Biochemistry

I never thought it would happen but, in my estimation, Richard Lenski has acquired a challenger for the title of “Best Experimental Evolutionary Scientist.” Lenski, of course, is the well-known fellow who has been growing E. coli in his lab at Michigan State for 50,000 generations in order to follow its evolutionary progress. His rival is Joseph Thornton of the University of Oregon who, by inferring the sequences of ancient proteins and then constructing (he calls it “resurrecting”) their genes in his lab, is able to characterize the properties of the ancestral proteins and discern how they may have evolved into more modern versions with different properties. I have written appreciatively about both Lenski and Thornton before, whose work indicates Read More ›

Dear Readers, Recently a paper appeared online in the journal Proceedings of the National Academy of Sciences, entitled “The reducible complexity of a mitochondrial molecular machine” (http://tinyurl.com/mhoh7w). As you might expect, I was very interested in reading what the authors had to say. Unfortunately, as is all too common on this topic, the claims made in the paper far surpassed the data, and distinctions between such basic ideas as “reducible” versus “irreducible” and “Darwinian” versus “non-Darwinian” were pretty much ignored. Since PNASpublishes letters to the editor on its website, I wrote in. Alas, it seems that polite comments by a person whose work is the clear target of the paper are not as welcome as one might suppose from reading the journal’s Read More ›

The May 1st issue of Science contains a “News Focus” article entitled “On the Origin of the Immune System.” While describing some current work in the area the author, John Travis, makes liberal use of myself as an unreasonably-skeptical foil. I wrote a letter to the editor of Science pointing out inaccuracies in the story but, gee whiz, they didn’t think the letter would be of sufficient interest to their readers to print it. Below I reproduce the unpublished letter for those who might be interested in my reaction to the article. To the editor:  In his article “On the Origin of the Immune System” (Science, May 1, 2009) John Travis makes the same mistake as did the judge in the 2005 Dover trial Read More ›

The January 2009 issue of Trends in Microbiology contains an article entitled “Bacterial flagellar diversity and evolution: seek simplicity and distrust it?”  Unfortunately, like many people, the authors have a mistaken view of irreducible complexity, as well as a very shallow idea of what a Darwinian “precursor” to an irreducibly complex system might be. I wrote a letter to the editor of the journal to point out these difficulties. Alas, they said they had no room to publish it. Below is the letter that I sent. To the editor: In their recent article “Bacterial flagellar diversity and evolution: seek simplicity and distrust it?” Snyder et al. (2009) [1] attribute to me a view of irreducible complexity concerning the flagellum that I do Read More ›

Dear Readers, This post continues directly from Part 2. Second, the authors assume that, in the absence of phenotypic mutations, the first genotypic mutation would be strictly neutral. That is, the selection coefficient for the first mutation is very, very close to zero. It turns out that this is a critical feature. If the first mutation were slightly positive itself (without considering look-ahead) then it could be selected on its own, and the look-ahead effect makes little difference. On the other hand, if the first mutation is slightly negative (including look-ahead), then it will not be positively selected and, again, the effect makes essentially no difference. It is only in a very restricted range of selection coefficients that any significant influence will be Read More ›

Dear Readers, When The Edge of Evolution  The Edge of Evolution: The Search for the Limits of Darwinism  was first published, some Darwinist reviewers sneered that the problem it focused on — the need for multiple mutations to form some protein features (such as binding sites), where intermediate mutations were deleterious — was a chimera. There were no such things, they essentially said. University of Wisconsin geneticist Sean Carroll, reviewing the book for Science, stressed examples where intermediate mutations were beneficial (I never said there weren’t such cases, and discussed several in the book). In the same vein, University of Chicago evolutionary biologist Jerry Coyne assured readers of The New Republic that “[i]n fact, interactions between proteins, like any complex interaction, were certainly built up step Read More ›

Dear Readers, Brown University Professor Kenneth Miller has gotten into a little tiffwith Discovery Institute’s Casey Luskin over what I said/meant about the blood clotting cascade in Darwin’s Black Box.  This is the first of two posts commenting on that. In Chapter 4 of Darwin’s Black Box I first described the clotting cascade and then, in a section called “Similarities and Differences”, analyzed it in terms of irreducible complexity. Near the beginning of that part I had written, “Leaving aside the system before the fork in the pathway, where details are less well known, the blood clotting system fits the definition of irreducible complexity…  The components of the system (beyond the fork in the pathway) are fibrinogen, prothrombin, Stuart factor, and proaccelerin.” Casey Luskin concludes that Read More ›

This is the second of five posts in which I reply to Dr. Ian Musgrave’s “Open Letter to Dr. Michael Behe” on the Panda’s Thumb blog. Musgrave: But by far the worst, you ignored her core argument. That in the space of a decade HIV-1 Vpu developed a series of binding sites that made it a viroporin, a multisubunit structure with a function previously absent from HIV-1. Behe: It is not clear to me why you call that Smith’s “core argument.” In her post, her writing meanders quite a bit; it’s hard for me to glean what she thinks is most important. After sneering a bit at me, Smith began her post by asserting that vpu is a “new” gene (even though Read More ›

Dear Readers, The latest issue of the journal Trends in Ecology and Evolution (TREE) carries a tediously disdainful review (1) of The Edge which revisits the blunders of previous reviews while adding new ones. This is the third of a three part series concerning the review. At the end of his essay our reviewer suddenly reveals his skill at mind reading: “It is clear that Behe is driven not by a truly scientific investigation, but instead metaphysics.” And this: “He is obsessed with ‘randomness,’ which he incorrigibly associates with ‘Darwinism’ and cosmic purposelessness.” Now, wait a darn second. Wasn’t it Darwin himself, we are constantly assured, who based his theory on “random” variation? So it’s “incorrigible” to associate with Darwin’s theory something which Darwin Read More ›

f you have any questions about my new book, Edge of Evolution, you might enjoy taking a look at this brief interview I just gave.   Question & Answer With Michael J. Behe, author of The Edge of Evolution: The Search for the Limits of Darwinism   What do you believe Darwinian evolutionary processes can actually do? THE EDGE OF EVOLUTION asks the sober question, what is it reasonable to think Darwinian evolutionary processes can actually do? Unprecedented genetic data on humans and our microbial parasites (malaria, HIV, E. coli) now allow us to answer that question with some precision. The astonishing result is that, even under intense selective pressure, and given an astronomical number of opportunities, random mutation and natural selection yield only trivial, Read More ›