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)

We advance an account that grounds cognition, specifically decision-making, in an activity all organisms as autonomous systems must perform to keep themselves viable—controlling their production mechanisms. Production mechanisms, as we characterize them, perform activities such as procuring resources from their environment, putting these resources to use to construct and repair the organism's body and moving through the environment. Given the variable nature of the environment and the continual degradation of the organism, these production mechanisms must be regulated by control mechanisms (...) that select when a production is required and how it should be carried out. To operate on production mechanisms, control mechanisms need to procure information through measurement processes and evaluate possible actions. They are making decisions. In all organisms, these decisions are made by multiple different control mechanisms that are organized not hierarchically but heterarchically. In many cases, they employ internal models of features of the environment with which the organism must deal. Cognition, in the form of decision-making, is thus fundamental to living systems which must control their production mechanisms. (shrink)

Living organisms act as integrated wholes to maintain themselves. Individual actions can each be explained by characterizing the mechanisms that perform the activity. But these alone do not explain how various activities are coordinated and performed versatilely. We argue that this depends on a specific type of mechanism, a control mechanism. We develop an account of control by examining several extensively studied control mechanisms operative in the bacterium E. coli. On our analysis, what distinguishes a control mechanism from other mechanisms (...) is that it relies on measuring one or more variables, which results in setting constraints in the control mechanism that determine its action on flexible constraints in other mechanisms. In the most basic arrangement, the measurement process directly determines the action of the control mechanism, but in more complex arrangements signals mediate between measurements and effectors. This opens the possibility of multiple responses to the same measurement and responses based on multiple measurements. It also allows crosstalk, resulting in networks of control mechanisms. Such networks integrate the behaviors of the organism but also present a challenge in tailoring responses to particular measurements. We discuss how integrated activity can still result in differential, versatile, responses. (shrink)

Despite numerous and increasing attempts to define what life is, there is no consensus on necessary and sufficient conditions for life. Accordingly, some scholars have questioned the value of definitions of life and encouraged scientists and philosophers alike to discard the project. As an alternative to this pessimistic conclusion, we argue that critically rethinking the nature and uses of definitions can provide new insights into the epistemic roles of definitions of life for different research practices. This paper examines the possible (...) contributions of definitions of life in scientific domains where such definitions are used most (e.g., Synthetic Biology, Origins of Life, Alife, and Astrobiology). Rather than as classificatory tools for demarcation of natural kinds, we highlight the pragmatic utility of what we call operational definitions that serve as theoretical and epistemic tools in scientific practice. In particular, we examine contexts where definitions integrate criteria for life into theoretical models that involve or enable observable operations. We show how these definitions of life play important roles in influencing research agendas and evaluating results, and we argue that to discard the project of defining life is neither sufficiently motivated, nor possible without dismissing important theoretical and practical research. (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)

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)

