Explaining the complex dynamics exhibited in many biological mechanisms requires extending the recent philosophical treatment of mechanisms that emphasizes sequences of operations. To understand how nonsequentially organized mechanisms will behave, scientists often advance what we call dynamic mechanistic explanations. These begin with a decomposition of the mechanism into component parts and operations, using a variety of laboratory-based strategies. Crucially, the mechanism is then recomposed by means of computational models in which variables or terms in differential equations correspond (...) to properties of its parts and operations. We provide two illustrations drawn from research on circadian rhythms. Once biologists identified some of the components of the molecular mechanism thought to be responsible for circadian rhythms, computational models were used to determine whether the proposed mechanisms could generate sustained oscillations. Modeling has become even more important as researchers have recognized that the oscillations generated in individual neurons are synchronized within networks; we describe models being employed to assess how different possible network architectures could produce the observed synchronized activity. (shrink)

In many fields of biology, researchers explain a phenomenon by characterizing the responsible mechanism. This requires identifying the candidate mechanism, decomposing it into its parts and operations, recomposing it so as to understand how it is organized and its operations orchestrated to generate the phenomenon, and situating it in its environment. Mechanistic researchers have developed sophisticated tools for decomposing mechanisms but new approaches, including modeling, are increasingly being invoked to recompose mechanisms when they involve nonsequential organization of (...) nonlinear operations. The results often are dynamical mechanistic explanations. The steps in mechanistic research are illustrated using research on circadian rhythms. (shrink)

Despite growing consumerism and skepticism about authority in the culture as a whole, most patients continue to be pliant. If there is a serious threat to physician autonomy, it is more likely to come from third‐party payers and new forms of medical practice, particularly the rise of for‐profit hospital chains, than from patients. Though physicians are restless, they will learn to adapt to the new conditions of practice.

This article argues that the basic account of mechanism and mechanistic explanation, involving sequential execution of qualitatively characterized operations, is itself insufficient to explain biological phenomena such as the capacity of living organisms to maintain themselves as systems distinct from their environment. This capacity depends on cyclic organization, including positive and negative feedback loops, which can generate complex dynamics. Understanding cyclically organized mechanisms with complex dynamics requires coordinating research directed at decomposing mechanisms into parts and operations with research (...) using computational models to recompose mechanisms and determine their dynamic behavior. This coordinated endeavor yields dynamic mechanistic explanations. (shrink)

Recently, Bechtel and Abrahamsen have argued that mathematical models study the dynamics of mechanisms by recomposing the components and their operations into an appropriately organized system. We will study this claim through the practice of combinational modeling in circadian clock research. In combinational modeling, experiments on model organisms and mathematical/computational models are combined with a new type of model—a synthetic model. We argue that the strategy of recomposition is more complicated than what Bechtel and Abrahamsen indicate. Moreover, synthetic (...) modeling as a kind of material recomposition strategy also points beyond the mechanistic paradigm. (shrink)

Accounts of mechanistic explanation have emphasized the importance of looking down—decomposing a mechanism into its parts and operations. Using research on visual processing as an exemplar, I illustrate how productive such research has been. But once multiple components of a mechanism have been identified, researchers also need to figure out how it is organized—they must look around and determine how to recompose the mechanism. Although researchers often begin by trying to recompose the mechanism in terms of sequential operations, they frequently (...) find that the components of a mechanism interact in complex ways involving positive and negative feedback and that the organization often exhibits highly interactive local networks linked by a few long-range connections (small-worlds organization) and power law distributions of connections. The mechanisms are themselves active systems that are perturbed by inputs but not set in motion by them. Researchers also need to look up —situate a mechanism in its context, which may be a larger mechanism that modulates its behavior. When looking down is combined with looking around and up, mechanistic research results in an integrated, multi-level perspective. (shrink)

