The advancement of computing technology makes it possible to build extremely accurate digital reconstructions of brain circuits. Are such unprecedented levels of biological accuracy essential for brain simulations to play the roles they are expected to play in neuroscientific research? The main goal of this paper is to clarify this question by distinguishing between various roles played by large-scale simulations in contemporary neuroscience, and by reflecting about what makes a simulation biologically accurate. It is argued that large-scale simulations may play (...) model-oriented and prediction-oriented roles in brain research, and that the concept of biological accuracy can be interpreted as related to the plausibility of the theoretical model implemented in the simulation system, to the accuracy of the computer implementation, and to the level of details of the implemented model. Building on these observations and distinctions, it is argued that biological accuracy is not essential for a computer simulation to play the epistemic roles it is expected to play in brain research. (shrink)

The received view of computation is methodologically bifurcated: it offers different accounts of computation in the mathematical and physical cases. But little in the way of argument has been given for this approach. This article rectifies the situation by arguing that the alternative, a unified account, is untenable. Furthermore, once these issues are brought into sharper relief we can see that work remains to be done to illuminate the relationship between physical and mathematical computation.

An adequate understanding of the ubiquitous practice of mechanistic explanation requires an account of what Craver termed “constitutive relevance.” Entities or activities are constitutively relevant to a phenomenon when they are parts of the mechanism responsible for that phenomenon. Craver’s mutual manipulability account extended Woodward’s account of manipulationist counterfactuals to analyze how interlevel experiments establish constitutive relevance. Critics of MM argue that applying Woodward’s account to this philosophical problem conflates causation and constitution, thus rendering the account incoherent. These criticisms, we (...) argue, arise from failing to distinguish the semantic, epistemic, and metaphysical aspects of the problem of constitutive relevance. In distinguishing these aspects of the problem and responding to these critics accordingly, we amend MM into a refined epistemic criterion, the “matched interlevel experiments” account. Further, we explain how this epistemological thesis is grounded in the plausible metaphysical thesis that constitutive relevance is causal betweenness. (shrink)

The free-energy principle states that all systems that minimize their free energy resist a tendency to physical disintegration. Originally proposed to account for perception, learning, and action, the free-energy principle has been applied to the evolution, development, morphology, anatomy and function of the brain, and has been called a postulate, an unfalsifiable principle, a natural law, and an imperative. While it might afford a theoretical foundation for understanding the relationship between environment, life, and mind, its epistemic status is unclear. Also (...) unclear is how the free-energy principle relates to prominent theoretical approaches to life science phenomena, such as organicism and mechanism. This paper clarifies both issues, and identifies limits and prospects for the free-energy principle as a first principle in the life sciences. (shrink)

It is commonly assumed that the concept of mechanism is a keytool for the scientific understanding of observable phenomena. However, there is no single definition of mechanism in the current philosophy of science. In fact, philosophers have developed several characterizations of what seemed to be a clear intuitive concept for scientists. In this paper, I will analyze these philosophical conceptions of mechanism, highlighting their problematic aspects and proposing a new mechanistic approach based on the idea that the pertinent levels of (...) organization for a mechanistic explanation can be identified with intervals of quasi-decompositionality. I argue that this approach allows us to consider that activities are directly derived from the entities’ structure. Consequently, a mechanistic explanation implies an arbitrary but not capricious choice of an organizational level. According to this approach, inter-level causation is merely apparent and there is no place for emergent properties. (shrink)

Mechanisms are now taken widely in philosophy of science to provide one of modern science’s basic explanatory devices. This has raised lively debate concerning the relationship between mechanisms, laws and explanation. This paper focuses on cases where a mechanism gives rise to a ceteris paribus law, addressing two inter-related questions: What kind of explanation is involved? and What is going on in the world when mechanism M affords behavior B described in a ceteris paribus law? We explore various answers offered (...) by ‘new mechanists’ and others before setting out and explaining our own answers: mechanistic explanations are a species of oldfashioned covering-law explanation and this often accounts in part for their explanatory power; and B is what it takes for some set of principles that govern the features of M’s parts in their arrangement in M all to be instanced together. (shrink)

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)

