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

["Tracy Ford" <tlford@ix.netcom.com>]

-----Original Message-----
From: owner-dinosaur@usc.edu [mailto:owner-dinosaur@usc.edu]On Behalf Of Ken
Kinman
Sent: Thursday, October 12, 2000 7:25 PM
To: dinosaur@usc.edu
Subject: RE: Gaia theropod follow-up: a "new" phylogeny

Tracy,
     In all fairness, I think cladistic analyses done well are one of our
most important systematic tools.  And generally the more characters a good
systematist has, the better the result will be.  But it isn't just a numbers
game, and quality of both character selection and analysis play an important
part as well.
     Like any other segment of society, there are going to be some slackards
out there, cutting corners and taking whatever the computer first spits out
at them.  There might even be a few really bad apples who set out to achieve
a certain end and manipulate the data until they get it (just like
statistics, cladograms will say anything if you torture them long enough).
     But I don't think you are going to find such bad apples on this list,
and most such people never make it out of graduate school, especially in a
discipline like systematic biology.
     Purposeful manipulation of data towards a preconceived result is
obviously a bad thing, but you can't therefore conclude that this makes
"tweaking" and testing bad.  In fact, the other extreme of no tweaking and
testing of results would be rather unscientific.  The best "tweakers" no
doubt learn from experience how much is too little and how much is overdoing
it.  In that way, it is probably just as much an art as it is a science.

This is one area I disagree with. ANY manipulation of the data from what
PAUP has given is wrong. It's abusing the system/program that it was made
for. The author (here will be the Scientist) will run the program. He will
get anywhere from 12 to 100 different trees. Which one is right? The author
decides the most parsimonious one (MPO, how does HE decide that?). But the
MPO isn't quite to his liking. So he re-codes some things, re classifies
others and there is the MPO, but it isn't the one the computer put forth. He
just manipulated the information to his liking. This is tweaking is
manipulation and should not be considered otherwise.
It's like this. I was at a Traffic court years and years ago. The Judge (who
will be PAUP) tells a young lady (who will be the author) in a none direct
way (because she really couldn't come out and tell the young lady) that if
she took a Traffic School Class her ticket wouldn't go on the books. She
said no. The Judge repeated again and then in a different way, but still she
said no. That is what the author does with the clade.
When you have a system that will tell you one group of animals, when just
the skull is used, is more closely related to the parareptilia, and then
when another author uses the skeleton, the animals come out closer to
lepidosauria. There is (AFIK) now consensus of characters used. I would like
there to be one. Then I would in brace it more. But there are hundreds of
trees, depending on which characters you use, which out groups you use,
which similar animals you use. Mononykus, what is it either a bird (one
author uses the PAUP) or a dinosaur (another author uses the PAUP, with the
same animal). How can this be correct?
Cladistics is a tool, that's all. How to use the tool can't even be agreed
upon. Some use morphology, others phylogeny. What it is to me is just
genealogy. Cladistics is the trees and the animals themselves are the
forest. Sometimes it just doesn't matter which animal from the same family
came first when they live together. You have to be able to use geology. You
can't have an ancestor after its kin.
Tracy