Embedded Mechanisms and Phylogenetics

A strong case has been made for the role and value of mechanistic explanation in neuroscience and molecular biology. A similar demonstration in other domains of scientific investigation, however, remains an important challenge of scope for the new mechanists. This article helps answer that challenge by demonstrating one valuable role mechanisms play in phylogenetics. Using the transition/transversion (ti/tv) rate parameter as a case example, this article argues that models embedded with mechanisms produce stronger phylogenetic tree hypotheses, as measured by maximum likelihood logL values. Two important implications for the new mechanistic account of explanation are considered.