: This contribution aims to address epistemological issues at the crossroads of philosophy of science and psychiatry by reflecting on the notions of organization and resilience. Referring to the debate on the notion of “organization” and its explanatory relevance in philosophical neo-mechanistic theories, I consider how such positions hold up when tentatively applied to the mental health context. More specifically, I show how reflections on psychiatric resilience, cognitive reserve, and accommodation strategies challenge attempts to embrace a mechanistic perspective on mental (...) disorders. A deeper focus on these aspects of mental health is relevant to theoretical discussions on explanatory models as well as for clinical practice, diagnosis, and treatment. Keywords: Psychiatric resilience; Cognitive Reserve; Organization; Mechanism Il ruolo esplicativo dell’organizzazione e la resilienza psichiatrica: sfide ad un approccio meccanicistico alla malattia mentale Riassunto: Questo articolo intende discutere alcuni temi epistemologici all’incrocio tra la filosofia della scienza e la psichiatria, riflettendo sulle nozioni di organizzazione e resilienza. Muovendo dalle riflessioni sulla nozione di “organizzazione” sviluppate nell’ambito delle teorie neo-meccaniciste, e dalla difesa del suo ruolo esplicativo, il lavoro analizza la possibilità di estendere alcune posizioni relative alla spiegazione scientifica al contesto delle scienze della salute mentale. Più nello specifico, si illustra come le indagini sulla resilienza psichiatrica, la riserva cognitiva e le strategie di compensazione possano mettere in discussione i tentativi di abbracciare una prospettiva meccanicistica quando si affronta il tema del disturbo psichiatrico. Una maggiore attenzione ai suddetti filoni di ricerca può avere un impatto significativo sia sulla discussione relativa ai modelli teorici di spiegazione della malattia mentale sia sui processi clinici di diagnosi e terapia. Parole chiave: Resilienza psichiatrica; Riserva cognitiva; Organizzazione; Meccanicismo. (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)

Organization figures centrally in the understanding of biological systems advanced by both new mechanists and proponents of the autonomy framework. The new mechanists focus on how components of mechanisms are organized to produce a phenomenon and emphasize productive continuity between these components. The autonomy framework focuses on how the components of a biological system are organized in such a way that they contribute to the maintenance of the organisms that produce them. In this paper we analyze and compare these two (...) accounts of organization and argue that understanding biological organisms as cohesively integrated systems benefits from insights from both. To bring together the two accounts, we focus on the notions of control and regulation as bridge concepts. We start from a characterization of biological mechanisms in terms of constraints and focus on a specific type of mechanism, control mechanisms, that operate on other mechanisms on the basis of measurements of variables in the system and its environment. Control mechanisms are characterized by their own set of constraints that enable them to sense conditions, convey signals, and effect changes on constraints in the controlled mechanism. They thereby allow living organisms to adapt to internal and external variations and to coordinate their parts in such a manner as to maintain viability. Because living organisms contain a vast number of control mechanisms, a central challenge is to understand how they are themselves organized. With the support of examples from both unicellular and multicellular systems we argue that control mechanisms are organized heterarchically, and we discuss how this type of control architecture can, without invoking top-down and centralized forms of organizations, succeed in coordinating internal activities of organisms. (shrink)

The new mechanists and the autonomy approach both aim to account for how biological phenomena are explained. One identifies appeals to how components of a mechanism are organized so that their activities produce a phenomenon. The other directs attention towards the whole organism and focuses on how it achieves self-maintenance. This paper discusses challenges each confronts and how each could benefit from collaboration with the other: the new mechanistic framework can gain by taking into account what happens outside individual mechanisms, (...) while the autonomy approach can ground itself in biological research into how the actual components constituting an autonomous system interact and contribute in different ways to realize and maintain the system. To press the case that these two traditions should be constructively integrated we describe how three recent developments in the autonomy tradition together provide a bridge between the two traditions: (1) a framework of work and constraints, (2) a conception of function grounded in the organization of an autonomous system, and (3) a focus on control. (shrink)

Ontic structural realism constitutes a promising take on scientific realism, one that avoids the well‐known issues that realist stances have with underdetermination and theory change. In its most radical versions, ontic structural realism proposes a type of eliminativism about theoretical entities, ascribing ontological commitment only to the structures, and not to the objects appearing in our theories. More moderate versions of ontic structural realism have also been proposed, allowing for ‘thin’ objects in the ontology. This work connects these takes on (...) structural realism with the independent notion that there are two categorically different kinds of scientific theories, namely those that deal with interactions and those that deal with structural constraints – what are known as interaction and framework theories, respectively. By taking this classification seriously, one can arrive at a selective version of ontic structural realism which is better adapted to our scientific knowledge, in which eliminativist ontic structural realism constitutes a natural fit to framework theories, whereas the moderate version is connected to interaction theories. (shrink)

