Does Behe’s “First Rule” Really Show that Evolutionary Biology Has a Big Problem?

Michael Behe has a new book coming out this month called Darwin Devolves. Nathan Lents, Joshua Swamidass, and I wrote a review of that book for the journal Science. (You can also find an open-access copy of our review here.) It provides an overview of the problems we see with his thesis and interpretations. As our review states, Behe points to many examples of evolution in which genes and their functions have been degraded, but he largely ignores the ways that evolution generates new functions and thereby produces complexity. That’s a severe problem because Behe uses the evidence for the ease of gene degradation to support his overarching implication that the current scientific understanding of the mechanisms of evolution is inadequate and, consequently, the field of evolutionary biology has a “big problem.”

I won’t attempt to summarize Behe’s entire book nor our short review, as people can read those for themselves if they want. Instead, I hope to accomplish three things in this post and two more that will follow. In this first post, I explain why Behe’s so-called “first rule of adaptive evolution” does not imply what he says it does about evolution writ large. In the second post, I’ll discuss whether my long-term evolution experiment (the LTEE for short) does or doesn’t provide strong support for Behe’s position in that regard. In my third post, I’ll explain why I think that Behe’s positions, taken as a whole, are scientifically untenable.

I. Behe’s “First Rule of Adaptive Evolution” Confounds Frequency and Importance

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.”

Let’s work through these two sentences, because they concisely express the thrust of Behe’s book. The first sentence regarding “the tendency of random mutation” is not too bad, though it is overly strong. I would tone it down as follows: “The tendency of random mutation is to degrade genes, and that is sometimes helpful.” My reasons for these subtle changes are that: (i) many mutations are selectively neutral or so weakly deleterious as to be effectively invisible to natural selection; (ii) while loss-of-function mutations are sometimes helpful to the organism, I wouldn’t say that’s “very often” the case (though it may be in some systems, as I’ll discuss in part II); and (iii) even those degradative mutations that are not helpful on their own sometimes persist and occasionally serve as “stepping stones” on the path toward new functionality. This last scenario is unlikely in any particular instance, but given the prevalence of degrading mutations it may nonetheless be important in evolution. (This scenario does not fit neatly within the old-fashioned caricature of Darwinian evolution as only proceeding by strictly adaptive mutations, but it is certainly part of modern evolutionary theory.)

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.

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.)

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. As one example, consider Tiktaalik or some relative thereof, in any case a transitional kind of fish whose descendants colonized land and eventually gave rise to all of the terrestrial vertebrates—amphibian, reptiles, birds, and mammals. That lineage left far more eventual descendants (including ourselves), and was far more consequential for the history of life on Earth, than 100 other lineages that might have gained a transient advantage by degrading some gene and its function before eventually petering out.

Asteroid impacts aren’t common either, but the dinosaurs (among other groups) sure felt the impact of one at the end of the Cretaceous. (There remains some debate about the cause of that mass extinction event, but whatever the cause its consequences were huge.) Luckily for us, though, some early mammals survived. Evolution often leads to dead ends, sometimes as a consequence of exogenous events like asteroids, and other times because adaptations that are useful under a narrow set of conditions (such as those caused by mutations that break or degrade genes) prove vulnerable over time to even subtle changes in the environment. It has been estimated that more than 99% of all species that have ever existed are now extinct. Yet here we are, on a planet that is home to millions of diverse species whose genomes record the history of life.

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.

[The picture below shows the Tiktaalik fossil discovered by Neil Shubin and colleagues.  It was posted on Wikipedia by Eduard Solà, and it is shown here under the indicated Creative Commons license.]

Tiktaalik

 

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54 Comments

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54 responses to “Does Behe’s “First Rule” Really Show that Evolutionary Biology Has a Big Problem?

