We argue that constructive approaches in epistemology and systems science, which are focused on normativity, knowledge, and communication of organisms and emphasize the primacy of activity, self-construction, and niche-construction in the cognitive agents, fit naturally to the both methodology and theory of biosemiotics. In particular, constructive view was already present in the works of the major precursors of biosemiotics: von Uexküll and Bateson, and to some extent Peirce. Biosemiotics has a chance to function as a mediating field in the theoretical (...) integration of semiotics with its construction-related sister disciplines (e.g., second order cybernetics, autopoiesis, constructivism, enactivism, and interactivism) because of its explicit assumption of the semiotic nature of life and agency and its objectified “first person” view to biosemiotic agents, the view that nevertheless avoids the agnostic attitude towards reality. (shrink)

The aim of this paper is to explore the connections between semiotics and biology by examining the behaviors of both humans and non-cognizant agents, using Bayesian and heuristic inference. The argument is that higher-level organisms use complex predictive reasoning to deal with uncertainty, while non-cognizant species, such as SARS-CoV-2, rely on an economy-driven heuristic to enter host cells. From this viewpoint, the current pandemic is characterized as a clash of representations resulting from the anthropocentric construction of the self, which neglects (...) the complexities of the natural world. (shrink)

The current article is the first in a series of review articles addressing biosemiotic terminology. The biosemiotic glossary project is inclusive and designed to integrate views of a representative group of members within the biosemiotic community based on a standard survey and related publications. The methodology section describes the format of the survey conducted in November–December 2013 in preparation of the current review and targeted on the terms ‘agent’ and ‘agency’. Next, I summarize denotation, synonyms and antonyms, with special emphasis (...) on the denotation of these terms in current biosemiotic usage. The survey findings include ratings of nine citations defining or making use of the two terms. I provide a summary of respondents’ own definitions and suggested term usage. Further sections address etymology, connotations, and related terms in English and other languages. A section on the notions’ mainstream meaning vs. their meaning in biosemiotics is followed by attempt at synthesis and conclusions. Although there is currently no consensus in the biosemiotic community on what constitutes a semiotic agent, i.e., an agent in the context of semiosis, most respondents agree that core attributes of an agent include goal-directedness, self-governed activity, processing of semiosis and choice of action, with these features being vital for the functioning of the living system in question. I agree that these four features are constitutive of biosemiotic agents, and stipulate that biosemiotic agents fall within three major categories, namely 1) sub-organismic biosemiotic agents, 2) organismic biosemiotic agents and 3) super-organismic biosemiotic agents. (shrink)

The target article by Denis Noble is an excellent overview of the illusions of the Modern Synthesis that still remains in textbooks despite of the recent criticism. Overcoming these illusions shows the active role of organisms in the evolutionary process and accounts for additional mechanisms such as plasticity of embryo development, epigenetic heredity, multilevel selection, Baldwin effect, and niche construction, which are components of the Extended Evolutionary Synthesis. Adding these mechanisms is certainly an important step forward, but I argue that (...) it is not sufficient for building a new theory of evolution. What is missing is a clear understanding of such notions as agency, autonomy, semiosis, interpretation, and goal-directedness, which so far belong to the humanities and have not been applied seriously in science. Organisms are autonomous and goal-directed semiotic agents capable of interpreting hereditary signs and making meaningful models of their environment. Evolutionary biology needs a semiotic vocabulary to talk about higher level functions in organisms, where specific molecules and mechanisms are only means for integrating functions over the life cycle and adapting to the environment without compromising organism integrity and identity. Such a vocabulary is being developed in biosemiotics; thus, I expect the emergence of a biosemiotic theory of evolution. (shrink)

Biological evolution is often viewed narrowly as a change of morphology or allele frequency in a sequence of generations. Here I pursue an alternative informational concept of evolution, as preservation, advance, and emergence of functional information in natural agents. Functional information is a network of signs that are used by agents to preserve and regulate their functions. Functional information is preserved in evolution via complex interplay of copying and construction processes: the digital components are copied, whereas interpreting subagents together with (...) scaffolds, tools, and resources, are constructed. Some of these processes are simple and invariant, whereas others are complex and contextual. Advance of functional information includes improvement and modification of already existing functions. Although the genome information may change passively and randomly, the interpretation is active and guided by the logic of agent behavior and embryonic development. Emergence of new functions is based on the reinterpretation of already existing information, when old tools, resources, and control algorithms are adopted for novel functions. Evolution of functional information progressed from protosemiosis, where signs correspond directly to actions, to eusemiosis, where agents associate signs with objects. Language is the most advanced form of eusemiosis, where the knowledge of objects and models is communicated between agents. (shrink)

