This chapter argues that scientific and philosophical progress in our understanding of the living world requires that we abandon a metaphysics of things in favour of one centred on processes. We identify three main empirical motivations for adopting a process ontology in biology: metabolic turnover, life cycles, and ecological interdependence. We show how taking a processual stance in the philosophy of biology enables us to ground existing critiques of essentialism, reductionism, and mechanicism, all of which have traditionally been associated with (...) substance ontology. We illustrate the consequences of embracing an ontology of processes in biology by considering some of its implications for physiology, genetics, evolution, and medicine. And we attempt to locate the subsequent chapters of the book in relation to the position we defend. (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)

Although contemporary metaphysics has recently undergone a neo-Aristotelian revival wherein dispositions, or capacities are now commonplace in empirically grounded ontologies, being routinely utilised in theories of causality and modality, a central Aristotelian concept has yet to be given serious attention – the doctrine of hylomorphism. The reason for this is clear: while the Aristotelian ontological distinction between actuality and potentiality has proven to be a fruitful conceptual framework with which to model the operation of the natural world, the distinction between (...) form and matter has yet to similarly earn its keep. In this chapter, I offer a first step toward showing that the hylomorphic framework is up to that task. To do so, I return to the birthplace of that doctrine - the biological realm. Utilising recent advances in developmental biology, I argue that the hylomorphic framework is an empirically adequate and conceptually rich explanatory schema with which to model the nature of organisms. (shrink)

Although they are continually compositionally reconstituted and reconfigured, organisms nonetheless persist as ontologically unified beings over time – but in virtue of what? A common answer is: in virtue of their continued possession of the capacity for morphological invariance which persists through, and in spite of, their mereological alteration. While we acknowledge that organisms‟ capacity for the “stability of form” – homeostasis - is an important aspect of their diachronic unity, we argue that this capacity is derived from, and grounded (...) in a more primitive one – namely, the homeodynamic capacity for the “specified variation of form”. In introducing a novel type of causal power – a „structural power‟ – we claim that it is the persistence of their dynamic potential to produce a specified series of structurally adaptive morphologies which grounds organisms‟ privileged status as metaphysically “one over many” over time. (shrink)

In this paper, we offer reasons to justify the explanatory credentials of dynamical modeling in the context of the metaplasticity thesis, located within a larger grouping of views known as 4E Cognition. Our focus is on showing that dynamicism is consistent with interventionism, and therefore with a difference-making account at the scale of system topologies that makes sui generis explanatory differences to the overall behavior of a cognitive system. In so doing, we provide a general overview of the interventionist approach. (...) We then argue that recent mechanistic attempts at reducing dynamical modeling to a merely descriptive enterprise fail given that the explanatory standard in dynamical modeling can be shown to rest on interventionism. We conclude that dynamical modeling captures features of nested and developmentally plastic cognitive systems that cannot be explained by appeal to underlying mechanisms alone. (shrink)

The biological sciences have always proven a fertile ground for philosophical analysis, one from which has grown a rich tradition stemming from Aristotle and flowering with Darwin. And although contemporary philosophy is increasingly becoming conceptually entwined with the study of the empirical sciences with the data of the latter now being regularly utilised in the establishment and defence of the frameworks of the former, a practice especially prominent in the philosophy of physics, the development of that tradition hasn’t received the (...) wider attention it so thoroughly deserves. This review will briefly introduce some recent significant topics of debate within the philosophy of biology, focusing on those whose metaphysical themes (in everything from composition to causation) are likely to be of wide-reaching, cross-disciplinary interest. (shrink)

Evolutionary developmental biology represents a paradigm shift in the understanding of the ontogenesis and evolutionary progression of the denizens of the natural world. Given the empirical successes of the evo-devo framework, and its now widespread acceptance, a timely and important task for the philosophy of biology is to critically discern the ontological commitments of that framework and assess whether and to what extent our current metaphysical models are able to accommodate them. In this paper, I argue that one particular model (...) is a natural fit: an ontology of dispositional properties coherently and adequately captures the crucial casual-cum-explanatory role that the fundamental elements of evo-devo play within that framework. (shrink)

