In this paper, I argue that informational semantics, the most well-known and worked-out naturalistic account of intentional content, conflicts with a fundamental psychological principle about the conditions of belief-formation. Since this principle is an important premise in the argument for informational semantics, the upshot is that the view is self-contradictory??indeed, it turns out to be guilty of a sophisticated version of the fallacy famously committed by Euthyphro in the eponymous Platonic dialogue. Criticisms of naturalistic accounts of content typically proceed piecemeal (...) by narrowly constructed counterexamples, but I argue that the current result is more robust. It affects a broad family of accounts, and provokes a wider doubt about the possibility of successful execution of the naturalistic project. (shrink)

One of the fundamental research goals for explanation-based Natural Language Inference (NLI) is to build models that can reason in complex domains through the generation of natural language explanations. However, the methodologies to design and evaluate explanation-based inference models are still poorly informed by theoretical accounts on the nature of explanation. As an attempt to provide an epistemologically grounded characterisation for NLI, this paper focuses on the scientific domain, aiming to bridge the gap between theory and practice on the notion (...) of a scientific explanation. Specifically, the paper combines a detailed survey of the modern accounts of scientific explanation in Philosophy of Science with a systematic analysis of corpora of natural language explanations, clarifying the nature and function of explanatory arguments from both a top-down (categorical) and a bottom-up (corpus-based) perspective. Through a mixture of quantitative and qualitative methodologies, the presented study allows deriving the following main conclusions: (1) Explanations cannot be entirely characterised in terms of inductive or deductive arguments as their main function is to perform unification; (2) An explanation typically cites causes and mechanisms that are responsible for the occurrence of the event to be explained; (3) While natural language explanations possess an intrinsic causal-mechanistic nature, they are not limited to causes and mechanisms, also accounting for pragmatic elements such as definitions, properties and taxonomic relations; (4) Patterns of unification naturally emerge in corpora of explanations even if not intentionally modelled; (5) Unification is realised through a process of abstraction, whose function is to provide the inference mechanism for subsuming the event to be explained under recurring patterns and high-level regularities. The paper contributes to addressing a fundamental gap in classical theoretical accounts on the nature of scientific explanations and their materialisation as linguistic artefacts. This characterisation can support a more principled design and evaluation of explanation-based AI systems which can better interpret, process, and generate natural language explanations. (shrink)

Current orthodoxy takes representation to be essential to computation. However, a philosophical account of computation that does not appeal to representation would be useful, given the difficulties involved in successfully theorizing representation. Piccinini's recent mechanistic account of computation proposes to do just that: it couches computation in terms of what certain mechanisms do without requiring the manipulation or processing of representations whatsoever (Piccinini 2015). Most crucially, mechanisms must process medium-independent vehicles. There are two ways to understand what "medium-independence" means on (...) this account; however, on either understanding, the account fails. Either too many things end up being counted as computational, or purportedly natural computations (e.g., neural computations) cannot be counted at all. In the end, illustrating this failure sheds some light on the way to revise the orthodoxy in the hope of a better account of computation. (shrink)

This paper proposes an extended version of the interventionist account for causal inference in the practical context of biological mechanism research. This paper studies the details of biological mechanism researchers’ practices of assessing the evidential legitimacy of experimental data, arguing why quantity and variety are two important criteria for this assessment. Because of the nature of biological mechanism research, the epistemic values of these two criteria result from the independence both between the causation of data generation and the causation in (...) question and between different interventions, not techniques. The former independence ensures that the interventions in the causation in question are not affected by the causation that is responsible for data generation. The latter independence ensures the reliability of the final mechanisms not only in the empirical but also the formal aspects. This paper first explores how the researchers use quantity to check the effectiveness of interventions, where they at the same time determine the validity of the difference-making revealed by the results of interventions. Then, this paper draws a distinction between experimental interventions and experimental techniques, so that the reliability of mechanisms, as supported by the variety of evidence, can be safely ensured in the probabilistic sense. The latter process is where the researchers establish evidence of the mechanisms connecting the events of interest. By using case studies, this paper proposes to use ‘intervention’ as the fruitful connecting point of literature between evidence and mechanisms. (shrink)

In this paper, we adopt a physiological perspective in order to produce an intelligible overview of biological transmission in all its diversity. This allows us to put forward the analysis of transmission mechanisms, with the aim of complementing the usual focus on transmitted factors. We underline the importance of the structural, dynamical, and functional features of transmission mechanisms throughout organisms’ life cycles in order to answer to the question of what is passed on across generations, how and why. On this (...) basis, we propose a vision of biological transmission as networks of heterogeneous physiological mechanisms, not restricted to transmission mechanisms stricto sensu. They prove to be themselves suited candidates for evolutionary explanations. They are processes both necessary for evolution to happen and resulting themselves from evolution. This leads us to call for a strategy of endogenization to account for transmission, and more specifically inheritance, as evolved and evolving physiological mechanisms. (shrink)