In contrast to the traditional relational semiotics, biosemiotics decisively deviates towards dynamical aspects of signs at the evolutionary and developmental time scales. The analysis of sign dynamics requires constructivism to explain how new components such as subagents, sensors, effectors, and interpretation networks are produced by developing and evolving organisms. Semiotic networks that include signs, tools, and subagents are multilevel, and this feature supports the plasticity, robustness, and evolvability of organisms. The origin of life is described here as the emergence of (...) simple self-constructing semiotic networks that progressively increased the diversity of their components and relations. Primitive organisms have no capacity to classify and track objects; thus, we need to admit the existence of proto-signs that directly regulate activities of agents without being associated with objects. However, object recognition and handling became possible in eukaryotic species with the development of extensive rewritable epigenetic memory as well as sensorial and effector capacities. Semiotic networks are based on sequential and recursive construction, where each step produces components that are needed for the following steps of construction. Construction is not limited to repair and reproduction of what already exists or is unambiguously encoded, it also includes production of new components and behaviors via learning and evolution. A special case is the emergence of new levels of organization known as metasystem transition. Multilevel semiotic networks reshape the phenotype of organisms by combining a mosaic of features developed via learning and evolution of cooperating and/or conflicting subagents. (shrink)

Principles of constructivism are used here to explore how organisms develop tools, subagents, scaffolds, signs, and adaptations. Here I discuss reasons why organisms have composite nature and include diverse subagents that interact in partially cooperating and partially conflicting ways. Such modularity is necessary for efficient and robust functionality, including mutual construction and adaptability at various time scales. Subagents interact via material and semiotic relations, some of which force or prescribe actions of partners. Other interactions, which I call “guiding”, do not (...) have immediate effects and do not disrupt the evolution and learning capacity of partner agents. However, they modify the extent of learning and evolutionary possibilities of partners via establishment of scaffolds and constraints. As a result, subagents construct reciprocal scaffolding for each other to rebalance their communal evolution and learning. As an example, I discuss guiding interactions between the body and mind of animals, where the pain system adjusts mind-based learning to the physical and physiological constraints of the body. Reciprocal effects of mind and behaviors on the development and evolution of the body includes the effects of Lamarck and Baldwin. (shrink)

The background target of the research going into the present article is to forge an intellectual alliance between, on the one hand, active inference and the free-energy principle (FEP), and on the other, Charles S. Peirce’s theory of semiotics and pragmatism. In the present paper, the focus is on the allegiance between the nomenclatures of active and abductive inferences as the proper place to begin reaching at that wider target. The paper outlines the key conceptual elements involved in a naturalistic (...) rendering of Peirce’s late semiotic and logical notion of abductive reasoning. The target is a cognitive-biological model of abduction which preserves the functional integrity of an organism and fulfils the existential imperative for living beings’ evidence of existence. Such a model is an adaptation of Peirce’s late logical schema of abduction proposed in his largely unpublished works during the early 20th century. The proposed model is argued to be a feasible sketch also of recent breakthroughs in computational (sensu Bayesian) cognitive science. (shrink)

As a field of scientific expertise, semiotics has the interesting property of being a relevant tool for understanding how scientists represent any domain of research, including the semiotic domain itself. This feature is particularly expressive in the case of biology, as it appears to be the case that a certain range of biological phenomena are of a semiotic character. However, it is not consensual the extent to which semiotics pervades biology. This paper deals with this issue for the particular case (...) of developmental biology, stressing the role of semiotics-as-a-discipline in delimiting the extent of semiotics-as-a-natural-phenomenon and, specifically, in disentangling semiotic mechanisms from semiotic metaphors aimed at clarifying non-semiotic developmental mechanisms. (shrink)