  1. I’ve been thinking about this a while and Behe has, what appears to me, to be a consistent problem. You can notice it all the way back to the Kitzmiller trial.
    He doesn’t understand populations. He talks about big numbers and mutations breaking things, but he’s referring to individuals and the effects on an individual.. not the population.
    Yes, if one offspring has a broken gene (depending on which gene) it may not survive. But that doesn’t mean that the parent’s lineage stops there. In some species, there’s another three thousand offspring.

    • Kevin: You’re referring to harmful mutations (“broken gene….may not survive”) which indeed won’t affect the population if that individual dies out. But Behe’s point is that a broken gene can be adaptive, not harmful, and thus can affect the population as it takes over through selection. That is by definition adaptive for the population as well, but can also mean a loss of function.

  2. Lino Di Ischia

    Lenski:

    “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.”

    From Behe’s response posted at Evolution News, it doesn’t appear that he’s confused at all. While I want to stay out of the fray, let me add my interpretation of what Behe has written: he’s said that since the likelihood of “breaking” or “blunting” a gene is much higher than that of any beneficial mutation–and here is the subtlety–the “broken” or “blunted” gene has a beneficial effect, meaning that the “broken” or “blunted” gene has a fitness advantage over the entire population. Hence, any beneficial mutaiton will have to override the likelihood of ‘breaking and blunting’ and its concomitant fitness advantage: or, IOW, a “slightly” advantageous mutation won’t stand a chance, and, so, RM + NS in a ‘positive’ direction will have to play ‘second-fiddle’ to the “breaking” and “blunting.”

    • Behe’s point doesn’t make sense to me, for the reasons in my post. As I explain, uncommon events can have large impacts that offset their relative rarity. I would expect mutations that improve existing functions, especially those that provide opportunities for adaptive radiations, to have larger advantages (potentially much larger) than those that provide incremental metabolic savings by “breaking or blunting” some gene under relaxed selection. You also say that the broken or blunted gene has an advantage “over the entire population.” Here a crucial distinction is whether that means an advantage relative to the average of the entire population, or relative to every other mutation in the population. The former may be true, even when the latter is not. For example, several common mutations that break unused genes might confer a 1% benefit, whereas a beneficial mutation that improves a gene’s encoded function in that same environment might confer a 5% benefit. For a while, all of them will increase in frequency (assuming they survive drift loss when they are rare) relative to the average member of the population (i.e., their common progenitor), but eventually the one with the larger advantage will prevail over those with blunted or broken genes. Things will get more complicated once we add recombination, allow sequential mutations, etc. And critically, one needs to be mindful of how long the environment remains in a state where previously useful functions are no longer needed (called “relaxed selection”). Even if a lineage with blunted or broken genes prevails in a particular population, that lineage may well go extinct when the environment changes again to require their functions. Meanwhile, other lineages that retained or even improved those functions (say, in other locales) may survive, proliferate, and diversify. Perhaps part II of my postings will help to clarify things for you.

  3. Pingback: Darwin Devolves: Behe Gets Polar Bear Evolution Very Wrong – The Human Evolution Blog

  4. Daniel Fisher

    Sir,

    Read your article with interest. But if I may humbly point out, there are certain “question-begging” fallacies throughout that I fear you are missing – perhaps because of your overwhelming confidence in the truth of Darwinian evolution, you may not notice that you are at times assuming the very conclusion you are arguing for.

    Specifically, you use Tiktaalik as a counter-example to Behe’s position. However, Tiktaalik can only serve as such a counter example if we first assume that it is such a transitional animal, and we assume its existence was a result of such unguided evolution. Professor Behe is asking whether this process can in fact explain such transitions. By assuming that such an animal has come about by the process under consideration simply does not answer his challenge; rather it simply begs the question, it simply assumes what you need to demonstrate.

    Similarly, you observe “It has been estimated that more than 99% of all species that have ever existed are now extinct. Yet here we are, on a planet that is home to millions of diverse species whose genomes record the history of life.” This is interesting, but irrelevant to the question at hand and does not answer Professor Behe’s challenge, unless you *assume* that the diverse species currently here are the few that demonstrate the reality of such beneficial mutations. But again, this is the point under discussion (whether or not this diversity could have been caused by such unguided beneficial mutations)… hence it cannot simply be assumed and thus used as counter-evidence.

