The organizational account of biological functions interprets functions as contributions of a trait to the maintenance of the organization that, in turn, maintains the trait. As has been recently argued, however, the account seems unable to provide a unified grounding for both intra- and cross-generation functions, since the latter do not contribute to the maintenance of the same organization which produces them. To face this ‘ontological problem’, a splitting account has been proposed, according to which the two (...) kinds of functions require distinct organizational definitions. In this article, we propose a solution for the ontological problem, by arguing that intra- and cross-generation functions can be said to contribute in the same way to the maintenance of the biological organization, characterized in terms of organizational self-maintenance. As a consequence, we suggest maintaining a unified organizational account of biological functions. (shrink)

This open access book assesses the prospects of (re)adopting organization as a pivotal concept in biology. It shows how organization can nourish biological thinking and practice, by reconnecting with the idea of biology as the science of organized systems. The book provides a comprehensive state-of-the-art picture of the characterizations and uses of the concept of organization in both biological science and philosophy of biology. It also deals with a variety of themes – including evolution, organogenesis, (...) heredity, cognition and ecology – with respect to which the concept of organization can guide the elaboration of original models and new experimental protocols. It will be of interest to biologists and scholars working in philosophy of science alike. (shrink)

We develop a conceptual framework that connects biological heredity and organization. We refer to heredity as the cross-generation conservation of functional elements, defined as constraints subject to organizational closure. While hereditary objects are functional constituents of biological systems, any other entity that is stable across generations—and possibly involved in the recurrence of phenotypes—belongs to their environment. The central outcome of the organizational perspective consists in extending the scope of heredity beyond the genetic domain without merging it with (...) the broad category of cross-generation stability. After discussing some implications, we conclude with a reflection on the relationship between stability and variation. 1Introduction2From Extended Heredity to Cross-generation Stability 2.1Extending the scope of heredity: A brief state of the art2.2Rethinking heredity: Conceptual challenges3Biological Heredity in Light of Organization 3.1Biological organization within organisms and beyond3.2Extending organization in time3.3What is biological heredity?4Implications and Objections 4.1Heredity as a specific kind of cross-generation stability4.2Heredity at various levels of description4.3Non-functional and dysfunctional objects5Conclusions: From Conservation to Variation. (shrink)

The concept of superorganism has a mixed reputation in biology—for some it is a convenient way of discussing supra-organismal levels of organization, and for others, little more than a poetic metaphor. Here, I show that a considerable step forward in the understanding of superorganisms results from a thorough review of the supra-organismal levels of organization now known to exist among the “unicellular” protists. Limiting the discussion to protists has enormous advantages: their bodies are very well studied and relatively (...) simple, and they exhibit an enormous diversity of anatomies and lifestyles. This allows for unprecedented resolution in describing forms of supra-organismal organization. Here, four criteria are used to differentiate loose, incidental associations of hosts with their microbiota from “actual” superorganisms: obligatory character, specific spatial localization of microbiota, presence of attachment structures and signs of co-evolution in phylogenetic analyses. Three groups—that have never before been described in the philosophical literature—merit special attention: Symbiontida, Oxymonadida and Parabasalia. Specifically, it is argued that in certain cases—for Bihospites bacati and Calkinsia aureus, Streblomastix strix, Joenia annectens and Mixotricha paradoxa and Kentrophoros —it is fully appropriate to describe the whole protist-microbiota assocation as a single organism and its elements as “tissues” or, arguably, even “organs”. To account for this level of biological complexity, I propose the term “structured superorganism”. (shrink)

