Evolution Redux

To many of us practicing science on a daily basis, the following claim may seem odd or even absurd at first pass: the recent report in Nature (PMID: 22992527; link) on the 30 year Escherichia coli experiment from Richard Lenski’s lab at Michigan State University has reintroduced the scientific method to one of the cornerstones of modern scientific thought—evolution.

Lenski began an experiment in evolutionary biology in 1988, when he propagated individual bacterial clones, splitting the cells daily, for nearly 55,000 generations, leading up to the present day. The purpose was to observe evolutionary change within this population in real time and to understand the role of various environmental and stochastic events in enabling selection. Every day for the last 30 years, one aliquot of those cells, amounting to a clonal sample of each of the ~55,000 generations, was frozen down by Lenski (or likely a grad student/post-doc). Herein lies the utility of this Herculean feat of patience and experimentation: because the ancestors to the current generation (and all those that will come after it…the experiment is still ongoing) are still alive and in the suspended animation of the -80°C freezer, this experiment in evolution can be repeated!

This is just what Lenski and his team did in the paper by Blount et al. Having observed spontaneous acquisition of a phenotype allowing utilization of citrate for an energy source, the lab traced the change to a genomic rearrangement that removed a block on citrate transporter expression around generation 30,000. However, this rearrangement alone was not enough to make the new phenotype an effective target for selection. Through elegant additional work, the lab proposes a model where 1) genomic rearrangements, in this case the transposition of an active promoter upstream of an evolutionarily silenced gene, can cause re-expression of a seemingly new protein for the given organism; 2) compounded by random potentiating mutations, and, of course, 3) selective pressures (in this case apparently positive ones, in the availability of oxygen and citrate in the growth media), new traits can arise. Because this bug was in the freezer, they thawed it and repeated the experiment, observing the emergence of this same phenotype a second time under the same controlled laboratory conditions.

That natural selection occurs is rarely denied, even by the non-scientific community, but proving evolution can occur has been more of a bugaboo. In fact this is true for many areas of science, where theories become adopted, due to the impracticality or impossibility of directly testing them (see PMID: 22914130, link, for a recent discussion of this point for the Higgs Boson and origin of the universe). Lenski and colleagues have taken evolution out of this fuzzy area of over-whelming evidence but experimental intractability. This feat is remarkable for many reasons including Lenski’s dedication to the task (What other mysteries will be revealed when the organism gets to generation 200,000? 1,000,000?), the scientific community’s support, the funding from the NSF, NIH and other sources (including several forward-thinking private foundations, per the paper's acknowledgements), and most of all, for the exciting discovery getting at the How? of evolution, that is, of the principles governing rapid emergence of phenotypes through slow genetic change over thousands of generations (or as Lenski and colleagues describe, potentiation, actualization and refinement of a trait). Perhaps most important, it is a victory against the defeatism of “it’s too complex to have happened by chance.”

Tom Vondriska -- September 25, 2012