The advent of contemporary evolutionary theory ushered in the eventual decline of Aristotelian Essentialism (Æ) – for it is widely assumed that essence does not, and cannot have any proper place in the age of evolution. This paper argues that this assumption is a mistake: if Æ can be suitably evolved, it need not face extinction. In it, I claim that if that theory’s fundamental ontology consists of dispositional properties, and if its characteristic metaphysical machinery is interpreted within the framework (...) of contemporary evolutionary developmental biology, an evolved essentialism is available. The reformulated theory of Æ offered in this paper not only fails to fall prey to the typical collection of criticisms, but is also independently both theoretically and empirically plausible. The paper contends that, properly understood, essence belongs in the age of evolution. (shrink)

Although it may seem like a truism to assert that biology is the science that studies organisms, during the second half of the twentieth century the organism category disappeared from biological theory. Over the past decade, however, biology has begun to witness the return of the organism as a fundamental explanatory concept. There are three major causes: (a) the realization that the Modern Synthesis does not provide a fully satisfactory understanding of evolution; (b) the growing awareness of the limits of (...) reductionism in molecular biology; and (c) the renewed interest in the nature of life as a genuine scientific problem. This essay examines these recent developments and considers the new epistemological roles being played by the organism in each of them. It also reflects on what the present resurgence of the organism means for the philosophy of biology. (shrink)

Comparing engineering to evolution typically involves adaptationist thinking, where well-designed artifacts are likened to well-adapted organisms, and the process of evolution is likened to the process of design. A quite different comparison is made when biologists focus on evolvability instead of adaptationism. Here, the idea is that complex integrated systems, whether evolved or engineered, share universal principles that affect the way they change over time. This shift from adaptationism to evolvability is a significant move for, as I argue, we can (...) make sense of these universal principles without making any adaptationism claims. Furthermore, evolvability highlights important aspects of engineering that are ignored in the adaptationist debates. I introduce some novel engineering examples that incorporate these key neglected aspects, and use these examples to challenge some commonly cited contrasts between engineering and evolution, and to highlight some novel resemblances that have gone unnoticed. (shrink)

This thesis explores and discusses foundational issues concerning the relationship between phenomenological philosophy and the enactive approach to cognitive science, with the aim of clarifying, developing, and promoting the project of enactive phenomenology. This project is framed by three general ideas: 1) that the sciences of mind need a phenomenological grounding, 2) that the enactive approach is the currently most promising attempt to provide mind science with such a grounding, and 3) that this attempt involves both a naturalization of phenomenology (...) and a phenomenologization of the concept of nature. More specifically, enactive phenomenology is the project of pursuing mutually illuminative exchanges between, on the one hand, phenomenological investigations of the structures of lived experience and embodied existence and, on the other, scientific accounts of mind and life – in particular those framed by theories of biological self-organization. The thesis consists of two parts. Part one is an introductory essay that seeks to clarify some of enactive phenomenology’s overarching philosophical commitments by tracing some of its historical roots. Part two is a compilation of four articles, each of which intervenes in a different contemporary debate relevant to the dissertation’s project. (shrink)

According to mainstream philosophical views causal explanation in biology and neuroscience is mechanistic. As the term ‘mechanism’ gets regular use in these fields it is unsurprising that philosophers consider it important to scientific explanation. What is surprising is that they consider it the only causal term of importance. This paper provides an analysis of a new causal concept—it examines the cascade concept in science and the causal structure it refers to. I argue that this concept is importantly different from the (...) notion of mechanism and that this difference matters for our understanding of causation and explanation in science. (shrink)

We provide three innovations to recent debates about whether topological or “network” explanations are a species of mechanistic explanation. First, we more precisely characterize the requirement that all topological explanations are mechanistic explanations and show scientific practice to belie such a requirement. Second, we provide an account that unifies mechanistic and non-mechanistic topological explanations, thereby enriching both the mechanist and autonomist programs by highlighting when and where topological explanations are mechanistic. Third, we defend this view against some powerful mechanist objections. (...) We conclude from this that topological explanations are autonomous from their mechanistic counterparts. (shrink)

Theory of illness causation is an important issue in all biomedical sciences, and solid etiological explanations are needed in order to develop therapeutic approaches in medicine and preventive interventions in public health. Until now, the literature about the theoretical underpinnings of illness causation research has been scarce and fragmented, and lacking a convenient summary. This interdisciplinary book provides a convenient and accessible distillation of the current status of research into this developing field, and adds a personal flavor to the discussion (...) by proposing the etiological stance as a comprehensive approach to identify modifiable causes of illness. (shrink)

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)

In this paper, we critically analyze the mechanicist approach to scientific explanation and propose to complement this view with a conception of level as interval of quasi-decompositionality. This conception allows us to metaphysically base the mechanicist proposals on characteristic systemic features. By means of concrete examples, we claim that this proposal is able to overcome some of the alleged limitations of predominant models of mechanistic explanation.