In this chapter we offer a critical analysis of organizational models about the process of origins of life and, thereby, a reflection about life itself (understood in a general, minimal sense). We begin by demarcating the idea of organization as an explanatory construct, linking it to the complex relationships and transformations that the material parts of (proto-)biological systems establish to maintain themselves under non-equilibrium dynamic conditions. The diverse ways in which this basic idea has been applied within the (...) prebiotic field are then reviewed in relative detail. We distinguish between “network” and “protocell” approaches, discussing their specific implications and explaining the greater relevance of the latter in the current state of affairs. Despite the key role that such organizational approaches play (and should keep playing) to advance on the problem of primordial biogenesis, the second half of our contribution is devoted to argue that they must be combined with other explanatory accounts, which go beyond the physiology of any single (proto-)organism. With that aim, we underline the fundamental differences between the autonomous, metabolic dynamics that individual (proto-)cells perform and the evolutionary and ecological dynamics that take place in a collective and trans-generational dimension. Apart from obvious gaps in the characteristic temporal and spatial scales involved, the corresponding causal and interactive regimes also reveal themselves as neatly distinct, what is reflected in the unpaired functional integration and the agent behavior displayed by biological individuals. Nevertheless, any living organism (and life in a wider, general sense) derives from the deep interweaving of those two phenomenological domains: namely, the “individual-metabolic” and the “collective-evolutionary” domains. At the end of the chapter, we propose the principle of dynamical decoupling as the core idea to develop a more comprehensive theoretical framework to understand how this intricate, causally asymmetric connection must be articulated during the actual process of biogenesis (as it happened here on Earth or anywhere else in the universe), so that life’s minimal complexity threshold is reached. (shrink)

This paper seeks to characterize how the study of nutrition processes contributed to revisit the problem of vital organization in the late eighteenth century. It argues that focusing on nutrition leads to reformulate the problem of the relation between life and organization in terms of processes, rather than static or given structures. This nutrition-centered approach to life amounts to acknowledge the specific strategic role nutrition played in the development of a materialist approach to the generation of vital (...) class='Hi'>organization. The paper proposes a clarification of the multiple meanings of the concept of organization in the context of Enlightenment physiology and nascent biology, before focusing on the century long analogy between nutrition and generation. It shows how, by contrasting different uses of this analogy, nutrition was employed as a key vital phenomenon in the development of epigenetic theories of generation, i.e. how a nutritive modeling of generation was used in the undermining of preformationism. To this purpose I contrast two seemingly opposite theories of generation, Buffon’s and Bonnet’s, and show that despite the obvious metaphysical discontent, their views of generation share a common mechanical conceptual frame in which nutrition is conflated with growth and repair. I then turn to the role nutrition played in the epigenetic conception of generation in C. F. Wolff’s embryology and analyze this rival understanding of nutrition as an organizing process. (shrink)

This chapter presents a displacement of the organism as a privileged level of analysis in evolutionary biology. It is concerned with the ontology of biology systems, with particular reference to hierarchical organization. It argues that the concept of a rank-free hierarchy can be transposed to the major transitions hierarchy, with interesting consequences. This chapter shows that the idea of rank freedom makes good sense of a number of facets of the recent discussion of evolutionary transitions and multilevel selection. It (...) suggests that the idea of rank freedom is already at work, implicitly, in much theorizing about evolutionary transitions and/or multilevel selection. (shrink)

This book offers a comprehensive account of vitalism and the Romantic philosophy of nature. The author explores the rise of biology as a unified science in Germany by reconstructing the history of the notion of “vital force,” starting from the mid-eighteenth through the early nineteenth century. Further, he argues that Romantic Naturphilosophie played a crucial role in the rise of biology in Germany, especially thanks to its treatment of teleology. In fact, both post-Kantian philosophers and naturalists were guided by teleological (...) principles in defining the object of biological research. The book begins by considering the problem of generation, focusing on the debate over the notion of “formative force.” Readers are invited to engage with the epistemological status of this formative force, i.e. the question of the principle behind organization. The second chapter provides a reconstruction of the physiology of vital forces as it was elaborated in the mid- to late-eighteenth century by the group of physicians and naturalists known as the “Göttingen School.” Readers are shown how these authors developed an understanding of the animal kingdom as a graded series of organisms with increasing functional complexity. Chapter three tracks the development of such framework in Romantic Naturphilosophie. The author introduces the reader to the problem of classification, showing how Romantic philosophers of nature regarded classification as articulated by a unified plan that connects all living forms with one another, relying on the idea of living nature as a universal organism. In the closing chapter, this analysis shows how the three instances of pre-biological discourse on living beings – theory of generation, physiology and natural history – converged to form the consolidated disciplinary matrix of a general biology. The book offers an insightful read for all scholars interested in classical German philosophy, especially those researching the philosophy of nature, as well as the history and philosophy of biology. (shrink)

