Autoinhibition is a design principle realized in many molecular mechanisms in biology. After explicating the notion of a design principle and showing that autoinhibition is such a principle, we focus on how researchers discovered instances of autoinhibition, using research establishing the autoinhibition of the molecular motors kinesin and dynein as our case study. Research on kinesin and dynein began in the fashion described in accounts of mechanistic explanation but, once the mechanisms had been discovered, researchers discovered that they exhibited a (...) second phenomenon, autoinhibition. The discovery of autoinhibition not only reverses the pattern in terms of which philosophers have understood mechanism discovery but runs counter to the one phenomenon-one mechanism principle assumed to relate mechanisms and the phenomena they explain. The ubiquity of autoinhibition as a design principle, therefore, necessitates a philosophical understanding of mechanisms that recognizes how they can participate in more than one phenomenon. Since mechanisms with this design are released from autoinhibition only when they are acted on by control mechanisms, we advance a revised account of mechanisms that accommodates attribution of multiple phenomena to the same mechanism and distinguishes them from other processes that control them. (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)

This paper focuses on physiological integration in multicellular systems, a notion often associated with biological individuality, but which has not received enough attention and needs a thorough theoretical treatment. Broadly speaking, physiological integration consists in how different components come together into a cohesive unit in which they are dependent on one another for their existence and activity. This paper argues that physiological integration can be understood by considering how the components of a biological multicellular system are controlled and coordinated in (...) such a way that their activities can contribute to the maintenance of the system. The main implication of this perspective is that different ways of controlling their parts may give rise to multicellular organizations with different degrees of integration. After defining control, this paper analyses how control is realized in two examples of multicellular systems located at different ends of the spectrum of multicellularity: biofilms and animals. It focuses on differences in control ranges, and it argues that a high degree of integration implies control exerted at both medium and long ranges, and that insofar as biofilms lack long-range control (relative to their size) they can be considered as less integrated than other multicellular systems. It then discusses the implication of this account for the debate on physiological individuality and the idea that degrees of physiological integration imply degrees of individuality. (shrink)

Among the notions of levels invoked in accounts of biological phenomena, I focus on two: levels of production mechanisms and levels of control mechanisms. I argue that these two notions of level exhibit different characteristics: production mechanisms are organized hierarchically while control mechanisms are often organized heterarchically. I illustrate the differences in these modes of organization by examining production and control mechanisms involved in cell division in Escherichia coli and in circulation of blood in mammals. I conclude by exploring how (...) these two notions of levels can be integrated by adopting a perspective in which organisms are autonomous systems maintaining themselves far from equilibrium. (shrink)

Unless one embraces activities as foundational, understanding activities in mechanisms requires an account of the means by which entities in biological mechanisms engage in their activities—an account that does not merely explain activities in terms of more basic entities and activities. Recent biological research on molecular motors exemplifies such an account, one that explains activities in terms of free energy and constraints. After describing the characteristic “stepping” activities of these molecules and mapping the stages of those steps onto the stages (...) of the motors’ hydrolytic cycles, researchers pieced together from images of the molecules in different hydrolyzation states accounts of how the chemical energy in ATP is transformed in the constrained environments of the motors into the characteristic activities of the motors. We argue that New Mechanism’s standard set of analytic categories—entities, activities, and organization—should be expanded to include constraints and energetics. Not only is such an expansion required descriptively to capture research on molecular motors but, more importantly from a philosophical point of view, it enables a non-regressive account of activities in mechanisms. In other words, this expansion enables a philosophical account of mechanistic explanation that avoids a regress of entities and activities “all the way down.” Rather, mechanistic explanation bottoms out in constraints and energetics. (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)

This paper proposes an integrated-structure notion of interlevel emergence, from a dynamic relational ontological perspective. First, I will argue that only the individualist essentialism of atomistic metaphysics can block the possibility of interlevel emergence. Then I will show that we can make sense of emergence by recognizing the formation of structures of transformative and interdependent causal relations in the generation and development of a particular class of mereological complexes called integrated systems. Finally, I shall argue that even though the emergent (...) structural attributes of such systems are not micro-determined nor micro-reducible, they can still be accounted for by an interlevel integrative neo-mechanistic form of explanation. (shrink)