Mechanistic approaches are very common in the causal interpretation of biological and neuroscientific experimental work in today’s philosophy of science. In the mechanistic literature a strict distinction is often made between causal relations and constitutive relations, where the latter cannot be causal. One of the typical reasons for this strict distinction is that constitutive relations are supposedly synchronic whereas most if not all causal relations are diachronic. This strict distinction gives rise to a number of problems, however. Our end goal (...) in this paper is to argue that it should be given up, at least in the context of the biological and the psychological sciences. To that effect, we argue that constitutive relations in this context are diachronic, thus undermining the aforementioned reason. We offer two cases from scientific practice in which constitutive relations are regarded as both diachronic and causally efficacious, review three existing ways of dealing with the apparent diachronic nature of interlevel relations in mechanisms and propose a new account of diachronic, causal constitutive relevance. (shrink)

A crucial question for a process view of life is how to identify a process and how to follow it through time. The genidentity view can contribute decisively to this project. It says that the identity through time of an entity X is given by a well-identified series of continuous states of affairs. Genidentity helps address the problem of diachronic identity in the living world. This chapter describes the centrality of the concept of genidentity for David Hull and proposes an (...) extension of Hull’s view to the ubiquitous phenomenon of symbiosis. Finally, using immunology as a key example, it shows that the genidentity view suggests that the main interest of a process approach is epistemological rather than ontological and that its principal claim is one of priority, namely that processes precede and define things, and not vice versa. (shrink)

This paper explores multiple experimental interventions in molecular biology. By “multiple,” we mean that molecular biologists often use different modes of experimental interventions in a series of experiments for one and the same subject. In performing such a series of experiment, scientists may use different modes of interventions to realize plural goals such as testing given hypotheses and exploring novel phenomena. In order to illustrate this claim, we develop a framework of multiple modes of experimental interventions to analyze a series (...) of experiments for a single subject. Our argument begins with a brief characterization of Craver and Darden’s taxonomy of experiments, because the taxonomy they have made implies various modes of interventions. We propose to extract two interventional directions and two interventional effects from their taxonomy as the basis of classification. The vertical or inter-level direction means that an intervention is performed between different levels of organization and the horizontal or inter-stage direction means that an intervention is performed between different stages of a mechanism. Interventions may produce an excitatory or an inhibitory effect. As a consequence, we can classify modes of interventions according to different directions and effects. We illustrate our claims by doing a case study of the PaJaMo experiment, which is a series of experiments for a single subject. The final goal in this paper is to provide a taxonomy of characteristics of experimentation in which the PaJaMo experiment is adequately located. (shrink)

Genetic explanation of complex human behavior presents an excellent test case for pluralism. Although philosophers agree that successful scientific investigation of behavior is pluralistic, there remains disagreement regarding integration and elimination—is the plurality of approaches here to stay, or merely a waystation on the road to monism? In this paper we introduce an issue taken very seriously by scientists yet mostly ignored by philosophers—the missing heritability problem—and assess its implications for disagreement among pluralists. We argue that the missing heritability problem, (...) which isn’t going anywhere any time soon, implies that pluralism in behavior genetics is both practically ineliminative and theoretically non-integrative. (shrink)

In contemporary philosophy of science, the consensus view seems to be that scientific explanations describe mechanisms responsible for the phenomena to be explained. Two kinds of explanatory relevance figure in mechanistic accounts of explanation: causal and constitutive. Following prominent accounts, it seems natural to analyze both these relations in terms of systematic interventions into some factor X with respect to another factor Y. However, such interventions are tailored to uncover causal relations only. Construing the constitutive relationship between parts and wholes (...) in terms of interventions thus raises metaphysical, conceptual, and epistemological questions. We here review the barriers that intervention-based inquiry into mechanisms encounters and consider some solutions. (shrink)

Multidisciplinary models aggregating ‘lower-level’ biological and ‘higher-level’ psychological and social determinants of a phenomenon raise a puzzle. How is the interaction between the physical, the psychological and the social conceptualized and explained? Using biopsychosocial models of pain as an illustration, I argue that these models are in fact level-neutral compilations of empirical findings about correlated and causally relevant factors, and as such they neither assume, nor entail a conceptual or ontological stratification into levels of description, explanation or reality. If inter-level (...) causation is deemed problematic or if debates about the superiority of a particular level of description or explanation arise, these issues are fueled by considerations other than empirical findings. (shrink)

Lack of clarity about underlying philosophical commitments leads to lack of clarity at other levels of analysis. Here I show that the literature on so-called “causal mechanisms” is rife with conceptual problems, stemming from insufficient rigor with respect to the metaphysics of causation.

