This essay considers how scholarly approaches to the development of molecular biology have too often narrowed the historical aperture to genes, overlooking the ways in which other objects and processes contributed to the molecularization of life. From structural and dynamic studies of biomolecules to cellular membranes and organelles to metabolism and nutrition, new work by historians, philosophers, and STS scholars of the life sciences has revitalized older issues, such as the relationship of life to matter, or of physicochemical inquiries to (...) biology. This scholarship points to a novel molecular vista that opens up a pluralist view of molecularizations in the twentieth century and considers their relevance to current science. (shrink)

This paper adds to the philosophical literature on mechanistic explanation by elaborating two related explanatory functions of idealisation in mechanistic models. The first function involves explaining the presence of structural/organizational features of mechanisms by reference to their role as difference-makers for performance requirements. The second involves tracking counterfactual dependency relations between features of mechanisms and features of mechanistic explanandum phenomena. To make these functions salient, we relate our discussion to an exemplar from systems biological research on the mechanism for countering (...) heat shock—the heat shock response system—in Escherichia coli bacteria. This research also reinforces a more general lesson: ontic constraint accounts in the literature on mechanistic explanation provide insufficiently informative normative appraisals of mechanistic models. We close by outlining an alternative view on the explanatory norms governing mechanistic representation. (shrink)

The usefulness of machine learning algorithms has led to their widespread adoption prior to the development of a conceptual framework for making sense of them. One common response to this situation is to say that machine learning suffers from a “black box problem.” That is, machine learning algorithms are “opaque” to human users, failing to be “interpretable” or “explicable” in terms that would render categorization procedures “understandable.” The purpose of this paper is to challenge the widespread agreement about the existence (...) and importance of a black box problem. The first section argues that “interpretability” and cognates lack precise meanings when applied to algorithms. This makes the concepts difficult to use when trying to solve the problems that have motivated the call for interpretability. Furthermore, since there is no adequate account of the concepts themselves, it is not possible to assess whether particular technical features supply formal definitions of those concepts. The second section argues that there are ways of being a responsible user of these algorithms that do not require interpretability. In many cases in which a black box problem is cited, interpretability is a means to a further end such as justification or non-discrimination. Since addressing these problems need not involve something that looks like an “interpretation” of an algorithm, the focus on interpretability artificially constrains the solution space by characterizing one possible solution as the problem itself. Where possible, discussion should be reformulated in terms of the ends of interpretability. (shrink)

We argue that mechanistic models elaborated by machine learning cannot be explanatory by discussing the relation between mechanistic models, explanation and the notion of intelligibility of models. We show that the ability of biologists to understand the model that they work with severely constrains their capacity of turning the model into an explanatory model. The more a mechanistic model is complex, the less explanatory it will be. Since machine learning increases its performances when more components are added, then it generates (...) models which are not intelligible, and hence not explanatory. (shrink)