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

[christopher brochu <cbrochu@fieldmuseum.org>]

>Regarding the last sentence - ALL matrices need to be tweaked to "work."
>All of us are professional tweakers.  I'm at home with my oatmeal now, but
>I'm on my way to the museum to tweak the day away.  Every paper in Syst Bio
>has some tweaking in it.  Why is this a problem?
>
><<
>
>Because the tweaking becomes the authors call and beliefs. I.e. he doesn't
>agree with the computer and changes the outcome. Then why use the computer?
>Tracy


We use computers because there are gazillions of possible trees for a given
reasonably large matrix, and a computer can sort through them much more
efficiently.

More to the point, the kind of "tweaking" that goes on is much more benign
than you imply.  If I see something really wierd on one of my trees, I
immediately go back to my matrix first.  Did I code something wrong?  And I
mean really wrong, as in typo.  I might re-evaluate the characters and,
better still, take another look at my photographs of the specimen.

One thing I don't do (and which good systematists don't do) is recode and
recode until I get a tree I like.  If the wierdness remains after I've
rethought the obvious sources of error, that's how it is.  I expect my
matrices and character lists to be peer-reviewed, and I stand by every
numeral in every cell - if someone sees the same specimen and wants to code
it differently, there'd better be a good reason for it.  My name goes on
the publication, and if the codings are crap, it reflects on my name.



chris

_________________________
Christopher A. Brochu
Department of Geology
Field Museum
1400 S. Lake Shore Drive
Chicago IL 60605

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