This paper describes a pattern of explanation prevalent in the biological sciences that I call a ‘lineage explanation’. The aim of these explanations is to make plausible certain trajectories of change through phenotypic space. They do this by laying out a series of stages, where each stage shows how some mechanism worked, and the differences between each adjacent stage demonstrates how one mechanism, through minor modifications, could be changed into another. These explanations are important, for though it is widely accepted (...) that there is an ‘incremental constraint’ on evolutionary change, in an important class of cases it is difficult to see how to satisfy this constraint. I show that lineage explanations answer important questions about evolutionary change, but do so by demonstrating differences between individuals rather than invoking population processes, such as natural selection.1. Introduction2. Turning a ‘Scale’ into a ‘Plume’3. Lineage Explanations in Biology3.1. The evolution of eyes3.2. The evolution of feathers4. The Two Dimensions of a Lineage Explanation4.1. The production dimension4.2. The continuity dimension4.3. The dual role of the parts5. Constraining the Explanations6. Operational and Generative Lineages7. Explaining Change Without Populations8. Conclusion. (shrink)

Philosophical accounts of scientific explanation are broadly divided into ontic and epistemic views. This paper explores the idea that the lexical ambiguity of the verb to explain and its nominalisation supports an ontic conception of explanation (Salmon 1989; Craver 2007). I analyse one argument which challenges this strategy by criticising the claim that explanatory talk is lexically ambiguous (Wright, European Journal of Philosophy of Science 2(3), 375–394, 2012). I propose that the linguistic mechanism of transfer of meaning (Nunberg, Journal of (...) Semantics 12(2), 109–132, 1995) provides a better account of the lexical alternations that figure in the systematic polysemy of explanatory talk, and evaluate the implications of this proposal for the debate between ontic and epistemic conceptions of scientific explanation. (shrink)

The paper presents, and discusses, four candidate explanations of the structure, and construction, of the bees’ honeycomb. So far, philosophers have used one of these four explanations, based on the mathematical Honeycomb Conjecture, while the other three candidate explanations have been ignored. I use the four cases to resolve a dispute between Pincock and Baker about the Honeycomb Conjecture explanation. Finally, I find that the two explanations focusing on the construction mechanism are more promising than those focusing exclusively on the (...) resulting, optimal structure. The main reason for this is that optimal structures do not uniquely determine the relevant optimization leading to the optimal structure. (shrink)

Causal reasoning is one of our most central cognitive competencies, enabling us to adapt to our world. Causal knowledge allows us to predict future events, or diagnose the causes of observed facts. We plan actions and solve problems using knowledge about cause-effect relations. Without our ability to discover and empirically test causal theories, we would not have made progress in various empirical sciences. In the past decades, the important role of causal knowledge has been discovered in many areas of cognitive (...) psychology. Despite the ubiquity of causal reasoning, textbooks of cognitive psychology have neglected this growing field. The goal of The Oxford Handbook of Causal Reasoning is to fill this gap. The handbook brings together the leading researchers in the field of causal reasoning and offers state-of-the-art presentations of theories and research. It provides introductions of competing theories of causal reasoning, and discusses its role in various cognitive functions and domains. The final section presents research from neighboring fields. 1. Causal Reasoning: An Introduction Michael R. Waldmann Part I: Theories of Causal Cognition 2. Associative Accounts of Causal Cognition Mike E. Le Pelley, Oren Griffiths, and Tom Beesley 3. Rules of Causal Judgment: Mapping Statistical Information Onto Causal Beliefs José C. Perales, Andrés Catena, Antonio Cándido, and Antonio Maldonado 4. The Inferential Reasoning Theory of Causal Learning: Toward a Multi- Process Propositional Account Yannick Boddez, Jan De Houwer, and Tom Beckers 5. Causal Invariance as an Essential Constraint for Creating a Causal Representation of the World: Generalizing the Invariance of Causal Power Patricia W. Cheng and Hongjing Lu 6. The Acquisition and Use of Causal Structure Knowledge Benjamin Margolin Rottman 7. Formalizing Prior Knowledge in Causal Induction Thomas L. Griffiths 8. Causal Mechanisms Samuel G. B. Johnson and Woo-kyoung Ahn 9. Force Dynamics and Causation Phillip Wolff and Robert Thorstad 10. Mental Models and Causation P. N. Johnson- Laird and Sangeet S. Khemlani 11. Pseudocontingencies Klaus Fiedler and Florian Kutzner 12. Singular Causation David Danks 13. Cognitive Neuroscience of Causal Reasoning Joachim T. Operskalski and Aron K. Barbey Part II: Basic Cognitive Functions 14. Visual Impressions of Causality Peter White 15. Goal-Directed Actions Bernhard Hommel 16. Planning and Control Magda Osman 17. Reinforcement Learning and Causal Models Samuel J. Gershman 18. Causation and the Probability of Causal Conditionals David E. Over 19. Causal Models and Conditional Reasoning Mike Oaksford and Nick Chater 20. Concepts as Causal Models: Categorization Bob Rehder 21. Concepts as Causal Models: Induction Bob Rehder 22. Causal Explanation Tania Lombrozo and Nadya Vasilyeva 23. Diagnostic Reasoning Björn Meder and Ralf Mayrhofer 24. Inferring Causal Relations by Analogy Keith J. Holyoak and Hee-Seung Lee 25. Causal Argument Ulrike Hahn, Roland Bluhm, and Frank Zenker 26. Causality in Decision- Making York Hagmayer and Philip M. Fernbach Part III: Domains of Causal Reasoning 27. Intuitive Theories Tobias Gerstenberg and Joshua B. Tenenbaum 28. Space, Time, and Causality Marc J. Buehner 29. Causation in Legal and Moral Reasoning David A. Lagnado and Tobias Gerstenberg 30. The Role of Causal Knowledge in Reasoning About Mental Disorders Woo-kyoung Ahn, Nancy S. Kim, and Matthew S. Lebowitz 31. Causality and Causal Reasoning in Natural Language Torgrim Solstad and Oliver Bott 32. Social Attribution and Explanation Denis Hilton Part IV: Development, Phylogeny, and Culture 33. The Development of Causal Reasoning Paul Muentener and Elizabeth Bonawitz 34. Causal Reasoning in Non-Human Animals Christian Schloegl and Julia Fischer 35. Causal Cognition and Culture Andrea Bender, Sieghard Beller, and Douglas L. Medin. (shrink)

