This book introduces semantic representations of multiscale, multidomain physiological systems that link to qualitative reasoning and to quantitative analysis of biophysical processes in health and disease. Two major public health problems, diabetes and hypertension, serve as use-cases to illustrate the depth and rigor of such representations for logical inference and quantitative analysis. Central to this approach is the Ontology of Physics for Biology (OPB) that formally represents the foundations of classical physics and engineering system dynamics that are the basis for our understanding of biomedical entities, processes, and functional relationships. Furthermore, we introduce OPB-based software for annotating and abstracting available biosimulation models for reuse, recombination, and for archiving of physics-based biomedical knowledge. We have formalized and leveraged physics-based biological knowledge as a working view of physiology and biophysics from three distinct perspectives: (1) biologists and biomedical investigators, (2) biophysicists and bioengineers, and (3) biomedical ontologists and informaticists. We present a logical and intuitive semantics of classical physics as a tool for mediating and translating biophysical knowledge among biomedical domains. Daniel L. Cook, MD, PhD John H. Gennari, PhD Maxwell L. Neal, PhD
Leading philosophers and scientists consider what conclusions about color can be drawn when the latest analytic tools are applied to the most sophisticated color science.Philosophers and scientists have long speculated about the nature of color. Atomists such as Democritus thought color to be "conventional," not real; Galileo and other key figures of the Scientific Revolution thought that it was an erroneous projection of our own sensations onto external objects. More recently, philosophers have enriched the debate about color by aligning the most advanced color science with the most sophisticated methods of analytical philosophy. In this volume, leading scientists and philosophers examine new problems with new analytic tools, considering such topics as the psychophysical measurement of color and its implications, the nature of color experience in both normal color-perceivers and the color blind, and questions that arise from what we now know about the neural processing of color information, color consciousness, and color language. Taken together, these papers point toward a complete restructuring of current orthodoxy concerning color experience and how it relates to objective reality. Kuehni, Jameson, Mausfeld, and Niederee discuss how the traditional framework of a three-dimensional color space and basic color terms is far too simple to capture the complexities of color experience. Clark and MacLeod discuss the difficulties of a materialist account of color experience. Churchland, Cohen, Matthen, and Westphal offer competing accounts of color ontology. Finally, Broackes and Byrne and Hilbert discuss the phenomenology of color blindness.Contributors Justin Broackes, Alex Byrne, Paul M. Churchland, Austen Clark, Jonathan Cohen, David R. Hilbert, Kimberly A. Jameson, Rolf Kuehni, Don I.A. MacLeod, Mohan Matthen, Rainer Mausfeld, Richard Niederée, Jonathan Westphal
Scientists use concepts and principles that are partly specific for their subject matter, but they also share part of them with colleagues working in different fields. Compare the biological notion of a 'natural kind' with the general notion of 'confirmation' of a hypothesis by certain evidence. Or compare the physical principle of the 'conservation of energy' and the general principle of 'the unity of science'. Scientists agree that all such notions and principles aren't as crystal clear as one might wish. An important task of the philosophy of the special sciences, such as philosophy of physics, of biology and of economics, to mention only a few of the many flourishing examples, is the clarification of such subject specific concepts and principles. Similarly, an important task of 'general' philosophy of science is the clarification of concepts like 'confirmation' and principles like 'the unity of science'. It is evident that clarfication of concepts and principles only makes sense if one tries to do justice, as much as possible, to the actual use of these notions by scientists, without however following this use slavishly. That is, occasionally a philosopher may have good reasons for suggesting to scientists that they should deviate from a standard use. Frequently, this amounts to a plea for differentiation in order to stop debates at cross-purposes due to the conflation of different meanings. While the special volumes of the series of Handbooks of the Philosophy of Science address topics relative to a specific discipline, this general volume deals with focal issues of a general nature. After an editorial introduction about the dominant method of clarifying concepts and principles in philosophy of science, called explication, the first five chapters deal with the following subjects. Laws, theories, and research programs as units of empirical knowledge (Theo Kuipers), various past and contemporary perspectives on explanation (Stathis Psillos), the evaluation of theories in terms of their virtues (Ilkka Niiniluto), and the role of experiments in the natural sciences, notably physics and biology (Allan Franklin), and their role in the social sciences, notably economics (Wenceslao Gonzalez). In the subsequent three chapters there is even more attention to various positions and methods that philosophers of science and scientists may favor: ontological, epistemological, and methodological positions (James Ladyman), reduction, integration, and the unity of science as aims in the sciences and the humanities (William Bechtel and Andrew Hamilton), and logical, historical and computational approaches to the philosophy of science (Atocha Aliseda and Donald Gillies).The volume concludes with the much debated question of demarcating science from nonscience (Martin Mahner) and the rich European-American history of the philosophy of science in the 20th century (Friedrich Stadler). - Comprehensive coverage of the philosophy of science written by leading philosophers in this field - Clear style of writing for an interdisciplinary audience - No specific pre-knowledge required
Could all or part of our taken-as-established scientific conclusions, theories, experimental data, ontological commitments, and so forth have been significantly different? Science as It Could Have Been focuses on a crucial issue that contemporary science studies have often neglected: the issue of contingency within science. It considers a number of case studies, past and present, from a wide range of scientific disciplines—physics, biology, geology, mathematics, and psychology—to explore whether components of human science are inevitable, or if we could have developed an alternative successful science based on essentially different notions, conceptions, and results. Bringing together a group of distinguished contributors in philosophy, sociology, and history of science, this edited volume offers a comprehensive analysis of the contingency/inevitability problem and a lively and up-to-date portrait of current debates in science studies.
