The application of molecular genetics, in particular comparative genomics, to the field of evolutionary biology is paving the way to an enhanced “New Synthesis.” Apart from their power to establish and refine phylogenies, understanding such genomic processes as the dynamics of change in genomes, even in hypothetical RNA-based genomes and the in vitro evolution of RNA molecules, helps to clarify evolutionary principles that are otherwise hidden among the nested hierarchies of evolutionary units. To this end, I outline the course of hereditary material and examine several issues including disparity, causation, or bookkeeping of genes, adaptation, and exaptation, as well as evolutionary contingency at the genomic level—issues at the heart of some of Stephen Jay Gould's intellectual battlegrounds. Interestingly, where relevant, the genomic perspective is consistent with Gould's agenda. Extensive documentation makes it particularly clear that exaptation plays a role in evolutionary processes that is at least as significant as—and perhaps more significant than—that played by adaptation.
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Vol. 31 • No. sp5