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 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. (shrink)

In this paper we identify six theses that constitute core results of philosophical investigation into the nature of mechanisms, and of the role that the search for and identification of mechanisms play in the sciences. These theses represent the fruits of the body of research that is now often called New Mechanism. We concisely present the main arguments for these theses. In the literature, these arguments are scattered and often implicit. Our analysis can guide future research in many ways: it (...) provides critics of New Mechanism with clear targets, it can reduce misunderstandings, it can clarify differences of opinion among New Mechanists and it helps to define a research agenda for New Mechanists. (shrink)

I provide a formally precise account of diachronic emergence of properties as described within scientific theories, extending a recent account of synchronic emergence using similarity structure on the theories’ models. This similarity structure approach to emergent properties unifies the synchronic and diachronic types by revealing that they only differ in how they delineate the domains of application of theories. This allows it to apply also to cases where the synchronic/diachronic distinction is unclear, such as spacetime emergence from theories of quantum (...) gravity. In addition, I discuss two further case studies—finite periodicity in van der Pol oscillators and two-dimensional quasiparticles in the fractional quantum Hall effect—to facilitate comparison of this approach to others in the literature on concepts of emergence applicable to the sciences. My discussion of the fractional quantum Hall effect in particular may be of independent interest to philosophers of physics concerned with its interpretation. (shrink)