The chronology of encoding amino acids in the genetic code, described by the self-referential model, prompted a search for the supporting biosynthesis pathways since the list of abiotic amino acids was not in close coherence with it. The prediction from the chronology was adequately satisfied with the identification of the Glycine-Serine Cycle of assimilation of C1-units. The start of encoding from C1-derived amino acids sits nicely at the fuzzy borders between methylotrophy and autotrophy. It is not possible to envisage the construction of metabolism from simpler nutrients. These indications support the notion that protein synthesis would be at the crux of the metabolic sink, and that metabolism is sink-driven. Relevance: In spite of the many unknowns in the area of the origin of life, it seems that the self-referential model offers a starting point for experimental verification of the formation of genetic codes. In the metabolic aspect, there is no possibility of getting simpler with respect to nutrients in the routes for metabolic contruction.

A biosemiotic view of living things is presented that supersedes the mechanistic view of life prevalent in biology today. Living things are active agents with autonomous subjectivity, whose structure is triadic, consisting of the individual organism, its Umwelt and the society. Sociality inheres in every living thing since the very origin of life on the earth. The temporality of living things is guided by the purpose to live, which works as the semantic boundary condition for the processes of embodiment of the subjectivity. Freedom at the molecular and cellular levels allows autonomy and spontaneity to emerge even in single cell organisms, and the presence of the dimension of mind in every living thing is deduced. Living things transcend their individualness, as they live in historically formed higher order structure consisting of the lineage-species and the society. They also transcend materiality, having the dimension of mind.

Key words: Subjectivity, Sociality, Triadic structure of subjectivity, Purposiveness, Microdynamic structural polymorphism, Freedom at the molecular and cellular levels

The nature of life has been a topic of interest from the earliest of times, and efforts to explain it in mechanistic terms date at least from the 18th century. However, the impressive development of molecular biology since the 1950s has tended to have the question put on one side while biologists explore mechanisms in greater and greater detail, with the result that studies of life as such have been confined to a rather small group of researchers who have ignored one another’s work almost completely, often using quite different terminology to present very similar ideas. Central among these ideas is that of closure, which implies that all of the catalysts needed for an organism to stay alive must be produced by the organism itself, relying on nothing apart from food (and hence chemical energy) from outside. The theories that embody this idea to a greater or less degree are known by a variety of names, including (M, R) systems, autopoiesis, the chemoton, the hypercycle, symbiosis, autocatalytic sets, sysers and RAF sets. These are not all the same, but they are not completely different either, and in this review we examine their similarities and differences, with the aim of working towards the formulation of a unified theory of life. – Highlights: There have been many isolated attempts to define the essentials of life, A major unifying feature is metabolic closure, Metabolic closure requires some molecules to fulfill more than one function, There can be no hierarchy in the overall organization of a living system.

Key words: Origin of life, (M, R) systems, Autopoiesis, Chemoton, Self-organization

Abstract: The notion of autopoiesis, as originally formulated in the seventies by Maturana and Varela, is first reviewed and it is pointed out how this view offers a definition of minimal life which differs in some respect from the more conventional view, which is based on the template recognition mechanism of nucleic acids. The main criterium for autopoiesis is self-maintenance of the autopoietic unity from within its own. Here it is shown, however, that self-reproduction, when it is originated from reactions taking place within the boundary of the autopoietic unity, can also be seen as a criterium for autopoiesis. Examples of self-reproducing micelles are then reviewed and it is discussed to what extent they can be considered as autopoietic unities. One experiment is discussed in some more detail, as it bears a relation with the origin of life: this is the case of caprylate micelles in water which are spontaneously build from the hydrolysis of water-insoluble ethylcaprylate (EC) – once the first micelles are formed, there is a fast autocatalytic hydrolysis of further EC which produces more micelles in a superexponentially accelerated process. The plan for future experiments in the area, e.g. core-and-shell-replication, is there also outlined. It is finally argued that the progress of this work on autopoietic structures, more than on micelles, must be based on vesicles and liposomes, and preliminary work on this field is discussed.

Spherical bounded structures such as those formed by surfactant aggregates (mostly micelles and vesicles), with an inside that is chemically and physically different from the outside medium, can be seen as primitive cell models. As such, they are fundamental structures for the theory of autopoiesis as originally formulated by Varela and Maturana. In particular, since self-reproduction is a very important feature of minimal cellular life, the study of self-reproduction of micelles and vesicles represents a quite challenging bio-mimetic approach. Our laboratory has put much effort in recent years into implementing self-reproduction of vesicles as models for self-reproduction of cellular bounded structures, and this article is a further contribution in this direction. In particular, we deal with the so-called matrix effect of vesicles, related to the fact that when fresh surfactant is added to an aqueous solution containing preformed vesicles of a very narrow size distribution, the newly formed vesicles (instead of being polydisperse, as is usually the case) have dimensions very close to those of the preformed ones. In practice, this corresponds to a mechanism of reproduction of vesicles of the same size. In this article, the matrix effect is re-elaborated in the perspective of the origin of life, and in particular in terms of the prebiotic mechanisms that might permit the growth and reproduction of vesicles. The data are analyzed by dynamic light scattering with a new program that permits the calculation of the number-weighted size distribution. It is shown that, on adding a stoichiometric amount of oleate micelles to preformed oleate vesicles extruded at 50 and 100 nm, the final distribution contains about twice the initial number of particles, centered around 50 and 100 nm. The same holds when oleate is added to preformed phospholipid liposomes. By contrast, when the same amount of oleate is added to an aqueous solution (as a control experiment), a very broad distribution ranging between 20 and 1000 nm is obtained. The data can then be seen as a kind of reproduction of the same size vesicles, and the argument is advanced that this may correspond to a simple prebiotic mechanism of vesicle multiplication in prebiotic times, when only physical forces might be responsible for the basic mechanisms of early protocell growth and division. Preliminary data also show that repeated addition of oleate maintains the same basic initial features, and that surfactants other than oleate also respect the reproductive mode of the matrix effect.

