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, 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. †To contact the author, please write to: Committee for Philosophy and the Sciences, Department of Philosophy, 1125A Skinner Building, University of Maryland, College Park, MD 20742 USA; e‐mail: [email protected]. (shrink)

Network analysis is increasingly used to discover and represent the organization of complex systems. Focusing on examples from neuroscience in particular, I argue that whether network models explain, how they explain, and how much they explain cannot be answered for network models generally but must be answered by specifying an explanandum, by addressing how the model is applied to the system, and by specifying which kinds of relations count as explanatory.

We provide a taxonomy of the two most important debates in the philosophy of the cognitive and neural sciences. The first debate is over methodological individualism: is the object of the cognitive and neural sciences the brain, the whole animal, or the animal--environment system? The second is over explanatory style: should explanation in cognitive and neural science be reductionist-mechanistic, inter-level mechanistic, or dynamical? After setting out the debates, we discuss the ways in which they are interconnected. Finally, we make some (...) recommendations that we hope will help philosophers interested in the cognitive and neural sciences to avoid dead ends. (shrink)

Arguments in favor of anti-representationalism in cognitive science often suffer from a lack of attention to detail. The purpose of this paper is to fill in the gaps in these arguments, and in so doing show that at least one form of anti- representationalism is potentially viable. After giving a teleological definition of representation and applying it to a few models that have inspired anti- representationalist claims, I argue that anti-representationalism must be divided into two distinct theses, one ontological, one (...) epistemological. Given the assumptions that define the debate, I give reason to think that the ontological thesis is false. I then argue that the epistemological thesis might, in the end, turn out to be true, despite a potentially serious difficulty. Along the way, there will be a brief detour to discuss a controversy from early twentieth century physics. (shrink)

We outline a framework of multilevel neurocognitive mechanisms that incorporates representation and computation. We argue that paradigmatic explanations in cognitive neuroscience fit this framework and thus that cognitive neuroscience constitutes a revolutionary break from traditional cognitive science. Whereas traditional cognitive scientific explanations were supposed to be distinct and autonomous from mechanistic explanations, neurocognitive explanations aim to be mechanistic through and through. Neurocognitive explanations aim to integrate computational and representational functions and structures across multiple levels of organization in order to explain (...) cognition. To a large extent, practicing cognitive neuroscientists have already accepted this shift, but philosophical theory has not fully acknowledged and appreciated its significance. As a result, the explanatory framework underlying cognitive neuroscience has remained largely implicit. We explicate this framework and demonstrate its contrast with previous approaches. (shrink)

Scientific models invariably involve some degree of idealization, abstraction, or nationalization of their target system. Nonetheless, I argue that there are circumstances under which such false models can offer genuine scientific explanations. After reviewing three different proposals in the literature for how models can explain, I shall introduce a more general account of what I call model explanations, which specify the conditions under which models can be counted as explanatory. I shall illustrate this new framework by applying it to the (...) case of Bohr's model of the atom, and conclude by drawing some distinctions between phenomenological models, explanatory models, and fictional models. (shrink)

Explaining the complex dynamics exhibited in many biological mechanisms requires extending the recent philosophical treatment of mechanisms that emphasizes sequences of operations. To understand how nonsequentially organized mechanisms will behave, scientists often advance what we call dynamic mechanistic explanations. These begin with a decomposition of the mechanism into component parts and operations, using a variety of laboratory-based strategies. Crucially, the mechanism is then recomposed by means of computational models in which variables or terms in differential equations correspond to properties of (...) its parts and operations. We provide two illustrations drawn from research on circadian rhythms. Once biologists identified some of the components of the molecular mechanism thought to be responsible for circadian rhythms, computational models were used to determine whether the proposed mechanisms could generate sustained oscillations. Modeling has become even more important as researchers have recognized that the oscillations generated in individual neurons are synchronized within networks; we describe models being employed to assess how different possible network architectures could produce the observed synchronized activity. (shrink)

