IDers already distorting Behe’s new paper

Over at the intelligent-design site Uncommon Descent, the ever befuddled Denyse O’Leary has already glommed onto the review I wrote yesterday of Michael Behe’s new paper. And, exactly as I predicted, she distorts Behe’s conclusions:

So, not only must the long, slow process of Darwinian evolution create every exotic form of life in the blink of a geological eye, but it must do so by losing or modifying what a life form already has.

In other words, she’s extended Behe’s conclusions, based on viral and bacterial evolution in the lab, to evolution of “every exotic form of life” on the planet.  This is exactly what one cannot do with Behe’s conclusions.

If you read Behe’s paper, or my take on it, you’ll see that Behe restricted his conclusions to the types of mutations that create adaptations in certain short-term laboratory experiments on viruses and bacteria.  He concluded that adaptive mutations in these experiments usually involved either inactivation of genes or genetic elements, or point mutations that modified, but did not qualitatitively change, gene function.  In these studies one doesn’t often observe the evolution of entire new genetic elements—Behe calls them “functional coded elements” or “FCTs”—in the lab.

Importantly, there were two critical caveats about his conclusions that restrict their relevance to evolution as it’s happened in nature. Indulge me while I repeat these:

1) The experiments Behe reviewed deliberately excluded important sources of mutations that create new genes and gene elements of evolution in naturally-occurring bacteria and viruses.  Those studies are not, then, a good model for what actually happens during microbial evolution in nature, which is known to involve uptake of new genes and genetic elements from other species via horizontal DNA transfer.  And this type of evolution involves the appropriation and creation of new FCTs.

2) Behe’s conclusions also can’t extend to eukaryotic species (those with “true” complex cells), because we know that in those groups the creation of new FCTs via gene duplication and other processes has been hugely important in evolution in nature.

See yesterday’s post for a more detailed explanation.

O’Leary either didn’t read what I wrote or, more probably, chose to ignore it.

She further distorts what I said:

This, apparently, got evolutionary biologist Jerry Coyne’s recent attention:

“Anyway, Behe reviews the last four decades of work on experimental evolution in bacteria and viruses (phage), and finds that nearly all the adaptive mutations in these studies fall into classes 1 and 3. We see very few “gain of FCT” mutations. Although this is not my field, the review seems pretty thorough to me, and the conclusions, as far as they apply to lab studies of adaptation in viruses and bacteria, seem sound.”

It looks as though Coyne must now actually take Behe’s argument seriously.

Bad of her to leave out these parts that I wrote:

Behe has provided a useful survey of mutations that cause adaptation in short-term lab experiments on microbes (note that at least one of these—Rich Lenski’s study— extends over several decades).  But his conclusions may be misleading when you extend them to bacterial or viral evolution in nature, and are certainly misleading if you extend them to eukaryotes (organisms with complex cells), for several reasons . . .

While Behe’s study is useful in summarizing how adaptive evolution has operated over the short term in bacteria and viruses in the lab, it’s far less useful in summarizing how evolution has happened over the longer term in bacteria or viruses in nature—or in eukaryotes in nature.  In this sense it says nothing about whether new genes and gene functions have been important in the evolution of life.  Granted, Behe doesn’t make such a sweeping statement—his paper wouldn’t have been published if he had—but there’s no doubt that his intelligent-design acolytes will use the paper in this way.

Thanks, Ms.O’Leary, for confirming my prediction.

_____

UPDATE:  I’ve changed the title from “Discovery Institute” to “IDers” to reflect the fact that O’Leary was commenting on Uncommon Descent which, as far as I know, is not a formal arm of the DI.  But the the DI’s approbation will surely come in time.

35 Comments

  1. Posted December 13, 2010 at 8:47 am | Permalink

    To be fair, predicting that the DI IDiots would distort your review is like predicting that the high temperature here in Tempe, Arizona will be over 100° F on the Fourth of July. You’ll have to do better to impress us with your prognostication skills, I’m afraid.

    Cheers,

    b&

    • whyevolutionistrue
      Posted December 13, 2010 at 8:51 am | Permalink

      Hey! I predicted it would be distorted in a particular way! Give me some credit. . . Anyway, somebody has to keep on top of this stuff.

      • Insightful Ape
        Posted December 13, 2010 at 10:13 am | Permalink

        I think Ben is too harsh. Thank you for yesterday’s post predicting the distortions and taking them apart pre-emptively in the middle of the Chicago blizzard.

        • Posted December 13, 2010 at 10:19 am | Permalink

          I presume he didn’t go outside to do it.

