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Thread: The book Darwin Devolves

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    tWebber lee_merrill's Avatar
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    Lightbulb The book Darwin Devolves

    I've just finished the book Darwin Devolves by Michael Behe, and it was a good read. His main argument is that usually the favorable mutations that natural selection has to work on are due to mutations that break or degrade genes. Devolution for survival is the norm, and mutations that restore original function are highly unlikely, so the mutated organism stays in the devolved state.

    Source: Darwin Devolves

    Burning down a gene or control region to help adapt to one demand means it is unavailable to help adapt to future ones. A fine illustration is Yersinia pestis, the bacterium that caused the Black Death in the fourteenth century. … About five thousand years ago Y. pestis apparently acquired two small DNA plasmids from other bacteria that carried several genes that allowed it to survive in fleas and so to be transmitted to people in a new way, by flea bite. Those are classified as gain-of-FCT [FCT: Functional Coded elemenT] events. The microbe then quickly adjusted to its new infectious lifestyle by losing a hundred and fifty genes that apparently were no longer needed in its new environment—which is of course a massive loss-of-FCT. It seems quite safe to say that the bug is now stuck where it is, as an obligatory blood-borne pathogen. Although random mutation and natural selection might adjust it a bit further—perhaps allowing it to infect a different host at some future point—it will never be free-living again.

    © Copyright Original Source



    This makes it difficult for the object or organism to be co-opted by mutation and selection for another purpose, since a loss of function reduces the raw material for evolution to work on. Behe thus describes mutation and natural selection as self-limiting, he investigates what evolution has actually done, in Darwin's finches for example, and concludes that the edge of evolution is at the level of biological "family". The finches presumably came from an original group of finches that landed on the islands many years ago, and produced, a finch.

    Blessings,
    Lee
    "What I pray of you is, to keep your eye upon Him, for that is everything. Do you say, 'How am I to keep my eye on Him?' I reply, keep your eye off everything else, and you will soon see Him. All depends on the eye of faith being kept on Him. How simple it is!" (J.B. Stoney)

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    Evolution is God's ID rogue06's Avatar
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    And yet in the real world we can see this taking place such as with Nylonase and Richard Lenski's E. coli long-term evolution experiment

    I'm always still in trouble again

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  3. Amen shunyadragon, gladiatrix amen'd this post.
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    tWebber HMS_Beagle's Avatar
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    Quote Originally Posted by lee_merrill View Post
    I've just finished the book Darwin Devolves by Michael Behe, and it was a good read. His main argument is that usually the favorable mutations that natural selection has to work on are due to mutations that break or degrade genes. Devolution for survival is the norm, and mutations that restore original function are highly unlikely, so the mutated organism stays in the devolved state.
    This latest turd by Behe has already been reviewed and soundly refuted by a large number of actual evolutionary biologists. For example this highly critical review in the journal Science

    A biochemist’s crusade to overturn evolution misrepresents theory and ignores evidence

    There are indeed many examples of loss-of-function mutations that are advantageous, but Behe is selective in his examples. He dedicates the better part of chapter 7 to discussing a 65,000-generation Escherichia coli experiment, emphasizing the many mutations that arose that degraded function—an expected mode of adaptation to a simple laboratory environment, by the way—while dismissing improved functions and deriding one new one as a “sideshow” (1). (Full disclosure: The findings in question were published by coauthor Richard Lenski.)

    Behe also ignores the fact that some of his prior arguments have been dismantled (2). He includes a lengthy appendix that argues that the blood-clotting cascade is irreducibly complex, for example, but fails to mention Kenneth Miller’s simple, elegant scheme for its stepwise evolution (3) or the fact that a progenitor fibrinogen gene has been discovered in echinoderms (4).

    Behe doubles down on his claim that the evolution of chloroquine resistance in malaria by random mutations is exceedingly unlikely because at least two mutations are required, neither of which is beneficial without the other. His calculations have already been refuted (5), and it has long been known that neutral and even deleterious mutations can provide stepping stones to future adaptations. Indeed, a 2014 study, unmentioned by Behe, reported discovery of two genetic paths through which malaria has evolved chloroquine resistance through multiple steps (6).

    Missing from Behe’s discussion is any mention of exaptation, the process by which nature retools structures for new function and possibly the most common mechanism that leads to the false impression of irreducible complexity. Some Sphingomonas bacteria, for example, have evolved the ability to digest a wood preservative, pentachlorophenol, by recruiting two unrelated biochemical pathways (7). Neither pathway can do that job alone, yet there they are together. The feathers of birds, gas bladders of fish, and ossicles of mammals have similar exaptive origins.

