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Posts tagged ‘cladistics’

Weekly reading: Cladistic matrices, Wagner trees, and optimizations “by hand”

This week our weekly lab discussion group shifts gears from the empiricism/realism debate to actual, and mostly still “manual” (as if hands could think), character matrix assembly, Wagner tree construction, and upward-/downward-pass parsimony-based character state optimization. Consistency and retention indices. And WinClada and NONA. Let’s see how far the first session will take us towards understanding the interaction between characters, parsimony, optimizations, and trees.

Weekly reading: Brady on the independence of systematics

Up next week, following Rieppel’s (2007) nuanced dissection of the limits of ‘direct reference’ (Kripke’s causal theory) and emerging lessons for comparative morphologists, we shall pivot to one of the more influential and sophisticated expositions of a pattern-centric view. Ronald Brady played a sometimes under-appreciated role in conversing and shaping views with cladists at the American Museum of Natural History starting in the late 1970s.

Brady, R.H. 1985. On the independence of systematics. Cladistics 1: 113-126. Availaible here.

Systematics and philosophy of science: some suggested readings

This is a developing post related to a prior entry on cladistic character coding. “Systematic philosophy”, naturally (in a historical science), is a rich topic with influential contributions from various competing philosophical schools such as empiricism or realism. Often these contributions acknowledge their heritage openly, however this is not always the case.

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Worthwhile reads on cladistic character coding

Some pointers to literature relevant to one of the most intellectually engaging topics I can think of in systematics – how to properly “code” cladistic characters. “Code” in quotation marks because there is more to it than a single verb or action might denote. For what it is worth, Olivier Rieppel’s (2007) “performance” paper is a must read in my assessment; he talks about the process of character “scoping”. Though practically all papers can be considered sincere (yes, that can matter) and scholarly contributions to advance the field, occasionally in an intellectual discourse setting overshadowed by too-easy dichotomies of pattern versus process, supposed methodological rigor versus eclecticism, or total evidence versus cherry picking (as I said, too easy, and no improvement here either in such a stenographic account).

Franz, N.M. 2014. Anatomy of a cladistic analysis. Cladistics 30: 294-321. pdf

I will update this listing, from time to time. My own current take is here, with corresponding WHS 2012 presentation:

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