Different cell lineages growing in microgravity undergo a spontaneous transition leading to the emergence of two distinct phenotypes. By returning these populations in a normal gravitational field, the two phenotypes collapse, recovering their original configuration. In this review, we hypothesize that, once the gravitational constraint is removed, the system freely explores its phenotypic space, while, when in a gravitational field, cells are “constrained” to adopt only one favored configuration. We suggest that the genome allows for a wide range of “possibilities” (...) but it is unable per se to choose among them: the emergence of a specific phenotype is enabled by physical constraints that drive the system toward a preferred solution. These findings may help in understanding how cells and tissues behave in both development and cancer. In microgravity, cells undergo spontaneous and reversible transitions between different phenotypes. In the absence of physical constraints, living systems could yield bi-stable decisions. On the contrary, physical ‘boundaries’ constrain cells to acquire only a specific configuration by selecting and shaping different gene expression patterns provided by the intrinsic genetic stochasticity. (shrink)

This book proposes the foundation of the relational approach to biology, rejecting the deterministic and reductionist approach of molecular biology. Although biology has made enormous progress in the last seventy years, onto genesis is still conceived as a “revelation” of information (DNA). Recovering the geometric tradition, relational biology conceives scientific and epistemological tools (cause, probability, space etc.) of science in a new way. If probabilistic biology and organicism still proposes a biology based on physics, with a fundamental invariant, relational biology (...) is based on variation: its fundamental invariant is variation, one of the most important elements of life. This is an indispensable book for academics who consider biology from a new theoretical approach, in particular for those working in the domains of cancer, ontogenesis and evolution. (shrink)

Biological systems are typically hierarchically organized, open, nonlinear systems, and inherit all of the characteristics of such systems that are found in the purely physical and chemical domains, to which all biological systems belong. In addition, biological systems exhibit functional properties, and they contain information in a form that is used internally to make required functional distinctions. The existence of these additional biological properties is widely granted, but their exact nature is controversial. I will address first (...) the issue of biological function, and then turn to the issue of information in biosystems. (shrink)

In this paper, I argue that starting with the organelles that constitute a cell - and continuing up the hierarchy of components in processes and subsystems of an organism - there exist clear instances of emergent biological phenomena that can be considered,,living" entities. These components and their attending processes are living emergent phenomena because of the way in which the components are organized to maintain homeostasis of the organism at the various levels in the hierarchy. I call this view (...) the homeostatic organization view of biological phenomena, and, as is shown, it comports well with the standard philosophical accounts of nomological emergence and representational emergence. To proffer HOV, I describe properties of biological entities that include internal-hierarchical data exchange, data selectivity, informational integration, and environmental-organismic information exchange. Further, a distinction is drawn between particularized homeostasis and generalized homeostasis, and I argue that because the various processes and subsystems of an organism are functioning properly in their internal environments, the organism is able to exist as a hierarchically-organized entity in some environment external to it. Stated simply: that components of biological phenomena are organized to perform some function resulting in homeostasis marks them out to be living emergent entities distinguishable, in description and in reality, from the very physico-chemical processes of which they are composed. German In diesem Aufsatz argumentiere ich dafür, daß - beginnend mit den Organellen, die eine Zelle bilden und die Hierarchie der Komponenten von Prozessen und Subsystemen eines Organismus hinaufführend - klare Fälle emergenter biologischer Phänomene existieren, die als,,lebende Entitäten betrachtet werden können. Diese Komponenten und die sie begleitenden Prozesse sind lebende emergente Phänomene wegen der Art, in der die Komponenten organisiert sind, um die Homöostase des Organismus auf den verschiedenen Ebenen in der Hierarchie aufrechtzuerhalten. Ich nenne diese Sichtweise die homöostatische Organisationssichtweise biologischer Phänomene, und es wird gezeigt, daß sie sich gut mit üblichen philosophischen Darstellungen nomologischer Emergenz und repräsentationaler Emergenz verträgt. Um HOV zu präsentieren, beschreibe ich Eigenschaften biologischer Entitäten, die den intern-hierarchischen Datenaustausch, die Datenselektivität, die informationelle Integration und den Umwelt-Organismus-Informationsaustausch einschließen. Des weiteren wird eine Unterscheidung zwischen partikularisierter und generalisierter Homöostase getroffen, und ich argumentiere dafür, daß ein Organismus fähig ist, als eine hierarchisch organisierte Entität in einigen Umwelten, die ihm extern sind, zu existieren, weil die verschiedenen Prozesse und Subsysteme eines Organismus in ihren internen Umwelten richtig funktionieren. Einfach formuliert: Daß Komponenten biologischer Phänomene organisiert sind, um eine Funktion zu erfüllen, die in Homöostase resultiert, zeichnet sie aus, lebende emergente Entitäten zu sein, die - in der Beschreibung und in der Wirklichkeit - von den physikalisch-chemischen Prozessen, aus denen sie zusammengesetzt sind, unterscheidbar sind. (shrink)

