Semiosis and Bio-Mechanism: towards Consilience

In biosemiotics, some oppose the study of sign relations to empirical work on bio-mechanisms. Urging consilience between these views, we show the value of Alain Berthoz’s concept of simplexity. Its heuristic power is to present molecules, cells, organisms and communities as using tricks to self-fabricate by agglomerating ‘simplex’ bio-mechanisms. Their properties enable living systems (including observers) to self-sustain, adapt and, at best, to thrive. But simplexity also empowers agents to engage with their surroundings in novel ways. Life thus not only generates know-how but also social organisation. With languaging, people can act and inhibit: they can also simplexify. As a result, we can see a fruit as ripe, feel when things are awry or behave in ways likely to be judged to be apt. While all living beings make situated use of the historical and the local, humans also bind these with the use of both practices and artifacts. As a result, brains come to emulate what occurs in-between persons and their surroundings. In pursuing the basis for our powers, we focus on inhibition. This simplex trick enables a plant to use dormancy, a bird to learn, and a person to mesh languaging with other aspects of action/perception. Indeed, inhibition enriches human style phenomenology as impersonal resources are used to expand our epistemic horizons. Experience links a self-fabricating body, ancient bio-mechanisms, community-based concerns and epigenetically derived know-how.     

Three Types of Semiosis

The existence of different types of semiosis has been recognized, so far, in two ways. It has been pointed out that different semiotic features exist in different taxa and this has led to the distinction between zoosemiosis, phytosemiosis, mycosemiosis, bacterial semiosis and the like. Another type of diversity is due to the existence of different types of signs and has led to the distinction between iconic, indexical and symbolic semiosis. In all these cases, however, semiosis has been defined by the Peirce model, i.e., by the idea that the basic structure is a triad of ‘sign, object and interpretant’, and that interpretation is an essential component of semiosis. This model is undoubtedly applicable to animals, since it was precisely the discovery that animals are capable of interpretation that allowed Thomas Sebeok to conclude that they are also capable of semiosis. Unfortunately, however, it is not clear how far the Peirce model can be extended beyond the animal kingdom, and we already know that we cannot apply it to the cell. The rules of the genetic code have been virtually the same in all living systems and in all environments ever since the origin of life, which clearly shows that they do not depend on interpretation. Luckily, it has been pointed out that semiosis is not necessarily based on interpretation and can be defined exclusively in terms of coding. According to the ‘code model’, a semiotic system is made of signs, meanings and coding rules, all produced by the same codemaker, and in this form it is immediately applicable to the cell. The code model, furthermore, allows us to recognize the existence of many organic codes in living systems, and to divide them into two main types that here are referred to as manufacturing semiosis and signalling semiosis. The genetic code and the splicing codes, for example, take part in processes that actually manufacture biological objects, whereas signal transduction codes and compartment codes organize existing objects into functioning supramolecular structures. The organic codes of single cells appeared in the first three billion years of the history of life and were involved either in manufacturing semiosis or in signalling semiosis. With the origin of animals, however, a third type of semiosis came into being, a type that can be referred to as interpretive semiosis because it became closely involved with interpretation. We realize in this way that the contribution of semiosis to life was far greater than that predicted by the Peirce model, where semiosis is always a means of interpreting the world. Life is essentially about three things: (1) it is about manufacturing objects, (2) it is about organizing objects into functioning systems, and (3) it is about interpreting the world. The idea that these are all semiotic processes, tells us that life depends on semiosis much more deeply and extensively than we thought. We realize in this way that there are three distinct types of semiosis in Nature, and that they gave very different contributions to the origin and the evolution of life.     

