The aim of this book is to show how supramolecular complexity of cell organization can dramatically alter the functions of individual macromolecules within a cell. The emergence of new functions which appear as a consequence of supramolecular complexity, is explained in terms of physical chemistry. The book is interdisciplinary, at the border between cell biochemistry, physics and physical chemistry. This interdisciplinarity does not result in the use of physical techniques but from the use of physical concepts to study (...) class='Hi'>biological problems. In the domain of complexity studies, most works are purely theoretical or based on computer simulation. The present book is partly theoretical, partly experimental and theory is always based on experimental results. Moreover, the book encompasses in a unified manner the dynamic aspects of many different biological fields ranging from dynamics to pattern emergence in a young embryo. The volume puts emphasis on dynamic physical studies of biological events. It also develops, in a unified perspective, this new interdisciplinary approach of various important problems of cell biology and chemistry, ranging from enzyme dynamics to pattern formation during embryo development, thus paving the way to what may become a central issue of future biology. (shrink)

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)

In this paper, I discuss the neo-Aristotelian approaches, which usually reinterpret Aristotle’s ideas on form and/or borrow the notion of formal cause without engaging with the broader implications of Aristotle’s metaphysics. In opposition to these approaches, I claim that biosemiotics can propose an alternative view on life’s form. Specifically, I examine the proposals to replace the formal cause with gene-centrism, functionalism, and structuralism. After critically addressing these approaches, I discuss the problems of reconciling Aristotelianism with the modern view of life’s (...) organization. I claim that the notion of the final cause proposes a cosmological hierarchy and that this is the main problem with applying the formal cause to biology. An alternative categorization of conceptualizing life’s form involves the processual identity, relational property clusters, and context-dependent transmission of representational units. The third category points to a semiotic basis of the form of life. In this context, I offer to readjust the focus of the problem of matter-form duality by pointing out that form is primarily an issue of the subject-object relation. Biosemiotics helps to understand the constructive role of symbolic representation in living systems, which is crucial to extend the analysis of the form from cognitive representations to external phenomena. Emergence of subjectivity and perspectivity of interactions are key elements to bridge the form and actual processes within a non-hylomorphic account. To demonstrate transitions from the physical influence of shapes to the organic recognition of forms, I address the biological studies on the synchronization of coincidental inputs and enzyme specificity. (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 article argues that the basic account of mechanism and mechanistic explanation, involving sequential execution of qualitatively characterized operations, is itself insufficient to explain biological phenomena such as the capacity of living organisms to maintain themselves as systems distinct from their environment. This capacity depends on cyclic organization, including positive and negative feedback loops, which can generate complex dynamics. Understanding cyclically organized mechanisms with complex dynamics requires coordinating research directed at decomposing mechanisms into parts and operations with research (...) using computational models to recompose mechanisms and determine their dynamic behavior. This coordinated endeavor yields dynamic mechanistic explanations. (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)

Enzymes are remarkable molecules which make metabolism possible. Their processing powers are considerable for not only are they catalysts they also contribute to information processing, integration, coherence and memory in the cell. This complex of attributes suggests that a complementary perspective to enzyme nature and activity is needed related to what enzymes and verbs have in common. The value of this kind of thinking is that it shifts the focus from objects and mechanisms to processes and information. In (...) order to support this idea a number of features which enzymes and verbs share are discussed including, context-dependence, occurrence, cases, voice, mood and glue/integrative capacities. The paper concludes with some reflections on the utility of a view of enzymes as verbs. (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)

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)

The aim of this paper is to compare various methods for the quantification of metabolic pathways dynamics. A Yates-Pardee metabolic pathway with enzyme organization, i.e. with spatial localization of the enzymes in a specific cellular compartment, was studied using: (i) the classical Henri-Michaelis-Menten (HMM) equations, (ii) linearization of the HMM equations in the vicinity of a steady state (linearized formalism), and (iii) Biochemical Systems Theory formalism (BST formalism). It is shown that transient solutions computed via either the linearized (...) formalism or the BST formalism can greatly differ from transient solutions computed with the HMM equations. However, in the studied example, results remain qualitatively the same for the three formalisms. This suggests that the study of the topology of the system may give useful insights into the metabolic pathways dynamics. (shrink)

