Rich Lenski continues his demolition of Michael Behe’s new book

As you probably know from reading this site, ID creationist Michael Behe has a new book coming out this week: Darwin Devolves: The New Science About DNA That Challenges Evolution (note the unclear antecedent, which could be either “New Science” or “DNA”).  Various scientists have weighed in, none of them positively, and there’s been considerable criticism by biologists Nathan Lents, Joshua Swamidass, and Rich Lenski, including a damning review in Science.

Lents continued his criticism on The Human Evolution Blog (see here,  here and here) and Lenski, whom Behe attacked strongly in the book, promised a three-part rebuttal of Behe’s ideas on his own website, Telliamed Revisited, which is now being extended (see here and here for Lenski’s parts 1 and 2).

Yesterday Lenski put up part 3 (screenshot below), which is an expansion of earlier criticism by Lents on whether a gene likely involved in the adaptive evolution of polar bears—a gene concerned with fat metabolism—was really “broken” or “damaged”.

One of Behe’s major theses in the book is that evolution is self-limiting, as, he argues, nearly all adaptations are based on damaged genes, and when a gene is damaged or inactivated, it can accumulate more mutations that eventually render it functionless and unable to revive. Thus, he concludes, evolution by natural selection runs itself into the ground. God An Intelligent Designer then has to step in to make things right.

Behe is wrong. Indeed, although we have examples of adaptive evolution based on inactivated genes, we also have many that don’t involve “broken genes”, and as long as a reasonable number of mutations involve changes in gene function or regulation, or things like gene duplication, chimeric genes, and so on, Behe’s claim holds no water.

One of the genes that Behe claimed was inactivated during adaptive evolution of polar bears from ancestral brownish bears was ApoB, which regulates the amount of fat in the blood. Behe claimed in his book that the gene’s evolution in polar bears involved many “inactivating” mutations. Lents pointed out that there was no evidence for this; on the contrary, even the authors of the paper analyzing the sequence of that gene found evidence that some of those substitutions were not involved in breaking the gene, but improved its function.

Behe replied, calling Lents an “incompetent reviewer” (without even giving his name!) and presenting some data that, he said, showed that the ApoB substitutions were “possibly damaging” or “probably damaging.

That was a mistake, for, as Lents showed, Behe was duplicitous in his reply, having omitted from his table all the mutations that the authors’ algorithm said were “benign”. Lents is charitable about this, but I can see no explanation except that Behe left out data inimical to his hypothesis. And that seems misleading and deceptive.  As I said, Lents is kinder to Behe than I would have been:

In Behe’s defense, he doesn’t explicitly say that he’s presenting the whole Table. So he isn’t lying exactly. Instead, he says that he is presenting “the relevant information” from the Table. I find this deeply misleading. This whole discussion is about the nature of adaptive mutations in the evolution of species and Behe’s arguments is that most of them are damaging. By presenting only the mutations that are predicted to fit that argument, he is intentionally leaving out evidence that is contrary to his position.

After all, what is the purpose of showing the chart at all? To show that some mutations that drove polar bear evolution are damaging? He didn’t need a chart to make that point and no one would argue with that. I suspect that if the unaltered Table S7 gave the impression that the overwhelming number of adaptive mutations were damaging, Behe would have shown the whole thing.

In reality, Table S7 does not give that impression at all, and so he slices it up with surgical precision so that he can present “the relevant information,” that is, the information that appears to support his position. And, at least when it comes to APOB, even the selectively edited information probably doesn’t support his position either, regardless of what the predictive algorithm says, as I (and the study’s authors!) explain above.

The evolution of polar bears is the opening story of Behe’s book, the example he uses to describe his concept of “devolution.” But if you actually consult the data itself, it tells a very different story than Behe does.

Lenski’s new post (click on screenshot), goes into the polar bear gene in detail, and also explains how scientists determine whether a mutation in a gene is advantageous, benign, or damaging—not an easy matter when all you have is its DNA sequence.

Lenski points out that the algorithm used by the real scientists who did the ApoB study is unable to detect adaptive changes that improve the function of the protein: it is limited to detecting “benign”, “possibly damaging” or “probably damaging” mutations. Not only did Behe leave out the “benign” mutations, but didn’t bother to mention that the algorithm can’t show changed or improved function for any mutations. And I call that duplicitous. Here’s Lenski’s take; the emphases are his.

