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)

The goal of this programmatic paper is to highlight a close connection between the core problem in the philosophy of medicine, i.e. the concept of health, and the core problem of the philosophy of mind, i.e. the concept of consciousness. I show when we look at these phenomena together, taking the evolutionary perspective of modern state-based behavioural and life-history theory used as the teleonomic tool to Darwinize the agent- and subject-side of organisms, we will be in a better position to (...) make sense of them both as natural phenomena. (shrink)

The idea that ambiguity can be productive in data science remains controversial. Efforts to make scientific publications and data intelligible to computers generally assume that accommodating multiple meanings for words, known as polysemy, undermines reasoning and communication. This assumption has nonetheless been contested by historians, philosophers, and social scientists, who have applied qualitative research methods to demonstrate the generative and strategic value of polysemy. Recent quantitative results from linguistics have also shown how polysemy can actually improve the efficiency of human (...) communication. I present a new conceptual typology based on a synthesis of prior research about the aims, norms, and circumstances under which polysemy arises and is evaluated. The typology supports a contextual pluralist view of polysemy’s value for scientific research practices: polysemy does both substantial positive and negative work in science, but its utility is context-sensitive in ways that are often overlooked by the norms people have formulated to regulate its use, including prior scholars researching polysemy. I also propose that historical patterns in the use of partial synonyms, i.e. terms with overlapping meanings, provide an especially promising phenomenon for integrative research addressing these issues. (shrink)

While philosophers of science have marginally discussed concepts such as ‘nutrient’, ‘naturalness’, ‘food’, or the ‘molecularization’ of nutrition, they have yet to seriously engage with the nutrition sciences. In this paper, I offer one way to begin this engagement by investigating conceptual challenges facing the burgeoning field of nutritional ecology and the question of how organisms construct a ‘balanced’ diet. To provide clarity, I propose the distinction between nutrient balance as a property of foods or dietary patterns and nutrient balancing (...) as an evolved capacity to regulate nutrient intake. This distinction raises conceptual and empirical issues, such as what properties constitute this capacity and whether they are the same in all organisms. Additionally, while scientists use the term ‘balancing’, its intension and extension need further clarification. Based on the literature, the properties of external nutrient detection, internal sensing of nutrient levels, and organismal regulation could provide a basic recipe for nutrient balancing. Next, using an evolutionary lens, I examine nutrient acquisition in some prokaryotes, slime molds, simple multicellular eukaryotes, and in the quirks of multicellular metabolism to raise questions about the origins and universality of balancing. Finally, I build on this explication of balance and balancing by considering how obesity and cancer might respectively elucidate problems of organismal nutrient imbalances versus disrupted cellular nutrient balancing. (shrink)

In recent years, the explanatory term “scaffold” has been gaining prominence in evolutionary biology. This notion has a long history in other areas, in particular, developmental psychology. In this paper, we connect these two traditions and identify a specific type of explanatory strategy shared between them, namely scaffolding explanations. We offer a new definition of “scaffold” anchored in the explanatory practices of evolutionary biologists and developmental psychologists that has yet to be clearly articulated. We conclude by offering a systematic overview (...) of the various dimensions of scaffolding explanations that further suggests both their usefulness and range of application. (shrink)

In this paper, I show how idealizations contribute to social activities in science, such as the recruitment of experts to a research project. These contributions have not been explicitly discussed by recent philosophical accounts of scientific idealization. These accounts have focused on how idealizations influence activities like scientific theorization, explanation, and modeling. Other accounts focus on how idealizations influence policy-making and science communication. I expand these accounts by exploring the uses of idealized phylogenetic trees in science. Trees are not only (...) useful for improving our understanding and public communication of evolutionary history, but they also help with the organization of laboratories and collaboration among scientists. Attending to the relation between idealizations and these social practices in science matters. It can help us understand why idealized models become entrenched and why certain social practices change over time. (shrink)

In recent philosophy of science there has been much discussion of both pluralism, which embraces scientific terms with multiple meanings, and eliminativism, which rejects such terms. Some recent work focuses on the conditions that legitimize pluralism over eliminativism – the conditions under which such terms are acceptable. Often, this is understood as a matter of encouraging effective communication – the danger of these terms is thought to be equivocation, while the advantage is thought to be the fulfilment of ‘bridging roles’ (...) that facilitate communication between different scientists and specialisms. These theories are geared towards regulating communication between scientists qua scientists. However, this overlooks an important class of harmful equivocation that involves miscommunication between scientists and nonscientists, such as the public or policymakers. To make my case, I use the example of theory of mind, also known as ‘mindreading’ and ‘mentalizing’, and broadly defined as the capacity to attribute mental states to oneself and others. I begin by showing that ‘theory of mind’ has multiple meanings, before showing that this has resulted in harmful equivocations of a sort and in a way not accounted for by previous theories of pluralism and eliminativism. (shrink)

Among those living systems, which are cognizers? Among the behaviours of, and causes of behaviour in, living systems, which are cognitive? Such questions sit at the heart of a sophisticated, ongoing debate, of which the recent papers by Corcoran et al. ( 2020 ) and Sims and Kiverstein ( 2021 ) serve as excellent examples. I argue that despite their virtues, both papers suffer from flawed conceptions of the point of the debate. This leaves their proposals ill-motivated—good answers to the (...) wrong question. Additionally, their proposals are unfit to serve the legitimate roles for characterizations of cognition. (shrink)