New mechanical philosophy posits that explanations in the life sciences involve the decomposition of a system into its entities and their respective activities and organization that are responsible for the explanandum phenomenon. This mechanistic account of explanation has proven problematic in its application to mathematical models, leading the mechanists to suggest different ways of aligning abstract models with the mechanist program. Initially, the discussion centered on whether the Hodgkin-Huxley model is explanatory. Network models provided another complication, as they apply to (...) a wide number of materially diverse systems. In this article, we examine the various attempts to integrate abstract models within the mechanist program, also presenting a further challenge: the Heimburg-Jackson model, which was introduced as an alternative to the Hodgkin-Huxley model. We argue that although the notion of abstraction as the omission of irrelevant mechanistic details appears to give a mechanistic solution for accommodating abstract models, this notion does not suit models whose epistemic strategy is not decompositional. As a result, the mechanist has to choose whether to dilute the mechanistic approach nearly beyond recognition or to claim that many, if not most, abstract theoretical models do not deliver mechanistic explanations, or qualify as explanatory at all. (shrink)

Functional decomposition is an important goal in the life sciences, and is central to mechanistic explanation and explanatory reduction. A growing literature in philosophy of science, however, has challenged decomposition-based notions of explanation. ‘Holists’ posit that complex systems exhibit context-sensitivity, dynamic interaction, and network dependence, and that these properties undermine decomposition. They then infer from the failure of decomposition to the failure of mechanistic explanation and reduction. I argue that complexity, so construed, is only incompatible with one notion of decomposition, (...) which I call ‘atomism’, and not with decomposition writ large. Atomism posits that function ascriptions must be made to parts with minimal reference to the surrounding system. Complexity does indeed falsify atomism, but I contend that there is a weaker, ‘contextualist’ notion of decomposition that is fully compatible with the properties that holists cite. Contextualism suggests that the function of parts can shift with external context, and that interactions with other parts might help determine their context-appropriate functions. This still admits of functional decomposition within a given context. I will give examples based on the notion of oscillatory multiplexing in systems neuroscience. If contextualism is feasible, then holist inferences are faulty—one cannot infer from the presence of complexity to the failure of decomposition, mechanism, and reductionism. (shrink)

Abstract Although noting the importance of organization in mechanisms, the new mechanistic philosophers of science have followed most biologists in focusing primarily on only the simplest mode of organization in which operations are envisaged as occurring sequentially. Increasingly, though, biologists are recognizing that the mechanisms they confront are non-sequential and the operations nonlinear. To understand how such mechanisms function through time, they are turning to computational models and tools of dynamical systems theory. Recent research on circadian rhythms addressing both intracellular (...) mechanisms and the intercellular networks in which these mechanisms are synchronized illuminates this point. This and other recent research in biology shows that the new mechanistic philosophers of science must expand their account of mechanistic explanation to incorporate computational modeling, yielding dynamical mechanistic explanations. Developing such explanations, however, is a challenge for both the scientists and the philosophers as there are serious tensions between mechanistic and dynamical approaches to science, and there are important opportunities for philosophers of science to contribute to surmounting these tensions. Content Type Journal Article Category Original paper in Philosophy of Science Pages 1-16 DOI 10.1007/s13194-012-0046-x Authors William Bechtel, Department of Philosophy, Center for Chronobiology, and Science Studies Program, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0119, USA Journal European Journal for Philosophy of Science Online ISSN 1879-4920 Print ISSN 1879-4912. (shrink)

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)

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)

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)

Chronobiology, especially the study of circadian rhythms, provides a model scientific field in which philosophers can study how investigators from a variety of disciplines working at different levels of organization are each contributing to a multi-level account of the responsible mechanism. I focus on how the framework of mechanistic explanation integrates research designed to decompose the mechanism with efforts directed at recomposition that relies especially on computation models. I also examine how recently the integration has extended beyond basic research to (...) the processes through which the disruption of circadian rhythms contributes to disease, including various forms of cancer. Understanding these linkages has been facilitated by discoveries about how circadian mechanisms interact with mechanisms involved in other physiological processes, including the cell cycle and the immune system. (shrink)

Chronobiology, especially the study of circadian rhythms, provides a model scientific field in which philosophers can study how investigators from a variety of disciplines working at different levels of organization are each contributing to a multi-level account of the responsible mechanism. I focus on how the framework of mechanistic explanation integrates research designed to decompose the mechanism with efforts directed at recomposition that relies especially on computation models. I also examine how recently the integration has extended beyond basic research to (...) the processes through which the disruption of circadian rhythms contributes to disease, including various forms of cancer. Understanding these linkages has been facilitated by discoveries about how circadian mechanisms interact with mechanisms involved in other physiological processes, including the cell cycle and the immune system. (shrink)

Cognitive science has always included multiple methodologies and theoretical commitments. The philosophy of cognitive science should embrace, or at least acknowledge, this diversity. Bechtel’s (2009a) proposed philosophy of cognitive science, however, applies only to representationalist and mechanist cognitive science, ignoring the substantial minority of dynamically oriented cognitive scientists. As an example of nonrepresentational, dynamical cognitive science, we describe strong anticipation as a model for circadian systems (Stepp & Turvey, 2009). We then propose a philosophy of science appropriate to nonrepresentational, dynamical (...) cognitive science. (shrink)

