Physiology, phylogeny, and the energetic roots of life

Before the days of molecular phylogenies, the standard way of viewing microbial evolution was as process of physiological evolution: the ordering of the sequence of events in which different pathways that microbes use to harness carbon and energy arose. The physiological view of microbial evolution was, of course, replaced in the 1980s by a gene centered view of microbial evolution that was built around the ribosomal RNA tree of life, also called the universal tree or the three domain tree. The universal tree installed long sought order into microbial systematics, but left physiological evolution out in the cold, because physiology never mapped properly onto the rRNA tree. That was not because the universal tree had an incorrect branching pattern. Rather it was because physiological characters have never mapped neatly onto any phylogenetic tree for prokaryotes, regardless of its topology. The reason is that prokaryotes, though they have an undeniable tendency to vertically inherit their ribosome, distribute the physiological traits that enable synthesis of ribosomes via lateral gene transfer (LGT). Geochemical isotope evidence harbors evidence for the existence of physiological processes, not for phylogeny, because LGT decouples physiology from phylogeny in prokaryotes. If we want a fuller picture of microbial evolution, we will have to incorporate aspects of physiology, phylogeny, and the geological record. The issue of how physiology got started has always been interesting. Non-fermentative substrate level phosphorylations as they occur in some acetogens and methanogens now look like good candidate reactions for that starting point, helping to put chemical roots on life's tree.