The present paper attempts to demonstrate semiotic arguments against the sequence → structure → function paradigm in protein studies. The unidirectional deterministic thinking in biological processes has been challenged by several disciplines of life sciences (epigenetics, proteomics, etc.) and philosophy (process philosophy). Biosemiotics comprehends living organisms as actively participating in their present and somehow creating or shaping their future, having a plurality of options for acting. Determinism and unidirectionality are in contradiction with a biosemiotic approach towards life, mostly when considering (...) Peirce’s triadic concept of semiosis. In this paper, a Peircean biosemiotic approach is applied to proteins and to the process of protein folding. Two main concepts are presented to support the arguments against the SSF paradigm in protein studies: the NonReduction Theorem and the notion of folded continuum. A processual approach is proposed as the most suitable for descriptions of proteins and their functions. (shrink)

The present paper attempts to demonstrate semiotic arguments against the sequence → structure → function paradigm in protein studies. The unidirectional deterministic thinking in biological processes has been challenged by several disciplines of life sciences and philosophy. Biosemiotics comprehends living organisms as actively participating in their present and somehow creating or shaping their future, having a plurality of options for acting. Determinism and unidirectionality are in contradiction with a biosemiotic approach towards life, mostly when considering Peirce’s triadic concept of semiosis. (...) In this paper, a Peircean biosemiotic approach is applied to proteins and to the process of protein folding. Two main concepts are presented to support the arguments against the SSF paradigm in protein studies: the NonReduction Theorem and the notion of folded continuum. A processual approach is proposed as the most suitable for descriptions of proteins and their functions. (shrink)

The present paper attempts to demonstrate semiotic arguments against the sequence → structure → function paradigm in protein studies. The unidirectional deterministic thinking in biological processes has been challenged by several disciplines of life sciences and philosophy. Biosemiotics comprehends living organisms as actively participating in their present and somehow creating or shaping their future, having a plurality of options for acting. Determinism and unidirectionality are in contradiction with a biosemiotic approach towards life, mostly when considering Peirce’s triadic concept of semiosis. (...) In this paper, a Peircean biosemiotic approach is applied to proteins and to the process of protein folding. Two main concepts are presented to support the arguments against the SSF paradigm in protein studies: the NonReduction Theorem and the notion of folded continuum. A processual approach is proposed as the most suitable for descriptions of proteins and their functions. (shrink)

Bacterial chemotaxis is often considered to be a textbook example of the rudimentary semiotic process. As such, it gives an excellent opportunity to better understand both semiosis and biology. Our study reviews this phenomenon in the light of up-to-date scientific knowledge to answer the most basic semiotic questions: what is the sign? What types of signs are there? What is the meaning understood on the molecular level, and by what means can it grow with time? As a case study, the (...) bacterial chemotaxis toward glucose in E. coli species is chosen, and the semiotic framework of Charles Sanders Peirce applied. The analyses provide us with the following results: the sign, in its ultimate nature, is a general process. Bacterial chemotaxis can be understood in terms of Peircean type, symbol, and argument. The meaning on the molecular level is entirely pragmatic and, in this case, reduced to a bacterial response to glucose. A sign can grow through sign generalization, the emergence of different sign categories, the integration of these categories in functional cycles, and the introduction of contextuality. The sign of bacterial chemotaxis extends from the cell signaling pathways up to the population level. The presented results advance our knowledge of sign processing in the context of semiotic evolution. (shrink)

Evolutionary biologists, evolutionary epistemologists, and biosemioticians have demonstrated that organisms not merely adapt to an external world, but that they actively construct their environmental, sociocultural, and cognitive niches. Denis Noble demonstrates that such is no different for those organisms that engage in science, and he lays bare several crucial assumptions that define the scientific dogmas and practices of evolutionary biology.

Drawing on research in posthumanism, science and technology studies and biosemiotics, this essay analyses the challenges epigenetic processes pose for our understanding of embodied subjectivity. It uses the work of Charles Sanders Peirce to argue that epigenetic processes are indexical in their patterned logic, that they are meaning-making processes and that, consequently, they can be conceived as a form of attention. To conceive of bodies as paying attention through epigenetic processes is to rupture the distinction between matter and meaning that (...) governs many philosophical categories. This in turn invites us to recalibrate our conception of the relationship between self, body and world. (shrink)

