it a “beneficial mutation,” therefore, seems a stretch.

Right – a deletion mutation has “deleted something”. This is an example of an irrelevant objection – point deletions are significant mutations, they change the resulting protein, and in this case the phenotype. Then they move the goalpost – mutations don’t count, only creating new proteins from scratch (btw – enzymes are proteins, so saying “protein or enzyme” is redundant).  Of course, none of this has anything to do with whether or not the mutation was beneficial – the researchers here demonstrated that it is.

And again we see the same old denialist strategy of denying a piece of evidence for what it is not, even though this is irrelevant to what it is. These deer mice are evidence that random mutations can crop up, provide a survival advantage, and predominate in a population – something creationists say is inherently unlikely. This is also not evidence for many aspects of evolution. No one piece of evidence is sufficient to establish all the various aspects of evolution – but creationists deny each piece of evidence in isolation partly by saying what it is not evidence for. But if you put it all together, we have a complete set of evidence for the evolution of life on earth through variation and natural selection.

The story of the sandy-colored deer mice can be added to the vast tapestry of evidence for organic evolution. It is one piece to a complex scientific puzzle, but it snaps into place quite nicely.

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86 responses so far

86 Responses to “Evolving Mice”

  1. artfulDon 01 Sep 2009 at 12:25 pm

    “But if you put it all together, we have a complete set of evidence for the evolution of life on earth through variation and natural selection.”
    Looks like a bit of evidence there for directed adaptation as well, but I expect you’ll deny it.

  2. Odin Xenobuilderon 01 Sep 2009 at 12:32 pm

    The last post here, “Facts are NOT Anti-Religious” made me think of this very topic of the mountain of evidence for evolution that is still denied. It seems like some people will not be convinced until they themselves see the process unfold all over again over the process of billions of years from start to finish.

    There are some things we just cannot behold, and if we want to take advantage of the knowledge in theories, we need to trust the evidence of things we cannot see because they are outside our normal scales of size or time. How much evidence is enough before we can stop calling the theory of evolution a theory? It seems like we’re already there.

  3. medmonkeyon 01 Sep 2009 at 12:51 pm

    Directed by what? Environmental selection? I agree. It took at least 4,000 years for this adaptation to first present itself and then become prevalent, exactly what is expected if random mutation in an individual and environmental selection are the predominating forces in this particular evolution.

  4. Mark F.on 01 Sep 2009 at 1:12 pm

    By an odd coincidence, Sean Carroll, in his 2006 book “The Making of the Fittest: DNA and the Ultimate Forensic Record of Evolution”, used as an example of just how quickly major changes in a species could occur through mutations a hypothetical, light-colored mouse population that had their environment altered by the introduction of a dark-colored lava flow. I can’t remember exactly how long he estimated in would take for the dark-color mutation to become predominant, but it was really not that long in a geologic time scale. This work seems to bear out his example very well.

  5. artfulDon 01 Sep 2009 at 1:17 pm

    Self-directed by the purposive trial and error activities of every organism. As man will contend that the Lenski experiments with E.coli indicate. As to the Agouti gene, the randomness involved in its mutation doesn’t preclude an element of direction being involved in its selection. The selection mechanisms are self-directed, are they not?

  6. Gorillahugon 01 Sep 2009 at 1:20 pm

    @artfulD and Dr. N,

    Looks like a bit of evidence there the divine noodly appendage as well, but I expect you’ll both deny that, too.

  7. medmonkeyon 01 Sep 2009 at 1:48 pm

    My understanding of your argument here is that genes can have a self-selecting capacity because genes define behavior and behavioral response to environmental changes is a component of environmental selection. OK. I don’t think there is another force at work there – behavior genes also being selected for by the environment – unless you are arguing that the actual mutation is being driven by some unknown force rather than being random, which I don’t think you are doing.

  8. artfulDon 01 Sep 2009 at 2:33 pm

    I think that in organisms such as E. coli, their learning experiences can effect changes in their physiological makeup and those changes can be replicated as part of their adaptive strategy. Random mutations have certainly played a part in their evolutionary history, but not the only part.
    In the case of the deer mice and other vertebrates, there’s evidence that their strategies will lead to changes in their physiology, but over a much longer period of time. There’s also evidence, such as from recent epigenetic research, that experiences can change behaviors that have limited heritability.
    The extent to which this involves directed mutation is unknown, but it appears that genes have flexibility in the way they carry out strategic instructions that should or could perhaps not be considered mutation at all.
    The concept of environmental selection is also bothersome in that it infers the environment is the active or choice making mechanism in the selection, and that the organism then must accept that decision. But what the organism must accept is that the environment has changed in a way that requires it to adapt, and from that point on, the operative decisions are the organism’s to make.

  9. Traveleron 01 Sep 2009 at 2:47 pm

    “The concept of environmental selection is also bothersome in that it infers the environment is the active or choice making mechanism in the selection, and that the organism then must accept that decision.”

    If hawks find it easier to spot dark mice on the light sand and eat them before they can breed, then yes the organism must accept the fact that it is dead. The remaining mice must accept the fact that there are fewer dark mice to breed with. I’m not seeing the problem with this.

  10. artfulDon 01 Sep 2009 at 3:45 pm

    Apples and oranges. Organisms don’t adapt for purposes of avoiding death – most will have no concept of an end to their existence. They also don’t adapt to become invincible to predation. They adapt to survive as a species in spite of predation and in spite of environmental change – whether that change involves choices made by other species or not.
    You’re hawk scenario doesn’t change the fact that the responsibility for adaptive choice lies with the mouse. One way that all such organisms adapt to such predation is to make their own changes in the environment, if not ultimately in themselves. They burrow, they learn other avoidance tactics, they deselect traits, they change their reproductive strategies, ad infinitum. But these are their operative choices, their strategic responses, not hawk’s.

    In short, the hawks choose to force the mice to choose. The mice must then take their operative turn in the choosing. If they choose wrong, they die. But they made the try and they made the error.

  11. artfulDon 01 Sep 2009 at 3:48 pm

    It should be “your hawk scenario,” but its my ‘ error.

  12. CertifiedCyborgon 01 Sep 2009 at 9:41 pm

    @artfulD

    Is your position that a change in the animals behaviour is itself a selective pressure which over time contributes to the evolution of that species?

    Well sure, that’s how selectionairy pressures such as sexual selection work. The problem is it’s unnecessary to invoke that as a pressure at work in this mouse adaption. About 4000 years ago this mutation arose and the percentage of mice carrying it increased as the gene had an obvious evolutionary advantage. The idea that the entire population simultaneously evolved (via cultural or genetic evolution) the desire to mate with these adapted mice as the incidence of the mutation increased is unnecessary to explain the increased prevalence of this gene. Therefore there’s no evidence for behaviourally directed adaption in this example.

