Taking the Relational Turn: Biosemiotics and Some New Trends in Biology

A cluster of similar trends emerging in separate fields of science and philosophy points to new opportunities to apply biosemiotic ideas as tools for conceptual integration in theoretical biology. I characterize these developments as the outcome of a “relational turn” in these disciplines. They signal a shift of attention away from objects and things and towards relational structures and processes. Increasingly sophisticated research technologies of molecular biology have generated an enormous quantity of experimental data, sparking a need for relational approaches that could help to find recurrent patterns in the mass of data. Earlier conceptions of relational biology and cybernetics, once deemed too abstract and speculative, are now resurrected and applied by means of new computational and simulation tools. I think this receptivity should be extended to incorporate nets of semiotic relations as heuristic guides for discerning global patterns of interactions in living systems. In this article I review aspects of systems biology and new directions in evolutionary theory, focusing on the role of circular and downward causation in relational structures and dynamical networks. I also indicate promising avenues of integration of some ideas of biosemiotics with those emerging from these new currents in biology. Relational developments in biology bear a telling similarity to a parallel relational turn presently manifest in the philosophy of science, rooted in the philosophy of physics and mathematics and in different varieties of structural and informational realism. The recognition of the relational nature of reality within these disciplines entails a tacit repudiation of nominalistic biases in science that have hindered the reception of semitiotic conceptions in biology. In previous investigations I explored connections between two kinds of relational structures: the networks of self-referential circular loops that appear pervasively in living systems, and the triadic relational structures that Peircean semiotics places at the basis of all semiotic transactions. Current relational views in the sciences seem oblivious to the difference between dyadic and triadic relations. Incorporating this essential distinction from biosemiotics into other fields could be a first step in seizing the opportunities opened by the relational turn for a renewal of biology and of natural philosophy in general, across disciplinary boundaries.     

Towards an Evolutionary Biosemiotics: Semiotic Selection and Semiotic Co-option

In biosemiotics, living beings are not conceived of as the passive result of anonymous selection pressures acted upon through the course of evolution. Rather, organisms are considered active participants that influence, shape and re-shape other organisms, the surrounding environment, and eventually also their own constitutional and functional integrity. The traditional Darwinian division between natural and sexual selection seems insufficient to encompass the richness of these processes, particularly in light of recent knowledge on communicational processes in the realm of life. Here, we introduce the concepts of semiotic selection and semiotic co-option which in part represent a reinterpretation of classical biological terms and, at the same time, keep explanations sensitive to semiosic processes taking place in living nature. We introduce the term ‘semiotic selection’ to emphasize the fact that actions of different semiotic subjects (selectors) will produce qualitatively different selection pressures. Thereafter, ‘semiotic co-option’ explains how semiotic selection may shape appearance in animals through remodelling existing forms and relations. Considering the event of co-option followed by the process of semiotic selection enables us to describe the evolution of semantic organs.     

Towards an ecosystem semiotics: Some basic aspects for a new research programme

The paper argues that ecosystem should be recognized as semiotic systems and that it is necessary to carry out studies of the ongoing semiotic processes in addition to traditional ecosystem research. It is suggested that interpretation of ecosystems within such a semiotic framework is of utmost importance and essential if we want to fully understand the complexity issue and how complex behaviour comes about at this level of biological hierarchy. This area—called ecosystem semiotics—is suggested to become a new direction of study dedicated to this understanding.As a consequence of the ontic character of ecosystem complexity, studies on the importance of semiotic processes can only be synthesized through modelling efforts. Hitherto, this type of process with a few exceptions has been neglected or at best only implicitly integrated and accounted for in ecosystem models. In the future, ecosystem models will need to integrate this type of behaviour in order to get full insight into the causal mechanisms behind the emergence of their complex behaviour. In addition, the concept of exergy in its classical form derived by Evans is suggested as a platform to integrate thermodynamic information of the systems as a complexity measure. The thermodynamic information may be split into parts that causally originate in the ontic existence of various ecosystem elements. Ecosystem semiotics is thought to considerably increase the thermodynamic efficiency of the ecosystem, leading to an increase in thermodynamic information and for instance ascendancy that would not have existed if it was not emerging from the semiotic processes.In other words, by incorporating semiotics, we add a “metaphysical” layer to our models, which may be referred to as the semiotype of the system. The semiotype acts as downward causation on the lower layers of interactions and allows for modification and adaptations of existing genotype or phenotype possibilities that would not be possible without the existence of semiosis and cognitive processes.     

Laws, constraints, and the modeling relation--history and interpretations

The modeling relation and models of complex systems expressed by non-integrable constraints were developed during ca. 1970-1987, when I worked most closely with Robert Rosen. I contrast the modeling relation within the organism itself as a necessary condition for life and evolution, as Rosen developed it in his fundamental work 'Anticipatory Systems', with the modeling relation within our brain as a necessary condition for understanding life, as Rosen developed it in 'Life Itself'. Our approaches to the modeling relation were complementary. Rosen focused on the formal relational conditions necessary for life, and on the limitations that formal mathematical-symbol systems impose on our models. I focused on the physical conditions necessary for these abstract relations to be realized, and on the symbolic control in organisms that allows open-ended evolution. I contrast Rosen's views on physics and evolution in 'Anticipatory Systems' and later papers with his views in 'Life Itself', and I speculate on why they differ so greatly.     

