In the last two decades few topics in philosophy of science have received as much attention as mechanistic explanation. A significant motivation for these accounts is that scientists frequently use the term “mechanism” in their explanations of biological phenomena. While scientists appeal to a variety of causal concepts in their explanations, many philosophers argue or assume that all of these concepts are well understood with the single notion of mechanism. This reveals a significant problem with mainstream mechanistic accounts– although philosophers (...) use the term “mechanism” interchangeably with other causal concepts, this is not something that scientists always do. This paper analyses two causal concepts in biology–the notions of “mechanism” and “pathway”–and how they figure in biological explanation. I argue that these concepts have unique features, that they are associated with distinct strategies of causal investigation, and that they figure in importantly different types of explanation. (shrink)

Much of the recent philosophical debate on causation and causal explanation in the biological and biomedical sciences has focused on the notion of mechanism. Mechanisms, their nature and epistemic roles have been tackled by a range of so-called neo-mechanistic theories, and widely discussed. Without denying the merits of this approach, our paper aims to show how lately it has failed to give proper credit to processes, which are central to the field, especially of contemporary molecular biology. Processes can be summed (...) up in the notion of ‘pathway’, which is far from being just equivalent to that of ‘mechanism’ and has a profound epistemological and explanatory relevance. It is argued that an adequate consideration of pathways impels some rethinking of scientific explanation in molecular biology, namely its functional and contextual features. A number of examples are given to suggest that the focus of philosophical attention in this disciplinary field should shift from the notion of mechanism to the notion of pathway. (shrink)

Understanding is a central aim of science and highly important in present-day society. But what precisely is scientific understanding and how can it be achieved? This book answers these questions, through philosophical analysis and historical case studies, and presents a philosophical theory of scientific understanding that highlights its contextual nature.

This volume argues for a new image of science that understands both natural and social phenomena to be the product of mechanisms, casting the work of science as an effort to understand those mechanisms. Glennan offers an account of the nature of mechanisms and of the models used to represent them in physical, life, and social sciences.

Models as Mediators discusses the ways in which models function in modern science, particularly in the fields of physics and economics. Models play a variety of roles in the sciences: they are used in the development, exploration and application of theories and in measurement methods. They also provide instruments for using scientific concepts and principles to intervene in the world. The editors provide a framework which covers the construction and function of scientific models, and explore the ways in which they (...) enable us to learn about both theories and the world. The contributors to the volume offer their own individual theoretical perspectives to cover a wide range of examples of modelling, from physics, economics and chemistry. These papers provide ideal case-study material for understanding both the concepts and typical elements of modelling, using analytical approaches from the philosophy and history of science. (shrink)

The Hodgkin–Huxley (HH) model of the action potential is a theoretical pillar of modern neurobiology. In a number of recent publications, Carl Craver ([2006], [2007], [2008]) has argued that the model is explanatorily deficient because it does not reveal enough about underlying molecular mechanisms. I offer an alternative picture of the HH model, according to which it deliberately abstracts from molecular specifics. By doing so, the model explains whole-cell behaviour as the product of a mass of underlying low-level events. The (...) issue goes beyond cellular neurobiology, for the strategy of abstraction exhibited in the HH case is found in a range of biological contexts. I discuss why it has been largely neglected by advocates of the mechanist approach to explanation. 1 Introduction2 A Primer on the HH Model2.1 The basic qualitative picture2.2 The quantitative model3 Interlude: What Did Hodgkin and Huxley Think?4 Craver’s View4.1 Mechanistic explanation4.2 Sketches4.3 Craver's view: The HH model as a mechanism sketch5 An Alternative View of the HH Model5.1 Another look at the equations5.2 The discrete-gating picture5.3 The road paved by Hodgkin and Huxley5.4 Summary and comparison to Craver6 Conclusion: The HH Model and Mechanistic Explanation6.1 Sketches and abstractions6.2 Why has aggregative abstraction been overlooked? (shrink)

