Review of T. Nickles (ed), Scientific Discovery: Case Studies.

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)

A scientific community cannot practice its trade without some set of received beliefs. These beliefs form the foundation of the "educational initiation that prepares and licenses the student for professional practice". The nature of the "rigorous and rigid" preparation helps ensure that the received beliefs are firmly fixed in the student's mind. Scientists take great pains to defend the assumption that scientists know what the world is like...To this end, "normal science" will often suppress novelties which undermine its foundations. Research (...) is therefore not about discovering the unknown, but rather "a strenuous and devoted attempt to force nature into the conceptual boxes supplied by professional education". (shrink)

This innovative book focuses on the development of the gene theory as a case study in scientific creativity.

Thomas S. Kuhn's classic book is now available with a new index.

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)

This paper analyzes the generation and function of hitherto ignored or misrepresented interfield theories , theories which bridge two fields of science. Interfield theories are likely to be generated when two fields share an interest in explaining different aspects of the same phenomenon and when background knowledge already exists relating the two fields. The interfield theory functions to provide a solution to a characteristic type of theoretical problem: how are the relations between fields to be explained? In solving this problem (...) the interfield theory may provide answers to questions which arise in one field but cannot be answered within it alone, may focus attention on domain items not previously considered important, and may predict new domain items for one or both fields. Implications of this analysis for the problems of reduction and the unity and progress of science are mentioned. (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.

Specifically designed to make the philosophy of mind intelligible to those not trained in philosophy, this book provides a concise overview for students and researchers in the cognitive sciences. Emphasizing the relevance of philosophical work to investigations in other cognitive sciences, this unique text examines such issues as the meaning of language, the mind-body problem, the functionalist theories of cognition, and intentionality. As he explores the philosophical issues, Bechtel draws connections between philosophical views and theoretical and experimental work in such (...) disciplines as cognitive psychology, artificial intelligence, linguistics, neuroscience, and anthropology. (shrink)

In this paper the common association between ontological reductionism and a methodological position called 'Mechanism' is discussed. Three major points are argued for: (1) Mechanism is not to be identified with reductionism in any of its forms; in fact, mechanism leads to a non-reductionist ontology. (2) Biological methodology is thoroughly mechanistic. (3) Mechanism is compatible with at least one form of teleology. Along the way the nature and value of scientific explanations, some recent controversies in biology and why reductionism has (...) proven to be such an attractive position are discussed. (shrink)

The first part of this paper has shown that the development of regulatory genetics and the lactose operon model stemmed from laboratory cultures rooted in local traditions. A "physiological" culture may be recognized in the Pasteurian context. The institutional continuity provided the basis for a tenuous link between Pasteur, Lwoff, and Monod. My claim is that the "national" value of regulatory and physiological genetics is an artifact produced in the course of the legitimization process accompanying the institutionalisation of the discipline. (...) In the 1960s, the lactose operon model was turned into a "flag-object," a symbol of the new culture. The work done by the Pasteurian group became therefore the most important, if not the only, exemplar of molecular biology in France.The second part o f the paper described the origins of general patterns that dominated the building of molecular biology in France. The study of the relationships between molecular biologists and biochemists or immunologists revealed the existence of alternatives to the development of operon research, or to the convergence with molecular biology. Both examples uncover specific paths leading to achievements that might be viewed as international trends: the expansion of RNA and translation studies, and the development of cellular immunology. They illustrate two possible patterns of linking local settings and disciplinary traditions: an oligopolistic situation where a few groups or one institution dominate an entire field, and the emergence of "collective" trends through collaboration networks or schools. (shrink)

(This insularity was further promoted by the guileless duplicity of scholars in other fields, who were all too prepared to bequeath "the problem of ...

