[Taxacom] Three Domains (was: Diversity of bacteria)

Kenneth Kinman kennethkinman at webtv.net
Wed Feb 8 11:58:29 CST 2012

Hi Brian, 
      It is widely accepted that the original eukaryote was
probably a chimaera formed from a fusion of an archaebacterium and a
eubacterium, although I believe it is still controversial whether the
archaebacterial element was the host cell or the nucleus. The close
relationship of eukaryotes and archaebacteria was initially discovered
through molecular sequences of the ribosomal machinery from the
archaebacterial component.
       However, many authors have strongly criticized
Woese and his 3 domains for ignoring the overwhelming similarities
between eubacteria and archaebacteria.  Ernst Mayr's 1998 paper "Two
Empires or Three?" is excellent (Proc. Natl. Acad. Sci., 95:9720-9723).
In the same journal is a paper by Margulis, Dolan and Guerrero, 2000
("The chimaeric eukaryote"; Proc. Natl. Acad. Sci., 97:6954-6959), in
which the first section is entitled "Two Domains, not Three", and they
give more data on the similarities between eubacteria and

      Then there are the many papers by R.S. Gupta which are

likewise highly critical of the Three Domain classification, and he
provides additional data which supports Thomas Cavalier-Smith's
hypothesis that archaebacteria evolved from a subclade of the
gram-positive bacteria (although Gupta refers to them as "Monoderms"
rather than Unibacteria; both terms refer to the fact that they have
only a single cell membrane, rather than two cell membranes in the
gram-negative bacteria, which Cavalier-Smith calls Negibacteria and
Gupta calls "Diderms"). 

      Anyway, these authors and many others may disagree on
the details (Cavalier-Smith thinks Negibacteria came first and the
Unibacteria arose by loss of the outer membrane, while Gupta thinks it
happened the other way around), but they are all strongly critical of
Woese's "Three Domains" for ignoring all the very fundamental
similarities between eubacteria and archaebacteria, as well as the
eubacterial component of the chimaeric eukaryotic cell. Woese should be
credited for discovering that archaebacteria are a very distinct group
of prokaryotes, but he went way overboard in elevating them to a
separate Domain.  This is even more irritating when you consider that
Hori and Osawa (1982), published their paper almost 30 years ago,
presenting molecular evidence that there was nothing particularly
"archaic" about Archaebacteria, and proposed that they be called
Metabacteria.  That proposal made perfect sense and yet they were
ignored.  Much of the confusion and the whole Three Domain mess could
have been avoided if their proposal had been followed.  

        There is actually no good evidence that I have
ever seen presented that the so-called archaebacteria are as old as
(much less older than) the eubacteria, and plenty of evidence to the
contrary.   Thus Mayr's criticism of Woese for replacing Archaebacteria
with Archaea (dropping the accurate last part of the name, -bacteria,
and retaining the inaccurate part, archae-). This has just perpetuated
the notion that life originated in boiling hot springs or deep-sea
hydrothermal vents. Many chemists would tell you that this is highly
unlikely and that life may have actually arisen at the opposite extreme
(in water near the freezing point). I still prefer something more
moderate (even the "warm little pond", which I believe originated with
       In any case, I would recommend reading the papers
in Proc. Acad. Nat. Sci. by Mayr and by Margulis, Dolan, and Guerrero.
These are freely available at the PNAS website (pnas.org). Also R.S.
Gupta, 1998 ("Life's third domain (Archaea): an established fact or an
endangererd paradigm"; Theor. Popul.Biol., 54:91-204). Here is a weblink

to the pubmed citation of the Mayr paper (and it has a link to the paper

where it says "Free PMC Article"):

P.S.  I didn't realize that Thomas Cavalier-Smith's kingdom (regnum)
level names were rejected by that committee in 2008.  I realize that the

Bacteriological Code doesn't deal with taxa at such high ranks, but
neither do the Zoological or Botanical Codes.  Not sure why they felt
the need to formlly reject the names, since there are no reasons given.
Perhaps the paraphyly of some of the taxa was an issue with some
members.  The notion that paraphyletic taxa are "unnatural" is certainly

widespread these days, but I frankly can't see how prokaryotes in
particular can be classified naturally without some paraphyletic taxa.
Empire (Superkingdom) Prokaryota is certainly paraphyletic with respect
to Empire (Superkingdom), so maybe that is why so many still gravitate
toward Three Domains (although the latter seems to simply ignore the
paraphyly that is obviously there beneath the window-dressing). 

Brian Patrick wrote:
Hi Ken et al., 
Okay, so Ken stated that the 3 domain system should be abandoned because

there seems to be more evidence that archaebacteria are indeed
monophyletic with eubacteria?  Thus, we should stay at the older
superkingdom system of Prokarya and Eukarya? 
I am definitely NOT an expert on bacteria, so I am genuinely asking
whether this is a viable line of reasoning?  I thought that the evidence

for archaebacteria being more closely related to eukaryotes was pretty
strong (ribosomes of archaebacteria are more similar to eukaryotes and
other evidence that is not coming to mind at this moment). 
What evidence exists for each side of this, i.e., for unifying all
prokaryotes into a single kingdom vs. the 3 domain system wherein the 2
superkingdom system creates paraphyly? 
This is fascinating!  The paradigm shift to 3 domains was interesting,
but if there is now evidence to throw that into doubt for a return to
the previous paradigm... 
Thanks again for your time! 
Best regards, Brian 
L. Brian Patrick, Ph.D. 
Assistant Professor of Biology and Chair 
Department of Biological Sciences 
Dakota Wesleyan University 
1200 W. University Ave. 
Mitchell, SD  57301

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