In this thesis I investigate causal inquiry in the social sciences, drawing on examples from various disciplines and in particular from conflict studies. In a backlash against the pervasiveness of statistical methods, in the last decade certain social scientists have focused on finding the causal mechanisms behind observed correlations. To provide evidence for such mechanisms, researchers increasingly rely on ‘process tracing’, a method which attempts to give evidence for causal relations by specifying the chain of events connecting a putative cause (...) and effect of interest. I will ask whether the causal claims process tracers make are defensible, and where they are not defensible I will ask how we can improve the method. Throughout these investigations, I show that the conclusions of process tracing are constrained both by the causal structure ofthe social world and by social scientists’ aims and values. My central argument is this: all instances of social phenomena have causally relevant differences, which implies that any research design that requires some comparison between cases is limited by how we systematize these phenomena. Moreover, such research cannot rely on stable regularities. Nevertheless, to forego causal conclusions altogether is not the right response to these limitations; by carefully outlining our epistemic assumptions we can make progress in causal inquiry. While I use philosophical theories of causation to comment on the feasibility of a social scientific method, I also do the reverse: by investigating a popular contemporary method in the social sciences, I show to what extent our philosophical theories of causation are workable in practice. Thus, this thesis is both a methodological and a philosophical work. Every chapter discusses both a fundamental philosophical position on the social sciences and a relevant case study from the social sciences. (shrink)

This chapter provides an introduction to the study of the philosophical notions of mechanisms and causality in biology and economics. This chapter sets the stage for this volume, Mechanism and Causality in Biology and Economics, in three ways. First, it gives a broad review of the recent changes and current state of the study of mechanisms and causality in the philosophy of science. Second, consistent with a recent trend in the philosophy of science to focus on scientific practices, it in (...) turn implies the importance of studying the scientific methods employed by researchers. Finally, by way of providing an overview of each chapter in the volume, this chapter demonstrates that biology and economics are two fertile fields for the philosophy of science and shows how biological and economic mechanisms and causality can be synthesized. (shrink)

Mechanistic models in molecular systems biology are generally mathematical models of the action of networks of biochemical reactions, involving metabolism, signal transduction, and/or gene expression. They can be either simulated numerically or analyzed analytically. Systems biology integrates quantitative molecular data acquisition with mathematical models to design new experiments, discriminate between alternative mechanisms and explain the molecular basis of cellular properties. At the heart of this approach are mechanistic models of molecular networks. We focus on the articulation and development of mechanistic (...) models, identifying five constraints which guide the articulation of models in molecular systems biology. These constraints are not independent of one another, with the result that modeling becomes an iterative process. We illustrate the use of these constraints in the modeling of the mechanism for bistability in the lac operon. (shrink)

This paper aims to provide Humean metaphysics for the interventionist theory of causation. This is done by appealing to the hierarchical picture of causal relations as being realized by mechanisms, which in turn are identified with lower-level causal structures. The modal content of invariances at the lowest level of this hierarchy, at which mechanisms are reduced to strict natural laws, is then explained in terms of projectivism based on the best-system view of laws.

