David Bourget (Western Ontario)
David Chalmers (ANU, NYU)
Rafael De Clercq
Jack Alan Reynolds
Learn more about PhilPapers
Acta Biotheoretica (2009)
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||No keywords specified (fix it)|
|Categories||categorize this paper)|
Setup an account with your affiliations in order to access resources via your University's proxy server
Configure custom proxy (use this if your affiliation does not provide a proxy)
|Through your library|
References found in this work BETA
No references found.
Citations of this work BETA
No citations found.
Similar books and articles
Peter Stone (2003). The Impossibility of Rational Politics? Politics, Philosophy and Economics 2 (2):239-263.
Howard Sankey (1995). The Problem of Rational Theory-Choice. Epistemologia 18 (2):299-312.
Robert S. Goldfarb, Thomas C. Leonard & Steven M. Suranovic (2001). Are Rival Theories of Smoking Underdetermined? Journal of Economic Methodology 8 (2):229-251.
Joel D. Velasco & Elliott Sober (2010). Testing for Treeness: Lateral Gene Transfer, Phylogenetic Inference, and Model Selection. Biology and Philosophy 25 (4):675-687.
W. S. Cooper (1989). How Evolutionary Biology Challenges the Classical Theory of Rational Choice. Biology and Philosophy 4 (4):457-481.
Duncan MacIntosh (1992). Buridan and the Circumstances of Justice (On the Implications of the Rational Unsolvability of Certain Co-Ordination Problems). Pacific Philosophical Quarterly 73 (2):150-173.
Mark Colyvan (2009). Naturalising Normativity. In David Braddon-Mitchell & Robert Nola (eds.), Conceptual Analysis and Philosophical Naturalism. MIT Press
Dag Olberg (1995). The Theory of Heroic Defeats: A Mixed Motivation Approach. Sociological Theory 13 (2):178-196.
Patricia Greenspan (2009). Resting Content: Sensible Satisficing? American Philosophical Quarterly 46 (4):305 - 317.
Richard C. Richards (2002). Kuhnian Values and Cladistic Parsimony. Perspectives on Science 10 (1):1-27.
Added to index2009-02-23
Total downloads23 ( #142,479 of 1,780,191 )
Recent downloads (6 months)1 ( #291,056 of 1,780,191 )
How can I increase my downloads?