Interactive Bodies: The Semiosis of Architectural Forms

In this paper architectural forms are presented as symbolic forms issued from the complex semiosis that characterises human cognition (Ferreira (2007, 2010)). Being semiotic objects, these symbolic forms are, consequently, context- dependent_they emerge and have meaning, i.e., they are assigned a functional and/or aesthetic value, in particular physical, social and cultural frameworks. As it happens with all semiotic objects, architectural forms, whatever their nature, are not static but highly interactive. In fact, they act as agents of specific semiotic processes, engaged in a permanent dialectic relationship with the environment they are embedded in. From this dialectics important physical, social, cultural and economic changes frequently arise, redefining this way the original framework for decades to come. As Pallasmaa (2009) points out: “Architecture is existentially rooted, and it expresses fundamental existential experiences, the complex condensation of how it feels to be human being in this world. Architecture grounds and frames existence and creates specific horizons of perception, understanding and identity.” Architecture happens in the context of particular landscapes both natural and man-made, individuating spaces, assigning them an identity, turning the frequently undifferentiated physical environment into “locus”, “place”, “site”, “ort”, definitely contributing to the definition of the mental map that individual minds are able to share collectively. The fundamental role played by architectural forms in the definition of “place” and identity and in the shaping or reshaping of a physical, social and cultural environment is analysed in this paper through a case study that observes the consequences of this dynamics in the development of the social and cultural tissue of a particular city.     

Semiosis as Individuation: Integration of Multiple Orders of Magnitude

This paper proposes Gilbert Simondon’s ontogenetic theory of individuation as an overarching framework for multilevel semiosis. What renders this theory suitable for this role is the fact that it shares a significant part of its heritage with biosemiotics, which provides compatibility between them. Unlike many philosophers who have worked on individuation, Simondon envisages a general process of individuation that starts with a metastable preindividual. This process ultimately constitutes an axiomatisation of ontogenesis and manifests itself in three basic modes: physical, vital and psycho-collective. In any of these modes a transductive operation is at work resolving the disparities of the preindividual whereby new structures emerge. Depending on the mode of individuation, the emerging structures can create new disparities that ask for further individuation. Simondon refers to such conversion of structure to operation and vice versa as allagmatics. He also extends his theory to scientific methodology establishing a healthy balance between reductionism and holism. His theory can be used to amend Peircean metaphysics to improve its compatibility with contemporary scientific discourse.     

Synergy of Energy and Semiosis: Cooperation Climbs the Tree of Life

The course of biological evolution is regarded by many authors as an ascending path toward higher levels of variety, complexity and integration. There are similar but partly conflicting accounts of the nature and causes of this ascending course. With the aim of reaching a unified conception I start by summarily reviewing three notable examples. These are, in their latest presentations, those of Hoffmeyer and Stjernfelt 2015, Szathmáry 2015, and Lane 2015a. Comparison of their commonalities and divergences, combined with further reflections, leads to the following views: 1) cooperation (synergy) between preexistent traits and processes is the primary determinant in the emergence of evolutionary novelty; 2) cooperation is a triadic relation similar to semiosis (while semiosis is a particular form of cooperation); 3) regulation, the key element of both metabolism and replication, results from the cooperation of energetic and semiotic causation; 4) conceptual generalization (as in scientific reasoning) and concrete generalization (as in biological evolution) are fruits of cooperation. Conceptual generalizations spring from the cooperation of ideas. I believe these realizations supply essential elements for a unified view of the ascent of biological evolution towards higher levels of organization. Some of these conceptions are also applicable to similar ascending trajectories through the stages of cultural and technological evolution.     

Semiotics of Communication: From Semiosis of Nature to Culture

Communication Studies currently undergoes a crisis of paradigms that requires an ontological review that must begin with a debate about the conditions of possibility of every communicational phenomena. In this article we argue that semiosis offers a conceptual framework that allows for the study of communication as qualitative action. Semiosis, or the action of the sign, is here defined as a fundamental process based on perception that models the world of species, creating cognition and culture. At the core of semiosis are dynamic structures that the authors have defined as ‘ontological diagrams’. The first purpose of Semiotics of Communication is to understand how these modeling systems evolve ontologically and phylogenically, producing, in the case of human culture, means of communication ever more varied and technologically advanced.     

