Biosemiotics is the synthesis of biology and semiotics, and its main purpose is to show that semiosis is a fundamental component of life, i.e., that signs and meaning exist in all living systems. This idea started circulating in the 1960s and was proposed independently from enquires taking place at both ends of the Scala Naturae. At the molecular end it was expressed by Howard Pattee’s analysis of the genetic code, whereas at the human end it took the form of Thomas Sebeok’s investigation into the biological roots of culture. Other proposals appeared in the years that followed and gave origin to different theoretical frameworks, or different schools, of biosemiotics. They are: (1) the physical biosemiotics of Howard Pattee and its extension in Darwinian biosemiotics by Howard Pattee and by Terrence Deacon, (2) the zoosemiotics proposed by Thomas Sebeok and its extension in sign biosemiotics developed by Thomas Sebeok and by Jesper Hoffmeyer, (3) the code biosemiotics of Marcello Barbieri and (4) the hermeneutic biosemiotics of Anton Markoš. The differences that exist between the schools are a consequence of their different models of semiosis, but that is only the tip of the iceberg. In reality they go much deeper and concern the very nature of the new discipline. Is biosemiotics only a new way of looking at the known facts of biology or does it predict new facts? Does biosemiotics consist of testable hypotheses? Does it add anything to the history of life and to our understanding of evolution? These are the major issues of the young discipline, and the purpose of the present paper is to illustrate them by describing the origin and the historical development of its main schools.

Key words: biosemiotics, signs, meaning, codes, interpretation, semiosis

The work of physicist and theoretical biologist Howard Pattee has focused on the roles that symbols and dynamics play in biological systems. Symbols, as discrete functional switching-states, are seen at the heart of all biological systems in the form of genetic codes, and at the core of all neural systems in the form of informational mechanisms that switch behavior. They also appear in one form or another in all epistemic systems, from informational processes embedded in primitive organisms to individual human beings to public scientific models. Over its course, Pattee’s work has explored (1) the physical basis of informational functions (dynamical vs. rule-based descriptions, switching mechanisms, memory, symbols), (2) the functional organization of the observer (measurement, computation), (3) the means by which information can be embedded in biological organisms for purposes of self-construction and representation (as codes, modeling relations, memory, symbols), and (4) the processes by which new structures and functions can emerge over time. We discuss how these concepts can be applied to a high-level understanding of the brain. Biological organisms constantly reproduce themselves as well as their relations with their environs. The brain similarly can be seen as a self-producing, self-regenerating neural signaling system and as an adaptive informational system that interacts with its surrounds in order to steer behavior.

Key words: Adaptive systems, biological cybernetics, biological semiotics, dynamical systems, emergence, epistemology, evolutionary robotics, genetic code, neural code, neurocomputation, self-organization, symbols.

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.

The deterministic component of the structure of the genetic code, derived from tRNA dimerization as proposed by the self-referential model, is described. Anticodon triplets form well defined modules of dimers that are sites for hosting the amino acid guests. The amino acids are the non-deterministic component, selected evolutionarily at the accomplishment of functions in the nucleoprotein ensembles and coevolving with metabolic pathways. The concomitance of the deterministic and the evolutionary components results in regionalization of the attributions in the matrix of encoded correspondences. The regionalized structure is what explains the error-minimizing property of the code structure. Relevance: Our utilization of the notion of self-reference may be relevant for the discussions on autopoiesis. Our model utilizes self-reference as the original and foundational attribute but compartmentalization is considered a derived function in the construction of the biomolecular machinery. The genetic code also reaches integration through the action of protein-protein interactions, between synthetases. Functional closure is reached when the punctuation subsystem is developed, but also in dependence on complex participation of other genes.

The model for the formation of the genetic code is called self-referential, indicating that producers (proto-tRNA dimers) are recognized by the products (peptides) through binding (back-looping) and formation of ribonucleoprotein (RNP) structures. If the binding results in stabilization of the structure, with conservation of the original function, this is equivalent to self-stimulation, which is at the root of the encoding process, which will develop specificity. This publication is the first where the model is presented in full, and from where the earlier publications (since 1996) could be rescued. Relevance: This is the first model for the genetic code that utilizes oligomers (proto-tRNAs) and proposes a clear mechanism (dimerization of the oligomers), traversing the whole set of attributions from the beginning to the end of the elongation attributions, also proposing the mechanism for setting the punctuation codes. It is also fully coherent with biological constructivism, starting all biosynthesis with one-carbon nutrients and running from simple to complex encodings.

The lack within AL of an agreed-upon notion of life and of a set of criteria for identifying life is considered. I propound a reflection upon the codified nature of the organization of living beings. The necessity of a guiding notion based on the coding is defended. After sketching some properties of the genetic code I proceed to consider the issue of functionalism as strategy for AL. Several distinctions ranging from plain multiple realizability to total implementation independence are made, arguing that the different claims should not be confused. The consideration of the semantic and intrinsically meaningful nature of the code leads to discuss the “symbol grounding” in AL. I suggest the principle of Semantic Closure as a candidate for confronting both problems inasmuch as it can be considered an accurate guiding notion to semantically ground Artificial Life.