Autopoiesis 40 years Later. A Review and a Reformulation

The concept of autopoiesis was proposed 40 years ago as a definition of a living being, with the aim of providing a unifying concept for biology. The concept has also been extended to the theory of knowledge and to different areas of the social and behavioral sciences. Given some ambiguities of the original definitions of autopoiesis, the concept has been criticized and has been interpreted in diverse and even contradictory ways, which has prevented its integration into the biological sciences where it originated. Here I present a critical review and conceptual analysis of the definition of autopoiesis, and propose a new definition that is more precise, clear, and concise than the original ones. I argue that the difficulty in understanding the term lies in its refined conceptual subtlety and not, as has been claimed by some authors, because it is a vacuous, trivial or very complex concept. I also relate the concept of autopoiesis to the concepts of closed systems, boundaries, homeostasis, self-reproduction, causal circularity, organization and multicellularity. I show that under my proposed definition the concept of a molecular autopoietic system is a good demarcation criterion of a living being, allowing its general integration into the biological sciences and enhancing its interdisciplinary use.     

Hylomorphism and the Metabolic Closure Conception of Life

This paper examines three exemplary theories of living organization with respect to their common feature of defining life in terms of metabolic closure: autopoiesis, (M, R) systems, and chemoton theory. Metabolic closure is broadly understood to denote the property of organized chemical systems that each component necessary for the maintenance of the system is produced from within the system itself, except for an input of energy. It is argued that two of the theories considered—autopoiesis and (M, R) systems—participate in a hylomorphist pattern of thinking which separates the “form” of the living system from its “matter.” The analysis and critique of hylomorphism found in the work of the philosopher Gilbert Simondon is then applied to these two theories, and on the basis of this critique it is argued that the chemoton model offers a superior theory of minimal life which overcomes many of the problems associated with the other two. Throughout, the relationship between hylomorphism and the understanding of living things as machines is explored. The paper concludes by considering how hylomorphism as a background ontology for theories of life fundamentally influences the way life is defined.     

Environment and individual: a dialectic relationship.

The role of development in current neo-Darwinian evolutionary theory is still underestimated. Only a few experimental and theoretical efforts have been made to bridge the gap, among which the theories of genetic assimilation, stabilising selection and autopoiesis. The relationship between the organism and its environment is a focal point for understanding development. The organism itself determines which environmental features are relevant to it, what represents a stimulus that would trigger its behaviour, and continuously affects the environment through its activities, in a dialectic relationship. Such a relationship is unique and diachronic, changing with time and defining the individual. Development in the broad sense and behavioural plasticity refer to the individual unlike evolution, which refers to populations.     

Dynamic causal models and autopoietic systems

Dynamic Causal Modelling (DCM) and the theory of autopoietic systems are two important conceptual frameworks. In this review, we suggest that they can be combined to answer important questions about self-organising systems like the brain. DCM has been developed recently by the neuroimaging community to explain, using biophysical models, the non-invasive brain imaging data are caused by neural processes. It allows one to ask mechanistic questions about the implementation of cerebral processes. In DCM the parameters of biophysical models are estimated from measured data and the evidence for each model is evaluated. This enables one to test different functional hypotheses (i.e., models) for a given data set. Autopoiesis and related formal theories of biological systems as autonomous machines represent a body of concepts with many successful applications. However, autopoiesis has remained largely theoretical and has not penetrated the empiricism of cognitive neuroscience. In this review, we try to show the connections that exist between DCM and autopoiesis. In particular, we propose a simple modification to standard formulations of DCM that includes autonomous processes. The idea is to exploit the machinery of the system identification of DCMs in neuroimaging to test the face validity of the autopoietic theory applied to neural subsystems. We illustrate the theoretical concepts and their implications for interpreting electroencephalographic signals acquired during amygdala stimulation in an epileptic patient. The results suggest that DCM represents a relevant biophysical approach to brain functional organisation, with a potential that is yet to be fully evaluated.     

