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.

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 9 we present and defend a causal account of multilevel mechanistic explanation by examining various case studies from biology. We argue that two key consequences of Causal Mechanism are (1) that levels and mechanisms are distinct notions and (2) that levels of multilevel explanations are levels of composition. This view is in stark contrast to Craver’s account, according to which levels in multilevel explanations are levels of mechanisms and multilevel explanations are instances of constitutive explanations. A key claim of the chapter is that whatever contributes to the phenomenon is part of the same pathway; but causal pathways can contain entities from multiple levels of composition. In order to motivate and illustrate our view, we use various examples from biology and medicine. We criticise some common views associated with the picture of a hierarchy of mechanistic levels and argue that our view allows for causation at higher levels.

Chapter 3 elucidates the link between national structures and foreign aid delivery. To that end, the chapter traces how national aid organizations vary in their bureaucratic structures and practices and how this variation maps onto my binary donor typology of neoliberal and traditional public sector donors. By tracing the link between particular institutional environments and aid delivery decisions, the chapter shows how bureaucratic structures and practices influence priorities of aid officials and authorize, enable, and justify particular delivery tactics and donor–recipient interactions, while precluding others. That is, I lay out why and how institutions of different ideological orientation constrain donor officials differently, and how they influence aid officials' decision-making.

It significantly strengthens the inferences drawn based on QCA results if we connect these results to theoretical knowledge and within-case evidence before, during, and after the analysis. In this chapter, we discuss two prominent tools of doing so after the analytic moment – set-theoretic theory evaluation and set-theoretic multi-method research (SMMR) – and demonstrate their implementation within R. Theory evaluation is a form of re-assessing theoretical hunches based on the results generated by QCA. While it can also be used for the identification of interesting cases for follow-up case studies, this task is better achieved with set-theoretic multi-method research. The latter is a tool for identifying typical and deviant cases for comparative or single within-case analysis.

Learning goals:

- Basic understanding of what theory-evaluation and set-theoretic multimethod research are.

- Familiarity with how to apply formal set-theoretic theory evaluation for re-assessing theoretical hunches based on the results generated by QCA.

- Familiarity with how to use set-theoretic multi-method research (SMMR) for the identification of cases for follow-up case studies after QCA.

- Ability to implement theory evaluation and SMMR in R.

Mediation analysis has been called \harder than it looks" (Bullock and Ha 2011) due to difficulties of experimental identification. However, recent work has clarified that, while hard, some experimental designs for mediation can be informative. Other recent work has provided “easier” substitutes for mediation analysis. This chapter has two goals. First, to summarize some of the findings published since Bullock and Ha (2011) and to consider the implications these findings have for mediation analysis. Second, to consider the situations in which a close alternative to mediation analysis would be useful (either as a supplement or a substitute). Such situations often depend on the motivation for the analysis.