1.  36
    Bengt Autzen (2011). Constraining Prior Probabilities of Phylogenetic Trees. Biology and Philosophy 26 (4):567-581.
    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 (...)
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  2.  7
    Bengt Autzen (2016). Significance Testing, P-Values and the Principle of Total Evidence. European Journal for Philosophy of Science 6 (2):281-295.
    The paper examines the claim that significance testing violates the Principle of Total Evidence. I argue that p-values violate PTE for two-sided tests but satisfy PTE for one-sided tests invoking a sufficient test statistic independent of the preferred theory of evidence. While the focus of the paper is to evaluate a particular claim about the relationship of significance testing and PTE, I clarify the reading of this methodological principle along the way.
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    Bengt Autzen (2016). Dissolving the Star-Tree Paradox. Biology and Philosophy 31 (3):409-419.
    While Bayesian methods have become very popular in phylogenetic systematics, the foundations of this approach remain controversial. The star-tree paradox in Bayesian phylogenetics refers to the phenomenon that a particular binary phylogenetic tree sometimes has a very high posterior probability even though a star tree generates the data. I argue that this phenomenon reveals an unattractive feature of the Bayesian approach to scientific inference and discuss two proposals for how to address the star-tree paradox. In particular, I defend the polytomy (...)
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