In last week’s edition of Phylogeny Fridays, I mentioned an essay that argued that biologists should refrain from using the term “prokaryote” because its definition is entirely negative. The author, Norman Pace, writes, “no one can define what is a prokaryote, only what it is not.” Furthermore, I pointed out that prokaryotes are a paraphyletic taxon (a statement that drew some criticism in the comments), and that alone should lead to the disuse of the term.
In a letter to Nature, Bill Martin and Eugene Koonin point out that there is a positive definition of prokaryotes:
Prokaryotes are cells with co-transcriptional translation on their main chromosomes; they translate nascent messenger RNAs into protein. The presence of this character distinguishes them from cells that possess a nucleus and do not translate nascent transcripts on their main chromosomes.
Pace, however, had mentioned that archaeal transcription differs from bacterial transcription; archaea use TATA-binding proteins, much like eukaryotes, whereas bacteria do not. While the coupling of transcription and translation is a unifying property of archaea and bacteria, it may be a shared ancestral character (a symplesiomorphy). Shared ancestral characters are phylogenetically uninformative and a bane of cladists.