Marcello Barbieri has presented code biology as an alternative to the Peircean approach to biosemiotics. Some critics questioned the viability of code biology on grounds that Barbieri’s conception of science is limited. It has been argued that code biology’s mechanistic tendency is the cause of the allegedly limited conception of science. In this paper, I evaluate the scientific viability of the code model from the perspective of scientific realism in the philosophy of science. To be more precise, I draw on (...) resources of the mechanistic view in philosophy to argue that far from harbouring a limited conception of science, code biology could indeed improve the scientific prospects of biosemiotics. I show that the mechanistic and model-based tendency of the code model enhances its vigour as a full-blooded scientific approach to the study of meaning in living systems. To consolidate my claim, I draw on some recent debates in the mechanistic philosophy to argue that even relational approaches to understanding the meaning in living systems—such as an approach that is defended by Vega in a recent paper—could be underpinned by mechanistic processes at a foundational level. (shrink)

According to new mechanists, mechanisms explain how specific biological phenomena are produced. New mechanists have had little to say about how mechanisms relate to the organism in which they reside. A key feature of organisms, emphasized by the autonomy tradition, is that organisms maintain themselves. To do this, they rely on mechanisms. But mechanisms must be controlled so that they produce the phenomena for which they are responsible when and in the manner needed by the organism. To account for how (...) they are controlled, we characterize mechanisms as sets of constraints on the flow of free energy. Some constraints are flexible and can be acted on by other mechanisms, control mechanisms, that utilize information procured from the organism and its environment to alter the flexible constraints in other mechanisms so that they produce phenomena appropriate to the circumstances. We further show that control mechanisms in living organisms are organized heterarchically—control is carried out primarily by local controllers that integrate information they acquire as well as that which they procure from other control mechanisms. The result is not a hierarchy of control but an integrated network of control mechanisms that has been crafted over the course of evolution. (shrink)

Research devoted to characterizing phenomena is underappreciated in philosophical accounts of scientific inquiry. This paper develops a diachronic analysis of research over 100 years that led to the recognition of two related electrophysiological phenomena, the membrane potential and the action potential. A diachronic perspective allows for reconciliation of two threads in philosophical discussions of phenomena—Hacking’s treatment of phenomena as manifest in laboratory settings and Bogen and Woodward’s construal of phenomena as regularities in the world. The diachronic analysis also reveals the (...) epistemic tasks that contribute to establishing phenomena, including the development of appropriate investigative techniques and concepts for characterizing them. (shrink)

A major approach to cancer research in the late twentieth century was to search for genes that, when altered, initiated the development of a cell into a cancerous state or failed to stop this development. But as researchers acquired the capacity to sequence tumors and incorporated the resulting data into databases, it became apparent that for many tumors no genes were frequently altered and that the genes altered in different tumors in the same tissue type were often distinct. To address (...) this heterogeneity problem, many researchers looked to a higher level of organization—to mechanisms in which gene products participated. They proposed to reduce heterogeneity by recognizing that multiple gene alterations affect the same mechanism and that it is the altered mechanism that is responsible for the cell developing one or more hallmarks of cancer. I examine how mechanisms figure in this research and focus on two heuristics researchers use to integrate proteins into mechanisms, one focusing on pathways and one focusing on clusters in networks. (shrink)

Dynamical systems play a central role in explanations in cognitive neuroscience. The grounds for these explanations are hotly debated and generally fall under two approaches: non-mechanistic and mechanistic. In this paper, I first outline a neurodynamical explanatory schema that highlights the role of dynamical systems in cognitive phenomena. I next explore the mechanistic status of such neurodynamical explanations. I argue that these explanations satisfy only some of the constraints on mechanistic explanation and should be considered pseudomechanistic explanations. I defend this (...) argument against three alternative interpretations of the neurodynamical explanatory schema. The independent interpretation holds that neurodynamical explanations and mechanisms are independent. The constitutive interpretation holds that neurodynamical explanations are constitutive but otherwise non-mechanistic. Both the independent and constitutive interpretations fail to account for all the features of neurodynamical explanations. The partial interpretation assumes that the targets of dynamical systems models are mechanisms and so holds that neurodynamical explanations are incomplete because they lack mechanistic details. I contend instead that the targets of those models are dynamical systems distinct from mechanisms and defend this claim against several objections. I conclude with a defense of the pseudomechanistic interpretation and a discussion of the source of their explanatory power in relation to a causal-mechanical description of the world. (shrink)

In this paper we investigate how inference to the best explanation (IBE) works in engineering science, focussing on the context of malfunction explanation. While IBE has gotten a lot of attention in the philosophy of science literature, few, if any, philosophical work has focussed on IBE in engineering science practice. We first show that IBE in engineering science has a similar structure as IBE in other scientific domains in the sense that in both settings IBE hinges on the weighing of (...) explanatory virtues. We then proceed to show that, due to the intimate connection between explanation and redesign in engineering science, there is a further engineering domain-specific virtue in terms of which engineering malfunction explanations are evaluated, viz. the virtue of redesign utility. This virtue entails that the explanatory information offered by a malfunction explanation should be instrumental in predicting counterfactual dependencies in redesigned systems. We illustrate and elaborate these points in terms of a number of engineering examples, focussing in particular on the 2009 crash of Air France Flight 447. Our extension of analyses of IBE and explanation to engineering science practice offers new insights by identifying a new explanatory virtue in malfunction explanation: redesign utility. (shrink)