Levels of organization are structures in nature, usually defined by part-whole relationships, with things at higher levels being composed of things at the next lower level. Typical levels of organization that one finds in the literature include the atomic, molecular, cellular, tissue, organ, organismal, group, population, community, ecosystem, landscape, and biosphere levels. References to levels of organization and related hierarchical depictions of nature are prominent in the life sciences and their philosophical study, and appear not only in (...) introductory textbooks and lectures, but also in cutting-edge research articles and reviews. In philosophy, perennial debates such as reduction, emergence, mechanistic explanation, interdisciplinary relations, natural selection, and many other topics, also rely substantially on the notion. -/- Yet, in spite of the ubiquity of the notion, levels of organization have received little explicit attention in biology or its philosophy. Usually they appear in the background as an implicit conceptual framework that is associated with vague intuitions. Attempts at providing general and broadly applicable definitions of levels of organization have not met wide acceptance. In recent years, several authors have put forward localized and minimalistic accounts of levels, and others have raised doubts about the usefulness of the notion as a whole. -/- There are many kinds of ‘levels’ that one may find in philosophy, science, and everyday life—the term is notoriously ambiguous. Besides levels of organization, there are levels of abstraction, realization, being, analysis, processing, theory, science, complexity, and many others. In this article, the focus will be on levels of organization and debates associated with them, and other kinds of levels will only be discussed when they are relevant to this main topic. (shrink)

During the last few years, various authors have called for the elaboration of a theoretical framework that would better take into account the role of organisms in evolutionary dynamics. In this paper, I argue that an organism-centered evolutionary theory, which implies the rehabilitation of an organizational thinking in evolutionary biology and should be associated with what I will call a heuristic of collaboration, may be completed by an organizational perspective of biological inheritance. I sketch this organizational perspective – which (...) allows going beyond gene-centrism –, show how it grounds a systemic concept of heritable variation suited to the new evolutionary framework, and highlight some of its explanatory value and theoretical implications for evolutionary thinking. (shrink)

The conceptual history of the term “organization” begins in Medieval times with the reception and transformation of Aristotle’s philosophy of life. It designates the corporeal structure and conditions of identity of natural “organic bodies,” a term that had been used to refer to living beings since antiquity. The term played an important role in specifying the ontological status of living beings. At the same time, it offered a basis for their mechanistic understanding. Starting with mechanistic models of life in (...) the second half of the seventeenth century, “organization” and “life” were increasingly used interchangeably. This conjunction of meaning transformed “living beings” into “organisms.” Within physiological accounts of the eighteenth century, the living organization was compared to a causal cycle of interdependency. Philosophically, this conjunction was adapted at the end of the century in Kant’s philosophy of “organized beings of nature” in which he located the idea of causal cyclicity within a teleological framework and specified an “organized being” in causal terms as a system of interacting and interdependent parts characterized by functional closure. Thus, “organization” refers to the constitution of living beings as a particular kind of causal system. In the nineteenth century, the term achieves the status of a signal word for the life sciences and starts being applied in a wide variety of contexts, from comparative anatomy to physiology and ecology. It was supplemented by two other fundamental notions, namely, “regulation” and “evolution,” the first referring to the stabilization and the second to the long-term transformation of natural organizations. The twentieth century saw a further intensification of the complementarity of the perspectives associated with these three terms. Finally, in recent years, a substantial improvement in understanding the causal structure of “organization” was achieved by analyzing it in terms of the “closure of constraints.”. (shrink)

