Lindley Darden

Lindley Darden
University of Maryland, College Park | UMD, UMCP, University of Maryland College Park · Department of Philosophy

Ph.D.

About

56
Publications
3,701
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3,882
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Introduction
Lindley Darden is a Professor Emerita and Research Professor in the Department of Philosophy, University of Maryland, College Park. Her research is in Philosophy of Science. She is working with John Moult's computational biology group at the University of Maryland's Institute for Bioscience and Biotechnology Research on the topic of "Discovery of genetic disease mechanisms." Their MecCog web-based system to aid discovery of genetic disease mechanisms: www.meccog.org
Additional affiliations
August 1974 - present
University of Maryland, College Park
Position
  • Professor of Philosophy

Publications

Publications (56)
Article
Motivation: Experimental findings on genetic disease mechanisms are scattered throughout the literature and represented in many ways, including unstructured text, cartoons, pathway diagrams, and network graphs. Integration and structuring of such mechanistic information greatly enhances its utility. Results: MecCog is a graphical framework for b...
Preprint
Full-text available
Motivation Experimental findings on genetic disease mechanisms are scattered throughout the literature and represented in many ways, including unstructured text, cartoons, pathway diagrams, and network graphs. Integration and structuring of such mechanistic information will greatly enhance its utility. Results MecCog is a graphical framework for b...
Article
Full-text available
Mechanism is a widely used concept in biology. In 2017, more than 10% of PubMed abstracts used the term. Therefore, searching for and reasoning about mechanisms is fundamental to much of biomedical research, but until now there has been almost no computational infrastructure for this purpose. Recent work in the philosophy of science has explored th...
Poster
Full-text available
This poster presents a conceptual framework, utilizing a newly developed analysis of disease mechanisms (Darden et al. 2018; forthcoming). The new mechanistic philosophy of science characterizes the components of mechanisms: entities and activities. Adapting this for genetic disease mechanisms yields the categories of "substate perturbations" plus...
Preprint
Full-text available
Mechanism is a widely used concept in biology: in 2017 more than 10% of PubMed abstracts used the term. Thus, searching for and reasoning about mechanisms is fundamental to much of biomedical research, but until now there has been almost no computational infrastructure for this purpose. Recent work in the philosophy of science has explored the cent...
Chapter
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 i...
Article
Full-text available
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 i...
Article
García-Sancho Miguel , Biology, Computing, and the History of Molecular Sequencing: From Proteins to DNA, 1945–2000 (Science, Technology and Medicine in Modern History) xv $+$ 242 pp., illus., apps., bibl., index (New York: Palgrave Macmillan, 2012), and paperback in 2015. $35.00, ISBN: 1137543329. - Volume 61 Issue 1 - Lindley Darden
Chapter
Explanatory and methodological reductionism in biology emphasises the importance of building explanations and pursuing research at ever-deeper levels of organisation. Integrationism, in contrast, emphasises the importance of building explanations at multiple levels of organisation or utilising findings from multiple scientific fields. Some of the p...
Preprint
Full-text available
This is a 2014 review of the history of the new mechanistic philosophy of science and discussion of some of the topics in philosophy of science and philosophy of biology to which it has been applied, such as scientific discovery, explanation, reduction, and function.
Book
This book uses case studies from across the life sciences to show how scientists open black boxes to reveal the hidden mechanisms that produce, underlie, or maintain phenomena characteristic of living things.
Chapter
Biologists use knowledge of mechanisms for explanation, prediction, and control. Philosophers of biology, working in the new mechanistic philosophy of science, have identified features of an adequate description of a biological mechanism. The very abstract schema term “cause” may refer to any of various components of a mechanism, or even conditions...
Chapter
The discovery of mechanisms occurs in cycles of generation, evaluation and revision of hypothesized mechanism sketches and schemata. A new analysis of the concept of a mechanism by Machamer, Darden and Craver (2000) points to hitherto unexplored aspects of mechanism discovery. Incomplete sketches have their black boxes filled as research proceeds....
Chapter
