Recently the terms “codes” and “information” as used in the context of molecular biology have been the subject of much discussion. Here I propose that a variety of structural realism can assist us in rethinking the concepts of DNA codes and information apart from semantic criteria. Using the genetic code as a theoretical backdrop, a necessary distinction is made between codes qua symbolic representations and information qua structure that accords with data. Structural attractors are also shown to be entailed by (...) the mapping relation that any DNA code is a part of (as the domain). In this framework, these attractors are higher-order informational structures that obviate any “DNA-centric” reductionism. In addition to the implications that are discussed, this approach validates the array of coding systems now recognized in molecular biology. (shrink)

Biological organisms appear to have agency, goals, and meaningful behaviour. One possibility is that this is mere appearance, where such properties are not real, but only ‘as if’ consequences of the physiological structure of organisms. Another possibility is that these properties are real, as emerging from the organism's structure and from how the organism interacts with its environment. Here I will discuss a recent theory showing that the latter position is most likely correct, and argue that the theory is largely (...) consistent with the basics of the field of biosemiotics. The theory can be represented as a triad that resembles the semiotic triad proposed by Peirce, which connects a sign with its object through a process of interpretation. In the theory presented, the sign is an internalized version of fitness which refers to the true fitness through a feedback loop that in effect produces interpretation. The feedback loop entangles deterministic and stochastic forms of causation in such a way that genuine agency, goal-directedness, and their associated meaning emerge. It produces a strong form of emergence not reducible to its constituents. The result is that novel phenomena arise that are real and necessary components for a complete understanding of living organisms. (shrink)

This essay employs Charles Peirce’s triadic semiotics in order to develop a biosemiotic theory of life that is capable of illuminating the function of information in living systems. Specifically, I argue that the relationship between biological information structures , selecting environments, and the adapted bodily processes of living organisms is aptly modelled by the irreducibly triadic relationship between Peirce’s sign, object, and interpretant, respectively. In each instance of information-based semiosis, the information structure is a complex informational sign that represents the (...) informational object ; and the bodily, behavioral, mental, or intellectual processes that are organized by the informational sign to more or less accurately interpret the present environment constitute a complex informational interpretant—a living, interpreting organism. The essay begins by discussing the precise sense in which this biosemiotic theory is based upon Charles Peirce’s semiotic theory. Next, the theory is developed at length in relation to genetic information structures. Finally, I present a brief outline of how the theory applies to neural and linguistic information structures. The essay concludes with a reflection upon the anti-reductionist implications of the theory. (shrink)

More than one researcher is currently proposing that the notion of information become an important element for defining living systems as well as for explaining conditions that make their origins possible. During the pre-biotic era, the type of compounds encountered would mainly have been very simple in nature and might have been immersed in the natural dynamic of the physical world and in processes of self-organization. It is furthermore quite possible that they formed a relationship between and among certain types (...) of processes that here we are specifically proposing as central for the emergence of cell organization. Consequently, an important initial step towards constructing a theory of biological information is to ask ourselves the question: how do biological systems process information? In this way, we will be contributing to the proposals of this paper where we seek to identify general principles that govern biological computing and that deal with biosemiotic approaches as they are defended in naturalistic normative terms. (shrink)

Any description of the emergence and evolution of different types of meaning processes (semiosis, sensu C.S.Peirce) in living systems must be supported by a theoretical framework which makes it possible to understand the nature and dynamics of such processes. Here we propose that the emergence of semiosis of different kinds can be understood as resulting from fundamental interactions in a triadically-organized hierarchical process. To grasp these interactions, we develop a model grounded on Stanley Salthe's hierarchical structuralism. This model can be (...) applied to establish, in a general sense, a set of theoretical constraints for explaining the instantiation of different kinds of meaning processes (iconic, indexical, symbolic) in semiotic systems. We use it to model a semiotic process in the immune system, namely, B-cell activation, in order to offer insights into the heuristic role it can play in the development of explanations for specific semiotic processes. (shrink)

