Eradicating typological thinking in prokaryotic systematics and evolution

In 1982, John Maynard Smith called for an evolutionary "New Synthesis" specific for prokaryotes, observing that "population thinking has been well developed for fully half a century, but has yet to be adopted by microbiology" (Maynard Smith 1982). Twenty-seven years later, typological thinking (population thinking's antithesis) still dominates the field. Evidence for this includes the continuing debates on the reality of prokaryotic species, the value of the term "prokaryote," and the significance of the tree of life (TOL). In each case, the unexpected prevalence of interlineage transfer of genetic information has been (or should now be) the catalyst for the final Darwinization of our discipline. With examples from phylogenomics, I argue that "species," "domains," and the "TOL" are reifications that we can do without, especially as genomics dissolves into metagenomics.