Thursday, May 10, 2007

Neutral origins of complexity?   posted by p-ter @ 5/10/2007 06:31:00 PM

Reading an agressively-stated scientific opinion is an acquired taste-- in published work, academics prefer to subtly hint that their colleague is ass, rather than just saying it directly like we do here on the internets. But when one is used to the dry writing of the scientific research articles, those subtle (or sometimes not so subtle) digs come to be rather enjoyable.

Which is why I enjoyed this piece by Michael Lynch [pdf], just published in PNAS. Dr. Lynch has long been an advocate for taking population genetics forces into account when studying genome evolution and innovation, and here he makes his case:
Although the basic theoretical foundation for understanding the mechanisms of evolution, the field of population genetics, has long been in place, the central significance of this framework is still occasionally questioned, as exemplified in this quote from Carroll (4), "Since the Modern Synthesis, most expositions of the evolutionary process have focused on microevolutionary mechanisms. Millions of biology students have been taught the view (from population genetics) that 'evolution is change in gene frequencies.' Isn't that an inspiring theme? This view forces the explanation toward mathematics and abstract descriptions of genes, and away from butterflies and zebras. . . The evolution of form is the main drama of life's story, both as found in the fossil record and in the diversity of living species. So, let's teach that story. Instead of 'change in gene frequencies,' let's try 'evolution of form is change in development'." Even ignoring the fact that most species are unicellular and differentiated mainly by metabolic features, this statement illustrates two fundamental misunderstandings. Evolutionary biology is not a story-telling exercise, and the goal of population genetics is not to be inspiring, but to be explanatory.
His argument is that many of the features of the eukaryotic cell, often assumed to be products of adaptations, may be largely the result of deleterious fixations due to a much smaller eukaryotic effective population size. It remains unclear how these features-- introns, large genomes, some aspects of gene regulation-- came to arise given their apparent costs. According to Lynch, population genetics provides a simple framework for testing neutral versus adaptive hypothesis on this subject (he favors neutral explanations). This has been largely ignored due to, well, the fact that math is hard:
The field of population genetics is technically demanding, and it is well known that most biologists abhor all things mathematical. However, the details do matter in the field of evolutionary biology.
Overall, he presents a sort of neutral theory of genome evolution, or at least the beginnings of one. And I must admit I'm intrigued by this possibility that "a long-term synergism may exist between nonadaptive evolution at the DNA level and adaptive evolution on the phenotypic level".

Some possibile examples of this: one of the current roles of the nuclear membrane is to segregate the actions of transcription from those of translation so that introns can be spliced out before a protein is made. It's an interesting hypothesis, then, that the nuclear membrane itself (one of the defining hallmarks of a eukaryotic cell) evolved in response to the existence of introns. Lynch cites another paper arguing that the nonsense-mediated decay pathway could also have evolved to prevent the translation of transcripts resulting from splicing errors. Finally, I've also heard much speculation that many of the regulatory mechanisms we take for granted-- methylation, histone modifications, etc.-- could have evolved to silence selfish DNA elements before taking on the broader roles they play today.

Sewall Wright put much emphasis on the role of genetic drift in allowing the evolutionary process to cross regions of low fitess to find other adaptive peaks. Maybe early population geneticists really did discover everything worth knowing about evolution.

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