Though the realm of biology has long been under the philosophical rule of the mechanistic magisterium, recent years have seen a surprisingly steady rise in the usurping prowess of process ontology. According to its proponents, theoretical advances in the contemporary science of evo-devo have afforded that ontology a particularly powerful claim to the throne: in that increasingly empirically confirmed discipline, emergently autonomous, higher-order entities are the reigning explanantia. If we are to accept the election of evo-devo as our best conceptualisation (...) of the biological realm with metaphysical rigour, must we depose our mechanistic ontology for failing to properly “carve at the joints” of organisms? In this paper, I challenge the legitimacy of that claim: not only can the theoretical benefits offered by a process ontology be had without it, they cannot be sufficiently grounded without the metaphysical underpinning of the very mechanisms which processes purport to replace. The biological realm, I argue, remains one best understood as under the governance of mechanistic principles. (shrink)

What should we do when two conflicting ontologies are both fruitful, though their fruitfulness varies by context or location? To achieve reconciliation, it is not enough to advocate pluralism. There are many varieties of pluralism and not all pluralisms will serve equally well; some may be inconsistent, others unhelpful. This essay considers another option: local ontology. For a pair of ontologies, a local ontology consists of two claims: (1) each location enjoys a unique ontology, and (2) neither ontology is most (...) fundamental nor most global. To argue for this view and provide an example, I develop a local ontology for two scientific ontologies: processualism and new mechanism. To further support this ontology, I argue against two varieties of pluralism: first, a pluralism based on directly unifying the assumptions of both ontologies and, second, one of allowing both ontologies to coexist within a discipline. I argue that the first option is inconsistent and the second is unhelpful. I conclude that this local ontology provides us with a consistent and fruitful account that includes elements from both mechanism and processualism. (shrink)

Substantialism, which is an extremely common paradigm in Western philosophy, has dominated the sciences over time. Arguing that the authentic structure of existence is fixed and unchangeable; over time, with the development of modern physics, this understanding, which was easily adopted due to the precision of mechanical and mathematical explanations and the ease of categorization, created a school of biology that tried to develop through quantitative propositions; thus, living things were considered static entities that could be understood through reverse engineering. (...) Findings regarding evolution, which has continued uninterrupted for millions of years, have led to the gradual abandonment of essentialism. In addition, when many new data were analyzed, such as the transition from genetics to epigenetics and the mutual interaction in nature and niche creation, it was realized that biology in particular and all natural sciences in general needed a new metaphysical approach, thus process philosophy came to the fore. In process philosophy and metaphysics, it is accepted that every structure in nature consists of processual structures, not substances. The living world is fundamentally dynamic, and the existence of things always depends on the existence of processes, the basic assumption of biology is stability, not change; more precisely, it is argued that it is a stability achieved through constant change. By presenting a methodology, metaphysics and perspective from the process perspective of John Dupré, one of today's most important philosophers of biology, it is aimed to draw attention to the flowing of existence and processes of nature, expressed by Heraclitus as panta rhei (everything flows). (shrink)

The history of developmental biology is interwoven with debates as to whether mechanistic explanations of development are possible or whether alternative explanatory principles or even vital forces need to be assumed. In particular, the demonstrated ability of embryonic cells to tune their developmental fate precisely to their relative position and the overall size of the embryo was once thought to be inexplicable in mechanistic terms. Taking a causal perspective, this Element examines to what extent and how developmental biology, having turned (...) molecular about four decades ago, has been able to meet the vitalist challenge. It focuses not only on the nature of explanations but also on the usefulness of causal knowledge – including the knowledge of classical experimental embryology – for further scientific discovery. It also shows how this causal perspective allows us to understand the nature and significance of some key concepts, including organizer, signal and morphogen. This title is also available as Open Access on Cambridge Core. (shrink)