This paper discusses a class of mechanistic explanations employed in engineering science where the activities and organization of nonstandard entities are cited as core factors responsible for failures. Given the use of mechanistic language by engineers and the manifestly mechanistic structure of these explanations, I consider several interpretations of these explanations within the new mechanical framework. I argue that these interpretations fail to solve several philosophical problems and propose an account of fictional mechanism explanations instead. According to this account, fictional (...) mechanism explanations provide descriptions of fictional mechanisms that enable the tracking of counterfactual dependencies of the physical system they model by capturing system constraints. Engineers use these models to learn about and understand properties of materials, to build computational simulations of their behaviour, and to design new materials. (shrink)

It is widely assumed that functional and dispositional properties are not identical to their physical base, but that there is some kind of asymmetrical ontological dependence between them. In this regard, a popular idea is that the former are realized by the latter, which, under the non-identity assumption, is generally understood to be a non-causal, constitutive relation. In this paper we examine two of the most widely accepted approaches to realization, the so-called ‘flat view’ and the ‘dimensioned view’, and we (...) analyze their explanatory relevance in the light of a number of examples from the life sciences, paying special attention to developmental phenomena. Our conclusion is that the emphasis placed by modern-day biology on such properties as variability, evolvability, and a whole collection of phenomena like modularity, robustness, and developmental constraint or developmental bias requires the adoption of a much more dynamic perspective than traditional realization frameworks are able to capture. (shrink)

Causal mediation mechanisms are well supported by available experimental evidence and provide a practicable way to reductive physicalism. According to the causal mediation account of mechanistic explanation, descriptions as diverse as ‘black-box’ phenomena, mechanistic sketches and schemas mixing physically interpreted and operationalized biological, psychological and social variables, and detailed descriptions of mechanisms refer to the same causal structure circumscribed within the spatiotemporal boundaries of a replicable experimental setup. The coreference of coarser- and finer-grained descriptions of causal structures opens new possibilities (...) for testing the reductive physicalism conjecture. I discuss experimental designs supporting the causal mediation account and show how recent studies demonstrating the biological mediation of mind-mind causal processes can provide evidence for reductive physicalism. (shrink)

According to contemporary ‘process ontology’, organisms are best conceptualised as spatio-temporally extended entities whose mereological composition is fundamentally contingent and whose essence consists in changeability. In contrast to the Aristotelian precepts of classical ‘substance ontology’, from the four-dimensional perspective of this framework, the identity of an organism is grounded not in certain collections of privileged properties, or features which it could not fail to possess, but in the succession of diachronic relations by which it persists, or ‘perdures’ as one entity (...) over time. In this paper, I offer a novel defence of substance ontology by arguing that the coherency and plausibility of the radical reconceptualisation of organisms proffered by process ontology ultimately depends upon its making use of the ‘substantial’ principles it purports to replace. (shrink)

Recent research on bacteria and other microorganisms has provided interesting insights into the nature of life, cooperation, evolution, individuality or species. In this paper, I focus on the capacity of bacteria to produce molecules that are usually classified as ’signals’ and I defend two claims. First, I argue that certain interactions between bacteria should actually qualify as genuine forms of communication. Second, I use this case study to revise our general theories of signaling. Among other things, I argue that a (...) plausible requirement for a state to qualify as a signal is that it is a minimal cause. (shrink)

The emphasis on the organization of entities and their activities and interactions has been labeled one of the most distinct contributions of mechanistic philosophy. In this paper I discuss the manner in which the organization of entities and their activities and interactions participates in bringing about phenomena. I present a well-known example from molecular biology—the functioning of the genetic switch in phage lambda—and discuss Marco J. Nathan’s notion of causation by concentration. Nathan introduces causation by concentration to account for the (...) irreducible causal role that the concentration ratio between two kinds of proteins possesses in the genetic switch mechanism in phage lambda. I discuss what the irreducibility of this causal role amounts to and provide a mechanistic interpretation of Nathan’s causation by concentration; that is, I explain this irreducible causal role as one organizational feature of this mechanism. The paper concludes that biological mechanisms need a causal pluralist framework [similar to Glennan’s account in, and but slightly modified] where organizational features such as the concentration ratio have a causally relevant role, yet all the causally productive relations occur at the level of entities or individuals. (shrink)

These preprints were automatically compiled into a PDF from the collection of papers deposited in PhilSci-Archive in conjunction with the PSA 2018.