We claim that in contemporary studies in molecular biology and biomedicine, the nature of ‘manipulation’ and ‘intervention’ has changed. Traditionally, molecular biology and molecular studies in medicine are considered experimental sciences, whereas experiments take the form of material manipulation and intervention. On the contrary “big science” projects in biology focus on the practice of data mining of biological databases. We argue that the practice of data mining is a form of intervention although it does not require material manipulation. We also (...) suggest that material manipulation, although still present in in the practice of data mining, fulfill a different epistemic role. (shrink)

This is the first textbook on pattern recognition to present the Bayesian viewpoint. The book presents approximate inference algorithms that permit fast approximate answers in situations where exact answers are not feasible. It uses graphical models to describe probability distributions when no other books apply graphical models to machine learning. No previous knowledge of pattern recognition or machine learning concepts is assumed. Familiarity with multivariate calculus and basic linear algebra is required, and some experience in the use of probabilities would (...) be helpful though not essential as the book includes a self-contained introduction to basic probability theory. (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)

It is often claimed—especially by scientific realists—that science provides understanding of the world only if its theories are (at least approximately) true descriptions of reality, in its observable as well as unobservable aspects. This paper critically examines this ‘realist thesis’ concerning understanding. A crucial problem for the realist thesis is that (as study of the history and practice of science reveals) understanding is frequently obtained via theories and models that appear to be highly unrealistic or even completely fictional. So we (...) face the dilemma of either giving up the realist thesis that understanding requires truth, or allowing for the possibility that in many if not all practical cases we do not have scientific understanding. I will argue that the first horn is preferable: the link between understanding and truth can be severed. This becomes a live option if we abandon the traditional view that scientific understanding is a special type of knowledge. While this view implies that understanding must be factive, I avoid this implication by identifying understanding with a skill rather than with knowledge. I will develop the idea that understanding phenomena consists in the ability to use a theory to generate predictions of the target system’s behavior. This implies that the crucial condition for understanding is not truth but intelligibility of the theory, where intelligibility is defined as the value that scientists attribute to the theoretical virtues that facilitate the construction of models of the phenomena. I will show, first, that my account accords with the way practicing scientists conceive of understanding, and second, that it allows for the use of idealized or fictional models and theories in achieving understanding. (shrink)

There is considerable disagreement about the epistemic value of novel predictive success, i.e. when a scientist predicts an unexpected phenomenon, experiments are conducted, and the prediction proves to be accurate. We survey the field on this question, noting both fully articulated views such as weak and strong predictivism, and more nascent views, such as pluralist reasons for the instrumental value of prediction. By examining the various reasons offered for the value of prediction across a range of inferential contexts , we (...) can see that neither weak nor strong predictivism captures all of the reasons for valuing prediction available. A third path is presented, Pluralist Instrumental Predictivism; PIP for short. (shrink)

Scientific and ‘intuitive’ or ‘folk’ theories are typically characterized as serving three critical functions: prediction, explanation, and control. While prediction and control have clear instrumental value, the value of explanation is less transparent. This paper reviews an emerging body of research from the cognitive sciences suggesting that the process of seeking, generating, and evaluating explanations in fact contributes to future prediction and control, albeit indirectly by facilitating the discovery and confirmation of instrumentally valuable theories. Theoretical and empirical considerations also suggest (...) why explanations may nonetheless feel intrinsically valuable. The paper concludes by considering some implications of the psychology of explanation for a naturalized philosophy of explanation. (shrink)

This article analyzes the epistemic value of understanding and offers an account of the role of understanding in science. First, I discuss the objectivist view of the relation between explanation and understanding, defended by Carl Hempel and J. D. Trout. I challenge this view by arguing that pragmatic aspects of explanation are crucial for achieving the epistemic aims of science. Subsequently, I present an analysis of these pragmatic aspects in terms of ‘intelligibility’ and a contextual account of scientific understanding based (...) on this notion. †To contact the author, please write to: Faculty of Philosophy, VU University Amsterdam, De Boelelaan 1105, 1081 HV Amsterdam, The Netherlands; e‐mail: [email protected]. (shrink)