Advocates of dynamical systems theory (DST) sometimes employ revolutionary rhetoric. In an attempt to clarify how DST models differ from others in cognitive science, I focus on two issues raised by DST: the role for representations in mental models and the conception of explanation invoked. Two features of representations are their role in standing-in for features external to the system and their format. DST advocates sometimes claim to have repudiated the need for stand-ins in DST models, but I argue that (...) they are mistaken. Nonetheless, DST does offer new ideas as to the format of representations employed in cognitive systems. With respect to explanation, I argue that some DST models are better seen as conforming to the covering-law conception of explanation than to the mechanistic conception of explanation implicit in most cognitive science research. But even here, I argue, DST models are a valuable complement to more mechanistic cognitive explanations. (shrink)

This article argues that the basic account of mechanism and mechanistic explanation, involving sequential execution of qualitatively characterized operations, is itself insufficient to explain biological phenomena such as the capacity of living organisms to maintain themselves as systems distinct from their environment. This capacity depends on cyclic organization, including positive and negative feedback loops, which can generate complex dynamics. Understanding cyclically organized mechanisms with complex dynamics requires coordinating research directed at decomposing mechanisms into parts and operations with research using computational (...) models to recompose mechanisms and determine their dynamic behavior. This coordinated endeavor yields dynamic mechanistic explanations. (shrink)

In many fields in the life sciences investigators refer to downward or top-down causal effects. Craver and Bechtel defended the view that such cases should be understood in terms of a constitution relation between levels in a mechanism and causation as solely an intra-level relation. Craver and Bechtel, however, provided insufficient specification as to when entities constitute a higher-level mechanism. In this paper I appeal to graph-theoretic representations of networks that are now widely employed in systems biology and neuroscience to (...) identify mechanisms with the modules that exhibit high clustering. As a result of the interconnections of nodes in these modules/mechanisms, they often exhibit complex dynamic behaviors that constrain how the individual components respond to external inputs, an important feature of cases viewed as involving top-down causation. (shrink)

Two widely accepted assumptions within cognitive science are that (1) the goal is to understand the mechanisms responsible for cognitive performances and (2) computational modeling is a major tool for understanding these mechanisms. The particular approaches to computational modeling adopted in cognitive science, moreover, have significantly affected the way in which cognitive mechanisms are understood. Unable to employ some of the more common methods for conducting research on mechanisms, cognitive scientists’ guiding ideas about mechanism have developed in conjunction with their (...) styles of modeling. In particular, mental operations often are conceptualized as comparable to the processes employed in classical symbolic AI or neural network models. These models, in turn, have been interpreted by some as themselves intelligent systems since they employ the same type of operations as does the mind. For this paper, what is significant about these approaches to modeling is that they are constructed specifically to account for behavior and are evaluated by how well they do so—not by independent evidence that they describe actual operations in mental mechanisms. (shrink)

One of the central objectives Shapiro and Sober pursue in is to show that what they call the master argument for epiphenomenalism, which is a type of causal exclusion argument, fails. Epiphe nomenalism, according to the terminology adopted in, designates the thesis that supervening macro properties have no causal influence on micro proper ties that are caused by the micro supervenience bases of those macro properties. Well-known classical exclusion arguments are designed to yield such macro-tomicro epiphenomenalism along the lines of (...) the following reasoning: subject to the widely accepted principle of the causal closure of the physical, there exists a causally sufficient micro cause for every micro effect; if it is additionally assumed that macro properties supervene on micro properties without being identical to the latter and if — in light of the rareness of cases of causal overdetermination — micro effects are assumed not to be systematically overdetermined, it follows that macro properties are causally inert with respect to effects of their micro supervenience bases. (shrink)

The first part of this paper presents an argument showing that the currently most highly acclaimed interventionist theory of causation, i.e. the one advanced by Woodward, excludes supervening macro properties from having a causal influence on effects of their micro supervenience bases. Moreover, this interventionist exclusion argument is demonstrated to rest on weaker premises than classical exclusion arguments. The second part then discusses a weakening of interventionism that Woodward suggests. This weakened version of interventionism turns out either to be inapplicable (...) to cases of downward causation involving supervening macro properties or to render corresponding causal claims meaningless. In sum, the paper argues that, contrary to what many non-reductive physicalists claim, interventionism does not render non-reductive physicalism immune to the problem of causal exclusion. (shrink)

