Rich Lenski answers ID creationist Michael Behe, dismantles “Behe’s First Rule of Adaptive Evolution”

Rich Lenski, a well known biologist at Michigan State University and head of the team which has conducted an equally well known long-term evolution experiment in E. coli (they have a generation every twenty minutes or so, and the experiment has run for 30 years), is the subject of a long attack in Michael Behe’s new Intelligent-Design (ID) book, Darwin Devolves.  Apparently Behe argued that Lenski’s work didn’t show real progressive evolution of a meaningful sort, but simply showed that bacteria could adapt to lab conditions by “breaking genes”: deactivating genes through missense or nonsense mutations. As Lenski and coauthors Nathan Lents and Joshua Swamidass showed in a short but damning review of Behe’s book in Science, Behe’s claim about Lenski’s experiment was wrong:

In the grand scheme of evolution, mutations serve only to break structures and degrade functions, Behe argues. He allows that mutation and natural selection can explain species- and genus-level diversification, but only through the degradation of genes. Something else, he insists, is required for meaningful innovation. Here, Behe invokes a “purposeful design” by an “intelligent agent.”

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.)

As I’ve written before, Behe’s thesis here is meant to show that, without the help of the “Intelligent Designer” (aka God), real progressive evolution is self-limiting, for all it does it create adaptations based on broken or deactivated genes. The accumulation of broken genes eventually makes further evolution impossible: once you have a genome full of broken genes, further progress is limited and so God has to step in to make those mutations that can’t occur naturally. (I’m always amused at the religious IDers diminution of God’s role from de novo creator of all organisms to that of a mutagen: a Divine Carcinogen.)

Behe’s thesis is expressed in his “First Rule of Adaptive Evolution”, which Lenski analyzes (and dismantles) in a post on his website (see link below).

I didn’t know that Lenski even had a website, but there you go. It’s called Telliamed Revisited, and his latest post (click below) is the first of three essays in which he’ll analyze Behe’s book. This is useful, as the three-authored Science critique was only 650 words long—not sufficient to analyze the scientific theses of a 352-page book. Lents has already expanded the criticism of Behe’s book on The Human Evolution Blog and on the AIPT site., but since Lenski and his microbial experiment were the targets of special criticism by Behe, it’s especially appropriate that Lenski himself respond.

First, Lenski summarizes Behe’s “First Rule” (my emphasis below):

Behe’s latest book is centered around what he calls “The First Rule of Adaptive Evolution: Break or blunt any gene whose loss would increase the number of offspring.” As he wrote in an immediate, dismissive response to our review: “The rule summarizes the fact that the overwhelming tendency of random mutation is to degrade genes, and that very often is helpful. Thus natural selection itself acts as a powerful de-volutionary force, increasing helpful broken and degraded genes in the population.

Then Lenski makes a simple point which appears to show that Behe is being intellectually dishonest. (He’s already been intellectually dishonest by implying that nearly all adaptive mutations are known to degrade or break genes, as we have many counterexamples.) Here’s what he says, referring to the sentence I’ve put in bold above (the bold below is Lenski’s):

Behe’s next sentence then asserts the power of the “de-evolutionary” process of gene degradation. This is an unjustifiable extrapolation, yet it is central to Behe’s latest book. (It’s not the sort of error I would expect from anyone who is deeply engaged in an earnest effort to understand evolutionary science and present it to the public.) Yes, natural selection sometimes increases the frequency of broken and degraded genes in populations. But when it comes to the power of natural selection, what is most frequent versus most important can be very different things. What is most important in evolution, and in many other contexts, depends on timescales and the cumulative magnitude of effects. As a familiar example, some rhinoviruses are the most frequent source of viral infections in our lives (hence the expression “common cold”), but infections by HIV or Ebola, while less common, are far more consequential.

. . . In the same vein, even if many more mutations destroy functions than produce new functions, the latter category has been far more consequential in the history of life. That is because a new function may enable a lineage to colonize a new habitat or realm, setting off what evolutionary biologists call an “adaptive radiation” that massively increases not only the numbers of organisms but, over time, the diversity of species and even higher taxa.

. . . Summing up, Behe is right that mutations that break or blunt a gene can be adaptive. And he’s right that, when such mutations are adaptive, they are easy to come by. But Behe is wrong when he implies these facts present a problem for evolutionary biology, because his thesis confuses frequencies over the short run with lasting impacts over the long haul of evolution.