          :- )

        • Posted December 13, 2010 at 11:01 am | Permalink

          To be fair, I think Jerry understood that my tongue was in my cheek….

          b&

      • truthspeaker
        Posted December 13, 2010 at 11:44 am | Permalink

        One could call it “specified dishonesty”.

  2. Posted December 13, 2010 at 8:53 am | Permalink

    Why do you limit the importance of gene duplication to eukaryotes? See, for example: http://www.biology-direct.com/content/4/1/46

    “Evolution by leaps: gene duplication in bacteria” Biology Direct 2009, 4:46doi:10.1186/1745-6150-4-46

    From the abstract:

    “Protein families seem likely to have arisen during evolution by gene duplication and divergence where the gene copies that have been retained are the variants that have led to distinct bacterial physiologies and taxa. Thus divergence of the duplicate enzymes has been a major process in the generation of different kinds of bacteria.”

    • whyevolutionistrue
      Posted December 13, 2010 at 9:08 am | Permalink

      I didn’t know of this paper, and was under the impression, which still may be correct, that gene duplication—and by that I mean duplication of a gene within a single individual—is less prevalent in bacteria than in eukaryotes. And it’s also possible that some of these “duplications” involve horizontal transfer of genes among individuals within E. coli by one of the two mechanisms that species has for exchanging genes. (Unlike many other bacteria, E. coli can’t simply take up naked DNA from the environment). That’s sort of a distinction without a difference! Nevertheless, to the extent that this process has been important in prokaryotes, and not just E. coli, it further shows the weakness of extending Behe’s conclusions to evolution in the wild. These types of duplications may be rare in the lab but important over long periods of time in the wild.

  3. Jeffrey Shallit
    Posted December 13, 2010 at 9:00 am | Permalink

    O’Leary is not a real journalist; she’s a partisan hack who almost never reports anything she disagrees with.

    • Badger3k
      Posted December 14, 2010 at 1:32 am | Permalink

      Plus her understanding of science is so limited that she probably wouldn’t pass a 4th grade science test.

  4. TBnSuch
    Posted December 13, 2010 at 9:22 am | Permalink

    In regards to point 1), won’t IDer’s simply say that horizontal DNA transfer does not result in new FCTs as the ‘information’ was already intact prior to the transfer?

    • whyevolutionistrue
      Posted December 13, 2010 at 9:25 am | Permalink

      They can’t really say this for two reasons:

      1. If the transfer comes from a completely different group, as it often does, then it leads to a brand new and novel genetic element within the species that acquires it, and thus a novel function within that species. This is clearly a “gain-of-FCT” mutation within the acquiring species.

      2. Behe counts gene duplication and subsequent divergence as a “gain-of-FCT” mutation.

  5. Posted December 13, 2010 at 9:35 am | Permalink

    Denyse O’Leary, the Catholic cookie baker, uses FTC in all her recipes.

  6. Tualha
    Posted December 13, 2010 at 9:37 am | Permalink

    O’Leary either didn’t read what I wrote or, more probably, chose to ignore it.

    Because, even more probably, she didn’t understand it.

    • steve oberski
      Posted December 13, 2010 at 10:25 am | Permalink

      She deliberately chooses not to understand it and is proud of her ignorance.

      Which she then puts on an alter and worships as a god.

      This is entirely consistent with the dogma of her cult.

      She is really no different from the more “sophisticated” motifs on this theme.

      I attended a talk by George V. Coyne, S.J., Jesuit priest, astronomer, and former director of the Vatican Observatory.

      After bashing creationism and ID he then processed to present a teleological argument for Homo sapiens somehow being singled out by his god for special treatment and being endowed with a soul. The tree of life has a direction ergo jesus. Or so his argument went.

      I see no difference between the creationists like O’Leary and the “theistic evolutionists” like George Coyne and Ken Miller except that O’Leary is being honest about her beliefs.

      • Tim Harris
        Posted December 13, 2010 at 4:09 pm | Permalink

        She may be being honest in her beliefs, but she is being thoroughly dishonest in every other respect. I think Jerry Coyne has been a bit too nice… These people really need to be called out on their dishonesty.

        • steve oberski
          Posted December 13, 2010 at 5:34 pm | Permalink

          Perhaps I shouldn’t have used the word “honest”.

          “Consistent” might be more accurate.

          O’Leary is just a clown and a buffoon, she is not the problem, she only speaks to those that have already closed their minds.

          I’d like to see the Millers and like minded “theistic evolutionists” call her out.

          I’ve heard George V. Coyne doing this and it isn’t pretty, but if anything has a chance of reaching the right audience and get them to re-evaluate their position, this is it.