Stem cells as probabilistic self-producing entities

Stem cells have the capacity both to self-renew and to give rise to differentiated progeny, and are vital to the organization of multicellular organisms. Stem cells raise a number of fundamental questions regarding lineage restriction and cellular differentiation, and they hold enormous promise for cell-based therapies. Here I propose a theoretical framework for stem cell biology based on the concepts of autopoiesis (self-production) and complementarity. I argue that stem cells are pivotal in the self-production of the organism and that we need complementary approaches to understand their probabilistic behavior. I discuss how this framework generates testable hypotheses regarding stem-cell functions.     

Time reverse automata patterns generated by Spencer-Brown's modulator: invertibility based on autopoiesis

In the present paper the self-consistency or operational closure of autopoiesis is described by introducing time explicitly. It is an extension of Spencer-Brown's idea of time, however. The definition of time is segregated into two parts, corresponding to the syntax and semantics of language, respectively. In this context, time reversibility is defined by the formalization of the relationship between time and self-consistency. This idea has also been discussed in the context of designation and/or naming. Here we will discuss it in the context of cellular automata and explain the structure of one-to-many type mappings. Our approach is the first attempt to extend autopoietic systems in terms of dynamics. It illustrates how to introduce an autopoietic time which looks irreversible, but without the concept of entropy.     

Maladie maniacodépressive et créativité

On the basis of pathological, empirical-statistical and experimental investigations of grand creatives and of normal patients of the manic-depressive spectrum, as well as leaning on my own observations comparing mental states and stiles of behaviour, the relationship between manicdepressive illness and creativity is investigated. With respect to cognitive stiles in manic-depressives as well as in creatives, the significance of tolerance respective intolerance of ambiguity in both groups is particularly informative. The significance of creativity as an autopoiesis in the context of the structuring of identity in manic-depressives not only illuminates the essence of the manic-depressive illness and of creativity, but can also provide us with basics for a therapy oriented to creativity in these patients.     

The autonomy of biological individuals and artificial models

This paper aims to offer an overview of the meaning of autonomy for biological individuals and artificial models rooted in a specific perspective that pays attention to the historical and structural aspects of its origins and evolution. Taking autopoiesis and the recursivity characteristic of its circular logic as a starting point, we depart from some of its consequences to claim that the theory of autonomy should also take into account historical and structural features. Autonomy should not be considered only in internal or constitutive terms, the largely neglected interactive aspects stemming from it should be equally addressed. Artificial models contribute to get a better understanding of the role of autonomy for life and the varieties of its organization and phenomenological diversity.     

Evolution by epigenesis: farewell to Darwinism, neo- and otherwise.

In the last 25 years, criticism of most theories advanced by Darwin and the neo-Darwinians has increased considerably, and so did their defense. Darwinism has become an ideology, while the most significant theories of Darwin were proven unsupportable. The critics advanced other theories instead of 'natural selection' and the survival of the fittest'. 'Saltatory ontogeny' and 'epigenesis' are such new theories proposed to explain how variations in ontogeny and novelties in evolution are created. They are reviewed again in the present essay that also tries to explain how Darwinians, artificially kept dominant in academia and in granting agencies, are preventing their acceptance. Epigenesis, the mechanism of ontogenies, creates in every generation alternative variations in a saltatory way that enable the organisms to survive in the changing environments as either altricial or precocial forms. The constant production of two such forms and their survival in different environments makes it possible, over a sequence of generations, to introduce changes and establish novelties--the true phenomena of evolution. The saltatory units of evolution remain far-from-stable structures capable of self-organization and self-maintenance (autopoiesis).     

Some aspects of interrelations between ants (Hymenoptera,Formicidae) and polistine wasps (Hymenoptera,Vespidae)

Embodied, situated and enactive aspects of relationships of polistine wasps with ants are considered within the framework of the theory of autopoiesis. The idea of the embodied interaction implies specific nestbuilding and protective behavior in polistine wasps. The paper examines the adaptive role of applying ant repellent on the petiole and nest and the latitude gradient of such behavior in re-social wasp species. The situated interaction is considered in the environmental context: the mortality of Polistes gallicus (L.) colonies as a result of predatory attacks of ants Myrmica bergi Ruzsky is analyzed in the Lower Dnieper basin (Ukraine). The enactive interaction includes both spontaneous autonomous activity of its participants as a result of self-organization and specific features of the spatial structure of the prey’s population forming under the impact of the predator. The applicability of some “predator-prey” models is discussed.     