Philosophy of science is positioned to make distinctive contributions to cognitive science by providing perspective on its conceptual foundations and by advancing normative recommendations. The philosophy of science I embrace is naturalistic in that it is grounded in the study of actual science. Focusing on explanation, I describe the recent development of a mechanistic philosophy of science from which I draw three normative consequences for cognitive science. First, insofar as cognitive mechanisms are information-processing mechanisms, cognitive science needs an (...) account of how the representations invoked in cognitive mechanisms carry information about contents, and I suggest that control theory offers the needed perspective on the relation of representations to contents. Second, I argue that cognitive science requires, but is still in search of, a catalog of cognitive operations that researchers can draw upon in explaining cognitive mechanisms. Last, I provide a new perspective on the relation of cognitive science to brain sciences, one which embraces both reductive research on neural components that figure in cognitive mechanisms and a concern with recomposing higher-level mechanisms from their components and situating them in their environments. (shrink)

Philosophy of science is positioned to make distinctive contributions to cognitive science by providing perspective on its conceptual foundations and by advancing normative recommendations. The philosophy of science I embrace is naturalistic in that it is grounded in the study of actual science. Focusing on explanation, I describe the recent development of a mechanistic philosophy of science from which I draw three normative consequences for cognitive science. First, insofar as cognitive mechanisms are information‐processing mechanisms, cognitive science needs an (...) account of how the representations invoked in cognitive mechanisms carry information about contents, and I suggest that control theory offers the needed perspective on the relation of representations to contents. Second, I argue that cognitive science requires, but is still in search of, a catalog of cognitive operations that researchers can draw upon in explaining cognitive mechanisms. Last, I provide a new perspective on the relation of cognitive science to brain sciences, one which embraces both reductive research on neural components that figure in cognitive mechanisms and a concern with recomposing higher‐level mechanisms from their components and situating them in their environments. (shrink)

Research in many fields of biology has been extremely successful in decomposing biological mechanisms to discover their parts and operations. It often remains a significant challenge for scientists to recompose these mechanisms to understand how they function as wholes and interact with the environments around them. This is true of the eukaryotic cell. Although initially identified in nineteenth-century cell theory as the fundamental unit of organisms, researchers soon learned how to decompose it into its organelles and chemical constituents (...) and have been highly successful in understanding how these carry out many operations important to life. The emphasis on decomposition is particularly evident in modern cell biology, which for the most part has viewed the cell as merely a locus of the mechanisms responsible for vital phenomena. The cell, however, is also an integrated system and for some explanatory purposes it is essential to recompose it and understand it as an organized whole. I illustrate both the virtues of decomposition (treating the cell as a locus) and recomposition (treating the cell as an object) with recent work on circadian rhythms. Circadian researchers have both identified critical intracellular operations that maintain endogenous oscillations and have also addressed the integration of cells into multicellular systems in which cells constitute units. Ó 2010 Elsevier Ltd. All rights reserved. (shrink)

Some recent accounts of constitutive relevance have identified mechanism components with entities that are causal intermediaries between the input and output of a mechanism. I argue that on such accounts there is no distinctive inter-level form of mechanistic explanation and that this highlights an absence in the literature of a compelling argument that there are such explanations. Nevertheless, the entities that these accounts call ‘components’ do play an explanatory role. Studying causal intermediaries linking variables Xand Y provides knowledge of the (...) counterfactual conditions under which X will continue to bring about Y. This explanatory role does not depend on whether intermediate variables count as components. The question of whether there are distinctively mechanistic explanations remains open. (shrink)

I argue against the claim, advanced by David Albert and Barry Loewer, that all non-fundamental laws can be derived from those required to underwrite the second law of thermodynamics.

This paper explores the cooperation mechanisms for the prisoner’s dilemma game, a canonical example for studying cooperation mechanisms, with Bayesian games. By the approach allowing simultaneous moves with the assumption that the players might be self-interested or norm-following, we establish four possible Bayesian game models, all of which are cooperation mechanisms for the prisoner’s dilemma game except for the model in which one of the two players must be self-interested.

