David Bourget (Western Ontario)
David Chalmers (ANU, NYU)
Rafael De Clercq
Ezio Di Nucci
Jack Alan Reynolds
Learn more about PhilPapers
Biology and Philosophy 26 (4):567-581 (2011)
Although Bayesian methods are widely used in phylogenetic systematics today, the foundations of this methodology are still debated among both biologists and philosophers. The Bayesian approach to phylogenetic inference requires the assignment of prior probabilities to phylogenetic trees. As in other applications of Bayesian epistemology, the question of whether there is an objective way to assign these prior probabilities is a contested issue. This paper discusses the strategy of constraining the prior probabilities of phylogenetic trees by means of the Principal Principle. In particular, I discuss a proposal due to Velasco (Biol Philos 23:455–473, 2008) of assigning prior probabilities to tree topologies based on the Yule process. By invoking the Principal Principle I argue that prior probabilities of tree topologies should rather be assigned a weighted mixture of probability distributions based on Pinelis’ (P Roy Soc Lond B Bio 270:1425–1431, 2003) multi-rate branching process including both the Yule distribution and the uniform distribution. However, I argue that this solves the problem of the priors of phylogenetic trees only in a weak form
|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
Daniel C. Dennett & Jon Hodge (1997). Darwin's Dangerous Idea: Evolution and the Meanings of Life. British Journal for the Philosophy of Science 48 (3):435-438.
John Earman (1992). Bayes or Bust? A Critical Examination of Bayesian Confirmation Theory. MIT Press.
John Maynard Keynes (1921/2004). A Treatise on Probability. Dover Publications.
Citations of this work BETA
Trevor Pearce (2012). Philosophy of Biology in the Twenty-First Century. Studies in History and Philosophy of Biological and Biomedical Sciences 43 (1):312-315.
Daniel Barker (2015). Seeing the Wood for the Trees: Philosophical Aspects of Classical, Bayesian and Likelihood Approaches in Statistical Inference and Some Implications for Phylogenetic Analysis. Biology and Philosophy 30 (4):505-525.
Similar books and articles
Joel D. Velasco (2008). The Prior Probabilities of Phylogenetic Trees. Biology and Philosophy 23 (4):455-473.
R. Festa (1993). Optimum Inductive Methods. Kluwer Academic Publishers: Dordrecht.
Joel D. Velasco (2013). Phylogeny as Population History. Philosophy and Theory in Biology 5 (20130604).
R. D. Rosenkrantz (1973). Probability Magic Unmasked. Philosophy of Science 40 (2):227-233.
Patrick Suppes (2007). Where Do Bayesian Priors Come From? Synthese 156 (3):441 - 471.
John C. Harsanyi (1983). Bayesian Decision Theory, Subjective and Objective Probabilities, and Acceptance of Empirical Hypotheses. Synthese 57 (3):341 - 365.
Timothy Herron, Teddy Seidenfeld & Larry Wasserman (1994). The Extent of Dilation of Sets of Probabilities and the Asymptotics of Robust Bayesian Inference. PSA: Proceedings of the Biennial Meeting of the Philosophy of Science Association 1994:250 - 259.
Jacob Feldman (2013). Tuning Your Priors to the World. Topics in Cognitive Science 5 (1):13-34.
Michael Huemer (2009). Explanationist Aid for the Theory of Inductive Logic. British Journal for the Philosophy of Science 60 (2):345-375.
David H. Glass (2005). Problems with Priors in Probabilistic Measures of Coherence. Erkenntnis 63 (3):375 - 385.
Joel D. Velasco (2009). When Monophyly is Not Enough: Exclusivity as the Key to Defining a Phylogenetic Species Concept. Biology and Philosophy 24 (4):473-486.
Olivier Rieppel (2010). The Series, the Network, and the Tree: Changing Metaphors of Order in Nature. Biology and Philosophy 25 (4):475-496.
Paul D. Thorn (2014). Defeasible Conditionalization. Journal of Philosophical Logic 43 (2-3):283-302.
Added to index2011-03-09
Total downloads28 ( #133,969 of 1,789,933 )
Recent downloads (6 months)2 ( #317,270 of 1,789,933 )
How can I increase my downloads?