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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 editor-in-chief of Bloggingheads TV, Robert Wright, has re-instated my interview with linguist John McWhorter (http://bloggingheads.tv/diavlogs/22075) on that website. Wright was away last week when the brouhaha occurred, and it’s good to see that a steady editorial hand is back in charge.

Dear readers, I’ve just been through the weirdest book-related experience I’ve had since a Canadian university professor with a loaded rat trap chased me around after a talk I gave a dozen years ago, threatening to spring it on me. Last week I got the following email bearing the title “Invitation to Appear on Bloggingheads TV” from a senior editor at that site: ************* Hi, Michael– I’d like to invite you to appear on Bloggingheads.tv, a web site that hosts video dialogues between journalists, bloggers, and scholars. We have a partnership with the New York Times by which they feature excerpts from some of our shows on their site. Past guests include prominent thinkers such as Paul Krugman, Paul Ehrlich, 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 Below I reproduce the unpublished letter for those who might be interested in my reaction to the article.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, This post continues directly from Part 1. Koonin is clearly very impressed with the new paper, which he calls “brilliant” and “a genuinely important work that introduces a new and potentially major mechanism of evolution…” His enthusiasm is a good indication that the problem is a major one, and that no other papers exist which deal effectively with it. So what is the paper (a theoretical, mathematical-modeling study) about?  When a mutationless gene is transcribed and translated into a protein, errors can creep in. It turns out that these error rates are much higher than for copying DNA. Using published mutation rates, Whitehead et al (2008) estimate that 1 in 10 standard-sized proteins will contain an error; that is, they 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, An interesting paper appeared several months ago in an issue of the journal Genetics, “Waiting for Two Mutations: With Applications to Regulatory Sequence Evolution and the Limits of Darwinian Evolution” (Durrett, R & Schmidt, D. 2008. Genetics 180: 1501-1509). This is the fifth of five posts that discusses it. Cited references appear in this post. The final conceptual error that Durrett and Schmidt commit is the gratuitous multiplication of probabilistic resources. In their original paper they calculated that the appearance of a particular double mutation in humans would have an expected time of appearance of 216 million years, if one were considering a one kilobase region of the genome. Since the evolution of humans from other primates took much less time Read More ›

An interesting paper appeared several months ago in an issue of the journal Genetics, “Waiting for Two Mutations: With Applications to Regulatory Sequence Evolution and the Limits of Darwinian Evolution” (Durrett, R & Schmidt, D. 2008. Genetics 180: 1501-1509). This is the fourth of five posts that discusses it. Cited references will appear in the last post.  Now I’d like to turn to a couple of other points in Durrett and Schmidt’s reply which aren’t mistakes with their model, but which do reflect conceptual errors. As I quote in a previous post, they state in their reply, “This conclusion is simply wrong since it assumes that there is only one individual in the population with the first mutation.” I have shown previously that, Read More ›