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.

Schaffner’s model of theory reduction has played an important role in philosophy of science and philosophy of biology. Here, the model is found to be problematic because of an internal tension. Indeed, standard antireductionist external criticisms concerning reduction functions and laws in biology do not provide a full picture of the limits of Schaffner’s model. However, despite the internal tension, his model usefully highlights the importance of regulative ideals associated with the search for derivational, and embedding, deductive relations among mathematical (...) structures in theoretical biology. A reconstructed Schaffnerian model could therefore shed light on mathematical theory development in the biological sciences and on the epistemology of mathematical practices more generally. *Received November 2006; revised March 2009. †To contact the author, please write to: Philosophy Department, University of California, Santa Cruz, 1156 High St., Santa Cruz, CA 95064; e‐mail: [email protected]. (shrink)

I analyze the importance of parts in the style of biological theorizing that I call compositional biology. I do this by investigating various aspects, including partitioning frames and explanatory accounts, of the theoretical perspectives that fall under and are guided by compositional biology. I ground this general examination in a comparative analysis of three different disciplines with their associated compositional theoretical perspectives: comparative morphology, functional morphology, and developmental biology. I glean data for this analysis from canonical textbooks and defend the (...) use of such texts for the philosophy of science. I end with a discussion of the importance of recognizing formal and compositional biology as two genuinely different ways of doing biology – the differences arising more from their distinct methodologies than from scientific discipline included or natural domain studied. Ultimately, developing a translation manual between the two styles would be desirable as they currently are, at times, in conflict. (shrink)

The dangers of character reification for cladistic inference are explored. The identification and analysis of characters always involves theory-laden abstraction—there is no theory-free “view from nowhere.” Given theory-ladenness, and given a real world with actual objects and processes, how can we separate robustly real biological characters from uncritically reified characters? One way to avoid reification is through the employment of objectivity criteria that give us good methods for identifying robust primary homology statements. I identify six such criteria and explore each (...) with examples. Ultimately, it is important to minimize character reification, because poor character analysis leads to dismal cladograms, even when proper phylogenetic analysis is employed. Given the deep and systemic problems associated with character reification, it is ironic that philosophers have focused almost entirely on phylogenetic analysis and neglected character analysis. (shrink)

A taxonomy of part‐whole or meronymic relations is developed to explain the ordinary English‐speaker's use of the term “part of” and its cognates. The resulting classification yields six types of meronymic relations: 1. component‐integral object (pedal‐bike), 2. member‐collection (ship‐fleet), 3. portion‐mass (slice‐pie), 4. stuff‐object (steel‐car), 5. feature‐activity (paying‐shopping), and 6. place‐area (Everglades‐Florida). Meronymic relations ore further distinguished from other inclusion relations, such as spatial inclusion, and class inclusion, and from several other semantic relations: attribution, attachment, and ownership. This taxonomy is (...) then used to explain cases of apparent intransitivity in merological syllogisms, and standard form syllogisms whose premises express different inclusion relations. The data suggest that intransitivities arise due to equivocations between different types of semantic relations. These results are then explained by means of the relation element theory which accounts for the character and behavior of semantic relations in terms of more primitive relational elements. The inferential phenomena observed are then explained by means of a single principle of element matching. (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)

The two major modern accounts of explanation are the causal and unification accounts. My aim in this paper is to provide a kind of unification of the causal and the unification accounts, by using the central technical apparatus of the unification account to solve a central problem faced by the causal account, namely, the problem of determining which parts of a causal network are explanatorily relevant to the occurrence of an explanandum. The end product of my investigation is a causal (...) account of explanation that has many of the advantages of the unification account. (shrink)

The concept of niche (setting, context, habitat, environment) has been little studied by ontologists, in spite of its wide application in a variety of disciplines from evolutionary biology to economics. What follows is a first formal theory of this concept, a theory of the relations between objects and their niches. The theory builds upon existing work on mereology, topology, and the theory of spatial location as tools of formal ontology. It will be illustrated above all by means of simple biological (...) examples, but the concept of niche should be understood as being, like concepts such as part, boundary, and location, a structural concept that is applicable in principle to a wide range of different domains. (shrink)