The program simply cannot detect or suggest that a protein might have some improved activity or altered function.

The authors of the paper recognized these limiting assumptions and their implications for the evolution of polar bears. In fact, they specifically interpreted the APOB mutations as follows (p. 789): “… we find nine fixed missense mutations in the polar bear … Five of the nine cluster within the N-terminal βα1 domain of the APOB gene, although the region comprises only 22% of the protein … This domain encodes the surface region and contains the majority of functional domains for lipid transport. We suggest that the shift to a diet consisting predominantly of fatty acids in polar bears induced adaptive changes in APOB, which enabled the species to cope with high fatty acid intake by contributing to the effective clearance of cholesterol from the blood.” In a news piece about this research, one of the paper’s authors, Rasmus Nielsen, said: “The APOB variant in polar bears must be to do with the transport and storage of cholesterol … Perhaps it makes the process more efficient.” In other words, these mutations may not have damaged the protein at all, but quite possibly improved one of its activities, namely the clearance of cholesterol from the blood of a species that subsists on an extremely high-fat diet.

It appears Behe either overlooked or ignored the authors’ interpretation. Determining whether those authors or Behe are right would require in-depth studies of the biochemical properties of the protein variants, their activities in the polar bear circulatory stream, and their consequences for survival and reproductive success on the bear’s natural diet. That’s a tall order, and we’re unlikely to see such studies because of the technical and logistical challenges. The point is that many proteins, including ApoB, are complex entities that have multiple biochemical activities (ApoB binds multiple lipids), the level and importance of which may depend on both intrinsic (different tissues) and environmental (dietary) contexts. In this example, Behe seems to have been too eager and even determined to describe mutations as damaging a gene, even when the evidence suggests an alternative explanation.

Now this may seem an arcane discussion about protein function, but if you’ve gathered anything from this post, Lenski’s post, and Lents’s posts, it should be that Behe has not been intellectually honest in treating the data in a key example used to make his case that natural selection nearly always relies on broken genes. But what do you expect from a creationist who’s deeply religious and who’s counting on the data to make the case for God?

I’m told that Behe really believes the kind of palaver he uses to make the case for “irreducible complexity” and Intelligent Design. But really, how can you leave out data and distort the conclusions of others, without being conscious of what you’re doing? One might almost conclude that Behe is lying for God.

Lenski isn’t done with taking Behe to the woodshed yet: as he says, “I initially planned to write three posts, but it will now be more than that, as I delve deeper into several issues.”  Behe’s tuchas is going to be smarting after this!

 

24 Comments

  1. grasshopper
    Posted February 23, 2019 at 1:39 pm | Permalink

    I pray that my descendants will still have at least one non-broken or non-damaged gene by the time of the Second Coming. It’s all been downhill since Creation, or at least since Adam ate that perfect apple.

    • Posted February 23, 2019 at 1:55 pm | Permalink

      Behe should make a graph of the rate of gene damage; and when the line hits the horizontal axis, we’ll have a prediction of the time of the Second Coming. This will at least be a falsifiable claim.

    • Posted February 23, 2019 at 4:55 pm | Permalink

      Moral: Never listen to a talking snake.

  2. Ken Pidcock
    Posted February 23, 2019 at 1:45 pm | Permalink

    I don’t believe that Michael Behe believes what he claims. There’s just too much purposeful duplicity. I think he believes that what he does undermines support for the evolutionary process as undirected and thereby buttresses theism, which he thinks essential to the little guys’ moral virtue.

    • Posted February 23, 2019 at 8:41 pm | Permalink

      I thought I read, though I don’t remember where, that Behe’s son (who has repudiated his father’s “science”) says that his dad really does believe the stuff he says.

      • Michael Fisher
        Posted February 23, 2019 at 9:24 pm | Permalink

        THE HUMANIST Interview with Leo Behe The son of intelligent design heavyweight Michael Behe discusses his journey to atheism by Ryan Shaffer, 23 August 2011

        The Humanist: Will your family see this interview?
        Behe: I already told my dad about it, and he had no objections. The rest of my family will most likely see it, as I will try to get news of it out to my circle of friends. My parents and older siblings will almost definitely disagree with opinions I’m presenting, and perhaps they’ll discuss said points with me, which I’m always more than ready to do.

