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. 
Leisola has delivered several books in Finnish, whose authors adopt a pseudo-scientific  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 .  Dictionaries published The first edition of the Evolutionary-Critical Analysis book in 2000.  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.