[Taxacom] sloppy cladistic analyses

[John Grehan]

I do agree with the apparent rush to large numbers at the expense of
detailed corroboration of individual features and adequate outgroup
sampling. I think this is an ironic consequence of many (?) 'cladists'
still thinking like pheneticist by invoking the 'law of large numbers'
that overrules the 'law of shared derived characters' (which may ore may
not be large). One sees this in the way the orangutan evidence (28
synapomorphies) is overruled by the "overwhelming' large numbers of DNA
base sequence simialrities in favor of the chimpanzee.

Coding errors do matter, and the more errors the more they matter. As
indicated by Thorpe, I also think that it is important to give detailed
accounts of each character state distribution, but this is often not the
case. The recent 'cladistic' analysis of the hobbit phylogeny for
example, is dreadful in this respect. Science and Nature types of
sensationalist phylogenies are often the worst.

John Grehan


> -----Original Message-----
> From: Stephen Thorpe [mailto:s.thorpe at auckland.ac.nz]
> Sent: Wednesday, February 03, 2010 3:18 PM
> To: John Grehan; taxacom at mailman.nhm.ku.edu
> Subject: RE: [Taxacom] sloppy cladistic analyses
> 
> > The problems outlined here by Thorpe (coding errors, mising data,
> subjectivity, polarity estimations, outgroup choice) are not just
those of
> cladistics, but of systematics in general
> 
> Perhaps Grehan is correct, but I still think that the problems are
worse
> for cladistics, or at least any methodology in systematics which
depends
> heavily on "number crunching". They have a tendency to lose the
> "narrative" - a huge data matrix and associated tree are not a
narrative!
> Each and every step to a conclusion needs to be fleshed out and
critically
> evaluated. The fleshing out is important in order to be able to spot
> errors which are otherwise virtually impossible to see within a huge
data
> matrix. I'm not sure if there have been any studies done on the amount
of
> influence on the conclusion that various amounts of coding errors can
> have? "People" have said to me "that doesn't matter!"  when I have
pointed
> out coding errors, but how do they know it doesn't matter? Matter to
whom?
> For every coding error I spot, how many others are there? At what
level
> does it start to matter?
> ________________________________________
> From: taxacom-bounces at mailman.nhm.ku.edu [taxacom-
> bounces at mailman.nhm.ku.edu] On Behalf Of John Grehan
> [jgrehan at sciencebuff.org]
> Sent: Thursday, 4 February 2010 2:06 a.m.
> To: taxacom at mailman.nhm.ku.edu
> Subject: Re: [Taxacom] sloppy cladistic analyses
> 
> The problems outlined here by Thorpe (coding errors, mising data,
> subjectivity, polarity estimations, outgroup choice) are not just
those
> of cladistics, but of systematics in general. Similarity, the problem
> identified by Ken with cladistic analyses where codings of previously
> analyses are cut and pasted with their own without critical
evaluation.
> This is a problem that is not necessarily confined to cladistic
analysis
> since any type of systematics may be underminded by this practice.
> Perhaps one of the few explicit attempts to demonstrate that probmem
has
> been with the recent hominid analyses where previously claimed
> characters have been subject to detailed critique whereas other
> analyeses claiming to support the chimpanzee relationship are plagued
> with the cut and paste recycling method - which of course means that
> they always get the same answer more or less.
> 
> I realize that Ken and various others are opposed to cladistics and
that
> is fine with me, but to attribute general problems of systematics to
> cladistics alone is (do doubt unintentionally) misleading.
> 
> John Grehan
> 
> 
> 
> > -----Original Message-----
> > From: taxacom-bounces at mailman.nhm.ku.edu [mailto:taxacom-
> > bounces at mailman.nhm.ku.edu] On Behalf Of Stephen Thorpe
> > Sent: Tuesday, February 02, 2010 10:52 PM
> > To: Kenneth Kinman; taxacom at mailman.nhm.ku.edu
> > Subject: Re: [Taxacom] sloppy cladistic analyses
> >
> > I'm not sure that the internet is to blame here. It seems to me to
be
> more
> > an intrinsic problem to cladistic analysis itself. Anything that
> involves
> > numbers is prone to transcription errors, and the nature of some
> people
> > increases the chances of this happening. How many cladistic analyses
> get
> > checked for coding errors? This problem on top of the other major
> problem
> > that most of the relevant data is missing (because only a minute
> fraction
> > of taxa have been informatively preserved as fossils), not to
mention
> > subjectivity in character weighting, polarity estimations, and
> outgroup
> > choice, and what is the worth of such analyses???
> >
> > ________________________________________
> > From: taxacom-bounces at mailman.nhm.ku.edu [taxacom-
> > bounces at mailman.nhm.ku.edu] On Behalf Of Kenneth Kinman
> > [kennethkinman at webtv.net]
> > Sent: Wednesday, 3 February 2010 4:18 p.m.
> > To: taxacom at mailman.nhm.ku.edu
> > Subject: [Taxacom] sloppy cladistic analyses
> >
> > Dear All:
> >       Although I don't ALWAYS agree with Michael Mortimer, his
> cladistic
> > analyses are far better than most.  Therefore, I find his following
> > critique of many recent cladistic practices and shortcomings very
> > seriously.  It reflects a broader problem among computer generated
> > so-called "information" and an alarming trend of  internet
> > DISINFORMATION now competing with or even outpacing good
information.
> >        What one now finds on the internet, including scientific
> > information, must increasingly be taken with a huge grain of salt.
> The
> > truism about computers in the hands of more sloppy users is
> > unfortunately an increasing reality:  "garbage in, garbage out."
This
> > is certainly true of cladistic analyses by those who just don't
> > critically evaluate the codings of previously analyses and just cut
> and
> > paste them and add a few of their own.  Adding a little new
> information
> > to a database riddled with garbage, and the garbage can overwhelm
the
> > new information (whether the new information might be helpful or
not).
> > As Mortimer says, it can give a false impression of consensus in
> > something that may or may not be true.  Here's a link to his
concerns:
> >
> > http://dml.cmnh.org/2010Feb/msg00010.html
> >
> >
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> >
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