Phylogenetic models traditionally represent the history of life as having a strictly-branching tree structure. However, it is becoming increasingly clear that the history of life is often not strictly-branching; lateral gene transfer, endosymbiosis, and hybridization, for example, can all produce lateral branching events. There is thus motivation to allow phylogenetic models to have a reticulate structure. One proposal involves the reconciliation of genealogical discordance. Briefly, this method uses patterns of disagreement – discordance – between trees of different genes to add (...) lateral branching events to phylogenetic trees of taxa, and to estimate the most likely cause of these events. I use this practice to argue for: (1) a need for expanded accounts of multiple-models idealization, (2) a distinction between automatic and manual de-idealization, and (3) recognition that idealization may serve the meso-level aims of science in a different way than hitherto acknowledged. (shrink)

Discussions on the status of definitions of life have long been dominated by a position known as definitional pessimism. Per the definitional pessimist, there is no point in trying to define life. This claim is defended in different ways, but one of the shared assumptions of all definitional pessimists is that our attempts to define life are attempts to provide a list of all necessary and sufficient conditions for something to count as alive. In other words, a definition of life (...) is a strict, descriptive definition. Against this, several pragmatic alternatives have been put forward. On these pragmatic accounts, definitions of life are not strictly, but rather loosely descriptive. Their purpose is not to be true, but to be useful to scientists by guiding scientific practice. More recently, this position has come under attack for not being able to explain how our attempts to define life are connected to scientific progress within the biological sciences. Here, I argue to the contrary by showing how pragmatic definitions of life can be, and in fact are, conducive to scientific progress. Additionally, I show how the pragmatic account of definitions of life can be brought to bear upon our normative discussions involving definitions of life. (shrink)

In earlier work, I criticized de Regt’s contextual theory of understanding, and advertised the advantages of my own, knowledge-based account. Using the early history of the standard model in particle physics as an illustration, I instead consider the benefits of unifying these two accounts of understanding. I argue that de Regt’s account substantially improves my own account of explanatory consideration, and that my account of explanatory comparison substantially improves upon his account of explanatory evaluation. De Regt and my apparent disagreement (...) about the so-called factivity of understanding is defused through a voluntaristic approach to the scientific realism debates. (shrink)