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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.

For someone entering the field of systematics it is minimally helpful to understand how philosophically minded papers in this field relate to the different philosophical schools, as this may confer an understanding of their underlying motivations and argumentative strategies. Some papers stay close to the assumptions of particular methods in use, others are explorations of parallels among such methods and certain philosophical tenets, and yet others utilize philosophy as a means to argue for the dominance of some methods to the detriment of others. Just as it is fair to assume that there is no bias-free science (nor should there be, according to many), there is likely no bias-free philosophy of systematics. Good science is in no small part characterized by an understanding (as opposed to abandonment) of one’s biases and inferential dependencies. Knowing one’s biases is a way of beginning to control for their influence on systematic inferences. This is why systematists can benefit from developing some expertise in the philosophical realm.

My own bias leans towards scientific realism in the sense of Boyd and Chakravartty, as summarized here: http://plato.stanford.edu/entries/scientific-realism/ [The Stanford Encyclopedia of Philosophy is an outstanding resource for scientists; look up the entries on Constructive Empiricism, Logical Empiricism, Kuhn, Naturalized Epistemology, and Simplicity; and you are well on your way.]

Below is an annotated list of papers that reflect different periods and viewpoints in the more recent (and largely North American) history of systematic philosophy.

To be continued.

  • Felsenstein, J. 1978. Cases in which parsimony or compatibility methods will be positively misleading. Systematic Zoology 27: 401-410. Link
    • …[the counter-factual case against parsimony as an a priori justified method of inference in systematics]
  • Platnick, N.I. 1979. Philosophy and the transformation of cladistics. Systematic Zoology 28: 537–546. Link
    • … [considered a landmark paper in “pattern cladistics”…]
  • Farris, J.S. 1983. The logical basis of phylogenetic analysis; pp. 7-36. In: Platnick, N.I. & V.A. Funk V.A., Eds. Advances in Cladistics, Volume 2. Columbia University Press, New York. Link
  • Brady, R.H. 1985. On the independence of systematics. Cladistics 1: 113–126. Link
    • …[a clear exposition of an independent research paradigm…]
  • Kluge, A.G. 1997. Testability and the refutation and corroboration of cladistic hypotheses. Cladistics 13: 81–96. Link
    • … [re-establishment of a certain interpretation of Popperianism…]
  • Hull, D.L. 1999. The use and abuse of Sir Karl Popper. Biology and Philosophy 14: 481–504. Link
  • Sober, E. 2004. The contest between parsimony and likelihood. Systematic Biology Biology 53 : 644–653. Link
  • Franz, N.M. 2005. Outline of an explanatory account of cladistic practice. Biology & Philosophy 20: 489-515. Link
  • Haber, M.H. 2005. On probability and systematics: possibility, probability, and phylogenetic inference. Systematic Biology 54: 831-841. Link
  • Plutynski, A. 2005. Parsimony and the Fisher–Wright debate. Biology and Philosophy 20: 697–713. Link
  • Haber, M.H. 2008. Phylogenetic inference. … Link
  • Rieppel, O. 2008. Hypothetico-deductivism in systematics: fact or fiction? Papéis Avulsos de Zoologia 48: 263-273. Link
    • …[critique of the Popperian line of argumentation…]
  • http://www.jstor.org/stable/25065585
  • http://ib.berkeley.edu/courses/ib200b/IB200B_Readings.shtml
  • http://joelvelasco.net/Papers/
  • http://www.philostv.com/matthew-haber-and-joel-velasco/
  • http://faculty.unlv.edu/jwood/unlv/Articles/PutnamVsPopper.pdf
  • http://www.sciencedirect.com/science/article/pii/S1055790305000023
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