  13. artfulDon 01 Sep 2009 at 9:58 pm

    Actually the behaviorally directed adaptation was more applicable to the bacteria, and as to the mouse, my argument is that the selective mechanism lies in the end with the mouse rather than just with the environment. But note a comment by Mark F. above about a light-colored mouse population that had their environment altered by the introduction of a dark-colored lava flow. It would seem there (although I haven’t refreshed any memories that I may have had of that study) that random mutations did not have to be the mechanism, but that the mice themselves had a role in the change of their coloring to match the surroundings.

  14. artfulDon 01 Sep 2009 at 10:31 pm

    CertifiedCyborg,
    Also there’s this statement of yours: “About 4000 years ago this mutation arose and the percentage of mice carrying it increased as the gene had an obvious evolutionary advantage.”
    This is an observation that explains nothing about the mechanism.
    It’s the common assumption that the process is random, but it’s not unanimous. It’s the common assumption that an evolutionary advantage is causative, when it can often or perhaps more often be the case that the advantage came from the effective strategy employed by the organism for the use of such a mutation.

  15. superdaveon 02 Sep 2009 at 12:25 am

    Ask any CREWATIONPIST if DELUETINHG some letters from this sentence takes away any information.

  16. [...] Evolving Mice (Steven Novella, 09/09) [...]

  17. CertifiedCyborgon 02 Sep 2009 at 10:32 am

    Artful D,

    It’s one of the many observations which is predicted by the modern theory of natural selection. It may also be predicted by the mechanism you purport, but the point I was making is that your mechanism requires more assumptions.

    But i’m having second thoughts, I don’t really understand your position well enough to make that judgement, and I am genuinely interested in it.

    Are you arguing that it may not be enough that a mouse is simply better camouflaged in its environment, that the mouse needs to take some kind of action to ensure the increased frequency of the gene? Or that the gene responsible for the lighter skin also codes for behavioral trait which is better for survival?

  18. artfulDon 02 Sep 2009 at 11:59 am

    Yes, I’m suggesting that the actions that ensure the increased frequency of the gene have to be taken by the organism, in this case the mouse. These actions are strategic, but not necessarily, or even likely in my view, connected to the gene itself. It’s these strategies that already have evolved in the organism that are in need of much more study, as it is arguably these strategies that account for selecting in mutations, whether the causation is random (a magical explanation in its own way) or directed by the organism itself (i.e., bacterial magic already under examination).

    Example of studies that underscore this need for more shining lights:
    Separate Neural Mechanisms Underlie Choices and Strategic Preferences in Risky Decision Making
    http://www.cell.com/neuron/abstract/S0896-6273(09)00288-8
    “Summary – Adaptive decision making in real-world contexts often relies on strategic simplifications of decision problems. Yet, the neural mechanisms that shape these strategies and their implementation remain largely unknown.”

  19. Mark F.on 02 Sep 2009 at 12:35 pm

    artfulD,

    I guess my comment wasn’t as clearly written as I would have liked. I was not referring to an actual study of mice populations and how their coat color was affected by a lava flow. I was referring to a hypothetical situation discussed in Sean Carroll’s book: “The Making of the Fittest: DNA and the Ultimate Forensic Record of Evolution.” As I wrote above he was using this as an example to estimate how long a random mutation that changed a characteristic (i.e. coat color) could become predominant within a population if it conferred a survival advantage. His calculations suggested it wouldn’t take very long at all (in a geological time scale). The real study described in Steven’s post here is entirely consistent with Carroll’s hypothetical calculations.

  20. artfulDon 02 Sep 2009 at 1:09 pm

    Hypothetical or not, the “study” produces the clearest of inferences that the mice themselves had a role in the change of their coloring to match the surroundings. And if pressed, I could reference a number of actual studies that demonstrate the same phenomena.

    But I’m persuaded that the farmer who lead the horse to the water, only to discover it couldn’t be made to drink, decided that it would have done just as well to point out where the water was and dispense with the leading.

  21. The skepTickon 02 Sep 2009 at 2:54 pm

    Point deletions or additions do not affect ID proponents. It’s humorous to think that before molecular biology, a sandy mouse turning into a black mouse would likely have held more sway. Now that we can point to a single mutation as the cause, creationists/IDists are unaffected. IDists are looking for a change in complexity – developments of whole new structures, for example. Perhaps even the bacterial flagellum changing into a five-bladed prop. They don’t exactly specify the level of specified complexity that must come about, although Behe gives it a shot in his new book which investigates the boundary between simple mutation and complex structure. Of course, without a definition that everyone can agree on, his arguments are little more than hand waving.

  22. artfulDon 02 Sep 2009 at 3:09 pm

    IDists are NOT looking at any form of self-directed evolution. With their “loss of information” thesis, they would seem to hate the concept that information comes from life itself as much as the traditional natural selectionists.

  23. tmac57on 02 Sep 2009 at 5:54 pm

    artfulD- Why are you so resistant to the idea that a random genetic mutation could accidentally convey a biological advantage that would then be more likely passed on due to making the organism more fit? Why does this scenario have to be ‘directed’ by anything other than natural selection?

  24. artfulDon 02 Sep 2009 at 7:35 pm

    Because the mechanism clearly involves an “intelligent” component that for those of us that don’t believe that intelligence comes from afar (with the exception of panspermia as a plausible possibility), would have to come from the organism itself.
    Your theory depends on the selection of random events being criteria driven, yet you don’t think it important to consider how the mechanism is regulated. But clearly the differences in species would require the regulatory process to reside with the organism and not with some unknown atmospheric presence hovering about and throwing a flag on the field arbitrarily.
    Whatever advantage an accident might convey, it’s something that’s taken rather than given. The taking is a choice made by a mechanism residing with the organism, not the causer, if any, of the accident.
    I neither require nor much care if you believe any of this. The question should be, in my view, why are you so resistant to the inclusion of direction as at least one of the processes, when we can already see through epigenetic research that it is.

  25. tmac57on 02 Sep 2009 at 9:48 pm

    “The taking is a choice made by a mechanism residing with the organism, not the causer, if any, of the accident.” The gene has to accept a mutation? It has to decide to be mutated? If I were caught in a crossfire of bullets (radiation) and my left index finger was blown off (mutation), would I have made that choice to be mutated?
    “The question should be, in my view, why are you so resistant to the inclusion of direction as at least one of the processes, when we can already see through epigenetic research that it is.” Well now you just shifted the argument from genetic to epigenetic.But as regards genetic mutations needing a director, that just seems unnecessary.Occam’s Razor.