Scientists cannot devise theories, construct models, propose explanations, make predictions, or even carry out observations, without first classifying their subject matter. The goal of scientific taxonomy is to come up with classification schemes that conform to nature's own. Another way of putting this is that science aims to devise categories that correspond to 'natural kinds.' The interest in ascertaining the real kinds of things in nature is as old as philosophy itself, but it takes on a different guise when one (...) adopts a naturalist stance in philosophy, that is when one looks closely at scientific practice and takes it as a guide for identifying natural kinds and investigating their general features. This Element surveys existing philosophical accounts of natural kinds, defends a naturalist alternative, and applies it to case studies in a diverse set of sciences. This title is also available as Open Access on Cambridge Core. (shrink)

Any successful account of the metaphysics of mechanistic causation must satisfy at least five key desiderata. In this article, I lay out these five desiderata and explain why existing accounts of the metaphysics of mechanistic causation fail to satisfy them. I then present an alternative account that does satisfy the five desiderata. According to this alternative account, we must resort to a type of ontological entity that is new to metaphysics, but not to science: constraints. In this article, I explain (...) how a constraints-based metaphysics fits best with the emerging consensus on the nature of mechanistic explanation. 1Introduction2Renormalizability2.1The first two desiderata: Intrinsicness and productivity2.2The third desideratum: Scientific validity or non-mysteriousness2.3The fourth desideratum: Directionality2.4The fifth desideratum: Perspectival nature of mechanisms3Constraints and Causation3.1Multi-perspectival realism and causal structure3.2Causal structure as laws3.3Causal structures in analytical mechanics: Constraints3.4A metaphysics inspired by analytical mechanics: Constraints as ontologically primitive modal structures4Constraints and Mechanistic Causal Powers 4.1Inter- versus intra-perspectival categories4.2Mechanistic causal powers are grounded by constraints4.3Intrinsicness and constraints4.4Constraints and productiveness4.5Constraints and directionality5Conclusion. (shrink)

The traditional practice of establishing morphological types and investigating morphological organization has found new support from evolutionary developmental biology (evo-devo), especially with respect to the notion of body plans. Despite recurring claims that typology is at odds with evolutionary thinking, evo-devo offers mechanistic explanations of the evolutionary origin, transformation, and evolvability of morphological organization. In parallel, philosophers have developed non-essentialist conceptions of natural kinds that permit kinds to exhibit variation and undergo change. This not only facilitates a construal of species (...) and higher taxa as natural kinds, but also broadens our perspective on the diversity of kinds found in biology. There are many different natural kinds relevant to the investigative and explanatory aims of evo-devo, including homologues and developmental modules. (shrink)

Evo-devo is a multidisciplinary field that investigates the interplay between evolutionary and developmental processes and brings together different kinds of explanatory strategies. This chapter examines the structure of paradigmatic explanations in evo-devo (e.g., the explanation of the origin of an evolutionary novelty) and raises philosophical questions about explanation in evo-devo. Much research in evo-devo is concerned with studying the developmental mechanisms that constrain and facilitate phenotypic evolution, which suggests that a distinctive feature of evo-devo is that it constructs mechanistic explanations. (...) In this chapter, I discuss three major challenges for thinking about evo-devo as providing mechanistic explanations. First, an explanation of an evolutionary novelty consists of several mechanistic explanations, rather than being a single one. Second, developmental mechanisms are ontogenetically and phylogenetically dynamic and thus difficult to individuate. Third, an explanation of an evolutionary novelty also has a non-mechanistic, historical part. Finally, I discuss whether evo-devo’s emphasis on mechanistic explanation promotes explanatory integration or results in a reductionist view of evolution. (shrink)

In this chapter we examine the relation between mechanisms and laws/counterfactuals by revisiting the main notions of mechanism found in the literature. We distinguish between two different conceptions of ‘mechanism’: mechanisms-of underlie or constitute a causal process; mechanisms-for are complex systems that function so as to produce a certain behavior. According to some mechanists, a mechanism fulfills both of these roles simultaneously. The main argument of the chapter is that there is an asymmetrical dependence between both kinds of mechanisms and (...) laws/counterfactuals: while some laws and counterfactuals must be taken as primitive (non-mechanistic) facts of the world, all mechanisms depend on laws/counterfactuals. (shrink)