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 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. 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. (shrink)

This paper examines the biosemiotic approach to the study of life processes by fashioning a series of questions that any worthwhile semiotic study of life should ask. These questions can be understood simultaneously as: (1) questions that distinguish a semiotic biology from a non-semiotic (i.e., reductionist–physicalist) one; (2) questions that any student in biosemiotics should ask when doing a case study; and (3) still currently unanswered questions of biosemiotics. In addition, some examples of previously undertaken biosemiotic case studies are examined (...) so as to suggest a broad picture of how such a biosemiotic approach to biology might be done. (shrink)

The majority of G protein-coupled receptors (GPCRs) self-assemble in the form dimeric/oligomeric complexes along the plasma membrane. Due to the molecular interactions they participate, GPCRs can potentially provide the framework for discriminating a wide variety of intercellular signals, as based on some kind of combinatorial receptor codes. GPCRs can in fact transduce signals from the external milieu by modifying the activity of such intracellular proteins as adenylyl cyclases, phospholipases and ion channels via interactions with specific G-proteins. However, in spite of (...) the number of cell functions they can actually control, both GPCRs and their associated signal transduction pathways are extremely well conserved, for only a few alleles with null or minor functional alterations have so far been found. This would seem to suggest that, beside a mechanism for DNA repairing, there must be another level of quality control that may help maintaining GPCRs rather stable throughout evolution. We propose here receptor oligomerization to be a basic molecular mechanism controlling GPCRs redundancy in many different cell types, and the plasma membrane as the first hierarchical cell structure at which selective categorical sensing may occur. Categorical sensing can be seen as the cellular capacity for identifying and ordering complex patterns of mixed signals out of a contextual matrix, i.e., the recognition of meaningful patterns out of ubiquitous signals. In this context, redundancy and degeneracy may appear as the required feature to integrate the cell system into functional units of progressively higher hierarchical levels. (shrink)

Mimicry and deception are two important issues in studies about animal communication. The reliability of animal signs and the problem of the benefits of deceiving in sign exchanges are interesting topics in the evolution of communication. In this paper, we intend to contribute to an understanding of deception by studying the case of aggressive signal mimicry in fireflies, investigated by James Lloyd. Firefly femmes fatales are specialized in mimicking the mating signals of other species of fireflies with the purpose of (...) attracting responding males to become their prey. These aggressive mimics are a major factor in the survival and reproduction of both prey and predator. It is a case of deception through active falsification of information that leads to efficient predation by femmes fatales fireflies and triggered evolutionary processes in their preys’ communicative behaviors. There are even nested coevolutionary interactions between these fireflies, leading to a remarkable system of deceptive and counterdeceptive signaling behaviors. We develop here a semiotic model of firefly deception and also consider ideas advanced by Lloyd about the evolution of communication, acknowledging that deception can be part of the explanation of why communication evolves towards increasing complexity. Increasingly complex sign exchanges between fireflies evolve in an extremely slow pace. Even if deceptive maneuvers are played out time and time again between particular firefly individuals, the evolution of the next level of complexity—and thus the next utterance in the dialogue between species—is likely to take an immense amount of generations. (shrink)

We sometimes have reasons to perform actions due to what they would communicate. Those who have discussed such reasons have understood what an action ‘communicates’ as what it conventionally expresses. Brennan and Jaworski argue that when a convention ensures that expressing the appropriate thing would be costly, we should change or flout the convention. I argue that what really matters is often what attitudes we indicate rather than conventionally express, using social science to show that indicating our attitudes is often (...) unavoidably costly, and sometimes worth the cost. I use this account to defend communicative arguments for egalitarian distributive policies. (shrink)