The persistent interpretation problem for quantum mechanics may indicate an unwillingness to consider unpalatable assumptions that could open the way toward progress. With this in mind, I focus on the work of David Bohm, whose earlier work has been more influential than that of his later. As I’ll discuss, I believe two assumptions play a strong role in explaining the disparity: 1) that theories in physics must be grounded in mathematical structure and 2) that consciousness must supervene on material processes. (...) I’ll argue that the first assumption appears to lead us toward Everett’s many worlds interpretation, which suggests a red flag. I’ll also argue that the second assumption is suspect due to the persistent explanatory gap for consciousness. Later, I explore ways that Bohm’s later work holds some promise in providing a better fit with our world, both phenomenologically and empirically. Also, I’ll address the possible problem of realism. (shrink)

Birth cohort studies can be used not only to generate population-level quantitative data, but also to recompose persons. The crux is how we understand data and persons. Recomposition entails scavenging for various (including unrecognised) data. It foregrounds the perspective and subjectivity of survey participants, but without forgetting the partiality and incompleteness of the accounts that it may generate. Although interested in the singularity of individuals, it attends to the historical and relational embeddedness of personhood. It examines the multiple and complex (...) temporalities that suffuse people’s lives, hence departing from linear notions of the life course. It implies involvement, as well as reflexivity, on the part of researchers. It embraces the heterogeneity and transformations over time of scientific archives and the interpretive possibilities, as well as incompleteness, of birth cohort studies data. Interested in the unfolding of lives over time, it also shines light on meaningful biographical moments. (shrink)

What is called ``orthodox'' quantum mechanics, as presented in standard foundational discussions, relies on two substantive assumptions --- the projection postulate and the eigenvalue-eigenvector link --- that do not in fact play any part in practical applications of quantum mechanics. I argue for this conclusion on a number of grounds, but primarily on the grounds that the projection postulate fails correctly to account for repeated, continuous and unsharp measurements and that the eigenvalue-eigenvector link implies that virtually all interesting properties are (...) maximally indefinite pretty much always. I present an alternative way of conceptualising quantum mechanics that does a better job of representing quantum mechanics as it is actually used, and in particular that eliminates use of either the projection postulate or the eigenvalue-eigenvector link, and I reformulate the measurement problem within this new presentation of orthodoxy. (shrink)

Cette nouvelle édition commentée des Fragments d'Héraclite est le fruit d'un travail totalement inédit. Alors que les éditions de référence (Hermann Diels en 1922 et Walter Kranz en 1934), comme celle de Jean Bollack et Heinz Wismann, se limitaient à les présenter selon un ordre alphabétique arbitraire, Marcel Conche procède ici à un mouvement d'ensemble du concret vers l'abstrait. Après des règles de méthodes viennent ainsi des lois universelles, puis les réalités elles-mêmes : le monde, les âmes, la cité... Le (...) schéma eût sans doute fait sourire Héraclite (ce qui n'eût pas été marque de désaveu), mais il rappelle qu'un fragment ne doit pas être interprété seul, et que les Fragments sont avant tout le reflet d'un système achevé en constante redéfinition. (shrink)

We show that the formulations of non-relativistic quantum mechanics can be derived from an extended least action principle. The principle can be considered as an extension of the least action principle from classical mechanics by factoring in two assumptions. First, the Planck constant defines the minimal amount of action a physical system needs to exhibit during its dynamics in order to be observable. Second, there is constant vacuum fluctuation along a classical trajectory. A novel method is introduced to define the (...) information metrics to measure additional observability due to vacuum fluctuations, which is then converted to an additional action through the first assumption. Applying the variational principle to minimize the total actions allows us to recover the basic quantum formulations including the uncertainty relation and the Schrödinger equation in the position representation. In the momentum representation, the same method can be applied to obtain the Schrödinger equation for a free particle while further investigation is still needed for a particle with an external potential. Furthermore, the principle brings in new results on two fronts. At the conceptual level, we find that the information metrics for vacuum fluctuations are responsible for the origin of the Bohm quantum potential. Even though the Bohm potential for a bipartite system is inseparable, the underlying vacuum fluctuations are local. Thus, inseparability of the Bohm potential does not justify a non-local causal relation between the two subsystems.responsible for manifesting entanglement effects without underlying physical interactions, implying that entanglement effects are non-causal. At the mathematical level, quantifying the information metrics for vacuum fluctuations using more general definitions of relative entropy results in a generalized Schrödinger equation that depends on the order of relative entropy. The extended least action principle is a new mathematical tool. It can be applied to derive other quantum formalisms such as quantum scalar field theory. (shrink)

Presents a guide to the basics of quantum mechanics and measurement.

