prokaryote evolution and globin proteins

Ken Kinman kinman at HOTMAIL.COM
Wed Oct 23 13:04:13 CDT 2002

      I wholeheartedly agree that it is indeed difficult to demonstrate what
is primitive among prokaryotes----it's probably the most difficult such case
in biology since we don't have an outgroup as a point of reference.  And
that has been my major criticism of Woesian "beliefs" (namely, using
Metabacteria as an outgroup in the study of eubacterial phylogeny), but how
badly that led us astray will only be apparent in retrospect.
     I think early life was "biased" toward H2O for many reasons, just one
of which is its extreme abundance.  And while H2S usage seems more "widely
spread" over Woesian evolutionary trees, I think the perspective of those
trees is probably just as biased as the old perspective that overly
minimized bacterial diversity.  Being one who has studied the diversity of
life from both perspectives (as zoologist and bacteriologist), I think the
"animals are just a little twig on the tree of life" thing was WAY overdone,
based on a single gene (and we all know how harmful one character
classifications can be).
      The Woesian belief system seems to have (from its very beginnings in
the 70's) assumed that lateral gene transfer was too rampant among early
prokaryotes for us to trace its phylogeny in any detail.  The Three
Urkingdoms were grudgingly transformed in Three Domains.  In the meantime,
workers like Cavalier-Smith were forging ahead in the belief that early life
was traceable (albeit difficult).  Unfortunately he is so erudite (and
published in less accessible journals) that the majority of biologists
naturally went for the simple Three Domain approach.  Popularity and good PR
does not necessarily mean good science.
     Until this trend changes, bacteriology is going to be as difficult to
navigate as the crippled Apollo 13 craft was back in the 1970's.  I look to
people like Cavalier-Smith to get us back on track, not that I fully agree
with all his ideas (like this new idea that "Archaebacteria" evolving only
750 million years ago), but he is way ahead of his time compared to the
continuing negative campaign that "rampant horizontal gene transfer" has
wiped away the phylogenetic signal of early life.  The discredited Three
Urkingdoms should have simply been abandoned in 1990, but was instead
spin-doctored into Three Domains.  So we still have that enormous monkey on
our backs, just dressed up in different clothing.
     Thanks to whole genome sequencing we are making great strides in spite
of such handicaps, but it certainly has made the going a lot tougher and
generated a lot of unnecessary confusion in my opinion.  I'll definitely
take Cavalier-Smith's brand of speculation any day, and I would advise more
biologists to do likewise.  His papers are not an easy read, but even his
older papers are standing up very well decades later, which is astounding
given the scope of his ideas.  He has certainly shown no signs of resting on
his laurels or beating dead horses, and he is very quick to admit his
mistakes and move forward.  If there were a Nobel Prize for Biology, Thomas
Cavalier-Smith would be deserving of one (maybe one for Medicine and
Physiology will come his way eventually).
           ------- Ken Kinman
P.S.  Guess I should drag out my bacteriology stuff and review all the
evidence for molecular oxygen and early life.  As I recall, there are
extensive banded iron formations even 3.4-3.5 billion years ago.  And
although the metabolic evidence is more equivocal, it also seems to support
very early oxygenic photosynthesis.  Whole genome evidence will be just
icing on the cake, but were just in the early stages of that.  I predict
that the almost finished Gloeobacter genome project will have some really
big surprises in store for us.  I can hardly wait.
Brian wrote:
>Ah, but the sulphide based systems also only use one photosystem. The other
>question is how do you prove that something is "primitive" (i.e. in its
>original state) or "secondarily simplified to look like the primitive
>form". Perhaps "belief" is the best answer ;-). From an evolutionary point
>of view the single photosystem H2S based system is more widely distributed
>across the evolutionary tree. The bias twoards H20 is based largely on the
>cyanobacteria and the fact that all eukaryotic photoautotrophs seem to have
>"taken a cyanobacterium captive". Ah well that's half the fun of healthy
>speculation I suppose.
>Thanks also for the link.

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