This paper examines tracer techniques in neuroscience, which are used to identify neural connections in the brain and nervous system. These connections capture a type of “structural connectivity” that is expected to inform our understanding of the functional nature of these tissues. This is due to the fact that neural connectivity constrains the flow of signal propagation, which is a type of causal process in neurons. This work explores how tracers are used to identify causal information, what standards they are (...) expected to meet, the forms of causal information they provide, and how an analysis of these techniques contributes to the philosophical literature, in particular, the literature on mark transmission and mechanistic accounts of causation. (shrink)

One big challenge faced by cognitive science is the development of a unified theory that integrates disparate scales of analysis of cognitive phenomena. In this paper, I offer a unified framework that provides a way to integrate neural and behavioral scales of analysis of cognitive phenomena—typically addressed by neuroscience and experimental psychology, respectively. The framework is based on the concept of resonance originated in ecological psychology and aims to be the foundation for a unified theory for radical embodiment; that is, (...) a unified theory for that dissident part of cognitive science that shares a methodological commitment to dynamic systems theory and remains skeptical about the adequacy of mechanism and representationalism as the guiding ideas in the field. In the course of my presentation, I analyze different issues regarding the requirements and constraints unification poses to radical embodiment. (shrink)

The aim of this paper is to present the ontic approach to the normativity of cognitive functions and mechanisms, which is directly related to the understanding of biological normativity in terms of normative mechanisms. This approach assumes the hypothesis that cognitive processes contain a certain normative component independent of external attributions and researchers’ beliefs. This component consists of specific cognitive mechanisms, which I call normative. I argue that a mechanism is normative when it constitutes given actions or behaviors of a (...) system. More precisely, it means that, on the one hand, it is their constitutive cause, and on the other hand, it determines a certain field of possibilities from which the system, guided by its own goals, preferences, environmental constraints, etc., chooses the appropriate action or behavior according to a given situation. The background for the analyses presented here is the predictive processing framework, in which it can be shown that at least some of the predictive mechanisms are in fact normative mechanisms. I refer here to the existence of a motivational relation which determines the normative dependence of the agent’s actions due to specific predictions and environmental constraints. (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)

Mechanistic approaches are very common in the causal interpretation of biological and neuroscientific experimental work in today’s philosophy of science. In the mechanistic literature a strict distinction is often made between causal relations and constitutive relations, where the latter cannot be causal. One of the typical reasons for this strict distinction is that constitutive relations are supposedly synchronic whereas most if not all causal relations are diachronic. This strict distinction gives rise to a number of problems, however. Our end goal (...) in this paper is to argue that it should be given up, at least in the context of the biological and the psychological sciences. To that effect, we argue that constitutive relations in this context are diachronic, thus undermining the aforementioned reason. We offer two cases from scientific practice in which constitutive relations are regarded as both diachronic and causally efficacious, review three existing ways of dealing with the apparent diachronic nature of interlevel relations in mechanisms and propose a new account of diachronic, causal constitutive relevance. (shrink)

In affective neuroscience, constructivist models are acutely influenced by the modern technological evolution, which underwrites an ongoing epistemological substitution of techne for episteme. Evidenced symptomatically in the influence of artificial intelligence (AI), affective artefacts, these models inform an ontological incursion of techne seen to coincide with posthumanist aspirations and anthropology. It is from the perspective of this neuroscientific techne that posthumanism views the human being as increasingly ill adapted to the modern technological civilization, which, conversely, is understood to require a (...) technical governance of the sort envisioned through AI. Among the projects thought necessary for implementing this framework is a recasting of the human emotional spectrum. Revealed through its techne recasting, however, are explanatory commitments to a metaphysic of extrinsic and contiguous causes, where malleability is ontologically constitutive. Aligned with posthumanist assertions malleability is invoked to argue for a rapid advance of the human form, normatively driven by enlightenment ideals. The ontological claim, however, dispenses with the stability of an a priori, intersubjective and interrelational metaphysical form that undergirds the emotions, leading to the collapse of a definitional anthropos. This paper will argue that techne models of the emotions selectively endorse philosophy of science commitments, thereby introducing a normative inversion that deconstructs the notion of anthropology pursued in posthumanist aspirations. (shrink)

