Re: Resending

[David Marjanovic <david.marjanovic@gmx.at>]

> They haven't been.  We still get long monographs (Clarke's on Ichthyornis,
> Chure's upcoming on Allosaurus, etc.),

To be fair, Chure's has been upcoming for years. How old is his thesis? --  
In that thesis he describes a complete skeleton (with furcula, gastralia, 
and apparently everything else you might wish for) as the holotype of the 
new species *Allosaurus jimmadseni*, we all know it, and we're all not even 
allowed to use the name. It's not validly published.

> and short papers existed in the past
> too (ever seen any original descriptions by Marsh?).

Or Cope, for that matter. Horrible. Typically, it seems, a few small pages 
of pure text where 3 vertebrae are "described" as 2 new taxa. "Pure text" as 
in "no illustration whatsoever".

> > From your description of the labile nature of current results, it should 
> > be
> clear identifying basic evolutionary patterns is NOT complete.  Most
> published morphological cladistic analyses are crap.  Too few characters 
> and
> taxa, too subjectively defined states.

The same applies to most, or perhaps all, molecular analyses published 
before 2001... and to several younger ones as well. The main reason is 
painfully obvious -- computers would have needed months (or would simply 
have crashed) trying to process today's matrices.

> You change some assumptions in Hutchinson's running model,
> and come up with completely different results. ;)

Yes, the elasticity of the tendons is probably an example... :o)

> Human thought is inferior to PAUP when it comes to calculating most 
> parsimonious trees in a realistic time.

In fact, most of classical guesswork at phylogenetic trees is parsimony with 
one character, or two, or five. Typically supported by ideology like "in 
Carnivora only the braincase is phylogenetically informative, because it 
isn't subject to adaptive pressures apart from some stabilizing selection".*

I have seen computer-free cladistics, however. Ax's recent three-volume book 
on systematic zoology is an example. It simply uses very few taxa and very 
few characters. Consequently, the results are very unreliable. Take the 
place where he explains why he thinks Articulata is monophyletic -- most of 
the characters there are of doubtful primary homology, and IIRC not a single 
proposed morphological synapomorphy of Ecdysozoa even gets considered.

For 9 taxa there are 135135 possible unrooted trees without polytomies. 
Almost regardless of the number of characters, it takes PAUP* less than a 
second to find out which of those are most parsimonious _in an exhaustive 
search_. Try to do that by hand. You will then understand why Hennig 
preached (and computer-free cladists still follow it) that the direction of 
phylogenetic reconstruction is opposite to that of cladogenesis** -- we are 
supposed to take one taxon and look for its sistergroup, then look for the 
sistergroup of the clade composed of the first two, and so on. It goes 
without saying that this approach routinely fails to take the real sister 
taxa into consideration.

* Which of course doesn't mean that the braincase is immune to _random_ 
convergence -- but people used to simply overlook that. However, the 
probability that the braincases will converge _in the same direction_ as the 
jaws and forelimbs and necks and whatnot is probably quite low -- and 
therefore ALL of those characters and more should be used, instead of 
declaring 90 % of them irrelevant.

** Which Hennig called speciation, trying to solve the species problem by 
violence...

> Okay, it technically does include a page of comparison with some
> other theropods, but you get the idea.

_One_ page?

> And I'd rather have that than unresolvable 'which
> character is more important' debates any day.

See above. Braincase! Braincase! ;-)