Acta Biotheoretica 57 (1-2):99-127 (2009)

Authors
Fabrizzio Mc Manus
Universidad Nacional Autonoma de Mexico
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.
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DOI 10.1007/s10441-009-9072-2
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References found in this work BETA

Four Decades of Scientific Explanation.Wesley C. Salmon & Anne Fagot-Largeault - 1989 - History and Philosophy of the Life Sciences 16 (2):355.
Conjectures and Refutations: The Growth of Scientific Knowledge.Mary Hesse - 1965 - Philosophical Quarterly 15 (61):372-374.
La estructura de las revoluciones científicas.Thomas Kühn - 2002 - Revista de Filosofía de la Universidad de Costa Rica 40 (101):179-190.

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