1. What’s all this fuss about mechanisms? Phyllis McKay University of Kent

2. Our approach to mechanisms and the philosophy of causality

3. From science to metaphysics: our case studies We aim to study scientific use of mechanisms to work out what mechanisms are, and what they do. We aim for both depth and breadth: 1.Physics: gravitational wave emission 2.Biochemistry: protein synthesis 3.Evolutionary biology: natural selection 4.Psychology: theory of mind mechanism 5.Economics: perhaps the transmission mechanism

4. Protein synthesisNatural selection

5. Experimental work on protein synthesis The use of various technologies to investigate microstructure. –‘Fifty years have passed since the discovery of the structure of DNA. This event … expanded understanding of all events in the pathway from DNA to protein. … In many instances determining structure has uncovered intricate details of their biological function.’ (Whitford p310.) Bare discovery of the chemicals present – or absent. –Eg Zamecnik and Hoagaland’s work in 40s and 50s. Manipulation experiments. –eg Crick and Brenner’s work in 1961. Replicated, but not repeated extensively.

6. Franklin’s X-ray diffraction photograph of DNA

7. Confirmation of the existence of replication forks

8. Experimental work on natural selection Artificial selection experiments, including extensive repetition of the same trial: –Eg Clayton and Roberton’s 1957 work on Drosophila. How-possibly constructions using simulations: –Eg Ridley on the eye; Bell on metabolism. Manipulation experiments: –Eg extensive work on clutch size in birds. Not uninterested in structure. Unexpected, non-replicable results common.

9. Conclusions on mechanisms to date

10. One important aim of science to use mechanisms in decompositional causal explanation to explain, in detail how a lower-level mechanism produces a higher-level phenomenon. They are characteristically: 1.Hierarchically nested 2.Functionally individuated In terms of the phenomenon produced and explained. 3.Real Entities that exist in the world that produce phenomena for the most part independently of how we describe them or of whether we even observe them. Note that independence comes in degrees: consider social and psychological mechanisms.

11. 4.Local Broadly nearby in space and time –Protein synthesis happens in the cell where proteins are produced. –Natural selection happens in the population which undergoes evolutionary change. –Psychological mechanisms involving content-bearing states may be a problem. Indexed to the phenomenon produced –Emission of gravitational waves versus social mechanisms. Note decompositional not etiological explanation NOT –a claim about intrinsicality imported from metaphysics –a locality claim imported from physics.

12. 5.Modular Might mean different things One phenomenon one mechanism – implausible. One mechanism one phenomenon – implausible. One section of the mechanism can be changed with no significant change to the rest of the mechanism. Comes in degrees. Possibly relative to a level of description in a mechanistic hierarchy. May be modular under a narrow range of conditions only. Required for success in this kind of scientific understanding and explanation. Allows sections of mechanisms to be isolated and understood to a certain extent in isolation from the other sections of the mechanism.

13. Philosophical questions about mechanisms

14. Methodology of science Explanation – how does mechanistic explanation work, and what are the similarities and differences in different disciplines? Beyond explanation – how, if at all, are mechanisms involved in prediction and control? Causal inference – how do mechanisms add to dependency relations in causal inference? Modularity and decomposition – how are we to understand it? Are associated practices analogous? For example, what is the relation between diagrams and DAGs?

16. Metaphysics of science Causation: How are mechanisms related to causation? Notice source of counterexamples to theories of causation. –Scientists see mechanistic explanation as causal explanation. Odd if there is no relation between mechanism and causation –Link to causal inference. Active versus passive metaphysics Want answers to these questions that cohere with the answers to the methodological questions.

17. What scientists say about their work ‘The main purpose of evolutionary biology is to provide a rational explanation for the extraordinarily complex and intricate organization of living things. To explain means to identify a mechanism that causes evolution and to demonstrate the consequences of its operation.’ (Bell 1997 and 2008 p1, emphasis added.) ‘Uncovering the cellular mechanisms resulting in sequential transfer of information from DNA (our genes) to RNA and then to protein represents one of major achievements of biochemistry in the 20th century.’ (Whitford p247, emphasis added.)

18. Metaphysics of science Causation: How are mechanisms related to causation? Notice source of counterexamples to theories of causation. –Scientists see mechanistic explanation as causal explanation. Odd if there is no relation between mechanism and causation –Link to causal inference. Active versus passive metaphysics Want answers to these questions that cohere with the answers to the methodological questions.