Theoretical accounts of development exhibit several internal tensions and face multiple challenges. They span from the problem of the identification of the temporal boundaries of development (beginning and end) to the characterization of the distinctive type of change involved compared to other biological processes. They include questions such as the role to ascribe to the environment or what types of biological systems can undergo development and whether they should include colonies or even ecosystems. In this chapter we discuss these conceptual (...) issues, and we argue that adopting an organizational approach may help solve or clarify them. -/- While development is usually identified with the achievement of an adult form with the capability to reproduce and therefore maintain a lineage, adopting the organizational approach may provide a different strategy, which focuses also on the maintenance of the current organization of the organism. By doing so an organizational approach favors a switch in perspective which consists in analyzing how organisms maintain their viability at each moment of development rather than considering them as going through intermediate stages of a process directed toward a specific goal state. This developmental dimension of biological organization has yet to be given a general and detailed analysis within the organizational theoretical perspective, apart from some preliminary attempts. How a biological organization is maintained through a series of radical organizational changes and what these changes are issues that still require clarification. In this chapter we offer the beginnings of such an analysis of developmental transitions, understood as changes in functionality brought forth by regulatory mechanisms in the context of the continued maintenance of organizational viability at every step. (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 definitions and conceptualizations of health, and the management of healthcare have been challenged by the current global scenarios (e.g., new diseases, new geographical distribution of diseases, effects of climate change on health, etc.) and by the ongoing scholarship in humanities and science. In this paper we question the mainstream definition of health adopted by the WHO—‘a state of complete physical, mental and social well-being and not merely the absence of disease or infirmity’ (WHO in Preamble to the constitution of (...) the World Health Organization as adopted by the international health conference, The World Health Organization, 1948)—and its role in providing tools to understand what health is in the contemporary context. More specifically, we argue that this context requires to take into account the role of the environment both in medical theory and in the healthcare practice. To do so, we analyse WHO documents dated 1984 and 1986 which define health as ‘coping with the environment’. We develop the idea of ‘coping with the environment’, by focusing on two cardinal concepts: adaptation in public health and adaptivity in philosophy of biology. We argue that the notions of adaptation and adaptivity can be of major benefit for the characterization of health, and have practical implications. We explore some of these implications by discussing two recent case studies of adaptivity in public health, which can be valuable to further develop adaptive strategies in the current pandemic scenario: community-centred care and microbiologically healthier buildings. (shrink)

Since it was inspired by Bernard and developed and named by Cannon, the conceptof homeostasis has been invoked by many as the central theoretical framework for physiology. Ithas also been the target of numerous criticisms that have elicited the introduction of a plethoraof alternative concepts. We argue that many of the criticisms actually target the more restrictiveaccount of homeostasis advanced by the cyberneticists. What was crucial to Bernard and Cannonwas a focus on the maintenance of the organism as the goal (...) of physiological regulation. We analysehow Bernard’s and Cannon’s broad conception of what was required to maintain the organismwas narrowed to negative feedback, characterized in terms of setpoints, by the cyberneticistsand demonstrate how many of the alternative concepts challenge the role of setpoints – treatingthem as variable in light of circumstances or in anticipation of future circumstances, or asdispensable altogether. To support our analysis, we draw on the experimental and theoreticalwork on thermoregulation, a phenomenon that has been considered as a paradigmatic example ofhomeostasis and has been a common focus of those advancing alternative concepts. To integratethe insights advanced by the original proponents of homeostasis and the theorists proposingreplacement notions we advance a framework in which regulation is viewed from the perspectiveof maintaining the organism. (shrink)

Eating is a fundamental behavior in which all organisms must engage in order to procure the material and energy from their environment that they need to maintain themselves. Since controlling eating requires procuring, processing, and assessing information, it constitutes a cognitive activity that provides a productive domain for pursuing cognitive biology as proposed by Ladislav Kováč. In agreement with Kováč, we argue that cognition is fundamentally grounded in chemical signaling and processing. To support this thesis, we adopt Cisek’s strategy of (...) phylogenetic refinement, focusing on two animal phyla, Porifera and Placozoa, organisms that do not have neurons, muscles, or an alimentary canal, but nonetheless need to coordinate the activity of cells of multiple types in order to eat. We review what research has revealed so far about how these animals gather and process information to control their eating behavior. (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)

This paper critically revises the organisational account of teleology, which argues that living systems are first and foremost oriented towards a goal: maintaining their own conditions of existence. It points out some limitations of this account, mainly in the capability to account for the richness and complexity of biological systems and their purposeful behaviours. It identifies the reason of these limitations in the theoretical grounding of this account, specifically in the too narrow notion of closure of constraints, focused on self-production. (...) It proposes to ground an organisational account of biological teleology in the capability of living system not just to produce and replace their parts, but to control their own internal dynamics and behaviours in such a way as to maintain themselves. This theoretical framework has two advantages. It better captures the distinctive features of biological organisations and consequently the richness and active nature of their purposeful behaviours. By doing so, it makes it possible to apply this framework beyond minimal theoretical models to real biological cases. (shrink)

