Functional information means an encoded network of functions in living organisms, which is represented by two components: code and an interpretation system, which together form a self-sustaining semantic closure. The interpretation system consists of inference rules that control the correspondence between the code and the function. The utility factor operates at multiple time scales: short-term selection drives evolution towards higher survival and reproduction rates within a given fitness landscape, and long-term selection favors those inference rules that support adaptability and lead to evolutionary expansion of certain lineages. Inference rules make short-term selection possible by shaping the fitness landscape and defining possible directions of evolution, but they are under the control of the long-term selection of lineages. Communication normally occurs within a set of agents with compatible interpretation systems, which I call a “communication system” (e.g., a biological species is a genetic communication system). This view of the relation between utility and inference can resolve the conflict between realism/positivism and pragmatism. Realism overemphasizes the role of inference in evolution of human knowledge because it assumes that logic is embedded in reality. Pragmatism substitutes usefulness for truth and therefore ignores the advantage of inference. The proposed concept of evolutionary pragmatism rejects the idea that logic is embedded in reality; instead, inference rules are constructed within each communication system to represent reality, and they evolve towards higher adaptability on a long time-scale. Relevance: This paper applies pragmatism and ineractivism (Bickhard) to biological evolution. It suggests that biosemiotics rests on evolutionary pragmatism.

Biosemiotics and cybernetics are closely related, yet they are separated by the boundary between life and non-life: biosemiotics is focused on living organisms, whereas cybernetics is applied mostly to non-living artificial devices. However, both classes of systems are agents that perform functions necessary for reaching their goals. I propose to shift the focus of biosemiotics from living organisms to agents in general, which all belong to a pragmasphere or functional universe. Agents should be considered in the context of their hierarchy and origin because their semiosis can be inherited or induced by higher-level agents. To preserve and disseminate their functions, agents use functional information – a set of signs that encode and control their functions. It includes stable memory signs, transient messengers, and natural signs. The origin and evolution of functional information is discussed in terms of transitions between vegetative, animal, and social levels of semiosis, defined by Kull. Vegetative semiosis differs substantially from higher levels of semiosis, because signs are recognized and interpreted via direct code-based matching and are not associated with ideal representations of objects. Thus, I consider a separate classification of signs at the vegetative level that includes proto-icons, proto-indexes, and proto-symbols. Animal and social semiosis are based on classification and modeling of objects, which represent the knowledge of agents about their body (Innenwelt) and environment (Umwelt). Relevance: The paper suggests an agency-based approach to biosemiotics. This approach is related to the interactivism of Mark Bickhard.

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

Open peer commentary on the article “A Critique of Barbieri’s Code Biology” by Alexander V. Kravchenko. Abstract: Biosemiotics assumes multiple levels of interpretation of signs. At the lowest level is protosemiosis, which is represented by intracellular information processes, and which can be seen as a semiotic alternative to code biology. Protosemiosis includes interpretation. However, it has fewer components in comparison to mental interpretation. In particular, protosemiosis lacks references to external objects in the sense of Peirce.