This isn’t rocket science. If Behe’s thesis is that broken genes present a big problem for continuing adaptive evolution, then one has to accept the thesis that nearly all broken or degraded genes are those genes involved in adaptation. And yes, some inactivated genes are involved in adaptations. But we also know of many adaptations based on non-broken genes, including those with changed functions as well as duplicated genes, cobbled-together genes, horizontally transferred genes, and so on. If, as I’ve said, only 50% of all adaptations involve these sorts of genes as opposed to “broken” genes, the natural selection will not lead to the stalling of evolution so important to Behe. Further, if a higher proportion of “changed function/new function mutations” are involved in major adaptations that are associated with the rise of new taxa, then the broken or blunted genes become even less important.

As Lenski notes, the frequency of mutations that degrade rather than change the function of genes does not tell us the frequency of degraded genes that are involved in adaptation, and the frequency of degraded genes that are involved in adaptation does not tell us the frequency of degraded genes involved in adaptations that are associated with new biological diversity. Behe surely realizes this, as he’s not stupid, but chooses not to make that point. Lenski had to make it for him.

Lenski is being quite kind when he says “it’s not the sort of error I would expect from anyone who is deeply engaged in an earnest effort to understand evolutionary science and present it to the public.” I would go farther and say “this is the sort of error that I would expect from a neo-creationist who’s trying to distort the empirical data in order to delude the public into thinking that there are severe problems with modern evolutionary theory.”

Behe is notoriously thin-skinned, and will undoubtedly go after Lenski at the intelligent-design Evolution News site, which, understandably, does not allow any comments. Behe’s ID buddies will also pitch in and help him out, as they’ve already been doing, for they want this book to sell well and create the widespread scientific acceptance of ID that the Wedge Document said would occur by 2018. LOL on that!

ID has not been widely accepted in science: it’s been scorned, laughed at, and deemed by the courts as religion and not science. If it were scientifically accepted, you’d get a better panoply of people endorsing the book than these four people who constitute the entirety of the editorial reviews on the Amazon page of Darwin Devolves:

Axe and Minnich are both associated with the ID-creationist Discovery Institute, and so are already in bed with Intelligent Design. Carlson is a member of the Christian Faculty Forum, has testified publicly about his deep faith, and thus shows that virtually all proponents of ID are religious. He’s also a Fellow of the Id-ish International Society for Complexity, Information, and Design; other fellows include William Lane Craig, Alvin Plantinga, and the whole Discovery Institute crew (Nelson, Behe, Dembski, and so on). Leisola is also an ID advocate and has written a book about his transformation from advocate of naturalism to worshiper of the Great Designer.  Leisola’s  Finnish Wikipedia page notes (translated by Google):

Leisola is a creationist . He believes that the world is only a few thousand years old and sees the flood of water as a historic global flood. [18]

Leisola has delivered several books in Finnish, whose authors adopt a pseudo-scientific [19] concept of ” intelligent design ” and make claims against the scientific theory of evolution . In 1981, he delivered AE Wilder-Smith’s Natural Sciences Not Known for Evolution (WSOY, 144 p.). Leisola founded the Datakirjatpublishing company in 2000 because Finnish publishers refused to publish his translation of the book ” Evolution – critical analysis ” by Siegfried Scherer and Reinhard Junker . [20] Dictionaries published The first edition of the Evolutionary-Critical Analysis book in 2000. [21]  The dictionaries have since published other pseudo-scientific and evolutionary works:

  • William A. Dembski, 2002, Intelligent Plan Idea , Data Books, 256 s.

  • Marwin Lubenow, 2005, Myth of Monkeys – Controversy over Timing of Fossils , Data Books, 380s .

 

These are hardly the brand of endorsements you want if you’re trying to divorce ID from creationism and make it part of mainstream science.

28 Comments

  1. ThyroidPlanet
    Posted February 17, 2019 at 10:05 am | Permalink

    Sub

  2. Randall Schenck
    Posted February 17, 2019 at 10:39 am | Permalink

    All proves if you are looking for g*d hard enough, you can find him anywhere. Not exactly the scientific method. Also shows something else that is often true or at least a good idea. Consider the source.

  3. Anonymous
    Posted February 17, 2019 at 10:41 am | Permalink

    It appears Behe is acknowledging the facts that deem all life forms to be reducibly non-complex.

    • Anonymous
      Posted February 17, 2019 at 1:38 pm | Permalink

      Awesome observation. Kinda puts the nail in the coffin of one of ID’s talking points.