Both physiological and evolutionary criteria of biological individuality are underpinned by the idea that an individual is a functionally integrated whole. However, a precise account of functional integration has not been provided so far, and current notions are not developed in the details, especially in the case of composite systems. To address this issue, this paper focuses on the organisational dimension of two representative associations of prokaryotes: biofilms and the endosymbiosis between prokaryotes. Some critical voices have been raised against the (...) thesis that biofilms are biological individuals. Nevertheless, it has not been investigated which structural and functional obstacles may prevent them from being fully integrated physiological or evolutionary units. By contrast, the endosymbiotic association of different species of prokaryotes has the potential for achieving a different type of physiological integration based on a common boundary and interlocked functions. This type of association had made it possible, under specific conditions, to evolve endosymbionts into fully integrated organelles. This paper therefore has three aims: first, to analyse the organisational conditions and the physiological mechanisms that enable integration in prokaryotic associations; second, to discuss the organisational differences between biofilms and prokaryotic endosymbiosis and the types of integration they achieve; finally, to provide a more precise account of functional integration based on these case studies. (shrink)

In this article we analyse the problem of emergence in its diachronic dimension. In other words, we intend to deal with the generation of novelties in natural processes. Our approach aims at integrating some insights coming from Whitehead’s Philosophy of the Process with the epistemological framework developed by the “autopoietic” tradition. Our thesis is that the emergence of new entities and rules of interaction (new “fields of relatedness”) requires the development of discontinuous models of change. From this standpoint natural evolution (...) can be conceived as a succession of emergences — each one realizing a novel “extended” present, described by distinct models — rather than as a single and continuous dynamics. This theoretical and epistemological framework is particularly suitable to the investigation of the origin of life, an emblematic example of this kind of processes. (shrink)

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

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)

Definition The authors’ definition of the autopoietic system has evolved through the years. One of them states that an autopoietic system is organized (defined as a unity) as a network of processes of production (transformation and destruction) of components that produces the components which: (1) through their interactions and transformations regenerate and realize the network of processes (relations) that produced them; and (2) constitute it (the machine) as a concrete unity in the space in which they exist by specifying the (...) topological domain of its realization as such a network (Varela 1979, p. 13). Nearly the same formula was earlier used to define an autopoietic machine (Maturana and Varela 1973/1980, 1984/1987, p. 135). (shrink)

Understanding how biological organisms are autonomous—maintain themselves far from equilibrium through their own activities—requires understanding how they regulate those activities. In multicellular animals, such control can be exercised either via endocrine signaling through the vasculature or via neurons. In C. elegans this control is exercised by a well-delineated relatively small but distributed nervous system that relies on both chemical and electric transmission of signals. This system provides resources to integrate information from multiple sources as needed to maintain the organism. Especially (...) important for the exercise of neural control are neuromodulators, which we present as setting agendas for control through more traditional electrical signaling. To illustrate how the C. elegans nervous system integrates multiple sources of information in controlling activities important for autonomy, we focus on feeding behavior and responses to adverse conditions. We conclude by considering how a distributed nervous system without a centralized controller is nonetheless adequate for autonomy. (shrink)

The aim of this article is to investigate the relevance and implications of synthetic models for the study of the interactive dimension of minimal life and cognition, by taking into consideration how the use of artificial systems may contribute to an understanding of the way in which interactions may affect or even contribute to shape biological identities. To do so, this article analyzes experimental work in synthetic biology on different types of interactions between artificial and natural systems, more specifically: between (...) protocells and between biological living cells and protocells. It discusses how concepts such as control, cognition, communication can be used to characterize these interactions from a theoretical point of view, which criteria of relevance and evaluation of synthetic models can be applied to these cases, and what are their limits. (shrink)

