grade represented by the prokaryote → eukaryote cellular transition as the major event in cell evolution. In lodging his objections to the paper of Woese, Kandler and Wheelis, he writes:
… as important as the molecular distance between the Archaebacteria and Eubacteria may seem to a specialist, as far as their general organization is concerned, the two kinds of prokaryotes are very much the same. By contrast, the series of evolutionary steps in cellular organization leading from the prokaryotes to the eukaryotes, including the acquisition of a nucleus, a set of chromosomes and the acquisition, presumably through symbiosis, of various cellular organelles (chloroplasts, mitochondria and so on) results in the eukaryotes in an entirely new level of organization … (Mayr, 1990).
Tom Cavalier-Smith (Cavalier-Smith, 1992) echoes this view:
Woese has repeatedly and mistakenly asserted that his recognition and firm establishment of the kingdom Archaebacteria (certainly a great and important breakthrough) invalidates the classical distinction between prokaryotes and eukaryotes. But as archaebacteria fall well within the scope of prokaryotes and bacteria as classically defined, it does nothing of the kind.
The questions that have to do with data rather than philosophy are: (i) what and how many traits distinguish the domains from each other (or betray a closer affinity between any two), (ii) how "fundamental" are these traits, and (iii) are such traits universally present within one (or two) groups and universally absent from the other(s) or is there in reality more of a mixing. For all the richness of our understanding of individual aspects of the biology of individual organisms, we are still very much in the dark, especially for answers to the second and third questions. Only recently, for instance (Cavalier-Smith, 1993), have we come to realize that archezoa (primitively amitochondrial eukaryotes) have 70S ribosomes, with rRNAs of the sizes and classes found in prokaryotes (archaebacteria or eubacteria). We know very little about possible forerunners of cytoskeletal proteins and functions in archaebacteria, although there have long been hints of such (Stein and Searcy, 1981). Even the eubacteria have not been plumbed in depth—newly discovered deeply branching lineages like Aquifex and the Thermotogales remain almost completely unknown in molecular or biochemical terms.
The Iwabe rooting and the renaming of the three domains as Bacteria, Archaea, and Eukarya (Figure 6) have found, in spite of these philosophical concerns, wide acceptance in the last 3 or 4 years. Together with increasing general understanding of gene and genome structure and function in the archaebacteria, the rooting has unavoidable impli-