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)

Biologists frequently draw on ideas and terminology from engineering. Evolutionary systems biology—with its circuits, switches, and signal processing—is no exception. In parallel with the frequent links drawn between biology and engineering, there is ongoing criticism against this cross-fertilization, using the argument that over-simplistic metaphors from engineering are likely to mislead us as engineering is fundamentally different from biology. In this article, we clarify and reconfigure the link between biology and engineering, presenting it in a more favorable light. We do so (...) by, first, arguing that critics operate with a narrow and incorrect notion of how engineering actually works, and of what the reliance on ideas from engineering entails. Second, we diagnose and diffuse one significant source of concern about appeals to engineering, namely that they are inherently and problematically metaphorical. We suggest that there is plenty of fertile ground left for a continued, healthy relationship between engineering and biology. (shrink)

Thought experiments de facto play many different roles in biology: economical, ethical, technical and so forth. This paper, however, is interested in whether there are any distinctive features of biological TEs as such. The question may be settled in the affirmative because TEs in biology have a function that is intimately connected with the epistemological and methodological status of biology. Peculiar to TEs in biology is the fact that the reflexive, typically human concept of finality may be profitably employed to (...) discover mechanical-experimental causal relations in all living beings—with the obvious caveat that we do not hypostatise and interpret this concept as an ontological quality, since this would land one in an implicitly animistic, pre-Galilean view of nature. From a methodical point of view, the concept of finality is an essential assumption as well as a powerful heuristic tool in the practice of biology, that is, in the investigation of living beings in an intersubjectively testable and reproducible way. (shrink)

Recognition of the plasticity of development — from gene expression to neuroplasticity — is increasingly undermining the traditional distinction between structure and function, or anatomy and behavior. At the same time, dynamic systems theory — a set of tools and concepts drawn from the physical sciences — has emerged as a way of describing what Maurice Merleau-Ponty calls the “dynamic anatomy” of the living organism. This article surveys and synthesizes dynamic systems models of development from biology, neuroscience, and psychology in (...) order to propose an integrated account of growth, learning, and behavior. Key to this account is the concept of self-differentiation or symmetry-breaking. I argue that development can be understood as a cascade of symmetry-breaking events brought about by the ongoing interactions of multiple, nested, nonlinear dynamic systems whose self-organizing behaviors gradually alter their own anatomical conditions. I begin by introducing the concept of symmetry-breaking as a way of understanding anatomical development. I then extend this approach to motor development by arguing that the organism’s behavior grows along with its body, like a new organ. Finally, I argue that the organism’s behavior and its world grow together dialectically, each driving the other to become more complex and asymmetrical through its own increasing asymmetry. Thus development turns out to be a form of cognition or sense-making, and cognition a form of development. (shrink)

Not only has the philosophical debate on causation been gaining ground in the last few decades, but it has also increasingly addressed the sciences. The biomedical sciences are among the most prominent fields that have been considered, with a number of works tackling the understanding of the notion of cause, the assessment of genuinely causal relations and the use of causal knowledge in applied contexts. Far from denying the merits of the debate on causation and the major theories it comprises, (...) this paper is meant as a stimulus for theorists of causation in the philosophy of biomedicine, with a focus on clinical matters. Without aiming at putting forward an original theory of causation and starting from the narration of two actual but paradigmatic cases at the joints between biomedical research and clinical practice, we want to point out that some pathological situations addressed by molecular medicine actually prove resistant to some of our major epistemological accounts of causal explanation. Given this scenario, which is very frequent in our hospitals, our analysis aims to provide a stimulus for the debate among theorists of causation in biomedicine interested in real cases in science in practice. We believe that this might in turn encourage some more general rethinking of the complex intertwinement of science, philosophy of science and ethics, as well as of the role of philosophy of science for clinical medicine itself. (shrink)

What has been called the new mechanistic philosophy conceives of mechanisms as the main providers of biological explanation. We draw on the characterization of the p53 gene in molecular oncology, to show that explaining a biological phenomenon implies instead a dynamic interaction between the mechanistic level—rendered at the appropriate degree of ontological resolution—and far more general explanatory tools that perform a fundamental epistemic role in the provision of biological explanations. We call such tools “explanatory frameworks”. They are called frameworks to (...) stress their higher level of generality with respect to bare mechanisms; on the other hand, they are called explanatory because, as we show in this paper, their importance in explaining biological phenomena is not secondary with respect to mechanisms. We illustrate how explanatory frameworks establish selective and local criteria of causal relevance that drive the search for, characterisation and usage of biological mechanisms. Furthermore, we show that explanatory frameworks allow for changes of scientific perspective on the causal relevance of mechanisms going beyond the account provided by the new mechanistic philosophy. (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)

