Limits of Evolution

Recently a new paper by Richard Lenski and colleagues (Meyer et al 2012) appeared in Science with, as usual, commentary in the New York Times. (Lenski’s lab must own a red phone with a direct line to The Gray Lady.) The gist of the paper is that a certain bacteriophage (a virus that infects bacteria) called “lambda” gained the ability to bind a different protein on the surface of its host, the bacterium E. coli, than the protein it usually binds. The virus has to bind to the cell’s surface as a prelude to invading it. The protein it normally binds is called LamB. Lenski’s lab, however, used a bacterial strain that had turned off the production of LamB in 99% of E. coli cells but, Read More ›

Recently a paper appeared by Ratcliff et al. (2012) entitled “Experimental evolution of mulitcellularity” and received a fair amount of press attention, including a story in the New York Times. (http://tinyurl.com/6va4fpp ) The authors discuss their results in terms of the origin of multicellularity on earth. The senior author of the paper is Michael Travisano of the University of Minnesota, who was a student of Richard Lenski’s in the 1990s. The paper, published in PNAS, was edited by Lenski. The gist is as follows. The authors repeated three steps multiple times: 1) they grew single-celled yeast in a flask; 2) briefly centrifuged it; and 3) took a small amount from the bottom of the flask to seed a new culture. This Read More ›

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 clear limits Read More ›

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 ›

At his blog (http://tinyurl.com/2cyetm7) University of Chicago professor of evolutionary biology Jerry Coyne has commented on my reply (http://tinyurl.com/383zqm7) to his analysis ((http://tinyurl.com/2fjenlt) of my new review (http://tinyurl.com/25c422s) in the Quarterly Review of Biology. This time he has involved two other prominent scientists in the conversation. I’ll discuss the comments of one of them in this post and the other in a second post. The first one is University of Texas professor of molecular biology James J. Bull, who works on the laboratory evolution of bacterial viruses (phages). I reviewed a number of Bull’s fascinating papers in the recent QRB publication. Coyne solicited Prof. Bull’s comments and put them up on his blog (http://tinyurl.com/2cyetm7). Bull says several nice things about 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 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 ›

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 ›