Re: Gaia theropod follow-up: a "new" phylogeny

["Jeffrey Martz" <jeffmartz@earthlink.net>]

philidor11 wrote...
>So the analyst intervenes with the data, trying to make them more 'right'.
>This is worthwile; the analyst is trying to improve the result, and the
>cladistic program is treated as a tool for doing calculations too complex
>for
>the analyst to do in her/his head, and not in itself a means of discovery.

>(except see below)  The results have to be verified and manipulated.
>The source data is assumed to be potentially misleading to the program.

    Something like that I think, although I'm not sure that I agree with
"not in itself a means of discovery".  If an analysis shows that the
availible character information puts a taxon in an unexpected place, its a
discovery regardless if it was noticed using a computer program or not.

>This conclusion is surprising to me.  Given that evolution works in various
>ways
>(including neotony and new features developed by adaptation), and sometimes
>over a comparatively brief period of time, the idea that the results of
>applying an
>algorithm to a set of samples would always conclusively show relationships
>appeared ambitious.  You are, presumably, assuming that the number of
>samples would be sufficient to allow the program to identify the
progression
>of
>taxa.


    Right.  In a statistical study, increasing the sample size brings the
results closer to reality, and (ideally) this is also sort of the case with
cladistics, assuming that the characters are coded in enough detail.

>The fact that an analysis
>is the result
>of using a cladistic computer program does not ipso facto give it extra
>credibility.

    No, not really.  It is possible to do a cladistic analysis with a pen
and paper and a calculator (although doing a big one would take forever).
However, the program should (hopefully) be less prone to making calculation
errors.

>The problem I see with these experiments, which are feedback loop
>interactions
>with the program, is that the algorithm is being made the judge of
accuracy.
>If I
>continuously rearrange my data and the taxa included in order to see if I
>can
>come to what the program sees as a 'good' result, then I have incorporated
>all
>and only the assumptions in the program as to the way evolution works.

    The basic assumption of the algorithm is that one character can change
into another, which I don't think anyone would refute as applying to
evolution in general, adaptive.  The other assumptions I mentioned before
(more characters = closer relationship, homology more likely then
convergence), which can be confounded by homoplasy, can be gotten around
either by tweaking or by more detailed coding.
    Keep in mind these are just MY personal opinions on what cladistic
analyses do and mean once you turn the technical jargon into english.  Dr.s
Holtz and Brochu may not agree and all or any of it.  Since I have never
actually RUN my own analysis (although I have read and tried to dissect
several), my opinion certainly isn't gospel.

LNJ
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Jeffrey W. Martz
Graduate student, Department of Geosciences, Texas Tech University
3002 4th St., Apt. C26
Lubbock, TX 79415
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