Learning Plants: Semiosis Between the Parts and the Whole

In this article, I explore plant semiosis with a focus on plant learning. I distinguish between the scales and levels of learning conceivable in phytosemiosis, and identify organism-scale learning as the distinguishing question for plant semiosis. Since organism-scale learning depends on organism-scale semiosis, I critically review the arguments regarding whole-plant functional cycles. I conclude that they have largely relied on Uexküllian biases that have prevented an adequate interpretation of modern plant neurobiology. Through an examination of trophic growth in plant roots, I expose some conceptual difficulties in attributing functional cycles to whole-plants. I conclude that the mapping of resource areas in the root system is a learning activity requiring higher-scale sign activity than is possible at the cellular scale, strongly suggesting the presence of organism-scale functional cycles. I do, however, question whether all perception-action cycles in organisms are accompanied with organism-scale semiosis.     

Overriding Semiosis: The Catastrophe of the Ambrym Eruption of 1913

ABSTRACT

The 1913 volcanic eruption on the island of Ambrym (Vanuatu) struck both groups composing the island’s population at the time, the Islanders and the British Presbyterians who had come to ‘civilise’ them. Through the lens of Peirce’s semiosis, particularly his notion of the ‘indexical sign’, this article examines the chronological development of the two groups’ divergent, and also at times convergent interpretations of the eruption as a sign. This semiotic analysis is then extended into the island’s socio-historical context, from the Presbyterians’ first attempts at missions to the catastrophic upheaval that decimated the island’s population until the 1940s, to study how the two groups interpreted themselves, each other, Western Christianity and the traditional Ambrymese belief and authority system.     

Demyelinating Disease: Evolution of a Paradigm

Multiple sclerosis was at one time viewed as a spiritual (God-given) disorder; only much later was it recognized as a scarring process. With advancing scientific knowledge, it was seen as a primarily demyelinating disease, later as thromboembolic in origin, and finally as inflammatory and destructive, probably an immunologic response to exogenous (infectious) agents or to one or more autoantigens. The pathogenesis of lesions was first ascribed to antibody, later to inflammatory cells, acting via a panoply of mediators, such as cytokines, adhesion molecules, chemokines, and complement components. It is now recognized as a complex disorder, in which many genetically controlled elements interact. Research on model diseases in experimental animals, both autoimmune and initiated by viral infection, has guided research on MS and similar demyelinating disorders of the CNS and PNS.     

Emergent morphogenesis: Elastic mechanics of a self-deforming tissue

Multicellular organisms are generated by coordinated cell movements during morphogenesis. Convergent extension is a key tissue movement that organizes mesoderm, ectoderm, and endoderm in vertebrate embryos. The goals of researchers studying convergent extension, and morphogenesis in general, include understanding the molecular pathways that control cell identity, establish fields of cell types, and regulate cell behaviors. Cell identity, the size and boundaries of tissues, and the behaviors exhibited by those cells shape the developing embryo; however, there is a fundamental gap between understanding the molecular pathways that control processes within single cells and understanding how cells work together to assemble multicellular structures. Theoretical and experimental biomechanics of embryonic tissues are increasingly being used to bridge that gap. The efforts to map molecular pathways and the mechanical processes underlying morphogenesis are crucial to understanding: (1) the source of birth defects, (2) the formation of tumors and progression of cancer, and (3) basic principles of tissue engineering. In this paper, we first review the process of tissue convergent extension of the vertebrate axis and then review models used to study the self-organizing movements from a mechanical perspective. We conclude by presenting a relatively simple “wedge-model” that exhibits key emergent properties of convergent extension such as the coupling between tissue stiffness, cell intercalation forces, and tissue elongation forces.     

Conceptualising a Child-Centric Paradigm

Since its inception, donor conception practices have been a reproductive choice for the infertile. Past and current practices have the potential to cause significant and lifelong harm to the offspring through loss of kinship, heritage, identity, and family health history, and possibly through introducing physical problems. Legislation and regulation in Australia that specifies that the welfare of the child born as a consequence of donor conception is paramount may therefore be in conflict with the outcomes. Altering the paradigm to a child-centric model, however, impinges on reproductive choice and rights of adults involved in the process. With some lobby groups pushing for increased reproductive choice while others emphasise offspring rights there is a dichotomy of interests that society and legislators need to address. Concepts pertaining to a shift toward a child-centric paradigm are discussed.     