19. Machamer, Darden and Craver

20. Two senses of Explanation 1.Epistemic: a human practice, aimed at increasing understanding of the world. Often involves the passing of information between people. Highly sensitive to the cognitive abilities and background knowledge of those improving, receiving and giving the information. Description of mechanism does the explaining. 2.Physical: mechanisms produce or are responsible for their phenomena. Independent of whether human beings understand or even observe them. Mechanism itself does the explaining. The distinction is made in the literature (explicitly in Craver 2007). Not always carefully maintained.

21. MDC claim Machamer, Darden and Craver: ‘Mechanisms are entities and activities organized such that they are productive of regular changes from start or set-up to finish or termination conditions.’ (p3.) Entities: they list ‘cell membrane, vesicles, microtubules, molecules, and ions.’ (p8.) Activities: they list ‘biosynthesis, transport, depolarization, insertion, storage, recycling, priming, diffusion, and modulation.’ (p8.) They add both that ‘Activities are the producers of change,’ (p3) and that, ‘Activities are types of causes.’ (p6.) Activity-Entity Dualism: They say that activities and entities are ontologically on a par. They argue against both substantivalists, who would reduce activity talk to talk of entities and their properties, and process ontologists, who would reduce entity talk to talk only of activities.

22. MDC issues The activity-entity dualism. –Activities crucial to their conception of causation in mechanisms, and to many other features of mechanisms. –Activities give you the intelligibility crucial for epistemic explanation. Note (p3) ‘Productive continuities are what make the connections between stages intelligible.’ Regularity: –‘Mechanisms are regular in that they work always or for the most part in the same way under the same conditions. The regularity is exhibited in the typical way that the mechanism runs from beginning to end; what makes it regular is the productive continuity between stages.’ (p3) –Sometimes regularity can be described by a law, sometimes not. –NOT mean produces phenomenon more than 50% or anything so crude.

23. MDC issues Productive continuity Functional individuation: –Note only partial. –MDC say the function of a mechanism is its role in a higher-level mechanism. –Potential topping-out problem Change: –homeostatic mechanisms exist to keep a system in a stable state. Set up and termination conditions: –Epistemic: features of a description of a mechanism, maybe not of the mechanism itself. Bottoming-out: –Also looks epistemic.

24. Extra comparative stuff

25. Protein synthesis and natural selection: a fair comparison Mechanisms and their sub-mechanisms are partially individuated in terms of their functions. –Protein synthesis is the mechanism for decoding DNA to produce proteins. –Natural selection is the mechanism for adaptation. Components in protein synthesis (objects, their structures, and sub-mechanisms) are also partially functionally individuated. For natural selection to be a decompositional mechanism and yield the same kind of explanation of its phenomenon we are looking for functionally individuated components – NOT barely physically similar components.

26. Function and explanation in protein synthesis ‘In addition to the promoter-like elements, the Xenopus intergenic spacer contains repetitive short sequences, the 60/81 bp elements, that are clustered in tandem (Fig. 9.10) and which stimulate transcription when placed at a variable distance from the promoter and when placed in either orientation…. They are thus analogous in their activity, but perhaps not in their mechanism, to the enhancers of RNA polymerase II …’ (Adams et al. p361.) The obsession with structure in protein synthesis exists because in this field, structure is most often a good guide to function. –Note aminoacyl-tRNA synthetases example of an exception.

27. Protein synthesis and natural selection: a fair comparison Mechanisms and their sub-mechanisms are partially individuated in terms of their functions. –Protein synthesis is the mechanism for decoding DNA to produce proteins. –Natural selection is the mechanism for adaptation. Components in protein synthesis (objects, their structures, and sub-mechanisms) are also partially functionally individuated. For natural selection to be a decompositional mechanism and yield the same kind of explanation of its phenomenon we are looking for functionally individuated components – NOT barely physically similar components.

28. The components of natural selection are also functionally individuated First division: directional selection, stabilizing selection, disruptive selection. Second division in directional selection: sorting, recombination, both sorting and recombination. Third division in recombination: structure of DNA and morphogenesis crucial. Consider gene linkage, epistasis and pleiotropy. Dozens of well-understood sub-mechanisms in the field. Population structure the kind of structure functionally relevant in this field. At its lowest levels, evolutionary biology collides with biochemistry in, for example, meiosis or autoselection.