Chapter 10 picks up the various threads and defends the main thesis of the book (Methodological Mechanism), namely, the claim that to be committed to mechanism is to adopt a certain methodological postulate, that is, to look for causal pathways for the phenomena of interest. We compare our view of Methodological Mechanism with an important discussion by Joseph Henry Woodger concerning the meaning of mechanism, which has been ignored in current discussions, as well as with the views of Robert Brandon. We then formulate a dilemma that new mechanists face, which arises from the unstable combination of two main tenets of New Mechanism, an ontological and a methodological, both of which depend on the general characterisation of mechanism but that pull in opposite directions. We argue that Causal Mechanism is able to resolve the dilemma, by providing the best defence of the methodological tenet of New Mechanism, while at the same time preventing the adoption of a robust version of the ontological tenet.

In the Finale we examine to what extent Causal Mechanism can be seen as a descendant of the original notion of mechanism developed in seventeenth century, by examining possible extensions of the seventeenth-century notion of mechanism and discussing whether they can be used to characterise mechanism as a concept-in-use. We identify two conditions that a biological explanation has to satisfy in order to count as mechanistic, both of which were central in Old Mechanism: the condition of intelligibility and the condition of the priority of the parts over the whole. We use these two conditions to distinguish between two notions of mechanism: a more narrow one that incorporates both the intelligibility condition and the condition of the priority of the parts and a broader one that incorporates only the intelligibility condition and is thus a weakened form of mechanism. We claim that an account of mechanism as a concept-in-use requires the weakened notion, which when viewed in terms of Causal Mechanism has nevertheless enough content so that it can be seen as a descendant of the original concept.

In Chapter 4 we build on the discussion in Chapter 3 in order to argue that understanding mechanisms in the Causal Mechanism sense is all that is needed in order to understand biological practice. We clarify the main commitments of our view by presenting three theses that together constitute Causal Mechanism: (1) Mechanisms are to be identified with causal pathways; (2) causal relations among the components of a pathway are to be viewed in terms of difference-making; and (3) Causal Mechanism is metaphysically agnostic. A key point is that, in contrast to mechanistic theories of causation, for Causal Mechanism causation as difference-making is conceptually prior to the notion of a mechanism. We examine in some detail the discovery of the mechanism of scurvy in order to argue that difference-making is what matters in practice. We then turn to the main inflationary accounts of mechanism and contrast them with our deflationary view and its metaphysical agnosticism. We argue that Causal Mechanism offers a general characterisation of mechanism as a concept-in-use in the life sciences that is deflationary and thin, but still methodologically important.

Chapter 1 examines the relationship between Old and New Mechanism and uses it to illuminate the relations between metaphysical and methodological conceptions of mechanism. This historical examination will directly motivate our new deflationary account of mechanism developed in the subsequent chapters. We start by focusing on the role of mechanistic explanation in seventeenth-century scientific practice, by discussing the views of René Descartes, Christiaan Huygens, Gottfried Wilhelm Leibniz and Robert Boyle, and the attempted mechanical explanations of gravity by Descartes and Ηuygens. We thereby illustrate how the metaphysics of Old Mechanism constrained scientific explanation. We then turn our attention to Isaac Newton’s critique of mechanism. The key point is that Newton introduced a new methodology that freed scientific explanation from the metaphysical constraints of the older mechanical philosophy. Last, we draw analogies between Newton’s critique of Old Mechanism and our critique of New Mechanism. The main point is that causal explanation in the sciences is legitimate even if we bracket the issue of the metaphysics of mechanisms.

The Introduction recounts the main aspects of the recent revival of the mechanical philosophy and outlines the main theses of the book (i.e., Causal Mechanism and Methodological Mechanism). It presents briefly the case for understanding mechanism as a methodological concept, introduces the main concepts and distinctions that will be discussed in the book, provides an outline of the central arguments and presents a summary of the chapters.

In Chapter 3 we present the first main part of our case for Causal Mechanism, by discussing in detail apoptosis, a central biological mechanism. We examine how John Kerr and his co-workers first introduced apoptosis in 1972. We then present the most important stages in scientific research regarding apoptosis during the last decades that led to its identification as a central biological mechanism, explaining the shift from morphological descriptions to biochemical descriptions of the mechanism. We generalise the molecular definition of a pathway to arrive at a more general notion of a causal pathway. We also show that several distinctions used by biologists in order to differentiate between causal pathways and identify the genuine biological mechanisms (active vs passive, programmed vs non-programmed, physiological vs accidental) do not correspond to internal features of causal pathways, but concern an external feature, that is, the role those processes play within the organism.

In Chapter 8 we examine Carl Craver’s well-known account of constitutive mechanisms, which takes the organised entities and activities that are the components of the mechanism to constitute the phenomenon to be explained. The main aim of the chapter is to criticise the adequacy of this view for illuminating mechanism as a concept-in-use in biological practice. We identify two main problems for the constitutive view: the problem of external components and the fact that some mechanisms can exist outside the entity the behaviour of which they underlie; we argue that both problems undermine the usefulness and appropriateness of viewing typical and paradigmatic cases of biological mechanisms in constitutive terms. The main claim of the chapter is that in order to understand the notion of mechanism as a concept-in-use, there is no need to posit a non-causal relation of constitution.

In Chapter 6, we defend the difference-making thesis of Causal Mechanism, that is, the view that mechanisms are underpinned by networks of difference-making relations, by showing that difference-making is more fundamental than production in understanding mechanistic causation. Our argument is two-fold. First, we criticise Stuart Glennan’s claim that mechanisms can be viewed as the truth-makers of counterfactuals and argue that counterfactuals should be viewed as metaphysically more fundamental. Second, we argue against the view that the productivity of mechanisms requires thinking of them as involving activities, qua a different ontic category. We criticise two different routes to activities: Glennan’s top-down approach and Phyllis Illari and Jon Williamson’s bottom-up approach. Given these difficulties with activities and mechanistic production, it seems more promising to start with difference-making and give an account of mechanisms in terms of it.

In Chapter 5, we examine the relation between mechanisms and laws/counterfactuals by revisiting the main notions of mechanism found in the literature. We distinguish between two different conceptions of ‘mechanism’: mechanisms-of and mechanisms-for. We argue that for both mechanisms-of and mechanisms-for, counterfactuals and laws are central for understanding within-mechanism interactions. Concerning mechanisms-for, we claim that the existence of irregular mechanisms is compatible with the view that mechanisms operate according to laws. The discussion in this chapter, then, points to an asymmetrical dependence between mechanisms and laws/counterfactuals: while some laws and counterfactuals must be taken as primitive (non-mechanistic) facts of the world, all mechanisms depend on laws/counterfactuals.

Given the centrality of counterfactual difference-making relations to the argument of the book, in Chapter 7 we say a few more things about contrary-to-fact conditionals. We offer a primer on the logic and the semantics of counterfactuals, focusing on the two main schools of thought: the metalinguistic and the possible-worlds approach. We also present and examine James Woodward’s interventionist counterfactuals and the Rubin-Holland model. We argue that the counterfactual approach is more basic than the mechanistic, but information about mechanisms can help sort out some of the methodological problems faced by the counterfactual account.