Although the relationship of part to whole is one of the most fundamental there is, this is the first full-length study of this key concept. Showing that mereology, or the formal theory of part and whole, is essential to ontology, Simons surveys and critiques previous theories--especially the standard extensional view--and proposes a new account that encompasses both temporal and modal considerations. Simons's revised theory not only allows him to offer fresh solutions to long-standing problems, but also has far-reaching consequences for (...) our understanding of a host of classical philosophical concepts. (shrink)

A classification of models of reduction into three categories — theory reductionism, explanatory reductionism, and constitutive reductionism — is presented. It is shown that this classification helps clarify the relations between various explications of reduction that have been offered in the past, especially if a distinction is maintained between the various epistemological and ontological issues that arise. A relatively new model of explanatory reduction, one that emphasizes that reduction is the explanation of a whole in terms of its parts is (...) also presented in detail. Finally, the classification is used to clarify the debate over reductionism in molecular biology. It is argued there that while no model from the category of theory reduction might be applicable in that case, models of explanatory reduction might yet capture the structure of the relevant explanations. (shrink)

The theory and practice of contemporary comparative biology and phylogeny reconstruction (systematics) emphasizes algorithmic aspects but neglects a concern for the evidence. The character data used in systematics to formulate hypotheses of relationships in many ways constitute a black box, subject to uncritical assessment and social influence. Concerned that such a state of affairs leaves systematics and the phylogenetic theories it generates severely underdetermined, we investigate the nature of the criteria of homology and their application to character conceptualization in the (...) context of transformationist and generative paradigms. Noting the potential for indeterminacy in character conceptualization, we conclude that character congruence (the coherence of character statements) relative to a hierarchy is a necessary, but not a sufficient, condition for phylogeny reconstruction. Specifically, it is insufficient due to the lack of causal grounding of character hypotheses. Conceptualizing characters as homeostatic property cluster natural kinds is in accordance with the empirical practice of systematists. It also accounts for the lack of sharpness in character conceptualization, yet requires character identification and re-identification to be tied to causal processes. (shrink)

In my book How the Mind Works, I defended the theory that the human mind is a naturally selected system of organs of computation. Jerry Fodor claims that 'the mind doesn't work that way'(in a book with that title) because (1) Turing Machines cannot duplicate humans' ability to perform abduction (inference to the best explanation); (2) though a massively modular system could succeed at abduction, such a system is implausible on other grounds; and (3) evolution adds nothing to our understanding (...) of the mind. In this review I show that these arguments are flawed. First, my claim that the mind is a computational system is different from the claim Fodor attacks (that the mind has the architecture of a Turing Machine); therefore the practical limitations of Turing Machines are irrelevant. Second, Fodor identifies abduction with the cumulative accomplishments of the scientific community over millennia. This is very different from the accomplishments of human common sense, so the supposed gap between human cognition and computational models may be illusory. Third, my claim about biological specialization, as seen in organ systems, is distinct from Fodor's own notion of encapsulated modules, so the limitations of the latter are irrelevant. Fourth, Fodor's arguments dismissing of the relevance of evolution to psychology are unsound. (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.

The goal of this paper is to encourage a reconfiguration of the discussion about typology in biology away from the metaphysics of essentialism and toward the epistemology of classifying natural phenomena for the purposes of empirical inquiry. First, I briefly review arguments concerning ‘typological thinking’, essentialism, species, and natural kinds, highlighting their predominantly metaphysical nature. Second, I use a distinction between the aims, strategies, and tactics of science to suggest how a shift from metaphysics to epistemology might be accomplished. Typological (...) thinking can be understood as a scientific tactic that involves representing natural phenomena using idealizations and approximations, which facilitates explanation, investigation, and theorizing via abstraction and generalization. Third, a variety of typologies from different areas of biology are introduced to emphasize the diversity of this representational reasoning. One particular example is used to examine how there can be epistemological conflict between typology and evolutionary analysis. This demonstrates that alternative strategies of typological thinking arise due to the divergent explanatory goals of researchers working in different disciplines with disparate methodologies. I conclude with several research questions that emerge from an epistemological reconfiguration of typology. (shrink)

"--Richard Grandy, Rice University "This is the first compelling diagnosis of what has gone awry in the raging 'science wars.

