Notes from the Biomass

You need to study molecular evolution longer than most of bioinformaticians grasp of it between writing Perl scripts designing XML interfaces before you can comment on progress in the understanding of molecular evolution. However, the forthcoming edition of Molecular Biology and Evolution includes a publication authored by Michael Lynch that has all the features of a landmark. It puts the view forward that evolution of the eukaryotic genome is largely dominated by the small population sizes that permits the creation and fixation of structures such as introns and long intergenic regions.

Or in Lynch's words:

However, by establishing an essentially permanent change in the population-genetic environment permissive to the genome-wide repatterning of gene structure, the eukaryotic condition also promoted a reliable resource from which natural selection could secondarily build novel forms of organismal complexity. Under this hypothesis, arguments based on molecular, cellular, and/or physiological constraints are insufficient to explain the disparities in gene, genomic, and phenotypic complexity between prokaryotes and eukaryotes.

According to Eike Staub, who notified me of the work, it gained much attention when it was presented at last year's conference of European Society for Evolutionary Biology in Krakow.
In addition to the hypothesis, the work builds upon a encompassing overview of the current state of our knowledge of molecular evolution and I can but recommend to take a couple of quiet hours to delve into it if you are interested in molecular evolution. And who isn't?