Signs of the Self: An Exploration in Semiotic Anthropology

Peirce's general theory of signs, or semiotic, as he called it, yields a theory of the self that sees it both as the object and the subject of semiotic systems. From this viewpoint, the locus, unity, and continuity of the self will be found in the systems of signs that constitute the dialogues between utterers and interpreters of the signs. Personal identity, in this theory, is also a social and cultural identity and is not confined to the individual organism. Peirce's anti-Cartesianism, which denies intuitive and introspective knowledge of the self, derived that knowledge from the fallible inferences we all make from the observations of external facts, including the signs of the self. This laid the foundation for a semiotic psychology as well as for a semiotic anthropology. [self, semiotic anthropology, personal identity, C. S. Peirce]     

生物网络研究进展述评

生物网络是一类典型的复杂适应性系统,包含了许多个体的多层次的各种相互作用和关系,在过去的十年里,利用复杂网络理论对生物网络进行研究引起了人们的注意并获得了快速发展.本文首先从从度分布、聚类系数及鲁棒性等角度对现阶段生物网络性质的研究进行了简要介绍,后进一步对生物网络的聚类算法及主要建模理论做出了概括.今后的研究趋势在于如何建立合理的生物网络模型,以深入研究生物网络的各种性质.     

Multiple relational equilibria: Polymorphism,metamorphosis and other possibly similar phenomena

In a preceding paper (Rashevsky, 1969. “Outline of a Unified Approach to Physics, Biology and Sociology.”Bulletin of Mathematical Biophysics,31, 159–198) certain isomorphisms between biological and social systems on the one hand and physical systems on the other were studied. The notion or relational forces, of which ordinary physical forces are a particular case, was introduced. In the present paper an attempt is made to establish analogies between stable equilibria in physical systems, equilibria due to physical forces, and stable equilibria in biological and social systems which are due to purely relational forces. The notion of relational forces causing multiple equilibria similar to multiple equilibria in some physical systems is studied, and it is outlined how this notion may possibly help the understanding of such phenomena as polymorphism, metamorphosis and the existence of rudimentary organs or rudimentary functions.     

Semiotic Mechanisms Underlying Niche Construction

The explanatory value of niche construction can be strengthened by firm footing in semiotic theory. Anthropologists have a unique perspective on the integration of such diverse approaches to human action and evolutionary processes. Here, we seek to open a dialogue between anthropology and biosemiotics. The overarching aim of this paper is to demonstrate that niche construction, including the underlying mechanism of reciprocal causation, is a semiotic process relating to biological development (sensu stricto) as well as cognitive development and cultural change. In making this argument we emphasize the semiotic mechanisms underlying the niche concept. We argue that the “niche” in ecology and evolutionary biology can be consistent with the Umwelt of Jakob von Uexkull. Following John Deely we therefore suggest that investigations into the organism—environment interface constituting niche construction should emphasize the semiotic basis of experience. Peircean signs are pervasive and allow for flexible interpretations of phenomena in relation to the perceptual and cognitive capacities of the behaving organism, which is particularly pertinent for understanding the relation of proximate/ultimate selective forces as co-productive (i.e., reciprocal). Additionally, theoretical work by Kinji Imanishi on the evolution of daily life and Gregory Bateson’s relational view of evolution both support the linkage between proximate and ultimate evolutionary processes of causation necessitated by the niche construction perspective. We will then apply this theoretical framework to two specific examples: 1) hominin evolution, including uniquely human cultural behaviors with niche constructive implications; and 2) the multispecies and anthropocentric niche of human-dog coevolution from which complex cognitive capacities and semiotic relationships emerged. The intended outcome of this paper is the establishment of concrete semiotic mechanisms and theory underlying niche constructive behavior which can then be applied to a broad spectrum of organisms to contextualize the reciprocal relation between proximate and ultimate drivers of behavior.     

Concept of energy in biological systems and the effects of irradiations of low energies on enzyme-substrate systems

The recent mathematical formalization of the concepts of matter and extrinsical energy, which are used for the relational representation of biological systems, is employed in the analysis of the important experimental discoveries of Comorosanet al. related to low energy electromagnetic irradiations on enzyme substrates. By means of the present analysis one of the properties inherent to the experimental phenomena is more precisely exposed, and theoretical developments corresponding to “energetical evolutions” in a biological system (Leguizamón, 1976) may now have an experimental basis. Important limitations are introduced for the validity of the commutativity and associativity of cartesian product of sets, when they represent matter and its linked extrinsical energy. In connection with this last aspect, new important knowledge is obtained for the relational mathematical representation of biological systems.     

A theory for environmental systems

A theory for environmental systems is defined on the basis of two elements, termed ‘environmental unity’ and ‘behavior’. Environmental systems are regarded as non-living systems, each one related with only one biological system. We construct a material-energetic environmental diagram, which is introduced in terms of the theory of categories, thereby giving rise to a new categoryE. By means of two biological conditions, and the definition of static property of the biological system (related to its own environment), a set of theorems is obtained, exhibiting mathematical consequences for the represented theory.     