    I am very interested in following the discussion, however, please note that using examples that depend on assuming that evolution has happened in the way you believe does little to little to convince skeptics like myself.

    • a

      are you guys aware that the tiktaalik is actually appearing after the first tetrapod fossil?:

      https://www.nature.com/articles/nature08623

      it means that the tiktaalik is actually in the wrong place from a ageological perspective since its appear to late in the fossil record.

    • Thank you, Daniel, for your comment. First, my post is meant to show the logical fallacy of Behe’s claim that, because vastly more mutations break things than improve things (he argues that’s true even for beneficial mutations, which I will set aside), that therefore means that standard evolutionary theory fails. It’s a logical fallacy, as my several examples show (viral infections, stock investments, and adaptive radiations) because it confuses the frequency of occurrence with the magnitude of consequences.
      Second, regarding your point of my begging the question, I would only claim that the Tiktaalik example fits well with everything we know from anatomy, paleontology, and genomics. It was even predicted, in terms of where it would be found (in terms of age and habitat). But no, science cannot absolutely prove it happened as evolutionary theory indicates. Instead, science recognizes that Tiktaalik fits well within a large body of accumulated knowledge and is consistent with theory that supports that accumulated knowledge.
      By contrast, Behe’s (and evidently your) notion of “guided” evolution is untestable and unscientific. I have no problem with anyone who believes that things small (say, a dream) or large (say, the laws of the universe), as they might prefer, are guided by a supernatural being. I completely disagree, however, that those ideas can be considered scientific — and worse yet, as Behe and the Discovery Institute are doing, that they can be claimed to undermine hard-won scientific understanding of the natural world. (What I’ve written here bears on part III of my response.)

      To “a” please note that I wrote “As one example, consider Tiktaalik or some relative thereof …” We’re not discussing whether Tiktaalik was the exact ancestor of terrestrial tetrapods. Science has a wonderful way of allowing for greater precision as more and more detailed discoveries are made. Rather, the point is that, whatever fish-lineage was progenitor to terrestrial tetrapods, it had remarkably important long-term consequences in comparison to many more common changes (losses of function, in particular) that were short lived.

    • Geo Bla

      You’ve made some excellent points Daniel and I don’t believe
      they were answered.
      The example of Tiktaalik has been brought into question on many
      grounds including the article noted in Nature as noted by another
      comment.

      The whole argument against Behe is that you have to assume
      that these speculated transitions of Speciation had to have
      occurred thru beneficial mutations and arrived at these fully
      developed complex forms of life.
      As you’ve also noted “Assumptions” are the norm for the
      premise of Abiogenesis and Speciation of life which
      I believe Professor Behe’s argument is that these
      type of mutations lack the capability of the claims
      that are regularly made.

      And from that point we have the extremely rare mutation that
      isn’t harmful having some minor benefit , but occasionally
      this benefit has a higher probability to harm then to benefit
      such as Sickle Cell Trait that offers protection from Malaria .

  5. Brett McIver

    How did all those genes get to the point where if they get broken or blunted , they then effect a population? Are they the results of broken or blunted attempts as well?What time period is required for all these changes to occur.?
    It seems to me from the arguements here that they had to be complete and then due to blunting and breaking we have the variations of animals we have today. I don’t see how breaking and blunting something can make a system more effective?

    • To “Geo Bla” — Sadly, your argumentative and muddled comment adds absolutely nothing of substance beyond empty assertions. I addressed Daniel’s comments explicitly and clearly. I’m sorry that you either couldn’t understand my points or refused to make the effort.

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  7. Frank Huggins

    OK, so how can we test the claim that random mutations can accumulate in such a way as to give rise to multi-protein complexes such as any bacterial flagellum?