Ernst Mayr proposed a distinction between “proximate”, mechanistic, and “ultimate”, evolutionary, causes of biological phenomena. This dichotomy has influenced the thinking of many biologists, but it is increasingly perceived as impeding modern studies of evolutionary processes, including study of “niche construction” in which organisms alter their environments in ways supportive of their evolutionary success. Some still find value for this dichotomy in its separation of answers to “how?” versus “why?”questions about evolution. But “why is A?” questions about evolution necessarily take (...) the form “how does A occur?”, so this separation is illusory. Moreover, the dichotomy distorts our view of evolutionary causality, in that, contra Mayr, the action of natural selection, driven by genotype-phenotype-environment interactions which constitute adaptations, is no less “proximate” than the biological mechanisms which are altered by naturally selected genetic variants. Mayr’s dichotomy thus needs replacement by more realistic, mechanistic views of evolution. From a mechanistic viewpoint, there is a continuum of adaptations from those evolving as responses to unchanging environmental pressures to those evolving as the capacity for niche construction, and intermediate stages of this can be identified. Some biologists postulate an association of “phenotypic plasticity” (phenotype-environment covariation with genotype held constant) with capacity for niche construction. Both “plasticity” and niche construction comprise wide ranges of adaptive mechanisms, often fully heritable and resulting from case-specific evolution. Association of “plasticity” with niche construction is most likely to arise in systems wherein capacity for complex learning and behavioral flexibility have already evolved. (shrink)

I maintain that quantum mechanics is fundamentally about a system of N particles evolving in three-dimensional space, not the wave function evolving in 3N-dimensional space.

People are motivated by shared social values that, when held with moral conviction, can serve as compelling mandates capable of facilitating support for ideological violence. The current study examined this dark side of morality by identifying specific cognitive and neural mechanisms associated with beliefs about the appropriateness of sociopolitical violence, and determining the extent to which the engagement of these mechanisms was predicted by moral convictions. Participants reported their moral convictions about a variety of sociopolitical issues prior to (...) undergoing functional MRI scanning. During scanning, they were asked to evaluate the appropriateness of violent protests that were ostensibly congruent or incongruent with their views about sociopolitical issues. Complementary univariate and multivariate analytical strategies comparing neural responses to congruent and incongruent violence identified neural mechanisms implicated in processing salience and in the encoding of subjective value. As predicted, neuro-hemodynamic response was modulated parametrically by individuals’ beliefs about the appropriateness of congruent relative to incongruent sociopolitical violence in ventromedial prefrontal cortex, and by moral conviction in ventral striatum. Overall moral conviction was predicted by neural response to congruent relative to incongruent violence in amygdala. Together, these findings indicate that moral conviction about sociopolitical issues serves to increase their subjective value, overriding natural aversion to interpersonal harm. (shrink)

This paper will examine the nature of mechanisms and the distinction between the relevant and irrelevant parts involved in a mechanism’s operation. I first consider Craver’s account of this distinction in his book on the nature of mechanisms, and explain some problems. I then offer a novel account of the distinction that appeals to some resources from Mackie’s theory of causation. I end by explaining how this account enables us to better understand what mechanisms are and their (...) various features. (shrink)

