In the beginning, there was the DN (Deductive Nomological) model of explanation, articulated by Hempel and Oppenheim (1948). According to DN, scientific explanation is subsumption under natural law. Individual events are explained by deducing them from laws together with initial conditions (or boundary conditions), and laws are explained by deriving them from other more fundamental laws, as, for example, the simple pendulum law is derived from Newton's laws of motion.

Introduction: Science and Common Sense Long before the beginnings of modern civilization, men ac- quired vast funds of information about their environment. ...

Philosophers have committed sins while studying science, it is said – philosophy of science focused on physics to the detriment of biology, reconstructed idealizations of scientific episodes rather than attending to historical details, and focused on theories and concepts to the detriment of experiments. Recent generations of philosophers of science have tried to atone for these sins, and by the 1980s the exculpation was in full swing. Marcel Weber’s Philosophy of Experimental Biology is a zenith mea culpa for philosophy of (...) science: it carefully describes several historical examples from twentieth century biology to address both ‘old’ philosophical topics, like reductionism, inference, and realism, and ‘new’ topics, like discovery, models, and norms. Biology, experiments, history – at last, philosophy of science, free of sin. (shrink)

A biochemical pathway is a sequence of chemical reactions in a biological organism. Such pathways specify mechanisms that explain how cells carry out their major functions by means of molecules and reactions that produce regular changes. Many diseases can be explained by defects in pathways, and new treatments often involve finding drugs that correct those defects. This paper presents explanation schemas and treatment strategies that characterize how thinking about pathways contributes to biomedical discovery. It discusses the significance of pathways for (...) understanding the nature of diseases, explanations, and theories. (shrink)

This essay has two goals. The first is to define the behavioristic study of natural events and to classify behavior. The second is to stress the importance of the concept of purpose.Given any object, relatively abstracted from its surroundings for study, the behavioristic approach consists in the examination of the output of the object and of the relations of this output to the input. By output is meant any change produced in the surroundings by the object. By input, conversely, is (...) meant any event external to the object that modifies this object in any manner. (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.

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 is a book about how we see: the environment around us (its surfaces, their layout, and their colors and textures); where we are in the environment; whether or not we are moving and, if we are, where we are going; what things are good for; how to do things (to thread a needle or drive an automobile); or why things look as they do.The basic assumption is that vision depends on the eye which is connected to the brain. The (...) author suggests that natural vision depends on the eyes in the head on a body supported by the ground, the brain being only the central organ of a complete visual system. When no constraints are put on the visual system, people look around, walk up to something interesting and move around it so as to see it from all sides, and go from one vista to another. That is natural vision—and what this book is about. (shrink)

One of the most notable aspects of Fodor's work is that it articulates features not only of speculative cognitive architectures but also of current research in ...

We argue that intelligible appeals to interlevel causes (top-down and bottom-up) can be understood, without remainder, as appeals to mechanistically mediated effects. Mechanistically mediated effects are hybrids of causal and constitutive relations, where the causal relations are exclusively intralevel. The idea of causation would have to stretch to the breaking point to accommodate interlevel causes. The notion of a mechanistically mediated effect is preferable because it can do all of the required work without appealing to mysterious interlevel causes. When interlevel (...) causes can be translated into mechanistically mediated effects, the posited relationship is intelligible and should raise no special philosophical objections. When they cannot, they are suspect. (shrink)

In Natural-Born Cyborgs, Clark argues that what makes humans so different from other species is our capacity to fully incorporate tools and supporting cultural ...

We will show that there is a strong form of emergence in cell biology. Beginning with C.D. Broad’s classic discussion of emergence, we distinguish two conditions sufficient for emergence. Emergence in biology must be compatible with the thought that all explanations of systemic properties are mechanistic explanations and with their sufficiency. Explanations of systemic properties are always in terms of the properties of the parts within the system. Nonetheless, systemic properties can still be emergent. If the properties of the components (...) within the system cannot be predicted, even in principle, from the behavior of the system’s parts within simpler wholes then there also will be systemic properties which cannot be predicted, even in principle, on basis of the behavior of these parts. We show in an explicit case study drawn from molecular cell physiology that biochemical networks display this kind of emergence, even though they deploy only mechanistic explanations. This illustrates emergence and its place in nature. (shrink)