The first part of this paper argues that if Craver’s ([2007a], [2007b]) popular mutual manipulability account (MM) of mechanistic constitution is embedded within Woodward’s ([2003]) interventionist theory of causation--for which it is explicitly designed--it either undermines the mechanistic research paradigm by entailing that there do not exist relationships of constitutive relevance or it gives rise to the unwanted consequence that constitution is a form of causation. The second part shows how Woodward’s theory can be adapted in such a way that (...) (MM) neither undermines the mechanistic paradigm nor reduces constitution to causation. However, it turns out that this modified theoretical embedding of (MM) makes it impossible to produce empirical evidence for constitutive relations. The paper ends by suggesting an additional criterion, the fat-handedness criterion, which, when combined with (MM), generates indirect empirical evidence for constitutive relevance. (shrink)

We address the question of whether and to what extent explanatory and modelling strategies in systems biology are mechanistic. After showing how dynamic mathematical models are actually required for mechanistic explanations of complex systems, we caution readers against expecting all systems biology to be about mechanistic explanations. Instead, the aim may be to generate topological explanations that are not standardly mechanistic, or to arrive at design principles that explain system organization and behaviour in general, but not specific mechanisms. These abstraction (...) strategies serve various aims, including prediction and control, that are central to understanding the epistemic diversity of systems biology. (shrink)

The received view of dynamical explanation is that dynamical cognitive science seeks to provide covering law explanations of cognitive phenomena. By analyzing three prominent examples of dynamicist research, I show that the received view is misleading: some dynamical explanations are mechanistic explanations, and in this way resemble computational and connectionist explanations. Interestingly, these dynamical explanations invoke the mathematical framework of dynamical systems theory to describe mechanisms far more complex and distributed than the ones typically considered by philosophers. Therefore, contemporary dynamicist (...) research reveals the need for a more sophisticated account of mechanistic explanation. (shrink)

In this paper I criticize the commonly accepted idea that the generalizations of the special sciences should be construed as ceteris paribus laws. This idea rests on mistaken assumptions about the role of laws in explanation and their relation to causal claims. Moreover, the major proposals in the literature for the analysis of ceteris paribus laws are, on their own terms, complete failures. I sketch a more adequate alternative account of the content of causal generalizations in the special sciences which (...) I argue should replace the ceteris paribus conception. (shrink)

Woodward's long awaited book is an attempt to construct a comprehensive account of causation explanation that applies to a wide variety of causal and explanatory claims in different areas of science and everyday life. The book engages some of the relevant literature from other disciplines, as Woodward weaves together examples, counterexamples, criticisms, defenses, objections, and replies into a convincing defense of the core of his theory, which is that we can analyze causation by appeal to the notion of manipulation.

This paper explores the question of whether all or most explanations in biology are, or ideally should be, ‘mechanistic’. I begin by providing an account of mechanistic explanation, making use of the interventionist ideas about causation I have developed elsewhere. This account emphasizes the way in which mechanistic explanations, at least in the biological sciences, integrate difference‐making and spatio‐temporal information, and exhibit what I call fine‐tunedness of organization. I also emphasize the role played by modularity conditions in mechanistic explanation. I (...) will then argue, in agreement with John Dupré, that, given this account, it is plausible that many biological systems require explanations that are relatively non‐mechanical or depart from expectations one associates with the behaviour of machines. (shrink)

A number of writers, myself included, have recently argued that an “interventionist” treatment of causation of the sort defended in Woodward, 2003 can be used to cast light on so-called “causal exclusion” arguments. This interventionist treatment of causal exclusion has in turn been criticized by other philosophers. This paper responds to these criticisms. It describes an interventionist framework for thinking about causal relationships when supervenience relations are present. I contend that this framework helps us to see that standard arguments for (...) causal exclusion involve mistaken assumptions about what it is appropriate to control for or hold fixed in assessing causal claims. The framework also provides a natural way of capturing the idea that properties that supervene on but that are not identical with realizing properties can be causally efficacious. (shrink)

This paper defends a counterfactual account of explanation, according to which successful explanation requires tracing patterns of counterfactual dependence of a special sort, involving what I call active counterfactuals. Explanations having this feature must appeal to generalizations that are invariant--stable under certain sorts of changes. These ideas are illustrated by examples drawn from physics and econometrics.

