Re: Ghosts of New Papers Past

[dinoboygraphics@aol.com]

> > > Hey, cool. BAND at last being done as science! At long last! :-) <<<

I'm afraid you spoke much, much to fast.  I finally waded through this 
unmitigated pile of tripe, and several things immediately leap out 
(well, as "immediate" as anything can be when reading a 78 page 
monograph).

First, it's astounding that the publication date is 2009, as the 
authors seem to have largely stopped reading the literature on homology 
in the 1990's (or at least they feel that in typical BANDit style they 
can quote papers from this time period and ignore or trivialize 
subsequent refutations).

Second, neither the authors nor the reviewer(s) have any knowledge of 
phylogenetic analysis (as a third hypothesis, the reviewers could have 
stopped reading in the first 10 pages, see below).

After opening with a summary of hypotheses on bird origins over the 
last few decades, and the introduction of several new acronyms (e.g. 
the Theropod Working Group's matrix is referred to as BMT, even though 
the cited literature they use already refers to it as the TWG matrix), 
and defining Aves a priori as including Archaeopteryx they start to lay 
out a promising sounding game plan.  They are going to explicitly 
define several of the competing hypotheses to a maniraptoran theropod 
origin of birds, and the relevant taxa and new characters, and analyze 
that.  They also plan to not polarize their characters (e.g. not assume 
that "0" is pri
mitive and "1" is advanced...which is a perfectly 
reasonable and interesting bit of data to publish)

Undoubtedly a worthwhile endeavor, and not dissimilar to Gauthier's 
classic 1986 paper in concept but with more taxa and characters and a 
couple methodological changes.  Alas, that's when we get to the real 
screw-ball portion...

...all of twelve pages in.

Prior to their analysis, they discuss how they plan to address the 
"problem" with assuming homology in characters where it "cannot be 
established with certainty" BY PROCEEDING TO THROW OUT EVERY CHARACTER 
WHOSE HOMOLOGY HAS EVER BEEN QUESTIONED BY A BANDIT.

I apologize for typing in caps, but please reread that and let it sink 
it.  Essentially any important character of the manus, pes, or skull is 
tossed out prior to the analysis because they don't want to burden the 
analysis with "assumptions" of homology.  They are committing the same 
old (and repeatedly refuted) mistake of thinking that scoring 
morphological similarity assumes homology, when in fact it TESTS 
homology.  Could every character in the manus, pes, and skull of 
theropods be homoplastic with birds?  Of course, but the point is to 
show you how much homoplasy you have to assume in order to favor a 
different phylogenetic hypothesis.  They side step this by simply 
throwing all of the characters out.  They claim to "test" their results 
later by including these characters, but they score all the=2
0
"questionable" characters with a? (Which is actually much worse and 
less honest, as it implies that the morphological state is not known 
when in fact it is).

Worse, they then commit the exact crime they claim they are avoiding, 
scoring "similarities" in tooth rooting in crocodilians and 
Archaeopteryx (how do they know these are homologous???) and other 
BANDit characters (ignoring the relevant literature on other 
maniraptoran tooth socketing), thus "assuming homology" in their 
parlance.  Of course what they are really doing is subjectively 
throwing out data that doesn't support their hypothesis and 
subjectively retaining characters that do support it.

And yet _even_ worst, they claim they are testing the idea that birds 
(and perhaps most maniraptorans) are not theropods by including 
non-dinosaurian taxa, which would be fair enough, except they don't 
actually sample the relevant taxa.  They include Longisquama (with some 
imaginary skull characters) but they don't bother to include any other 
theropod except the ones that the TWG's tree was rooted on (Allosaurus 
and Sinraptor).  No basal theropods, no basal tetanurans.  They prune 
enough taxa away by the end to basically reduce non-maniraptoran 
coelurosaurs to "tyrannosaurs" and all other theropods to "Allosaurus, 
Sinraptor, and Ceratosaurus" and seem to not even grasp that this is a 
problem.

BTW, I've seen this a lot lately in informal publications (and whatever 
you call F
educcia's unrefereed opinion and review pieces), where people 
want to shove "maniraptorans" including birds out of Theropoda, without 
bothering themselves with the huge number of other theropods that would 
be relevant to the question.  Ignoring virtually all other theropod 
taxa is NOT a test of where maniraptorans go.

