Evolutionary Biology

In my last post I reported that University of Chicago evolutionary biologist Jerry Coyne, who had critiqued (http://tinyurl.com/2fjenlt) my recent Quarterly Review of Biology article (http://tinyurl.com/25c422s) concerning laboratory evolution studies of the last four decades and what they show us about evolution, had asked several other prominent scientists for comments (http://tinyurl.com/2cyetm7). I replied (http://tinyurl.com/4lq8sre) to those of experimental evolutionary biologist John Bull. In a subsequent post Coyne discussed (http://tinyurl.com/4tqoq7c) a recent paper (http://tinyurl.com/4shw456) by the group of fellow University of Chicago biologist Manyuan Long on gene duplication in fruitflies. After a bit of delay due to the holidays, I will comment on that here. Try as one might to keep Darwinists focused on the data, some can’t help reverting to Read More ›

In its most recent issue The Quarterly Review of Biology has published a review by myself of laboratory evolution experiments of microbes going back four decades. The paper (entitled “Experimental Evolution, Loss-of-Function Mutations, and ‘The First Rule of Adaptive Evolution’”) is available as a free pdf on my Lehigh University website (http://www.lehigh.edu/~inbios/pdf/Behe/QRB_paper.pdf). The chief question asked in the paper is the following: does evolution more often proceed by endowing an organism with a new function, by taking away an existing function, or by tweaking (modifying) a pre-existing function? Darwin himself realized that evolution did not always have to proceed by gain-of-function events. For example, in some of his writings he described male barnacles that had undergone gross simplification. For most Read More ›

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 ›

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 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 ›