        […]

        The Humanist: About your father, you previously blogged: “I believe that he does have doubts and does see conflicts between science and the Bible, and he therefore continues to reshape his faith so as to dodge those conflicts.” [see note at bottom] Why do you think he has doubts and why does he continue to reshape his faith?
        Behe: I think that all scientists who hold to a particular religious creed must experience conflicts with their sacred texts and their scientific observations. I can’t speak for my father’s personal beliefs specifically, but I believe that the constant reinterpretation of sacred texts to correct conflicts between theological claims and scientific discoveries says something about the faith upon which those claims are based. For irreducible complexity particularly, the glaring inefficiencies apparent in life—along with a universe that appears more chaotic and indifferent the more we learn about it—will challenge the religious beliefs of any scientist and continue to force additional reinterpretations of sacred texts. It is my hope that eventually such texts will lose all credibility.

        The Humanist: While you have been critical of intelligent design, you have defended your father as a nice and honest person. What more would you like the public to know about him?
        Behe: I would like everyone to realize that he doesn’t have any sort of religious agenda and he’s not trying to denigrate science in any way. Long-held beliefs, especially beliefs developed during childhood, operate on a very deep and basic level of thought—almost subconsciously. These beliefs can exist independently in a perfectly honest and intelligent scientist who is simply doing his part to further theories or ideas that he believes are supported by the scientific data. The best way to progress is through respectful and thoughtful discussion and debate, as it has always been.

        NOTE:
        Leo Behe’s blog is THE JOYFUL ATHEIST I haven’t found Leo’s quote there yet that I bolded, but I’m still looking.

      • Michael Fisher
        Posted February 23, 2019 at 9:50 pm | Permalink

        I suspect Leo Behe’s statements about his father can’t be trusted – Leo isn’t going to say his dad is a fraud even if he knows he is. Leo likes his peace & quiet too much – I found his current social media & he’s interested in sustainability, veganism & the glamour side of tech [shiny SpaceX rocketry] – I don’t think he’s that interested in the good fight & “atheist” isn’t in his lingo today. I think other people [that’s us] made a big deal about Leo splitting from the family Catholic beliefs, but it hasn’t seemingly impinged on homeschooled Leo much.

        I did a word search for “conflicts” at Leo Behe’s blog The Joyful Atheist & it doesn’t appear anywhere in Leo’s posts. The most likely explanation is Leo has deleted this quote: “I believe that he does have doubts and does see conflicts between science and the Bible, and he therefore continues to reshape his faith so as to dodge those conflicts”

        I cant find the quote as an original source & I can’t find another Leo Behe blog, thus I assume Leo has been cleaning up his past web presence.

      • Michael Fisher
        Posted February 23, 2019 at 10:16 pm | Permalink

        Ha! I found Leo’s LinkedIn – shortly after the atheist thing Leo started to study Physics at LeHigh University [2012] which was & still is his dad’s place. And all his education & internships since then have been close to the family hearth [same town].

        I wouldn’t be amazed if he still lives at home & pops footed his education. No waves of discontent from Leo.

  3. Ken Pidcock
    Posted February 23, 2019 at 1:46 pm | Permalink

    I don’t believe that Michael Behe believes what he claims. There’s just too much purposeful duplicity. I think he believes that what he does undermines support for the evolutionary process as undirected and thereby buttresses theism, which he thinks essential to the little guys’ moral virtue. (Sorry if this is duplicated. I didn’t appear to post.)

  4. Jonathan Gallant
    Posted February 23, 2019 at 2:50 pm | Permalink

    The discussion has left out the old story of the ebg gene of E. coli, in which certain missense (amino acid substitution) mutations confer the ability to hydrolyze lactose [see: The EBG system of E. coli: origin and evolution of a novel beta-galactosidase for the metabolism of lactose. Hall BG. Genetica. 2003 Jul;118(2-3):143-56.] This example of adaptive mutations became mired in a complicated story about a possible “instructive” role of the selection regime on the mutation process, which eventually turned out to be a red herring. Still, the changes in the “unbroken” ebg gene would seem a good example of acquisition or change of function in a protein through mutational change. Since the original work by B.G. Hall, others have shown a large variety of ebg missense mutations that produce galactosidase activity (see Chem Biol. 2005 Dec;12(12):1291-300.).

    I haven’t read Behe’s book, so don’t know if he comments on this. I believe he got involved in the controversy over the red herring part of the ebg story.

