Rational Disagreements in Phylogenetics

Abstract

This paper addresses the general problem of how to rationally choose an algorithm for phylogenetic inference. Specifically, the controversy between maximum likelihood (ML) and maximum parsimony (MP) perspectives is reframed within the philosophical issue of theory choice. A Kuhnian approach in which rationality is bounded and value-laden is offered and construed through the notion of a Style of Modeling. A Style is divided into four stages: collecting remnant models, constructing models of taxonomical identity, implementing modeling algorithms, and finally inferring and confirming evolutionary trees or cladograms. The identification and investigation of styles is useful for exploring sociological and epistemological issues such as individuating scientific communities and assessing the rationality of algorithm choice. Regarding the last point, this paper suggests that the values motivating ML and MP perspectives are justified but only contextually; these algorithms also have normative force because they can be therapeutic by allowing us to rationally choose among several competing trees, nonetheless this force is limited and cannot be used in order to decide the controversy tout court.

A revised classification of the Sphacelariales (Phaeophyceae) inferred from apsbC andrbcL based phylogeny

“…There was also incongruence between the results of different phylogenetic inference methods. There has been a long-standing debate whether parsimony or model based methods (ML and BI) perform better without general agreement (Sober, 2004;Yang, 2006;Mc Manus, 2009). The fact that MP analysis of data sets including only the more conservative first and second codon positions resulted in the same topology as the BI and ML trees supports this being the correct topology.…”

The Structure of Explanations and Counter-Explanations of Homosexuality

“…In other words, what these explanations have in common is the idea that sexuality corresponds to a family of traits in which sexual orientation can be conceived as a particular trait homologous among different animals and with different character states that correspond to what we in the West call "homosexuality", "heterosexuality" and "bisexuality" (this corresponds to what I have labeled as models of taxonomic identity [Mc Manus, 2009]).…”