  26. Ryan261357on 02 Sep 2009 at 10:11 pm

    artfulD,

    I don’t think anyone understands why this study shows a “mechanism [that] clearly involves an ‘intelligent’ component”.
    To me it shows a random mutation conveying a beneficial trait, in this case a coat of a lighter shade that is propagated through subsequent populations. I don’t understand why this is directed.

    What is going on with all the “choosing” you keep mentioning as well? I don’t see the mice choosing anything. A mouse doesn’t get to choose its coat color; it is born with it.

    Why do we need to hypothesize strategic choices made by the mice given their new coat color? Light colored mice could behave in the exact same way as their darker brethren but still be selected for given their superior camouflage.

    I don’t see how the study you provided supports anything that you are proposing?

  27. Ryan261357on 02 Sep 2009 at 10:32 pm

    artfulD

    Before making a case for a new mechanism that needs to be added to the standard explanation, you should really look to see if the standard explanation is deficient in some way. Are there anomalies, which require some kind of direction? I have yet to see you demonstrate any reason why the standard evolutionary explanation needs to be modified or added to.

    Others on this forum have already mentioned Occam’s Razor. Try to understand why your proposed “directed evolution” is an unnecessary addition that is not needed to explain this mouse study. In fact the entire theory of evolution has no need of your new mechanism to explain the life we see around us.

  28. artfulDon 02 Sep 2009 at 10:35 pm

    The organism has to take advantage of the mutation. Mutations, if accidental, don’t come with directions as well, or did you think somehow they did? If your finger is blown off, who decides whether to find the advantage in that, if any? Not the bullet.
    The second part is not a shift at all. Epigenetics may find part of the answer to the apparent lack of direction included with your radiated bullet.
    Ockham’s Razor is an advisory “rule” and not a requirement to pick the dumbest solution because to the relatively ignorant, it’s the simplest.

  29. tmac57on 02 Sep 2009 at 11:01 pm

    The organism does not need to be aware of the advantage in order to benefit from it. The sand colored mice are probably totally unaware that their color has given them an edge over their darker cousins. They just ‘naturally’ survive easier in their environment. Also, I thought that it was clear that Dr Novella was describing a strictly genetic case not an epigenetic one, so again, you seem to want to drag that into the discussion to bolster your position, rather than address the case given.

  30. artfulDon 02 Sep 2009 at 11:24 pm

    Each and every of those statements, sentence by sentence, is just dumb.
    Do you think being aware is a conscious phenomenon? Did the mutation change all these mice at once, and the benefit that helped the first mutated individual automatically spread to them all?
    How in your view do you know in advance that a case you have presented as strictly genetic was in fact not that simple? Do you perhaps tell everyone that if the answer could involve epigenetics (which is part of genetics by the way but for sake of your argument we’ll pretend it isn’t), please refrain from presenting such a solution, as you wish to remain ignorant?

  31. artfulDon 02 Sep 2009 at 11:36 pm

    But hey, tmac7, if you want to have the last word here, just say something else dumb and I’m gone.

  32. HHCon 02 Sep 2009 at 11:54 pm

    There is not a city with a population of more than 6,000 in the Sand Hills of Nebraska. 30 miles north of the Platt River and East of the Nebraska Panhandle, the population is sparse, and there is many more cattle than people. Cattle ranching is a primary industry out there. The colors of the mice blend into the terrain.

  33. Surakyon 03 Sep 2009 at 5:26 am

    artfulD … seems you’ve run out of steam, reduced to ad hominems … you’re not really worth the effort now, but I’ll bite.

    The mouse takes advantage of the mutation by not getting eaten as often amongst the sand dunes as it’s non-mutated relatives.

    It is not a choice on the mouse’s part, it the mutation did not need to affect a large group of mice all at once … it’s simply a random change that left the mouse better adapted to the new environment, where it could survive and reproduce better than it’s non-mutated relatives. If anything, the Hawk makes choice.

    The mutation could have happened several times over several thousands of years with the mouse not surviving before the change finally was successful … the mutation could have happened to mice that were not in the dunes, where it offered no advantage or was actually a disadvantage, reducing survival.

    Does the mouse scream to the hawk … Hey! Don’t eat me! I’m choosing to blend into the environment better!

    No, it does not.

    The only thing resembling a choice in this matter is that the mutated mouse was able to find a mate that was not turned off by the different appearance.

    … Now careful on this point artfulD, You’re on a slippery slope and might not realize it …

    … If to support your argument, you agree that this is a reproductive choice made by the mouse, then you must accept that this type of choice also starts the mouse down the road of speciation if mutated and non-mutated mice happen to chose to mate only within their colour and therefore become sexually isolated populations long enough for their genomes to drift into incompatibility.

    … due to other random, undirected, chance mutations given enough time.

    … With no ID and no god required.

  34. Steven Novellaon 03 Sep 2009 at 8:01 am

    This case does seem to be purely genetic – the article did not mention any epigenetic factors that control coat color, just the genotype.

    artfulD – you are degrading to ad hominems. I think the point here is that your hypothesis about intention in the mice is simply unnecessary. The favorable gene could spread through the population without any intention from the mice themselves, as a passive consequence of the survival advantage of the phenotype. You have not put forward any argument that says that intention is necessary nor that it is actually present. The mice do not have to sexually favor light-colored mates (btw – when such a thing does happen it is called sexual selection, to distinguish it from natural selection). They did not will the mutation into existence, nor will it to spread and predominate – it just happens as a natural consequence of the survival advantage. Computer models show this quite nicely – without any AI.

  35. artfulDon 03 Sep 2009 at 12:55 pm

    Sursky, as to ad hominem, I didn’t attack the person, I attacked the statements. Your statements are equally dumb. It would be just as pointless to refute them one by one as it would have been with tmacs. Organisms are choice making apparati. If you don’t understand that basic fact, you should refrain from talking about choice as if you did.

    Dr. Novella, I said nothing anywhere about intention, unless you consider all choices made as intentional. But then there would be no need to differentiate the intentional from the unintentional, or the conscious from the unconscious, etc.

    Computer models show what happens, they don’t show why. The simulation of the organism as a maker of choices is (or should be) built into the model. If not, the experiments will be worthless. Evolutionary biologists know this. Apparently you don’t.

    Directed or adaptive mutations are recognized as hypothetically plausible, and in that sense factual. Direction by an organism means the organism contains the directive choice making apparatus. There is large body of scientific work out there that supports this. You don’t have to agree with it, but it’s silly to deny it’s there.

  36. weingon 03 Sep 2009 at 1:46 pm

    “Computer models show what happens, they don’t show why.”

    I prefer to see how something happens. What genes are activated, in what sequence, by whom, or what.
    Asking questions such as why donkeys don’t have wings leads to answers like because they would damage your roof upon landing, etc.