We will show that there is a strong form of emergence in cell biology. Beginning with C.D. Broad's classic discussion of emergence, we distinguish two conditions sufficient for emergence. Emergence in biology must be compatible with the thought that all explanations of systemic properties are mechanistic explanations and with their sufficiency. Explanations of systemic properties are always in terms of the properties of the parts within the system. Nonetheless, systemic properties can still be emergent. If the properties of the components (...) within the system cannot be predicted, even in principle, from the behavior of the system's parts within simpler wholes then there also will be systemic properties which cannot be predicted, even in principle, on basis of the behavior of these parts. We show in an explicit case study drawn from molecular cell physiology that biochemical networks display this kind of emergence, even though they deploy only mechanistic explanations. This illustrates emergence and its place in nature. (shrink)

In the context of mechanistic explanation, reductionistic research pursues a decomposition of complex systems into their component parts and operations. Using research on the mechanisms responsible for circadian rhythms, I consider both the gains that have been made by discovering genes and proteins that figure in these intracellular oscillators and also highlight the increasingly recognized need to understand higher-level integration, both between cells in the central oscillator and between the central and peripheral oscillators. This history illustrates a common need to (...) complement reductionistic inquiry with investigations at higher-levels. Unlike most other accounts of reduction, the mechanistic framework accommodates this complementary relationship between reductionistic and systems approaches. (shrink)

Explanations in the life sciences frequently involve presenting a model of the mechanism taken to be responsible for a given phenomenon. Such explanations depart in numerous ways from nomological explanations commonly presented in philosophy of science. This paper focuses on three sorts of differences. First, scientists who develop mechanistic explanations are not limited to linguistic representations and logical inference; they frequently employ diagrams to characterize mechanisms and simulations to reason about them. Thus, the epistemic resources for presenting mechanistic explanations are (...) considerably richer than those suggested by a nomological framework. Second, the fact that mechanisms involve organized systems of component parts and operations provides direction to both the discovery and testing of mechanistic explanations. Finally, models of mechanisms are developed for specific exemplars and are not represented in terms of universally quantified statements. Generalization involves investigating both the similarity of new exemplars to those already studied and the variations between them. (shrink)

Animate vision systems have gaze control mechanisms that can actively position the camera coordinate system in response to physical stimuli. Compared to passive systems, animate systems show that visual computation can be vastly less expensive when considered in the larger context of behavior. The most important visual behavior is the ability to control the direction of gaze. This allows the use of very low resolution imaging that has a high virtual resolution. Using such a system in a controlled way provides (...) additional constraints that dramatically simplify the computations of early vision. Another important behavior is the way the environment “behaves‘. Animate systems under real-time constraints can further reduce their computational burden by using environmental cues that are perspicuous in the local context. A third source of economy is introduced when behaviors are learned. Because errors are rarely fatal, systems using learning algorithms can amortize computational cost over extended periods. Further economies can be achieved when the learning system uses indexical reference, which is a form of dynamic variable binding. Animate vision is a natural way of implementing this dynamic binding. (shrink)

Between 1940 and 1970 pioneers in the new field of cell biology discovered the operative parts of cells and their contributions to cell life. They offered mechanistic accounts that explained cellular phenomena by identifying the relevant parts of cells, the biochemical operations they performed, and the way in which these parts and operations were organised to accomplish important functions. Cell biology was a revolutionary science but in this book it also provides fuel for yet another revolution, one that focuses on (...) the very conception of science itself. Laws have traditionally been regarded as the primary vehicle of explanation, but in the emerging philosophy of science it is mechanisms that do the explanatory work. Bechtel emphasises how mechanisms were discovered, focusing especially on the way in which new instruments made these inquiries possible. He also describes how new journals and societies provided institutional structure to this new enterprise. (shrink)

A variety of scientific disciplines have set as their task explaining mental activities, recognizing that in some way these activities depend upon our brain. But, until recently, the opportunities to conduct experiments directly on our brains were limited. As a result, research efforts were split between disciplines such as cognitive psychology, linguistics, and artificial intelligence that investigated behavior, while disciplines such as neuroanatomy, neurophysiology, and genetics experimented on the brains of non-human animals. In recent decades these disciplines integrated, and with (...) the advent of techniques for imaging activity in human brains, the term cognitive neuroscience has been applied to the integrated investigations of mind and brain. This book is a philosophical examination of how these disciplines continue in the mission of explaining our mental capacities. (shrink)

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)