In the last few decades, philosophy of science has increasingly focused on multilevel models and causal mechanistic explanations to account for complex biological phenomena. On the one hand, biological and biomedical works make extensive use of mechanistic concepts; on the other hand, philosophers have analyzed an increasing range of examples taken from different domains in the life sciences to test—support or criticize—the adequacy of mechanistic accounts. The article highlights some challenges in the elaboration of mechanistic explanations with a focus on (...) cancer research and neuropsychiatry. It jointly considers fields, which are usually dealt with separately, and keeps a close eye on scientific practice. The article has a twofold aim. First, it shows that identification of the explananda is a key issue when looking at dynamic processes and their implications in medical research and clinical practice. Second, it discusses the relevance of organizational accounts of mechanisms, and questions whether thorough self-sustaining mechanistic explanations can actually be provided when addressing cancer and psychiatric diseases. While acknowledging the merits of the wide ongoing debate on mechanistic models, the article challenges the mechanistic approach to explanation by discussing, in particular, explanatory and conceptual terms in the light of stances from medical cases. (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)

The classical theories of the genetic code claimed that its coding rules were determined by chemistry—either by stereochemical affinities or by metabolic reactions—but the experimental evidence has revealed a totally different reality: it has shown that any codon can be associated with any amino acid, thus proving that there is no necessary link between them. The rules of the genetic code, in other words, obey the laws of physics and chemistry but are not determined by them. They are arbitrary, or (...) conventional, rules. The result is that the genetic code is not a metaphorical entity, as implied by the classical theories, but a real code, because it is precisely the presence of arbitrary rules that divides a code from all other natural processes. In the past 20 years, furthermore, various independent discoveries have shown that many other organic codes exist in living systems, which means that the genetic code has not been an isolated case in the history of life. These experimental facts have one outstanding theoretical implication: they imply that in addition to the concept of information we must introduce in biology the concept of meaning, because we cannot have codes without meaning or meaning without codes. The problem is that at present we have two different theoretical frameworks for that purpose: one is Code Biology, where meaning is the result of coding, and the other is Peircean biosemiotics, where meaning is the result of interpretation. Recently, however, a third party has entered the scene, and it has been proposed that Robert Rosen’s relational biology can provide a bridge between Code Biology and Peircean biosemiotics. (shrink)

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)

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)

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)

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)

Various scientists and philosophers have heavily criticized what they see as problematic forms of ‘nutritional reductionism’ or ‘nutritionism’ whereby studying food–health interactions at the level of isolated food components produces largely misguided science and misleading interpretations. However, the exact target of these diverse criticisms remains elusive, and its implications are overstated, which may hinder scientific understanding. To better identify the types of flaws supposedly hindering reductionist research, we disentangle three types of reductionist claims to better determine what the debate is (...) about and to propose ways to move it forward. We then present a qualified defence of the reductionist programme that hinges on the ability to identify nutritional causes that make a difference, which we illustrate through central examples in the history of nutrition. This defence is taken further by using insights from the philosophy of mechanisms to analyse how the field of nutritional ecology offers a synthetic framework to explain, generate, and test predictions about nutrient–organism interactions, which is premised on the biological mechanisms of nutrient-specific appetite regulation. The result, which we call ‘synthetic reductionism’, avoids many, though perhaps not all, of the challenges raised by anti-reductionists, and also highlights the potential of reductionism to identify nutritional difference makers. (shrink)

This paper critiques the new mechanistic explanatory program on grounds that, even when applied to the kinds of examples that it was originally designed to treat, it does not distinguish correct explanations from those that blunder. First, I offer a systematization of the explanatory account, one according to which explanations are mechanistic models that satisfy three desiderata: they must 1) represent causal relations, 2) describe the proper parts, and 3) depict the system at the right ‘level.’ Second, I argue that (...) even the most developed attempts to fulfill these desiderata fall short by failing to appropriately constrain explanatorily apt mechanistic models. -/- *This paper used to be called "The Emperor's New Mechanisms". (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)

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)

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

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)