Throughout, this book questions our accepted definitions and biases, showing the self-reflective nature of scientific activity within society.

Extreme variation in the meaning of the term “species” throughout the history of biology has often frustrated attempts of historians, philosophers and biologists to communicate with one another about the transition in biological thinking from the static species concept to the modern notion of evolving species. The most important change which has underlain all the other fluctuations in the meaning of the word “species” is the change from it denoting such metaphysical entities as essences, Forms or Natures to denoting classes (...) of individual organisms. Several authors have taken notice of the role of metaphysics in the work of particular biologists. An attempt will be made in this paper to present a systematic investigation of the role which metaphysics has played in the work of representative biologists throughout the history of biology, especially as it relates to their species concepts. (shrink)

The unifying theme of these thirteen essays is understanding.

The focus of this volume, which collects both recent and now-classic essays, is the historical emergence of concepts and objects, through new uses of words and ...

Required reading at more than 100 colleges and universities throughout North America.

Philosophers of science typically associate the causal-mechanical view of scientific explanation with the work of Railton and Salmon. In this paper I shall argue that the defects of this view arise from an inadequate analysis of the concept of mechanism. I contrast Salmon's account of mechanisms in terms of the causal nexus with my own account of mechanisms, in which mechanisms are viewed as complex systems. After describing these two concepts of mechanism, I show how the complex-systems approach avoids certain (...) objections to Salmon's account of causal-mechanical explanation. I conclude by discussing how mechanistic explanations can provide understanding by unification. (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)

University of Copenhagen University of Copenhagen University of Copenhagen Blegdamsvej 17 Njalsgade 80 Njalsgade 80 DK-2100 Copenhagen Ø DK 2300 Copenhagen S DK-2300 Copenhagen S Denmark.

With this manifesto, John Dupré systematically attacks the ideal of scientific unity by showing how its underlying assumptions are at odds with the central conclusions of science itself.

In exploring the nature of psychological explanation, this book looks at how psychologists theorize about the human ability to calculate, to speak a language and the like. It shows how good theorizing explains or tries to explain such abilities as perception and cognition. It recasts the familiar explanations of "intelligence" and "cognitive capacity" as put forward by philosophers such as Fodor, Dennett, and others in terms of a theory of explanation that makes established doctrine more intelligible to professionals and their (...) students.In particular, the book shows that vestigial adherence to the positivists' D-N model has distorted the view of philosophers of science about what psychologists (and biologists) do and has masked the real nature of explanation. Major sections in the book cover Analysis and Subsumption; Functional Analysis; Understanding Cognitive Capacities; and Historical Reflections.Robert Cummins is Associate Professor of Philosophy at the University of Illinois, Chicago Circle. A Bradford Book. (shrink)

Despite the traditional focus on metaphysical issues in discussions of natural kinds in biology, epistemological considerations are at least as important. By revisiting the debate as to whether taxa are kinds or individuals, I argue that both accounts are metaphysically compatible, but that one or the other approach can be pragmatically preferable depending on the epistemic context. Recent objections against construing species as homeostatic property cluster kinds are also addressed. The second part of the paper broadens the perspective by considering (...) homologues as another example of natural kinds, comparing them with analogues as functionally defined kinds. Given that there are various types of natural kinds, I discuss the different theoretical purposes served by diverse kind concepts, suggesting that there is no clear-cut distinction between natural kinds and other kinds, such as functional kinds. Rather than attempting to offer a unique metaphysical account of ‘natural’ kind, a more fruitful approach consists in the epistemological study of how different natural kind concepts are employed in scientific reasoning. (shrink)

