Andrew Bollhagen

This article offers a novel take on what philosophers have called problems of “practical underdetermination” in order to identify a form of creative epistemic agency operative in the means by which researchers cope with such problems. In developing my analysis, I contrast my “experimental dead-space” (EDS) formulation of practical underdetermination with the more standard “epistemic gap” formulation. Drawing on prior work, I embed the idea of an EDS within a broader unit of analysis—a “research platform”—and identify an experimental dead-space with what I call, borrowing terms from Stuart Kauffman, an “epistemic adjacent possible.” This enables me to characterize the form of creativity I have in mind. Finally, I revisit the case study for which I originally formulated the idea of an EDS in order to show how my expanded analysis enables us to appreciate how research platforms in experimental science can creatively develop in genuinely novel, “unprestatable” ways.

This paper analyzes an episode of scientific work that was prompted by observations of a novel defect in early embryonic development, which was unexpectedly induced in an experimental context and has tentatively been dubbed “xenogastrulation.” The researchers worked to individuate this as a novel phenomenon—both by distinguishing it from what it is not (e.g., exogastrulation) and by forming a positive conception of what it is—in order to facilitate further inquiry. Our analysis provides new insights into the role of explanatory reasoning in nascent experimental research programs. We argue that the researchers’ efforts to individuate the novel phenomenon were entangled with their efforts to explain it. By this, we mean that tentative answers to the individuative question, “what is it?” also served as tentative answers to the explanatory question, “by what means does it occur?” This case study therefore demonstrates that explanation need not wait until an explanandum has been clearly individuated but instead can be deeply entangled with the process of individuating the explanandum in the first place.

Autoinhibition is a design principle realized in many molecular mechanisms in biology. After explicating the notion of a design principle and showing that autoinhibition is such a principle, we focus on how researchers discovered instances of autoinhibition, using research establishing the autoinhibition of the molecular motors kinesin and dynein as our case study. Research on kinesin and dynein began in the fashion described in accounts of mechanistic explanation but, once the mechanisms had been discovered, researchers discovered that they exhibited a second phenomenon, autoinhibition. The discovery of autoinhibition not only reverses the pattern in terms of which philosophers have understood mechanism discovery but runs counter to the one phenomenon-one mechanism principle assumed to relate mechanisms and the phenomena they explain. The ubiquity of autoinhibition as a design principle, therefore, necessitates a philosophical understanding of mechanisms that recognizes how they can participate in more than one phenomenon. Since mechanisms with this design are released from autoinhibition only when they are acted on by control mechanisms, we advance a revised account of mechanisms that accommodates attribution of multiple phenomena to the same mechanism and distinguishes them from other processes that control them.

Unless one embraces activities as foundational, understanding activities in mechanisms requires an account of the means by which entities in biological mechanisms engage in their activities—an account that does not merely explain activities in terms of more basic entities and activities. Recent biological research on molecular motors exemplifies such an account, one that explains activities in terms of free energy and constraints. After describing the characteristic “stepping” activities of these molecules and mapping the stages of those steps onto the stages of the motors’ hydrolytic cycles, researchers pieced together from images of the molecules in different hydrolyzation states accounts of how the chemical energy in ATP is transformed in the constrained environments of the motors into the characteristic activities of the motors. We argue that New Mechanism’s standard set of analytic categories—entities, activities, and organization—should be expanded to include constraints and energetics. Not only is such an expansion required descriptively to capture research on molecular motors but, more importantly from a philosophical point of view, it enables a non-regressive account of activities in mechanisms. In other words, this expansion enables a philosophical account of mechanistic explanation that avoids a regress of entities and activities “all the way down.” Rather, mechanistic explanation bottoms out in constraints and energetics.

The paper takes a novel approach to a classic problem—Hempel’s Raven Paradox. A standard approach to it supposes the solution to consist in bringing our inductive logic into “reflective equilibrium” with our intuitive judgements about which inductive inferences we should license. This approach leaves the intuitions as a kind of black box and takes it on faith that, whatever the structure of the intuitions inside that box might be, it is one for which we can construct an isomorphic formal edifice, a system of inductive logic. By popping open the box we can see whether that faith is misplaced. I aim, therefore, to characterize our pre-theoretical, intuitive understanding of generalizations like “ravens are black” and argue that, intuitively, we take them to mean, for instance: “ravens are black by some indeterminate yet characteristic means.” I motivate and explicate this formulation and bring it to bear on Hempel’s Problem.

New Mechanist philosophical models of "phenomenon reconstitution" understand the process to be driven by explanatory considerations. Here I discuss an episode of phenomenon reconstitution that occurred entirely within an experimental program dedicated to characterizing the phenomenon of kinesin motility. Rather than being driven by explanatory considerations, as standard mechanist views maintain, I argue that the phenomenon of kinesin motility was reconstituted to enhance researchers’ primary experimental tool—the single molecule motility assay.