This paper summarizes some initial empirical results from a new computer model (artificial chemistry) which exhibits spontaneous emergence and persistence of autopoietic organization. the model is based on a system originally presented by Varela, Maturana, and Uribe. In carrying out this reimplementation it was found that an additional interaction (chain-based bond inhibition), not documented in the original description by Varela et al., is critical to the realization of the autopoietic phenomena. This required interaction was rediscovered only following careful examination of (unpublished) source code for an early version of the original model. The purpose of the paper is thus two-fold: firstly, to identify and discuss this previously undocumented, but essential, interaction; and secondly, to argue, on the basis of this particular case, for the importance of exploiting the emerging technologies which support publication of completely detailed software models (in addition, of course, to conventional publication of summary experimental results).

Key words: autopoieses, artificial life, artificial chemistry, origin of life

All sciences have epistemic assumptions, a language for expressing their theories or models, and symbols that reference observables that can be measured. In most sciences the languages in which their models are expressed are not the focus of their attention, although the choice of language is often crucial for the model. On the contrary, biosemiotics, by definition, cannot escape focusing on the symbol-matter relationship. Symbol systems first controlled material construction at the origin of life. At this molecular level it is only in the context of open-ended evolvability that symbol-matter systems and their functions can be objectively defined. Symbols are energy-degenerate structures not determined by laws that act locally as special boundary conditions or constraints on law-based energy-dependent matter in living systems. While this partial description holds for all symbol systems, cultural languages are much too complex to be adequately described only at the molecular level. Genetic language and cultural languages have common basic requirements, but there are many significant differences in their structures and functions. Relevance: The paper expresses the classical epistemological mind-matter problem at the simplest evolutionary level, which begins with self-replication. At this level I call it the symbol-matter problem, and I discuss the physical and epistemic conditions for symbol systems and languages to arise.

Life is a complex phenomenon that not only requires individual self-producing and self-sustaining systems but also a historical-collective organization of those individual systems, which brings about characteristic evolutionary dynamics. On these lines, we propose to define universally living beings as autonomous systems with open-ended evolution capacities, and weclaim that all such systems must have a semi-permeable active boundary (membrane), an energy transduction apparatus (set of energy currencies) and, at least, two types of functionally interdependent macromolecular components (catalysts and records). The latter is required to articulate a `phenotype-genotype’ decoupling that leads to a scenario where the global network ofautonomous systems allows for an open-ended increase in the complexity of the individual agents. Thus, the basic-individual organization of biological systems depends critically on being instructed by patterns (informational records) whose generationand reliable transmission cannot be explained but take into account the complete historical network of relationships amongthose systems. We conclude that a proper definition of life should consider both levels, individual and collective: livingsystems cannot be fully constituted without being part of theevolutionary process of a whole ecosystem. Finally, we alsodiscuss a few practical implications of the definition fordifferent programs of research.

Key words: artificial life, astrobiology, autonomous agents, definition of life, generalization of biology, genotype-phenotype decoupling, open-ended evolution, origin of life, origins of (genetic) information

This paper focuses in upon a model of abiotic (proto) semiosis, giving some suggestions concerning the origin of life. In doing this, the paper utilizes the Peircean triadic concept of semiosis along with the maximum energy dispersion principle in connection with the concept of dissipative structures. It is suggested that the origin of biosemiosis via the genetic system allowed mediation of physiosemiosis into zoosemiosis. Thus, biosemiosis is taken to not be on the direct line of descent of anthroposemiosis. I argue that the characteristic gesture of natural science was to eliminate final cause from its texts, which amounted to eliminating the contexts of examined phenomena as being critical in understanding their behavior. But, I argue, context is crucial for any semiotic interpretation, and must be brought back into our conception of the abiotic world if semiosis is to be understood as arising naturally during evolution.

Development of artificial cognition, one of the major challenges of contemporary science, requires better understanding of the nature and function of mind. This paper follows the idea of Searle that mind is more than computation, and explores the notion that mind has to be embodied in agency that actively interacts with the outside world. To avoid anthropocentrism and dualism, I develop the concept of agency using principles of biosemiotics, a new discipline that integrates semiotics (science on signification and meaning) with biology. In evolutionary terms, human cognition is an advanced form of agency that emerged from simpler ancestral forms in animals, plants, and single-cell organisms. Agency requires autonomy, informed choice, and goal-directedness. These features imply a capacity of agents to select and execute actions based on internal goals and perceived or stored signs. Agents are always constructed by parental agents, except for the most simple primordial molecular-scale self-reproducing agents, which emerged from non-living components. The origin of life coincides with the emergence of agency and primitive communication, where signs are not yet associated with objects, and instead used to activate or regulate actions directly. The capacity of agents to perceive and categorize objects appeared later in evolution and marks the emergence of minimal mind and advanced communication via object-associated signs. Combining computation with agential features such as goal-directedness, adaptability, and construction may yield artificial systems comparable in some respects to human mind.

Key words: biosemiotics, constructivism, multi-levelness, autonomy, protosemiosis, eusemiosis, autonomous learning