In this paper I offer an anti-Humean critique to Williamson and Russo’s approach to medical mechanisms. I focus on one of the specific claims made by Williamson and Russo, namely the claim that micro-structural ‘mechanisms’ provide evidence for the stability across populations of causal relationships ascertained at the (macro-) level of (test) populations. This claim is grounded in the epistemic account of causality developed by Williamson, an account which—while not relying exclusively on mechanistic evidence for justifying causal judgements—appeals nevertheless to (...) mechanisms, and rejects their anti-Humean interpretation in terms of capacities, powers, potencies, etc. By using (and expanding on) Cartwright’s basic critique against Humean mechanisms, I suggest that, in order to move beyond the level of plausibility, Williamson and Russo’s position is in need of a clarification as to the occurent reading of the components, functioning and interferences of mechanisms. Relatedly, as concerns Williamson’s epistemic account of causation, I argue that this account is in need of a more straightforward answer as to what truth-makers its causal claims should have. (shrink)

Stem cell biology and systems biology are two prominent new approaches to studying cell development. In stem cell biology, the predominant method is experimental manipulation of concrete cells and tissues. Systems biology, in contrast, emphasizes mathematical modeling of cellular systems. For scientists and philosophers interested in development, an important question arises: how should the two approaches relate? This essay proposes an answer, using the model of Waddington’s landscape to triangulate between stem cell and systems approaches. This simple abstract model represents (...) development as an undulating surface of hills and valleys. Originally constructed by C. H. Waddington to visually explicate an integrated theory of genetics, development and evolution, the landscape model can play an updated unificatory role. I examine this model’s structure, representational assumptions, and uses in all three contexts, and argue that explanations of cell development require both mathematical models and concrete experiments. On this view, the two approaches are interdependent, with mathematical models playing a crucial but circumscribed role in explanations of cell development. (shrink)

The concept of technical function is a key concept to describe technical artifacts and artifacts-to-be-designed. Engineers often give such descriptions in terms of functional decomposition models, which represent relationships between functions and sets of other functions. Despite the importance of the concept of function there is no consensus among engineers about its meaning. Models of functional decomposition are likewise conceptually divergent. Although this conceptual diversity hampers information exchange between engineers, they accept and maintain it. Engineers do not, by and large, (...) engage in a focused debate to establish commonly shared functional conceptualizations. This contrasts with science where both debates on the adequacy of key conceptualizations and convergence toward shared conceptualizations are common. This book investigates the side-by-side usage of different functional decomposition models in engineering. It explains this phenomenon by applying and extending the analysis of theory choice in terms of methodological incommensurability to engineering functional decomposition, rather than to science. This analysis shows that engineers’ usage of competing functional decomposition models is rational from a practical point of view. This book furthermore investigates the communication problems that the side-by-side usage of different models engenders and presents a strategy that supports the exchange and re-use of functional information between engineers. (shrink)

This paper addresses questions about how the levels of causality (generic and single-case causality) are related. One question is epistemological: can relationships at one level be evidence for relationships at the other level? We present three kinds of answer to this question, categorised according to whether inference is top-down, bottom-up, or the levels are independent. A second question is metaphysical: can relationships at one level be reduced to relationships at the other level? We present three kinds of answer to this (...) second question, categorised according to whether single-case relations are reduced to generic, generic relations are reduced to single-case, or the levels are independent. We then explore causal inference in autopsy. This is an interesting case study, we argue, because it refutes all three epistemologies and all three metaphysics. We close by sketching an account of causality that survives autopsy—the epistemic theory. (shrink)

The hunt for a biologically respectable definition for the folk concept of innateness is still on. I defend Ariew’s Canalization account of innateness against the criticisms of Griffiths and Machery, but highlight the remaining flaws in this proposal. I develop a new analysis based on the notion of environmental induction. A trait is innate, I argue, iff it is not environmentally induced. I augment this definition with a novel analysis of environmental induction that draws on the contrastive nature of causal (...) explanation. Whether a trait is environmentally induced, I argue, depends on a context sensitive contrast class. I argue that a “Noninduction” analysis of innateness allows the concept an explanatory role in biology. I show how my proposal co-opts the successes of the Canalization account whilst avoiding its pitfalls, and I account for why biologists associate a range of disparate properties with innateness. (shrink)

