Research

Abstract: Positively misleading errors are errors of statistical reasoning in which adding data to an analysis will systematically and reliably strengthen support for an erroneous hypothesis over a correct one.  This pattern distinguishes them from other errors of statistical inference and pattern recognition.  Here I provide a general account of positively misleading errors by describing an exemplar case from biology along with a candidate case from clinical medicine.  Though well known in biology (phylogenetic systematics, to be precise), positively misleading errors are likely more widespread and deserve to be brought to the attention of the wider research community.  This will facilitate a better understanding of them and sharpen our ability to assess statistical and probabilistic methods, providing resources for researchers to more effectively identify, diagnose, and dislodge these errors of statistical inference.  This reflects the way we have gained a better understanding of scientific reasoning from studying other errors of statistical and probabilistic reasoning.

Abstract: We are currently in the midst of what I call biology’s Einstein moment. This is the rejection of absolute biological history, the idea that there is an invariant, privileged biological history against which other histories are measured or deviate from. Instead, biologists must specify theoretically and empirically motivated frames of lineal reference. This is already informing and advancing biological practice, theory, methods, and more, and is a significant and important feature of contemporary biology. Here I argue that it is worth identifying and naming this shift, and encouraging a deeper and broader embrace of it.

Abstract: There is an "under-representation problem” in philosophy departments and journals. Empirical data suggest that while we have seen some improvements since the 1990s, the rate of change has slowed down. Some posit that philosophy has disciplinary norms making it uniquely resistant to change. We present results from an empirical case study of a philosophy department that achieved and maintained male-female gender parity among its faculty as early as 2014. Our analysis extends beyond matters of gender parity because that is only one, albeit important, dimension of inclusion. We build from the study to reflect on strategies that may catalyze change.

Abstract: I spell out and update the individuality thesis, that species are individuals, and not classes, sets, or kinds. I offer three complementary presentations of this thesis. First, as a way of resolving an inconsistent triad about natural kinds; second, as a phylogenetic systematics theoretical perspective; and, finally, as a novel recursive account of an evolved character (individuality). These approaches do different sorts of work, serving different interests. Presenting them together produces a taxonomy of the debates over the thesis, and isolates ways it has been (and may continue to be) productive. This goes to the larger point of this paper: a defense of the individuality thesis in terms of its utility, and an update of it in light of recent theoretical developments and empirical work in biology.

Abstract: Biological lineages move through time, space, and each other. As they do, they diversify, diverge, and grade away from and into one another. One result of this is genealogical discordance; i.e., the lineages of a biological entity may have different histories. We see this on numerous levels, from microbial networks, to holobionts, to population-level lineages. This paper considers how genealogical discordance impacts our study of species. More specifically, I consider this in the context of three framing questions: (1) How, if at all, does genealogical discordance challenge, modify, or revise how we conceive of species? (2) How has growing appreciation of genealogical discordance impacted scientific practice? Of systematics in particular? (3) How do lineages at different levels diverge and diversify? All told, genealogical discordance enriches and complicates our taxonomic ontology, as well as the practice of reconstructing phylogenies. This presents both challenges and opportunities for the study of divergence and diversification.

Abstract: The relation among method, concept, and theory in science is complicated. I seek to shed light on that relation by considering an instance of it in systematics: the additional challenges phylogeneticists face when reconstructing phylogeny not at a single level but simultaneously at multiple levels of the hierarchy. How does this complicate the task of phylogenetic inference, and how might it inform and shape the conceptual foundations of phylogenetics? This offers a lens through which the interplay of method, theory, and concepts may be understood in systematics, which, in turn, provides data for a more general account.

Abstract: Type specimens are used to designate species. What is the nature of the relation between a type specimen and the species it designates? If species names are rigid designators, and type specimens ostensively define species, then that relation is, at the very least, a close one. Levine (Biol Philos 16(3):325–338, 2001) argues that the relationship of type specimen to a named species is one of necessity—and that this presents problems for the individuality thesis. Namely, it seems odd that a contingently selected specimen should belong to a species of necessity. In considering Levine’s argument, LaPorte (Biol Philos 18:583–588, 2003) suggests that recognizing the distinction between de re and de dicto necessity resolves Levine’s worries. I reconsider the motivating question: does a type specimen belong of necessity to the species that it designates? In light of taxonomic cases and practice the answer is clear: definitively not. This is particularly clear in the case of re-designation of types by taxonomic decree. I explain how this helps reveal how taxonomists prioritize competing (and sometimes conflicting) theoretical commitments, and offer a defense of the individuality thesis as applied to these particular cases. In short, I demonstrate how to misidentify a type specimen.

Abstract: Phylogenetics is the study of the evolutionary history and relationships among individuals, groups of organisms (e.g., populations, species, or higher taxa), or other biological entities with evolutionary histories (e.g., genes, biochemicals, or developmental mechanisms). Phylogenetic inference is the task of inferring this history, and as with other problems of inference, there are interesting and difficult questions regarding how these inferences are justified.

In this entry, we examine what phylogenetic inference is and how it works. In the first section, we briefly introduce the field of phylogenetics and its history. In section 2, we explore how phylogenetic inference provides useful problems for philosophers to examine, and where philosophical approaches have contributed to the scientific examination of phylogenetics. This will help display why phylogenetic inference is not merely a biological research problem, but a philosophical one as well. Finally in section 3, we will move to a discussion of some of the contemporary debates about foundational issues in phylogenetics, and what the future of phylogenetic inference looks like.

Abstract: Michael Ghiselin and David Hull’s individuality thesis is that biological species are individuals. Philosophers often treat the term “individual” as synonymous with “mereological sum” and characterize it in terms of mereology (an axiomatic system of parts and wholes analogous to set theory). It is easy to see how the biological project (that species are individuals) has been interpreted as a mereological one (that species are mereological sums). This chapter argues that this is a mistake, that biological part/whole relations often violate the axioms of mereology. Conflating these projects confuses the central issues at stake in both, and makes the job of evaluating either unnecessarily burdensome. Clarifying this helps identify the genuine metaphysical implications of the individuality thesis, which serves as an exemplar of scientifically informed metaphysics.