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 ...

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)

The relationship of part to whole is one of the most fundamental there is; this is the first and only full-length study of this concept. This book shows that mereology, the formal theory of part and whole, is essential to ontology. Peter Simons surveys and criticizes previous theories, especially the standard extensional view, and proposes a more adequate account which encompasses both temporal and modal considerations in detail. 'Parts could easily be the standard book on mereology for the next twenty (...) or thirty years.' Timothy Williamson, Grazer Philosophische Studien. (shrink)

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)

The Dappled World: A Study of the Boundaries of Science. nancy cartwright. Plato's Reception of Parmenides. john a. palmer.

Artificial intelligence research has foundered on the issue of representation. When intelligence is approached in an incremental manner, with strict reliance on interfacing to the real world through perception and action, reliance on representation disappears. In this paper we outline our approach to incrementally building complete intelligent Creatures. The fundamental decomposition of the intelligent system is not into independent information processing units which must interface with each other via representations. Instead, the intelligent system is decomposed into independent and parallel activity (...) producers which all interface directly to the world through perception and action, rather than interface to each other particularly much. The notions of central and peripheral systems evaporateeverything is both central and peripheral. Based on these principles we have built a very successful series of mobile robots which operate without supervision as Creatures in standard office environments. (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)

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)

Modularity has been the subject of intense debate in the cognitive sciences for more than 2 decades. In some cases, misunderstandings have impeded conceptual progress. Here the authors identify arguments about modularity that either have been abandoned or were never held by proponents of modular views of the mind. The authors review arguments that purport to undermine modularity, with particular attention on cognitive architecture, development, genetics, and evolution. The authors propose that modularity, cleanly defined, provides a useful framework for directing (...) research and resolving debates about individual cognitive systems and the nature of human evolved cognition. Modularity is a fundamental property of living things at every level of organization; it might prove indispensable for understanding the structure of the mind as well. (shrink)

The official model of explanation proposed by the logical empiricists, the covering law model, is subject to familiar objections. The goal of the present paper is to explore an unofficial view of explanation which logical empiricists have sometimes suggested, the view of explanation as unification. I try to show that this view can be developed so as to provide insight into major episodes in the history of science, and that it can overcome some of the most serious difficulties besetting the (...) covering law model. (shrink)

In the beginning, there was the DN (Deductive Nomological) model of explanation, articulated by Hempel and Oppenheim (1948). According to DN, scientific explanation is subsumption under natural law. Individual events are explained by deducing them from laws together with initial conditions (or boundary conditions), and laws are explained by deriving them from other more fundamental laws, as, for example, the simple pendulum law is derived from Newton's laws of motion.

This paper addresses the general problem of how to rationally choose an algorithm for phylogenetic inference. Specifically, the controversy between maximum likelihood (ML) and maximum parsimony (MP) perspectives is reframed within the philosophical issue of theory choice. A Kuhnian approach in which rationality is bounded and value-laden is offered and construed through the notion of a Style of Modeling. A Style is divided into four stages: collecting remnant models, constructing models of taxonomical identity, implementing modeling algorithms, and finally inferring and (...) confirming evolutionary trees or cladograms. The identification and investigation of styles is useful for exploring sociological and epistemological issues such as individuating scientific communities and assessing the rationality of algorithm choice. Regarding the last point, this paper suggests that the values motivating ML and MP perspectives are justified but only contextually; these algorithms also have normative force because they can be therapeutic by allowing us to rationally choose among several competing trees, nonetheless this force is limited and cannot be used in order to decide the controversy tout court. (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.

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, defences, objections, and replies into a convincing defence of the core of his theory, which is that we can analyse 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.

There are many ways of construing the claim that some categories are more “natural" than others. One can ask whether a system of categories is innate or acquired by learning, whether it pertains to a natural phenomenon or to a social institution, whether it is lexicalized in natural language or requires a compound linguistic expression. This renders suspect any univocal answer to this question in any particular case. Yet another question one can ask, which some authors take to have a (...) bearing on the issue of the naturalness of categories, is whether a system of categories constitutes a unique way of organizing a particular set of entities or phenomena, or whether there are other legitimate classification schemes that can coexist with it. Another way of putting this is by asking whether systems of categories can cut across one another, and if so, under what circumstances. Some philosophers have claimed that crosscutting systems of categories cannot exist as genuine natural kinds. This paper examines that claim and puts forward some counterexamples, concluding that this notion of natural kind is not in tune with scientific classification and ought to be rejected in favor of an alternative. (shrink)

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)

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)

Cognitivism in psychology and philosophy is roughly the position that intelligent behavior can (only) be explained by appeal to internal that is, rational thought in a very broad sense. Sections 1 to 5 attempt to explicate in detail the nature of the scientific enterprise that this intuition has inspired. That enterprise is distinctive in at least three ways: It relies on a style of explanation which is different from that of mathematical physics, in such a way that it is not (...) basically concerned with quantitative equational laws; the states and processes with which it deals are in the sense that they are regarded as meaningful or representational; and it is not committed to reductionism, but is open to reduction in a form different from that encountered in other sciences. Spelling these points out makes it clear that the Cognitivist study of the mind can be rigorous and empirical, despite its unprecedented theoretical form. The philosophical explication has another advantage as well: It provides a much needed framework for articulating questions about whether the Cognitivist approach is right or wrong. The last three sections take that advantage of the account, and address several such questions, pro and con. (shrink)

The unifying theme of these thirteen essays is understanding.

The rosy dawn of my title refers to that optimistic time when the logical concept of a natural kind originated in Victorian England. The scholastic twilight refers to the present state of affairs. I devote more space to dawn than twilight, because one basic problem was there from the start, and by now those origins have been forgotten. Philosophers have learned many things about classification from the tradition of natural kinds. But now it is in disarray and is unlikely to (...) be put back together again. My argument is less founded on objections to the numerous theories now in circulation, than on the sheer proliferation of incompatible views. There no longer exists what Bertrand Russell called ‘the doctrine of natural kinds’—one doctrine. Instead we have a slew of distinct analyses directed at unrelated projects. (shrink)

Selectionist evolutionary theory has often been faulted for not making novel predictions that are surprising, risky, and correct. I argue that it in fact exhibits the theoretical virtue of predictive capacity in addition to two other virtues: explanatory unification and model fitting. Two case studies show the predictive capacity of selectionist evolutionary theory: parallel evolutionary change in E. coli, and the origin of eukaryotic cells through endosymbiosis.

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