From the mechanical complexity in biology

From the mechanical complexity in biology. Through history, each century has brought new discoveries and beliefs that have resulted in different perspectives to study life organisms. In this essay, 1 define three periods: in the first, organisms were studied in the context of their environment, in the second, on the basis of physical and chemical laws, and on the third, systemically. My analysis starts with primitive humans, continues to Aristoteles and Newton, Lamarck and Darwin, the DNA doble helix discovery, and the beginnings of reduccionism in science. I propose that life is paradigmatical, that it obeys physical and chemical laws but cannot be explained by them I review the systemic theory, autopoiesis, discipative structures and non- linear dynamics. 1 propose that the deterministic, lineal and quantitative paradigm of nature are not the only way to study nature and invite the reader to explore the complexity paradigm.     

Autogenesis: the evolution of replicative systems

Questions concerning the nature and origin of living systems and the hierarchy of their evolutionary processes are considered, and several problems which arise in connection with formerly developed theories--the autopoiesis of Maturana & Varela, the POL theory of Haukioja and the earlier developed evolutionary theory of Csányi--are discussed. The organization of living systems, the use of informational terms and the question how reproduction can enter into their characterization, problems of autonomy and identity are included in the list. It is suggested that replication--a copying process achieved by a special network of interrelatedness of components and component-producing processes that produces the same network as that which produced them--characterizes the living organization. The information "used" in this copying process, whether it is stored by special means or distributed in the whole system, is called replicative information. A theoretical model is introduced for the spontaneous emergence of replicative organization, called autogenesis. Autogenesis commences in a system by an organized "small" subsystem, referred to as AutoGenetic System Precursor (AGSP), which conveys replicative information to the system. During autogenesis, replicative information increases in system and compartment(s) form. A compartment is the co-replicating totality of components. The end state of autogenesis is an invariantly self-replicating organization which is unable to undergo further intrinsic organizational changes. It is suggested that replicative unities--such as living organisms--evolve via autogenesis. Levels of evolution emerge as a consequence of the relative autonomy of the autogenetic unities. On the next level they can be considered as components endowed with functions and a new autogenetic process can commence. Thus evolution proceeds towards its end state through the parallel autogenesis of the various levels. In terms of applications, ontogenesis is dealt with in detail as an autogenetic process as is the autogenesis of the biosphere and the global system.     

The microbial experience of environmental phosphate fluctuations. An essay on the possibility of putting intentions into cell biochemistry

We present a model of microbial information processing that contains characteristic features of the phenomenon of physiological adaptation. The backbone of the model is the "adaptive event" in which energy-converting subsystems of the cell interact with the changing environment. In this process, the subsystems pass, via an adaptive operation mode, from one adapted state to the next. An adaptive operation mode takes place when an adapted state is disturbed by an environmental alteration. These two manifestations of an adaptive event were differently treated in the simulation, based on an application of linear irreversible thermodynamics to the energy transduction of adaptive subsystems. In adapted states, the conductivity coefficients of the flow-force relationships employed remained constant, whereas during an adaptive operation mode, these coefficients were altered in a directional manner during the simulation. An example dealing with the complex relationship between phosphate uptake and cyanobacterial growth is given. In this example, the simulation of adapted states of two subsystems of the incorporating machinery, namely the phosphate carrier in the cell membrane and the F-ATPase in the thylakoid membrane, was in accordance with the measured uptake kinetics, and when fixed, predetermined conductivity coefficients were used. In the adaptive operation mode, however, the simulated behavior was in agreement with experimental observations when the program was able to "interpret" its own performance in the light of environmental phosphate fluctuations, experienced by the cell in the past, and to reconstruct the two subsystems according to this interpretation. Via transitions between adapted states and adaptive modes, information is transferred from one adaptive event to the next: the latter "inherits" the results of former interpretations. By appropriating them selectively, it is entering into a future in which its own interpretation is passed on to the following adaptive event. The model is discussed with respect to the concept of autopoiesis.     