This article demonstrates that non-mechanistic, dynamical explanations are a viable approach to explanation in the special sciences. The claim that dynamical models can be explanatory without reference to mechanisms has previously been met with three lines of criticism from mechanists: the causal relevance concern, the genuine laws concern, and the charge of predictivism. I argue, however, that these mechanist criticisms fail to defeat non-mechanistic, dynamical explanation. Using the examples of Haken et al.’s model of bimanual coordination, and Thelen et al.’s (...) dynamical field model of infant perseverative reaching, I show how each mechanist criticism fails once the standards of Woodward’s interventionist framework are applied to dynamical models. An even-handed application of Woodwardian interventionism reveals that dynamical models are capable of producing genuine explanations without appealing to underlying mechanistic details. 1Introduction2Interventionism and Mechanistic Explanation 2.1Causal relevance and ideal interventions2.2Invariance2.3Explanation3Covering-Laws and Dynamical Explanation 3.1Dynamical models3.2Covering-law explanation3.3Prediction4Causal Relevance 4.1The causal relevance concern4.2Intervening on dynamical models4.3Test case I: The Haken–Kelso–Bunz model4.4Test case II: Dynamical field model5Genuine Laws 5.1The genuine laws concern5.2Using invariance in place of laws5.3Test case I: The Haken–Kelso–Bunz model5.4Test case II: Dynamical field model6Prediction 6.1Predictivism6.2Crude and invariant prediction7Interventionist Criticism of the Haken–Kelso–Bunz Model8Dynamical Explanation8Conclusion. (shrink)

Despite the importance of network analysis in biological practice, dominant models of scientific explanation do not account satisfactorily for how this family of explanations gain their explanatory power in every specific application. This insufficiency is particularly salient in the study of the ecology of the microbiome. Drawing on Coyte et al. (2015) study of the ecology of the microbiome, Deulofeu et al. (2021) argue that these explanations are neither mechanistic, nor purely mathematical, yet they are substantially empirical. Building on their (...) criticisms, in the present work we make a step further elucidating this kind of explanations with a general analytical framework according to which scientific explanations are ampliative, specialized embeddings (ASE), which has recently been successfully applied to other biological subfields. We use ASE to reconstruct in detail the Coyte et al.’s case study and on its basis, we claim that network explanations of the ecology of the microbiome, and other similar explanations in ecology, gain their epistemological force in virtue of their capacity to embed biological phenomena in non-accidental generalizations that are simultaneously ampliative and specialized. (shrink)

In this paper, I propose a theory of living organisms that captures the insights of both traditional Aristotelian hylomorphism and John Dupré's “biological processualism”. Like traditional Aristotelian hylomorphism, the proposed theory understands material objects to be comprised of both matter and form. Unlike contemporary structural varieties of hylomorphism, however, it does not understand the form of a material object to be a relation, configuration, or structure exhibited by its parts but an activity or process in which its matter is continuously (...) engaged. Following Mark Steen, I call the proposed theory “Hyloenergeism”. As a version of hylomorphism, hyloenergeism better captures the inherent dynamism of living organisms than contemporary structural approaches. And it does so not by abandoning the substantialist paradigm, as Dupré's biological processualism does, but by reconceptualizing the nature of material substances as possessing a processual core. Hyloenergeism, then, paves a middle way for those looking for a substance view of living organisms sensitive to the concerns raised by contemporary processualist philosophers of biology. (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)

Current debates about the integration of traditional and academic ecological knowledge struggle with a dilemma of division and assimilation. On the one hand, the emphasis on differences between traditional and academic perspectives has been criticized as creating an artificial divide that brands TEK as “non-scientific” and contributes to its marginalization. On the other hand, there has been increased concern about inadequate assimilation of Indigenous and other traditional perspectives into scientific practices that disregards the holistic nature and values of TEK. The (...) aim of this article is to develop a practice-based account of the epistemic relations between TEK and AEK that avoids both horns of the dilemma. While relations between TEK and AEK are often described in terms of the “holistic” nature of the former and the “mechanistic” character of the latter, we argue that a simple holism–mechanism divide misrepresents the epistemic resources of both TEK and AEK. Based on the literature on mechanistic explanations in philosophy of science, we argue that holders of TEK are perfectly capable of identifying mechanisms that underlie ecological phenomena while AEK often relies on non-mechanistic strategies of dealing with ecological complexity. Instead of generic characterizations of knowledge systems as either mechanistic or holistic, we propose to approach epistemic relations between knowledge systems by analyzing their heuristics in practice. (shrink)

