Cladism, Monophyly and Natural Kinds

Cladism, today the dominant school of systematics in biology, includes a classification component—the view that classification ought to reflect phylogeny only, such that all and only taxa are monophyletic (i.e. consist of an ancestor and all its descendants)—and a metaphysical component— the view that all and only real groups or kinds of organisms are monophyletic. For the most part these are seen as amounting to much the same thing, but I argue they can and should be distinguished, in particular that cladists about classification need not accept the typically cladist view about real groups or kinds. Cladists about classification can and should adopt an explanatory criterion for the reality of groups or kinds, on which being monophyletic is neither necessary nor sufficient for being real or natural. Thus the line of reasoning that has rightly led to cladism becoming dominant within systematics, and the attractive line of reasoning in the philosophical literature that advocates a more liberal approach to natural kinds, are seen to be, contrary to appearances, compatible

Pluralism, Realism and the Units of Selection

I consider two attempts to combine realism with pluralism about the units of selection: Sober and Wilson’s combination of “model” and “unit” pluralism, and Sterelny and Griffiths’ “local pluralism”. I argue that both of these attempts fail to show that realism and pluralism are compatible. Sober and Wilson’s pluralism turns out, on closer inspection, to be a kind of monism in disguise, while Sterelny and Griffiths’ local pluralism involves a combination of realism and anti-realism about interactors, and the units of selection, that is fundamentally unstable. My conclusion is that one must choose whether to be a realist or a pluralist in this area: one cannot be both. The question of which we should choose is a further question that I do not take a stand on

Conceptual Engineering and Conceptual Extension in Science

I argue that the Conceptual Ethics and Conceptual Engineering framework, in its pragmatist version as recently defended by Thomasson, provides a means of articulating and defending the conventionalist interpretation of projects of conceptual extension (e.g. the extended mind, the extended phenotype) in biology and psychology. This promises to be illuminating in both directions: it helps to make sense of, and provides an explicit methodology for, pragmatic conceptual extension in science, while offering further evidence for the value and fruitfulness of the Conceptual Ethics/Engineering framework itself, in particular with respect to conceptual change within science, which has thus-far received little attention in the literature on Conceptual Ethics/Engineering

A computational approach to linguistic knowledge

The rejection of behaviorism in the 1950s and 1960s led to the view, due mainly to Noam Chomsky, that language must be studied by looking at the mind and not just at behavior. It is an understatement to say that Chomskyan linguistics dominates the field. Despite being the overwhelming majority view, it has not gone unchallenged, and the challenges have focused on different aspects of the theory. What is almost universally accepted, however, is Chomsky’s view that understanding language demands a theory that posits mental states that represent rules of language. Call this claim, following Cowie (1999), Representationalism or (R). According to (R), ‘‘[e]xplaining language mastery and acquisition requires the postulation of contentful mental states and processes involving their manipulation’’ (Cowie, 1999, p. 154). Although (R) is nothing more than the general assumption on which cognitive psychology is founded applied to the case of language, even it has had its detractors. Critics have argued that linguistic competence should not in fact be thought of as based on the possession of a body of linguistic knowledge but should be thought of, rather, as a kind of skill. This is an important challenge because one might be inclined to think that no recognizable form of Chomskyan linguistics could withstand the falsification of (R). In this paper we attempt to show that in fact (R) could be false without doing much damage to Chomskyan linguistics at all. Indeed, it is possible that the Chomskyan position could be made more coherent by adopting the view we will sketch. Our claim, therefore, is that critics of (R) might be right, but that this does not obviously make them serious critics of the Chomskyan program

Multiple novel prostate cancer susceptibility signals identified by fine-mapping of known risk loci among Europeans

Genome-wide association studies (GWAS) have identified numerous common prostate cancer (PrCa) susceptibility loci. We have fine-mapped 64 GWAS regions known at the conclusion of the iCOGS study using large-scale genotyping and imputation in 25 723 PrCa cases and 26 274 controls of European ancestry. We detected evidence for multiple independent signals at 16 regions, 12 of which contained additional newly identified significant associations. A single signal comprising a spectrum of correlated variation was observed at 39 regions; 35 of which are now described by a novel more significantly associated lead SNP, while the originally reported variant remained as the lead SNP only in 4 regions. We also confirmed two association signals in Europeans that had been previously reported only in East-Asian GWAS. Based on statistical evidence and linkage disequilibrium (LD) structure, we have curated and narrowed down the list of the most likely candidate causal variants for each region. Functional annotation using data from ENCODE filtered for PrCa cell lines and eQTL analysis demonstrated significant enrichment for overlap with bio-features within this set. By incorporating the novel risk variants identified here alongside the refined data for existing association signals, we estimate that these loci now explain ∼38.9% of the familial relative risk of PrCa, an 8.9% improvement over the previously reported GWAS tag SNPs. This suggests that a significant fraction of the heritability of PrCa may have been hidden during the discovery phase of GWAS, in particular due to the presence of multiple independent signals within the same regio