    • Mark Joseph
      Posted February 17, 2019 at 1:44 pm | Permalink

      Awesome observation. Kinda puts the nail in the coffin of one of ID’s talking points.

  4. W.T. Effingham
    Posted February 17, 2019 at 10:45 am | Permalink

    It seems Behe is acknowledging the data indicate all lifeforms aren’t so irreducible in their complexity.

  5. Posted February 17, 2019 at 10:50 am | Permalink

    Thanks for this Jerry. His polar bear example is tremendously wrong and I’ve updated my article to more fully fleshed out just how misleading he is about it. There is no other way to see this as a ton of egg on Behe’s face. Yikes.

    https://thehumanevolutionblog.com/2019/02/12/behe-polar-bears/

    • Steve Gerrard
      Posted February 17, 2019 at 1:05 pm | Permalink

      Oh my, that willful editing of table S7 is really appalling. It pretty much damns the whole book. How ridiculous!

      • Posted February 18, 2019 at 12:01 pm | Permalink

        Reminds me of the grade 11 economics texts that were used in some Quebec high schools. They included a table which showed the amount and direction of transfer payments from Ottawa to the provinces. Except for the row corresponding to Quebec. (It is a myth amongst some Quebec nationalists that Quebec at the time was a net contributor by this narrow measure, which was false.)

  6. Posted February 17, 2019 at 11:04 am | Permalink

    Among the different mutant strains that Dr Lenski and his students generated in the LTEE, one of the most consequential ones was a citT mutation where the gene that encoded the citrate transporter protein was duplicated, and the duplicated gene came under control of a strong promoter so that it was also expressed when oxygen was present. So instead of being able to take up citrate in the absence of oxygen, which is one of the diagnostic characters of E. coli, this new strain could always take up and use citrate as a nutrient, giving it a powerful growth advantage. Maybe it was not common, but it sure was consequential. It is just this sort of mutation that leads to lineages becoming established in new environments.

  7. Roger
    Posted February 17, 2019 at 11:48 am | Permalink

    “Darwin Devolves” seems like an odd title for a scientifically serious book. It’s like if Einstein wrote a book called “Newton Is So Stupid.”

    • Zetopan
      Posted February 20, 2019 at 4:35 pm | Permalink

      “It’s like if Einstein wrote a book called “Newton Is So Stupid.””

      It’s much worse than that since both Newton and Einstein did actual science. Behe in contrast is peddling a form of creationism that lost their argument in the advancement of science well over a century ago. If you still want an analogy, Behe’s book is the equivalent of Samuel Rowbotham’s flat Earth book “proving” that the Earth is not a globe.

  8. Roger
    Posted February 17, 2019 at 12:01 pm | Permalink

    Hmm I coulda swore that a few days ago there were about four or five five-star customer reviews at the Amazon page. They seem to be gone now.

    • Posted February 17, 2019 at 12:13 pm | Permalink

      Yes, I remember them too! But they are indeed gone, and no telling why, unless they took them down because the book isn’t officially released yet.

      • Heather Hastie
        Posted February 18, 2019 at 5:17 pm | Permalink

        I think these days they insist all reviews are from confirmed purchasers in an attempt to stop friends padding the reviews. That way, at least the friends have to buy the book from Amazon.

  9. Posted February 17, 2019 at 12:12 pm | Permalink

    Would there be any other way for him to respond but lamely?
    The much bigger question is when will mankind evolve past this need to identify ourselves with a Supreme Being and Eternal Life and accept what is here before him?

  10. Posted February 17, 2019 at 12:15 pm | Permalink

    The “cdesign proponentsists” (and people should know what that infamous term means) have long sought to concentrate on the technical and obscure. Instead of basing their claims on highly visible and more broadly known areas like anatomy and the fossil record, they go for the obscure and molecular. So they claim there is design and irreducible complexity in bacteria flagella and mammalian blood clotting pathways. The genetics of pigmentation in polar bears? Citrate metabolism in bacteria? Not many people are learned enough to see the bullshit they claims they make there! By doing so they can be fairly safe from rebuttal from a freshman college student, museum curator, and book-learned naturalist. Now they mainly have to deal with the rarified molecular biologist. Also, the inevitable rebuttals that do come from those special sorts of experts will of course be rather technical in nature and beyond the ken of their target audience, which is the average god fearing Christian.
    This is their only strategy these days. Make a clear declaration of ‘we found design! The “experts” are wrong! Their audience understands that. If they don’t understand the details of the claims (and most of them won’t), then they won’t see the falsehoods either, let alone understand the absolutely crushing rebuttals from those so-called experts.