The subject of this edited volume is the idea of levels of organization: roughly, the idea that the natural world is segregated into part-whole relationships of increasing spatiotemporal scale and complexity. The book comprises a collection of essays that raise the idea of levels into its own topic of analysis. Owing to the wide prominence of the idea of levels, the scope of the volume is aimed at theoreticians, philosophers, and practicing researchers of all stripes in the life sciences. (...) The volume’s contributions reflect this diversity, and draw from fields such as developmental biology, evolutionary biology, molecular biology, ecology, cell biology, and neuroscience. The book presents wide-ranging novel insights on causation and levels, the hierarchical structure of evolution, the role of levels in biological theory, and more. (shrink)

Abstract.Stuart Kauffman's proposal in Investigations to ground a “general biology” in the laws of self‐organization governing systems of autonomous agents runs up against the methodological problem of how to integrate formal mathematical with semantic and semiotic approaches to the study of evolutionary development. Gilles Deleuze's concept of the virtual and C. S. Peirce's system of existential graphs provide a theoretical framework and practical art for answering this problem of method by modeling the creative event of collective self‐organization as (...) both represented and practiced in the scientific community. (shrink)

Here we discuss the challenge posed by self-organization to the Darwinian conception of evolution. As we point out, natural selection can only be the major creative agency in evolution if all or most of the adaptive complexity manifest in living organisms is built up over many generations by the cumulative selection of naturally occurring small, random mutations or variants, i.e., additive, incremental steps over an extended period of time. Biological self-organization—witnessed classically in the folding of a protein, (...) or in the formation of the cell membrane—is a fundamentally different means of generating complexity. We agree that self-organizing systems may be fine-tuned by selection and that self-organization may be therefore considered a complementary mechanism to natural selection as a causal agency in the evolution of life. But we argue that if self-organization proves to be a common mechanism for the generation of adaptive order from the molecular to the organismic level, then this will greatly undermine the Darwinian claim that natural selection is the major creative agency in evolution. We also point out that although complex self-organizing systems are easy to create in the electronic realm of cellular automata, to date translating in silico simulations into real material structures that self-organize into complex forms from local interactions between their constituents has not proved easy. This suggests that self-organizing systems analogous to those utilized by biological systems are at least rare and may indeed represent, as pre-Darwinists believed, a unique ascending hierarchy of natural forms. Such a unique adaptive hierarchy would pose another major challenge to the current Darwinian view of evolution, as it would mean the basic forms of life are necessary features of the order of nature and that the major pathways of evolution are determined by physical law, or more specifically by the self-organizing properties of biomatter, rather than natural selection. (shrink)

Developmental biology is the science of explaining how a variety of interacting processes generate the heterogeneous shapes, size, and structural features of an organism as it develops rom embryo to adult, or more generally throughout its life cycle (Love, 2008b; Minelli, 2011a). Although it is commonplace in philosophy to associate sciences with theories such that the individuation of a science is dependent on a constitutive theory or group of models, it is uncommon to find presentations of developmental biology making reference (...) to a theory or theories of development. For example, in the third edition of Essential Developmental Biology (Slack, 2013), three families of approaches are described (developmental genetics, experimental embryology, and molecular and cell biology), and the appendix contains a catalogue of ‘key molecular components’ (genes, transcription factor, families, inducing factor families, cytoskeleton, cell adhesion molecules, and extracellular matrix components); however, no standard theory or group of models provides a theoretical scaffolding to the book nor is any mentioned. (shrink)