    In the LTEE didn’t anyone wonder if it was random that the CiT+ gene was duplicated, the only gene that could transport citrate through the membrane, and just happened to be put under the control of an existing binding site that was not affected by the presence of oxygen?

    The point being is Dr. Behe is OK with the premise that organisms were intelligently designed with the ability to evolve and adapt.

    • Frank: It ain’t science if it invokes some unidentifiable and untestable intelligent agent working behind the scenes. And there’s NOTHING in the duplication of the citT gene that suggests it was intelligently designed to be evolvable in that way. Even after 70,000 generations, it’s only happened in one of the 12 LTEE populations. And growth on citrate required not only that duplication mutation, but a series of other mutations, before and after the duplication, to allow the cell to gain any meaningful advantage from the citrate. Not a very impressive design.

    • Frank Huggins

      Thank you for your response. However you didn’t answer my question.

      OK, so how can we test the claim that random mutations can accumulate in such a way as to give rise to multi-protein complexes such as any bacterial flagellum?

      We identified the designers and builders of Stonehenge by first determining it was intelligently designed and then studying it and all relevant evidence. We still can’t test their capabilities but just assume what they are capable of by what they have left behind. That is true with ID. We can test to see if intelligent design exists. And to falsify any given design inference all one has to do is step up and show that nature is capable.

      Your LTEE and CiT did not start out with the designed bacteria. The bacteria that started the experiment were already degraded. But even so still managed to find the right gene, but duplicate and put it under the control of an existing binding site. And that binding site just happened to be unaffected by the presence of oxygen.

      What are the odds that blind and mindless processes can do that along with those other necessary mutations?

    • Frank asked: “What are the odds that blind and mindless processes can do that [produce citrate-using cells] along with those other necessary mutations?”
      Our best estimate, given the population sizes and other conditions of the LTEE, is that the odds are about 1 in 12 after 70,000 generations.

    • Frank Huggins

      No, that assumes the processes were blind and mindless.

    • Frank wrote: “No, that assumes the processes were blind and mindless.” Where “that” refers to the fact that 1 of 12 LTEE populations evolved citrate use within 70,000 generations.

      There’s a huge literature on the meaning(s) for and randomness of mutations in evolution. For any readers interested in an early, elegant experiment in this respect:
      https://telliamedrevisited.wordpress.com/2013/08/29/luria-and-delbruck-1943-genetics/

      However, if you prefer to imagine that a mysterious, supreme intelligence intervened in the LTEE, and that it specifically favored population Ara-3 by endowing those cells with the necessary mutations to allow it to partake of the citrusy substrate therein, be my guest. Does that imply, though, that this intelligence has something against the other 11 populations? Or perhaps the intelligence bungled the design in the other 11 populations? Or what?

    • Kevin: We’ve been over all that.
      https://telliamedrevisited.wordpress.com/2016/02/20/on-the-evolution-of-citrate-use/
      A little advice: If your getting your evolution news from “Evolution News”, then you’re getting a very distorted perspective of science and scientific understanding.
      https://ncse.com/creationism/general/wedge-document
      https://en.wikipedia.org/wiki/Discovery_Institute

  8. Kevin Carlson

    Thank you for your article. However Daniel Fisher’s comment remains valid and unanswered. You merely assume what you should be trying to prove (stock market analogies notwithstanding): that Darwinian evolution (or whatever term you prefer) is solely capable of producing the changes necessary for the transition from a fully aquatic to a fully terrestrial organism or vice versa.

    Behe, on the other hand, has shown with real-world examples the strict limitations of the capabilities of evolution, most notably in The Edge of Evolution (EoE). His critics have mystifyingly failed to grasp at every level the book and Behe’s subsequent defense of it. I say this based on 1) the fact you and the other authors of the review of Darwin Devolves were unaware that he quite vociferously answered his critics time and time again, 2) you three inferring that Summers et al contradicted Behe when in fact it vindicated him and 3) completely misunderstanding and misrepresenting the main thesis of EoE to this day.

