I. Finally, I discussed non-cladists' objections to cladistics. there were four major ones:
B. Cladograms as an end in themselves: Non-cladists often complain that cladists are ONLY interested in generating trees, but are not interested in using them to address larger issues. This complaint hits home to varying degrees with different researchers. It is true that when one's only tool is a hammer, all problems start to look like nails. Thoughtful cladists must remember that phylogenies are tool with which larger issues of paleobiology, evolutionary processes, and biogeography (to name a few) can be addressed.
C. No ancestors: For ages, paleontologists prided themselves on their ability to find the direct ancestors to things. In so doing, they erroneously viewed evolution as a ladder rather than a tree. (For an example of this, check out the fossil horse exhibit at the National Museum of Natural History.) Generally, we should not expect to find direct ancestors and, indeed, the hypothesis that one organisms is directly ancestral to another may be very hard to falsify. Nevertheless, there are circumstances under which the identification of ancestors ought to be both possible and useful (as in the evolution of Homo.) Never forget that the phylogenetic systematic method cannot, in principle, identify ancestors. Indeed, if your data set incudes a taxon that is directly ancestral to another, PAUP will place it at the end of its own branch.
D. Inconvenient: Whatever its shortcomings, the Linnean system is a great way to store and retrieve information. By revolutionizing the way we describe evolution and taxonomy, we inconvenience the non-specialists who have to deal with this information: high school teachers, librarians, etc. Change is the nature of science, but where possible, we should strive for taxonomic stability.
E. Our own worst enemies: In the movement's exuberant youth, its proponents made many extravagant claims. the most extreme is that phylogenetic systematics is a fully objective approach to reconstructing evolutionary history. Anyone who has decided which taxa to include or exclude from a matrix or has puzzled over the most informative way to phrase character state descriptions knows that much subjectivity goes into a phylogenetic analysis. The strength of phylogenetic systematics is not that it is so objective. Rather, it is that it is explicit. If you publish your matrix, character list, and search methods, I can repeat your analysis. Before cladistics, such repeatability was impossible.
You who have studied and used the method, and are familiar with the body of knowledge it has generated, can easily see through ad-hoc and rhetorically dishonest arguments.
Take this example: Ornithologist Alan Feduccia and his colleagues claim that birds could not be theropods, because birds appear in the Late Jurassic, but the theropods that the cladists like to group birds with, such as dromaeosaurids (raptors), don't show up until the middle of the Cretaceous. How, then, could birds have evolved from dromaeosaurids?
Viewed in a phylogenetic perspective, this is nonsense. No one has actually claimed that birds evolved from dromaeosaurids, but if you were not familiar with the concept of sister-taxon relationships - if you did not know how to interpret a cladogram - this might seem like a compelling argument. That's the rub. To critically examine these issues, you really need a decent store of prerequisite knowledge and some experience dealing with the concepts of the tree of evolution. (Actually, the Feduccia argument is precisely analogous to the creationist argument that humans couldn't ahve evolved from apes, because if they had then the apes shouldn't still be here.
Skillfully employed, cladistics not only show us the speciousness of such arguments, they provide students a depth of understanding of evolution that our current emphasis on evolutionary processes, by itself, can't. It's hard to claim that that you can't see how birds could have evloved from reptiles, if you had been taken, step by step, through the internested hierarchy of evolutionary novelties that link the comon ancestor of repiles with that of birds.
It's been fun.