Scholars in science and technology studies, as well as economics and innovation studies, utilize the trajectory metaphor in describing a technology’s maturation. Impetus and purpose may differ, but the trajectory serves as a shared tool for assessing social change either in society at large or within a market sector, a firm, or a discipline. In reverse, the lens of a technology trajectory can be a basis for assessing technology, estimating economic growth, and selecting among plausible product development pathways. Emerging technologies (...) pose a challenge in that the promissory claims that attracted investment may also challenge social safeguards, leading to necessary, but unforeseen hurdles to later technology acceptance. The experiences with biotechnology and nanotechnology demonstrate that knowledge gained in the intervening years was to have tempered exaggerations and addressed the criteria and the responsibilities of those who would later be deciding on product acceptability. In particular, the promissory claim for nanotechnology, unique phenomena, challenged regulatory practice, while claims for biotechnology products were often the fruition of themes found in the educational experience common to both the biotechnology researcher and the regulator. The social science and humanities literature mirrored these points as did the responses of civil society organizations. A prospective trajectory for artificial intelligence is developed using the example of driverless cars and then qualitatively compared to the retrospective trajectories for nanotechnology and biotechnology. Experience with automation, algorithm transparency, and computational modeling of biological mechanisms are identified as pertinent to responsible AI development. (shrink)

Moral rationalism has long been an attractive position within moral philosophy. However, among empirical-minded philosophers, it is widely dismissed as scientifically untenable. In this essay, I argue that moral rationalism’s lack of uptake in the empirical domain is due to the widespread supposition that moral rationalists must hold that moral judgments and actions are produced by rational capacities. But this construal is mistaken: moral rationalism’s primary concern is not with the relationship between moral judgments and rational capacities per se, but (...) rather with developing a conception objectivity normativity that avoids Platonism. In light of this, I develop an alternative approach to translating moral rationalism into the empirical domain that builds on the common rationalist view that normative requirements are explained by the relationship between agents and the social structures and practices in which they are embedded. I propose that this social conception of normativity can be translated into a scientific framework by interpreting it as a claim about the importance of constraint-based explanation when accounting for norm-governed behavior. In order to develop this point more concretely and show that it is empirically tractable, I turn to research on macaque social organization that highlights the ways in which normative standards are generated by empirically observable social structures. The insights garnered from the macaque case allow me to then locate moral rationalism’s core claims about the relationship between morality and the standards of practical rationality within an empirically plausible framework. (shrink)

This article explores the use of model organisms in studying the cognitive phenomenon of decision-making. Drawing on the framework of biological control to develop a skeletal conception of decision-making, we show that two core features of decision-making mechanisms can be identified by studying model organisms, such as E. coli, jellyfish, C. elegans, lamprey, and so on. First, decision mechanisms are distributed and heterarchically structured. Second, they depend heavily on chemical information processing, such as that involving neuromodulators. We end by discussing (...) the implications for studying distinctively human decision-making. (shrink)

This paper aims to provide a philosophical and theoretical account of biological communication grounded in the notion of organisation. The organisational approach characterises living systems as organised in such a way that they are capable to self-produce and self-maintain while in constant interaction with the environment. To apply this theoretical framework to the study of biological communication, we focus on a specific approach, based on the notion of influence, according to which communication takes place when a signal emitted by a (...) sender triggers a change in the behaviour of the receiver that is functional for the sender itself. We critically analyse the current formulations of this account, that interpret what is functional for the sender in terms of evolutionary adaptations. Specifically, the adoption of this etiological functional framework may lead to the exclusion of several phenomena usually studied as instances of communication, and possibly even of entire fields of investigation such as synthetic biology. As an alternative, we reframe the influence approach in organisational terms, characterising functions in terms of contributions to the current organisation of a biological system. We develop a theoretical account of biological communication in which communicative functions are distinguished from other types of biological functions described by the organisational account (e.g. metabolic, ecological, etc.). The resulting organisational-influence approach allows to carry out causal analyses of current instances of phenomena of communication, without the need to provide etiological explanations. In such a way it makes it possible to understand in terms of communication those phenomena which realise interactive patterns typical of signalling interactions – and are usually studied as such in scientific practice – despite not being the result of evolutionary adaptations. Moreover, this approach provides operational tools to design and study communicative interactions in experimental fields such as synthetic biology. (shrink)

