We characterize a type of functional explanation that addresses why a homologous trait originating deep in the evolutionary history of a group remains widespread and largely unchanged across the group’s lineages. We argue that biologists regularly provide this type of explanation when they attribute conserved functions to phenotypic and genetic traits. The concept of conserved function applies broadly to many biological domains, and we illustrate its importance using examples of molecular sequence alignments at the intersection of evolution and cell biology. (...) We use these examples to show how the study of conserved functions can integrate knowledge of a trait’s causal effects on fitness and its history of natural selection without invoking adaptation. We also show how conserved function provides a novel basis for addressing objections against evolutionary functions raised by Robert Cummins. (shrink)

In this paper, I introduce the notion of ‘philosophy moves’: prominent tropes featured in contemporary academic philosophy. Moves are more than patterns – they are tools for advancing and enriching philosophical debates. By recognizing these patterns in the philosophical literature, we collect an ensemble of moves for deployment in novel contexts, each with the potential to forge new paths of philosophical investigation through a given topic. The moves featured in this paper are constructive and progressive, with the potential to push (...) past stalemates and open up a wider conceptual landscape. Following a presentation of five exemplars taken from the philosophy of biology literature, I show how different moves could be made within a current interdisciplinary debate. Overall, I aim to demonstrate that recognizing these patterns is insightful pedagogically and potentially useful when put to use as part of one’s philosophical methodology. (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)

Mechanisms, in the prominent biological sense of the term, are historical entities. That is, whether or not something is a mechanism for something depends on its history. Put differently, while your spontaneously-generated molecule-for-molecule double has a heart, and its heart pumps blood around its body, its heart does not have a mechanism for pumping, since it does not have the right history. My argument for this claim is that mechanisms have proper functions; proper functions are historical entities; so, mechanisms are (...) historical entities, too. This thesis runs against the mainstream new mechanist way of thinking about mechanisms, where mechanisms are generally thought of in an ahistorical way. After arguing for this thesis, I draw out some consequences for philosophy of science and metaphysics. (shrink)

Philosophers who study the problem of biological function often begin their deliberations by reflecting on the functions of parts of animals, or the behavior of animals. Applying theories of biological function to unconventional or borderline cases can help us to better evaluate and refine those theories. This is the case when we consider whether parts of transposable elements —bits of “selfish” DNA that move about within a host genome—have functions of their own, that is, whether the parts of TEs have (...) the function of helping the TE move about within the genome. Here I argue that whether or not the parts of TEs have functions depends crucially on whether collections of TEs form “populations,” by which I mean, here, a group of individuals of the same type that impact one another’s chances of persistence or multiplication, by impacting one another’s access to a shared resource. I think there is suggestive, but not conclusive, evidence that some TEs have functions of their own. Considering the problem of TE functionality, then, has value both for philosophy and for biology. (shrink)