Neuroscience and cognitive science seek to explain behavioral regularities in terms of underlying mechanisms. An important element of a mechanistic explanation is a characterization of the operations of the parts of the mechanism. The challenge in characterizing such operations is illustrated by an example from the history of physiological chemistry in which some investigators tried to characterize the internal operations in the same terms as the overall physiological system while others appealed to elemental chemistry. In order for biochemistry to become (...) successful, researchers had to identify a new level of operations involving operations over molecular groups. Existing attempts at mechanistic explanation of behavior are in a situation comparable to earlier approaches to physiological chemistry, drawing their inspiration either from overall psychology activities or from low-level neural processes. Successful mechanistic explanations of behavior require the discovery of the appropriate component operations. Such discovery is a daunting challenge but one on which success will be beneficial to both behavioral scientists and cognitive and neuroscientists. (shrink)

Ontic structural realism constitutes a promising take on scientific realism, one that avoids the well‐known issues that realist stances have with underdetermination and theory change. In its most radical versions, ontic structural realism proposes a type of eliminativism about theoretical entities, ascribing ontological commitment only to the structures, and not to the objects appearing in our theories. More moderate versions of ontic structural realism have also been proposed, allowing for ‘thin’ objects in the ontology. This work connects these takes on (...) structural realism with the independent notion that there are two categorically different kinds of scientific theories, namely those that deal with interactions and those that deal with structural constraints – what are known as interaction and framework theories, respectively. By taking this classification seriously, one can arrive at a selective version of ontic structural realism which is better adapted to our scientific knowledge, in which eliminativist ontic structural realism constitutes a natural fit to framework theories, whereas the moderate version is connected to interaction theories. (shrink)

The emphasis on the organization of entities and their activities and interactions has been labeled one of the most distinct contributions of mechanistic philosophy. In this paper I discuss the manner in which the organization of entities and their activities and interactions participates in bringing about phenomena. I present a well-known example from molecular biology—the functioning of the genetic switch in phage lambda—and discuss Marco J. Nathan’s notion of causation by concentration. Nathan introduces causation by concentration to account for the (...) irreducible causal role that the concentration ratio between two kinds of proteins possesses in the genetic switch mechanism in phage lambda. I discuss what the irreducibility of this causal role amounts to and provide a mechanistic interpretation of Nathan’s causation by concentration; that is, I explain this irreducible causal role as one organizational feature of this mechanism. The paper concludes that biological mechanisms need a causal pluralist framework [similar to Glennan’s account in, and but slightly modified] where organizational features such as the concentration ratio have a causally relevant role, yet all the causally productive relations occur at the level of entities or individuals. (shrink)

Mechanisms are now taken widely in philosophy of science to provide one of modern science’s basic explanatory devices. This has raised lively debate concerning the relationship between mechanisms, laws and explanation. This paper focuses on cases where a mechanism gives rise to a ceteris paribus law, addressing two inter-related questions: What kind of explanation is involved? and What is going on in the world when mechanism M affords behavior B described in a ceteris paribus law? We explore various answers offered (...) by ‘new mechanists’ and others before setting out and explaining our own answers: mechanistic explanations are a species of oldfashioned covering-law explanation and this often accounts in part for their explanatory power; and B is what it takes for some set of principles that govern the features of M’s parts in their arrangement in M all to be instanced together. (shrink)

An epistemic account of constitutive relevance lists the criteria by which scientists can identify the components of mechanisms in empirical practice. Three prominent claims from Craver form a promising basis for an account. First, constitutive relevance is established by means of interlevel experiments. Second, interlevel experiments are executions of interventions. Third, there is no interlevel causation between a mechanism and its components. Currently, no account on offer respects all three claims. I offer my causal situationist account of constitutive relevance that (...) respects the claims. By situating a part of a mechanism on the causal chain between the mechanism’s input and output, components can be identified with interventions, without the interventions suggesting interlevel causation. The causal situationist account is the only account on offer so far that clearly fits within Craver’s framework. (shrink)

The aim of this paper is to begin developing a version of Gualtiero Piccinini’s mechanistic account of computation that does not need to appeal to any notion of proper (or teleological) functions. The motivation for doing so is a general concern about the role played by proper functions in Piccinini’s account, which will be evaluated in the first part of the paper. I will then propose a potential alternative approach, where computing mechanisms are understood in terms of Carl Craver’s perspectival (...) account of mechanistic functions. According to this approach, the mechanistic function of ‘performing a computation’ can only be attributed relative to an explanatory perspective, but such attributions are nonetheless constrained by the underlying physical structure of the system in question, thus avoiding unlimited pancomputationalism. If successful, this approach would carry with it fewer controversial assumptions than Piccinini’s original account, which requires a robust understanding of proper functions. Insofar as there are outstanding concerns about the status of proper functions, this approach would therefore be more generally acceptable. (shrink)

