Discovery proceeds in stages of construction, evaluation, and revision. Each of these stages is constrained by what is known or conjectured about what is being discovered. A new characterization of mechanism aids in specifying what is to be discovered when a mechanism is sought. Guidance in discovering mechanisms may be provided by the reasoning strategies of schema instantiation, modular subassembly, and forward/backward chaining. Examples are found in mechanisms in molecular biology, biochemistry, immunology, and evolutionary biology.

Philosophers have proposed various kinds of relations between Mendelian genetics and molecular biology: reduction, replacement, explanatory extension. This paper argues that the two fields are best characterized as investigating different, serially integrated, hereditary mechanisms. The mechanisms operate at different times and contain different working entities. The working entities of the mechanisms of Mendelian heredity are chromosomes, whose movements serve to segregate alleles and independently assort genes in different linkage groups. The working entities of numerous mechanisms of molecular biology are larger (...) and smaller segments of DNA plus related molecules. Discovery of molecular DNA mechanisms filled black boxes that were noted, but unilluminated, by Mendelian genetics. (shrink)

The dominant neuroscientific theory of spatial memory is, like many theories in neuroscience, a multilevel description of a mechanism. The theory links the activities of molecules, cells, brain regions, and whole organisms into an integrated sketch of an explanation for the ability of organisms to navigate novel environments. Here I develop a taxonomy of interlevel experimental strategies for integrating the levels in such multilevel mechanisms. These experimental strategies include activation strategies, interference strategies, and additive strategies. These strategies are mutually reinforcing, (...) providing a kind of interlevel and intratheoretic robustness that has not previously been recognized. (shrink)

The dominant neuroscientific theory of spatial memory is, like many theories in neuroscience, a multilevel description of a mechanism. The theory links the activities of molecules, cells, brain regions, and whole organisms into an integrated sketch of an explanation for the ability of organisms to navigate novel environments. Here I develop a taxonomy of interlevel experimental strategies for integrating the levels in such multilevel mechanisms. These experimental strategies include activation strategies, interference strategies, and additive strategies. These strategies are mutually reinforcing, (...) providing a kind of interlevel and intratheoretic robustness that has not previously been recognized. (shrink)

We currently have on offer a variety of different theories of causation. Many are strikingly good, providing detailed and plausible treatments of exemplary cases; and all suffer from clear counterexamples. I argue that, contra Hume and Kant, this is because causation is not a single, monolithic concept. There are different kinds of causal relations imbedded in different kinds of systems, readily described using thick causal concepts. Our causal theories pick out important and useful structures that fit some familiar cases—cases we (...) discover and ones we devise to fit. (shrink)

In their rich and intricate paper ‘Independence, Invariance, and the Causal Markov Condition’, Daniel Hausman and James Woodward ([1999]) put forward two independent theses, which they label ‘level invariance’ and ‘manipulability’, and they claim that, given a specific set of assumptions, manipulability implies the causal Markov condition. These claims are interesting and important, and this paper is devoted to commenting on them. With respect to level invariance, I argue that Hausman and Woodward's discussion is confusing because, as I point out, (...) they use different senses of ‘intervention’ and ‘invariance’ without saying so. I shall remark on these various uses and point out that the thesis is true in at least two versions. The second thesis, however, is not true. I argue that in their formulation, the manipulability thesis is patently false and that a modified version does not fare better. Furthermore, I think their proof that manipulability implies the causal Markov condition is not conclusive. In the deterministic case it is valid but vacuous, whereas it is invalid in the probabilistic case. 1 Introduction 2 Intervention, invariance and modularity 3 The causal Markov condition: CM1 and CM2 4 From MOD to the causal Markov condition and back 5 A second argument for CM2 6 The proof of the causal Markov condition for probabilistic causes 7 ‘Cartwright's objection’ defended 8 Metaphysical defenses of the causal Markov condition 9 Conclusion. (shrink)

Machamer, Darden, and Craver argue that causal explanations explain effects by describing the operations of the mechanisms which produce them. One of this paper’s aims is to take advantage of neglected resources of Mechanism to rethink the traditional idea that actual or counterfactual natural regularities are essential to the distinction between causal and non-causal co-occurrences, and that generalizations describing natural regularities are essential components of causal explanations. I think that causal productivity and regularity are by no means the same thing, (...) and that the Regularists are mistaken about the roles generalizations play in causal explanation. Humean, logical empiricist, and other Regularist accounts of causal explanation have had the unfortunate effect of distracting philosophers’ from important non-explanatory scientific uses of laws and lesser generalizations which purport to describe natural regularities. My second aim is to characterize some of these uses, illustrating them with examples from neuroscientific research. (shrink)