Although prediction has been largely absent from discussions of explanation for the past 40 years, theories of explanation can gain much from a reintroduction. I review the history that divorced prediction from explanation, examine the proliferation of models of explanation that followed, and argue that accounts of explanation have been impoverished by the neglect of prediction. Instead of a revival of the symmetry thesis, I suggest that explanation should be understood as a cognitive tool that assists us in generating new (...) predictions. This view of explanation and prediction clarifies what makes an explanation scientific and why inference to the best explanation makes sense in science. *Received August 2009; revised September 2009. †To contact the author, please write to: Department of Philosophy, University of Tennessee, 801 McClung Tower, Knoxville, TN 37920‐0480; e‐mail: [email protected]. (shrink)

Approaches to explanation -- Causal and explanatory relevance -- The kairetic account of /D making -- The kairetic account of explanation -- Extending the kairetic account -- Event explanation and causal claims -- Regularity explanation -- Abstraction in regularity explanation -- Approaches to probabilistic explanation -- Kairetic explanation of frequencies -- Kairetic explanation of single outcomes -- Looking outward -- Looking inward.

Carl Craver investigates what we are doing when we sue neuroscience to explain what's going on in the brain.

In this book Bruno Latour brings together these different approaches to provide a lively and challenging analysis of science, demonstrating how social context..

Despite their best efforts, scientists may be unable to construct models that simultaneously exemplify every theoretical virtue. One explanation for this is the existence of tradeoffs: relationships of attenuation that constrain the extent to which models can have such desirable qualities. In this paper, we characterize three types of tradeoffs theorists may confront. These characterizations are then used to examine the relationships between parameter precision and two types of generality. We show that several of these relationships exhibit tradeoffs and discuss (...) what consequences those tradeoffs have for theoretical practice. (shrink)

This paper is an interpretation and defense of Richard Levins’ “The Strategy of Model Building in Population Biology,” which has been extremely influential among biologists since its publication 40 years ago. In this article, Levins confronted some of the deepest philosophical issues surrounding modeling and theory construction. By way of interpretation, I discuss each of Levins’ major philosophical themes: the problem of complexity, the brute-force approach, the existence and consequence of tradeoffs, and robustness analysis. I argue that Levins’ article is (...) concerned, at its core, with justifying the use of multiple, idealized models in population biology. (shrink)

Not all models are explanatory. Some models are data summaries. Some models sketch explanations but leave crucial details unspecified or hidden behind filler terms. Some models are used to conjecture a how-possibly explanation without regard to whether it is a how-actually explanation. I use the Hodgkin and Huxley model of the action potential to illustrate these ways that models can be useful without explaining. I then use the subsequent development of the explanation of the action potential to show what is (...) required of an adequate mechanistic model. Mechanistic models are explanatory. (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.

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)

Causal relations among components and activities are intentionally misrepresented in mechanistic explanations found routinely across the life sciences. Since several mechanists explicitly advocate accurately representing factors that make a difference to the outcome, these idealizations conflict with the stated rationale for mechanistic explanation. We argue that these idealizations signal an overlooked feature of reasoning in molecular and cell biology—mechanistic explanations do not occur in isolation—and suggest that explanatory practices within the mechanistic tradition share commonalities with model-based approaches prevalent in population (...) biology. (shrink)

What do biologists want? If, unlike their counterparts in physics, biologists are generally wary of a grand, overarching theory, at what kinds of explanation do biologists aim? A history of the diverse and changing nature of biological explanation in a particularly charged field, "Making Sense of Life" draws our attention to the temporal, disciplinary, and cultural components of what biologists mean, and what they understand, when they propose to explain life.

