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

[chris brochu <cbrochu@fieldmuseum.org>]

OK, as one of the resident cladocentrists, I'll go against my better
judgment and jump in.

Dinogeorge:

>Is it just me, or do other people find this endless hunt for ever more
>"characters" just plain CRAZY?

What?  You find the constant search for evidence of relationships unwise
(or even unintelligent)?  We're searching for more characters because we
keep finding new fossils and turning new technologies (and new search
patterns) toward older discoveries.

Phylogenetics, from a morphological perspective, is a feedback loop.  Dr. X
publishes a phylogenetic hypothesis.  It suggests something unorthodox
about taxa A, B, and C.  So Dr. Y takes a closer look at A, B, and C
(perhaps Dr. X only read about one of these from the literature, and was
unable to study them first-hand).  Dr. Y sees something Dr. X missed, and
recodes a few characters she feels were inadequately described.  She also
comes up with a new hypothesis, which looks a whole lot like its
predecessor from Dr. X, but has some nuances.  Then Dr. Z takes a look....


And it isn't restricted to morphology.  A really strange molecular tree
could be strange because the gene is whacked, or it could be strange
because the real phylogeny is strange.  One way to check is to look more
closely at morphology (another is to get more genes).




The computer will, of course, grind out trees
>as long as you give it "characters" to chew on, but do you really BELIEVE in
>the resulting phylogenies, or are they just so much nonsense, to be
>discarded
>when the next batch of computer-generated trees, crunching even more
>"characters," emerges?


But preceeding trees aren't "discarded" as much as they're modified.  I
really liked Tom Holtz' poster session at last year's SVP - it showed that
most of the theropod trees published since the 1980's are basically
modifications of each other; they aren't fundamentally different.

What I will chide my fellow theropod systematists for is a relative lack of
attention paid to nodal support within trees.  This is changing, but older
papers didn't always apply currently-available stats.




 If so, why not hold out until you've found ALL
>possible "characters," grind out the one big tree and be done with it?


Because at that point, I couldn't publish it.  The only way to achieve that
condition is to die and have God reveal the One True Phylogeny.  Believe
me, I can't wait to have God tell me exactly what's going on with Gavialis
and Tomistoma, and a few molecular people and I have a case of beer riding
on it.  I only hope they let us drink beer in Heaven.



 But
>then how would you CHECK this tree against reality? Are synapomorphy wars
>what the search for truth in paleontology is really like? <<


Since these are phylogenetic hypotheses (or, in likelihood circles,
"estimates"), there is no way to check any phylogenetic hypothesis against
reality.  But I'll take a tree built with a repeatable methodology and an
explicit data set over one built with intuition any day.  I can check the
algorithmic tree without killing the scientist and eating his or her brain.

And I disagree with your perspective on whether one should check over a
matrix.  I do it all the time, and people go over mine as well.


Tracy Ford:

>
>Crazy, that's to kind a word. I've just seen an article redescribing a
>Jurassic lizard with 100 or so characters The Character matrix is nearly as
>long as the article.

Well, lizards are rather complicated objects, having lots of bones and stuff...




It's getting way out of hand. Tom says his article in
>Gaia is going to torn apart at the SVP. Give me a break!!!


Yes!  How dare Tom do science by attempting to falsify a hypothesis!  Tom,
shame!


 It's constantly
>changing.

See above - it's not really changing as much as people think.


Now instead of naming a node, cladis just say unnamed node. They
>don't have to worry about Order, Family, etc. so they just place new nodes
>were ever they want.


Not correct - sorry.

1.  We stopped worrying about Linnean ranks because they have no biological
reality and can seriously mislead people.  They were made for a world view
that did not account for evolution.  Good riddance to them.


2.  We don't "place new nodes" where WE want.  We observe them as the
MATRIX wants.  The act of naming a node is, of course, arbitrary - but
recognition of the node itself is not.

chris

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

phone 312-665-7633
fax 312-665-7641
electronic cbrochu@fmppr.fmnh.org