Explanations in the life sciences frequently involve presenting a model of the mechanism taken to be responsible for a given phenomenon. Such explanations depart in numerous ways from nomological explanations commonly presented in philosophy of science. This paper focuses on three sorts of differences. First, scientists who develop mechanistic explanations are not limited to linguistic representations and logical inference; they frequently employ diagrams to characterize mechanisms and simulations to reason about them. Thus, the epistemic resources for presenting mechanistic explanations are (...) considerably richer than those suggested by a nomological framework. Second, the fact that mechanisms involve organized systems of component parts and operations provides direction to both the discovery and testing of mechanistic explanations. Finally, models of mechanisms are developed for specific exemplars and are not represented in terms of universally quantified statements. Generalization involves investigating both the similarity of new exemplars to those already studied and the variations between them. (shrink)

The philosophical analysis of mathematical explanations concerns itself with two different, although connected, areas of investigation. The first area addresses the problem of whether mathematics can play an explanatory role in the natural and social sciences. The second deals with the problem of whether mathematical explanations occur within mathematics itself. Accordingly, this entry surveys the contributions to both areas, it shows their relevance to the history of philosophy and science, it articulates their connection, and points to the philosophical pay-offs to (...) be expected by deepening our understanding of the topic. (shrink)

Stathis Psillos divides his account into three sections: causation, laws of nature, and explanation. He begins the causation section with Hume's classic "reductive" account and then focuses on the subsequent division between Humean and non-Humean accounts, examining topics such as regularities and singular causation, causation and counterfactuals, and causation and mechanism.

Comparisons of rival explanations or theories often involve vague appeals to explanatory power. In this paper, we dissect this metaphor by distinguishing between different dimensions of the goodness of an explanation: non-sensitivity, cognitive salience, precision, factual accuracy and degree of integration. These dimensions are partially independent and often come into conflict. Our main contribution is to go beyond simple stipulation or description by explicating why these factors are taken to be explanatory virtues. We accomplish this by using the contrastive-counterfactual approach (...) to explanation and the view of understanding as an inferential ability. By combining these perspectives, we show how the explanatory power of an explanation in a given dimension can be assessed by showing the range of answers it provides to what-if-things-had-been-different questions and the theoretical and pragmatic importance of these questions. Our account also explains intuitions linking explanation to unification or to exhibition of a mechanism. (shrink)

This paper presents a counterfactual account of what a mechanism is. Mechanisms consist of parts, the behavior of which conforms to generalizations that are invariant under interventions, and which are modular in the sense that it is possible in principle to change the behavior of one part independently of the others. Each of these features can be captured by the truth of certain counterfactuals.

This paper presents a counterfactual account of what a mechanism is. Mechanisms consist of parts, the behavior of which conforms to generalizations that are invariant under interventions, and which are modular in the sense that it is possible in principle to change the behavior of one part independently of the others. Each of these features can be captured by the truth of certain counterfactuals.

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 develops an account of explanation in biology which does not involve appeal to laws of nature, at least as traditionally conceived. Explanatory generalizations in biology must satisfy a requirement that I call invariance, but need not satisfy most of the other standard criteria for lawfulness. Once this point is recognized, there is little motivation for regarding such generalizations as laws of nature. Some of the differences between invariance and the related notions of stability and resiliency, due respectively to (...) Sandra Mitchell and Brian Skyrms, are explored. (shrink)

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)

This paper attempts to elucidate three characteristics of causal relationships that are important in biological contexts. Stability has to do with whether a causal relationship continues to hold under changes in background conditions. Proportionality has to do with whether changes in the state of the cause “line up” in the right way with changes in the state of the effect and with whether the cause and effect are characterized in a way that contains irrelevant detail. Specificity is connected both to (...) David Lewis’ notion of “influence” and also with the extent to which a causal relation approximates to the ideal of one cause–one effect. Interrelations among these notions and their possible biological significance are also discussed. (shrink)

Stuart Glennan, and the team of Peter Machamer, Lindley Darden, and Carl Craver have recently provided two accounts of the concept of a mechanism. The main difference between these two versions rests on how the behavior of the parts of the mechanism is conceptualized. Glennan considers mechanisms to be an interaction of parts, where the interaction between parts can be characterized by direct, invariant, change-relating generalizations. Machamer, Darden, and Craver criticize traditional conceptualizations of mechanisms which are based solely on parts (...) interacting and introduce a new conceptactivity. This essay is an attempt at carving out a relationship between these two philosophical interpretations of a mechanism. I will claim that, rather than being in conflict, Glennan's concept of interaction and Machamer, Darden, and Craver's notion of activity actually complement one another, each emphasizing a missing element of the other. (shrink)