    “Direction by an organism means the organism contains the directive choice making apparatus.” What does this directive choice apparatus? A gene or cascade of genes activated by specific conditions in the environment.

  37. Ryan261357on 03 Sep 2009 at 2:08 pm

    artfulD,

    “There is large body of scientific work out there that supports this. You don’t have to agree with it, but it’s silly to deny it’s there.”

    Ok provide us with some links so that we can better understand your position.

    And maybe some links that better explain your ideas on choice and intention.

  38. artfulDon 03 Sep 2009 at 2:48 pm

    Weing, I think you will find that activated means the phenotype was prompted to exercise the strategies that differentiated it from others of its genotype. The apparatus you are questioning is the one that then makes the choice to act in accordance with its strategic plan. The plan contains the options available to the organism for responding to this particular contingency. Thus does it direct its actions in response to the environment – including the part of that environment that zaps it with these mutational forces.

    Here’s a reference that might help, but then again leading some of you to the water hasn’t been a very effective strategy.
    http://www.plosone.org/article/info:doi/10.1371/journal.pone.0006356

  39. HHCon 03 Sep 2009 at 7:39 pm

    Natural predators of the sandy-colored deer mice are hawks and buzzards. There are eagles along the Niobrara River in the Northern Sand Hills which search for mice to feed their young.

  40. CertifiedCyborgon 03 Sep 2009 at 9:27 pm

    artfulD – That link seems to have nothing to do with your position.

    I’m perplexed as to why you think it is part of “a large body of scientific work” supporting your position. It deals with how the copying mechanisms themselves might bias some mutations over others, and the extent to which selectionairy pressures affect gene expression. Yes it questions the how great a role natural selection plays and yes it looks like there are other factors involved. It’s interesting research, but what has that got to do with Directed Adaptation? It doesn’t mention any motivation on the plants behalf. It doesn’t talk about certain behaviours the plants use which in themselves select for certain genes. As far as I can tell it’s got nothing to do with your position.

    Please correct me.

  41. artfulDon 03 Sep 2009 at 10:11 pm

    That link was offered in response to Weing’s question, not an attempt to answer the other joker who should know all he has to do is google directed adaptation or variations on that theme.
    Then he might get something like this:
    http://www.springerlink.com/content/f81j83umg08553v6/
    But then he’d likely find some way to deny its relevance.

    In your case, if your interest is genuine, you can also do some Googling, or Binging or whatever. The stuff is out there and I’ve cited much of it before on other posts.

    The water is there. It’s for you to decide if it’s drinkable.

  42. Ryan261357on 03 Sep 2009 at 10:45 pm

    I sure hope I am that other joker!

    I also agree with CertifiedCyborg, the evidence you have presented so far has not been very impressive. But I am taking your advice and am googleing like mad. Ill let you know if I decide to drink the water.

  43. CertifiedCyborgon 03 Sep 2009 at 10:56 pm

    I’ve already read the article you’re referring to, we’re not all as daft as you like to think we are. I don’t think anyone’s ruling out the fact that in some cases animal behaviour can create a selectionairy feedback loop of sorts. I’ve already mentioned sexual selection which is but one of these feedback loops.

    I simply still question its relevance or necessity in the mouse example Steven brought up.

  44. dwayneon 03 Sep 2009 at 11:13 pm

    Horse: “This guy keeps telling me there’s water here, but all I see is a metaphor.”

  45. artfulDon 03 Sep 2009 at 11:30 pm

    Maybe it’s because the horse is also a metaphor for a questioner of relevance who finds satisfaction in his bit and his blinders.

  46. Ryan261357on 04 Sep 2009 at 12:33 am

    artfulD,

    First, you should know that some of us including me where genuinely interested in your ideas. Instead of defending your position against perfectly reasonable criticism you have become increasingly hostile. Most of us here are skeptics and as such we require a reasonable amount of evidence before rejecting the standard evolutionary explanation for the results of this study. There is no need to disparage people simply because they have questions, do not understand your position or need clarification.

    Secondly, you are the one with the new radical idea. It is not up to any of us to “discover” what knew modulations you have for the theory of evolution. Instead the burden of proof is on you and it requires a lot more then leading us to the “water”, to use your metaphor. In fact we prefer to be drowned in evidence before overturning such a robust theory as evolution. None of your arguments on this forum topic have done anything of the sort. Your evidence is less then stellar as well.

    Both links you provided in this forum did not support your position in the context of this mice study. Taking your advice I did a search for directive adaptation. I found a number of sources dealing with directed adaptation. Most of them dealt with mathematics and computer science. Computer modeling of evolutionary theory is of course important and can lead scientists in new directions of discovery. However I found nothing in those sources compelling enough to “drink the water”. Instead I came away with the impression that given your arguments in this forum, you do not understand the research. Maybe I didn’t look at the correct articles or am not smart enough but once again it really is not my job to find the evidence to support your position. I also dont feel that articles written in a book about computer science make a real argument against the standard theory of evolution.

    As far as I can tell your arguments seem to take on a weird mixture of lysenkoism, information theory, and computer science. When presented with questions you do not give a cogent answer, but instead present us with your vague philosophical definitions of concepts like choice and intention. I say vague because you do not supported them with an explanation or a single link even when presented with specific questions. Most of your posts make no sense and after reading a number of the articles you suggested I look up, I cannot help the feeling that I might have to classify your ideas as pseudoscience.

  47. artfulDon 04 Sep 2009 at 1:50 am

    Ryan261357,
    Your particular questions have been hostile from the beginning. Only Cyborg professed an interest, but it turns out it was more of a tactic to probe for errors. There’s nothing radical about the ideas of directed mutation. The fact that you pretend a lack of familiarity with the subject until now says a lot about the depth of your understanding of the selection process in general. Pseudoscience? I’m tempted to name the very prominent biologists, and yes, philosophers, who teach and write on the subject here in the US as well as Europe, Asia, Australia, and elsewhere who would be laughing their asses off to hear that. Or maybe not, considering the source.

    Why don’t I name them? Because I’ve done so numerous times in the past with no discernible effects on the level of discourse here.
    Your strategy of deliberate ignorance is just too much to overcome.
    Sites like this will be more to your liking:
    http://blogs.bnet.com/bnet1/?p=382

  48. Ryan261357on 04 Sep 2009 at 2:50 am

    artfulD,

    I have never been exposed to your theories. I am not someone you have met in the past nor should you presume that I have anything against your ideas. Show me the evidence. Show me the people you are referring to. “Name the very prominent biologists [and] philosophers, who teach and write on the subject here in the US as well as Europe, Asia, Australia, and elsewhere.” Let me know who they are so I can read them and understand what you are writing about. Give me a list. I swear I will read them. Give me the first bit of reading you want me to do in order to understand your theory.