    Although Darwin Devolves gives passing reference to EoE, I have my suspicions as to why it factored prominently in the review. EoE has shown with empirical data – not story telling – what evolution can and cannot accomplish. With a population of 10^20 organisms, after a decade, evolution was eventually able to stumble upon the two necessary mutations that led to full chloroquine resistance. To equal that population, you would have to continue your LTEE for another hundred million years.

    Yet malaria, despite its enormous population, short generation time and the selective pressure it’s under, has not figured out how to overcome sickle-cell disease or reproduce below 60 degrees F. Why is that?

    Because…there’s an edge to evolution.

    I look forward to your other 2 posts.

    • Kevin: Your post is argumentative and muddled, but I’ll let it slide for this time. I did indeed directly answer Daniel’s comments. The ability to use citrate effectively (potentiation, actualization, and on-going refinement) in the LTEE involves more than two mutations, yet it happened in a tiny experiment. See this post for how tiny the LTEE is, in the grand scheme of nature:
      https://telliamedrevisited.wordpress.com/2014/04/02/on-time-and-space/
      Meanwhile, all of the LTEE lineages have accumulated dozens or even hundreds of mutations in only a few decades. (That’s the number of mutations that any given late-generation cell has relative to the ancestral strain; each population as a whole has had billions of mutations.) And the mutations don’t all break things, as I’ll elaborate in my next post. And even in my own research group, in other experiments we’ve seen adaptations that exceed the supposed “edge of evolution.”
      Perhaps it’s time to stop worshipping Michael Behe. There’s a lot to be learned by anyone who actually wants to understand the natural world. I would think that would be far more more rewarding than misrepresenting science. Here’s some reading for you and others who might want to break free from the shackles of anti-evolution misinformation:
      https://telliamedrevisited.wordpress.com/2014/02/19/resources-for-people-interested-in-learning-about-evolution/

  9. Mike Behe

    Hi, Professor Lenski. Thanks very much for amplifying on your concerns about the argument in Darwin Devolves. Your post makes interesting points, and I look forward to reading the next two you said you would write. I will think about all of them and then probably post my own reflections over at Discovery Institute’s Evolution News. I very much admire and appreciate all the work you have done in the past decades.

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  12. Daniel Fisher

    Sir, I very much appreciate your willingness to so thoroughly respond, and while I’m afraid it didn’t exactly answer my core concern, I do appreciate what you see as the logical fallacy you perceive in Behe’s position (granted having not read his work yet), that even if 99.9% of mutations are harmful, that the entire process would be fueled from that other 0.1%.

    As you were so kind to offer such a thorough answer to my question, I wonder if I could be so bold to ask you a much more general question about your work and it’s relation to the larger evolutionary question…. but please tell me if there is a better forum, page, or avenue to ask: I have followed your long-term evolution experiments with fascination over the years, and you may be surprised that it is the results of your (and similar) work that has been perhaps most instrumental in my deepening skepticism about unguided evolution.

    Please let me know if you might have the time or inclination to engage with my questions on the topic, and if so, what the best forum to do so might be.

    • If our work has somehow contributed to your skepticism about unguided evolution, then I think you’re looking at evidence and/or inferences in a peculiar way. I don’t have the time to engage further individually — indeed, the recent book review and these follow-up posts and comments are proving overly time-consuming.

      In any case, I encourage you to keep reading and thinking. You might be interested in these papers from our work, showing the evolution of new functions and how they arise. The middle one is from the LTEE, but the other two are from other experimental systems.
      http://science.sciencemag.org/content/335/6067/428
      https://www.nature.com/articles/nature11514
      https://www.nature.com/articles/nature01568
      (Drop me an email if you need pdf reprints.)