This paper describes an alternative to the common view that explanation in the special sciences involves subsumption under laws. According to this alternative, whether or not a generalization can be used to explain has to do with whether it is invariant rather than with whether it is lawful. A generalization is invariant if it is stable or robust in the sense that it would continue to hold under a relevant if it is stable or robust in the sense that it (...) would continue to hold under a relevant class of changes. Unlike lawfulness, invariance comes in degrees and has other features that are well suited to capture the characteristics of explanatory generalizations in the special sciences. For example, a generalization can be invariant even if it has exceptions or holds only over a limited spatio-temporal interval. The notion of invariance can be used to resolve a number of dilemmas that arise in standard treatments of explanatory generalizations in the special sciences. (shrink)

Mechanistic explanation has an impressive track record of advancing our understanding of complex, hierarchically organized physical systems, particularly biological and neural systems. But not every complex system can be understood mechanistically. Psychological capacities are often understood by providing cognitive models of the systems that underlie them. I argue that these models, while superficially similar to mechanistic models, in fact have a substantially more complex relation to the real underlying system. They are typically constructed using a range of techniques for abstracting (...) the functional properties of the system, which may not coincide with its mechanistic organization. I describe these techniques and show that despite being non-mechanistic, these cognitive models can satisfy the normative constraints on good explanations. (shrink)

In this paper, I outline two strands of evidence for the conclusion that the dynamical approach to cognitive science both seeks and provides covering law explanations. Two of the most successful dynamical models—Kelso’s model of rhythmic finger movement and Thelen et al.’s model of infant perseverative reaching—can be seen to provide explanations which conform to the famous explanatory scheme first put forward by Hempel and Oppenheim. In addition, many prominent advocates of the dynamical approach also express the provision of this (...) kind of explanation as a goal of dynamical cognitive science. I conclude by briefly outlining two consequences. First, dynamical cognitive science’s explanatory style may strengthen its links to the so-called “situated” approach to cognition, but, secondly, it may also undermine the widespread intuition that dynamics is related to emergentism in the philosophy of mind. (shrink)

According to the dominant computational approach in cognitive science, cognitive agents are digital computers; according to the alternative approach, they are dynamical systems. This target article attempts to articulate and support the dynamical hypothesis. The dynamical hypothesis has two major components: the nature hypothesis (cognitive agents are dynamical systems) and the knowledge hypothesis (cognitive agents can be understood dynamically). A wide range of objections to this hypothesis can be rebutted. The conclusion is that cognitive systems may well be dynamical systems, (...) and only sustained empirical research in cognitive science will determine the extent to which that is true. (shrink)

The overall goal of this target article is to demonstrate a mechanism for an embodied cognition. The particular vehicle is a much-studied, but still widely debated phenomenon seen in 7–12 month-old-infants. In Piaget's classic “A-not-B error,” infants who have successfully uncovered a toy at location “A” continue to reach to that location even after they watch the toy hidden in a nearby location “B.” Here, we question the traditional explanations of the error as an indicator of infants' concepts of objects (...) or other static mental structures. Instead, we demonstrate that the A-not-B error and its previously puzzling contextual variations can be understood by the coupled dynamics of the ordinary processes of goal-directed actions: looking, planning, reaching, and remembering. We offer a formal dynamic theory and model based on cognitive embodiment that both simulates the known A-not-B effects and offers novel predictions that match new experimental results. The demonstration supports an embodied view by casting the mental events involved in perception, planning, deciding, and remembering in the same analogic dynamic language as that used to describe bodily movement, so that they may be continuously meshed. We maintain that this mesh is a pre-eminently cognitive act of “knowing” not only in infancy but also in everyday activities throughout the life span. Key Words: cognitive development; dynamical systems theory; embodied cognition; infant development; motor control; motor planning; perception and action. (shrink)