I argue (1) that what (ontic) New Mechanistic philosophers of science call mechanisms would be material Gestalten, and (2) that Merleau-Ponty’s engagement with Gestalt theory can help us frame a standing challenge against ontic conceptions of mechanisms. In short, until the (ontic) New Mechanist can provide us with a plausible account of the organization of mechanisms as an objective feature of mind-independent ontic structures in the world which we might discover – and no ontic Mechanist has done so – it (...) is more conservative to claim that mechanistic organization is instead a mind-dependent aspect of our epistemic strategies of mechanistic explanation. (shrink)

Mechanistic accounts of explanation have recently found popularity within philosophy of science. Presently, we introduce the idea of an extended mechanistic explanation, which makes explicit room for the role of environment in explanation. After delineating Craver and Bechtel’s account, we argue this suggestion is not sufficiently robust when we take seriously the mechanistic environment and modeling practices involved in studying contemporary complex biological systems. Our goal is to extend the already profitable mechanistic picture by pointing out the importance of the (...) mechanistic environment. It is our belief that extended mechanistic explanations, or mechanisms that take into consideration the temporal sequencing of the interplay between the mechanism and the environment, allow for mechanistic explanations regarding a broader group of scientific phenomena. (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)

After a decade of intense debate about mechanisms, there is still no consensus characterization. In this paper we argue for a characterization that applies widely to mechanisms across the sciences. We examine and defend our disagreements with the major current contenders for characterizations of mechanisms. Ultimately, we indicate that the major contenders can all sign up to our characterization.

In this paper, I argue that looking at the concept of neural function through the lens of cognition alone risks cognitive myopia: it leads neuroscientists to focus only on mechanisms with cognitive functions that process behaviorally relevant information when conceptualizing “neural function”. Cognitive myopia tempts researchers to neglect neural mechanisms with noncognitive functions which do not process behaviorally relevant information but maintain and repair neural and other systems of the body. Cognitive myopia similarly affects philosophy of neuroscience because scholars overlook (...) noncognitive functions when analyzing issues surrounding e.g., functional decomposition or the multifunctionality of neural structures. I argue that we can overcome cognitive myopia by adopting a patchwork approach that articulates cognitive and noncognitive “patches” of the concept of neural function. Cognitive patches describe mechanisms with causally specific effects on cognition and behavior which are likely operative in transforming sensory or other inputs into motor outputs. Noncognitive patches describe mechanisms that lack such specific effects; these mechanisms are enabling conditions for cognitive functions to occur. I use these distinctions to characterize two noncognitive functions at the mesoscale of neural circuits: subsistence functions like breathing are implemented by central pattern generators and are necessary to maintain the life of the organism. Infrastructural functions like gain control are implemented by canonical microcircuits and prevent neural system damage while cognitive processing occurs. By adding conceptual patches that describe these functions, a patchwork approach can overcome cognitive myopia and help us explain how the brain’s capacities as an information processing device are constrained by its ability to maintain and repair itself as a physiological apparatus. (shrink)

We contrast reactive and endogenously active perspectives on brain activity. Both have been pursued continuously in neurophysiology laboratories since the early 20thcentury, but the endogenous perspective has received relatively little attention until recently. One of the many successes of the reactive perspective was the identification, in the second half of the 20th century, of the distinctive contributions of different brain regions involved in visual processing. The recent prominence of the endogenous perspective is due to new findings of ongoing oscillatory activity (...) in the brain at a wide range of time scales, exploiting such techniques as single-cell recording, EEG, and fMRI. We recount some of the evidence pointing to ways in which this endogenous activity is relevant to cognition and behavior. Our major objective is to consider certain implications of the contrast between the reactive and endogenous perspectives. In particular, we relate these perspectives to two different characterizations of explanation in the new mechanistic philosophy of science. In a basic mechanistic explanation, the operations of a mechanism are characterized qualitatively and as functioning sequentially until a terminating condition is realized. In contrast, a dynamic mechanistic explanation allows for non-sequential organization and emphasizes quantitative modeling of the mechanisms's behavior. For example, with appropriate parameter values a set of differential equations can be used to demonstrate ongoing oscillations in a system organized with feedback loops. We conclude that the basic conception of mechanistic explanation is adequate for reactive accounts of brain activity, but dynamical accounts are required to explain sustained, endogenous activity. (shrink)

In this talk I present the main results from Anta (2021), namely, that the theoretical division between Boltzmannian and Gibbsian statistical mechanics should be understood as a separation in the epistemic capabilities of this physical discipline. In particular, while from the Boltzmannian framework one can generate powerful explanations of thermal processes by appealing to their microdynamics, from the Gibbsian framework one can predict observable values in a computationally effective way. Finally, I argue that this statistical mechanical schism contradicts the Hempelian (...) (1958) thesis that the predictive power of a scientific theory is directly proportional to its explanatory potential, and vice versa. (shrink)