reweighting characters, cladistics, and Woese

[Ken Kinman]

Dear Taxacomers:
      This may seem a little strange coming from one who is so often
criticizing the "strict cladists", but I think this thread is dumping a
little too heavily on "cladistics" in general.  I make a very big
distinction between the utility and heuristic value of cladistic analysis
(and in that sense I am a cladist) and the strict cladism that took it to
the extremes of total "paraphylophobia".  I know some "strict cladists" find
the term "paraphylophobia" to be an "erudite insult" (as one called it), but
it is meant to sort of shock them into realizing that perhaps the cladistic
pendulum did swing too far (especially in the United States) and at least
some seem to realize that if some middle ground isn't found, that there is
going to be an increasing backlash against "strict cladism" in the years to
come.
     Cladistic analysis is a powerful tool, and it can do great things if it
is used properly, but it can be very destructive if used improperly.  This
is precisely why I am so critical of many of the ideas of Carl Woese.  He is
so stubbornly attached to the notion that Eubacteria (sensu lato) and
Metabacteria (his "Archaea") are sister groups (and thus equivalent
Urkingdoms or Domains) that he continues the short-sighted practice of using
Metabacteria as outgroup to the Eubacteria.   Not only does this result in
totally misrooted and "mangled" eubacterial phylogenies, but it also falsely
props up (with circular reasoning) his precious false assumption that life
(or at least the cenancestor or LUCA of extant life) was thermophilic.  If
he continues to stubbornly refuse to recognize past errors, he will only
damage his reputation in the long run, and the important contributions that
he did make will be overshadowed by the damage caused by his more grandious
pronouncements.
     The criticisms of Woese by Ernst Mayr, Thomas Cavalier-Smith, Lynn
Margulis and others just scratch the surface of this damage, but you would
think Woese would at least have modified his position somewhat in light of
criticism from such eminent scientists (and many other eminent scientists
regarding this nonsense about thermophilic origins).  It is, of course,
totally up to Woese, and his place in the history of science may well depend
on what he does in the next several years.  Although I was rather saddened
by the tone of his weak rebuttal of Mayr's article (both appearing in Proc.
Natl. Acad. Sci., in the fall of 1998), I cannot help but be irritated by
his selective view of what evidence he chooses to embrace, and what he
simply chooses to explain away to fit preconceived notions.  Hopefully he
will begin modifying his position before it is to late, and science leaves
him behind.
                  -------Ken Kinman

>From: Alexander Martynov <doris at AM3963.SPB.EDU>
>Reply-To: Alexander Martynov <doris at AM3963.SPB.EDU>
>To: TAXACOM at USOBI.ORG
>Subject: Re: reweighting characters, few and many
>Date: Thu, 28 Oct 1999 00:41:32 +0300
>
>Wed, 27 Oct 99 15:54 +0300 MSK Thomas Schlemmermeyer wrote to
>TAXACOM at USOBI.ORG:
> > Already a few months ago, an anonymous list member told me that
>cladistics
> > functions like that: Figure out a tree that you personally like! In the
>next
> > step choose a suitable program and algorithm which generate exactly this
>tree.
> >
> > Yesterday, at night, I made my first exciting experiences of this kind.
>
>Dear Thomas,
>  Despite that I am so far from  phylogenetic's softs I always suspected
>that
>cladistic's programs was created exactly for this deal.
>
>Alexander Martynov (doris at AM3963.spb.edu)
>Zoological Institute, St. Petersburg
>Thu, 28 Oct 99 00:21 +0300 MSK

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