To understand how complex dynamic systems, living or non-living, linguistic or non-linguistic, come to be organized as systems, to understand how their inherent dynamic nature gives rise to organisations and forms that have found a balance between potentiality for change and evolution on the one hand, and requisite stability in a given environment on the other, is the main ambition of the study of evolutionary systems. The aim of the present volume is to elucidate the scientific and philosophical backgrounds that (...) play a role in one of the major debates taking place in that field, namely that on the relation between selection and self-organization. The book represents a genuine interdisciplinary forum in which the major representatives of evolutionary systems take part. Audience: This volume will be interest to biologists, philosophers of science, systems scientists, mathematicians, physicists, sociologists of science. It is highly recommended to those interested in an interdisciplinary and complex approach to evolution, as well as to those interested in developing a genuinely historical viewpoint in the sciences. (shrink)

In this article an epistemological framework is proposed in order to integrate the emergentist thought with systemic studies on biological autonomy, which are focused on the role of organization. Particular attention will be paid to the role of the observer’s activity, especially: (a) the different operations he performs in order to identify the pertinent elements at each descriptive level, and (b) the relationships between the different models he builds from them. According to the approach sustained here, organization (...) will be considered as the result of a specific operation of identification of the relational properties of the functional components of a system, which do not necessarily coincide with the intrinsic properties of its structural constituents. Also, an epistemological notion of emergence—that of “complex emergence”—will be introduced, which can be defined as the insufficiency, even in principle, of a single descriptive modality to provide a complete description of certain classes of systems. This integrative framework will allow us to deal with two issues in biological and emergentist studies: (1) distinguishing the autonomy proper of living systems from some physical processes like those of structural stability and pattern generation, and (2) reconsidering the notion of downward causation not as a direct or indirect influence of the whole on its parts, but instead as an epistemological problem of interaction between descriptive domains in which the concept of organization proposed and the observational operations related to it play a crucial role. (shrink)

In this paper, I argue that starting with the organelles that constitute a cell – and continuing up the hierarchy of components in processes and subsystems of an organism – there are clear instances of emergent biological phenomena that can be considered “living” entities. These components and their attending processes are living emergent phenomena because of the way in which the components are organized to maintain homeostasis of the organism at the various levels in the hierarchy. I call this (...) view the homeostatic organization view of biological phenomena and, as is shown, it comports well with the standard philosophical accounts of nomological emergence and representational emergence. To proffer HOV, I describe properties of biological entities that include internal-hierarchical data exchange, data selectivity, informational integration, and environmental-organismic information exchange. Further, a distinction is drawn between particularized homeostasis and generalized homeostasis, and I argue that because the various processes and subsystems of an organism are functioning properly in their internal environments , the organism is able to exist as a hierarchically-organized entity in some environment external to it . Stated simply: that components of biological phenomena are organized to perform some function resulting in homeostasis marks them out to be living emergent entities distinguishable, in description and in reality, from the very physico-chemical processes of which they are composed. (shrink)

The philosophical foundations of the theory of molecular self-organization (TMS) are reconstructed and compared with the explicit methodological statements made by occasions by its author(s). Special attention is paid to those philosophical fundamentals of TMS which can turn out helpful in answering the question evoking vivid discussions in the philosophy of nature of the recent decades: whether it is possible to search for a physico-chemical explanation of the genesis of life and at the same time defend its specific character. (...) In other words: do the latest findings in self-organization of prebiological molecules allow to overcome the traditional disjunction “either physics or evolution” and to replace it with the conjunction “physics and evolution”? (shrink)

Despite its pervasiveness, the concept of ‘levels of organization’ has received relatively little attention in its own right. I propose here an emerging approach that posits ‘levels’ as a fragmentary concept situated within an interest-relative matrix of operational usage within scientific practice. To this end I propose one important component of meaning, namely the epistemic goal motivating the term’s usage, which recovers a remarkably conserved and sufficiently unifying significance attributable to ‘levels’ across different instances of usage. This epistemic goal, (...) to provide structure to scientific problems, delegates tasks whose execution generates the term’s expressed content in a given instance. This treatment of levels does not diminish the concept’s general importance to science, but rather allows for its use in, and usefulness for, scientific practice to be better contextualized to particular tasks encompassing varying breadths of activity. (shrink)

Apparently factual disagreement on the level(s) at which selection operates often results from different interpretations of the term selection. Attempts to resolve terminological problems must come to grips with a dilemma: a narrow interpretation of selection may lead to a restricted view on evolution; a broader, less precise, definition may wrongly suggest that selection is the centre of a unified, integrated theory of evolution. Different concepts of selection, therefore, should carefully be kept apart.

