Unjustifiable assumptions of homology incorporated
into data matrices.—The most glaring example of
this problem is the coding of avian and theropod
manual, carpal, and tarsal characters as if they were homologous, despite the ambiguity of the data, and despite the assumption this coding entails that
the BMT [birds are maniraptor theropods] hypothesis is correct a priori.
Because of the above ambiguities, these five
sets of characters [the palate, the basipterygoid process, the carpus, the manus, and the tarsus] cannot be coded for birds and theropods without unjustified assumptions of
homology. They were not included in the primary
analysis of our matrix. This decision is
understood to be especially controversial, so
we have documented our reasoning, which was
based on careful review of the anatomical evidence,
in Appendix 3.
Criticisms of the James and Pourtless study:
James and Pourtless excluded the characteristics that are in dispute. That is impartial.
The critics object to that. The critics want things scored their way.