The question of the proper role of metaphysics in philosophy of science is both significant and contentious. The last few decades have seen considerable engagement with philosophical projects aptly described as "the metaphysics of science:" inquiries into natural laws and properties, natural kinds, causal relations, and dispositions. At the same time, many metaphysicians have begun moving in the direction of more scientifically-informed ("scientistic" or "naturalistic") metaphysics. And yet many philosophers of science retain a deep suspicion about the significance of metaphysical investigations into science. This volume of new essays explores a broadly methodological question: what role should metaphysics play in our philosophizing about science? These new essays, written by leading philosophers of science, address this question both through ground-level investigations of particular issues in the metaphysics of science and by more general methodological inquiry.
Over the past three decades, the philosophy of biology has emerged from the shadow of the philosophy of physics to become a respectable and thriving philosophical subdiscipline. The authors take a fresh look at the life sciences and the philosophy of biology from a strictly realist and emergentist-naturalist perspective. They outline a unified and science-oriented philosophical framework that enables the clarification of many foundational and philosophical issues in biology. This book will be of interest both to life scientists and philosophers.
Ontology is the philosophical discipline which aims to understand how things in the world are divided into categories and how these categories are related together. This is exactly what information scientists aim for in creating structured, automated representations, called ‘ontologies,’ for managing information in fields such as science, government, industry, and healthcare. Currently, these systems are designed in a variety of different ways, so they cannot share data with one another. They are often idiosyncratically structured, accessible only to those who created them, and unable to serve as inputs for automated reasoning. This volume shows, in a non-technical way and using examples from medicine and biology, how the rigorous application of theories and insights from philosophical ontology can improve the ontologies upon which information management depends.
This volume is the first systematic and thorough attempt to investigate the relation and the possible applications of mereology to contemporary science. It gathers contributions from leading scholars in the field and covers a wide range of scientific theories and practices such as physics, mathematics, chemistry, biology, computer science and engineering. Throughout the volume, a variety of foundational issues are investigated both from the formal and the empirical point of view. The first section looks at the topic as it applies to physics. The section addresses questions of persistence and composition within quantum and relativistic physics and concludes by scrutinizing the possibility to capture continuity of motion as described by our best physical theories within gunky space times. The second part tackles mathematics and shows how to provide a foundation for point-free geometry of space switching to fuzzy-logic. The relation between mereological sums and set-theoretic suprema is investigated and issues about different mereological perspectives such as classical and natural Mereology are thoroughly discussed. The third section in the volume looks at natural science. Several questions from biology, medicine and chemistry are investigated. From the perspective of biology, there is an attempt to provide axioms for inferring statements about part hood between two biological entities from statements about their spatial relation. From the perspective of chemistry, it is argued that classical mereological frameworks are not adequate to capture the practices of chemistry in that they consider neither temporal nor modal parameters. The final part introduces computer science and engineering. A new formal mereological framework in which an indeterminate relation of part hood is taken as a primitive notion is constructed and then applied to a wide variety of disciplines from robotics to knowledge engineering. A formal framework for discrete mereotopology and its applications is developed and finally, the importance of mereology for the relatively new science of domain engineering is also discussed.
This text focuses on two major issues: the nature of scientific inquiry and the relations between scientific disciplines. Designed to introduce the basic issues and concepts in the philosophy of science, Bechtel writes for an audience with little or no philosophical background. The first part of the book explores the legacy of Logical Positivism and the subsequent post-Positivistic developments in the philosophy of science. The second section examines arguments for and against using a model of theory reduction to integrate scientific disciplines. The book concludes with a chapter describing non-reductionist approaches for relating scientific disciplines using psycholinguistic and cognitive neuroscience models.
