Acta Biotheoretica

, Volume 57, Issue 1–2, pp 99–127 | Cite as

Rational Disagreements in Phylogenetics

  • Fabrizzio Guerrero Mc Manus
Regular article


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.


Phylogenetic inference Rationality Rational disagreements Styles of modeling Maximum parsimony Maximum likelihood 



First and foremost I want to thank Rasmus Winther and Paco Vergara. They have been, are, and surely will remain as great influences in my life. They have been my teachers and also my friends. Thanks for inviting me to join this particular project as well. I also want to thank Martha Martínez and Helga Ochoterena, who have also taught me a lot about Systematics and motivated, by doing that, many of the points here presented; any failure is of course only mine. I would also like to thank Gabriela Guerrero’s technical assistance when writing this paper. And lastly, I want to thank those philosophers who have greatly influenced my thinking: Ana Rosa Pérez Ransanz (How could I possibly understand Kuhn without your guidance), Sergio Martínez and Ángeles Eraña (your reflections on rationality have been an inspiration), and finally I want to thank Carlos López Beltrán for teaching me how history matters even in the realm of reason.


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Copyright information

© Springer Science+Business Media B.V. 2009

Authors and Affiliations

  1. 1.Graduate Program in Philosophy of Science, Instituto de Investigaciones FilosóficasUNAMMexico CityMexico

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