Cognitive science has always included multiple methodologies and theoretical commitments. The philosophy of cognitive science should embrace, or at least acknowledge, this diversity. Bechtel’s (2009a) proposed philosophy of cognitive science, however, applies only to representationalist and mechanist cognitive science, ignoring the substantial minority of dynamically oriented cognitive scientists. As an example of nonrepresentational, dynamical cognitive science, we describe strong anticipation as a model for circadian systems (Stepp & Turvey, 2009). We then propose a philosophy of science appropriate to nonrepresentational, dynamical (...) cognitive science. (shrink)

The philosophical theory of scientific explanation proposed here involves a radically new treatment of causality that accords with the pervasively statistical character of contemporary science. Wesley C. Salmon describes three fundamental conceptions of scientific explanation--the epistemic, modal, and ontic. He argues that the prevailing view is untenable and that the modal conception is scientifically out-dated. Significantly revising aspects of his earlier work, he defends a causal/mechanical theory that is a version of the ontic conception. Professor Salmon's theory furnishes a robust (...) argument for scientific realism akin to the argument that convinced twentieth-century physical scientists of the existence of atoms and molecules. To do justice to such notions as irreducibly statistical laws and statistical explanation, he offers a novel account of physical randomness. The transition from the "reviewed view" of scientific explanation to the causal/mechanical model requires fundamental rethinking of basic explanatory concepts. (shrink)

This paper discusses several distinct process theories of causality offered in recent years by Phil Dowe and me. It addresses problems concerning the explication of causal process, causal interaction, and causal transmission, whether given in terms of transmission of marks, transmission of invariant or conserved quantities, or mere possession of conserved quantities. Renouncing the mark-transmission and invariant quantity criteria, I accept a conserved quantity theory similar to Dowe's--differing basically with respect to causal transmission. This paper also responds to several fundamental (...) constructive criticisms contained in Christopher Hitchcock's discussion of both the mark-transmission and the conserved quantity theories. (shrink)

We sketch a framework for building a unified science of cognition. This unification is achieved by showing how functional analyses of cognitive capacities can be integrated with the multilevel mechanistic explanations of neural systems. The core idea is that functional analyses are sketches of mechanisms , in which some structural aspects of a mechanistic explanation are omitted. Once the missing aspects are filled in, a functional analysis turns into a full-blown mechanistic explanation. By this process, functional analyses are seamlessly integrated (...) with multilevel mechanistic explanations. (shrink)

It is argued that once biological systems reach a certain level of complexity, mechanistic explanations provide an inadequate account of many relevant phenomena. In this article, I evaluate such claims with respect to a representative programme in systems biological research: the study of regulatory networks within single-celled organisms. I argue that these networks are amenable to mechanistic philosophy without need to appeal to some alternate form of explanation. In particular, I claim that we can understand the mathematical modelling techniques of (...) systems biologists as part of a broader practice of constructing and evaluating mechanism schemas. This argument is elaborated by considering the case of bacterial chemotactic networks, where some research has been interpreted as explaining phenomena by means of abstract design principles. (shrink)

The concept of mechanism is analyzed in terms of entities and activities, organized such that they are productive of regular changes. Examples show how mechanisms work in neurobiology and molecular biology. Thinking in terms of mechanisms provides a new framework for addressing many traditional philosophical issues: causality, laws, explanation, reduction, and scientific change.

We argue that dynamical and mathematical models in systems and cognitive neuro- science explain (rather than redescribe) a phenomenon only if there is a plausible mapping between elements in the model and elements in the mechanism for the phe- nomenon. We demonstrate how this model-to-mechanism-mapping constraint, when satisfied, endows a model with explanatory force with respect to the phenomenon to be explained. Several paradigmatic models including the Haken-Kelso-Bunz model of bimanual coordination and the difference-of-Gaussians model of visual receptive fields are (...) explored. (shrink)

Recently, it has been provocatively claimed that dynamical modeling approaches signal the emergence of a new explanatory framework distinct from that of mechanistic explanation. This paper rejects this proposal and argues that dynamical explanations are fully compatible with, even naturally construed as, instances of mechanistic explanations. Specifically, it is argued that the mathematical framework of dynamics provides a powerful descriptive scheme for revealing temporal features of activities in mechanisms and plays an explanatory role to the extent it is deployed for (...) this purpose. It is also suggested that more attention should be paid to the distinctive methodological contributions of the dynamical framework including its usefulness as a heuristic for mechanism discovery and hypothesis generation in contemporary neuroscience and biology. (shrink)