his monograph examines the metaphysical commitments of the new mechanistic philosophy, a way of thinking that has returned to center stage. It challenges a variant of reductionism with regard to higher-level phenomena, which has crystallized as a default position among these so-called New Mechanists. Furthermore, it opposes those philosophers who reject the possibility of interlevel causation. Contemporary philosophers believe that the explanation of scientific phenomena requires the discovery of relevant mechanisms. As a result, new mechanists are, in the main, (...) concerned solely with epistemological questions. But, the author argues, their most central claims rely on metaphysical assumptions. Thus, they must also take into account metaphysics, a system of thought concerned with explaining the fundamental nature of being and the world around it. This branch of philosophy does indeed matter to the empirical sciences. The chapters investigate the nature of mechanisms, their components, and the ways in which they can bring about different phenomena. In addition, the author develops a novel account of causation in terms of activities. The analysis provides the basis for many further research projects on mechanisms and their relations to, for example, the mind-body problem, realization, multiple realization, natural kinds, causation, laws of nature, counterfactuals, and scientific levels. (shrink)

This book explores the prospects of rivaling ontological and epistemic interpretations of quantum mechanics (QM). It concludes with a suggestion for how to interpret QM from an epistemological point of view and with a Kantian touch. It thus refines, extends, and combines existing approaches in a similar direction. -/- The author first looks at current, hotly debated ontological interpretations. These include hidden variables-approaches, Bohmian mechanics, collapse interpretations, and the many worlds interpretation. He demonstrates why none of these ontological interpretations can (...) claim to be the clear winner amongst its rivals. Next, coverage explores the possibility of interpreting QM in terms of knowledge but without the assumption of hidden variables. It examines QBism as well as Healey’s pragmatist view. The author finds both interpretations or programs wanting in certain respects. As a result, he then goes on to advance a genuine proposal as to how to interpret QM from the perspective of an internal realism in the sense of Putnam and Kant. -/- The book also includes two philosophical interludes. One details the notions of probability and realism. The other highlights the connections between the notions of locality, causality, and reality in the context of violations of Bell-type inequalities. (shrink)

The purpose of the present paper is to consider the traditional interpretive problems of quantum mechanics from the viewpoint of a modal ontology of properties. In particular, we will try to delineate a quantum ontology that (i) is modal, because describes the structure of the realm of possibility, and (ii) lacks the ontological category of individual. The final goal is to supply an adequate account of quantum non-individuality on the basis of this ontology.

What ontology does realism about the quantum state suggest? The main extant view in contemporary philosophy of physics is wave-function realism . We elaborate the sense in which wave-function realism does provide an ontological picture, and defend it from certain objections that have been raised against it. However, there are good reasons to be dissatisfied with wave-function realism, as we go on to elaborate. This motivates the development of an opposing picture: what we call spacetime state realism , a view (...) which takes the states associated to spacetime regions as fundamental. This approach enjoys a number of beneficial features, although, unlike wave-function realism, it involves non-separability at the level of fundamental ontology. We investigate the pros and cons of this non-separability, arguing that it is a quite acceptable feature, even one which proves fruitful in the context of relativistic covariance. A companion paper discusses the prospects for combining a spacetime-based ontology with separability, along lines suggested by Deutsch and Hayden. (shrink)

Even though the evidence‐based medicine movement (EBM) labels mechanisms a low quality form of evidence, consideration of the mechanisms on which medicine relies, and the distinct roles that mechanisms might play in clinical practice, offers a number of insights into EBM itself. In this paper, I examine the connections between EBM and mechanisms from several angles. I diagnose what went wrong in two examples where mechanistic reasoning failed to generate accurate predictions for how a dysfunctional mechanism (...) would respond to intervention. I then use these examples to explain why we should expect this kind of mechanistic reasoning to fail in systematic ways, by situating these failures in terms of evolved complexity of the causal system(s) in question. I argue that there is still a different role in which mechanisms continue to figure as evidence in EBM: namely, in guiding the application of population‐level recommendations to individual patients. Thus, even though the evidence‐based movement rejects one role in which mechanistic reasoning serves as evidence, there are other evidentiary roles for mechanistic reasoning. This renders plausible the claims of some critics of evidencebased medicine who point to the ineliminable role of clinical experience. Clearly specifying the ways in which mechanisms and mechanistic reasoning can be involved in clinical practice frames the discussion about EBM and clinical experience in more fruitful terms. (shrink)