Jonathan Y. Tsou examines and defends positions on central issues in philosophy of psychiatry. The positions defended assume a naturalistic and realist perspective and are framed against skeptical perspectives on biological psychiatry. Issues addressed include the reality of mental disorders; mechanistic and disease explanations of abnormal behavior; definitions of mental disorder; natural and artificial kinds in psychiatry; biological essentialism and the projectability of psychiatric categories; looping effects and the stability of mental disorders; psychiatric classification; and the validity of the DSM's (...) diagnostic categories. The main argument defended by Tsou is that genuine mental disorders are biological kinds with harmful effects. This argument opposes the dogma that mental disorders are necessarily diseases that result from biological dysfunction. Tsou contends that the broader ideal of biological kinds offers a more promising and empirically ascertainable naturalistic standard for assessing the reality of mental disorders and the validity of psychiatric categories. (shrink)

Abstraction and idealization are the two notions that are most often discussed in the context of assumptions employed in the process of model building. These notions are also routinely used in philosophical debates such as that on the mechanistic account of explanation. Indeed, an objection to the mechanistic account has recently been formulated precisely on these grounds: mechanists cannot account for the common practice of idealizing difference-making factors in models in molecular biology. In this paper I revisit the debate and (...) I argue that the objection does not stand up to scrutiny. This is because it is riddled with a number of conceptual inconsistencies. By attempting to resolve the tensions, I also draw several general lessons regarding the difficulties of applying abstraction and idealization in scientific practice. Finally, I argue that more care is needed only when speaking of abstraction and idealization in a context in which these concepts play an important role in an argument, such as that on mechanistic explanation. (shrink)

It is generally believed that two rival non-relativistic quantum theories, the realist interpretation of quantum mechanics and Bohmian mechanics, are empirically equivalent. In this paper, I use these two quantum theories to show that it is possible to offer a solution to underdetermination in some local cases, by specifying what counts as relevant empirical evidence in empirical equivalence and underdetermination. I argue for a _domain-sensitive_ approach to underdetermination. Domain sensitivity on theories’ predictions plays a role in determining whether two or (...) more theories are empirically equivalent and underdetermined. To support my argument for the denial of the empirical equivalence between Bohmian mechanics and the realist interpretation of quantum mechanics, I argue that they are not empirically equivalent when we consider their predictions for domains outside their application, using the relativistic domain as an example. (shrink)

What features will something have if it counts as an explanation? And will something count as an explanation if it has those features? In the second half of the 20th century, philosophers of science set for themselves the task of answering such questions, just as a priori conceptual analysis was generally falling out of favor. And as it did, most philosophers of science just moved on to more manageable questions about the varieties of explanation and discipline-specific scientific explanation. Often, such (...) shifts are sound strategies for problem-solving. But leaving fallow certain basic conceptual issues can also result in foundational debates. (shrink)

Existing accounts of mechanistic causation are not suited for understanding causation in biological and neural mechanisms because they do not have the resources to capture the unique causal structure of control heterarchies. In this paper, we provide a new account on which the causal powers of mechanisms are grounded by time-dependent, variable constraints. Constraints can also serve as a key bridge concept between the mechanistic approach to explanation and underappreciated work in theoretical biology that sheds light on how biological systems (...) channel energy to actively respond to the environment in adaptive ways, perform work, and fulfill the requirements to maintain themselves far from equilibrium. We show how the framework applies to several concrete examples of control in simple organisms as well as the nervous system of complex organisms. (shrink)

Objects appear to causally interact with one another in virtual worlds, such as video games, virtual reality, and training simulations. Is this causation real or is it illusory? In this paper I argue that virtual causation is as real as physical causation. I achieve this in two steps: firstly, I show how virtual causation has all the important hallmarks of relations that are causal, as opposed to merely accidental, and secondly, I show how virtual causation is genuine according to one (...) influential metaphysical theory of causation: the mechanistic approach. (shrink)

The scope of this paper can be clarified by means of a well-known phenomenon that is usually called ‘industrial melanism’: the fact that the melanic form of the peppered moth became dominant in industrial areas in England in the second half of the nineteenth century. Such changes in relative phenotype frequencies are important explananda for population biologists. Apart from trying to explain such changes over time, population biologists also often try to explain differences between populations, e.g. why yellow shell colour (...) is dominant in certain colonies of land snails and almost absent in other colonies. The causal explanations that are given to address such explananda are the objects of analysis in this paper. Our primary aim is to explicate their structure: we want to capture the typical ingredients of causal explanations in population biology, and their organisation. Based on this explication, we discuss how natural selection fits into recent mechanical philosophy of science, and engage in the debate on the nature of evolutionary theory. (shrink)

