[Taxacom] Taxonomy DOES matter (not why it doesn't)

[Kenneth Kinman]

Hi Bob and Richard,
      Well, most investigators may be only interested in evolutionary
"signals" (as am I most of the time), but I am also constantly on the
look out for mis-signals.  While homoplasy is a major source of
mis-signals, I am even more interested in a different class of major
mis-signals from mis-rooting (which can be even more of a problem in
many cases).    
        In my opinion, the three biggest such cases are:
    (1) properly rooting prokaryotes (and thus virtually the entire Tree
of Life;
     (2) Mollusca (did bivalves actually come first in that group as I
have suggested?; and 
     (3) Arthropoda (did they really evolve from a worm-like animal with
many serial segments?).  
         I've been harping on all three of those cases for years, and I
have seen no significant progress in any of them.  Misrooting is the
number one problem in such cases.  Homoplasy seems to come in second as
a problem when it comes to these broader taxonomic challenges.
            -------------Ken Kinman             
----------------------------------------------------------      
Bob Mesibov wrote:
Richard Zander wrote: 
"This is done by coming up with a scientific 
theory of evolutionary process for each group that explains and
conciliates results of alpha taxonomy, morphological analysis, and
molecular analyses... What is important is not to let any one member
demand that his/her analytical method must control or will explain the
results of any other method, but that all results be explained by a
separate unified theory... This is possible." 
      Just as hard as wrangling your team members will be dealing with
incongruence and fitting it within your evolutionary picture. Who does
this now? Is there anyone who seriously examines incongruence, instead
of dismissing it as noise and an obstacle to discovering the One True
Tree? 
If I understand you correctly, that's what 'explains and conciliates'
would be tackling. Do you have a plan for this? 
Regardless of what group is being studied, what I read in the literature
suggests that investigators are looking for evolutionary 'signal' in
their data. The 'signal' is regarded as evolution, the rest isn't. This
is a very strange idea. Surely *all* the data reflect what's happened
during evolution? 
Maybe someday there'll be well-funded Departments of Evolutionary
Incongruence and Centres of Excellence for the Study of Homoplasy, with
PR pronouncements like 'We thought it was just random mutation in that
intron, but it turns out this be a very clever redesign of the protein
to take advantage of the warmer temperatures in the habitat this lineage
moved into.' 
-- 
Dr Robert Mesibov