          The cognitive dissonance must be strong in those folks.

  7. Umkomasia
    Posted December 13, 2010 at 9:40 am | Permalink

    Many of the ID creationists are on record as saying they will not accept the evolution of complex structures (ones they would call irreducibly complex)until it can be shown in the laboratory in real time. This is based on their highly restrictive view of science that underplays the importance of model building and inference based on phylogenies. Trying then to convince them of the reality of macroevolution is impossible even in principle.

  8. Kevin
    Posted December 13, 2010 at 10:08 am | Permalink

    I propose a new metric.

    DI = amount of time it takes a Discovery Institute n00b to quote mine a critique of a DI-sponsored or “supportive” paper.

    I propose 1 hour as the standard DI.

    My my reckoning, it took about 4 hours for O’Leary to quote-mine Coyne. Therefore, 4 DIs.

    We could call it the O’Leary.

  9. justsearching
    Posted December 13, 2010 at 10:19 am | Permalink

    Such blatant distortions indicate she and her DI cohorts are either deceptive or dumb. I’ll give them some credit on this one and say they’re just the first.

  10. MadScientist
    Posted December 13, 2010 at 10:58 am | Permalink

    They’re so predictable that it’s not even worth asking James Randi if he’d hand over the million bucks …

  11. Luke
    Posted December 13, 2010 at 10:59 am | Permalink

    It seems to me that one of the main problems with extrapolating results on this kind of issue from the lab to nature is in the complexity of the selection pressures. In experimental evolution, there is usually a single, simple, specified and quantitative goal. All the other needs of the organism are artificially met, so many changes may be permissible that otherwise would not be in nature, where there are many different aspects of the environment which must be dealt with simultaneously. In nature, evolution occurs more slowly, but it seems to be more meticulous as well.

    In other words, in the lab, it doesn’t matter if the bacteria “gum the works,” to quote Behe, as long as they increase fitness with respect to a single quantitative trait. This would not be the case in nature.

  12. Posted December 13, 2010 at 11:36 am | Permalink

    the long, slow process of Darwinian evolution create every exotic form of life in the blink of a geological eye

    Apropos of very little, one thing I always have to remind myself of is that evolution is a parallel process. A massively parallel process, in fact.

    Sometimes it seems just staggering that so many different organisms could have evolved even in the billions of years they had to do it in. Sometimes it’s tempting to think, “I’d believe a few hundred in that time, but not all the species we see!”

    But that’s serial thinking. Natural selection is operating in every single organism all of the time. It’s like a computer with (literally) trillions of processors. It’s not like natural selection first turns it’s attention to this phylum, and then when that phylum’s done, it goes and adds diversity to some other phyla. It’s all happening all at the same time, everywhere, in every organism.

    That’s an easy thing to forget, I think.

    • Torbjörn Larsson, OM
      Posted December 13, 2010 at 3:57 pm | Permalink

      True. Coevolution happens too, so the local algorithmic processors (learning genomes) interact as parts of their respective environments. Massively parallel and massively interlinked.

  13. Ken Pidcock
    Posted December 13, 2010 at 11:57 am | Permalink

    Those studies are not, then, a good model for what actually happens during microbial evolution in nature, which is known to involve uptake of new genes and genetic elements from other species via horizontal DNA transfer.

    Too few evolutionary biologists appreciate the magnitude of horizontal gene transfer among bacteria, and its significance in bacterial evolution. It makes Behe’s analyses kind of meaningless. (It also, of course, reveals how limited Lenski’s work is, but it is limited by design.)

    • Torbjörn Larsson, OM
      Posted December 13, 2010 at 4:04 pm | Permalink

      The magnitude isn’t all that great, as I understand it. If you do massive genome analysis (many genes and species) and add transition analysis you find:

      a) more than 1 HGT/gene*4.5 Gy on _all_ genes, including ribosomal DNA; but not much more, as I understand it. [Duh, can't find the ref as I write.]

      b) The dominant VGT is “easily” traceable by phylogenic trees for prokaryotes, as “per usual”.

      Darwin was “right”, Woese was “wrong”!?

      • Ken Pidcock
        Posted December 13, 2010 at 6:11 pm | Permalink

        How is Woese wrong again?

  14. Gayle Stone
    Posted December 13, 2010 at 12:41 pm | Permalink

    Oleary’s comments sound about as SOUND as the ramblings of Sarah Palin. We see VERY FEW mutations. Although this is NOT MY FIELD, the review SEEMS PRETTY thorough TO ME, and the etc.,etc., etc. SEEM SOUND. Serious reasoning?
    But Coyne MUST take Behe seriously!