Woodward present an argument for the Causal Markov Condition (CMC) on the basis of a principle they dub ‘modularity’ ([1999, 2004]). I show that the conclusion of their argument is not in fact the CMC but a substantially weaker proposition. In addition, I show that their argument is invalid and trace this invalidity to two features of modularity, namely, that it is stated in terms of pairwise independence and ‘arrow-breaking’ interventions. Hausman & Woodward's argument can be rendered valid through a (...) reformulation of modularity, but it is doubtful that the argument so revised provides any substantially new insight regarding the basis of the CMC. Introduction The CMC versus Hausman & Woodward's conclusion Hausman & Woodward's argument Modularity and independent error terms Conclusion Appendix: D-separation. (shrink)

In this volume, the authors discuss what practical contributions ecology can and can't make in applied science and environmental problem solving. In the first section, they discuss conceptual problems that have often prevented the formulation and evaluation of powerful, precise, general theories, explain why island biogeography is still beset with controversy and examine the ways that science is value laden. In the second section, they describe how ecology can give us specific answers to practical environmental questions posed in individual case (...) studies, and argue for a new way to look at scientific error. A case study using the Florida panther is examined in the light of these findings. (shrink)

Because of the problems associated with ecological concepts, generalizations, and proposed general theories, applied ecology may require a new "logic" of explanation characterized neither by the traditional accounts of confirmation nor by the logic of discovery. Building on the works of Grunbaum, Kuhn, and Wittgenstein, we use detailed descriptions from research on conserving the Northern Spotted Owl, a case typical of problem solving in applied ecology, to (1) characterize the method of case studies; (2) survey its strengths; (3) summarize and (...) respond to its shortcomings; and (4) investigate and defend its underlying "logic". (shrink)

Van Fraassen and others have urged that judgements of explanations are relative to why-questions; explanations should be considered good in so far as they effectively answer why-questions. In this paper, I evaluate van Fraassen's theory with respect to mathematical explanation. I show that his theory cannot recognize any proofs as explanatory. I also present an example that contradicts the main thesis of the why-question approach—an explanation that appears explanatory despite its inability to answer the why-question that motivated it. This example (...) shows how explanatory judgements can be context-dependent without being why-question-relative. (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 presents a drastically revised version of the theory of causality, based on analyses of causal processes and causal interactions, advocated in Salmon (1984). Relying heavily on modified versions of proposals by P. Dowe, this article answers penetrating objections by Dowe and P. Kitcher to the earlier theory. It shows how the new theory circumvents a host of difficulties that have been raised in the literature. The result is, I hope, a more satisfactory analysis of physical causality.

Ecologists may apply their science either to manage ecosystems to increase the long-run benefits nature offers man or to protect ecosystems from anthropogenie insults and injuries. Popular reasons for supposing that these two tasks (management and protection) are complementary turn out not to be supported by the evidence. Nevertheless, society recognizes the protection of the “health” and “integrity” of ecosystems to be an important ethical and cultural goal even if it cannot be backed in detail by utilitarian or prudential arguments. (...) It is a legitimate purpose of ecological science, moreover, to describe and help society preserve ecosystem “health” and “integrity,” insofar as these are considered as privative qualities. (shrink)

I analyze here biological regression equations known in the literature as allometries and scaling laws. My focus is on the alleged lawlike status of these equations. In particular I argue against recent views that regard allometries and scaling laws as representing universal, non-continent, and/or strict biological laws. Although allometries and scaling laws appear to be generalizations applying to many taxa, they are neither universal nor exceptionless. In fact there appear to be exceptions to all of them. Nor are the constants (...) in allometries and scaling laws truly constant, stable, or universal in character, but vary in value across different taxa and background conditions. Moreover, these equations represent evolutionary, strongly contingent generalizations, which threatens their lawlike status. Lastly, allometries and scaling laws do not offer stable probabilities to which they hold in different backgrounds. I further suggest that many allometries and scaling laws function to elucidate explananda rather than explanantia or covering laws. (shrink)

James Woodward offers a conception of explanation and mechanism in terms of interventionist counterfactuals. Based on a case from ecology, I show that ecologists’ approach to that case satisfies Woodward’s conditions for explanation and mechanism, but his conception does not fully capture what ecologists view as explanatory. The new mechanistic philosophy likewise aims to describe central aspects of mechanisms, but I show that it is not sufficient to account for ecological mechanisms. I argue that in ecology explanation involves identification of (...) invariant and insensitive causal relationships and descriptions of the mechanistic characteristics that make these relations possible. †To contact the author, please write to: Department of Philosophy, University of Dayton, 300 College Park, Dayton, OH 45469‐1546; e‐mail: [email protected]. (shrink)

