David Faguy writes:
>Bacteria and archaea are both prokaryotes (no nucleus). They share a
>negative characteristic this implies nothing about their phylogenetic
Huh? Who mentioned nuclei? My post mentioned the numerous similarities
between flagellar-based motility in archaebacteria and eubacteria that are
not shared with eukaryotes. These are *positive* characteristics likely to
have existed in the most recent common ancestor. If these and a few other
important characters (circular chromosomes, operons, shine-dalgarno sites,
etc) were present in the common ancestor, as is likely, then archaebacteria
and eubacteria have a common heritage that I would call "bacterial."
>The shear mass of data - cell walls, lipids, protein
>translation, rRNA, and yes flagellins- that supports the distinct
>nature of each domain makes it clear that archaea are not bacteria.
No one said that "Archaea" (=archaebacteria) are "Bacteria" (=eubacteria).
Furthermore, the uniqueness of the archaebacteria is not a valid argument
against calling them "bacteria" _sensu latu_: _Homo sapiens_ has many
distinctive features, yet we still call it a "primate", and for good
reason. Archaebacteria have been considered "bacteria" in the past, as is
obvious from numerous taxon names (e.g., Archaebacteria, Metabacteria,
Halobacterium halobium, Methanobacterium, Halobacteriacea, etc). If Woese,
Kandler and Wheelis wish to formally drop "-bacteria" from "archaebacteria"
and declare these "Archaea" a "third from of life" distinct from
"Bacteria", then they are obliged to explain why the former usage is
incorrect. So far, all Woese has done is to mount an agressive campaign
against his own misunderstanding of the term "prokaryote" (which he
inevitably takes to be a false clade designator, instead of an accurate but
not always useful grade designator).
This gives the unfortunate impression that the entire taxonomic debate is
just so much noise about words. But, in fact, taxonomic arguments like
this are not empty semantic proposals: they represent (sometimes only
indirectly) evolutionary hypotheses. The Cavalier-Smith proposal (Empire
Bacteria: Kingdoms Archaebacteria, Eubacteria) implies that the most recent
common ancestor of archaebacteria and eubacteria had features that would be
recognized as "bacterial." The Woese-Kandler-Wheelis proposal implies that
there is no such common bacterial heritage: instead, these shared bacterial
features (rotary motors, r-protein operons, circular chromosomes, etc)
evolved twice, in parallel, from a "progenotic" common ancestor. Before
adopting a taxonomy one should ask oneself which evolutionary hypothesis is
better supported by available evidence.