Rational Disagreements in Phylogenetics
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Rational Disagreements in Phylogenetics Fabrizzio Guerrero Mc Manus
Received: 17 January 2009 / Accepted: 3 February 2009 / Published online: 20 February 2009 Ó Springer Science+Business Media B.V. 2009
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. Keywords Phylogenetic inference Rationality Rational disagreements Styles of modeling Maximum parsimony Maximum likelihood
1 Introduction Systematics, as a discipline that has the aim of inferring the phylogenetic relationships among taxa, has been dominated by different positions such as evolutionism, pheneticism and cladism (Hull 1988). Nevertheless, Cladists— F. G. Mc Manus (&) Graduate Program in Philosophy of Science, Instituto de Investigaciones Filoso´ficas, UNAM, Mexico City, Mexico e-mail: [email protected]; [email protected]
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understood as the defenders of the criterion of maximum parsimony (MP)—are now facing new opponents: the Likelihoodists—who believe that the criterion of parsimony should be abandoned in favor of an inductive methodology based in the probabilistic relation known as likelihood (ML)—and, more recently, the Bayesians—who endorse a position in which the full Bayesian Methodology (BM) and not only the likelihood relation should be employed when we are reconstructing phylogenies. This development has placed systematists in a complicated situation in which they have to choose one of the three modern proposals (MP, ML and BM). The choice is unavoidable because, in principle, we know that only one true representation of the tree of life1 can be given and, sometimes, these methodologies produce different and irreconcilable representations of it. Lots of papers have been written defending one of these three methodologies and although no common strategy can be identified, there have been some general trends utilized here and there to defend and criticize the use
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