The mechanistic framework traditionally comes bundled with a multi-level view. Some ascribe ontological weight to these levels, whereas others claim that characterising a higher-level entity and the corresponding lower-level mechanism are only different descriptions of the same thing. The goal of this paper is to develop a consistent metaphysical picture that can underly the latter position. According to this flat view, wholes and their parts are embedded in the same network of interacting units. The flat view preserves the original virtues (...) of the mechanistic approach and is able to avoid the problems associated with the multi-level view. (shrink)

⦿ In my dissertation I introduce, motivate and take the first steps in the implementation of, the project of naturalising modal metaphysics: the transformation of the field into a chapter of the philosophy of science rather than speculative, autonomous metaphysics. -/- ⦿ In the introduction, I explain the concept of naturalisation that I apply throughout the dissertation, which I argue to be an improvement on Ladyman and Ross' proposal for naturalised metaphysics. I also object to Williamson's proposal that modal metaphysics (...) --- or some view in the area --- is already a quasi-scientific discipline. -/- ⦿ Recently, some philosophers have argued that the notion of metaphysical modality is as ill defined as to be of little theoretical utility. In the second chapter I intend to contribute to such skepticism. First, I observe that each of the proposed marks of the concept, except for factivity, is highly controversial; thus, its logical structure is deeply obscure. With the failure of the "first principles" approach, I examine the paradigmatic intended applications of the concept, and argue that each makes it a device for a very specific and controversial project: a device, therefore, for which a naturalist will find no use for. I conclude that there is no well-defined or theoretically useful notion of objective necessity other than logical or physical necessity, and I suggest that naturalising modal metaphysics can provide more stable methodological foundations. -/- ⦿ In the third chapter I answer a possible objection against the in-principle viability of the project: that the concept of metaphysical modality cannot be understood through the philosophical analysis of any scientific theory, since metaphysical necessity "transcends'' natural necessity, and science only deals with the latter. I argue that the most important arguments for this transcendence thesis fail or face problems that, as of today, remain unsolved. -/- ⦿ Call the idea that science doesn't need modality, "demodalism''. Demodalism is a first step in a naturalistic argument for modal antirealism. In the fourth chapter I examine six versions of demodalism to explain why a family of formalisms, that I call "spaces of possibility'', are (i) used in a quasi-ubiquitous way in mathematised sciences (I provide examples from theoretical computer science to microeconomics), (ii) scientifically interpreted in modal terms, and (iii) used for at least six important tasks: (1) defining laws and theories; (2) defining important concepts from different sciences (I give several examples); (3) making essential classifications; (4) providing different types of explanations; (5) providing the connection between theory and statistics, and (6) understanding the transition between a theory and its successor (as is the case with quantisation). -/- ⦿ In fifth chapter I propose and defend a naturalised modal ontology. This is a realism about modal structure: my realism about constraints. The modal structure of a system are the relationships between its possible states and between its possible states and those of other systems. It is given by the plurality of restrictions to which said system is subject. A constraint is a factor that explains the impossibility of a class of states; I explain this concept further. First, I defend my point of view by rejecting some of its main rivals: constructive empiricism, Humean conventionalism, and wave function realism, as they fail to make sense of quantum chaos. This is because the field requires the notion of objective modal structure, and the mentioned views have trouble explaining the modal facts of quantum dynamics. Then, I argue that constraint realism supersedes these views in the context of Bohm's standard theory and mechanics, and underpins the study of quantum chaos. Finally, I consider and reject two possible problems for my point of view. -/- ⦿ A central concern of modal metaphysicians has been to understand the logical system that best characterises necessity. In the sixth chapter I intend to recover the logical project applied to my naturalistic modal metaphysics. Scientists and philosophers of science accept different degrees of physical necessity, ranging from purely mathematically necessary facts that restrict physical behaviour, to kinetic principles, to particular dynamical constraints. I argue that this motivates a multimodal approach to modal logic, and that the time dependence of dynamics motivates a logic of historical necessity. I propose multimodal propositional (classical) logics for Bohmian mechanics and the Everettian theory of many divergent worlds, and I close with a criticism of Williamson's approach to the logic of state spaces of dynamic systems. (shrink)