    • Posted February 17, 2019 at 12:24 pm | Permalink

      “they can be fairly safe from rebuttal from a freshman college student…”

      Maybe I am too optimistic, but we teach evolution of gene families to freshmen!

  11. Ken Pidcock
    Posted February 17, 2019 at 1:15 pm | Permalink

    It’s not the sort of error I would expect from anyone who is deeply engaged in an earnest effort to understand evolutionary science and present it to the public.

    Duh.

  12. Michael Fisher
    Posted February 17, 2019 at 1:31 pm | Permalink

    Richard Lenski over at his site:

    “Or consider an investor who bought stocks in 100 different companies 25 years ago, of which 80 have been losers. Ouch? Maybe not! A stock can’t lose more than the price that was paid for it, and so 20 winners can overcome 80 losers. Imagine if that investor had picked Apple, for example. That single stock has increased in value by well over 100-fold in that time, more than offsetting even 80 total wipeouts all by itself. (In fact, research on the stock market has shown the vast majority of long-term gains result from a small minority of companies that, like Apple, eventually become big winners.)”

    Coincidentally? John Templeton, during the Depression of the 1930s, also bought 100 shares of each NYSE listed company which was then selling for less than $1 a share ($18 today) (104 companies, 34 in bankruptcy, in 1939), later making many times the money back when USA industry picked up as a result of World War II. According to Templeton, he called his broker the day World War II began and instructed him to purchase every stock trading at less than a dollar. This stratagem helped make him a wealthy man. [I’ve copy/pasted that from Templeton’s Wiki]

    • rickflick
      Posted February 17, 2019 at 7:22 pm | Permalink

      It’s pretty clear that Templeton was unable to use his (financial) cunning to grok evolution. Too much bias. I guess the lesson is, where there’s a will there’s a way.

      • Michael Fisher
        Posted February 17, 2019 at 7:33 pm | Permalink

        Puntastic! 🙂

        Yes – yet another who must have spookiness in the gaps & doesn’t consider how evil that spooky agent would have to be to match what we see.

  13. Posted February 17, 2019 at 3:00 pm | Permalink

    Behe also fails to recognize the adaptation that arose to combat the idea of gene degradation is to have a back-up copy of the gene (or allele) in question. Problem solved!
    If you have a degradation in one, the other copy can pick up where the other fails. And having this ability to tinker with the genetic amalgam, without significant consequence for errors, results in allowing the adaptive trait to spread and the error to be silent or weeded out. The monkeys banging on the type writer will have written War and Peace in no time (geologically speaking)if the good words are preserved and the nonsense words are discarded.

    • James
      Posted February 18, 2019 at 6:47 am | Permalink

      Gene duplication has interesting consequences. Duplicating genes can increase the concentration of the products of their expression to dangerous levels. So some genes go dormant. The best example of this is calico cats–the color pattern is a result of X chromosomes (which carry the gene for color) going dormant.

      • ThyroidPlanet
        Posted February 18, 2019 at 6:53 am | Permalink

        Cool biology textbook level fact (this is meant as a good thing)

  14. aljones909
    Posted February 17, 2019 at 4:22 pm | Permalink

    If Intelligent Design exists in our Universe it must have happened in all species (at least, that’s my understanding of Behe’s claims).

    The existence of a single parasitic species, exquisitely designed to exploit a sentient host while causing great suffering, would seem to be inconsistent with the God Behe worships.

    Maybe he (or his supporters) have attempted to answer that challenge?.

  15. Torbjörn Larsson
    Posted February 17, 2019 at 4:31 pm | Permalink

    Thanks for the tip!

    Nitpick:

    they have a generation every twenty minutes or so, and the experiment has run for 30 years

    The minimal replication cycle time for E. coli is twenty minutes at optimal growth condition, and at that they have to start new replication forks before they have fully divided. The experiment seems to purposefully not be at those conditions:

    “Each day, 1% of each population is transferred to a flask of fresh DM25 growth medium. The dilution means that each population experiences 6.64 generations, or doublings, each day.” [ https://en.wikipedia.org/wiki/E._coli_long-term_evolution_experiment ]

    So a generation time of 4 hours or so.


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