Emergent properties have been described by Mill, Lewes, Broad, Morgan and others, as novel, nonadditive, nonpredictable and nondeducible within a hierarchical context. I have developed a more definitive concept of a hierarchy that can be used to inspect the phenomenon of emergence in a new and detailed manner. A hierarchy is held together by descending constraints and new features can arise when an upper level entity restrains its components in new combinations that are not expected when viewing these components alone. (...) Examples of emergent features are matching anticodons and amino acids by aminoacetyl-tRNA synthetase enzymes appearing early among the first forms of life, negative feedback in end-product inhibition first occurring in microbes, memory in animals and apical cells in plants. Until recently, life was considered only in terms of physics and chemistry, but now it is known to have a third aspect of information that along with the descendant constraints in its hierarchical organization makes emergentism possible within a reductionist’s framework. (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)

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)

The Darwinian concept of natural selection was conceived within a set of Newtonian background assumptions about systems dynamics. Mendelian genetics at first did not sit well with the gradualist assumptions of the Darwinian theory. Eventually, however, Mendelism and Darwinism were fused by reformulating natural selection in statistical terms. This reflected a shift to a more probabilistic set of background assumptions based upon Boltzmannian systems dynamics. Recent developments in molecular genetics and paleontology have put pressure on Darwinism once again. Current work (...) on self-organizing systems may provide a stimulus not only for increased problem solving within the Darwinian tradition, especially with respect to origins of life, developmental genetics, phylogenetic pattern, and energy-flow ecology, but for deeper understanding of the very phenomenon of natural selection itself. Since self-organizational phenomena depend deeply on stochastic processes, self-organizational systems dynamics advance the probability revolution. In our view, natural selection is an emergent phenomenon of physical and chemical selection. These developments suggest that natural selection may be grounded in physical law more deeply than is allowed by advocates of the autonomy of biology, while still making it possible to deny, with autonomists, that evolutionary explanations can be modeled in terms of a deductive relationship between laws and cases. We explore the relationship between, chance, self-organization, and selection as sources of order in biological systems in order to make these points. (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)

Over the last two decades there has been a significant increase of interest in Schelling’s philosophy, and in particular his philosophy of nature. However, even the most generous of Schelling’s interpreters are confused by one of Schelling’s key theses: his view that nature as a whole (including non-living nature) is “organized,” and his related rejection of the hard-and-fast distinction between living and non-living. My aim is to offer an explanation of these two related points. Given that Schelling regards all of (...) nature as organized, it makes most sense to begin with the basic stuff of nature—matter. For if we can understand how matter can be organized, then we can also understand how non-living material beings are also organized. Accordingly, I focus on Schelling’s first work in the philosophy of nature, the 1797 Ideen zu einer Philosophie der Natur (Ideas for a Philosophy of Nature), where he deals with matter most directly and challenges mechanistic accounts of matter. I show that the crucial influence on the Ideen was not (as many interpretations have it) Fichte, but Kant, and explicate how and why Schelling departs from Kant’s understanding of both matter and organization. Finally, I will briefly point to the ways in which Schelling’s understanding of organization can be brought to bear on current questions in theoretical biology. (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 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)

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)

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)

The primary method by which science endeavors to order the world is the analytic approach, consistent with Cartesian principles of dividing the problem in as many sections as required for an optimal solution, and progressing from the simplest to the most complex reasoning. When the interactions among the various elements of the system being studied are minimal, such a procedure indeed makes it possible to formulate laws that describe chains of causality. However, when the variables are interdependent and linked by (...) non-linear equations, the atomistic method cannot account for the phenomenon in its entirety. Spurred by this inadequacy, scientists sought to discover synthetic methods which, early in the twentieth century, led to the conceptualization of holistic theories in a number of disciplines. The most highly developed fields are the psychology of form, structural anthropology (1), and the various systems theories (2). More recently, the development of epigenetic concepts in biology has corresponded to the appearance of different theories of pattern in physics and mathematics (3, 4) and to the progressive emergence of the concept of self-organization (5, 6, 7). The objective is to explain the production of complex structures on the basis of interacting elements, none of which contains a guiding scheme that dictates these structures. In biology, the challenge is to locate the constraints that are expressed in a space of possibilities (8) in order to develop a theory of organization that is capable of predicting the finite number of forms that living creatures can assume (9). This school of thought can be described as structuralist, emergentist, self-organizational, or epigeneticist, depending on the theoretical version that is emphasized. (shrink)

Biology lacks a central organism concept that unambiguously marks the distinction between organism and non-organism because the most important questions about organisms do not depend on this concept. I argue that the two main ways to discover useful biological generalizations about multicellular organization--the study of homology within multicellular lineages and of convergent evolution across lineages in which multicellularity has been independently established--do not require what would have to be a stipulative sharpening of an organism concept.