The periodic table is one of the best-known systems of classification in science. Because of the information it contains, it raises explanation-seeking questions. Quantum mechanical models of the behaviour of electrons may be seen as providing explanations in response to these questions. In this paper we first address the question ‘Do quantum mechanical models of atoms provide legitimate explanations?’ Because our answer is positive, our next question is ‘Are the explanations provided by quantum mechanical models of atoms mechanistic explanations?’. This (...) question is motivated by the fact that in many scientific disciplines, mechanistic explanations are abundant. Because our answer to the second question is negative, our last question is ‘What kind of explanation do quantum mechanical models of atom provide?’ By addressing these questions, we shed light on the nature of an important type of chemical explanation. (shrink)

I show how Sir William Rowan Hamilton’s philosophical commitments led him to a causal interpretation of classical mechanics. I argue that Hamilton’s metaphysics of causation was injected into his dynamics by way of a causal interpretation of force. I then detail how forces are indispensable to both Hamilton’s formulation of classical mechanics and what we now call Hamiltonian mechanics (i.e., the modern formulation). On this point, my efforts primarily consist of showing that the contemporary orthodox interpretation of potential energy is (...) the interpretation found in Hamilton’s work. Hamilton called the potential energy function the “force-function” because he believed that it represents forces at work in the world. Various non-historical arguments for this orthodox interpretation of potential energy are provided, and matters are concluded by showing that in classical Hamiltonian mechanics, facts about the potential energies of systems are grounded in facts about forces. Thus, if one can tolerate the view that forces are causes of motion, then Hamilton provides one with a road map for transporting causation into one of the most mathematically sophisticated formulations of classical mechanics, viz., Hamiltonian mechanics. (shrink)

I will argue, pace a great many of my contemporaries, that there's something right about Boltzmann's attempt to ground the second law of thermodynamics in a suitably amended deterministic time-reversal invariant classical dynamics, and that in order to appreciate what's right about (what was at least at one time) Boltzmann's explanatory project, one has to fully apprehend the nature of microphysical causal structure, time-reversal invariance, and the relationship between Boltzmann entropy and the work of Rudolf Clausius.

This paper adds to the philosophical literature on mechanistic explanation by elaborating two related explanatory functions of idealisation in mechanistic models. The first function involves explaining the presence of structural/organizational features of mechanisms by reference to their role as difference-makers for performance requirements. The second involves tracking counterfactual dependency relations between features of mechanisms and features of mechanistic explanandum phenomena. To make these functions salient, we relate our discussion to an exemplar from systems biological research on the mechanism for countering (...) heat shock—the heat shock response system—in Escherichia coli bacteria. This research also reinforces a more general lesson: ontic constraint accounts in the literature on mechanistic explanation provide insufficiently informative normative appraisals of mechanistic models. We close by outlining an alternative view on the explanatory norms governing mechanistic representation. (shrink)

The causal efficacy of a material system is usually thought to be produced by the law-like actions and interactions of its constituents. Here, a specific system is constructed and explained that produces a cause that cannot be understood in this way, but instead has novel and autonomous efficacy. The construction establishes a proof-of-feasibility of strong emergence. The system works by utilizing randomness in a targeted and cyclical way, and by relying on sustained evolution by natural selection. It is not vulnerable (...) to standard arguments against strong emergence, in particular ones that assume that the physical realm is causally closed. Moreover, it does not suffer from epiphenomenalism or causal overdetermination. The system uses only standard material components and processes, and is fully consistent with naturalism. It is discussed whether the emergent cause can still be viewed as ‘material’ in the way that term is commonly understood. (shrink)

I argue that introspection recruits the same mental mechanism as that which is required for the production of ordinary speech acts. In introspection, in effect, we intentionally tell ourselves that we are in some mental state, aiming thereby to produce belief about that state in ourselves. On one popular view of speech acts, however, this is precisely what speakers do when speaking to others. On this basis, I argue that every bias discovered by social epistemology applies to introspection and other (...) forms of self-directed representation. If so, it becomes unclear in what sense social epistemology is social. (shrink)

Mechanisms consist of component parts and processes organized in a specific way to produce changes that may give rise to one or more phenomena. I aim to examine the generative mechanism of generative material models in the production of new material models. A generative material model in biology is a living material model that is capable of generating new material models. I contend that generative mechanisms of a generative material model are not to be conflated with biological mechanisms: the former (...) is a mechanism manipulated and altered by the modeler while the latter is a naturally occurring mechanism. I examine the ways in which idealization may contribute to the generative mechanism in generating new model organisms. I articulate that the component parts and activities in a generative mechanism are to a large extent shaped by idealization in generative material modeling. Although biological mechanisms do have a role to play in the generation of model organisms, I propose that we shall view the generative mechanism as a hybrid of biological mechanisms and modeling activities. I shall argue that the notion of generative mechanisms as hybrid mechanisms is different from the extant conceptions of mechanisms in various aspects. (shrink)

In our article, “Past Facts and The Nature of History”, we unpack a broadly realist view of the nature of history and historical narratives. Paul Roth’s The Philosophical Structure of Historical Explanation serves as our primary foil. Fons DeWulf and Roth have replied, and this is our response to their response.