Biosemiotics and Hominidae history: technicity,animals, and the limitations of human exceptionalism

This article is focused on problematic distinctions of difference among animals in the lineage of great apes. It combines several theoretical perspectives on evolutionary relationships, technological innovation, the development of body parts as tools, and a semiotic interpretation of what André Leroi-Gourhan called technicity. Foundational questions in social theory are developed using biosemiotics, particularly as concerns a materialist understanding of religion and the magical aspects of cultural representation. This, it is argued, provides a framework for theorizing social history in terms of real ecological relations, embodied meaning, and the transference of meaning onto objects. Understood semiotically, the material history of Hominidae, encompassing animals with different kinds of motility, dexterity, and techno-semiotic orientations towards the world, is inclusive and relational rather than exclusively anthropocentric, as is the case for social theory based on the artifice of language and articulations of belief, creativity, and cultural distinction that are thought to be distinctive of the genus Homo.     

Relational forces and structures produced by them

After giving a brief review of the theory of organismic sets (Bull. Math. Biophysics,29, 139–152, 1967;31, 159–198, 1969), in which the concept of relational forces, introduced earlier (Bull. Math. Biophysics,28, 283–308, 1966a) plays a fundamental role, the author discusses examples of possible different structures produced by relational forces. For biological organisms the different structures found theoretically are in general agreement with observation. For societies, which are also organismic sets as discussed in the above references, the structures can be described only in an abstract space, the nature of which is discussed. Different isomorphisms between anatomical structures, as described in ordinary Euclidean space, and the sociological structures described in an abstract space are noted, as should be expected from the theory of organismic sets.     

The dynamic systems approach to control and regulation of intracellular networks

Systems theory and cell biology have enjoyed a long relationship that has received renewed interest in recent years in the context of systems biology. The term 'systems' in systems biology comes from systems theory or dynamic systems theory: systems biology is defined through the application of systems- and signal-oriented approaches for an understanding of inter- and intra-cellular dynamic processes. The aim of the present text is to review the systems and control perspective of dynamic systems. The biologist's conceptual framework for representing the variables of a biochemical reaction network, and for describing their relationships, are pathway maps. A principal goal of systems biology is to turn these static maps into dynamic models, which can provide insight into the temporal evolution of biochemical reaction networks. Towards this end, we review the case for differential equation models as a 'natural' representation of causal entailment in pathways. Block-diagrams, commonly used in the engineering sciences, are introduced and compared to pathway maps. The stimulus-response representation of a molecular system is a necessary condition for an understanding of dynamic interactions among the components that make up a pathway. Using simple examples, we show how biochemical reactions are modelled in the dynamic systems framework and visualized using block-diagrams.     

On the semiotic dimension of ecological theory: The case of island biogeography

The Macarthur-Wilson equilibrium theory of island biogeography has had a contradictory role in ecology. As a lasting contribution, the theory has created a new way of viewing insular environments as dynamical systems. On the other hand, many of the applications of the theory have reduced to mere unimaginative curve-fitting. I analyze this paradox in semiotic terms: the theory was mainly equated with the simple species-area relationship which became a signifier of interesting island ecology. The theory is, however, better viewed as a theoretical framework that suggests specific hypotheses on the ecology of colonization of insular environments. This paradox is inherent in the use of simplifying analytic models. Analytic models are necessary and fruitful in the work of ecologists, but they ought to be supplemented with a broader, pluralistic appreciation of the role of theories in general.     

Computer simulation of biological systems

The current status of mathematical models of biological systems is reviewed. Advances in supercomputer hardware allows more complex models to be constructed. The new generation of microcomputers are quite adequate for many computer simulations of biological systems. A theory of modeling is being developed to improve the relationship between the real biological system and the model. Deterministic models, stochastic models and applications of control theory and optimization methods are discussed. Examples given include models of molecular structure, of experimental techniques, and of biochemical reactions. It is recommended that experimental biologists consider the use of microcomputers to model the system under study as a part of their research program.     

Lattices and lattice-valued relations in biology

Rashevsky's treatment of general binary relations between sets of biological elements is extended using the novel mathematical concept of lattice-valued relation (l.v.r.). This yields a quantitative measure of the strength of the relations between components of a biological organism, and some illustrative examples are given. Specific l.v.r.'s are used to define (more precisely than in Rashevsky's preliminary theory of binary relations) the biologically important relationships amongst hormones, metabolism and energy exchange involved in metabolic reactions. The ‘strongest link’ between the set of hormones and the set of metabolic reactions is quantified using a special l.v.r., and other specific biological realisations of lattice-valued relations in abstract-relational biology are presented. L.v.r.'s may also be regarded as a form ofG-relation in relational biology, or as a particular case of generating diagrams. Further possible developments of this approach, using more complex tools of the newly developed mathematical theory of lattice-valued relations, such as function space l.v.r., group l.v.r., l.v.r. morphisms, l.v.r. homology andn-ary l.v.r.'s are suggested.