Much of the recent philosophical debate on causation and causal explanation in the biological and biomedical sciences has focused on the notion of mechanism. Mechanisms, their nature and epistemic roles have been tackled by a range of so-called neo-mechanistic theories, and widely discussed. Without denying the merits of this approach, our paper aims to show how lately it has failed to give proper credit to processes, which are central to the field, especially of contemporary molecular biology. Processes can be summed (...) up in the notion of ‘pathway’, which is far from being just equivalent to that of ‘mechanism’ and has a profound epistemological and explanatory relevance. It is argued that an adequate consideration of pathways impels some rethinking of scientific explanation in molecular biology, namely its functional and contextual features. A number of examples are given to suggest that the focus of philosophical attention in this disciplinary field should shift from the notion of mechanism to the notion of pathway. (shrink)

Much contemporary debate on the nature of mechanisms centers on the issue of modulating negative causes. One type of negative causability, which I refer to as "causation by absence," appears difficult to incorporate into modern accounts of mechanistic explanation. This paper argues that a recent attempt to resolve this problem, proposed by Benjamin Barros, requires improvement as it overlooks the fact that not all absences qualify as sources of mechanism failure. I suggest that there are a number of additional types (...) of effects caused by absences that need to be incorporated to account for the diversity of causal connections in the biological sciences. Furthermore, it is argued that recognizing natural variability in mechanisms, such as attenuation, leads to some interesting line-drawing issues for contemporary philosophy of mechanisms. (shrink)

Developing models of biological mechanisms, such as those involved in respiration in cells, often requires collaborative effort drawing upon techniques developed and information generated in different disciplines. Biochemists in the early decades of the 20th century uncovered all but the most elusive chemical operations involved in cellular respiration, but were unable to align the reaction pathways with particular structures in the cell. During the period 1940-1965 cell biology was emerging as a new discipline and made distinctive contributions to understanding the (...) role of the mitochondrion and its component parts in cellular respiration. In particular, by developing techniques for localizing enzymes or enzyme systems in specific cellular components, cell biologists provided crucial information about the organized structures in which the biochemical reactions occurred. Although the idea that biochemical operations are intimately related to and depend on cell structures was at odds with the then-dominant emphasis on systems of soluble enzymes in biochemistry, a reconceptualization of energetic processes in the 1960s and 1970s made it clear why cell structure was critical to the biochemical account. This paper examines how numerous excursions between biochemistry and cell biology contributed a new understanding of the mechanism of cellular respiration. (shrink)

An important strategy in the discovery of biological mechanisms involves the piecing together of experimental results from interventions. However, if mechanisms are investigated by means of ideal interventions, as defined by James Woodward and others, then the kind of information revealed is insufficient to discriminate between modular and non-modular causal contributions. Ideal interventions suffice for constructing webs of causal dependencies that can be used to make some predictions about experimental outcomes, but tell us little about how causally relevant factors are (...) organized together and how they interact with each other in order to produce a phenomenon. I argue that lab research relies on more elaborated types of interventions targeting in a controlled fashion multiple variables at the same time in order to probe the temporal organization of causally-relevant factors along distinct causal pathways and to test for non-modular interaction effects, thus providing crucial spatial-temporal constraints guiding the formulation of more detailed mechanistic explanations. (shrink)

This paper examines a case of failed interdisciplinary collaboration, between experimental stem cell research and theoretical systems biology. Recently, two groups of theoretical biologists have proposed dynamical systems models as a basis for understanding stem cells and their distinctive capacities. Experimental stem cell biologists, whose work focuses on manipulation of concrete cells, tissues and organisms, have largely ignored these proposals. I argue that ‘failure to communicate’ in this case is rooted in divergent views of explanation: the theoretically-inclined modelers are committed (...) to a version of the covering-law view, while experimental stem cell biologists aim at mechanistic explanations. I propose a way to reconcile these two explanatory approaches to cell development, and discuss the significance of this result for interdisciplinary collaboration in systems biology and beyond. (shrink)

The paper starts by distinguishing between two kinds of economic practice: theoretical economic practice (TEP) (model and theory building) and direct economic practice (DEP) (the practical operation upon real economies). Most of the epistemological and philosophical considerations have been directed to the first type of practice, one of whose main goals is the discovery of particular sorts of economic laws, mechanisms and other regularities which throw light on relevant economic patterns. We do not deny that in some restricted domains these (...) kinds of regularities may be found. Rather, we claim that the realm of economics is best understood as consisting of processes whose regular structure (if they have one at all) is not guaranteed beforehand but may be crucially influenced and successfully enforced by what we call DEP. We claim that (a) some economic processes are a particular type of social process that will be referred to as Expectations-Based Processes (EBP). Characteristically, an EBP shows a connection between the information that individuals receive from the relevant economic context, the expectations they form, and the actions they perform; (b) in those cases in which EBP exhibit a regular behaviour, they depend on agents' expectations and, crucially, we argue, on interventions upon them. Authorities as well as other economic actors may intervene to change agents' expectations (and therefore, their decisions), contributing to shape EBP and helping to produce the patterns that lead to some targeted economic phenomena. These features of EBP show that they are not shielded from external influences and they do not run autonomously once triggered. Therefore they cannot be conceived as mechanisms or as economic machines. Rather they are open-ended processes that require continuous prodding on the part of policy makers to keep them running in the intended way. (shrink)