      Also, there are many superb books about evolution that i’d recommend. Here are a few thought-provoking books that I really like:
      Zimmer: Evolution: The Triumph of an Idea
      Shubin: Your Inner Fish
      Pennock: Tower of Babel
      Losos: Improbable Destinies
      Judson: Dr. Tatiana’s Sex Advice to All Creation
      Grant & Grant: 40 Years of Evolution: Darwin’s Finches on Daphne Major Island
      Gould: Wonderful Life
      Dugatkin & Trut: How to Tame a Fox (and Build a Dog)
      Dennett: Darwin’s Dangerous Idea
      Dawkins: The Selfish Gene
      Dawkins: Greatest Show on Earth
      Coyne: Why Evolution is True

      Good luck in your pursuit of understanding.

    • Isn’t Behe’s point that if a population has repeatedly suffered 999 mutations that damage genes that may be needed in different circumstances, and then 1 constructive mutation takes place, then another 999 damaging mutations take place before yet another constructive mutation takes place, then that process is self limiting – you will end up with an organism that has lost a lot of its flexibility to survive in different situations – drought, disease, etc. when those genes would have been valuable.

    • To David Bailey: If that’s Behe’s claim, it’s total nonsense. Even in the LTEE
      https://telliamedrevisited.wordpress.com/2019/02/26/is-the-ltee-breaking-bad/
      which is the best case scenario for Behe’s “devolution” claims, we see nothing remotely like that extreme bias toward damaging and destructive mutations. And when environments change, what Behe presumes are damaging mutations may not be damaging at all, as I explain in his polar bear example:
      https://telliamedrevisited.wordpress.com/2019/02/22/on-damaged-genes-and-polar-bears/
      Why the public buys Behe’s claims and books is beyond me.

  13. Behe is talking science backed by evidence. It is true that an atom bomb will outdo a thousand hand grenades, but so what. That is explosives. Stock are stocks. Let’s stick to genetics and the reality of mutational load. Behe’s detractors are supported by assumptions, what ifs, could haves, and maybes with no evidence. They seem to have an abundance of faith. I want to see the science. Their faith is so strong that they don’t even know when they are assuming. We can not simply assume that something is not designed for a purpose, when it appears to many that it is designed for that purpose. We can’t dismiss design based on faith and a false definition of science. We need to see the evidence that genetic information can be added into the system. How is genetic information added into the system to evolve a novel feature like an articulating limb. The fact that some scientists are blind to the evidence of design is meaningless to me.

    • Walt: Your comment confuses what science can, and cannot, say about the world. Feel free to contemplate a supernatural designer, if you choose. But don’t confuse science, which examines the material universe, with appeals to supernatural beings and forces.

  14. D. Carraher

    Dr. Lenski,
    A well written response. I have a few quibbles, however.
    1) The problem with the stock analogy is that the 80 bad stocks don’t kill off the 20 good stocks (or vice versa) through competition before they can succeed. Which is what I think Behe says will happen?
    2) Claiming that positive mutations will overpower the broken/blunted ones is certainly a valid rebuttal. The question becomes, however, does empirical evidence support such an assertion? I believe the point of Behe’s book is that empirical evidence does not support such a conclusion, based on the lack of evidence for positive change, and the significant evidence for broken/blunted adaptations taking over a population.
    3) To use the example of your incredible experiments, do you believe that the citrate mutation constitutes an example of a) positive change that will b) overpower negative mutations in the population? I.e. if these populations were released in the wild, do you believe the citrate mutation would thrive above and beyond the current wild populations and their broken adaptations?

    (My apologies for any inaccurate terminology, hopefully the ideas are clear).

    • Science does not appeal to design as much as it can point to design. Science can and does point us in a direction. Design is an evidence based inference. Materialism science is defined and based on an assumption and not evidence. That is my point. I want evidence based inferences and not faith based assumptions. Science is not required to eliminate any potential conclusions at the onset of exploration. Materialism science begins the exploration of evidence of “origin of life and diversity of species” with the conclusion in hand. That would be a close-minded definition of science. Science does not have to be close-minded. Science for me is unbridled in its search. Anyone is welcome to close off possible answers, but could in the process be closing off the truth.