During the past two decades, philosophers of biology have increasingly turned their attention to mechanisms of biological phenomena. Through analyses of mechanistic proposals advanced by biologists, the goal of these philosophers is to understand what a mechanism is and how mechanisms explain. These analyses have generally focused on mechanistic proposals for phenomenon that occur at the cellular or sub-cellular level, such as synapse firing, protein synthesis, or metabolic pathway operation. Little is said about the mechanisms of the macromolecular reactions that (...) underpin these phenomena. These reactions comprise a diverse family of reaction types, and include protein folding, macromolecular complex formation, receptor-ligand interactions, and enzyme catalysis. In this paper, I develop an account of mechanism that focuses exclusively on macromolecular reactions. I begin by reviewing how mechanism is understood in enzymology, and how mechanistic concepts of enzymology apply to macromolecular reactions in general. We will see that the mechanism of a macromolecular reaction is most accurately described as a progression of reaction intermediates, where the evolution of intermediates, from one to the next, is characterized by an energetic coupling between chemistry and protein dynamics. I then make the case that this description necessitates a grounding in a process ontology. To describe the mechanism by which a macromolecular reaction occurs is to describe a process. (shrink)

We show how more general knowledge can be built in information security, by the building of knowledge of mechanism clusters, some of which are multifield. By doing this, we address in a novel way the longstanding philosophical problem of how, if at all, we come to have knowledge that is in any way general, when we seem to be confined to particular experiences. We also address the issue of building knowledge of mechanisms by studying an area that is new to (...) the mechanisms literature: the methods of what we shall call mechanism discovery in information security. This domain offers a fascinating novel constellation of challenges for building more general knowledge. Specifically, the building of stable communicable mechanistic knowledge is impeded by the inherent changeability of software, which is deployed by malicious actors constantly changing how their software attacks, and also by an ineliminable secrecy concerning the details of attacks not just by attackers, but also by information security defenders as they protect their methods from both attackers and commercial competitors. We draw out ideas from the work of the mechanists Darden, Craver, and Glennan to yield an approach to how general knowledge of mechanisms can be painstakingly built. We then use three related examples of active research problems from information security to develop philosophical thinking about building general knowledge using mechanisms, and also apply this to develop insights for information security. We show that further study would be instructive both for practitioners and for philosophers. (shrink)

Proponents of the extended mind have suggested that phenomenal transparency may be important to the way we evaluate putative cases of cognitive extension. In particular, it has been suggested that in order for a bio-external resource to count as part of the machinery of the mind, it must qualify as a form of transparent equipment or transparent technology. The present paper challenges this claim. It also challenges the idea that phenomenological properties can be used to settle disputes regarding the constitutional (...) status of bio-external resources in episodes of extended cognizing. Rather than regard phenomenal transparency as a criterion for cognitive extension, we suggest that transparency is a feature of situations that support the ascription of certain cognitive/mental dispositional properties to both ourselves and others. By directing attention to the forces and factors that motivate disposition ascriptions, we arrive at a clearer picture of the role of transparency in arguments for extended cognition and the extended mind. As it turns out, transparency is neither necessary nor sufficient for cognitive extension, but this does not mean that it is entirely irrelevant to our understanding of the circumstances in which episodes of extended cognizing are apt to arise. (shrink)

Examples of extended cognition typically involve the use of technologically low-grade bio-external resources (e.g., the use of pen and paper to solve long multiplication problems). The present paper describes a putative case of extended cognizing based around a technologically advanced mixed reality device, namely, the Microsoft HoloLens. The case is evaluated from the standpoint of a mechanistic perspective. In particular, it is suggested that a combination of organismic (e.g., the human individual) and extra-organismic (e.g., the HoloLens) resources form part of (...) a common mechanism that realizes a bona fide cognitive routine. In addition to demonstrating how the theoretical resources of neo-mechanical philosophy might be used to evaluate extended cognitive systems, the present paper illustrates one of the ways in which mixed reality devices, virtual objects (i.e., holograms), and online (Internet-accessible) computational routines might be incorporated into human cognitive processes. This, it is suggested, speaks to the recent interest in mixed/virtual reality technologies across a number of disciplines. It also introduces us to issues that cross-cut disparate fields of philosophical research, such as the philosophy of science and the philosophy of technology. (shrink)