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Re: Ghosts of New Papers Past

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
"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


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I take it book reviews are not peer-reviewed...?Â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

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
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
Barrett, P.M., and Han, F.-L. 2009. Cranial anatomy of JeholosaurusÂ
shangyuanensis (Dinosauria: Ornithischia) from the Early Cretaceous
China. Zootaxa 2072:31-55.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 >
and interpretation of the facies.Â
Gamma rays?Â
What next, death rays? Or machine guns? What does one need that kind of power for?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
sand sheet: MarÃlia Formation (North-West Bauru Basin, Brazil).Â
Sedimentology. doi: 10.1111/j.1365-3091.2009.01061.x.Â
That's where all those crocodiles were running around. Literally.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:
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
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
this species on the basis of an unequivocal set of characters, >
to the long awaited revision of the Asiatosuchus-like taxa.Â
Always good to see that someone is working on this kind of problem. There are so many such problems out there...Â
Remember when the diagnosis of *Tyrannosaurus rex* was "it's dead, Jim"? Â