    Exaptation also challenges Behe’s notion of “devolution” by showing that loss of one function can lead to gain of another. The evolutionary ancestors of whales lost their ability to walk on land as their front limbs evolved into flippers, for example, but flippers proved advantageous in the long run.

    Behe is skeptical that gene duplication followed by random mutation and selection can contribute to evolutionary innovation. Yet there is overwhelming evidence that this underlies trichromatic vision in primates (8), olfaction in mammals (9), and developmental innovations in all metazoans through the diversification of HOX genes (10). And in 2012, Andersson et al. showed that new functions can rapidly evolve in a suitable environment (11). Behe acknowledges none of these studies, declaring an absence of evidence for the role of duplications in innovation.
    Dr. Richard Lenski of LTEE fame has written a four part detailed dismembering of Behe's nonsense

    More criticisms of Behe’s new ID book

    In my first post, I explained that Behe’s arguments confuse and conflate what is easy and commonplace over the short run (i.e., mutations that break or blunt functional genes) with the lasting impacts of less frequent but constructive adaptations (i.e., new functions and subsequent diversification) over the long haul of evolution. My second post examined a case involving polar bears, which Behe highlighted as a compelling example of degradative evolution, but where a careful review of the science suggests that gene function improved. Behe also highlighted results from my lab’s long-term evolution experiment with bacteria, but in my third post I explained that he overstates his case by downplaying or dismissing evidence that runs counter to his argument.

    In this post, I’ll discuss an experiment that Behe ignores in Darwin Devolves. (Behe clearly knows the work, because he wrote about it on the Discovery Institute’s anti-evolution blog. But as usual, he spun the story to obscure the problems for his arguments, all the while accusing the scientists who collect data to test hypotheses of spinning the story.) In fact, as I’ll explain, the results also undermine the claims in Behe’s two previous books, Darwin’s Black Box and The Edge of Evolution, about the supposed shortcomings of evolution.
    and another highly critical review

    Intelligent Design Gets Even Dumber

    Bottom line is this is one more scientifically worthless propaganda book sponsored by the DI with cherry-picked data, misrepresentations, and outright lies about actual evolutionary theory.

  5. Amen Tassman, shunyadragon, Seeker, gladiatrix amen'd this post.
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    Evolution is God's ID rogue06's Avatar
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    Yup the hand waving off of an example of improved functions in Lenski's experiment as a "sideshow" since it demolishes his case is very telling.

    I'm always still in trouble again

    "You're by far the worst poster on TWeb" and "TWeb's biggest liar" --starlight (the guy who says Stalin was a right-winger)
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    tWebber lee_merrill's Avatar
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    Quote Originally Posted by HMS_Beagle View Post
    This latest turd by Behe has already been reviewed and soundly refuted by a large number of actual evolutionary biologists. For example this highly critical review in the journal Science
    Well, here is some of the review of Lenski's work:
    Source: Darwin Devolves

    In order to best accommodate the gene rearrangement that gave it the talent to eat citrate, several other mutations were found that fine-tuned its metabolism. Even before the critical mutation occurred, a different mutation in a gene for a protein that makes citrate in E. coli degraded the protein’s ability to bind another metabolite, abbreviated NADH, which normally helps regulate its activity. Another, later, mutation to the same gene decreased its activity by about 90 percent. Why were those mutations helpful? As the authors write, “When citrate is the sole carbon source, [computer analysis] predicts optimal growth when there is no flux through [the enzyme]. In fact, any [of that enzyme] activity is detrimental.” And if something is detrimental, random mutation will quickly get rid of it. Further computer analysis by the authors suggested that the citrate mutant would be even more efficient if two other metabolic pathways that were normally turned off were both switched on. They searched and discovered that two regulatory proteins that usually suppress those pathways had been degraded by point mutations; the traffic lights were now stuck on green.

    © Copyright Original Source


    So the point is clearly made here, deleterious, favorable mutations predominate.

    Dr. Richard Lenski of LTEE fame has written a four part detailed dismembering of Behe's nonsense …
    And here is Behe's first response to Lenski.
    Source: Behe

    Experimental evidence strongly supports my conclusion (disputed without good reason by Lenski and others) that highly selected mutations in the polar bear genome work by breaking or blunting pre-existing functions.