We argue that living systems process information such that functionality emerges in them on a continuous basis. We then provide a framework that can explain and model the normativity of biological functionality. In addition we offer an explanation of the anticipatory nature of functionality within our overall approach. We adopt a Peircean approach to Biosemiotics, and a dynamical approach to Digital-Analog relations and to the interplay between different levels of functionality in autonomous systems, taking an integrative approach. We then apply (...) the underlying biosemiotic logic to a particular biological system, giving a model of the B-Cell Receptor signaling system, in order to demonstrate how biosemiotic concepts can be used to build an account of biological information and functionality. Next we show how this framework can be used to explain and model more complex aspects of biological normativity, for example, how cross-talk between different signaling pathways can be avoided. Overall, we describe an integrated theoretical framework for the emergence of normative functions and, consequently, for the way information is transduced across several interconnected organizational levels in an autonomous system, and we demonstrate how this can be applied in real biological phenomena. Our aim is to open the way towards realistic tools for the modeling of information and normativity in autonomous biological agents. (shrink)

In this work, we propose a computational approach to the triadic model of Peircean semiosis (meaning processes). We investigate theoretical constraints about the feasibility of simulated semiosis. These constraints, which are basic requirements for the simulation of semiosis, refer to the synthesis of irreducible triadic relations (Sign–Object–Interpretant). We examine the internal organization of the triad S–O–I, that is, the relative position of its elements and how they relate to each other. We also suggest a multi-level approach based on self-organization principles. (...) In this context, semiosis is described as an emergent process. Nevertheless, the term ‘emergence’ is often used in a very informal way in the so called ‘emergent’ computation, without clear explanations and/or definitions. In this paper, we discuss in some detail the meaning of the theoretical terms ‘emergence’ and ‘emergent’, showing how such an analysis can lead to improvements of the algorithm proposed. (shrink)

This inaugural handbook documents the distinctive research field that utilizes history and philosophy in investigation of theoretical, curricular and pedagogical issues in the teaching of science and mathematics. It is contributed to by 130 researchers from 30 countries; it provides a logically structured, fully referenced guide to the ways in which science and mathematics education is, informed by the history and philosophy of these disciplines, as well as by the philosophy of education more generally. The first handbook to cover the (...) field, it lays down a much-needed marker of progress to date and provides a platform for informed and coherent future analysis and research of the subject. -/- The publication comes at a time of heightened worldwide concern over the standard of science and mathematics education, attended by fierce debate over how best to reform curricula and enliven student engagement in the subjects There is a growing recognition among educators and policy makers that the learning of science must dovetail with learning about science; this handbook is uniquely positioned as a locus for the discussion. -/- The handbook features sections on pedagogical, theoretical, national, and biographical research, setting the literature of each tradition in its historical context. Each chapter engages in an assessment of the strengths and weakness of the research addressed, and suggests potentially fruitful avenues of future research. A key element of the handbook’s broader analytical framework is its identification and examination of unnoticed philosophical assumptions in science and mathematics research. It reminds readers at a crucial juncture that there has been a long and rich tradition of historical and philosophical engagements with science and mathematics teaching, and that lessons can be learnt from these engagements for the resolution of current theoretical, curricular and pedagogical questions that face teachers and administrators. (shrink)

This book provides a comprehensive overview of my recent theoretical work that aims to explain some of the more puzzling properties of life and mind, in particular agency, goal-directedness and consciousness. It contains published papers as well as new material. Table of contents: Preface - PART I: GROUNDWORK - 1. Introduction - 2. The basic mechanism - 3. Inclusive and extensive fitness - 4. Components of F and X - 5. The consequences: a preview - PART II: LIFE - 6. (...) What qualifies as life? - 7. Biological meaning - 8. Biological functions - PART III: MIND - 9. Minimal agency, goal-directedness and value - 10. Intentionality and meaning - 11. Language - 12. Consciousness - 13. The human self - PART IV: PHILOSOPHY - 14. Strong emergence - 15. The real, the true and the good - 16. Philosophical problems of consciousness - Epilogue - Appendix A: Summaries of computational simulations - Appendix B: Examples of minimal intentionality - References. -/- . (shrink)