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Opponents of [new names 4 old groups]

arlin at ac.dal.ca arlin at ac.dal.ca
Fri Oct 21 09:11:40 EST 1994

Jonathan Badger writes:
>> it "Empire"), and argues that there is no reason to change the familiar names
>> to the new names, which are misleading about the similarities of organisms,
>> as well as being inconsistent with previous usage (i.e., of the word
>> "bacteria", which obviously was formerly applied to organisms such
>> as "archaeBACTERIA" as well as "euBACTERIA").
>I don't get this. Woese-Kandler-Wheelis aren't trying to change taxonomy on
>a whim -- they are trying to change it in accordance with the (extremely)
>well supported hypothesis that Archaes are more closely related to eukaryotes
>than either are the bacteria. Taxonomy should reflect phylogeny -- what good
>is it if it doesn't? The only rational reason for rejecting the taxonomic
>change is if there is substantial evidence rejecting the three domain
>hypothesis as phylogentically incorrect. At present this doesn't seem to be
>the case, but I suggest that the detractors of the three domain hypothesis
>find data to support their cause if they wish to have it considered.

First, the "domains" proposal of Woese, Kandler and Wheelis (WKW) is a 
taxonomic proposal, to be considered in light of other options, among 
which thinking biologists have a choice:

i) adopting the prior formal proposal of Cavalier-Smith (the C-S scheme)
for two "Empires": "Eukaryota" (containing several eukaryotic Kingdoms) and
"Bacteria" (containing Kingdoms "Archaebacteria" and "Eubacteria"); and

ii) formalizing the informal taxonomy already in place, three "urkingdoms"
or "primary kingdoms" called "archaebacteria", "eubacteria" and

Second, the issue is not evidence.  None of these proposals is "wrong" in
some empirically demonstrable sense.  The issues concern rankings and names, 
and not the validity of the
phylogenetic tree suggested by Iwabe, et al. and Gogarten, et al.  These
issues may sound trivial at first glance, but that's what these taxonomic
choices are about: which formal rankings and which formal names are

The rooted tree is not an issue because a set of three equally ranked taxa 
(i.e., as in the WKW scheme) will inevitably be consistent with any rooted 
tree of three clades:

(eubacteria (eukaryotes, archaebacteria)) 
(eukaryotes (eubacteria ,archaebacteria)) 
(archaebacteria (eukaryotes, eubacteria))

The C-S scheme is also consistent with these three rooted trees, given
Cavalier-Smith's taxonomic principles.  Cavalier-Smith allows paraphyletic
groups, and since the "bacterial" features shared by eubacteria and
archaebacteria (prokaryotic cell structure, circular chromosome, operons,
Shine-Dalgarno sites, etc) are likely shared by descent from a common
ancestor with these properties, there is a clear justification for uniting
archaebacteria and eubacteria into an "Empire Bacteria".  

Personally, I'm not fond of paraphyletic groups, but even if I were a
table-banging cladist I would not support the unrevised WKW scheme, because
the names are so irrational.  Why does it have to be such a big deal to
substitute some better names for three "domains" that do not conflict with
past usage of "bacteria" and don't perpetuate the irrational myth that 
there is something peculiarly archaic or primitive about the "archae"-
bacteria?  For instance, "Larry", "Moe" and "Curly" would be an improvement.  
I also think that "Archaebacteria", "Eubacteria" and "Eukaryotes" would 
be an excellent choice of names for the three "domains" (I'm prepared to
accept the irrational "archae" bit for the sake of consistency with
prior usage and prior literature).  


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