Autopoiesis and Interpretive Semiosis

Translation has long been viewed as ‘code-switching’ either within or between languages. Hence, most translation discussions center on its linguistic and cultural aspects. However, the fundamental mechanism of ‘translation as interpretative semiosis’ has yet to be studied with appropriate rigor. Susan Petrilli (2008) has identified ‘iconicity’ as the key that enables translative semiosis. Nevertheless, as her model is restricted to a discussion of literary translation activity in verbal sign systems, a fundamental mechanism to explain translation as interpretative semiosis is still needed. By analyzing the interactions between the source sign (the translated) and the target sign (the translatant) in the translating process, it can be discerned that Humberto Maturana’s notion of autopoiesis may provide some crucial insights into translative semiosis. By identifying the autopoietic nature of translation, that is, the interlocked structural coupling between the Translated and Translatant, translation is no longer the ‘one-to-one-correspondence’ between sign systems, but rather a recursive process of interpretation—an interpretive semiosis. Moreover, it is by this autopoietic, self-productive mechanism of translation that I would suggest translation becomes a recursive generation of new inter-connections between semiotics systems.     

Autonomy: an information theoretic perspective

We present a tentative proposal for a quantitative measure of autonomy. This is something that, surprisingly, is rarely found in the literature, even though autonomy is considered to be a basic concept in many disciplines, including artificial life. We work in an information theoretic setting for which the distinction between system and environment is the starting point. As a first measure for autonomy, we propose the conditional mutual information between consecutive states of the system conditioned on the history of the environment. This works well when the system cannot influence the environment at all and the environment does not interact synergetically with the system. When, in contrast, the system has full control over its environment, we should instead neglect the environment history and simply take the mutual information between consecutive system states as a measure of autonomy. In the case of mutual interaction between system and environment there remains an ambiguity regarding whether system or environment has caused observed correlations. If the interaction structure of the system is known, we define a "causal" autonomy measure which allows this ambiguity to be resolved. Synergetic interactions still pose a problem since in this case causation cannot be attributed to the system or the environment alone. Moreover, our analysis reveals some subtle facets of the concept of autonomy, in particular with respect to the seemingly innocent system-environment distinction we took for granted, and raises the issue of the attribution of control, i.e. the responsibility for observed effects. To further explore these issues, we evaluate our autonomy measure for simple automata, an agent moving in space, gliders in the game of life, and the tessellation automaton for autopoiesis of Varela et al. [Varela, F.J., Maturana, H.R., Uribe, R., 1974. Autopoiesis: the organization of living systems, its characterization and a model. BioSystems 5, 187-196].     

Lipid-cholesterol interactions. Monte Carlo simulations and theory.

Results of Monte Carlo calculations of order parameter profiles of lipid chains interacting with cholesterol are presented. Cholesterol concentrations in the simulations are sufficiently large that it is possible to analyze profiles for chains which are near neighbors of two or more cholesterol molecules, chains which are neighbors to a single cholesterol, and chains which are not near any cholesterol molecules. The profiles, show that cholesterol acts to significantly decrease the ability of neighboring chains to undergo trans-gauche isomeric rotations, although these chains are not all forced into all-trans conformations. The effect is significantly greater for chains which are neighbors to more than one cholesterol. The Monte Carlo results are next used as a guide to develop a theoretical model for lipid-cholesterol mixtures. The properties of this model and the phase diagram which it predicts are described. The phase diagram is then compared with experimentally determined phase diagrams. The model calculations and the computer simulations upon which they are based yield a molecular mechanism for several of the observed phases exhibited by lipid-cholesterol mixtures. The theoretical model predicts that at low temperatures the system should exhibit solid phase immiscibility.