Philosophy and Neuroscience: A Ruthlessly Reductive Account is the first book-length treatment of philosophical issues and implications in current cellular and molecular neuroscience. John Bickle articulates a philosophical justification for investigating "lower level" neuroscientific research and describes a set of experimental details that have recently yielded the reduction of memory consolidation to the molecular mechanisms of long-term potentiation (LTP). These empirical details suggest answers to recent philosophical disputes over the nature and possibility of psycho-neural scientific reduction, including the multiple realization (...) challenge, mental causation, and relations across explanatory levels. Bickle concludes by examining recent work in cellular neuroscience pertaining to features of conscious experience, including the cellular basis of working memory, the effects of explicit selective attention on single-cell activity in visual cortex, and sensory experiences induced by cortical microstimulation. (shrink)

This study synthesizes current information from the various fields of cognitive science in support of a new and exciting theory of mind. Most psychologists study horizontal processes like memory and information flow; Fodor postulates a vertical and modular psychological organization underlying biologically coherent behaviors. This view of mental architecture is consistent with the historical tradition of faculty psychology while integrating a computational approach to mental processes. One of the most notable aspects of Fodor's work is that it articulates features not (...) only of speculative cognitive architectures but also of current research in artificial intelligence. (shrink)

Philosophy of Experimental Biology explores some central philosophical issues concerning scientific research in experimental biology, including genetics, biochemistry, molecular biology, developmental biology, neurobiology, and microbiology. It seeks to make sense of the explanatory strategies, concepts, ways of reasoning, approaches to discovery and problem solving, tools, models and experimental systems deployed by scientific life science researchers and also integrates developments in historical scholarship, in particular the New Experimentalism. It concludes that historical explanations of scientific change that are based on local laboratory (...) practice need to be supplemented with an account of the epistemic norms and standards that are operative in science. This book should be of interest to philosophers and historians of science as well as to scientists. (shrink)

Although the mechanics of how the eye works are well understood, debate still exists as to how the complex machinery of the brain interprets neural impulses...

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)

2. Daugman, J. G. Brain metaphor and brain theory 3. Mundale, J. Neuroanatomical Foundations of Cognition: Connecting the Neuronal Level with the Study of Higher Brain Areas.

Second, this collection of cognitive programs evolved in the Pleistocene to solve the adaptive problems regularly faced by our hunter-gatherer ancestors-...

The mechanistic perspective has dominated biological disciplines such as biochemistry, physiology, cell and molecular biology, and neuroscience, especially during the 20th century. The primary strategy is reductionist: organisms are to be decomposed into component parts and operations at multiple levels. Researchers adopting this perspective have generated an enormous body of information about the mechanisms of life at scales ranging from the whole organism down to genetic and other molecular operations.

First published in 1995, The Visual Brain in Action remains a seminal publication in the cognitive sciences. It presents a model for understanding the visual processing underlying perception and action, proposing a broad distinction within the brain between two kinds of vision: conscious perception and unconscious 'online' vision. It argues that each kind of vision can occur quasi-independently of the other, and is separately handled by a quite different processing system. In the 11 years since publication, the book has provoked (...) considerable interest and debate - throughout both cognitive neuroscience and philosophy, while the field has continued to flourish and develop. -/- For this new edition, the text from the original edition has been left untouched, standing as a coherent statement of the authors' position. However, a very substantial epilogue has been added to the book in which Milner and Goodale review some of the key developments that support or challenge the views that were put forward in the first edition. The new chapter summarizes developments in various relevant areas of psychology, neuroscience and behaviour. It notably supplements the main text by updating the reader on the contributions that have emerged from the use of functional neuroimaging, which was in its infancy when the first edition was written. Neuroimaging, and functional MRI in particular, has revolutionized the field over the past 11 years by allowing investigators to plot in detail the patterns of activity within the visual brains of behaving and perceiving humans. The authors show how its use now allows scientists to test and confirm their proposals, based as they then were largely on evidence accrued from primate neuroscience in conjunction with studies of neurological patients. (shrink)

Anydomainofscientificresearchhasitssustainingorthodoxy. Thatis, research on a problem, whether in astronomy, physics, or biology, is con- ducted against a backdrop of broadly shared assumptions. It is these as- sumptionsthatguideinquiryandprovidethecanonofwhatisreasonable-- of what "makes sense." And it is these shared assumptions that constitute a framework for the interpretation of research results. Research on the problem of how we see is likewise sustained by broadly shared assump- tions, where the current orthodoxy embraces the very general idea that the business of the visual system is to (...) create a detailed replica of the visual world, and that it accomplishes its business via hierarchical organization and by operatingessentiallyindependently of other sensorymodalitiesas well as independently of previous learning, goals, motor planning, and motor execution. (shrink)