Processes produce changes: rivers erode their banks and thunderstorms cause floods. If I am right that organisms are a kind of process, then the causally efficacious behaviours of organisms are also examples of processes producing change. In this paper I shall try to articulate a view of how we should think of causation within a broadly processual ontology of the living world. Specifically, I shall argue that causation, at least in a central class of cases, is the interaction of processes, (...) that such causation is the exercise of a capacity inherent in that process and, negatively, that causation should not be understood as the instantiation of universal laws. The approach I describe has substantial similarities with the process causality articulated by Wesley Salmon and Phil Dowe for physical causation, making it plausible that the basic approach can be applied equally to the non-living world. It is an approach that builds at crucial points on the criticisms of determinism and universal causality famously articulated by Elizabeth Anscombe. (shrink)

In this paper we identify six theses that constitute core results of philosophical investigation into the nature of mechanisms, and of the role that the search for and identification of mechanisms play in the sciences. These theses represent the fruits of the body of research that is now often called New Mechanism. We concisely present the main arguments for these theses. In the literature, these arguments are scattered and often implicit. Our analysis can guide future research in many ways: it (...) provides critics of New Mechanism with clear targets, it can reduce misunderstandings, it can clarify differences of opinion among New Mechanists and it helps to define a research agenda for New Mechanists. (shrink)

Epidemiological explanation often has a “black box” character, meaning the intermediate steps between cause and effect are unknown. Filling in black boxes is thought to improve causal inferences by making them intelligible. I argue that adding information about intermediate causes to a black box explanation is an unreliable guide to pragmatic intelligibility because it may mislead us about the stability of a cause. I diagnose a problem that I call wishful intelligibility, which occurs when scientists misjudge the limitations of certain (...) features of an explanation. Wishful intelligibility gives us a new reason to prefer black box explanations in some contexts. (shrink)

We address the controversy in the literature concerning the definition of holobionts and the apparent constraints on their evolution using concepts from community population genetics. The genetics of holobionts, consisting of a host and diverse microbial symbionts, has been neglected in many discussions of the topic, and, where it has been discussed, a gene-centric, species-centric view, based in genomic conflict, has been predominant. Because coevolution takes place between traits or genes in two or more species and not, strictly speaking, between (...) species, it may affect some traits but not others in either host or symbiont. Moreover, when interacting species pairs are embedded in a larger community, indirect ecological effects can alter the expected pairwise dynamics. Mode of symbiont transmission and the degree of host inbreeding both affect the extent of microbial mixing across host lineages and thereby the degree to which selection on one trait of either partner affects other aspects of a holobiont phenotype. We discuss several potential defining criteria for holobionts using community genetics and population genetics models, suggesting their application and limitations. Using community genetics models, we show how conflict between genomes can be self-limiting, while cooperation and mutualism tend to be self-accelerating. It is likely that this bias in the evolutionary dynamics of interaction between hosts and symbionts is an important feature of holobionts. This bias in the evolutionary dynamic could contribute to explaining the absence of cheaters from natural mutualisms, although cheaters are predicted by gene-centered conflict theory to cause the evolutionary instability of mutualisms. Additionally, it may help explain the more frequent origin of mutualisms from parasitic than from free-living systems, an evolutionary trajectory opposite to that predicted by genome conflict theory. (shrink)

Recently, it has been provocatively claimed that dynamical modeling approaches signal the emergence of a new explanatory framework distinct from that of mechanistic explanation. This paper rejects this proposal and argues that dynamical explanations are fully compatible with, even naturally construed as, instances of mechanistic explanations. Specifically, it is argued that the mathematical framework of dynamics provides a powerful descriptive scheme for revealing temporal features of activities in mechanisms and plays an explanatory role to the extent it is deployed for (...) this purpose. It is also suggested that more attention should be paid to the distinctive methodological contributions of the dynamical framework including its usefulness as a heuristic for mechanism discovery and hypothesis generation in contemporary neuroscience and biology. (shrink)

