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.

This set contains Murray's renowned _English Grammar_, and his textbooks. The unique study of Murray's life and work, by Colin Eaton West is here updated with new notes by David A. Reibel.

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

Reasoning in Biological Discoveries brings together a series of essays, which focus on one of the most heavily debated topics of scientific discovery. Collected together and richly illustrated, Darden's essays represent a groundbreaking foray into one of the major problems facing scientists and philosophers of science. Divided into three sections, the essays focus on broad themes, notably historical and philosophical issues at play in discussions of biological mechanism; and the problem of developing and refining reasoning strategies, including interfield relations and (...) anomaly resolution. Darden summarizes the philosophy of discovery and elaborates on the role that mechanisms play in biological discovery. Throughout the book, she uses historical case studies to extract advisory reasoning strategies for discovery. Examples in genetics, molecular biology, biochemistry, immunology, neuroscience and evolutionary biology reveal the process of discovery in action. (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)

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)

David Hume's claim that necessary connection is essential to causality was at the expense of a useful causal distinction we sometimes note with the words ‘necessity’ and ‘contingency’. And since, as J. L. Mackie has stated, Hume made ‘the most significant and influential single contribution to the theory of causation’, subsequent writers on causality, regardless of their support for, or opposition to, Hume, have joined him in trampling this distinction. The object of this paper is not so much to undermine (...) one of Hume's conclusions as it is to describe a use of ‘necessary’ that, while surviving in popular usage, is ignored or obfuscated in the literature on causality. (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)

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.

The new research program to understand mechanisms in biology has developed rapidly in the last 10 years. Reconsideration of the characterization of mechanisms in biology in the light of this recent work is now in order. This article discusses the perspectival aspect of the characterization of mechanisms, refinements in claims about working entities and kinds of activities, challenges and responses to claims about regularity, productive continuity, and the organizational aspects of a mechanism, and issues about representations of mechanisms in schemas (...) and sketches. †To contact the author, please write to: Committee for Philosophy and the Sciences, Department of Philosophy, 1125A Skinner Building, University of Maryland, College Park, MD 20742 USA; e‐mail: [email protected]. (shrink)

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

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

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)

Podemos dizer que a predominância da forma sobre a matéria - ontologicamente, em hierarquia e em dignidade - no pensamento medieval é quase unânime. Na maior parte das propostas medievais de compatibilização entre filosofia e religião, a matéria sensível foi vista como bastarda, como fonte da imperfeição, da carência e da falha, e, por vezes, associada diretamente ao mal e ao pecado. A imagem da matéria como mulher pecadora de origem duvidosa está já presente em Ibn Sina e passa a (...) Maimônides que, comparando-a à adúltera, afirma que, apesar de manter um vínculo marital com uma forma, não cessa de mover-se, buscando constantemente outra forma para substituí-la. Pelas particularidades de sua doutrina, Ibn Gabirol não teve problemas ao abordar essa questão, inclusive quanto a indicar a origem da matéria – tema evitado pela maioria dos filósofos - mas não sem despertar fortes críticas de seus leitores contemporâneos e ao longo especificamente em relação à matéria, levantamos aqui as seguintes: 1) matéria não é corpo; 2) a matéria inteligível não é essencialmente distinta da matéria sensível; 3) a matéria não é a fonte da diversidade e da multiplicidade; 4) a matéria provém diretamente da Essência de Deus. Portanto, ainda que Ibn Gabirol mantenha as qualidades que, por outros filósofos, foram entendidas como sendo o caráter volúvel dessa mulher – ou seja, o fato de que ela está sempre apta a receber muitas formas – nada há que desabone sua conduta. (shrink)

Democracy establishes relationships of political equality, ones in which citizens equally share authority over what they do together and respect one another as equals. But in today's divided public square, democracy is challenged by political thinkers who disagree about how democratic institutions should be organized, and by antidemocratic politicians who exploit uncertainties about what democracy requires and why it matters. Democratic Equality mounts a bold and persuasive defense of democracy as a way of making collective decisions, showing how equality of (...) authority is essential to relating equally as citizens. James Lindley Wilson explains why the US Senate and Electoral College are urgently in need of reform, why proportional representation is not a universal requirement of democracy, how to identify racial vote dilution and gerrymandering in electoral districting, how to respond to threats to democracy posed by wealth inequality, and how judicial review could be more compatible with the democratic ideal. What emerges is an emphatic call to action to reinvigorate our ailing democracies, and a road map for widespread institutional reform. Democratic Equality highlights the importance of diverse forms of authority in democratic deliberation and electoral and representative processes—and demonstrates how that authority rests equally with each citizen in a democracy. (shrink)

What does the abundance of data and proliferation of data-making methods mean for the ordinary person, the person on the street? And, what could they come to mean? In this paper, we present an overview of a year-long project to examine just such questions and complicate, in some ways, what it is to ask them. The project is a collective exercise in which we – a mixture of social scientists, designers and makers – and those living and working on one (...) street in Cambridge, Tenison Road, are working to think through how data might be materialised and come to matter. The project aims to better understand the specificities and contingencies that arise when data is produced and used in place. Mid-way through the project, we use this commentary to give some background to the work and detail one or two of the troubles we have encountered in putting locally relevant data to work. We also touch on a methodological standpoint we are working our way into and through, one that we hope complicates the separations between subject and object in data-making and opens up possibilities for a generative refiguring of the manifold relations. (shrink)

Philosophy & Public Affairs, Volume 50, Issue 2, Page 169-201, Spring 2022.