Biosemiotics argues that “sign” and “meaning” are two essential concepts for the explanation of life. Peircean biosemiotics, founded by Tomas Sebeok from Peirce’s semiotics and Jacob von Uexkül’s studies on animal communication, today makes up the mainstream of this discipline. Marcello Barbieri has developed an alternative account of meaning in biology based on the concept of code. Barbieri rejects Peircean biosemiotics on the grounds that this discipline opens the door to nonscientific approaches to biology through its use of the concept (...) of “interpretation.” In this article, it is noted that Barbieri does not adequately distinguish among Peirce’s semiotics, Peircean biosemiotics, and “interpretation-based” biosemiotics. Two key arguments of Barbieri are criticized: his limited view of science and his rejection of “interpretation-based” biosemiotics. My argument is based on tools taken from a different approach: Robert Rosen’s relational biology. Instead of “signs” and “meanings,” the study begins in this case from the “components” and “functions” of the organism. Rosen pursues a new definition of a law of nature, introduces the anticipatory nature of organisms, and defines the living being as a system closed to efficient cause. It is shown that Code Biosemiotics and Peircean biosemiotics can share a common field of study. Additionally, some proposals are suggested to carry out a reading of Rosen’s biology as a biosemiotic theory. (shrink)

Within biology and in society, living creatures have long been described using metaphors of machinery and computation: ‘bioengineering’, ‘genes as code’ or ‘biological chassis’. This paper builds on Lakoff and Johnson’s argument that such language mechanisms shape how we understand the world. I argue that the living machines metaphor builds upon a certain perception of life entailing an idea of radical human control of the living world, looking back at the historical preconditions for this metaphor. I discuss how design is (...) perceived to enable us to shape natural beings to our will, and consider ethical, epistemological and ontological implications of the prevalence of this metaphor, focusing on its use within synthetic biology. I argue that we urgently need counter-images to the dominant metaphor of living machines and its implied control and propose that artworks can provide such counter-images through upsetting the perception of life as controllable. This is argued through discussion of artworks by Oron Catts and Ionat Zurr, by Tarsh Bates and by Ai Hasegawa, which in different ways challenge mechanistic assumptions through open-ended engagement with the strangeness and messiness of life. (shrink)

This paper argues that there is no single universal conception of scientific explanation that is consistently employed throughout the whole domain of Higgs physics—ranging from the successful experimental search for a standard model Higgs particle and the hitherto unsuccessful searches for any particles beyond the standard model, to phenomenological model builders in the Higgs sector and theoretical physicists interested in how the core principles of quantum field theory apply to spontaneous symmetry breaking and the Higgs mechanism. Yet the coexistence of (...) deductive-statistical, unificationist, model-based, and statistical-relevance explanations does not amount to a fragmentation of the discipline, but allows elementary particle physicists to simultaneously pursue a plurality of research strategies and keep the field together by joint convictions about the SM and shared explanatory ideals. These convictions include that the SM both represents a successful explanation of the available particle data and contains aspects in need of further explanation. Especially in the domain of BSM physics, explanatory ideals typically appear as stories motivating the different models and linking them to the whole of the discipline. (shrink)

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)

Examining tensions between the past and present uses of scientific concepts can help clarify their contributions as tools in experimental practices. This point can be illustrated by considering the concepts of mental imagery and hallucinations: despite debates over their respective referential reliabilities remaining unresolved within their interdependent histories, both are used as independently stable concepts in neuroimaging experiments. Building on an account of how these concepts function as tools structured for pursuit of diverging goals in experiments, this paper explores this (...) tension by re-examining the continued reliance of each concept on inverse characterisations inherited from the nominally-discarded ‘mediator-view’ of sensory-like mental phenomena (SLMP). In doing so, I seek to demonstrate how examining unresolved tensions can help highlight that entrenched associations can remain both integral to, and obscured by, the uses of concepts as goal-directed tools within experimental practices. (shrink)

Biological processes are often explained by identifying the underlying mechanisms that generate a phenomenon of interest. I characterize a basic account of mechanistic explanation and then present three challenges to this account, illustrated with examples from molecular biology. The basic mechanistic account is insufficient for explaining nonsequential and nonlinear dynamic processes, is insufficient for explaining the inherently stochastic nature of many biological mechanisms, and fails to give a proper framework for analyzing organization. I suggest that biological processes are best approached (...) as a multidimensional gradient—with some processes being paradigmatic cases of mechanisms and some being marginal cases. (shrink)

The conventional historical account of the concept of brain death credits developments and discoveries of the twentieth century with its inception, emphasizing the role of technological developments and professional conferences, notably the 1968 Ad Hoc Committee of the Harvard Medical School to Examine the Definition of Brain Death. This essay argues that the French physician Eugène Bouchut anticipated the concept of brain death as early as 1846. Correspondence with Bouchut’s understanding of brain death and one important contemporary concept of brain (...) death is established then contrasted with current trends of defining death as the death of the brain. The philosophical factors that influenced Bouchut and the later developments of concepts of brain death are considered, with special reference to mechanistic philosophy and vitalism. (shrink)

Current Perspectives in Philosophy of Biology.