Abstract While agreeing that dynamical models play a major role in cognitive science, we reject Stepp, Chemero, and Turvey's contention that they constitute an alternative to mechanistic explanations. We review several problems dynamical models face as putative explanations when they are not grounded in mechanisms. Further, we argue that the opposition of dynamical models and mechanisms is a false one and that those dynamical models that characterize the operations of mechanisms overcome these problems. By briefly considering examples involving the generation (...) of action potentials and circadian rhythms, we show how decomposing a mechanism and modeling its dynamics are complementary endeavors. (shrink)

This paper argues that besides mechanistic explanations, there is a kind of explanation that relies upon “topological” properties of systems in order to derive the explanandum as a consequence, and which does not consider mechanisms or causal processes. I first investigate topological explanations in the case of ecological research on the stability of ecosystems. Then I contrast them with mechanistic explanations, thereby distinguishing the kind of realization they involve from the realization relations entailed by mechanistic explanations, and explain how both (...) kinds of explanations may be articulated in practice. The second section, expanding on the case of ecological stability, considers the phenomenon of robustness at all levels of the biological hierarchy in order to show that topological explanations are indeed pervasive there. Reasons are suggested for this, in which “neutral network” explanations are singled out as a form of topological explanation that spans across many levels. Finally, I appeal to the distinction of explanatory regimes to cast light on a controversy in philosophy of biology, the issue of contingence in evolution, which is shown to essentially involve issues about realization. (shrink)

To explain the phenomena in the world of our experience, to answer the question “why?” rather than only the question “what?”, is one of the foremost objectives of all rational inquiry; and especially, scientific research in its various branches strives to go beyond a mere description of its subject matter by providing an explanation of the phenomena it investigates. While there is rather general agreement about this chief objective of science, there exists considerable difference of opinion as to the function (...) and the essential characteristics of scientific explanation. In the present essay, an attempt will be made to shed some light on these issues by means of an elementary survey of the basic pattern of scientific explanation and a subsequent more rigorous analysis of the concept of law and of the logical structure of explanatory arguments. (shrink)

In this paper I offer an analysis of causation based upon a theory of mechanisms-complex systems whose internal parts interact to produce a system's external behavior. I argue that all but the fundamental laws of physics can be explained by reference to mechanisms. Mechanisms provide an epistemologically unproblematic way to explain the necessity which is often taken to distinguish laws from other generalizations. This account of necessity leads to a theory of causation according to which events are causally related when (...) there is a mechanism that connects them. I present reasons why the lack of an account of fundamental physical causation does not undermine the mechanical account. (shrink)

In a 2008 paper, Walmsley argued that the explanations employed in the dynamical approach to cognitive science, as exemplified by the Haken, Kelso and Bunz model of rhythmic finger movement, and the model of infant preservative reaching developed by Esther Thelen and her colleagues, conform to Carl Hempel and Paul Oppenheim’s deductive-nomological model of explanation (also known as the covering law model). Although we think Walmsley’s approach is methodologically sound in that it starts with an analysis of scientific practice rather (...) than a general philosophical framework, we nevertheless feel that there are two problems with his paper. First, he focuses only on the deductivenomological model and so neglects the important fact that explanations are causal. Second, the explanations offered by the dynamical approach do not take the deductive-nomological format, because they do not deduce the explananda from exceptionless laws. Because of these two points, Walmsley makes the dynamical explanations in cognitive science appear problematic, while in fact they are not. (shrink)

This paper considers the applicability of standard accounts of causation to living systems. In particular it examines critically the increasing tendency to equate causal explanation with the identification of a mechanism. A range of differences between living systems and paradigm mechanisms are identified and discussed. While in principle it might be possible to accommodate an account of mechanism to these features, the attempt to do so risks reducing the idea of a mechanism to vacuity. It is proposed that the solution (...) to this problem requires the development of a philosophical account of process adequate to apply to living systems. (shrink)