Explanatory and methodological reductionism in biology emphasizes the importance of building explanations and pursuing research at ever-deeper levels of organization. Explanatory and methodological integrationism, in contrast, emphasize the importance of building explanations and pursuing research at and between multiple levels of organization in h...
Article
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 perspectivai aspect of the characterization of mechanisms (and ways of mitigating rampant perspectivali...
Article
Generally speaking, making models for unknown mechanisms is the creative process in science. INTRODUCTION: MECHANISMS AND MODELS Biologists often seek to discover mechanisms. Knowledge of biological mechanisms is valuable because descriptions of them often play the roles attributed to general scientific theories. They provide explanations of puzzli...
Article
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,...
Article
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 wo...
Article
Full-text available
Book review of Michael Ruse's Darwin and Design: Does Evolution Have a Purpose? in ISIS, 95 (2004): 338-339. ISIS is the journal of the History of Science Society.
Article
Bulletin of the History of Medicine 77.4 (2003) 987-989 This book admirably succeeds in its goal of debunking myths about Barbara McClintock—myths created by previous biographers, scientists, and even McClintock herself. McClintock (1902-92) was a Nobel Prize-winning corn cytogeneticist whose career spanned the twentieth century. Nathaniel Comfort...
Article
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 st...
Article
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 f...
Conference Paper
A task in the philosophy of discovery is to find reasoning strategies for discovery, which fall into three categories: strategies for generation, evaluation and revision. Because mechanisms are often what is discovered in biology, a newc haracterization of mechanism aids in their discovery. A computational system for discovering mechanisms is sketc...
Article
Full-text available
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, re...
Article
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...
Article
Experiment design and execution is a central activity in the natural sciences. The SeqER system provides a general architecture for the integration of automated planning techniques with a variety of domain knowledge in order to plan scientific experiments. These planning techniques include rule-based methods and, especially, the use of derivational...
Article
Woodward and Devonis in their article, Toward a New Understanding of Scientific Change: Applying interfield theory to the history of psychology, extend the examples of interfield theories (such as those discussed in Darden & Maull, 1977) to cases from the history of psychology. In addition, they develop a comprehensive model of scientific change th...
Article
The processes scientists use to form new hypotheses are often regarded as mysterious and outside the scope of philosophy of science. Yet, some philosophers have addressed the issue and suggested that scientists use prior knowledge to guide the formation of new hypotheses by reasoning by analogy (Hanson, 1965; Hesse, 1966). This chapter examines met...
Chapter
The synthetic theory of evolution is a multi-level theory that serves to synthesize knowledge from fields at different levels of organization. It provides a solution to the problem of the origin of species. Biologists attempted to solve this problem for years, during which time the key fields emerged and developed to the point that the synthesis wa...
Article
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.
Chapter
This chapter discusses the recent tradition in the philosophy of science of understanding the rational means by which science changes. It discusses that the procedures exist for determining the postulates of a theory, as opposed to others, that are more likely to be in need of modification when evidence necessitates a change. In at least some cases...
Article
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...
Chapter
Philosophers of science have had relatively little to say about theory construction. Theories were treated by Popper (1960) and the logical empiricists (e.g., Hempel, 1966) as if they arose all at once by a creative leap of the imagination of a scientist, a process whose study was viewed as the province of the psychologist. Only after the creative...
Article
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...

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Project (1)
Project
The goal is to develop a computational representation system for disease mechanisms, based on the Machamer, Darden, Craver ("Thinking about Mechanisms" Philosophy of Science 2000) characterization of mechanisms, in terms of entities and activities. This will aid those with GWAS data about statistical association of mutations with diseases in exploring whether a mechanism connect the mutation with disease symptom(s). Expands discussion from Carl Craver and Lindley Darden (2013) In Search of Mechanisms (UChicago Press), Chapters 3 & 11.