The current antireductionist consensus rests in part on the indefensibility of the deductive-nomological model of explanation, on which classical reductionism depends. I argue that the DN model is inessential to the reductionist program and that mechanism provides a better framework for thinking about reductionism. This runs counter to the contemporary mechanists’ claim that mechanism is an alternative to reductionism. I demonstrate that mechanists are committed to reductionism, as evidenced by the historical roots of the contemporary mechanist program. This view shares (...) certain core commitments with reductionism. It is these shared commitments that constitute the essential elements of the reductionist program. (shrink)

This essay is concerned with concentrations of entities, which play an important—albeit often overlooked—role in scientific explanation. First, I discuss an example from molecular biology to show that concentrations can play an irreducible causal role. Second, I provide a preliminary philosophical analysis of this causal role, suggesting some implications for extant theories of causation. I conclude by introducing the concept of causation by concentration, a form of statistical causation whose widespread presence throughout the sciences has been unduly neglected and which (...) deserves to be studied in more depth. 1 Introduction2 Solving Lillie's Paradox: Lysogenic Induction in Phage λ3 Repressor Concentration and the Tuning of the Switch4 Concentration and Causality5 Preemption in Concentrations: Analysis and Implications6 Causation by Concentration: General Definition, Refinements, and Further Applications. (shrink)

Resurgent interest in both mechanistic and counterfactual theories of explanation has led to a fair amount of discussion regarding the relative merits of these two approaches. James Woodward is currently the pre-eminent counterfactual theorist, and he criticizes the mechanists on the following grounds: Unless mechanists about explanation invoke counterfactuals, they cannot make sense of claims about causal interactions between mechanism parts or of causal explanations put forward absent knowledge of productive mechanisms. He claims that these shortfalls can be offset if (...) mechanists will just borrow key tenets of his counterfactual theory of causal claims. What mechanists must bear in mind, however, is that by pursuing this course they risk both the assimilation of the mechanistic theories of explanation into Woodward’s own favored counterfactual theory, and they risk the marginalization of mechanistic explanations to a proper subset of all explanations. An outcome more favorable to mechanists might be had by pursuing an actualist-mechanist theory of the contents of causal claims. While it may not seem obvious at first blush that such an approach is workable, even in principle, recent empirical research into causal perception, causal belief, and mechanical reasoning provides some grounds for optimism. (shrink)

Emergent antireductionism in biological sciences states that even though all living cells and organisms are composed of molecules, molecular wholes are characterized by emergent properties that can only be understood from the perspective of cellular and organismal levels of composition. Thus, an emergence claim (molecular wholes are characterized by emergent properties) is thought to support a form of antireductionism (properties of higher-level molecular wholes can only be understood by taking into account concepts, theories and explanations dealing with higher-level entities). I (...) argue that this argument is flawed: even if molecular wholes are characterized by emergent properties and even if many successful explanations in biology are not molecular, there is no entailment between the two claims. (shrink)

Philosophers of science have developed an account of causal-mechanical explanation that captures regularity, but this account neglects variation. In this article I amend the philosophy of mechanisms to capture variation. The task is to explicate the relationship between regular causal mechanisms responsible for individual development and causes of variation responsible for variation in populations. As it turns out, disputes over this relationship have rested at the heart of the nature–nurture debate. Thus, an explication of the relationship between regular causal mechanisms (...) and causes of variation and between individual development and variation offers both the necessary amendment to the philosophy of mechanisms and the resources to mediate the dispute. (shrink)

This article addresses the following problems: What is a mechanism, how can it be discovered, and what is the role of the knowledge of mechanisms in scientific explanation and technological control? The proposed answers are these. A mechanism is one of the processes in a concrete system that makes it what it is — for example, metabolism in cells, interneuronal connections in brains, work in factories and offices, research in laboratories, and litigation in courts of law. Because mechanisms are largely (...) or totally imperceptible, they must be conjectured. Once hypothesized they help explain, because a deep scientific explanation is an answer to a question of the form, "How does it work, that is, what makes it tick—what are its mechanisms?" Thus, by contrast with the subsumption of particulars under a generalization, an explanation proper consists in unveiling some lawful mechanism, as when political stability is explained by either coercion, public opinion manipulation, or democratic participation. Finding mechanisms satisfies not only the yearning for understanding, but also the need for control. Key Words: explanation • function • mechanism • process • system • systemism. (shrink)