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Archaebacteria and the Three Domains

arlin at ac.dal.ca arlin at ac.dal.ca
Thu Apr 14 09:44:47 EST 1994

My two cents (which, IMHO, is worth at least 25 cents) is that there are
better taxonomies available than the Woese-Kandler-Wheelis scheme, which is
fatally mired in rRNA mythology.  Back when it was difficult to relate the
16S oligonucleotide catalogs between the "urkingdoms", this was erroneously
taken to be a statement about evolution, instead of a lack of data: it was
proposed that the three groups were truly unrelated at the genomic level,
in the sense of having emerged independently from an RNA "progenote."  The
shared "bacterial" properties would then be separately derived, so that
bacteria _sensu latu_ would be polyphletic and therefore not a good taxon.

The "progenote-as-common-ancestor" scheme is multiply contradicted, for
instance by the dozens of long homologous DNA genes (i.e., not RNA
mini-genes) just mentioned by James Brown, the godfather of molecular
evolution. One doesn't need a supercomputer and a genome sequencing factory
to figure out that (regardless of how euks arose) the most recent common
ancestor of those organisms now called "archaebacteria" and "eubacteria"
was a microscopic cellular organism with a single circular DNA chromosome
of less than 8 Mbp, multigene operons (for ribosomal proteins, RNAP
subunits, etc), Shine-Dalgarno sites, probably a rotary external flagellum:
a bacterium, that is, not a "progenote".  Nevertheless, a holy trinity of
three separate-but-equal groups has become a central tenet in the catechism
of the Woesian school, and is a major flaw of the WKW scheme.

Nearly all the disputants in the current debate on taxonomy agree that a
single kingdom of bacteria is not enough: the archaes and the eubs should
be recognized at the kingdom level, at least. What is needed is a proposal
that recognizes the uniqueness of the archaebacteria without exaggerating
it. Such a proposal would leave room for the almost inevitable possibility
of additional distinctive groups of bacteria that presently remain to be
discovered or fully characterized. Calling archaes a "3rd form of life" and
giving them the highest possible taxonomic ranking really sets an
unreasonable standard.  By this standard, planctomyces-ologists could make
alot of hoopla and declare a "4th form of life", since they truly are quite
distinct from other organisms called "eubacteria" (e.g their
*non-peptidoglycan* cell walls exclude them from the eubacteria by most

The first formal proposal to recognize bacterial diversity was by the
systematist Tom Cavalier-Smith, who suggested an "Empire" called,
appropriately, "Bacteria" that would contain the kingdoms "Archaebacteria"
and "Eubacteria."  The WKW scheme is inferior to this.  It misleadingly
uses "Bacteria" to refer only to "eubacteria" and not "archaebacteria",
though both terms are now widely accepted as informal taxon names.  In its
choice of the term "Archaea," the WKW scheme drops the "-bacteria" part
from "archaebacteria", but keeps the "archae-" part, in effect giving more
weight to unsubstantiated and parochial lore (that they are somehow more
primitive or more characteristic of the archaen geological period) than to
the documented features that suggest a common *bacterial* heritage.


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