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.

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)

Contents: Preface. - Introduction. - Science as a caricature of reality. - Three methodological revolutions. - The method of idealization. - Explanations and applications. - Truth and idealization. - A generalization of idealization. - References.

Frederick Suppe has come to enjoy a position of undisputed leadership in the post-positivistic philosophy of science.

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)

Philosophers of science increasingly recognize the importance of idealization: the intentional introduction of distortion into scientific theories. Yet this recognition has not yielded consensus about the nature of idealization. e literature of the past thirty years contains disparate characterizations and justifications, but little evidence of convergence towards a common position.

The modern history of verisimilitude can be divided into three periods. The first began in 1960, when Karl Popper proposed his qualitative definition of what it is for one theory to be more truthlike than another theory, and lasted until 1974, when David Miller and Pavel Trichý published their refutation of Popper's definition. The second period started immediately with the attempt to explicate truthlikeness by means of relations of similarity or resemblance between states of affairs (or their linguistic representations); the (...) work within this similarity approach was summarized in the books of Graham Oddie [1986] and Ilkka Niiniluoto [1987]. During the subsequent third period, studies in verisimilitude have been actively continued, and interesting results and applications have been achieved, but not many dramatic novelties. While it is now obsolete to claim that truthlikeness with reasonable properties cannot be defined at all, there is still a lot of controversy about the best and least arbitrary approach to doing this. (shrink)

Approaches to explanation -- Causal and explanatory relevance -- The kairetic account of /D making -- The kairetic account of explanation -- Extending the kairetic account -- Event explanation and causal claims -- Regularity explanation -- Abstraction in regularity explanation -- Approaches to probabilistic explanation -- Kairetic explanation of frequencies -- Kairetic explanation of single outcomes -- Looking outward -- Looking inward.

Excerpts from Robert Nozick's "Invariances" Necessary truths are invariant across all possible worlds, contingent ones across only some.

Counterfactuals is David Lewis' forceful presentation of and sustained argument for a particular view about propositions which express contrary to fact conditionals, including his famous defense of realism about possible worlds and his theory of laws of nature.

Ever since David Hume, empiricists have barred powers and capacities from nature. In this book Cartwright argues that capacities are essential in our scientific world, and, contrary to empiricist orthodoxy, that they can meet sufficiently strict demands for testability. Econometrics is one discipline where probabilities are used to measure causal capacities, and the technology of modern physics provides several examples of testing capacities (such as lasers). Cartwright concludes by applying the lessons of the book about capacities and probabilities to the (...) explanation of the role of causality in quantum mechanics. (shrink)

In this sequence of philosophical essays about natural science, the author argues that fundamental explanatory laws, the deepest and most admired successes of modern physics, do not in fact describe regularities that exist in nature. Cartwright draws from many real-life examples to propound a novel distinction: that theoretical entities, and the complex and localized laws that describe them, can be interpreted realistically, but the simple unifying laws of basic theory cannot.

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.

Accounts of the relation between theories and models in biology concentrate on mathematical models. In this paper I consider the dual role of models as representations of natural systems and as a material basis for theorizing. In order to explicate the dual role, I develop the concept of a remnant model, a material entity made from parts of the natural system(s) under study. I present a case study of an important but neglected naturalist, Joseph Grinnell, to illustrate the extent to (...) which mundane practices in a museum setting constitute theorizing. I speculate that historical and sociological analyses of institutions can play a specific role in the philosophical analysis of model-building strategies. (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.

Scientific models may be more useful for false assumptions they make than true ones when one is interested not in the fit of the model, but in the form of the residuals. Modeling Darwin’s “blending” theory of inheritance shows how it illuminates features of Mendelian theory. Insufficient understanding of it leads to incorrect moves in modeling population structure. But it may prove even more useful for organizing a theory of cultural evolution. Analysis of “blending” inheritance gives new tools for recognizing (...) population structure for culture and for understanding differences between biological and cultural inheritance. (shrink)