We will show that there is a strong form of emergence in cell biology. Beginning with C.D. Broad's classic discussion of emergence, we distinguish two conditions sufficient for emergence. Emergence in biology must be compatible with the thought that all explanations of systemic properties are mechanistic explanations and with their sufficiency. Explanations of systemic properties are always in terms of the properties of the parts within the system. Nonetheless, systemic properties can still be emergent. If the properties of the components (...) within the system cannot be predicted, even in principle, from the behavior of the system's parts within simpler wholes then there also will be systemic properties which cannot be predicted, even in principle, on basis of the behavior of these parts. We show in an explicit case study drawn from molecular cell physiology that biochemical networks display this kind of emergence, even though they deploy only mechanistic explanations. This illustrates emergence and its place in nature. (shrink)

An analysis of two heuristic strategies for the development of mechanistic models, illustrated with historical examples from the life sciences. In Discovering Complexity, William Bechtel and Robert Richardson examine two heuristics that guided the development of mechanistic models in the life sciences: decomposition and localization. Drawing on historical cases from disciplines including cell biology, cognitive neuroscience, and genetics, they identify a number of "choice points" that life scientists confront in developing mechanistic explanations and show how different choices result in divergent (...) explanatory models. Describing decomposition as the attempt to differentiate functional and structural components of a system and localization as the assignment of responsibility for specific functions to specific structures, Bechtel and Richardson examine the usefulness of these heuristics as well as their fallibility—the sometimes false assumption underlying them that nature is significantly decomposable and hierarchically organized. When Discovering Complexity was originally published in 1993, few philosophers of science perceived the centrality of seeking mechanisms to explain phenomena in biology, relying instead on the model of nomological explanation advanced by the logical positivists (a model Bechtel and Richardson found to be utterly inapplicable to the examples from the life sciences in their study). Since then, mechanism and mechanistic explanation have become widely discussed. In a substantive new introduction to this MIT Press edition of their book, Bechtel and Richardson examine both philosophical and scientific developments in research on mechanistic models since 1993. (shrink)

Stuart Kauffman here presents a brilliant new paradigm for evolutionary biology, one that extends the basic concepts of Darwinian evolution to accommodate recent findings and perspectives from the fields of biology, physics, chemistry and mathematics. The book drives to the heart of the exciting debate on the origins of life and maintenance of order in complex biological systems. It focuses on the concept of self-organization: the spontaneous emergence of order widely observed throughout nature. Kauffman here argues that self-organization plays an (...) important role in the emergence of life itself and may play as fundamental a role in shaping life's subsequent evolution as does the Darwinian process of natural selection. Yet until now no systematic effort has been made to incorporate the concept of self-organization into evolutionary theory. The construction requirements which permit complex systems to adapt remain poorly understood, as is the extent to which selection itself can yield systems able to adapt more successfully. This book explores these themes. It shows how complex systems, contrary to expectations, can spontaneously exhibit stunning degrees of order, and how this order, in turn, is essential for understanding the emergence and development of life on Earth. Topics include the new biotechnology of applied molecular evolution, with its important implications for developing new drugs and vaccines; the balance between order and chaos observed in many naturally occurring systems; new insights concerning the predictive power of statistical mechanics in biology; and other major issues. Indeed, the approaches investigated here may prove to be the new center around which biologicalscience itself will evolve. The work is written for all those interested in the cutting edge of research in the life sciences. (shrink)

Observation and conceptual interpretation constitute the two major ways through which human beings engage the world. _The World Observed/The World Conceived _presents an innovative analysis of the nature and role of observation and conceptualization. While these two actions are often treated as separate, Hans Radder shows that they are inherently interconnected-that materially realized observational processes are always conceptually interpreted and that the meaning of concepts depends on the way they structure observational processes and abstract from them. He examines the role (...) of human action and conceptualization in realizing observational processes and develops a detailed theory of the relationship between observation, abstraction, and the meaning of concepts. This book provides a critical analysis of the work of various other philosophers and their accounts of scientific and ordinary-life observation and conceptualization. Radder discusses the formation and nature of concepts and demonstrates how concepts structure the phenomenal world. He then introduces and defines the notions of extensible concepts, abstraction and nonlocal meanings and explores the philosophical implications of his theory. _The World Observed/The World Conceived_ offers fresh insights in practices of observation and conceptualization, that will prove useful to many areas of scholarly study including ontology, epistemology, philosophy of language, philosophy of science, science studies, and cognitive science. (shrink)

This book offers a philosophy for error-prone humans trying to understand messy systems in the real world.