Functionalism and structuralism as philosophical stances: van Fraassen meets the philosophy of biology

I consider the broad perspectives in biology known as 'functionalism' and 'structuralism', as well as a modern version of functionalism, 'adaptationism'. I do not take a position on which of these perspectives is preferable; my concern is with the prior question, how should they be understood? Adapting van Fraassen's argument for treating materialism as a stance, rather than a factual belief with propositional content, in the first part of the paper I offer an argument for construing functionalism and structuralism as stances also. The argument draws especially on Gould's (The structure of evolutionary theory. Harvard University Press, Cambridge, 2002) insights concerning functionalism and structuralism, in particular their apparent historical continuity from the pre-Darwinian period through to today. In the second part of the paper I consider Godfrey-Smith's distinction between empirical and explanatory adaptationism, and suggest that while the former is an empirical scientific hypothesis, the latter is closely related to the functionalist stance

What is a philosophical stance? Paradigms, policies and perspectives

Since van Fraassen first put forward the suggestive idea that many philosophical positions should be construed as 'stances' rather than factual beliefs, there have been various attempts to spell out precisely what a philosophical stance might be, and on what basis one should be adopted. In this paper I defend a particular account of stances, the view that they are pragmatically justified perspectives or ways of seeing the world, and compare it to some other accounts that have been offered. In Sect. 2 I consider van Fraassen's argument for construing empiricism as a stance, and look at some responses to it. In Sect. 3 I outline my conception of stances as perspectives or ways of seeing, and explain how stances so understood may be justified. I illustrate this conception by way of a discussion of the model pluralist position with respect to the units of selection debate in biology, and suggest that on the model pluralist view different perspectives on the units of selection, such as the gene's eye view, are in fact van Fraassian stances. In Sect. 4 I discuss the view put forward by Teller and Chakravartty among others that stances should be understood as epistemic policies, and argue that it is consistent with the conception of stances as perspectives. In the final section I criticise Rowbottom's attempt to assimilate stances to Kuhnian paradigms. I argue that he has overlooked some important disanalogies between stances and paradigms, so that the comparison obscures more than it reveals

Stances and Epistemology: Values, Pragmatics, and Rationality

Bas van Fraassen has argued that many philosophical positions should be understood as stances rather than factual beliefs. This paper discusses the vexed question of whether and how such stances can be rationally justified. It argues that stances may be justified pragmatically, in terms of both their epistemic fruits and their coherence with our values, both epistemic and non‐epistemic. It also examines van Fraassen's version of epistemological voluntarism, which has received considerable attention of late, and shows that it provides a theoretical framework, and approach to epistemology, within which the pragmatic and value‐based forms of justification appropriate to stance choice find a natural home

Gould on Species, Metaphysics and Macroevolution: A critical appraisal

Stephen Jay Gould's views on the ontology of species were an important plank of his revisionist program in evolutionary theory. In this paper I cast a critical eye over those views. I focus on three central aspects of Gould's views on species: the relation between the Darwinian and the metaphysical notions of individuality, the relation between the ontology of species and macroevolution, and the issue of contextualism and conventionalism about the metaphysics of species

Conceptual engineering and conceptual extension in science

I argue that the Conceptual Ethics and Conceptual Engineering framework, in its pragmatist version as recently defended by Thomasson (2017, 2020), provides a means of articulating and defending the conventionalist interpretation of projects of conceptual extension (e.g. the extended mind, the extended phenotype) in biology and psychology. This promises to be illuminating in both directions: it helps to make sense of, and provides an explicit methodology for, pragmatic conceptual extension in science, while offering further evidence for the value and fruitfulness of the conceptual ethics/engineering framework itself, in particular with respect to conceptual change within science, which has thus-far received little attention in the literature on conceptual ethics/engineering