natural selection

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 ›

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, Why Evolution is True (http://tinyurl.com/2fjenlt), Jerry Coyne, professor of evolutionary biology at the University of Chicago, has been analyzing my recent paper, “Experimental Evolution, Loss-of-Function Mutations, and ‘The First Rule of Adaptive Evolution’” (http://www.lehigh.edu/~inbios/pdf/Behe/QRB_paper.pdf), which appears in the latest issue of the Quarterly Review of Biology. Although I usually don’t respond to blog posts I will this time, both because Coyne is an eminent scientist and because he does say at least one nice thing about the paper. First, the nice thing. About half-way through his comments Professor Coyne writes: My overall conclusion: Behe has provided a useful survey of mutations that cause adaptation in short-term lab experiments on microbes (note that at least one of these 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 ›

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 ›

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 ›

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 ›