Contributors: Rodney A. Brooks, Paul M. Churchland, Andy Clark, Daniel C. Dennett, Hubert L. Dreyfus, Jerry A. Fodor, Joseph Garon, John Haugeland, Marvin...

FEW HEROES LOWER their sights in the prime of their lives; triumph leads inexorably on, often to destruction. Alexander wept because he had no new worlds to conquer; Napoleon, overextended, sealed his doom in the depth of a Russian winter. But Charles Darwin did not follow the Origin of Species (1859) with a general defense of natural selection or with its evident extension to human evolution (he waited until 1871 to publish The Descent of Man). Instead, he wrote his most (...) obscure work, a book entitled: On the Various Contrivances by Which British and Foreign Orchids Are Fertilized by Insects (1862). (shrink)

Carl Craver investigates what we are doing when we sue neuroscience to explain what's going on in the brain.

As Aristotle stated, scientific explanation is based on deductive argument--yet, Wesley C. Salmon points out, not all deductive arguments are qualified explanations. The validity of the explanation must itself be examined. _Four Decades of Scientific Explanation_ provides a comprehensive account of the developments in scientific explanation that transpired in the last four decades of the twentieth century. It continues to stand as the most comprehensive treatment of the writings on the subject during these years. Building on the historic 1948 essay (...) by Carl G. Hempel and Paul Oppenheim, "Studies in the Logic of Explanation,” which introduced the deductive-nomological model on which most work on scientific explanation was based for the following four decades, Salmon goes beyond this model's inherent basis of describing empirical knowledge to tells us “not only _what,_ but also _why_.” Salmon examines the predominant models in chronological order and describes their development, refinement, and criticism or rejection. _Four Decades of Scientific Explanation_ underscores the need for a consensus of approach and ongoing evaluations of methodology in scientific explanation, with the goal of providing a better understanding of natural phenomena. (shrink)

This article began as a review of a conference, organized by Gerhard Schlosser, entitled “Modularity in Development and Evolution.” The conference was held at, and sponsored by, the Hanse Wissenschaftskolleg in Delmenhorst, Germany in May, 2000. The article subsequently metamorphosed into a literature and concept review as well as an analysis of the differences in current perspectives on modularity. Consequently, I refer to general aspects of the conference but do not review particular presentations. I divide modules into three kinds: structural, (...) developmental, and physiological. Every module fulfills none, one, or multiple functional roles. Two further orthogonal distinctions are important in this context: module-kinds versus module-variants-of-a-kind and reproducer versus nonreproducer modules. I review criteria for individuation of modules and mechanisms for the phylogenetic origin of modularity. I discuss conceptual and methodological differences between developmental and evolutionary biologists, in particular the difference between integration and competition perspectives on individualization and modular behavior. The variety in views regarding modularity presents challenges that require resolution in order to attain a comprehensive, rather than a piecemeal and fragmentary, evolutionary developmental biology. (shrink)

Maximum Parsimony (MP) and Maximum Likelihood (ML) are two methods for evaluating which phlogenetic tree is best supported by data on the characteristics of leaf objects (which may be species, populations, or individual organisms). MP has been criticized for assuming that evolution proceeds parsimoniously -- that if a lineage begins in state i and ends in state j, the way it got from i to j is by the smallest number of changes. MP has been criticized for needing to assume (...) some model or other of the evolutionary process even though biologists often do not know what that process really is. This paper critically evaluates both criticisms. (shrink)