A new paper from Richard Lenski’s group has appeared in Nature and has garnered a fair amount of press attention. 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 whole genomes — each and every nucleotide — sequenced of the E. coli that they have been growing for the past twenty years. Since they froze away portions of their bacterial culture at different times along the way, they now have the exact sequences of the evolving culture at many time points, from inception to 2000 generations to 10,000 to 40,000. Thus they can know exactly which mutations appeared when — an almost-complete paper trail. Very very cool!

From that information they identify a couple score of mutations which they say are likely beneficial ones. That is almost certainly true, but what they don’t emphasize is that many of the beneficial mutations are degradative — that is, they eliminate a gene or its protein’s function. About half of the mutations they initially identified in previous work, but some they report here for the first time. They don’t discuss what the new ones do (they may not yet know), but odds are high that most of them also are degradative, causing proteins either to stop working or to work less well. In any event, there is no indication that any of these are on their way to building some complex new system.
Interestingly, in this paper they report that the E. coli strain became a “mutator.” That means it lost at least some of its ability to repair its DNA, so mutations are accumulating now at a rate about seventy times faster than normal. Lenski had reported years earlier that a number of other lines of the evolving population (they started with 12 separate cultures) had become mutators, too. So it seems that loss of ability to repair DNA is a common occurrence under these conditions.
Lenski is a very good self-promoter (no criticism intended; that’s a good thing — scientists have to interest other people in their work), and he always accentuates the positive. So if a gene is blasted to bits by a mutation, he talks cheerfully about how it is a beneficial change that helps the bacterium grow faster. One has to dig hard into the data to see that the bacterium is losing genetic info. In press coverage for this paper, he avows a “new dynamic relationship was established” in the bacterium’s evolution, and one has to read the details of the paper to find out that this is due to a degradative mutation that compromises its normal ability to repair its DNA.
Despite his understandable desire to spin the results his way, Lenski’s decades-long work lines up wonderfully with what an ID person would expect — in a huge number of tries, one sees minor changes, mostly degradative, and no new complex systems. So much for the power of random mutation and natural selection. For his work in this area we should be very grateful. It gives us solid results to point to, rather than having to debate speculative scenarios.
References
Barrick, J.E., Yu, D.S., Yoon, S.H., Jeong, H., Oh, T.K., Schneider, D., Lenski, R.E., and Kim,J.F. 2009. Genome evolution and adaptation in a long-term experiment with Escherichia coli. Nature, doi:10.1038/nature08480.
Sniegowski, P.D., Gerrish, P.J., and Lenski, R.E. 1997. Evolution of high mutation rates in experimental populations of E. coli. Nature 387:703-705.