Apparently factual disagreement on the level at which selection operates often results from different interpretations of the term “selection”. Attempts to resolve terminological problems must come to grips with a dilemma: a narrow interpretation of “selection” may lead to a restricted view on evolution; a broader, less precise, definition may wrongly suggest that “selection” is the centre of a unified, integrated theory of evolution. Different concepts of selection, therefore, should carefully be kept apart.

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)

This paper argues that biological organisation can be legitimately conceived of as an intrinsically teleological causal regime. The core of the argument consists in establishing a connection between organisation and teleology through the concept of self-determination: biological organisation determines itself in the sense that the effects of its activity contribute to determine its own conditions of existence. We suggest that not any kind of circular regime realises self-determination, which should be specifically understood as self-constraint: in biological systems, (...) in particular, self-constraint takes the form of closure, i.e. a network of mutually dependent constitutive constraints. We then explore the occurrence of intrinsic teleology in the biological domain and beyond. On the one hand, the organisational account might possibly concede that supra-organismal biological systems could realise closure, and hence be teleological. On the other hand, the realisation of closure beyond the biological realm appears to be highly unlikely. In turn, the occurrence of simpler forms of self-determination remains a controversial issue, in particular with respect to the case of self-organising dissipative systems. (shrink)

This selective review explores biologically inspired learning as a model for intelligent robot control and sensing technology on the basis of specific examples. Hebbian synaptic learning is discussed as a functionally relevant model for machine learning and intelligence, as explained on the basis of examples from the highly plastic biological neural networks of invertebrates and vertebrates. Its potential for adaptive learning and control without supervision, the generation of functional complexity, and control architectures based on self-organization is brought forward. (...) Learning without prior knowledge based on excitatory and inhibitory neural mechanisms accounts for the process through which survival-relevant or task-relevant representations are either reinforced or suppressed. The basic mechanisms of unsupervised biological learning drive synaptic plasticity and adaptation for behavioral success in living brains with different levels of complexity. The insights collected here point toward the Hebbian model as a choice solution for “intelligent” robotics and sensor systems. Keywords: Hebbian learning; synaptic plasticity; neural networks; self-organization; brain; reinforcement; sensory processing; robot control . (shrink)

Our aim in this article is to attempt to discuss propagating organization of process, a poorly articulated union of matter, energy, work, constraints and that vexed concept, “information”, which unite in far from equilibrium living physical systems. Our hope is to stimulate discussions by philosophers of biology and biologists to further clarify the concepts we discuss here. We place our discussion in the broad context of a “general biology”, properties that might well be found in life anywhere in the (...) cosmos, freed from the specific examples of terrestrial life after 3.8 billion years of evolution. By placing the discussion in this wider, if still hypothetical, context, we also try to place in context some of the extant discussion of information as intimately related to DNA, RNA and protein transcription and translation processes. While characteristic of current terrestrial life, there are no compelling grounds to suppose the same mechanisms would be involved in any life form able to evolve by heritable variation and natural selection. In turn, this allows us to discuss at least briefly, the focus of much of the philosophy of biology on population genetics, which, of course, assumes DNA, RNA, proteins, and other features of terrestrial life. Presumably, evolution by natural selection—and perhaps self-organization—could occur on many worlds via different causal mechanisms. Here we seek a non-reductionist explanation for the synthesis, accumulation, and propagation of information, work, and constraint, which we hope will provide some insight into both the biotic and abiotic universe, in terms of both molecular self reproduction and the basic work energy cycle where work is the constrained release of energy into a few degrees of freedom. The typical requirement for work itself is to construct those very constraints on the release of energy that then constitute further work. Information creation, we argue, arises in two ways: first information as natural selection assembling the very constraints on the release of energy that then constitutes work and the propagation of organization. Second, information in a more extended sense is “semiotic”, that is about the world or internal state of the organism and requires appropriate response. The idea is to combine ideas from biology, physics, and computer science, to formulate explanatory hypotheses on how information can be captured and rendered in the expected physical manifestation, which can then participate in the propagation of the organization of process in the expected biological work cycles to create the diversity in our observable biosphere. Our conclusions, to date, of this enquiry suggest a foundation which views information as the construction of constraints, which, in their physical manifestation, partially underlie the processes of evolution to dynamically determine the fitness of organisms within the context of a biotic universe. (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)