  49. pope111on 04 Sep 2009 at 4:19 am

    Much as it pains me to say it, there may be a just a grain of truth to what ArtfulD says (why so arogant? If you want to convince someone of your position on this, tell them and provide information, don’t belittle and provide rubbish links). Although i do not think that it takes away from the importance of natural selection in this case.

    http://jn.nutrition.org/cgi/content/full/132/8/2393S

    From this article it appears that mouse diet can influence coat colour through effects on the expression of the agouti gene in offspring.

    That is, it is possible that a behavior in a mouse can effect its offsprings coat colour and even possibly subsequent offsprings coat colours. In this case it appears that exposure to a particular diet in mice with a particular allele for coat colour can lead to a range of different coat colours in offspring (all of whom have the same geneotype). Mice with other alleles for coat colour showed no epigenetic effects of diet (that is no matter what they ate it had no effect on offsprings coat clour)

    I am not a biologist and although i think i understand most of this study and its implications i could always do with some back up.

    I have seen articles like this before and they are interesting but i dont see where choice comes into it ArtfulD. I think it is at least the wrong word, and i fear may indicate that you do not understand the phenomenon that you are trying to promote.

    In this article i think the experiements controlled the maternal mouse diet (in only mice with the allele which was suscptible to epigenetic effects). So they were controling the environment, this affected the offsprings phenotype (colour of the mouse) without affecting their genotype (DNA). The animal had not choise here, the experimenters did though.

    In the natural environment a mouse might make a descision to eat a particular diet which might influence its colour (or really its offsprings) and thus its liklihood of survival and reprduction. But its propensity to make such a dietary “choice” has to in turn be controlled either by the availabilty of food (the environemnt) or by something else. If something else what? Did it know that if it ate a specific food its children would be more likely to survive? Did eating that diet provide some benefit for it at the time unrelated to the colour of its offspring?

    In any case overall the allele which is susceptible to epigenetic effects and affects coat colour seems also to give some rather nasty side effects to mice who do “choose” to become lighter coloured so it is unlikely to explain the differentiation discussed in Steven article.

  50. artfulDon 04 Sep 2009 at 5:21 am

    pope111, to understand what I mean by choice in this context, read books like the following to start with – I expect from your post you will understand it. I can’t say as much for the ones that decide I’m wrong first, and then in effect dare me to prove they are wrong by proving I’m right, and they’ll be the judge of my efforts. Easily seen as the tactics of the deliberately ignorant.

    Check out this from your library:
    The Life and Behavior of Living Organisms
    A General Theory Elliott Jaques
    Especially read the chapter on The Choice Making Functions of All Living Organisms

    That will give you the key to understanding almost anything else about biological strategies.

    I write comments that I expect people who specialize in the subject area will understand. I’m not interested in the spoon feeding process. If that comes off as arrogant, it’s not by accident. If I get the signal that someone is open to the idea, I’ll gladly expand on the theory. If they just want to poke holes in something they lack the capacity to understand, the hell with them.

  51. CertifiedCyborgon 04 Sep 2009 at 2:13 pm

    So I’m a joker, a poker and I simply lack the capacity to understand the subjects you’re talking about.

    Look artfulD, I’m sorry I haven’t had a formal education in computational biology, and that I’m probably not as passionate about it as you are. I’m in over my head in a topic I don’t have much background knowledge of and I don’t yet understand. You’ve motivated me to fix this, so for that I thank you.

    But let’s get somethings straight.

    In your very first comment I thought you said that the mouse study was evidence for directed adaptation and that Novella was denying this – not that he was simplifying the subject, and glossing over some of the gaps (I thought that to be obvious). I objected to that and questioned the relevance of directed adaption of your idea in the context of this mouse study. I quickly realized I should not have made that judgement without a better understanding of directed adaptation. I said as much and thus begun this escapade.

    I don’t know about you, but usually when someone I start talking about a subject, and fair number of people don’t understand what I’m talking about, it indicates to me I’m haven’t been successful in communicating my ideas – not that my audience is intellectually beneath me. You’ve made it clear that if the people reading the blog had the prerequisite knowledge, they would have understood you perfectly well. You were not trying to educate those of us less informed and it wasn’t your responsibility. If I wanted to take part of the discourse with you I should have taken the time to do a bit of research first.

    The thing is, I did. I opened Google Scholar and the university databases I had access to, and I entered the phrase “Directed Adaptation.” The articles I read were on specific models of computational biology. They were interesting, but seemed unrelated to what you were talking about. Hence why I asked you to clarify and explain your ideas. I was genuinely interested, I wasn’t just searching for errors. I just couldn’t make the connection between the articles and your position.

    Again, not your responsibility. If you don’t care about educating others then that’s fair enough. But why the name calling? Why the patronizing language? If you don’t care for helping those who don’t already understand you then simply say so next time. The venom and ridicule is unnecessary.

  52. CertifiedCyborgon 04 Sep 2009 at 2:15 pm

    Third paragraph should read “Questioned the relevance of directed adaptation in the context of the mouse study.”

  53. artfulDon 04 Sep 2009 at 2:55 pm

    Look at directed mutation. That’s the phrase I used several times here as well. Some people who need to get on with the research prefer to separate the concepts, because as you can see, to talk of directed mutation is utter heresy in this type of crowd. Directed adaptation doesn’t raise as much ire among the more religious devotees of the god of the zaps. They are slow to realize that you don’t have one without the other. Not something they are motivated to think about.

  54. Ryan261357on 04 Sep 2009 at 5:32 pm

    artfulD,

    Wouldn’t you have saved a lot of electronic ink if you would have mentioned this book when we asked for reference materials a day ago? Ill have to check it out.

    CertifiedCyborgon,

    Good post.

  55. Ryan261357on 04 Sep 2009 at 5:49 pm

    If anyone wants to read artfulD’s book suggestion “The Life and Behavior of Living Organisms” by Elliott Jaques, you can read it online at google books.

  56. artfulDon 04 Sep 2009 at 6:08 pm

    Who was it that wrote this: “Try to understand why your proposed “directed evolution” is an unnecessary addition that is not needed to explain this mouse study. In fact the entire theory of evolution has no need of your new mechanism to explain the life we see around us.”
    Whoever that was pronounced himself as knowing it all already.
    Asking a question from such a position is a challenge to put up or shut up.
    So I decided not to put up, and the guy just wouldn’t shut up. He went from scoffing, to asking, to begging. Now it seems he wants to read a book about the things he already knows don’t exist. Because if they existed it would have to be because they were needed, and he knows they aren’t.

    Finally someone asks who really wants to know, and gets a prompt answer, and the denier is all cranky and stuff. I guess he’s not all that content with maintaining a state of ignorance as a strategy.

