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Re: Phylogenies, science, tea-time and more...

Enough for an introduction. I was reading the discussion following Nick's
intervention in favor of getting rid of silly postcranial characters and
fragmentary taxa in theropod phylogenetic analysis, and was suddenly cought by the
need of telling what I think about all this.

I hate to spoil all the fun... but apparently someone needs to kill the joke by explaining it: Nick is parodizing the way ornithischian phylogenetics is almost always done. By applying it to theropods, he demonstrates what nonsense results when one only puts a few skulls into one's matrix. He is crying desperately for someone to do a serious phylogenetic analysis of Ornithischia. (Probably he'll end up doing it himself, alone.)

It certainly was a good  thing to
nuke the old crumbling linnean tree and get rid of "thecodonts" and
"carnosaurs", which were mostly synonyms of ignorance.

Unfortunately (IMNSHO), the name Carnosauria was _immediately_ reintroduced to designate the sistergroup of Coelurosauria (...a name that should have been dropped as well...). So, while *Tyrannosaurus* and *Megalosaurus* are no longer carnosaurs, *Allosaurus*, *Carcharodontosaurus*, *Sinraptor* and *Monolophosaurus* are still carnosaurs.

I know this also depends on money, research credits, and anyway
everydoby wants to be as modern and up to date as possible... But I dare to think
this is NOT science. For me, dinosaur paleontology is mostly anatomy,
stratigraphy, paleobiology and paleoecology. The first two items are the dry and hard
data on which the other two more attractive ones are based.
But where does phylogenetic systematics fit in there?

It is based on anatomy, it is partly based on paleobiology, and paleobiology including -ecology are partially based on it.

But after this is done, I can't see the sheer utility of those numerous analyses.
You add some abscure species known from two
teeth and one caudal vertebra and the tree gets completely changed... Get rid
of some characters you don't like and Corythosaurus might appear as a brand
new ankylosaur!

If your tree is so unstable, you clearly have far too few characters*, and probably too few taxa as well.

* Get a look at the "Basal Tetanurae" chapter in The Dinosauria II. The analysis in there has 638 characters. It will teach you what I mean by "too few characters".

I think Nick is right at pointing  that part of the rampant phylogenetic
instability comes from including too  fragmentary taxa,

Ironically, missing data are usually much more harmless than one might think. There are theoretical studies on this to supplement my personal experience (and doubtless the much richer one of others).

but doesn't it come also from inadequate study of those
reasonably well preserved specimens we have at hand?

Of course. My bird matrix http://www.unet.univie.ac.at/~a0000265/cladogram.htm is an extreme case of this. I haven't seen any of the specimens I've coded there, I have relied completely on the literature which is often very superficial. By examining the specimens -- or reading good monographs on them, which don't exist -- I could perhaps cut the number of question marks in half. (That's the most important reason why I don't consider it publishable -- even though I fear it is better than any published analysis of Mesozoic birds, for example in the sheer number of taxa that aren't included anywhere else).

As a student in social sciences, I have got quite a good knowledge of the
good and bad points of quantitative and qualitative methods. Cladistics are a
quantitative method, everyting being based on the NUMBER of shared apomorphies,
and the like. When reading sociology works, I tend to strongly dislike
studies based on pure statistics, while I believe interviews of "real" people are
often thrilling. Is it that silly to say that we could somewhat turn back to
actually thoroughly interviewing fossils instead of comfortably use some
unreliable statistical method?

I don't think this metaphor works. In sociology you have to cope with plenty of phenomena that are not quantifiable to start with. In morphology, those are rare... and actually just causes of ignorance. An example is the question whether a particular character should be ordered, and if so, in which way, or even which characters to include in the analysis at all. Learning more about the ontogeny, inheritability, variability etc. of the character in question (and on its dependence on other characters!) can force us to exclude several possibilities, ideally all except one. (Unfortunately, papers on phylogenetic analyses rarely explain the choices that were made in coding.)

BTW, I wouldn't call parsimony statistics... maximum likelihood and especially Bayesian methods do use statistics... and as long as we aren't talking about molecular data of taxa with long branches, I wouldn't call any of them "unreliable"!

And, more generally, is it really more interesting
to know  where Torvosaurus fit on the cladistic tree than to
know what it looked like and  how it lived?

This is a false dichotomy! If we don't know its place in the tree of life, we _cannot_ find out certain aspects of what it looked like and how it lived. "Nothing in evolution makes sense without a good phylogeny."

The best thing about cladistics is that it has introduced tree-thinking.