Pharyngula

Oops, missed the first part of this talk due to the distractions of Lunch. Walked in as he was talking about tree vs. ladder thinking (people have a hard time conceptualizing trees) and history as a chronicle — barebones description of events — or a narrative — events linked by causal explanations.

It took a century for biologists to use systematics to make testable hypotheses about evolution. Darwin himself talked at length about all kinds of evidence for evolution, but strangely neglected fossils and dinosaurs altogether. Sereno blames this on rivalry with Richard Owen, who was the big dinosaur man of the day. One fossil Darwin was pleased with was Archaeopteryx, and Huxley in particular made the link between Archy and birds. Sereno brought in fossil of Confuciusornis — very cool.

We have begun to separate out the chronology from the narrative; chronology is a limiting factor in our hypotheses. We are interested in the trajectory of change over time, and Sereno confesses to baldly exploiting that to get a publication in nature of Raptorex, but he carefully omitted any causal discussion in the paper, trusting readers to infer a narrative from the story, because that’s what we do.

Deplores the thinness of work in the philosophy of phylogeny.

History: Darwin crystallized many of the pieces of an existing chronology into an evolutionary narrative. The next big breakthrough was Hennig (1950) who atomized morphological transformations and branching patterns, defining specific terms to describe phenomena important for understanding trees. Quantitative cladistics (1969) put it on a solid empirical foundation. Character states were coded as mathematical variables.

Problem: everyone has a different matrix for the analysis of characters for each phylogeny examined. The matrix is a black box. We are searching for a methodology that will link everything together. A modern comparative cladistics would open up the black box for universal analysis. Need to figure out what the characters are, and need to be able to do comparative analysis. There is no global understanding of what a character or character state are. There is currently a movement to develop a universal character ontology.

He makes a strong case that we have a serious problem with different investigators studying the same phylogenies, but using different characters and even scoring them differently. We need to standardize to enable full comparisons of multiple data sets.