The main purpose of the present chapter is to argue in favor of the claim that, contrary to what is usually and tacitly assumed, organization is not necessary for organicism. To this purpose, I first set up the stage by providing a working characterization of organicism that involves two free parameters, whose variations allow for covering the rich and diverse conceptual landscape of organicism, past and present. In particular, I contend that organization is usually construed as a “mean (...) to an end” notion, or as a tool put at the service of vindicating organicism’s twofold defining assumption, namely, that organisms are determinative entities in their own right, to the effect that (organismic) biology is epistemologically autonomous from physico-chemistry. After a short detour devoted to show that organicism generally collapses on a spectrum of variants of emergentism, I take inspiration from a recent account of emergence called “transformational emergence” to put forward a transformational version of organicism. For such a version meets organicism’s defining standards in a way that is free of any commitment to organization, arguing for its very conceptual soundness finally allows for legitimizing the claim that organicism doesn’t really need organization. (shrink)

Reductionism encompasses a set of ontological, epistemological, and methodological claims about the relation of different scientific domains. The basic question of reduction is whether the properties, concepts, explanations, or methods from one scientific domain (typically at higher levels of organization) can be deduced from or explained by the properties, concepts, explanations, or methods from another domain of science (typically one about lower levels of organization). Reduction is germane to a variety of issues in philosophy of science, including the (...) structure of scientific theories, the relations between different scientific disciplines, the nature of explanation, the diversity of methodology, and the very idea of theoretical progress, as well as to numerous topics in metaphysics and philosophy of mind, such as emergence, mereology, and supervenience. (shrink)

In contrast to the “normativist” view, “naturalist” theorists claim that the concept of health refers to natural or normal states and propose different characterizations of healthy and diseased conditions that are meant to be objectivist and biologically grounded. In this article, we examine the core concept of these naturalist accounts of disease, i.e., the concept of biological malfunction, and develop a new formulation of the notion of malfunction following the recent organizational approach to functions in the philosophy of biology. (...) We focus on the notions of adaptive regulation and functional presupposition to develop a new conceptual framework that justifies the ascription of malfunctional behaviors to biological systems according to the embodied normativity of biological organizations. (shrink)

Systems Biology and the Modern Synthesis are recent versions of two classical biological paradigms that are known as structuralism and functionalism, or internalism and externalism. According to functionalism (or externalism), living matter is a fundamentally passive entity that owes its organization to external forces (functions that shape organs) or to an external organizing agent (natural selection). Structuralism (or internalism), is the view that living matter is an intrinsically active entity that is capable of organizing itself from within, with (...) purely internal processes that are based on mathematical principles and physical laws. At the molecular level, the basic mechanism of the Modern Synthesis is molecular copying, the process that leads in the short run to heredity and in the long run to natural selection. The basic mechanism of Systems Biology, instead, is self-assembly, the process by which many supramolecular structures are formed by the spontaneous aggregation of their components. In addition to molecular copying and self-assembly, however, molecular biology has uncovered also a third great mechanism at the heart of life. The existence of the genetic code and of many other organic codes in Nature tells us that molecular coding is a biological reality and we need therefore a framework that accounts for it. This framework is Code biology, the study of the codes of life, a new field of research that brings to light an entirely new dimension of the living world and gives us a completely new understanding of the origin and the evolution of life. (shrink)