[Taxacom] Three Domains (follow up)

Kenneth Kinman kennethkinman at webtv.net
Thu Feb 9 11:59:32 CST 2012


Hi Dan, 
       Yes, it is too bad Cavalier-Smith didn't designate
types for those Kingdom and Phylum taxa, but most such taxa don't have
types and they don't cause confusion (Metazoa, Eukaryota, Mollusca,
Arthropoda, etc.). At least they weren't pure neologisms, like Woese et
al. changing Eukaryota to Eukarya, and Archaebacteria to Archaea. And I
don't think they designated types for those Domain names, so maybe those

names should be rejected as well.  Probably too late to change to
Metabacteria, but I'll take Archaebacteria any day over Archaea.  

      Anyway, I believe that Cavalier-Smith's division of
Prokaryota into two large taxa (Negibacteria and Unibacteria) will be so

useful that it will eventually catch on, so much so that they may be
elevated to full Kingdoms (which would make Archaebacteria a Subkingdom,

the highest rank that I would give it).  

      And I can certainly understand Brian Tindall's
viewpoints. I never liked Margulis' "spirochaete" theory of eukaryotic
origins, and only mentioned the paper to show how many different
researchers (with differing hypotheses) all agree that the Three Domain
classification was a very bad idea. As for the unique membrane lipids in

Archaebacteria, that could easily be an apomorphy which arose after
Eukaryota inherited its ribosomal machinery from them, explaining why
the lipid chemistry in the membranes of eukaryotes are similar to
eubacteria. Early members of Archaebacteria (now extinct?) could have
originally had the same membrane chemistry, but then they specialized in

novel chemistries which allowed them to occupy extreme environments (and

retained them even when secondarily re-invading non-extreme
environments).  And moving into extreme environments explains the
accelerated mutation rates, which would make Archaebacteria appear older

than they actually are on molecular trees.  Like the other hydrothermal
vent inhabitants, I view them as specialists (which enabled them to
invade that niche), not as primitive hold-overs.  In any case, using
archaebacteria to root eubacterial trees is a very bad idea, because it
tends to pull hyperthermophilic eubacteria towards the base and can
obscure the true phylogeny.   

        And I certainly have expressed my disagreement
with Cavalier-Smith on several issues. As I have said in the past, I
believe Eukaryota is more like 2 billion years old, and Archaebacteria
perhaps 2 1/2 billion years old, while Eubacteria are the oldest at
around 3.4-3.5 billion years old. If so, the major split in prokaryotes,

between Negibacteria and Unibacteria would have happened somewhere
between 3.5 and 2.5 billion years ago. 

       I also dislike his Kingdom Chromista for reasons I
have given previously on Taxacom, but I find his "obcell" theory (for
the origins of cellular life on Earth) very convincing. It elegantly
explains acquisition of a double membrane without the problems that a
"de novo" second membrane would cause.  Unibacteria evolved by a simple
loss of the outer membrane. 

       His papers may be difficult reading, but they contain mountains
of valuable data. I admire him for readily admiting his mistakes and
moving forward, and I continue to learn interesting new things from his
research. On the other hand, the Three Domain hypothesis seems to be
just a warmed over version of the old "Three Urkingdoms" (1977).  That
was over 30 years ago, and it's time to move on.  Cavalier-Smith may not

be perfect, but he is always informative and on the cutting edge of new
ideas.
             ---------Ken Kinman
---------------------------------------------- 
Dan Lahr wrote: 
Hi Ken, 
"However, I still don't see why they felt compelled to reject the
kingdom and phylum level names, since the Code does not deal with taxa
at that level." 
The committee of nomenclature issued an opinion in a nomenclatural
matter. It is their responsibility to issue opinions in matters they
believe are consistent with the principles established by their code. In

this case, the relevant is Principle 1 "1. Aim at stability of names. 

2. Avoid or reject the use of names which may cause error or confusion. 
3. Avoid the useless creation of names." By not providing types, the
proposed names generate confusion - of course the Committee could have
decided on a type as this is predicted by the bacterial code, so there
must have been something else as well. 
Committees are living breathing organisms which exist with the very
purpose of dealing with issues that are consistent with the spirit of
the code, but perhaps not spelled out in detail in the current form of
the code. While there are indeed very specific rules and a general
concern for homonymy and priority in lower taxonomic levels, the
principles should be followed at all levels. At least the ICZN, which I
have more familiarity with, states this explicitly in article 1.2.2.
I´d expect the other codes to contain similar claims. cheers, 
Dan 
On Wed, Feb 8, 2012 at 4:23 PM, Kenneth Kinman <kennethkinman at
webtv.net>wrote: 
Hi All, 
          I just reread the minutes of the Judicial
Committee >in 2008. It seems that they did provide one reason for
rejecting the >taxa proposed by Thomas Cavalier-Smith in 2002, namely
not providing >nomenclatural types. However, I still don't see why they
felt compelled >to reject the kingdom and phylum level names, since the
Code does not >deal with taxa at that level. 
        ---------Ken 






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