March of "progress"

["Ken Kinman" <kinman@hotmail.com>]

Tim,
    The old "march of progress" idea is criticized mainly because progress 
is such a loaded word (just like "superior" is a loaded word).
    But it does reflect the directionality of evolution, certainly in the 
time dimension, and often in complexity as well (although the latter is 
somewhat reversible, as in Mesozoans, pentastomid "worm" crustaceans, and 
parasites in general).   Single cells must precede multicellularity.  
Amphibians and reptiles had to precede birds and mammals.  [and I strongly 
believe Eubacteria were around almost a billion years before giving rise to 
the Metabacteria-Eukaryota clade].
    So because of this directionality and the natural preoccupation of 
humans with their own ancestry, we have unfortunately shown these biases 
with unfortunate words like "progress" and "superior".  And the poorly known 
bacteria and protists were unduly neglected in our classifications and 
studies for a long time.
    But let's not get carried away in trying mitigate those errors, 
swinging the taxonomic pendulum too far the other way----which is what Three 
Domains (and a preoccupation with a few select genes) is doing.  This was an 
overreaction and we are now facing a taxonomic arms race (although that's 
the least of the problems it is causing).
    Life on Earth (Geobiota) is optimally divided into a handful of 
Kingdoms (about 4-6), and everyone's education should include a basic 
understanding of their relationships.  On the surface, a cladified Three 
Domain system seems even simpler, but there is not a doubt in my mind that 
it is simplistic, erroneous, and damaging.  The confusion it is generating 
is just a tip of the iceberg, and the now overused crutch of ad hoc 
"horizontal gene transfer" is just sweeping the confusion under the rug.
    But just one simple step-----Stop using "Archaea" as outgroup to 
Eubacteria-----would go a long way to mitigating the mess (and the name 
"Archaea" is helping to perpetuate such misrooting).  That has been my main 
message to bacteriologists all along, whether they believe my other ideas or 
not.  Otherwise medicine, agriculture, and other important fields (that 
depend on accurate bacterial phylogenies) will suffer as a result.  That is 
why I am so critical of Woese's "paradigm".  And I also worry that cladistic 
"analysis" will get a lot of the blame, even though any good tool will cause 
damage when used inappropriately.
                ----Gotta run,   Ken
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