Molecular biologists use different kinds of reasoning strategies for different tasks, such as hypothesis formation, experimental design, and anomaly resolution. More specifically, the reasoning strategies discussed in this paper may be characterized as (1) abstraction-instantiation, in which an abstract skeletal model is instantiated to produce an experimental system; (2) the systematic scan, in which alternative hypotheses are systematically generated; and (3) modular anomaly resolution, in which components of a model are stated explicitly and methodically changed to generate alternative changes to (...) resolve an anomaly. This work grew out of close observation over a period of six months of an actively functioning molecular genetics laboratory. (shrink)

Since the 1930s, scientists studying the neurological disease scrapie had assumed that the infectious agent was a virus. By the mid 1960s, however, several unconventional properties had arisen that were difficult to reconcile with the standard viral model. Evidence for nucleic acid within the pathogen was lacking, and some researchers considered the possibility that the infectious agent consisted solely of protein. In 1982, Stanley Prusiner coined the term `prion' to emphasize the agent's proteinaceous nature. This infectious protein hypothesis was denounced (...) by many scientists as `heretical'.This two-part essay asks why the concept of an infectious protein was considered controversial. Some biologists justified their evaluation of this hypothesis on the grounds that an infectious protein contradicted the `central dogma of molecular biology'. Others referred to vague theoretical constraints such as molecular biology's `theoretical structure' or `framework'. Examination of the objections raised by researchers reveals exactly what generalizations were being challenged by a protein model of infection.This two-part survey of scrapie and prion research reaches several conclusions: A theoretical framework is present in molecular biology, exerting its influence in hypothesis formation and evaluation; This framework consists of several related, yet separable, generalizations or `elements', including Francis Crick's Central Dogma and Sequence Hypothesis, plus notions concerning infection, replication, protein synthesis, and protein folding; The term `central dogma' has stretched beyond Crick's original 1958 definition to encompass at least two other `framework elements': replication and protein synthesis; and From the study of scrapie and related diseases, biological information has been delineated into at least two classes: sequential and what I call `conformational'.In Part I of this essay, a brief review of the central dogma was given, and the developments in scrapie research from 1965 to 1972 were traced. This section summarized many of the puzzling, non-virus-like properties of the scrapie agent. Alternative hypotheses to the viral explanation were presented, including early versions of a protein-only hypothesis. Part II of this essay will follow the developments in scrapie and prion research from the mid-1970s through 1991. The growing prominence of a protein-only model of infection will be countered by continued objections from many researchers to a pathogen devoid of nucleic acid. These objections will help illuminate those generalizations in molecular biology that were indeed challenged by a protein-only model of infection. (shrink)

In the above pages I have sketched a history of the genesis and comparative evaluation of the repressor model of genetic regulation of enzyme induction. I have not attempted in this article to carry out an analysis of the more scientifically interesting fully developed Jacob-Monod operon theory of genetic regulations but such an analysis of the operon theory would not, I believe, involve any additional logical or epistemological features than have been discussed above. I have argued that the above account (...) of the development of a theory of enzyme induction involved inferential moves and well-characterized desiderata, of both empirical and non-empirical character, in the genesis and evaluation of new hypotheses and theories. I have also contended that the reasoning displayed in the genesis of a theory is in a large measure identical to that utilized in evaluating a theory. Both of these conclusions are at variance with the views of philosophers such as H. Reichenbach, Sir Karl Popper, and C.G. Hempel who have argued that the genesis of new hypotheses is primarily an irrational affair and that only the context of justification is susceptible of rational reconstruction. In the alternative view presented here, scientific discovery and scientific justification represent the application in contexts, which are primarily telically distinguishable, of a fundamentally unitary logic of scientific inquiry. (shrink)

Selection type theories solve adaptation problems. Natural selection, clonal selection for antibody production, and selective theories of higher brain function are examples. An abstract characterization of typical selection processes is generated by analyzing and extending previous work on the nature of natural selection. Once constructed, this abstraction provides a useful tool for analyzing the nature of other selection theories and may be of use in new instances of theory construction. This suggests the potential fruitfulness of research to find other theory (...) types and construct their abstractions. (shrink)