The author presents a history of the attempts to find the final "theory of everything," gives a forceful argument that one can never be found, and a warning that the compromises necessary to produce a final theory may well undermine the rules of doing good science. At the heart of the story is the rise of the particle physicists and their attempts to reach far out into the cosmos for a unifying theory. Unable to subject their findings and theories to (...) experimental scrutiny, they have moved into a world governed entirely by mathematical and highly speculative theories, none of which can be empirically verified. "Does physics then become a branch of aesthetics?" Lindley asks. For an opposing viewpoint, see Stephen Weinberg's Dreams of a Final Theory. Annotation copyright by Book News, Inc., Portland, OR. (shrink)

This paper examines the hypothesis that analogies may play a role in the generation of new ideas that are built into new explanatory theories. Methods of theory construction by analogy, by failed analogy, and by modular components from several analogies are discussed. Two different analyses of analogy are contrasted: direct mapping (Mary Hesse) and shared abstraction (Michael Genesereth). The structure of Charles Darwin's theory of natural selection shows various analogical relations. Finally, an "abstraction for selection theories" is shown to be (...) the structure of a number of theories. (shrink)

The nature of the product to be discovered guides the reasoning to discover it. Biologists and medical researchers often search for mechanisms. The "new mechanistic philosophy of science" provides resources about the nature of biological mechanisms that aid the discovery of mechanisms. Here, we apply these resources to the discovery of mechanisms in medicine. A new diagrammatic representation of a disease mechanism chain indicates both what is known and, most significantly, what is not known at a given time, thereby guiding (...) the researcher and collaborators in discovery. Mechanisms of genetic diseases provide the examples. (shrink)

This note discusses lecture plates at the Hugo de Vries Laboratorium that may be relevant to Hugo de Vries's claim to have independently discovered Mendel's law of segregation. Dating when the plates were made is problematic.

In the early seventeenth century Galileo broke free from the hold of ancient Platonic and Aristotelian philosophy. He drastically changed the framework through which we view the natural world when he asserted that we should base our theory of reality on what we can observe rather than pure thought. In the process, he invented what we would come to call science. This set the stage for all the breakthroughs that followed--from Kepler to Newton to Einstein. But in the early twentieth (...) century when quantum physics, with its deeply complex mathematics, entered into the picture, something began to change. Many physicists began looking to the equations first and physical reality second. As we investigate realms further and further from what we can see and what we can test, we must look to elegant, aesthetically pleasing equations to develop our conception of what reality is. As a result, much of theoretical physics today is something more akin to the philosophy of Plato than the science to which the physicists are heirs. In The Dream Universe, Lindley asks what is science when it becomes completely untethered from measurable phenomena? (shrink)

Few revolutions in science have been more far-reaching--but less understood--than the quantum revolution in physics. Everyday experience cannot prepare us for the sub-atomic world, where quantum effects become all-important. Here, particles can look like waves, and vice versa; electrons seem to lose their identity and instead take on a shifting, unpredictable appearance that depends on how they are being observed; and a single photon may sometimes behave as if it could be in two places at once. In the world of (...) quantum mechanics, uncertainty and ambiguity become not just unavoidable, but essential ingredients of science--a development so disturbing that to Einstein "it was as if God were playing dice with the universe." And there is no one better able to explain the quantum revolution as it approaches the century mark than David Lindley. He brings the quantum revolution full circle, showing how the familiar and trustworthy reality of the world around us is actually a consequence of the ineffable uncertainty of the subatomic quantum world--the world we can't see. (shrink)

In 1958, Francis Crick distinguished the flow of information from the flow of matter and the flow of energy in the mechanism of protein synthesis. Crick’s claims about information flow and coding in molecular biology are viewed from the perspective of a new characterization of mechanisms and from the perspective of information as holding a key to distinguishing work in molecular biology from that of biochemistry in the 1950s–1970s . Flow of matter from beginning to end does not occur in (...) the protein synthesis mechanism; flow of information does. The flow of information and coding in molecular biological mechanisms are distinguished, on the one hand, from formal information theory, and, on the other, from information as used in cognitive neuroscience, where information and representation are often coupled. (shrink)

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)