Probabilism and Phylogenetic Inference

Abstract

The maximum likelihood approach to phylogenetics rests on frequency probability theory. This stands in stark contrast to the logical probability of corroboration-based cladistic parsimony. History is particular and cannot be described in terms of universal statements about abstract generalities, the task of the historical sciences being one of explanation, not prediction. Thus, frequency probability methods of estimation are inappropriate for making historical inferences. Maximum likelihood estimation procedures are deconstructed from numerous perspectives in spite of their supposed impressive technicalities. Charges of parsimony's inconsistency are rendered mute, because its justification lies elsewhere, yet maximum likelihood is still subject to Wald's dilemma if realism is of any interest. Although all epistemologies make assumptions, the models employed by maximum likelihood are problematic and deterministic, as opposed to the unproblematic background knowledge characteristic of cladistics. Apart from issues of logical and sampling dependencies, the requirements of frequency probability theory are non-trivial and the maximum likelihood estimation of phylogeny can neither escape, nor satisfy the tenets of calculus independence (e.g. i.i.d.) inherent in the multiplicative relations of the method. If phylogeneticists are to maintain a rational foundation for their epistemology, neo-justificationist appeals to some metaphysical truth must be abandoned in favour of the realism of sophisticated falsification.