This paper is the first one of a series devoted to the analysis of metabolic networks. Its aim is to establish the theoretical framework for this analysis. Two different lines of research are considered: the one about metabolism-repair systems ((M, R), introduced by Robert Rosen as an abstract representation of cell metabolic activity, and the concept of autopoiesis developed by Humberto Maturana and Francisco Varela. Both concepts have been recently connected by Letelier et al., determining that the set of autopoietic systems is a subset of the set of general abstract (M, R) systems. In fact, every specific (M, R) system is an autopoietic one, being the boundary, which specifies each system as a unity, the main element of autopoietic systems which is not formalized in Rosen’s representation. This paper introduces the definition of boundary – a physical boundary and a functional one – for (M, R) systems in the context of a representation using category theory. The concept of complete (M, R) system is also introduced by means of a process of completion in categories which is functorial, natural and universal.

Key words: (m, r) systems, autopoiesis, relational biology, metabolic networks, theory of categories.

A formalization, computerization and extension of the original Varela-Maturana-Uribe model of autopoiesis is presented. Autopoietic systems are driven by sets of simple “rules” which guide the behavior of components in a given milieu. These rules are capable of producing systemic structures that are far more complex than we could ever achieve by a direct arrangement of components, i.e., by a method of systems analysis and design. The study of autopoietic systems indicates that the traditional emphasis on internal qualities of a system’s components has been misplaced. It is the organization of components, rather than the components themselves (or their structural manifestations), that provides the necessary and sufficient conditions of autopoiesis and thus of life itself. The dynamic autonomy of autopoietic systems contrasts significantly with non-autonomous, allopoietic mechanistic systems. Relevance: This paper discusses the theory of autopoietic systems based on the work of Maturana, Varela and Uribe.

An alternative view of the emergence of “living” systems and a special concept of “life” itself are advanced here. We assume that the first “living” things must have emerged from “non-living” ones. There is no escaping from this simple logic. The transformation from non-life to life must have been natural, long and evolutionary – certainly not sudden, like a bolt of lightning. The key is autopoiesis – the cyclical and unity-maintaining organization of even the simplest, inorganic components that may lead to the initial auto-organization of life, or autogenesis. Living organisms are complex composites of both organic and inorganic elements. Nature does not make such distinctions, only some men do. By means of absorption and adsorption of primordial monomers, under the favorable thermodynamic conditions of the vast tidal zones, the autopoietic biomatrix and its self-renewing structures were gradually transformed from predominantly inorganic-molecular to mostly organic-polymeric. Continually, they spilled out into the waters from myriads of sources, and started on their parallel, predifferentiated evolutionary paths. Relevance: This paper discusses the theory of autopoietic systems based on the work of Maturana, Varela and Uribe.

First paragraph: Readers working their way through this volume will learn about autopoiesis from 15 different expositions, including those of the very creators of the concept: Maturana, Varela, and Uribe. But experience shows that a careful tutorial orientation, before a plunge into the articles themselves, can go a long way toward providing a framework for understanding. One acquires a template, a point of reference, and the subsequent reading and study can take place in a directed, selective, and therefore creative way. Relevance: This paper is an introduction to the concept of autopoiesis, discusses the basic concepts of its definition, presents a computer model, and offers an annotated bibliography.

Key words: Autopoiesis, computer modeling

All living systems, e.g., cells, organisms, groups, and species (including humans) are tied together in communication networks (social systems) as well as into a hypernetwork of all social systems. Their interaction forms the entire terrestrial biosphere or Gaia, a social system akin to the unified organism of a living cell, which itself is a social system of its constitutive organelles. Connecting different species into a coherent, interactive, and self-organizing system cannot happen without death and birth (autopoiesis) – the fuel of environmental adaptation. The natural death of species does not signal maladaptability of the species, but harmony, adaptability, and systemic perseverance of the social network of species. Death is a cosmological event – the most exquisite assurance of life yet to be. Relevance: This paper strongly relates to the theory of autopoietic systems based on the work of Maturana, Varela and Uribe.

Every organism, even if temporarily isolated, can emerge, survive, and reproduce only as part of a larger societal network of organisms. Similarly, any cell, organelle, or neuron can exist only as part of a group or society of cells, organelles, or neurons. Each component of an autopoietic system can emerge, persist, and reproduce only within the complex of relationships that constitute the network of interconnected components and component-producing processes. Before any organism can reproduce, it must first be produced (or self-produced), and it must survive. Autopoiesis therefore precedes, and in fact creates, the conditions for a subsequent reproduction. Survival activities of individual organisms (economic and ecological) directly form and re-form local societies of interactive populations, which are further concatenated into regional networks and full ecosystems. Reproductive organismic activities can take place only within such preformed networks and thus assure their own (networks’) reinforcement and self-production. In fact, autopoietic systems can, and many do, adapt and evolve without their own reproduction; only their components may reproduce. Social networks are demonstrably biotic systems. Relevance: This paper builds and relates to the theory of autopoietic systems based on the work of Maturana, Varela and Uribe.

A newly emerging organizational mode shifts our thinking from the traditional vertical hierarchy of command to horizontal patterns of market-oriented networks of autonomous agents. This organizational mode is characterized by self-management, autonomy and self-sustainability, the trio of prerequisites for a successful and self-sustainable enterprise. Self-sustainable systems must be autopoietic, i.e., self-producing. They must be capable of producing themselves, not only of producing something else. Employees, managers and community stakeholders are striving to create a self-sustaining organizational milieu by pursuing decisional autonomy, self-management and shared participatory ownership. Like biological “amoebas,” they should adapt to the ever changing circumstances in terms of size, shape, function and interaction. Relevance: This paper builds on the theory of autopoietic systems based on the work of Maturana, Varela and Uribe.

The free-market economy is being continually challenged – by governments, monopolies, “too big to fail” enterprises, global banks and social experimentation. Crisis is still considered to be a failure of the capitalistic system rather than a failure of the politicized state and governmental institutions unable to abstain from interfering with free-market fundamentals. Crisis represents a necessary catharsis which periodically renews and regenerates prevailing business ecology. At the same time, especially with the current crisis, the system is undergoing fundamental transformation, change of paradigm and change of dominant business models. Transformations get naturally confounded with crises. Man’s failure and challenge is that we repeatedly fail to do the catharsis of crisis – without the crisis. Disentangling the phenomena of crisis from those of transformation is the main aim of this paper. We address the issues of unemployment in the post-crisis environment, especially in the U.S. We trace the difficulties to treating the economy as a deterministic machine while it behaves as an adaptive organism. Relevance: It is claimed that the theory of autopoiesis is applicable to social, business and management systems because they are mostly natural, spontaneous, self-organizing and self-equilibrating organisms, not mechanistic contrivances.

Advanced and mature societies are undergoing a fundamental transformation of their economic, political, technological and social lives. Developing countries are rapidly catching on and accelerating their participation in the transformation, which is equally rapidly becoming global. Yet, at the same time, the process of globalization itself is exhibiting signs of a reversal towards relocalization, i.e., rebounding after the strong global outbound of the past fifty years. The change of paradigms and change of dominant business models accompany such transformations. Yet transformations get naturally confounded with ongoing recessions and crises. Disentangling the phenomena of crisis from those of transformation remains a challenge, especially for politicians. In this paper we primarily address the issues of unemployment and the changing nature of employment in mature economies. Relevance: It is claimed that the autopoietic cycle of self-production or self-renewal forms the organization of all living and self-sustaining systems.