The history of science is articulated by moments of discovery. Yet, these 'moments' are not simple or isolated events in science. Just as a scientific discovery illuminates our understanding of nature or of society, and reveals new connections among phenomena, so too does the history of scientific activity and the analysis of scientific reasoning illuminate the processes which give rise to moments of discovery and the complex network of consequences which follow upon such moments. Understanding discovery has not been, until (...) recently, a major concern of modem philosophy of science. Whether the act of discoyery was regarded as mysterious and inexplicable, or obvious and in no need of explanation, modem philosophy of science in effect bracketed the question. It concentrated instead on the logic of scientific explanation or on the issues of validation or justification of scientific theories or laws. The recent revival of interest in the context of discovery, indeed in the acts of discovery, on the part of philosophers and historians of science, represents no one particular method'ological or philosophical orientation. It proceeds as much from an empiricist and analytical approach as from a sociological or historical one; from considerations of the logic of science as much as from the alogical or extralogical contexts of scientific tho'¢tt and practice. But, in general, this new interest focuses sharply on the actual historical and contem porary cases of scientific discovery, and on an examination of the act or moment of discovery in situ. (shrink)

This paper investigated the part played by collaborative practices in chaneling the work of prominent biochemists into the development of molecular biology. The RNA collaborative network that emerged in the 1960s in France encompassed a continuum of activities that linked laboratories to policy-making centers. New institutional frameworks such as the DGRST committees were instrumental in establishing new patterns of funding, and in offering arenas for multidisciplinary debates and boundary assessment. It should be stressed however, that although this collaborative network was (...) based on centralized initiatives aimed at developing molecular biology as a new biological specialty, it operated above all as a nexus of practices. The main argument of this paper is that the central allocation of funds and resources, exemplified by the DGRST operation, actually enhanced the creation of a self-conscious community of biochemists turned molecular biologists by virtue of an increased circulation of tools, skills, and results that took place within the RNA network and a few analogous systems of exchange.Having hands on “things” viewed as identical for all practical purposes was a potent factor in changing the experimental systems and their meanings. Limited but shared means of doing helped to reduce uncertainties, change representations, and turn contingent decisions into meaningful choices. The collaborative enterprises then resulted in personal contacts and the transfer of skills and materials, which gradually incorporated the biochemical tools into systems producing facts relevant to molecular biology as defined by its early practitioners. In that sense, networking was a regulatory process that stabilized new research objects and acculturated French biochemists.The mere existence of such a collaborative network also changed the scale of the disciplining process. Collaborations may have been started for contingent motives, but multiple exchanges resulted in the emergence of a new collective, and amplified small displacements. Collaborations, however, worked both ways, and the RNA network may be viewed as an efficient “trading-post.” An unexpected outcome of the development of a conversion zone is the fact that, by the late 1960s, the former biochemists dominated the “new” world of molecular biology — both in terms of research habits, since interests in structural studies dominated the field, and in terms of institutional initiatives such as the creation of laboratories and institutes for molecular biology.As an example of the cognitive displacements achieved by the network, I have focused here on the stabilization of “messenger RNA” as a new biological entity. This process illustrates the role of “boundary objects” and other mediating innovations in the development of disciplinary structures. Students of science trained in the symbolic interactionism tradition have proposed that “boundary objects” enhance the multiple interactions between heterogeneous social worlds: they are robust enough to enhance unity, but plastic enough to be manipulated in different social and cultural contexts.81 Within the emerging network, messenger RNA was a weakly structured “genetic information carrier” in common use, but it could, at the same time, be a strongly structured “macromolecular structure” adapted to practical and local uses. Consequently, messenger RNA favored the association of groups of heterogeneous scientists with backgrounds and interests in medical biochemistry, genetics, physical chemistry, organic chemistry, and so forth. This contrast between general and local uses was also instrumental in integrating the manipulation of things and the negotiation of aims. In contrast to transfer RNAs, which in the French context remained objects for chemical (and mainly structural) studies, messenger RNA became a key component of the new culture of “genetic information”. Messenger RNA was a loose theoretical entity described as a “genetic information carrier” in the policy-making documents, while operational but tacit and more conflicting definitions prevailed at the bench. In other words, messenger RNA was not only a classical “boundary object” but also a “flag object,” which tightened the collaborative network by mediating between the DGRST offices and the laboratories. (shrink)

The discovery that some B vitamins are constituents of respiratory coenzymes led to the development of an interfield theory of the kind discussed by Darden and Maull. In this paper it is shown that the development of a useful interfield connection was made possible by two reconceptualizations: a reconceptualization that united two then-distinct fields giving rise to the concept of vitamins as dietary substances; and another reconceptualization that united two approaches to respiratory metabolism producing the idea that coenzymes are transport (...) vehicles. (shrink)