The modern history of verisimilitude can be divided into three periods. The first began in 1960, when Karl Popper proposed his qualitative definition of what it is for one theory to be more truthlike than another theory, and lasted until 1974, when David Miller and Pavel Trich published their refutation of Popper's definition. The second period started immediately with the attempt to explicate truthlikeness by means of relations of similarity or resemblance between states of affairs (or their linguistic representations); the (...) work within this similarity approach was summarized in the books of Graham Oddie [1986] and Ilkka Niiniluoto [1987]. During the subsequent third period, studies in verisimilitude have been actively continued, and interesting results and applications have been achieved, but not many dramatic novelties. While it is now obsolete to claim that truthlikeness with reasonable properties cannot be defined at all, there is still a lot of controversy about the best and least arbitrary approach to doing this. (shrink)

In the 1950s and 1960s, an interfield interaction between molecular biologists and biochemists integrated important discoveries about the mechanism of protein synthesis. This extended discovery episode reveals two general reasoning strategies for eliminating gaps in descriptions of the productive continuity of mechanisms: schema instantiation and forward chaining/backtracking. Schema instantiation involves filling roles in an overall framework for the mechanism. Forward chaining and backtracking eliminate gaps using knowledge about types of entities and their activities. Attention to mechanisms highlights salient features of (...) this historical episode while providing general reasoning strategies for mechanism discovery. (shrink)

Using the Schwarzschild calculation of the Relativistic bending of starlight near the sun as an illustration, it is shown that the relationship between theory and data requires a hierarchy of structures of different logical type. An essential feature of this hierarchy is the use of idealizations and approximate truths. On the basis of a counterfactual analysis of these concepts, it is shown that confirmation is possible even though statistical measures of goodness of fit are not satisfied. The consequences of this (...) view of confirmation and hierarchical structure for scientific realism are then considered. (shrink)

This book comes to the rescue of scientific realism, showing that reports of its death have been greatly exaggerated. Philosophical realism holds that the aim of a particular discourse is to make true statements about its subject matter. Ilkka Niiniluoto surveys different kinds of realism in various areas of philosophy and then sets out his own critical realist philosophy of science.

The naive structuralist definition of truthlikeness is an idealization in the sense that it assumes that all mistaken models of a theory are equally bad. The natural concretization is a refined definition based on an underlying notion of structurelikeness.In Section 1 the naive definition of truthlikeness of theories is presented, using a new conceptual justification, in terms of instantial and explanatory mistakes.

This paper is an interpretation and defense of Richard Levins’ “The Strategy of Model Building in Population Biology,” which has been extremely influential among biologists since its publication 40 years ago. In this article, Levins confronted some of the deepest philosophical issues surrounding modeling and theory construction. By way of interpretation, I discuss each of Levins’ major philosophical themes: the problem of complexity, the brute-force approach, the existence and consequence of tradeoffs, and robustness analysis. I argue that Levins’ article is (...) concerned, at its core, with justifying the use of multiple, idealized models in population biology. (shrink)

Two decades of critique have sensitized historians and philosophers of science to the inadequacies of conventional dichotomies between theory and practice, thereby prompting the search for new ways of writing about science that are less beholden than the old ways to the epistemological mores of theoretical physics, and more faithful to the actual practices not only of physics but of all the natural sciences. The need for alternative descriptions seems particularly urgent if one is to understand the place of theory (...) (and, in parallel, the role of modeling) in contemporary molecular biology, a science where, until now, no division between theory and experiment has obtained, and where distinctions between representing and intervening, and more generally, between basic and applied science, are daily becoming more blurred. Indeed, the very division between theory and experiment threatens to slight the extensive and sophisticated theoretical analyses (and even modeling) on which experimental work in contemporary molecular biology so often depends. My aim in this paper is to find a way of talking about theoretical practices in biology that is directly rooted in the mix of conceptual and material work that biologists do. As an example of such theoretical practices, I choose for the focus of my analysis the development of a model for gene regulation out of the experimental work of Eric Davidson and his colleagues at Cal Tech. (shrink)

We distinguish dynamical and statistical interpretations of evolutionary theory. We argue that only the statistical interpretation preserves the presumed relation between natural selection and drift. On these grounds we claim that the dynamical conception of evolutionary theory as a theory of forces is mistaken. Selection and drift are not forces. Nor do selection and drift explanations appeal to the (sub-population-level) causes of population level change. Instead they explain by appeal to the statistical structure of populations. We briefly discuss the implications (...) of the statistical interpretation of selection for various debates within the philosophy of biologythe `explananda of selection' debate and the `units of selection' debate. (shrink)

