[Taxacom] sloppy cladistic analyses

[John Grehan]

Or reword to ask " how many systematics analyses are checked to see that
atomized traits, no matter how homologous, may not be probabilistically
analyzed in many cases."

"Morphological analyses are never checked as to the degree of linkage of
traits in each species in the data set in any adaptive environment."

On the other hand molecular analyses are never checked to see whether
the proof claims made about phylogeny hae any epirical foundation.

"We should not extend that approximation as though we have done a
satisfactory evolutionary analysis."

Tell the molecular supporters who claim to have the holy grail on
phylogeny.

John Grehan

> -----Original Message-----
> From: taxacom-bounces at mailman.nhm.ku.edu [mailto:taxacom-
> bounces at mailman.nhm.ku.edu] On Behalf Of Richard Zander
> Sent: Wednesday, February 03, 2010 10:11 AM
> To: Stephen Thorpe; Kenneth Kinman; taxacom at mailman.nhm.ku.edu
> Subject: Re: [Taxacom] sloppy cladistic analyses
> 
> And . . .  how many cladistic analyses are checked to see that
atomized
> traits, no matter how homologous, may not be probabilistically
analyzed in
> many cases. Cladistics assumes that:  when you have 3 traits
supporting
> (AB)C and only 2 supporting (AC)B, then chances are the shared
ancestor
> had the three traits. But suppose the three traits are selected for as
a
> package, i.e. all three are necessary to survive in a particular
> environment, and the other two are unlinked. Then, chances are (AC)B
is
> correct. Morphological analyses are never checked as to the degree of
> linkage of traits in each species in the data set in any adaptive
> environment.
> 
> I think this is because systematics is 2-stepped: 1. an evolutionary
> analysis, then 2. classification reflecting the results. And few
> systematists also do professional research in evolution. Instead, we
rely
> on software imposing one and only one simple model of evolution on all
> exemplars in the data set. Yet evolution may be quite complex
depending on
> the expressed traits and environmental history of each different
organism.
> 
> We are depending on the fact that parsimony and intuitive cluster
analyses
> group organisms so they approximate the results of molecular analyses
> (genetic continuity and isolation events). Good stuff, but . . . We
should
> not extend that approximation as though we have done a satisfactory
> evolutionary analysis.
> 
> _______________________
> Richard H. Zander
> Missouri Botanical Garden
> PO Box 299
> St. Louis, MO 63166 U.S.A.
> richard.zander at mobot.org
> 
> 
> ________________________________
> 
> From: taxacom-bounces at mailman.nhm.ku.edu on behalf of Stephen Thorpe
> Sent: Tue 2/2/2010 9:51 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.
> 
> 
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