  57. HHCon 04 Sep 2009 at 10:15 pm

    The sandy-colored mice in the Sand Hills of Nebraska mainly eat grains ,i.e., wheat.

  58. Seadiveron 04 Sep 2009 at 10:56 pm

    Re birds being transistional, back in ’86 Nature said there were true birds before Archaeopteryx (Tim Beardsley, “Fossil Bird Shakes Evolutionary Hypotheses,” Nature, Vol. 322, 21 August 1986, p. 677). Gould said ‘Smooth intermediates between Bauplane [body plans] are almost impossible to construct, even in thought experiments: there is certainly no evidence for them in the fossil record (curious mosaics like Archaeopteryx do not count)” – Gould, S.J. and N. Eldredge. “Punctuated equilibria: the tempo and mode of evolution reconsidered.” Paleobiology, 3 (1977): 115-151. (p. 147)’. Once at a public lecture I asked Gould what he thought about one of his own students (which he graduated with a PhD in paleontology) who believed that most fossils were the result of the flood described in the Bible. He replied ‘I just don’t think one flood can account for all fossils’ [which side-stepped my question, as I did not ask about all fossils].

  59. pope111on 05 Sep 2009 at 8:33 am

    Having thought about it some more i now more firmly think that natural selection is a more likely reason for mouse colour change in this situation.

    Thats not to say that some epigenetic effect is not possible, its just not probable in this case.

    I think there are several things getting confused here. Please anyone comment if they think i am way off track here, as i say i’m not a biologist but i do find this interesting.

    There is a diferrence between epigenetics and adaptive mutation as i read it.

    Epigenetics suggests that changes in phenotype (how the organism looks or functions) can come about without changes in the DNA. Like for instance the mouse diet influencing expresion of certain alleles in either itself (through altering the process of cell division) or possibly its offspring. This is not a terribly contentious idea i dont think, although how important its role is in evolution is i guess much more debatable.

    Adaptive mutation suggests that something other than blind chance is directing mutations (changes in DNA). This to me is the much more challenging idea and i’m not at all convinced that it exists.

    Theoretically it may be possible for changes occuring in an animals lifetime (by epigenetic mechanism for instance) to change or regulate the rate of mutation (or type of mutations?). I think this idea is what ArtfulD is trying to get at.

    I think this is a pretty contencious idea and i dont think alot of mainstream biologists are advancing it. When you see the term epigenetic mutation i think they are refering to a mutation in the epigenetic system (changes in the methyl groups attached to the DNA which regulate its expression), not mutations in the DNA (which is what results in speciation).

    Just thinking out loud now…. i have no evidence for these next comments….It may also be theoretically possible for epigenetic changes to differentiate groups of organisms within a species to an extent that they no longer interbreed as often (not because they can not) but because they do not, say for instance, reside in the same environment as frequently (as is hypothetically possible in the case of these mice). Then the two groups who are initially genotypically identical may slowly drift apart (via normal evolutionary processes) and speciation may take place. In this case the mechanism of speciation is still normal random mutation and natural selection but perhaps you could say that epigenetics rather than envirnemental change per se is the thing which contributes to the speciation.

  60. CertifiedCyborgon 05 Sep 2009 at 10:04 am

    Yeah that’s the way I read it.

  61. CertifiedCyborgon 05 Sep 2009 at 10:21 am

    Sorry, the comment got cut short.

    Yeah that’s the way I read it. Some people use the term as a reference to ontogenic evolution, others to a form of Lamarckism. One of the quirkier articles I read suggested that conscious thought itself had the potential to actively invoke mutations in the DNA; they didn’t present much evidence to back up their position. The common theme is that not all mutations are random. It does run counter to mainstream Neo-Darwinism and it’s still the subject of debate.

  62. HHCon 05 Sep 2009 at 10:54 am

    It is sunny much of the year in the Sand Hills. In the summer it is 100 degrees plus. Sunlight impacts hair coloration in humans as well as mice. Note some of the sandy-bottomed lakes are alkaline. This is a water source which effects physiology. The sandy color of the mice reflects its environment.

  63. artfulDon 05 Sep 2009 at 2:19 pm

    Conscious thought might (and likely will) result from the same stressful experiences that in the aggregate will drive the epigenetic process, but conscious thought can’t be said to have willed any such change as a result of being itself a result. There is no proximate causation to be found in that sequence that I’m aware of.
    If you want to really understand this general subject, you will of course be trying to critique it at the same time, but it’s in the latter process that most of you are going wrong. And particularly in your understanding of causation.

    You (or some of you) can get familiar with that subject here:
    http://plato.stanford.edu/entries/causation-metaphysics/

    Folks, unfortunately for most of you that reject these ideas out of hand, this IS a form of rocket science.

  64. artfulDon 05 Sep 2009 at 4:30 pm

    Think on this a bit for example: The effects of silent mutations were being examined in the thread that followed this one, but that examination said nothing about the proximate causes of the silent mutations themselves. In the literature involving silent mutations the best explanation is always an assumption such as the following, to quote from the Seed magazine article:
    “The fact that silent mutations are not harmless anomalies of nature means that they are not neutral. In contrast, some, if not all, silent sites must be subject to the forces of Darwinian natural selection.”
    Back again to an invocation of something like the god of the zaps as a proximate cause.

    By the way, I hereby claim the copyright to the use of the phrase “God of the Zaps,” and at the same time release that right to any creationist who will find it useful as a bolster to their positions. Because it sure as hell represent the weakest spot in the traditional Darwinian’s perspective. (Which Darwin himself was well aware of as insufficient for a proper explanation of the mechanisms for his proposals.)

  65. weingon 05 Sep 2009 at 4:44 pm

    Rocket science is easy, if you know it. Try as much as I could, I could never figure out how many angels could fit on the head of a pin. If you can define your terms, I’m sure we can all follow. The time spent learning all the technical terms of rocket science in Harry Potter novels, is better spent learning something else if you want to learn how to fly but fine if you are just looking for a diversion. What to do if someone claims to have learned the subtleties of rocket science from Harry Potter?

  66. artfulDon 05 Sep 2009 at 4:52 pm

    Dumb.

  67. John2on 05 Sep 2009 at 7:43 pm

    Artful ID, don’t be so hard on yourself, please!

    I mean, I know that you are struggling to put your ideas into words, but you’re probably not dumb, so don’t give up just yet!

  68. artfulDon 05 Sep 2009 at 7:58 pm

    Holy zap, batspeople, I forgot to define my terms again.

    The God of the Zaps is the deistic entity that routinely intercedes with random bursts of otherwise neutral mutational energy to piggyback and directly zap down the various strategic algorithms that allow life forms to be and remain uninvolved in the selections for the various traits most suitable for not only adaptation but preadaptation.