This paper discusses the epistemic status of biology from the standpoint of the systemic approach to living systems based on the notion of biological autonomy. This approach aims to provide an understanding of the distinctive character of biological systems and this paper analyses its theoretical and epistemological dimensions. The paper argues that, considered from this perspective, biological systems are examples of emergent phenomena, that the biological domain exhibits special features with respect to other domains, and that biology as a discipline (...) employs some core concepts, such as teleology, function, regulation among others, that are irreducible to those employed in physics and chemistry. It addresses the claim made by Jacques Monod that biology as a science is marginal. It argues that biology is general insofar as it constitutes a paradigmatic example of complexity science, both in terms of how it defines the theoretical object of study and of the epistemology and heuristics employed. As such, biology may provide lessons that can be applied more widely to develop an epistemology of complex systems. (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)

Open peer commentary on the article “Circularity and the Micro-Macro-Difference” by Manfred Füllsack. Upshot: The target article defends the fundamental role of circularity for systems sciences and the necessity to develop a conceptual and methodological approach to it. The concept of circularity, however, is multifarious, and two of the main challenges in this respect are to provide distinctions between different forms of circularities and explore in detail the roles they play in organizations. This commentary provides some suggestions in this direction (...) with the aim to supplement the perspective presented in the target article with some insights from theoretical biology. (shrink)

El prefijo “auto” en autoorganización y autopoiesis se refiere a la existencia de una identidad o agencialidad implicada en el orden, organización o producción de un sistema que se corresponde con el sistema mismo, en contraste con el diseño o la influencia de carácter externo. La autoorganización (AO) estudia la manera en la que los procesos de un sistema alcanzan de forma espontánea un orden u organización complejo, bien como una estructura o patrón emergente, bien como algún tipo de finalidad (...) o identidad autoconstruida. En este trabajo nos ocupamos del concepto de AO en el contexto de la problemática sobre la naturaleza la vida y de los organismos vivientes. Este concepto se elabora en diferentes tradiciones científicas y filosóficas, a partir de su origen en la filosofía kantiana. La cibernética trata de emular la organización de los seres vivos y su teleología mediante la construcción de máquinas; desarrolla una perspectiva centrada en la regulación y en la causalidad mutua entre componentes del sistema. Estos trabajos, a veces complementados con la teoría de sistemas y la teoría de la información, son fundamentales para el desarrollo de la ciencia del siglo XX, especialmente las ciencias computacionales y la biología. Una segunda corriente surge desde la termodinámica de los procesos irreversibles alejados del equilibrio a partir, entre otros, de los trabajos de la escuela de Bruselas, en la que la AO se explora como la formación espontánea de estructuras de orden disipativo. Una tercera tradición, tal vez la más profundamente kantiana, se desarrolla en el contexto de la biología del desarrollo e integra a las dos mencionadas previamente, pues combina aspectos de las dos previas en el desarrollo ontogenético. Podemos decir que cada una de estas concepciones de la AO se relaciona con modelos paradigmáticos diferentes. La noción de autopoiesis (AP), por su parte, fue propuesta en los años 70 por los biólogos chilenos Humberto Maturana y Francisco Varela para explicar la organización individual de los seres vivos como un proceso dinámico que genera una identidad desde las operaciones del sistema (Maturana y Varela 1973). Puede decirse que hereda y reorganiza ideas de la tradición de la AO, especialmente la kantiana y la cibernética, para proponer una teoría biológica alternativa. El enfoque autopoiético concibe el fenómeno de la vida y a los seres vivos de forma muy diferente a la teoría de la evolución o la biología molecular que constituían las líneas de investigación predominantes en la biología de su tiempo. La teoría subraya como propiedad básica de un sistema viviente su autoconstitución dinámica como unidad dotada de identidad a partir de interacciones entre sus componentes. Sin embargo, aquellas propiedades de la vida consideradas primordiales en el enfoque darwiniano, como la reproducción o la evolución, se ven como secundarias, pues requieren de la existencia previa de sistemas autopoiéticos. El objetivo de esta voz es examinar diferentes aspectos que configuran las tradiciones autoorganizativa y autopoiética, en especial las tensiones conceptuales internas que permiten comprender los desafíos a los que se enfrentan ambas en el marco de la filosofía y la teoría de la biología, así como la forma en que sus posiciones e intuiciones contrastan con otras perspectivas en biología. (shrink)