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Re: BCF in perspective (LONG!)



A final, brief reply to G.O. (I feel the discussion is getting a bit
pedantic and longwinded for most of the list, so I'll agree to hush now):

>"The more characters used, the more accurate the cladogram will
>be." How do you _know_ this?

Generally accepted by most cladists I know. Throwing out characters a
priori because you _think_ they might be homoplastic or whatever is
generally naughty.

What's good character choice? Read the dozens of publications on it, e.g.
Hennig, Carpenter and Currie's Dinosaur Systematics, yada yada yada.

>Ha! When is the last time you heard a cladist say, "Well, my
>cladogram says thus and so, but the stratigraphy says otherwise;
>so its back to the drawing board for me!"

Just yesterday, when Michel Laurin (basal tetrapod cladistics guy) admitted
to me that his cladograms don't match the fossil record perfectly, and
hence are probably wrong in some places. Good cladists (and there are
plenty) don't make a cladogram and then sit back and say, "OK, marsupials
are done. On to edentates." It's a process of refinement that really never
ends, but keeps getting closer to the truth.

>I don't think
>there is any more validity to using parsimony to sift through a
>bunch of cladograms _after_ they are generated than there is in
>using parsimony to eliminate a bunch of long-shot possibilities
>_before_ the cladograms are created.

You won't find many real (i.e. professional) cladists that agree with you
on that one.

>I _don't
>really care_ whether the archosaur phylogeny that my methods and
>analysis have generated overturn BADD or not.

If you do care whether anyone believes you, then you'd better try to
convince them by their rules. Dinosaur phylogeny is currently done by
professionals via cladistics. If you're inventing some new method to use in
place of cladistics, you'd better publish that first and subject it to peer
review.

>No--if I play by the same rules, then I can expect to get much
>the same results, and we have made no progress.

I'd say you're wrong. If you replicate the same phylogeny, that would
support that phylogeny. If you use more characters and taxa than previous
studies, and don't omit included taxa, and come up with a different
phylogeny, _then_ you've got something, if your methods are sound and the
fossil record does not contradict it.

>The objectivity
>of cladistics is compromised by the unavoidable subjectivity of
>the data-gathering process

True in part, but name for me a 100% objective systematic method. Right,
there is none really. Name for me another method that uses compiled data
(ostensibly objectively measured) and produces parsimonious phylogenies.
Right, there is none really. Good characters can be recognized by
researchers trying to replicate your study, objectivity is in the hands of
the researcher.

>I have arrived at a
>phylogeny for archosaurs (excluding crocs and Cenozoic birds,
>which I know very little about)

Ummm....that's not good. You have a paraphyletic phylogeny, which is very
naughty as you know. Might want to tidy that up a bit; if you're going to
do a revision of Archosauria, you'd better include ALL of Archosauria.
Yeah, it's a lot of work, but if you're right, then I'll eat my words with
a spork.

>I'm always interested in hearing from anyone and everyone who
>disagrees with my phylogeny

Good, at least we're both being civilized here. I'd like to add, G.O., that
I enjoy your contributions to the list (as you know, it wouldn't be the
same without ya), and I'm not poo-pooing BCF because I don't want to
believe it, but because I see fundamental flaws in it.

                        John R. Hutchinson
                  Evolving Evolutionary Biologist
                 Department of Integrative Biology
                  3060 Valley Life Sciences Bldg
                University of California - Berkeley
                        Berkeley, CA 94720
                          (510) 643-2109
         http://ucmp1.berkeley.edu/people/jrh/homepage.html