Recently, biologists have argued that data - driven biology fosters a new scientific methodology; namely, one that is irreducible to traditional methodologies of molecular biology defined as the discovery strategies elucidated by mechanistic philosophy. Here I show how data - driven studies can be included into the traditional mechanistic approach in two respects. On the one hand, some studies provide eliminative inferential procedures to prioritize and develop mechanistic hypotheses. On the other, different studies play an exploratory role in providing useful (...) generalizations to complement the procedure of prioritization. Overall this paper aims to shed light on the structure of contemporary research in molecular biology. (shrink)

Proponents of mechanistic explanation all acknowledge the importance of organization. But they have also tended to emphasize specificity with respect to parts and operations in mechanisms. We argue that in understanding one important mode of organization—patterns of causal connectivity—a successful explanatory strategy abstracts from the specifics of the mechanism and invokes tools such as those of graph theory to explain how mechanisms with a particular mode of connectivity will behave. We discuss the connection between organization, abstraction, and mechanistic explanation and (...) illustrate our claims by looking at an example from recent research on so-called network motifs. (shrink)

We argue that dynamical and mathematical models in systems and cognitive neuro- science explain (rather than redescribe) a phenomenon only if there is a plausible mapping between elements in the model and elements in the mechanism for the phe- nomenon. We demonstrate how this model-to-mechanism-mapping constraint, when satisfied, endows a model with explanatory force with respect to the phenomenon to be explained. Several paradigmatic models including the Haken-Kelso-Bunz model of bimanual coordination and the difference-of-Gaussians model of visual receptive fields are (...) explored. (shrink)

We argue that mechanistic models elaborated by machine learning cannot be explanatory by discussing the relation between mechanistic models, explanation and the notion of intelligibility of models. We show that the ability of biologists to understand the model that they work with severely constrains their capacity of turning the model into an explanatory model. The more a mechanistic model is complex, the less explanatory it will be. Since machine learning increases its performances when more components are added, then it generates (...) models which are not intelligible, and hence not explanatory. (shrink)

The considerations set out in the paper are intended to suggest that in practical contexts predictive power does not play the outstanding roles sometimes accredited to it in an epistemic framework. Rather, predictive power is part of a network of other merits and achievements. Predictive power needs to be judged differently according to the specific conditions that apply. First, predictions need to be part of an explanatory framework if they are supposed to guide actions reliably. Second, in scientific expertise, the (...) demand for accurate predictions is replaced with the objective of specifying a robust corridor of estimates. Finally, it is highly uncertain to predict the success of research projects. The overall purpose of the paper is to enlarge the debate about predictions by addressing specifically the roles of predictions in application-oriented research. (shrink)

This paper analyzes two ways idealized biological models produce factive scientific understanding. I then argue that models can provide factive scientific understanding of a phenomenon without providing an accurate representation of the features of their real-world target system. My analysis of these cases also suggests that the debate over scientific realism needs to investigate the factive scientific understanding produced by scientists’ use of idealized models rather than the accuracy of scientific models themselves.

Recent claims, mainly from computer scientists, concerning a largely automated and model-free data-intensive science have been countered by critical reactions from a number of philosophers of science. The debate suffers from a lack of detail in two respects, regarding the actual methods used in data-intensive science and the specific ways in which these methods presuppose theoretical assumptions. I examine two widely-used algorithms, classificatory trees and non-parametric regression, and argue that these are theory-laden in an external sense, regarding the framing of (...) research questions, but not in an internal sense concerning the causal structure of the examined phenomenon. With respect to the novelty of data-intensive science, I draw an analogy to exploratory as opposed to theory-directed experimentation. (shrink)

With In Search of Mechanisms, Carl F. Craver and Lindley Darden offer both a descriptive and an instructional account of how biologists discover mechanisms. Drawing on examples from across the life sciences and through the centuries, Craver and Darden compile an impressive toolbox of strategies that biologists have used and will use again to reveal the mechanisms that produce, underlie, or maintain the phenomena characteristic of living things. They discuss the questions that figure in the search for mechanisms, characterizing the (...) experimental, observational, and conceptual considerations used to answer them, all the while providing examples from the history of biology to highlight the kinds of evidence and reasoning strategies employed to assess mechanisms. At a deeper level, Craver and Darden pose a systematic view of what biology is, of how biology makes progress, of how biological discoveries are and might be made, and of why knowledge of biological mechanisms is important for the future of the human species. (shrink)

In biology—as in other scientific fields—there is a lively opposition between big and small science projects. In this commentary, I try to contextualize this opposition in the field of biomedicine, and I argue that, at least in this context, big science projects should come first.