    • To D. Carraher:
      1) The companies/businesses behind stocks most certainly DO kill off their competitors. Look at what Walmart and Amazon have done to many local businesses, as well as some national competitors. And Apple, for example, came very close to being wiped out by Microsoft, before storming back to success. In both biology and business, however, competitive extinction is rarely instantaneous. It’s a dynamic process, subject to reversal, as a losing competitor evolves and adapts. We’ve certainly seen cases in our experiments where the “side” that appears to be losing recovers and eventually drives the apparent “winner” extinct.

      2) The fossil record of the history of life on Earth, coupled with the diversity of living species we see around us today, provides overwhelming evidence “that positive mutations [have] overpower[ed] the broken/blunted ones.” Behe’s book seems to imply that, too, since he apparently accepts common descent and the paleontological evidence. However, he attributes those positive changes to some hidden designer that inserts novel genes here and there during evolution, without any evidence that it has happened or how it could happen.

      3) I doubt that our citrate-using LTEE population would last very long in nature. But not because of a few broken genes it may have accumulated during its time in the lab. Rather, nature is full of other bacterial species that make good use of any available citrate in mammalian digestive tracts, so that “niche” is already filled. Adaptive radiations, such as the earliest terrestrial vertebrates or the finches that found their way to the Galapagos islands, typically occur when they are newcomers to an un- or under-exploited realm. So additional conditions would likely be required for our little guys to have success. But given an “island” rich in citrate and devoid of citrate-users, I’m pretty sure that a few less-than-perfectly-functioning genes wouldn’t hold them back.

  15. To Walt: I’ve copied my response here to a comment from “Daniel Fisher” on my subsequent post. Maybe it will provide helpful insight. But, alas, I won’t have the time to engage further.
    “Science already has identified a set of evolutionary processes — mutation, recombination (including horizontal gene transfer in some cases), drift, and selection — that can produce, improve, and change functions, giving the appearance of “top down” design in nature. Thus, science doesn’t appear to require an additional “intelligent design” process to explain the diversity of life. But if Michael Behe, or anyone else, produces evidence for how that “top-down” design occurs — I’m talking about real evidence, not the usual hand-waving god-of-the-gaps evolution-can’t-do-that incredulity — I’ll pay it a lot of attention! But it hasn’t happened yet, and I’m not holding my breath …”

    • None of these evolutionary processes — mutation, recombination (including horizontal gene transfer in some cases), drift, and selection — can produce a limb on a lame and limbless organism. None of these evolutionary processes have been shown to gradually evolve and produce functional genitalia in an organism with no functional genitalia. Functional genitalia is somewhat necessary and not something that can wait on evolutionary processes — mutation, recombination (including horizontal gene transfer in some cases), drift, and selection. A species with no gene Italia will be extinct, soon.
      Natural science is confined to exploration and testing of natural phenomena. How could something confined to natural phenomena ever explain the supernatural? You tell me that I can’t jump 36 inches, while you have a 24 inch tether on my ankles. In that case you will always be correct, if you get to set the parameters. Natural science is tethered and confined to “inside the box thinking”. By your definition thinking untethered and “outside the box thinking” is prohibited. Who made the rules? Einstein and Newton did not exclude the supernatural as they explained the natural.

    • Walt: There are some thriving organisms, like yeast, that reproduce — yes, even sexually — just fine without genitalia. Anyhow, Behe also accepts common descent and the history of life as seen in the fossil record, but he thinks an intelligent agent purposefully designed and somehow added new genetic information (presumably encoding genitalia) along the way. So please ask him to explain when, where, and how that happened. Early science may once have considered what most scientists today would regard as unscientific, supernatural forces. But that work never panned out, and so it’s widely viewed as nonscientific today.

