Is Carl Woese losing a Kingdom?

Dave Edgell dedgell at
Mon Sep 23 17:49:44 EST 1996

jos van den broek wrote:
> The complete genome of Methanococcus jannaschii reported in Science of 23 August
> is another great achievement of Craig Venter c.s. According to Carl Woese it
> gives an extra proof of the fact that Archaea are closer related to Eukaryotes
> than to Bacteria. But not according to e.g. Margulis and Gupta, who now even
> stronger believe that Eukaryotes originated by a merger of archaebacteria and
> eubacteria. To my humble opinion they are right and Woese - although he's a
> great scientist - is wrong, and about to lose a paradigm... and a Kingdom. Who
> is interested in a non-published article I wrote on this subject? Where can I
> get it published? Please e-mail me (at my home address), and send your comment!

First of all, what Kingdom is Woese losing?  If you are referring to
Eukaryota, he placed it at the level of domain while Cavalier-Smith placed
it at the level of Empire.  But taxonomy aside, Eukaryota is not Woese's
kingdom/domain to lose anyway.  The distinctness of eukaryotes has been known
for many years. Thoughts about this crystallized in the 60's--
Stanier and Van Neil were the first to put these thoughts in the context
we normally think of them-- emphasizing the huge gulf in cell structure
between prokaryotes and eukaryotes.

Margulis reawakened everyone to endosymbiosis (which had been
more or less out of style for 30-40 years in the West) and everyone
now pretty much accepts an endosymbiotic origin for mitochondria and plastids.
So we already know that most eukaryotes are chimaeras in this sense.
That this had something to do with the origin of eukaryotes per se is much
less clear. There is no evidence that flagella are of endosymbiotic
origin. Moreover, there are a few eukaryotic groups which lack organelles
of symbiotic origin. So it is possible that the eukaryotic condition
(having nucleus, endomembranes and cytoskeleton etc.) arose prior to any

As for Gupta. He has shown that there are many trees which look like:
(Archaebacteria,Gm+ve)(Eukaryotes,G,-ves) IF (and this is the big catch)
you sample few enough taxa from each group.

All 7 of Gupta and Goldings proteins showing the above topology are
complicated by one or several of the following problems:
-multiple phylogenetically distinct homologs in single organisms 
(GS, proC, GDH)
-group polyphyly (all)
-probable cases of lateral transfer (GS, GDH, aat, hsp70)  
-comparisons of NON-HOMOLOGOUS proteins (ferredoxins of 2FE-2S and 4Fe-4S types)

If you look at this data close enough (and believe me I have), you are
left with a distinct feeling that there is a lot of lateral transfer and/or
paralogy at the deepest phylogenetic levels and that none of the 7 proteins
are clean gene phylogenies which are likely to reflect organismal relationships only.
Until the confusing influences of paralogy and transfer are understood 
in these datasets we must be very careful interpreting this evidence
solely in terms of organismal relationships.

So...has Woese lost a kingdom?

A- it was never his
B- there is no clear evidence for eukaryotes being chimaeric beyond
organellar endosymbiosis

Andrew J. Roger

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