This paper explores the question of whether all or most explanations in biology are, or ideally should be, ‘mechanistic’. I begin by providing an account of mechanistic explanation, making use of the interventionist ideas about causation I have developed elsewhere. This account emphasizes the way in which mechanistic explanations, at least in the biological sciences, integrate difference‐making and spatio‐temporal information, and exhibit what I call fine‐tunedness of organization. I also emphasize the role played by modularity conditions in mechanistic explanation. I (...) will then argue, in agreement with John Dupré, that, given this account, it is plausible that many biological systems require explanations that are relatively non‐mechanical or depart from expectations one associates with the behaviour of machines. (shrink)

The concept of levels of organization, despite its widespread scientific currency, has recently been criticized by a number of philosophers of science. This paper diagnoses the main source of problems facing theories of levels. On this basis, the problems with the usual criteria for distinguishing levels are evaluated: compositional relations, organizational types, and spatial scales. Drawing on some work on hierarchies in ecology, I argue in favor of an alternative conception of levels defined by the criterion of rates or time (...) scales of processes. (shrink)

A crucial question for a process view of life is how to identify a process and how to follow it through time. The genidentity view can contribute decisively to this project. It says that the identity through time of an entity X is given by a well-identified series of continuous states of affairs. Genidentity helps address the problem of diachronic identity in the living world. This chapter describes the centrality of the concept of genidentity for David Hull and proposes an (...) extension of Hull’s view to the ubiquitous phenomenon of symbiosis. Finally, using immunology as a key example, it shows that the genidentity view suggests that the main interest of a process approach is epistemological rather than ontological and that its principal claim is one of priority, namely that processes precede and define things, and not vice versa. (shrink)

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

Life poses a threat to materialism. To understand the phenomena of animate nature, we make use of a teleological form of explanation that is peculiar to biology, of explanations in terms of what I call the ‘vital categories’ – and this holds even for accounts of underlying physico-chemical ‘mechanisms’. The materialist claims that this teleological form of explanation does not capture what is metaphysically fundamental, whereas her preferred physical form of explanation does. In this essay, I do three things. (1) (...) I argue that the ‘vital categories’, such as life form and life-process, do not reduce to the ‘physical categories’ and show that there are no grounds for the materialist's metaphysically limiting claim; (2) I sketch a positive view on how vital and physical explanations can both apply to a given phenomenon, and on how they interrelate; and (3) I show that this view meshes nicely with evolutionary theory, despite being committed to a form of ‘biological essentialism’. (shrink)

I propose a cautionary assessment of the recent debate concerning the impact of the dynamical approach on philosophical accounts of scientific explanation in the cognitive sciences and, particularly, the cognitive neurosciences. I criticize the dominant mechanistic philosophy of explanation, pointing out a number of its negative consequences: In particular, that it doesn’t do justice to the field’s diversity and stage of development, and that it fosters misguided interpretations of dynamical models’ contribution. In order to support these arguments, I analyze a (...) case study in computational neuroethology and show why it should not be understood through a mechanistic lens; I specially focus on Zednik’s mechanistic interpretation of the case study. In addition, I argue for a greater appreciation of the relation between explanation and other epistemic goals in the field, as well as an increased sensitivity towards the associated contextual factors. (shrink)

This work addresses biological explanations and aims to provide a philosophical account which brings together logical-procedural and historical-processual aspects when considering molecular pathways. It is argued that, having molecular features as explananda, a particular non-classical logical language – Zsyntax – can be used to formally represent, in terms of logical theorems, types of molecular processes, and to grasp how we get from one molecular interaction to another, hence explaining why a given outcome occurs. Expressing types of molecular biology processes in (...) terms of the Zsyntax language allows us to represent causal interactions by taking into account their context-sensitivity, and amounts to partly reviving the spirit of the so-called received view of explanation – which aimed to capture scientific explanatory accounts in terms of their logical structure and their appealing to nomological relations. Such a partial revival is pursued by invoking here non-classical deductions and empirical generalisations, which are called to provide the epistemic norms to explain the behavior of molecular pathways. (shrink)