    [Source]

    © Copyright Original Source




    and another highly critical review

    Intelligent Design Gets Even Dumber[/QUOTE]
    Source: Washington Post

    First, they pointed out numerous scenarios in which a system fitting Behe’s definition of “irreducible complexity” could evolve in a step-by-step manner (one is the hormone pathway studied by my Chicago colleague Joe Thornton).

    © Copyright Original Source


    Simple IC systems can evolve, though with difficulty, Behe discusses evolution of a new disulfide bond, for instance. But no evolutionary scenarios for the evolution of flagella have been found, only comparative protein studies, which though highly touted, are not demonstrations of evolutionary pathways.

    Source: Washington Post

    Further, Behe’s rationale for designed mutations is circular. He claims that biochemical pathways are designed rather than evolved because they’re based on the “purposeful arrangement of parts.” But which arrangements are those designed with a purpose? They’re simply the pathways that Behe sees as too complex to have evolved. This is a classic example of begging the question: assuming what you’re supposed to prove (purposefulness).

    © Copyright Original Source


    Well, no, his argument depends on probability of evolution producing an object, "pathways that Behe sees as too complex to have evolved." The question is not begged.

    Source: Washington Post

    Perhaps Behe’s most ludicrous claim is this: Evolution within the lowest levels of biological classification — genera and species — might be purely Darwinian, but the origin of higher-level groups — families, orders and so on — requires designed mutations. Yet as every biologist knows, groupings above the level of species are purely subjective. That is, whether you call a group a family or a genus is arbitrary, depending on the tastes of the scientists who work on that group.

    © Copyright Original Source


    But this is silly, higher orders are not purely subjective.

    Source: Washington Post

    Mutation supposedly acts as a brake on evolution because, argues Behe, most genes that fuel adaptation have been irreparably broken and inactivated by mutations (a gene that doesn’t do anything can still be better than one making an unneeded product). And a dead gene, because it tends to degrade further, can’t easily be reactivated. Evolution, then, must eventually grind to a halt.

    © Copyright Original Source


    Yes, this is Behe's argument.

    Source: Washington Post

    … but he simply ignores the large number of adaptive mutations that do not inactivate genes. These include duplications, in which a gene is accidentally copied twice, with the copies diverging in useful ways (this is how primates acquired our three-color vision, as well as different forms of hemoglobin); changes not in gene function but in how and when a gene is turned on and off, like mutations producing lactose tolerance in milk-drinking human populations; the repurposing of ancient genes acquired from viruses (one source of the mammalian placenta); “chimeric genes” cobbled together from odd bits of DNA (e.g., genes producing antifreeze proteins in fish blood ); and simple changes in DNA sequence that alter proteins without breaking them (tolerance of low oxygen levels in high-flying geese). As long as a substantial number of genetic mutations don’t break genes, which seems to be the case, evolution can work just fine.

    © Copyright Original Source


    Yes, Behe acknowledges that beneficial, non-destructive mutations occur, only that these are rare compared to deleterious favorable mutations.

    Blessings,
    Lee
    "What I pray of you is, to keep your eye upon Him, for that is everything. Do you say, 'How am I to keep my eye on Him?' I reply, keep your eye off everything else, and you will soon see Him. All depends on the eye of faith being kept on Him. How simple it is!" (J.B. Stoney)

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    tWebber TheLurch's Avatar
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    Quote Originally Posted by rogue06 View Post
    Yup the hand waving off of an example of improved functions in Lenski's experiment as a "sideshow" since it demolishes his case is very telling.
    That's the thing that amazes me about Behe. His ideas get completely dismantled with regularity - his "Edge of Evolution" ignored 80 years of developments in the field of population genetics, to give on example. But he just dismisses everything without engaging it, and keeps going like nothing ever happened. You'd think at some point embarrassment would become a factor, but apparently not. I really wonder what's going on personality wise to drive behavior like that.

  9. Amen shunyadragon, gladiatrix amen'd this post.
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    tWebber TheLurch's Avatar
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    Quote Originally Posted by lee_merrill View Post
    Simple IC systems can evolve, though with difficulty, Behe discusses evolution of a new disulfide bond, for instance. But no evolutionary scenarios for the evolution of flagella have been found, only comparative protein studies, which though highly touted, are not demonstrations of evolutionary pathways.
    But that's one of the many fundamental flaws with ID. Its basic premise is that there is no possible way for a class of systems to evolve. All you need to do is show that such pathways could exist to demonstrate that this claim is wrong - you don't need to actually show that anything did evolve down those pathways.