The paper draws a parallel between natural language symbols and the symbolic mode in living systems. The inextricability of symbols and the dynamics with which they are functionally related shows that much of their structuring is due to dynamics and self-organization. It is also stressed that important factors that determine the shape of language structure lie outside individual mind/brains and they draw on time-scales quite different from those of phenomenological experience. Analysis of language into units and subsystems is thus (...) not straightforward, since they show functionality on many levels and many time-scales. Finally it is recognized that, as a specific and specialized system of inter-individual coordination, natural language is many hierarchical levels away form simpler forms of information transmission in biological systems. (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)

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)

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)

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)

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)

An apparent conflict between preferences for hierarchical as opposed to distributed organizations is evident in arguments about disciplinary and interdisciplinary organization. It characterizes as well a wide array of other arenas ranging from the biological to the political. In this article, parallels between biological, neurobiological, and social observations are explored in an effort to outline a general approach that may be useful in thinking about interdisciplinary and transdisciplinary activities as well as forms of social organization in (...) general. A key element in the approach is an ongoing individual and collective process of story creation, sharing, and revising. The article is offered both as a contribution to better understanding interdisciplinary and transdisciplinary work and as an illustrative example of the potentials and problems of such work. (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)

I claim that explanations of human behaviour by Edward O. Wilsonand Charles Lumsden are constituted by a religiously functioningmetaphysics: emergent materialism. The constitutive effects areidentified using six criteria, beginning with a metaphorical re-description of dissimilarities between levels of organization interms of the lower level, and consist of conceptual andexplanatory reductions (CER). Wilson and Lumsden practice CER,even though CER is not required by emergent materialism. Theypreconceive this practice by a re-description which conflates thelevels of organization and explain failure of (...) CER in terms oftechnical, not ontological or epistemological reasons. Iinterpret these three practices as a reaction of Wilson againsthis early Christian religious beliefs. Statements by Wilsonindicate this reaction ultimately constitutes his explanations ofsocial, moral and religious behaviour.Tested knowledge about matter at the lower level functions as ametaphysical belief when applied to the higher level becausethere it is untested. I offer twelve criteria for the diagnosisof religious functions of this metaphysical materialism, five ofwhich are satisfied. I show that the constitutive effects of thismaterialism in sociobiology are due to its religious functions,are beneficial for science and do not destroy its public nature. (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 article describes how empirical discoveries in the 1930s–1950s regarding population variation for chromosomal inversions affected Theodosius Dobzhansky and Richard Goldschmidt. A significant fraction of the empirical work I discuss was done by Dobzhansky and his coworkers; Goldschmidt was an astute interpreter, with strong and unusual commitments. I argue that both belong to a mechanistic tradition in genetics, concerned with the effects of chromosomal organization and systems on the inheritance patterns of species. Their different trajectories illustrate how scientists’ commitments (...) affect how they interpret new evidence and adjust to it. Dobzhansky was moved to revised views about selection, while Goldschmidt moved his attention to different genetic phenomena. However different, there are significant connections between the two that enrich our understanding of their views. I focus on two: the role of developmental considerations in Dobzhansky’s thought and the role of neutrality and drift in Goldschmidt’s evolutionary account. Dobzhansky’s struggle with chromosomal variation is not solely about competing schools of thought within the selectionist camp, as insightfully articulated by John Beatty, but also a story of competition between selectionist thinking and developmental perspectives. In contraposition, Goldschmidt emphasized the role of low penetrance mutations that spread neutrally and pointed out that drift could result from developmental canalization. This account adds to the dominant story about Goldschmidt’s resistance to the splitting of development from genetics, as told by Garland Allen and Michael Dietrich. The story I tell illustrates how developmental thinking and genetic thinking conflicted and influenced researchers with different convictions about the significance of chromosomal organization. (shrink)