Molecular biologists and biochemists often use diagrams to present hypotheses. Analysis of diagrams shows that their content can be expressed with linguistic representations. Why do biologists use visual representations instead? One reason is simple comprehensibility: some diagrams present information which is readily understood from the diagram format, but which would not be comprehensible if the same information was expressed linguistically. But often diagrams are used even when concise, comprehensible linguistic alternatives are available. I explain this phenomenon by showing why diagrammatic (...) representation is especially well suited for a particular kind of explanation common in molecular biology and biochemistry: namely, functional analysis, in which a capacity of the system is explained in terms of capacities of its component parts. (shrink)

Beatty, Brandon, and Sober agree that biological generalizations, when contingent, do not qualify as laws. Their conclusion follows from a normative definition of law inherited from the Logical Empiricists. I suggest two additional approaches: paradigmatic and pragmatic. Only the pragmatic represents varying kinds and degrees of contingency and exposes the multiple relationships found among scientific generalizations. It emphasizes the function of laws in grounding expectation and promotes the evaluation of generalizations along continua of ontological and representational parameters. Stability of conditions (...) and strength of determination in nature govern projectibility. Accuracy, ontological level, simplicity, and manageability provide additional measures of usefulness. (shrink)

In this article I consider the challenges for exporting causal knowledge raised by complex biological systems. In particular, James Woodward’s interventionist approach to causality identified three types of stability in causal explanation: invariance, modularity, and insensitivity. I consider an example of robust degeneracy in genetic regulatory networks and knockout experimental practice to pose methodological and conceptual questions for our understanding of causal explanation in biology. †To contact the author, please write to: Department of History and Philosophy of Science, University of (...) Pittsburgh, 1017 Cathedral of Learning, Pittsburgh, PA 15260; e‐mail: [email protected]. (shrink)

Biological knowledge does not fit the image of science that philosophers have developed. Many argue that biology has no laws. Here I criticize standard normative accounts of law and defend an alternative, pragmatic approach. I argue that a multidimensional conceptual framework should replace the standard dichotomous law/ accident distinction in order to display important differences in the kinds of causal structure found in nature and the corresponding scientific representations of those structures. To this end I explore the dimensions of stability, (...) strength, and degree of abstraction that characterize the variety of scientific knowledge claims found in biology and other sciences. (shrink)

It has been claimed that ceteris paribus laws, rather than strict laws are the proper aim of the special sciences. This is so because the causal regularities found in these domains are exception-ridden, being contingent on the presence of the appropriate conditions and the absence of interfering factors. I argue that the ceteris paribus strategy obscures rather than illuminates the important similarities and differences between representations of causal regularities in the exact and inexact sciences. In particular, a detailed account of (...) the types and degrees of contingency found in the domain of biology permits a more adequate understanding of the relations among the sciences. (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.

One of the motivations for Salmon's (1984) causal theory of explanation was the explanatory irrelevance exhibited by many arguments conforming to Hempel's covering-law models of explanation. However, the nexus of causal processes and interactions characterized by Salmon is not rich enough to supply the necessary conception of explanatory relevance. Salmon's (1994) revised theory, which is briefly criticized on independent grounds, fares no better. There is some possibility that the two-tiered structure of explanation described by Salmon (1984) may be pressed into (...) service, but more work would have to be done. Ironically, Salmon's difficulties are similar to those suffered by his seventeenth-century predecessors. (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)

This paper explores the relationship between a manipulability conception of causation and the causal Markov condition (CM). We argue that violations of CM also violate widely shared expectations—implicit in the manipulability conception—having to do with the absence of spontaneous correlations. They also violate expectations concerning the connection between independence or dependence relationships in the presence and absence of interventions.

This essay explains what the Causal Markov Condition says and defends the condition from the many criticisms that have been launched against it. Although we are skeptical about some of the applications of the Causal Markov Condition, we argue that it is implicit in the view that causes can be used to manipulate their effects and that it cannot be surrendered without surrendering this view of causation.

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)

Philosophers of science increasingly believe that much of science is concerned with understanding the mechanisms responsible for the production of natural phenomena. An adequate understanding of scientific research requires an account of how scientists develop and test models of mechanisms. This paper offers a general account of the nature of mechanical models, discussing the representational relationship that holds between mechanisms and their models as well as the techniques that can be used to test and refine such models. The analysis is (...) supported by study of two competing models of a mechanism of speech perception. (shrink)

Carl F. Craver investigates what we are doing when we use neuroscience to explain what's going on in the brain. When does an explanation succeed and when does it fail? Craver offers explicit standards for successful explanation of the workings of the brain, on the basis of a systematic view about what neuroscientific explanations are.