    Quote Originally Posted by lee_merrill View Post
    But this is silly, higher orders are not purely subjective.
    Then i'm sure you can explain how we measure the amount of change that's sufficient to produce a new order, but not a new class.

  11. Amen shunyadragon amen'd this post.
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    tWebber HMS_Beagle's Avatar
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    Quote Originally Posted by lee_merrill View Post
    Yes, Behe acknowledges that beneficial, non-destructive mutations occur, only that these are rare compared to deleterious favorable mutations.
    (facepalm) "deleterious favorable mutations" is an oxymoron with the emphasis on moron. If a mutation is favorable or beneficial then it can't be deleterious by definition.

    Science has known for almost 70 years evolution works by modifying existing structures. It matters not one iota if the old configuration is "degraded" since in the new environment the new configuration works better than the old. Behe apparently is counting on his readers being pitifully scientifically ignorant and not understanding basic evolutionary mechanisms like gene duplication followed by subsequent mutations to the new copy. Behe also completely ignore the effect of neutral drift in providing new raw materials for mutations to act on. Part IV of Dr. Lenski's review gives a verified example of a multi-stage IC forming mutation happening, something Behe has repeatedly claims is impossible for evolution to do.

    All in all this was another stinker by Behe full of brutally bad cherry-picked and misrepresented science. Just like his other two books this was also was beaten into mist by actual evolutionary scientists. Behe has given up all pretense of writing scientifically valuable works and now churns out this crappola just to make money from the few remaining IDiots dumb enough to pay it.

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    tWebber HMS_Beagle's Avatar
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    Quote Originally Posted by TheLurch View Post
    That's the thing that amazes me about Behe. His ideas get completely dismantled with regularity - his "Edge of Evolution" ignored 80 years of developments in the field of population genetics, to give on example. But he just dismisses everything without engaging it, and keeps going like nothing ever happened. You'd think at some point embarrassment would become a factor, but apparently not. I really wonder what's going on personality wise to drive behavior like that.
    Either Behe has decided to sacrifice his scientific integrity to push his religious beliefs, or he's in it for the easy money from the IDiot true believers, or both.

  14. Amen shunyadragon amen'd this post.
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    tWebber shunyadragon's Avatar
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    Quote Originally Posted by lee_merrill View Post
    I've just finished the book Darwin Devolves by Michael Behe, and it was a good read. His main argument is that usually the favorable mutations that natural selection has to work on are due to mutations that break or degrade genes. Devolution for survival is the norm, and mutations that restore original function are highly unlikely, so the mutated organism stays in the devolved state.

    Source: Darwin Devolves

    Burning down a gene or control region to help adapt to one demand means it is unavailable to help adapt to future ones. A fine illustration is Yersinia pestis, the bacterium that caused the Black Death in the fourteenth century. … About five thousand years ago Y. pestis apparently acquired two small DNA plasmids from other bacteria that carried several genes that allowed it to survive in fleas and so to be transmitted to people in a new way, by flea bite. Those are classified as gain-of-FCT [FCT: Functional Coded elemenT] events. The microbe then quickly adjusted to its new infectious lifestyle by losing a hundred and fifty genes that apparently were no longer needed in its new environment—which is of course a massive loss-of-FCT. It seems quite safe to say that the bug is now stuck where it is, as an obligatory blood-borne pathogen. Although random mutation and natural selection might adjust it a bit further—perhaps allowing it to infect a different host at some future point—it will never be free-living again.

    © Copyright Original Source



    This makes it difficult for the object or organism to be co-opted by mutation and selection for another purpose, since a loss of function reduces the raw material for evolution to work on. Behe thus describes mutation and natural selection as self-limiting, he investigates what evolution has actually done, in Darwin's finches for example, and concludes that the edge of evolution is at the level of biological "family". The finches presumably came from an original group of finches that landed on the islands many years ago, and produced, a finch.

    Blessings,
    Lee
    This is voodoo science. I cannot even comprehend this in terms of the contemporary science.
    Glendower: I can call spirits from the vasty deep.
    Hotspur: Why, so can I, or so can any man;
    But will they come when you do call for them? Shakespeare’s Henry IV, Part 1, Act III:

    go with the flow the river knows . . .

    Frank

    I do not know, therefore everything is in pencil.

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