    • Tulse
      Posted December 13, 2010 at 2:51 pm | Permalink

      Hey, Gayle, what’s with the shouting?

  15. Wayne Robinson
    Posted December 13, 2010 at 6:53 pm | Permalink

    Behe’s paper is available online:

    http://www.lehigh.edu/~inbios/pdf/Behe/QRB_paper.pdf

    One thing that bemuses me is that when he’s discussing Lenski’s experiment, he persists in referring to a’cumulative population size’ of 10 to the 14th power E coli over 50,000 generations.

    From my understanding of the experimental protocol, at the start of each day, approximately 1% of the previous day’s flask is inoculated into a fresh flask (reducing the number from roughly 500 million to 4 million, since each day would be the equivalent of 6 or 7 doublings or generations).

    Behe has just multiplied 12 (the number of lines) by 50,000 (the number of generations) by 500 million (the maximum number of E coli in each flask at the end of each day) to give 10 to the power of 14, which he claims is the number microbes that are being looked at for mutations.

    I’d argue that it’s actually much less. For a really beneficial mutation to survive into the next day’s flask, it has to occur very early in the day’s incubation. If the mutation occurs in the first doubling, then at the end of the day there will only be about 128 mutant bacteria of which only 1 or 2 will be randomly selected in the 1% inoculum. So actually, the population being studied is actually just 48 million over 20 years, which make the changes much more impressive.

  16. sparc
    Posted December 13, 2010 at 11:25 pm | Permalink

    UPDATE: I’ve changed the title from “Discovery Institute” to “IDers” to reflect the fact that O’Leary was commenting on Uncommon Descent which, as far as I know, is not a formal arm of the DI. But the the DI’s approbation will surely come in time.

    Actually, the original title is still true because Casey Luskin did exactly that on DI’s propaganda page evolutionnews.org.

  17. Posted December 14, 2010 at 7:42 am | Permalink

    Gene duplication? I hope you realize that not only does the gene need to be duplicated but also all the regulatory stuff,including a nucleotide binding site, has to be there too.

    Not only that Dr Spetner went over gene duplications in his book “Not By Chance”- that was back in 1997.

    The bottom line is there isn’t any justification in saying that gene duplication followed by integration into the existing gene network is a blind watchmaker processes.

    Ya see guys neither ID nor Creation say that mutations do not happen. They just say that not all mutations are genetic mistakes/ errors/ accidents.

    As for horizontal transfer- again what methodology demonstrates that this is a blind, undirected chemical process?

    And what evidence do you have that genetic mistakes can accumulate in such a way as to give rise to novel protein machinery, novel body parts and novel body plans?

    Look it is a fact that all you guys can do is throw vast amounts of time around as if that solves all of your problems.

    But is that science?

    • Tulse
      Posted December 14, 2010 at 8:33 am | Permalink

      there isn’t any justification in saying that gene duplication followed by integration into the existing gene network is a blind watchmaker processes

      So every time that has happened, God did it?

  18. Insightful Ape
    Posted December 13, 2010 at 6:48 pm | Permalink

    You don’t have a clue what you are talking about. Dogs are EUKARYOTES. Behe’s paper deals with prokaryotes exclusively. The mutation mechanisms are different. Read Coyne’s analysis on Behe’s article from yesterday.


7 Trackbacks/Pingbacks

  1. [...] Jerry Coyne is now attacking me, re Behe’s recent paper. To judge from his blog post’s title, he has me confused with Discovery Institute.* . Dr. Coyne claims that Behe’s findings apply [...]

  2. [...] expected, the IDers are completely ignoring the limitations of this paper (see my analyses here and here), and asserting that it makes a powerful statement about evolution in [...]

  3. [...] and no one is really up in arms about Behe’s paper itself. But isn’t it interesting how quickly the creationist intelligent design crowd started distorting the facts? Over at the intelligent-design site Uncommon Descent, the ever befuddled Denyse O’Leary has [...]

  4. [...] Michael Behe published a paper which appears to be sound. That does NOT make the case for intelligent design [...]

  5. [...] did not, and could not, say this in the paper, but intelligent-design advocates certainly did (see here and here, for instance), and now Behe himself has said the same thing on his blog at Uncommon [...]

  6. [...] I predicted, the IDers completely ignore the limitations of this paper (see my analyses here and here), and assert, wrongly, that Behe has made a powerful statement about evolution in [...]

  7. [...] Jerry Coyne has published several blog articles reflecting on this paper (Behe’s new paper; IDers already distorting Behe’s new paper; Casey Luskin distorts Behe’s paper; An experimental evolutionist replies to Behe), so [...]

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