Various laws and theories in the natural and social sciences are presented with a view to discerning the syntactic and semantic characteristics of many idealizations in science. Three different kinds of idealizations are discussed: ideal conditions, ideal cases, and idealized theories. An ideal condition is a formula in which state variables occur, whose existential closure is false, and for which there is another formula that can be constructed out of the original formula such that the existential closure of the new (...) formula is true. An ideal case is a statement which is logically equivalent to a universal conditional which has an ideal condition as its antecedent. And an idealized theory is a set of false universal conditional statements. Alternative syntactic and semantic analyses are viewed and criticized. (shrink)

Consider the reasonable axioms of subjunctive conditionals if p → q1 and p → q2 at some world, then p → at that world, and if p1 → q and p2 → q at some world, then → q at that world, where p → q is the subjunctive conditional. I show that a Lewis-style semantics for subjunctive conditionals satisfies these axioms if and only if one makes a certain technical assumption about the closeness relation, an assumption that is probably (...) false. I will then show how Lewisian semantics can be modified so as to assure and even when the technical assumption fails, and in fact in one sense the semantics actually becomes simpler then. (shrink)

In this article I offer an approach to counterfactuals based on a notion of objective probability. It is in the spirit of, though it does not fall squarely under, the metalinguistic model. Thus, it is not developed in terms of possible worlds, or notions parasitic on them (e.g., similarity). Its dominant features are rooted in objective probability and causal relevance (analyzed probabilistically), and thus it is not close in spirit to a maximal similarity or a minimal change approach.

Scientific models may be more useful for false assumptions they make than true ones when one is interested not in the fit of the model, but in the form of the residuals. Modeling Darwin's “blending” theory of inheritance shows how it illuminates features of Mendelian theory. Insufficient understanding of it leads to incorrect moves in modeling population structure. But it may prove even more useful for organizing a theory of cultural evolution. Analysis of “blending” inheritance gives new tools for recognizing (...) population structure for culture and for understanding differences between biological and cultural inheritance. (shrink)

Two decades of critique have sensitized historians and philosophers of science to the inadequacies of conventional dichotomies between theory and practice, thereby prompting the search for new ways of writing about science that are less beholden than the old ways to the epistemological mores of theoretical physics, and more faithful to the actual practices not only of physics but of all the natural sciences. The need for alternative descriptions seems particularly urgent if one is to understand the place of theory (...) in contemporary molecular biology, a science where, until now, no division between theory and experiment has obtained, and where distinctions between representing and intervening, and more generally, between basic and applied science, are daily becoming more blurred.Indeed, the very division between theory and experiment threatens to slight the extensive and sophisticated theoretical analyses on which experimental work in contemporary molecular biology so often depends. My aim in this paper is to find a way of talking about theoretical practices in biology that is directly rooted in the mix of conceptual and material work that biologists do. As an example of such theoretical practices, I choose for the focus of my analysis the development of a model for gene regulation out of the experimental work of Eric Davidson and his colleagues at Cal Tech. (shrink)

: Despite its amazing morphological diversity, life as we know it on Earth today is remarkably similar in its basic molecular architecture and biochemistry. The assumption that all life on Earth today shares these molecular and biochemical features is part of the paradigm of modern biology. This paper examines the possibility that this assumption is false, more specifically, that the contemporary Earth contains as yet unrecognized alternative forms of microbial life. The possibility that more than one form of life arose (...) on Earth is consistent with our current understanding of conditions on the early Earth and the biochemical and molecular possibilities for life. Arguments that microbial descendents of an alternative origin of life could not co-exist with familiar life are belied by what we know of the complexity and diversity of microbial communities. Furthermore, the tools that are currently used to explore the microbial world – microscopy (with the aid of techniques such as DAPI staining and fluorescence in situ hybridization), cultivation and PCR amplification of rRNA genes – could not detect such organisms if they existed. Thus, the fact that we have not discovered any alternative life forms cannot be taken as evidence that they do not exist. (shrink)