Appendix 3 is where they justify all of the characters they feel should 
be ignored because they may not be homologous.  It reads very much like 
classic BANDit papers from the 1980s and 1990s (actually, large 
sections are verbatim quotes from those papers), and they evince the 
usual selective quotation of papers to justify those assumptions.  But 
as I mention above, the real problem isn't that they like or don't like 
certain characters, it's that they misunderstand phylogenetic analysis 
so poorly that they feel they can throw out entire reams of data they 
don't like, while keeping (and not questioning the homology of) other 
characters they do like.

The paper completely garbles phylogenetic methodology, but instead of 
the classic BANDit tact of simply saying "cladistics sucks" they have 
shifted their rhetoric (in a way more befitting of political 
mudslinging than scientific discourse) to "we understand phylogenetics 
better than you, which is why we are throwing out all of this data".

This may seem harsh, but given how frequently papers and opinion pieces 
of this "quality" seem to show up in AOU publications, I20think they 
should consider restricting themselves to publications on extant or 
recently extinct members of Aves.  They seem to be ill equipped to 
review these papers, and it casts an unfortunate and unfair pall over 
other research that gets published by them.


Scott Hartman
Science Director
Wyoming Dinosaur Center
110 Carter Ranch Rd.
Thermopolis, WY 82443
(800) 455-3466 ext. 230
Cell: (307) 921-8333

www.skeletaldrawing.com


-----Original Message-----
From: David Marjanovic <david.marjanovic@gmx.at>
To: DML <dinosaur@usc.edu>
Sent: Tue, 21 Apr 2009 4:32 pm
Subject: Re: Ghosts of New Papers Past


> Feduccia, A. 2009. A colorful Mesozoic menagerie. Trends in Ecology 
andÂ
> Evolution. doi: 10.1016/j.tree.2009.03.002.Â
> Â
> (Book review of John Long's _Feathered Dinosaurs_.)Â
Â
I take it book reviews are not peer-reviewed...?Â
Â
> James, F.C., and Pourtless, J.A., IV. 2009. Cladistics and the origin 
ofÂ
> birds: a review and two new analyses. Ornithological Monographs 
66:1-78.Â
Â

Â
This approach (looking for mistakes in published data matrices) is what 
I've been doing with three matrices on tetrapod phylogeny and the 
origin of lissamphibians. Yields interesting results each time.Â
Â
I bet, of course, that these authors introduced more mistakes than they 
corrected ("questionable homologies in [...] the carpus", yeah right). 
But it will be interesting to loo
k at that in detail.Â
Â
> Barrett, P.M., and Han, F.-L. 2009. Cranial anatomy of JeholosaurusÂ
> shangyuanensis (Dinosauria: Ornithischia) from the Early Cretaceous 
ofÂ
> China. Zootaxa 2072:31-55.Â
Â
:-) :-) :-)Â
Â
> Combination of traditional sedimentological fieldÂ
> analysis with modern digital data capture techniques (e.g. spectralÂ
> gamma-ray, LIDAR terrestrial scanner imaging) allows a detailed > 
descriptionÂ
> and interpretation of the facies.Â
Â
Gamma rays?Â
Â
What next, death rays? Or machine guns? What does one need that kind of 
power for?Â
Â
> Basilici, G., FÃr dal BÃ, P.F., and Bernardes Ladeira, F.S. 2009.Â
> Climate-induced sediment-palaeosol cycles in a Late Cretaceous dry 
aeolianÂ
> sand sheet: MarÃlia Formation (North-West Bauru Basin, Brazil).Â
> Sedimentology. doi: 10.1111/j.1365-3091.2009.01061.x.Â
Â
That's where all those crocodiles were running around. Literally.Â
Â
> Maxwell, E.E. 2009. Comparative ossification and development of the 
skull > inÂ
> palaeognathous birds (Aves: Palaeognathae). Zoological Journal of theÂ
> Linnean Society 156(1):184-200. doi: 
10.1111/j.1096-3642.2009.00480.x.Â
Â
Always good. There are people out there who like doing phylogenetics 
with ossification sequences of four or five taxa; increasing the 
dataset really can't hurt.Â
Â
> All these remains belong toÂ
> one singl
e taxon which clearly represents the long known but never > 
properlyÂ
> described 'C.'depressifrons. They allow, for the first time, the 
diagnosisÂ
> this species on the basis of an unequivocal set of characters, > 
contributingÂ
> to the long awaited revision of the Asiatosuchus-like taxa.Â
Â
Always good to see that someone is working on this kind of problem. 
There are so many such problems out there...Â
Â
Remember when the diagnosis of *Tyrannosaurus rex* was "it's dead, 
Jim"? Â