  5. Steve Gerrard
    Posted February 23, 2019 at 3:34 pm | Permalink

    Gotta say, it feels like piling on now. Behe is wrong; his opening argument has been decimated; case closed as far as I’m concerned.

    • Michael Fisher
      Posted February 23, 2019 at 4:33 pm | Permalink

      It’s not what I would describe as piling on. My only concern is that his [mainly] Christian audience doesn’t get to see posts such as these as they stay inside their tribal bubble.

      Behe’s fake science creationism has to be thoroughly shredded at every point where he misrepresents the science. His ‘authoritative’ nonsense is widely & uncritically disseminated as sound bites within the creationist network for the purposes of garnering more followers, subscribers, donors & buyers of lying creationist products: Homeschooling books, DVDs, posters, mugs, T-shirts. I think it was one of the Hovinds or Ham who was distributing this crap as a tax deductible to prison libraries a few years back.

      The biz is still bringing in 10s of millions of dollars cash per year in the USA alone & some unknown additional amount of profit in the form of legally dodged income tax, property tax & interest free loans.

    • Posted February 23, 2019 at 8:42 pm | Permalink

      It’s not piling on; the book makes many claims and gives many examples, and discrediting one is not sufficient to discredit the whole book–not for any reasonable person. After all, it could just be a lone mistake.

      The case may be closed for you, but I doubt it’s closed for the most of the others who haven’t yet read the book but will.

  6. Posted February 23, 2019 at 4:51 pm | Permalink

    I still want to know what is proposed as the ‘god intervening mechanism’? Crossing the numinous/physical barrier – it sounds like the real deal breaker to me, especially if doesn’t contravene Core Theory. Almost magical….

    rz

    • Roger
      Posted February 23, 2019 at 6:43 pm | Permalink

      One thing you won’t hear from religous people is questions about how the the mechanism of god magic works. As far as things religious people inexplicably won’t do, it’s right up there with praying for Satan’s salvation.

    • Posted February 23, 2019 at 8:44 pm | Permalink

      There is no mechanism proposed (there never is). It’s just “we can’t see how natural selection did this, so God must have done it.” The methods that god (or space aliens) use is not specified. But if the Designer is an alien, then he/she/it/hir must have to use physical methods to mutate the genes. If God did it, well, it’s supernatural and God works in mysterious and unfathomable ways.

      • Posted February 28, 2019 at 3:21 pm | Permalink

        I think they’ve finally dropped the it-could-have-been-space-aliens argument that they’ve been using publicly at least since Dover.
        For some time now (and with his newest book) Meyer has tied evidence for intelligent design to evidence that the universe was created- and only a god can create a universe

  7. Posted February 23, 2019 at 5:29 pm | Permalink

    So Behe’s God didn’t think to allow for advantageous mutations to begin with and now has to waste His time continually intervening in order to keep evolution from grinding to a halt. Pretty dumb God to worship.

    • JezGrove
      Posted February 24, 2019 at 11:02 am | Permalink

      Nicely put.

  8. Roger
    Posted February 23, 2019 at 6:53 pm | Permalink

    Sadly in spite of all criticism Behe’s book will no doubt have a 4 to 4 1/2 star rating just like the rest of his books.

    • rickflick
      Posted February 23, 2019 at 10:31 pm | Permalink

      4 stars? Probably most readers/reviewers are Christians looking to fortify their faith with a little “science”. Critical thinkers probably don’t want to waste the time.

  9. Posted February 23, 2019 at 9:06 pm | Permalink

    Great job Dr. Coyne. It has been a pleasure to be working with Lenski on this. We were gob-stopped by the exchange over polar bears. As a computational biologist, this is an example of trying to claim 1+1=3. I’m honestly not sure how he could have made a mistake this large and consequential. Any ideas?

  10. Posted February 23, 2019 at 9:10 pm | Permalink

    You might enjoy how this played out at PS: https://discourse.peacefulscience.org/t/lents-and-hunt-behe-and-the-polar-bears-fat/4473 I also covered this in our response to his trainwreck response. https://discourse.peacefulscience.org/t/behes-trainwreck-response-to-science/4548

  11. Torbjörn Larsson
    Posted February 24, 2019 at 3:55 pm | Permalink

    how can you leave out data and distort the conclusions of others, without being conscious of what you’re doing? One might almost conclude that Behe is lying for [magic].

    I am less surprised that when “gaps open for superstition” disappears superstitious in general feels compelled to lie. But if scientists do it too I would find it surprising.


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