In this paper, we address the question whether a mechanistic approach can account for evolutionary causes. The last decade has seen a major attempt to account for natural selection as a mechanism. Nevertheless, we stress the relevance of broadening the debate by including the other evolutionary causes inside the mechanistic approach, in order to be a legitimate conceptual framework on the same footing as other approaches to evolutionary theory. We analyse the current debate on natural selection as a mechanism, and (...) extend it to the rest of the evolutionary causes. We focus on three approaches that we call the stochastic view, the functional view, and the minimalist view. We argue that all of them are unable to account for evolutionary causes as mechanisms. It is concluded that the current mechanistic proposals cannot be accepted as a common framework for evolutionary causes. Finally, we outline some guidelines and requirements that any mechanistic proposal should meet in order to be applied to evolutionary theory. (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)

The writings of Joseph Henry Woodger (1894–1981) are often taken to exemplify everything that was wrongheaded, misguided, and just plain wrong with early twentieth-century philosophy of biology. Over the years, commentators have said of Woodger: (a) that he was a fervent logical empiricist who tried to impose the explanatory gold standards of physics onto biology, (b) that his philosophical work was completely disconnected from biological science, (c) that he possessed no scientific or philosophical credentials, and (d) that his work was (...) disparaged – if not altogether ignored – by the biologists and philosophers of his era. In this paper, we provide the first systematic examination of Woodger’s oeuvre, and use it to demonstrate that the four preceding claims are false. We argue that Woodger’s ideas have exerted an important influence on biology and philosophy, and submit that the current consensus on his legacy stems from a highly selective reading of his works. By rehabilitating Woodger, we hope to show that there is no good reason to continue to disregard the numerous contributions to the philosophy of biology produced in the decades prior to the professionalization of the discipline. (shrink)

The machine conception of the organism (MCO) is one of the most pervasive notions in modern biology. However, it has not yet received much attention by philosophers of biology. The MCO has its origins in Cartesian natural philosophy, and it is based on the metaphorical redescription of the organism as a machine. In this paper I argue that although organisms and machines resemble each other in some basic respects, they are actually very different kinds of systems. I submit that the (...) most significant difference between organisms and machines is that the former are intrinsically purposive whereas the latter are extrinsically purposive. Using this distinction as a starting point, I discuss a wide range of dissimilarities between organisms and machines that collectively lay bare the inadequacy of the MCO as a general theory of living systems. To account for the MCO’s prevalence in biology, I distinguish between its theoretical, heuristic, and rhetorical functions. I explain why the MCO is valuable when it is employed heuristically but not theoretically, and finally I illustrate the serious problems that arise from the rhetorical appeal to the MCO. (shrink)

Biological atomism postulates that all life is composed of elementary and indivisible vital units. The activity of a living organism is thus conceived as the result of the activities and interactions of its elementary constituents, each of which individually already exhibits all the attributes proper to life. This paper surveys some of the key episodes in the history of biological atomism, and situates cell theory within this tradition. The atomistic foundations of cell theory are subsequently dissected and discussed, together with (...) the theory’s conceptual development and eventual consolidation. This paper then examines the major criticisms that have been waged against cell theory, and argues that these too can be interpreted through the prism of biological atomism as attempts to relocate the true biological atom away from the cell to a level of organization above or below it. Overall, biological atomism provides a useful perspective through which to examine the history and philosophy of cell theory, and it also opens up a new way of thinking about the epistemic decomposition of living organisms that significantly departs from the physicochemical reductionism of mechanistic biology. (shrink)

Although the analogy between macroscopic machines and biological molecular devices plays an important role in the conceptual framework of both neo-mechanistic accounts and nanotechnology, it has recently been claimed that certain complex molecular devices cannot be considered machines since they are subject to physicochemical forces that are different from those of macroscopic machines. However, the structural and physicochemical conditions that allow both macroscopic machines and microscopic devices to work and perform new functions, through a combination of elemental functional parts, have (...) not yet been examined. In order to fill this void, this paper has a threefold aim: first, to clarify the structural and organisational conditions of macroscopic machines and microscopic devices; second, to determine whether the machine-like analogy fits nanoscale devices; and third, to assess whether the machine-like analogy is appropriate for describing the behaviour of some biological macromolecules. Finally, the paper gives an account of ‘machine’ which, while acknowledging the physicochemical and organisational differences between man-made machines and biological microscopic devices, nevertheless identifies a common conceptual core that allows us to consider the latter ‘machines’. (shrink)