  16. Rob Stadler

    Prof. Lenski,
    Thank you for taking the time to blog here and to respond to comments. I also greatly appreciate the tone of this dialogue, which is so uncommon in these kinds of debates.
    What I find puzzling about your response to Behe is that you are the world authority on evolutionary evidence that is prospective, directly observable, and repeatable. Your type of evolutionary evidence provides a level of confidence that far exceeds the vast majority of evidence for evolution (e.g., the fossil record, homology, vestigial organs) that cannot be repeated, directly observed, or studied prospectively. But in response here to Behe’s alternative interpretation of your prospective, directly observed evolutionary data, you resort largely to lower confidence evidence – stories about Tiktalik, and about asteroid impacts. As mentioned by Daniel Fischer here, your response is based on narrative that starts by assuming what you are arguing. Why would you prioritize this approach over your own high-confidence evidence? My book, The Scientific Approach to Evolution, speaks to this in depth.

    • I’d love to perform an experiment on the vast scales of space and time over which evolution has operated, but I haven’t had the time (billions of years) or space (replicate planets). Yes, I’m proud that our experiments have contributed some small measure of insight into the evolutionary process. But comparative biology (including genomics) and the fossil record leave no room for reasonable doubt that organic evolution has occurred. Even Behe apparently accepts that fact — although he also proposes that some unknown agent reached in and provided new genetic information along the way. As a scientist, that’s totally unsatisfying, all the more so since science has discovered natural processes that can accomplish the same thing.
      (Perhaps God created a world that only looked like evolution had taken place. Or perhaps God pre-programmed the universe so it looked like mutations were random with respect to their utility, but just the right ones would pop up at just the right moments. If so, I can’t shed any light on how God did such things. But I’d wonder why …)
      Of course, a perfect — or sometimes even satisfactory — understanding of exactly what happened so long ago is shrouded by time. (Or as some creationists like to say, you weren’t there when it happened, so how do you know?) Nonetheless, science has made predictions — and made new discoveries based on those predictions — about past events, from the asteroid impact to Tiktaalik to the introgression of Neanderthal and Denisovan DNA into living humans.
      These evolutionary narratives, all supported by solid science (and subject to revision as scientists learn more) are, in my view, far more consequential to our understanding of where we came from and how we got here than an experiment with bacteria in the lab, as much as I love my experiment for its ability to show evolution as an ongoing process.
      In any case, as Lents, Swamidass, and I wrote in our book review (and I’ve said in response to some other comments), modern evolutionary theory provides a coherent set of core processes that are consistent with what we see using comparative methods and paleontological records. And science has observed those core processes, including improved and sometimes even new functions.

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  19. Louie

    Dr. Lenski,

    Thanks so much for your very thoughtful and well-reasoned response to Michael Behe’s critique. Please keep up the good work. I am following this dialogue closely trying to make up my mind about what the evidence says. This type of dialogue is very enlightening for me. I appreciate your insights.

    Sincerely,
    Louie

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  22. JimV

    A few previous commenters have made the point that all logical conclusions (e.g., math theorems) depend on initial assumptions. This of course applies to their own assumptions and biases. How do we resolve differences of opinion that depend on different assumptions? Science was developed to do exactly this, by comparing evidence and predictions in statistically-valid ways. As far as I know, there are essentially no reliable predictions of what the assumed Intelligent Designer will do next, whereas the ToE does product reliable results. For example, the evolutionary algorithm has been used in computer simulations to improve many products, such as the GE-90 jet engine. (Unless one assumes the Intelligent Designer is also juggling the random-number generators in those computers.)

    Speaking of assumptions, if I recall correctly Dr. Behe did his calculation of the probablility of a certain mutation in his “Edge” book assuming there were only two possible pathways for that mutation to occur, whereas those who study it have so far found seven pathways. See Dr. Ken Miller’s website for details. Unfortunately, Dr, Behe’s books are published without prior peer review.

    (Off topic, but the very concept of Intelligent Design being some sort of magic based on human design work seems very problematical to me. In my 38 years as a design engineer, trial-and-error played just as large a role in human design as it does in ToE. See Edison and his 1000-odd trials of light-bulb filaments. I often wonder if the ID theorists such as Dr. Behe have ever been part of a working design team.)

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