  69. pope111on 05 Sep 2009 at 9:37 pm

    ArtfulD i think you are slipping outside of the science now and into philisophy…. I have read quite a few scientific papers on adaptive mutation and epigenetics now… there are a very small group of researchers (mainly one group actually) proposing what you seem to be suggesting and the rest of the scientific community has strongly criticised them…

    This is always a warning sign, if an idea, which has been around since the 80′s i might add, does not start to become part of mainstream science it often means that its a poor theory. Not always i will grant you, but in the vast majority of cases.

    Most of the experimental data looking at adaptive mutation involve bacteria, as far as we are aware they do not have conscious thought, as they do not a have a central nervous system it seems very unlikely. So using the term concious seems misleading.

    In animals such as mice, sure its possible they make conscious decisions which influence epigenetic outcomes as i already noted. Its just that i have not seen a scientific paper which shows evidence that this can result or is heavily involved in speciation.

    I would think your explination fits better into the God of the zaps category, in this case the concept of “Choice” it the god of the zaps. I have yet to hear a cogent explanation of it from you (and there was certainly not one in the research paper) linking to a textbook on the philosophy of causation is not terribly impressive.

    If you understand the subject in which you claim to be an expert then you should be able to explain it to this group in terms they can understand, if you can not then you either:
    A) do not understand it as well as you think you do, or
    B) the subject is not rational and can not be understood in any normal sense of the word (i.e. its a load of baloney).

  70. artfulDon 05 Sep 2009 at 11:18 pm

    pope111,
    First of all I specifically stated that the choices involved were NOT conscious. It was Cyborg who said he’d read of some such theory and I posted this response:
    “- but conscious thought can’t be said to have willed any such change as a result of being itself a result.”

    Can’t is of course a contraction of cannot. This is about as close as I’ve come to positing a certainty, and I went on to explain why. Which involves having some understanding of the nature of causation, and this is what philosophy, which has formed the basis of every scientific hypothesis, does best.

    Then you come along and read the entirely opposite meaning, stating, in essence, that because I’m positing a conscious thought process on the part of not only mice but bacteria, I’m full of baloney.

    But why then do you think I specifically referred you to a book about organisms, not philosophy, and asked that you “Especially read the chapter on The Choice Making Functions of All Living Organisms.”

    Does that sound like I expected them to confirm that bacteria make conscious choices?

    You don’t want to accept the importance of some of the work done on adaptive mutation or what is actually work being done at almost every large university on epigenetics, that’s your right.

    I didn’t use terms you could understand when I said choices were not conscious, and you naturally misunderstood me to say the opposite? You have to be lying to base your present diatribe on such a flimsy premise.

    Don’t justify the state of your ignorance by lying about what I actually said and did here. Anyone who cares to go back and read this stuff will know you’re not only ignorant, but a fool in the bargain.

  71. Ryan261357on 06 Sep 2009 at 3:35 am

    Im so tired of you. We are happy to invite people with different opinins on this forum. You have made a mockery of the hard work that people like opope111, CertifiedCyborg myself have been doing it trying to understand your position. You have not aswered anyone with real answers. Your hostility has grown untill its almost disgusting to watch. In short you are a jerk. The way I see it, your only purpose on this forum is not to share information or to learn from others but to Sh**t on people who you dont believe are as smart as you. Though you may feel that you are correct, you are in a skeptics forum where we look at every idea critically. This should be a place for you to go in order to seek people who can vette your ideas and tell you what needs to be done to make them better. Instead you talk down to people-you twist there words and meanings, all under the cover of whatever ideological slant you may have. You have no idea what free discource is and I hope you get banned from this forum.

  72. Ryan261357on 06 Sep 2009 at 3:40 am

    Sorry everyone. I know that what I wrote had nothing to do with science or Dr. Novella’s last post. I just had to get it out.

  73. artfulDon 06 Sep 2009 at 4:51 am

    Yo, ski bum,
    I’m on a skeptics forum where many or most people look at new ideas, as opposed to a persistent and vocal few who are not true skeptics, just disciples of the blog owner. These few will always jump to his defense (even though he has no reason to need it) and parrot the party line as if they really understood it.
    You’re a scoffer first, then at last a beggar. You don’t know diddly squat about natural selection and the fact that you and certain others had never heard of either directed mutation or directed adaptation proves that beyond any real doubt. You may be the biggest fraud of the bunch, pretending to give advice about doing something you not only have never done but most likely never will.
    “We are happy to invite people” you say. Who the hell are you to be issuing invitations? I’ve been posting here much longer than you and already know what to expect from the likes of you and the other ignoramuses.
    You want information, ask an intelligent question. Those who did got answers. Those like yourself who try confrontation first will get nothing from me, and hopefully from no-one else that has observed your tactics.
    Were you in one of my classes, your ass would be out the door in a flash. So would a good many of these others although you may just be the dumbest.
    You say pope111 and yourself have been doing hard work to understand me? I wrote you off from the start so how is that my problem. Pope does such hard work that he doesn’t even read what I actually wrote, and then lies about it. Then he comes up with his gratuitous insults which may have been his purpose all along.
    I suppose I should just let bozos like you and others I don’t need to name make asses of themselves and not bother to reply. Dr. Novella does that (until really provoked), but then he has a reputation to be concerned with.
    I don’t. You and certain others are just rats in my experimental maze. You may choose to learn nothing from me, but you’d be amazed how much I learn from knee jerkers like you.

  74. pope111on 06 Sep 2009 at 8:08 am

    Wow… and you called my post a diatribe.

    Once you start to think that the reason everyone does not concur with your ideas is just because they are far too dumb to understand such weighty issues, you are in trouble….

    Look at the chap who started this all off, Cairns in the 80′s. He published a paper with this theory, he recieved a lot of criticism and from the look of it he is still engaged in publications in the literature trying to convince the rest of the scientific world of his ideas. He did not throw up his hands call the rest of the world idiots and refuse to get into dialogue.

    You also seem to have some kind of persecution complex, i did not start off my posts to try and insult you i am genuinely interested in the subject and think i made this perfectly clear, i also posted the only article on epigenetics specifically relevant to the subject Steven was discussing.

    You still have not provided a simple or at least clear response to my request of an explination of what you mean by choice, you have now told us what it isn’t (conscious) so what do you mean?

  75. artfulDon 06 Sep 2009 at 1:10 pm

    Yo, Popery
    It’s not everyone who doesn’t concur that bothers me, it’s the dummies who put down an idea out of hand and the frauds like the ski bum above. And the ones like you that I start out by helping, and when they don’t get it, they insult me first and use lies to back it up. I choose not to help such people. I gave you a book chapter on biological choice to read and you pretended all I offered was some philosophy that had no role in scientific matters. Go read the book chapter. I’m done responding to you.

