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University of California evolutionary biologist John Avise has penned a book, Inside the Human Genome: A Case for Non-Intelligent Design, and gotten it published by a top academic publishing house, Oxford University Press. Avise, a member of the National Academy of Sciences, has for decades been a leading researcher in evolutionary and ecological genetics. He has written hundreds of research articles and over a dozen books. Clearly he has an impressive scientific mind. Which makes it all the more astonishing that his new book shows all the intellectual savvy of a typical late-night college dormroom bull session. As his subtitle announces, Avise is anxious to show that, despite the claims of certain renegade biochemists, the molecular features of the human genome Read More ›

The science writer Carl Zimmer posted an invited replyhttp://tinyurl.com/yhpm3t7 on his blog from Joseph Thornton of the University of Oregon to my recent comments about Thornton’s work. This is the last of four posts addressing it. References appear at the bottom of this post. At the end of his post Thornton waxes wroth. Behe’s argument has no scientific merit.  It is based on a misunderstanding of the fundamental processes of molecular evolution and a failure to appreciate the nature of probability itself.  There is no scientific controversy about whether natural processes can drive the evolution of complex proteins.  The work of my research group should not be misintepreted by those who would like to pretend that there is. Well, now. I’ll Read More ›

The science writer Carl Zimmer posted an invited replyhttp://tinyurl.com/yhpm3t7 on his blog from Joseph Thornton of the University of Oregon to my recent comments about Thornton’s work. This is the third of several posts addressing it. References will appear in the last post. Now back to Thornton’s first point, the role of neutral mutations (which he sometimes labels “permissive” mutations). At several places in his post Thornton implies I’m unaware of the possibilities opened up by genetic drift: “Behe’s discussion of our 2009 paper in Nature is a gross misreading because it ignores the importance of neutral pathways in protein evolution…. Behe’s first error is to ignore the fact that adaptive combinations of mutations can and do evolve by pathways involving neutral intermediates…. Read More ›

The science writer Carl Zimmer posted an invited replyhttp://tinyurl.com/yhpm3t7 on his blog from Joseph Thornton of the University of Oregon to my recent comments about Thornton’s work. This is the second of several posts addressing it. References will appear in the last post. Now to Professor Thornton’s reply. He writes at length but makes just two substantive points: 1) that neutral mutations occur and can serendipitously help a protein evolve some function (“[Behe] ignores the key role of genetic drift in evolution”); and 2) that just because a protein may not be able to evolve a particular function one way does not mean that it, or some other kind of protein, can’t evolve the function another way (“nothing in our results Read More ›

The science writer Carl Zimmer posted an invited replyhttp://tinyurl.com/yhpm3t7 on his blog from Joseph Thornton of the University of Oregon to my recent comments about Thornton’s work. This is the first of several posts addressing it. References will appear in the last post. I must say, it never ceases to amaze me how otherwise-very-smart folks like Zimmer and Thornton fail to grasp pretty simple points when it comes to problems for Darwinian mechanisms. Let me start slowly with a petty complaint in Carl Zimmer’s intro to the post. Zimmer is annoyed that I think Thornton’s latest work is “great”, yet I thought his previous work published a few years ago was “piddling”. “Why the change of heart?”, wonders Zimmer. It’s really Read More ›

A new paper from Richard Lenski’s group has appeared in Nature http://tinyurl.com/ygtcflq and has garnered a fair amount of press attention (for example, herehttp://tinyurl.com/yh7nqht ). Some people asked me for my thoughts about it. The new paper continues the grand experiment that Lenski has been publishing about lo these many years — allowing a culture of the bacterium E. coli to continuously grow and evolve under his close observation. The only really new thing reported is a technical improvement — these days one can have the entire genome of E. coli “re-sequenced” (that is, determine the sequence of the entire DNA of the particular E. coli you’re working with) done for an affordable cost. (There are companies which will do it for a fee.) So Lenski and collaborators had the Read More ›

Nature has recently published an interesting paper which places severe limits on Darwinian evolution. The manuscript, from the laboratory of Joseph Thornton at the University of Oregon, is entitled “An epistatic ratchet constrains the direction of glucocorticoid receptor evolution”. ( http://tinyurl.com/yeq2cy8 ) The work is interpreted by its authors within a standard Darwinian framework, but the results line up very well with arguments I made in The Edge of Evolution. ( http://tinyurl.com/yba6vba ) This is the last of three posts discussing it. Bridgham et al (2009) are interested in the reversibility of evolution, and discuss their results in terms of something called “Dollo’s law.” Louis Dollo, an early 20thcentury paleobiologist, was interested in discerning phylogenies. He maintained that one could always distinguish ancestral forms from descendant Read More ›

Nature has recently published an interesting paper which places severe limits on Darwinian evolution. The manuscript, from the laboratory of Joseph Thornton at the University of Oregon, is entitled “An epistatic ratchet constrains the direction of glucocorticoid receptor evolution”. ( http://tinyurl.com/yeq2cy8 ) The work is interpreted by its authors within a standard Darwinian framework, but the results line up very well with arguments I made in The Edge of Evolution. ( http://tinyurl.com/yba6vba )This is the second of several posts discussing it. Using clever synthetic and analytical techniques, Bridgham et al (2009) show that the more recent hormone receptor protein that they synthesized, a GR-like protein, can’t easily revert to the ancestral structure and activity of an MR-like protein because its structure has been adjusted by selection Read More ›

Nature has published an interesting paper recently which places severe limits on Darwinian evolution. This is the first of several posts discussing it. The manuscript, from the laboratory of Joseph Thornton at the University of Oregon, is entitled “An epistatic ratchet constrains the direction of glucocorticoid receptor evolution”. ( http://tinyurl.com/yeq2cy8 ) The work is interpreted by its authors within a standard Darwinian framework. Nonetheless, like the important work over the years of Michigan State’s Richard Lenski on laboratory evolution of E. coli, which has shown trillions of bacteria evolving under selection for tens of thousands of generations yielding just broken genes and minor changes, the new work demonstrates the looming brick wall which confronts unguided evolution in at least one system. And it points Read More ›

In a new segment, http://bloggingheads.tv/diavlogs/22300 , Bloggingheads chief Robert Wright and Bloggingheads correspondent George Johnson go on for 75 minutes about the trauma of a pair of heretics (me and Paul Nelson, on separate segments) appearing on their site. I would urge everyone who doesn’t have pressing matters to attend to, such as the need to wash your hair, to tune in for the full time. It’s really fascinating in its way to see two grown men in such a hand-wringing lather. It’s also fascinating to see that neither of them in 75 minutes offers a reason for the correctness of their own views, or the wrongness of ours. The closest they come is when George Johnson invokes the hoary “methodological naturalism.” Read More ›