The study seeks to contribute to the concept of semiotic causation by building a nomenclature of effects (interpretants) produced by signs. As a starting point, the suggested approach uses Charles Peirce’s idea that the interpretant itself is a sign that is produced by another sign. From this, the study suggests that Peirce’s ten-fold division of signs can be used as a basis for the division of interpretants and, thus, proposes a nomenclature that distinguishes poti-interpretants (interpretants that are quali-signs), sin-interpretants (interpretants (...) that are sin-signs), and legi-interpretants (interpretants that are legi-signs), also differentiating between iconic, indexical, and symbolic interpretants, as well as rhematic, dicent, and argumentive interpretants. The article uses Peirce’s famous whistle example (EP 2:4–5) to illustrate how the proposed systematics of interpretants works and demonstrates that it aligns well with Peirce’s distinction of feeling, reaction, and thinking, as feeling corresponds to the production of iconic poti-interpretants and iconic sin-interpretants, reaction corresponds to the production of indexical sin-interpretants, and thinking corresponds to the production of legi-interpretants. The article also suggests how the proposed ten-fold systematics of interpretants can be reconciled with Peirce’s original classifications of interpretants, as immediate-dynamical-final interpretants correspond to the triad of poti-, sin-, and legi-interpretants, while emotional-energetic-logical interpretants correspond to the three sub-classes of sin-interpretants, i.e. iconic sin-interpretants, rhematic indexical sin-interpretants, and dicent indexical sin-interpretants. The study then explores how the suggested classification of interpretants can be used to draw distinctions between different kinds of semiosis in different agents. In particular, the study shows how the proposed ten-fold classification can be applied to analyze diverse biosemiotic and anthroposemiotic processes. It also tests how different capacities to produce interpretants can be used to distinguish full-fledged signs from quasi-signs and demonstrates that in some cases of zoösemiosis, as well as in proto-semiosis and tardo-semiosis, the production of symbolic interpretants is diminished. (shrink)

The concept of protosemiosis or semiosis at the lower levels of the living goes back to Giorgio Prodi, Thomas A. Sebeok and others. More recently, a typology of proto-signs was introduced by Sharov and Vehkavaara. Kull uses the term of vegetative semiosis, defined by iconicity, when referring to plants and lower organism semiosis. The criteria for the typology of proto-signs by Sharov and Vehkavaara are mostly based on two important presuppositions: agency and a lack of representation in low-level semiosis. We (...) would like to focus on an alternative approach to protosign classification. In particular, we aim to provide a sign-typological characteristic of proteins (in analogy to Maran’ s classification of environmental signs). Our approach is focused on representation, that is, we only consider the relation between a sign and its object. We are considering representation independently from the role of interpretant and interpretation (which is an epiphenomenon of agency). Two hypotheses are investigated and accordingly evaluated in this paper: (I) Proteins are indexical protosigns. (II) Proteins are iconic protosigns. The conclusion our argumentation leads to supports the hypothesis (II). (shrink)

In this article two questions are discussed with regard to semiosis in protein biosynthesis for nano engines. (1) What kind of semiosis is involved in the construction of these proteins? and (2) How can we explain the semiotic process observed? With regard to the first issue we draw attention to comparisons between semiosis in protein biosynthesis and human natural language. The notion of normativity appears to be of great importance for both. A comparison also demonstrates differences. Nevertheless, because of the (...) normative symbolic information processing in it, we suggest to employ the term symbolic reference (employed in linguistics as a distinguishing feature of human language) to indicate the semiotic processes in protein biosynthesis. With regard to explaining semiosis in protein synthesis we compare different approaches. We conclude that a Kantian approach should be preferred. In such an approach strengths of the mechanistic and organicist approaches can be combined, and the observed symbolic information processing acknowledged. (shrink)

Both biosemiotics and evolutionary epistemology are concerned with how knowledge evolves. (Applied) Evolutionary Epistemology thereby focuses on identifying the units, levels, and mechanisms or processes that underlie the evolutionary development of knowing and knowledge, while biosemiotics places emphasis on the study of how signs underlie the development of meaning. We compare the two schools of thought and analyze how in delineating their research program, biosemiotics runs into several problems that are overcome by evolutionary epistemologists. For one, by emphasizing signs, biosemiotics (...) needs to delineate a semiotic threshold, which is a problem not encountered by evolutionary epistemologists. Instead, the latter recognizes that all organisms are knowers that evolve knowledge, which they recognize to extend toward phenomena produced by organisms such as behavior, cognition, language, culture, science, and technology. Secondly, biosemiotics attempts at continuing adaptationist notions on how organisms relate to their environment, while especially Applied Evolutionary Epistemology comes to redefine the nature of the organism–environment relationship in such a way that it recognizes the spatiotemporal boundedness of existence, which in turn makes adaptationist accounts obsolete. (shrink)