  76. CertifiedCyborgon 08 Sep 2009 at 2:41 am

    To be fair pope111, you did misread his post. I was the one who first brought up the idea of consciousness affecting mutation. artfulD agreed with me that it was unlikely due to problems in causality, though he suggested that their may be environmental stresses which cause both (at least that’s how I read his response).

    I don’t like the way he assumes an underlying motive when people misinterpretation his post, nor do I enjoy reading the ad-hominen’s with which he liberally peppers his posts. But hey that’s life.

    artfulD – While I currently disagree with you when it comes to the overall significance that non-random mutations have in the process of evolution, I’m not a mindless disciple of Novella.

    For example I think he’s flat out wrong when he supports the idea of falsifiability as a criteria of whether or not an idea is scientific. Falsification relies on the hidden premise that the data used to falsify an idea will forever remain accurate. I think this is a false assumption; ideas which have been ‘falsified’ can be ‘unfalsified’ when the data used to falsify them is replaced by new, higher resolution data which points in the other direction. I prefer to use the criterion of testability instead.

    What I’m saying is that even though I may respect Novella, and agree with him on many issues, it doesn’t mean I’ll leap to defend him no matter what. I simply didn’t think the mouse study was evidence of behaviourally directed non-random mutation. In contrast, the plant study you linked to does provide evidence that there is a bias in the mutation process of that species.

  77. CertifiedCyborgon 08 Sep 2009 at 2:44 am

    Second paragraph should read “when people misinterpret his posts, nor do I enjoy reading the ad-hominen’s he liberally peppers them with.”

  78. artfulDon 08 Sep 2009 at 5:05 am

    Cyborg, I wasn’t including you as a disciple. As to these others, and to ascribing motives, I’ve run across most of these guys before, and I decided a change in tactics would be an interesting experiment. And so it has been. Too many of them are students or worse pretending to be practicing science – and if one argues from such a deceptive position, this goes to their motives, and they should expect to be called on it. A person who knows his subject will come at you from a different direction than one who merely pretends such knowledge. Dr. Novella tolerates this, as it’s his blog, and he needs to tolerate the dummies and frauds if he’s to make information available to the rest. I don’t have to, and as you can see, what I’ve already decided to do is stop dealing with these bozos, and letting them know why, and exposing them as frauds in the bargain – something I’m sure they never expected. As a consequence, this will prevent me from participating in any substantive discussion here in future, but I knew that going in, and there are more hospitable venues out there in any case.

  79. pope111on 08 Sep 2009 at 7:26 am

    It shouldn’t matter whether someone is a student or a practicing scientist, if their arguments are sound and logic is good then whats the difference.

    I am a practicing scientist but have had my students point out my own mistakes before.

    I would guess that no one (including you Artful) is really qualified to talk definatively about these issues as none of us is involved in research in this precise area.

    An attitude of intellectualy superiority will thus not get you very far, particularly with a crowd such as this, who are also likely to have more than a passing familiarity with science and are likely to be on the higher side of the IQ scale. Best of luck finding a more hospitable venue.

  80. artfulDon 08 Sep 2009 at 12:54 pm

    Your alleged students didn’t lie about being students, did they? If those I’m referring to here did in fact have sound and logical arguments, the lying wouldn’t have been so obvious. In your case, some of the explanations you initially proposed were laughable. I didn’t attack any of them on that basis, as at least you were trying to understand, or so it seemed. Turns out you can’t read all that well, and I may have mistaken that disability for deliberateness.

  81. pope111on 08 Sep 2009 at 7:19 pm

    ..no no, i wouldn’t want you to hold back on your criticism, please do offer you critique and counter points, thats the idea of this kind of thread is it not?

    If i have badly erred in my simplified explinations of epigenetics and adaptive mutations please do tell.

  82. artfulDon 08 Sep 2009 at 8:20 pm

    Maybe the way mice change color to match the environment is to coincidentally adopt a different diet? (Sorry, couldn’t resist the bait.)

  83. pope111on 09 Sep 2009 at 1:45 am

    ….different environment=different diet, no co-incidence, they dont have a choice in the matter they have to eat whatever happens to be around, thats the point…

  84. artfulDon 09 Sep 2009 at 3:05 am

    A (possible) new source of food in the sand dunes coincides with the mice becoming the same color as the dunes, and that becomes your scientific assessment of either the how or the why? Where’s the nexus, the proximate cause, the proposed mechanism? How do you ignore the inconsistencies with other examples reported of this rather ubiquitous natural camouflage phenomena? How would you settle on such improbable speculation as the best explanation? You scoffed at my suggestion of reading, not a book, but an in depth article on causation. You say you’re a practicing scientist and that you have students in some such capacity? And you think causation is just some sort of philosophical side issue? It’s as central to the scientific method and discovery as any concept could be.

    That’s it. My last comment on the subject.

  85. pope111on 09 Sep 2009 at 6:24 am

    You misunderstand, i do not think that the mouse diet did influnce their colour in this case (although it is theoretically possible as shown by the colour changes caused by epigenetic changes seen in mice fed a certain diet, c.f. the paper i linked to previously).

    I think it is exceeding unlikely in fact, the chances that a mouse will just happen to have find itself in an environment in which its new diet will just happen to have the effect of changing its colour to the colour which will be advantageous in that particular environment is exceeding small. If you recall, the only reason i started out on that track was to give you a little support in your contention that what an organimsm does (chooses) in its life can influence its (or at least its offsprings) phenotype without the necessity of a random mutation.

    If you can not understand that , read the article.

    I think its much more likely that a traditional random mutation/ natural selection type explination is correct in this case (as i have already stated).

  86. artfulDon 09 Sep 2009 at 2:10 pm

    Musings on the subject of relevance:

    The mice “experience” that they are in an environment of a different color. Coincidentally, or so it seems, they evolve to take on that same color. And it also seems that epigenetic mechanisms may turn out to be one way in which the effects of such experience on an organism can be heritable.
    So we have here a physiological change that seems to have been dictated by experience and with an eery specificity to the organism’s observations. Of course we don’t know if the selection process was epigenetic. But we know, or should know, there is a selection process here that has little to do with the type of choices involved, conscious or otherwise, in adapting to new or different food sources.
    Assuming we know that choices are involved at all, or know a particular example of hypothetical behavioral changes would have relevance to physiological changes because we have a sufficient understanding of the nature of biological choice.
    But then where an ultimate denial that choice was involved in the process at all, even though the organism’s experience clearly was, would seem to belie the notion of such an understanding.
    Leaving one free to see relevance in the web of causality without any purpose to the singling out of a particular section or strand.

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