The myofibroblast: Paradigm for a mechanically active cell

Tissues lose mechanical integrity when our body is injured. To rapidly restore mechanical stability a multitude of cell types can jump into action by acquiring a reparative phenotype—the myofibroblast. Here, I review the known biomechanics of myofibroblast differentiation and action and speculate on underlying mechanisms. Hallmarks of the myofibroblast are secretion of extracellular matrix, development of adhesion structures with the substrate, and formation of contractile bundles composed of actin and myosin. These cytoskeletal features not only enable the myofibroblast to remodel and contract the extracellular matrix but to adapt its activity to changes in the mechanical microenvironment. Rapid repair comes at the cost of tissue contracture due to the inability of the myofibroblast to regenerate tissue. If contracture and ECM remodeling become progressive and manifests as organ fibrosis, the outcome of myofibroblast activity will have more severe consequences than the initial damage. Whereas the pathological consequences of myofibroblast occurrence are of great interest for physicians, their mechano-responsive features render them attractive for physicists and bioengineers. Their well developed cytoskeleton and responsiveness to a plethora of cytokines fascinate cell biologists and biochemists. Finally, the question of the myofibroblast origin intrigues stem cell biologists and developmental biologists—what else can you ask from a truly interdisciplinary cell?     

Functions and Roles of Proteins: Diabetes as a Paradigm

Molecular and cellular biology has moved towards complete and accurate knowledge of how molecules behave in space and time. Protein is considered as the primary group of molecules responsible for mediating most physiological processes. Changes in the levels of proteins may lead to the altered function and are responsible for many diseases. This review provides a partial molecular explanation of biological force-ratio generation that may act to split protein into branches, and shows molecular functional divergence. Developing a non-reductionist theory of the cellular function in medicine is clearly not sufficient. Finding effective parameters of the models by characterizing molecular interactions becomes necessary. Protein interactivity and stability provides a basis for an integrated understanding of pathologies such diabetes. One example of how a mechanistic analysis of such physiological processes can be of value is the time-delay between mRNA and translation that can act as a fork allowing a slowdown in gene expression.     

Emergent growth: an auxin-mediated response

Restoration of oxygenated conditions following 15 minutes to 2 hours of anoxia causes light-grown pea (Pisum sativum L. var. Alaska) stem segments to elongate 100 to 200% more than continuously aerated segments. This "emergent growth" response takes place in the presence of 5 mm F(-), an inhibitor of anaerobic respiration; therefore, a build-up of glycolytic products does not appear to be the mechanism underlying emergent growth. "Acid growth" does not appear to account directly for the hyperelongation, as extracellular pH does not drop following a return to aerobic conditions. Studies with (14)C-indoleacetic acid indicate that auxin is freed from some previously unavailable pool during O(2)-limited treatments. We suggest, therefore, that emergent growth is a response to auxin which is released during anaerobiosis: the newly mobile or diffusible auxin promoting growth when O(2) is no longer limiting.     

Emergent properties from organisms to ecosystems: towards a realistic approach

More realistic approaches are needed to understand the complexity of ecological systems. Emergent properties of real systems can be used as a basis for a new, neither reductionist nor holistic, approach. Three systems, termed here BUBBLEs, WAVEs and CRYSTALs, have been identified as exhibiting emergent properties. They are non-hierarchical assemblages of individual components, with amplification and connectedness being two main principles that govern their build-up, maintenance and mutual relationships. Examples from various fields of biological and ecological science are referred to, ranging from individual organisms to landscapes.     

Toward a Unified Paradigm of Race

Racism in Mind. Michael Levine and Tamas Pataki, eds. Ithaca, NY: Cornell University Press, 2004. 320 pp.
Only Skin Deep: Changing Visions of the American Self. Coco Fusco and Brian Wallis, eds. New York: Harry N. Abrams, 2003. 416 pp.