The new research program to understand mechanisms in biology has developed rapidly in the last 10 years. Reconsideration of the characterization of mechanisms in biology in the light of this recent work is now in order. This article discusses the perspectival aspect of the characterization of mechanisms (and ways of mitigating rampant perspectivalism), refinements in claims about working entities and kinds of activities, challenges and responses to claims about regularity, productive continuity, and the organizational aspects of a mechanism, and issues about representations of mechanisms in schemas and sketches.

Chemists take mechanisms to be an important way of explaining chemical change. I examine the usefulness of the mechanism approach in the recent philosophical literature in explicating the explanatory use of mechanisms by organic chemists. I argue that chemists consider a mechanism to be explanatory because it accounts for the “dynamic process of bringing about” (Tabery 2004, 10) chemical change. For chemists, mechanisms are causal explanations based on interventions that show “how some possibilities depend on others” (Woodward 2003, 375). Only possibilities are achievable because chemists face a number of challenges when they explain by means of a mechanism.

Cognitive psychologists, like biologists, frequently describe mechanisms when explaining phenomena. Unlike biologists, who can often trace material transformations to identify operations, psychologists face a more daunting task in identifying operations that transform information. Behavior provides little guidance as to the nature of the operations involved. While not itself revealing the operations, identification of brain areas involved in psychological mechanisms can help constrain attempts to characterize the operations. In current memory research, evidence that the same brain areas are involved in what are often taken to be different memory phenomena or in other cognitive phenomena is playing such a heuristic function.

This article examines the role of experimental generalizations and physical laws in neuroscientific explanations, using Hodgkin and Huxley's electrophysiological model from 1952 as a test case. I show that the fact that the model was partly fitted to experimental data did not affect its explanatory status, nor did the false mechanistic assumptions made by Hodgkin and Huxley. The model satisfies two important criteria of explanatory status: it contains invariant generalizations and it is modular (both in James Woodward's sense). Further, I argue that there is a sense in which the explanatory heteronomy thesis holds true for this case.

This article considers claims that biology should seek general theories similar to those found in physics but argues for an alternative framework for biological theories as collections of prototypical interlevel models that can be extrapolated by analogy to different organisms. This position is exemplified in the development of the Hodgkin-Huxley giant squid model for action potentials, which uses equations in specialized ways. This model is viewed as an “emergent unifier.” Such unifiers, which require various simplifications, involve the types of heuristics discussed in Wimsatt's writings on reduction, but with a twist. Here, the heuristics are used to generate emergent rather than reductive explanations.

Hodgkin and Huxley's model of the action potential is an apparent dream case of covering-law explanation in biology. The model includes laws of physics and chemistry that, coupled with details about antecedent and background conditions, can be used to derive features of the action potential. Hodgkin and Huxley insist that their model is not an explanation. This suggests either that subsuming a phenomenon under physical laws is insufficient to explain it or that Hodgkin and Huxley were wrong. I defend Hodgkin and Huxley against Weber's heteronomy thesis and argue that explanations are descriptions of mechanisms.

I claim that the Hodgkin-Huxley (HH) current equations owe a great deal of their importance to their role in bringing results from experiments on squid giant action preparations to bear on the study of the action potential in other neurons in other in vitro and in vivo environments. I consider ideas from Weber and Craver about the role of Coulomb's and other fundamental equations in explaining the action potential and in HH's development of their equations. Also, I offer an embellishment to Schaffner's emergent unifier conception of the HH model.