[Taxacom] sloppy cladistic analyses

[Stephen Thorpe]

> 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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