I have been asked to discuss how computers have affected my work in philosophy. This paper discusses the use of artificial intelligence (AI) models to investigate both the representation of scientific knowledge and reasoning strategies for scientific change. The focus is on the reasoning strategies used to revise a theory, given an anomaly, which is a failed prediction of the theory.
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 (and ways of mitigating rampant perspectivalism), 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: firstname.lastname@example.org. (shrink)
Reasoning in Biological Discoveries brings together a series of essays which focus on one of the most heavily debated topics of scientific discovery today. Collected together and richly illustrated for the first time in this edition, Darden's essays represent a ground-breaking 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. Published here for the first time, 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)
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.
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)
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)
Summary 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.
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)
This paper analyzes features of the emergence of new fields in science by examining the cases of cytology and biochemistry. The first step in the emergence of these new fields was the discovery of a new entity. A subsequent claim was made that entities of this kind are found more generally; making this generalization constituted the construction of a new theory. As a line of research to test the theory began, a new domain was formed and the new field (...) emerged. In each case the theory proposed a new solution to an old problem in science. Some implications of this analysis for understanding the emergence of other fields are indicated. (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)