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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 third of five posts that discusses it. Cited references will appear in the last post. The third problem also concerns the biology of the system. I’m at a bit of a loss here, because the problem is not hard to see, and yet in their reply they stoutly deny the mistake. In fact, they confidently assert it is I who am mistaken. I had written in my letter, ‘‘… their model is incomplete on its own terms because it 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 second of five posts that discusses it. Cited references will appear in the last post.  Interesting as it is, there are some pretty serious problems in the way they applied their model to my arguments, some of which they owned up to in their reply, and some of which they didn’t. When the problems are fixed, however, the resulting number is remarkably close to the empirical value of 1 in 10^20. I will go through the difficulties in turn. 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 first of five posts that discusses it. Cited references will appear in the last post.  As the title implies, it concerns the time one would have to wait for Darwinian processes to produce some helpful biological feature (here, regulatory sequences in DNA) if two mutations are required instead of just one. It is a theoretical paper, which uses models, math, and computer simulations to reach conclusions, rather than empirical data from field or lab experiments, as The Edge does. The authors Read More ›

Dear Readers, In a long book review in The New Republic, University of Chicago evolutionary biologist Jerry Coyne calls Brown University cell biologist Ken Miller a creationist. No surprise there — “creationist” has a lot of negative emotional resonance in many intellectual circles, so it makes a fellow’s rhetorical task a lot easier if he can tag his intellectual opponent with the label. (Kind of like calling someone a “communist” back in the 1950s.) No need for the hapless “creationist” to be a Biblical literalist, or to believe in a young earth, or to be politically or socially conservative, or have any other attribute the general public thinks of when they hear the “C” word. For Coyne, one just has to think that Read More ›

Dear Readers,At the end of his first post squabbling with Discovery Institute’s Casey Luskin, Brown University Professor Kenneth Miller refers to some great new work by UC San Diego Professor and member of the National Academy of Science, Russell Doolittle. Doolittle, of course, has worked on the blood clotting cascade for about fifty years! (I discussed some of his work in Chapter 4 of Darwin’s Black Box.) In a new paper Doolittle and co-workers analyze DNA sequence data from a primitive vertebrate, the lamprey, thinking that it might have a simpler clotting cascade than higher vertebrates. (1) It is difficult work, because the sequences of lamprey proteins — even ones that are indeed homologous to the proteins of other vertebrates — are significantly 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 ›

Dear Readers, Kenneth R. Miller, a professor of biology at Brown University, has written a new book Only a Theory: Evolution and the Battle for America’s Soul, in which he defends Darwinism, attacks intelligent design, and makes a case for theistic evolution (defined as something like “God used Darwinian evolution to make life”). In all this, it’s pretty much a re-run of his previous book published over a decade ago,Finding Darwin’s God: A Scientist’s Search for Common Ground between God and Evolution. So if you read that book, you’ll have a very good idea of what 90% of the new book concerns. For people who think that a mousetrap is not irreducibly complex because parts of it can be used as Read More ›

Dear Readers, An interesting paper has just appeared in the Proceedings of the National Academy of Sciences, “Historical contingency and the evolution of a key innovation in an experimental population of Escherichia coli.” (1) It is the “inaugural article” of Richard Lenski, who was recently elected to the National Academy. Lenski, of course, is well known for conducting the longest, most detailed “lab evolution” experiment in history, growing the bacterium E. coli continuously for about twenty years in his Michigan State lab. For the fast-growing bug, that’s over 40,000 generations! I discuss Lenski’s fascinating work in Chapter 7 of The Edge of Evolution, pointing out that all of the beneficial mutations identified from the studies so far seem to have been degradative ones, where functioning genes are knocked out or Read More ›

Dear Readers, An interesting paper appeared recently in the New England Journal of Medicine. (1) The workers there discovered some new mutations which confer some resistance to malaria on human blood cells in the lab. (Their usefulness in nature has not yet been nailed down.) The relevance to my analysis in The Edge of Evolution is that, like other mutations that help with malaria, these mutations, too, are ones which degrade the function of a normally very useful protein, called pyruvate kinase. As the workers note: “[H]eterozygosity for partial or complete loss-of-function alleles . . . may have little negative effect on overall fitness (including transmission of mutant alleles), while providing a modest but significant protective effect against malaria. Although speculative, this situation Read More ›

Dear Readers, California State University emeritus Professor Mark Perakh (author of Unintelligent Design) and I recently taped an episode of the program “Voice of Reason”,http://www.cn8.tv/channel/article.asp?lArticleID=5 195&lChannelID=603 with the venerable Philadelphia newsman Larry Kane. We discussed intelligent design, The Edge of Evolution, and other topics for thirty minutes. The show will air Sunday March 2nd at 9:30 p.m. on CN8, the Comcast Network.