Bayesianism and likelihoodism are two of the most important frameworks philosophers of science use to analyse scientific methodology. However, both frameworks face a serious objection: much scientific inquiry takes place in highly idealized frameworks where all the hypotheses are known to be false. Yet, both Bayesianism and likelihoodism seem to be based on the assumption that the goal of scientific inquiry is always truth rather than closeness to the truth. Here, I argue in favour of a verisimilitude framework for inductive (...) inference. In the verisimilitude framework, scientific inquiry is conceived of, in part, as a process where inference methods ought to be calibrated to appropriate measures of closeness to the truth. To illustrate the verisimilitude framework, I offer a reconstruction of parsimony evaluations of scientific theories, and I give a reconstruction and extended analysis of the use of parsimony inference in phylogenetics. By recasting phylogenetic inference in the verisimilitude framework, it becomes possible to both raise and address objections to phylogenetic methods that rely on parsimony. 1Introduction2Problems with the Law of Likelihood3Introducing Verisimilitude-Based Inference4Examples of Verisimilitude-Based Inference Procedures4.1Parsimony inference over theories4.2Parsimony inference in phylogenetics5Conclusion. (shrink)

Essay review of Michael Ruse (ed.), The Oxford Handbook of the Philosophy of Biology (2008).

The three main approaches in statistical inference—classical statistics, Bayesian and likelihood—are in current use in phylogeny research. The three approaches are discussed and compared, with particular emphasis on theoretical properties illustrated by simple thought-experiments. The methods are problematic on axiomatic grounds, extra-mathematical grounds relating to the use of a prior or practical grounds. This essay aims to increase understanding of these limits among those with an interest in phylogeny.

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. (shrink)

Bayesianism and likelihoodism are two of the most important frameworks philosophers of science use to analyse scientific methodology. However, both frameworks face a serious objection: much scientific inquiry takes place in highly idealized frameworks where all the hypotheses are known to be false. Yet, both Bayesianism and likelihoodism seem to be based on the assumption that the goal of scientific inquiry is always truth rather than closeness to the truth. Here, I argue in favor of a verisimilitude framework for inductive (...) inference. In the verisimilitude framework, scientific inquiry is conceived of, in part, as a process where inference methods ought to be calibrated to appropriate measures of closeness to the truth. To illustrate the verisimilitude framework, I offer a reconstruction of parsimony evaluations of scientific theories, and I give a reconstruction and extended analysis of the use of parsimony inference in phylogenetics. By recasting phylogenetic inference in the verisimilitude framework, it becomes possible to both raise and address objections to phylogenetic methods that rely on parsimony. (shrink)