I develop an interdisciplinary framework for understanding the nature of agents and agency that is compatible with recent developments in the metaphysics of science and that also does justice to the mechanistic and normative characteristics of agents and agency as they are understood in moral philosophy, social psychology, neuroscience, robotics, and economics. The framework I develop is internal perspectivalist. That is to say, it counts agents as real in a perspective-dependent way, but not in a way that depends on an (...) external perspective. Whether or not something counts as an agent depends on whether it is able to have a certain kind of perspective. My approach differs from many others by treating possession of a perspective as more basic than the possession of agency, representational content/vehicles, cognition, intentions, goals, concepts, or mental or psychological states; these latter capabilities require the former, not the other way around. I explain what it means for a system to be able to have a perspective at all, beginning with simple cases in biology, and show how self-contained normative perspectives about proper function and control can emerge from mechanisms with relatively simple dynamics. I then describe how increasingly complex control architectures can become organized that allow for more complex perspectives that approach agency. Next, I provide my own account of the kind of perspective that is necessary for agency itself, the goal being to provide a reference against which other accounts can be compared. Finally, I introduce a crucial distinction that is necessary for understanding human agency: that between inclinational and committal agency, and venture a hypothesis about how the normative perspective underlying committal agency might be mechanistically realized. (shrink)

The aim of this paper is to provide a theoretical framework to understand how multicellular systems realize functionally integrated physiological entities by organizing their intercellular space. From a perspective centered on physiology and integration, biological systems are often characterized as organized in such a way that they realize metabolic self-production and self-maintenance. The existence and activity of their components rely on the network they realize and on the continuous management of the exchange of matter and energy with their environment. One (...) of the virtues of the organismic approach focused on organization is that it can provide an understanding of how biological systems are functionally integrated into coherent wholes. Organismic frameworks have been primarily developed by focusing on unicellular life. Multicellularity, however, presents additional challenges to our understanding of biological systems, related to how cells are capable to live together in higher-order entities, in such a way that some of their features and behaviors are constrained and controlled by the system they realize. Whereas most accounts of multicellularity focus on cell differentiation and increase in size as the main elements to understand biological systems at this level of organization, we argue that these factors are insufficient to provide an understanding of how cells are physically and functionally integrated in a coherent system. In this paper, we provide a new theoretical framework to understand multicellularity, capable to overcome these issues. Our thesis is that one of the fundamental theoretical principles to understand multicellularity, which is missing or underdeveloped in current accounts, is the functional organization of the intercellular space. In our view, the capability to be organized in space plays a central role in this context, as it enables (and allows to exploit all the implications of) cell differentiation and increase in size, and even specialized functions such as immunity. We argue that the extracellular matrix plays a crucial active role in this respect, as an evolutionary ancient and specific (non-cellular) control subsystem that contributes as a key actor to the functional specification of the multicellular space and to modulate cell fate and behavior. We also analyze how multicellular systems exert control upon internal movement and communication. Finally, we show how the organization of space is involved in some of the failures of multicellular organization, such as aging and cancer. (shrink)

Endocrinologists apply the idea of feedback loops to explain how hormones regulate certain bodily functions such as glucose metabolism. In particular, feedback loops focus on the maintenance of the plasma concentrations of glucose within a narrow range. Here, we put forward a different, organicist perspective on the endocrine regulation of glycaemia, by relying on the pivotal concept of closure of constraints. From this perspective, biological systems are understood as organized ones, which means that they are constituted of a set of (...) mutually dependent functional structures acting as constraints, whose maintenance depends on their reciprocal interactions. Closure refers specifically to the mutual dependence among functional constraints in an organism. We show that, when compared to feedback loops, organizational closure can generate much richer descriptions of the processes and constraints at play in the metabolism and regulation of glycaemia, by making explicit the different hierarchical orders involved. We expect that the proposed theoretical framework will open the way to the construction of original mathematical models, which would provide a better understanding of endocrine regulation from an organicist perspective. (shrink)