In addition to theorizing about the role and value of mechanisms in scientific explanation or the causal structure of the world, there is a fundamental task of getting straight what a ‘mechanism’ is in the first place. Broadly, this paper is about the challenge of application: the challenge of aligning one's philosophical account of a scientific concept with the manner in which that concept is actually used in scientific practice. This paper considers a case study of the challenge of application (...) as it pertains to the concept of a mechanism: the debate about whether natural selection is a mechanism. By making clear what is and is not at stake in this debate, this paper considers various strategies for dealing with the challenge of application and makes a case for definitional pluralism about mechanism concepts. (shrink)

Although the concept of modularity is pervasive across fields and disciplines, philosophers and scientists use the term in a variety of different ways. This paper identifies two distinct ways of thinking about modularity, and considers what makes them similar and different. For philosophers of mind and cognitive science, cognitive modularity helps explain the capacities of brains to process sundry and distinct kinds of informational input. For philosophy of biology and evolutionary science, biological modularity helps explain the capacity of random evolutionary (...) processes to give rise to highly complex and sophisticated biological systems. Although these different ways of thinking about modularity are largely distinct, this paper proposes a unifying feature common to both: isolability, or the capacity of subsystems to undergo changes without resulting in substantial changes to neighboring or interconnected subsystems. (shrink)

Species are considered the basic unit of biological classification and evolution. Hence, they are used as a benchmark in several fields, although the ontological status of such a category has always been a matter of debate. This paper aims to discuss the problem of the definition of species within the new mechanistic approach. Nevertheless, the boundary between entities, activities, and mechanisms remains difficult to establish and always requires an analysis of what is meant by explanation. As a case study, the (...) paper describes the debate concerning the species category by considering different kingdoms: Animals, Bacteria, and Fungi. The inherently biological differences between those groups prevent the use of a single, universally applicable concept of species that could fit the mechanisms responsible for the variability present in these kingdoms. The same issue is encountered within each group, as highlighted through a focus on mammals and microbes. This controversy has given rise to opposite approaches, namely: monism, which looks for a single definition that might account for all species, and pluralism, which admits that different groups of organisms require somewhat different definitions. In order to develop an adequate definition of species, we propose to apply a new mechanistic framework, which considers the ontic-epistemic dimensions of scientific explanation in close parallel. The apt correlation between epistemic and the ontic aspects highlights the way in which the concept of species and the reference to data are strictly co-determined. This suggests that the concept of species is better understandable within a dual ontic-epistemic approach. (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)

I distinguish three theses associated with the new mechanistic philosophy – concerning causation, explanation and scientific methodology. Advocates of each thesis are identified and relationships among them are outlined. I then look at some recent work on natural selection and mechanisms. There, attention to different kinds of New Mechanism significantly affects of what is at stake.

Most defenders of the new mechanistic approach accept ontic constraints for successful scientific explanation (Illari 2013; Craver 2014). The minimal claim is that scientific explanations have objective truthmakers, namely mechanisms that exist in the physical world independently of any observer and that cause or constitute the phenomena-to- be-explained. How can this idea be applied to type-level explanations? Many authors at least implicitly assume that in order for mechanisms to be the truthmakers of type-level explanation they need to be regular (Andersen (...) 2012; Sheredos 2015). One problem of this assumption is that most mechanisms are (highly) stochastic in the sense that they “fail more often than they succeed” (Bogen 2005; Andersen 2012). How can a mechanism type whose instances are more likely not to produce an instance of a particular phenomenon type be the truthmaker of the explanation of that particular phenomenon type? In this paper, I will give an answer to this question. I will analyze the notion of regularity and I will discuss Andersen's suggestion for how to cope with stochastic mechanisms. I will argue that her suggestion cannot account for all kinds of stochastic mechanisms and does not provide an answer as to why regularity grounds type-level explanation. According to my analysis, a mechanistic type- level explanation is true if and only if at least one of the following two conditions is satisfied: the mechanism brings about the phenomenon more often than any other phenomenon (comparative regularity) or the phenomenon is more often brought about by the mechanism than by any other mechanism/causal sequence (comparative reverse regularity). (shrink)