Biological Information

Humans are cognitive entities. Our ongoing interactions with the environment are threaded with creations and usages of meaningful information. Animal life is also populated with meaningful information related to survival constraints. Information managed by artificial agents can also be considered as having meanings, as derived from the designer. Such perspective brings us to propose an evolutionary approach to cognition based on meaningful information management. We use a systemic tool, the Meaning Generator System (MGS), and apply it consecutively to animals, humans (...) and artificial agents [1, 2]. The MGS receives information from its environment and compares it with its constraint. The generated meaning is the connection existing between the received information and the constraint. It triggers an action aimed at satisfying the constraint. The action modifies the environment and the generated meaning. Meaning generation links agents to their environments. The MGS is a system: a set of elements linked by a set of relations. Any system submitted to a constraint and capable of receiving information can lead to a MGS. Animals, humans and robots are agents containing MGSs dealing with different constraints. Similar MGSs carrying different constraints will generate different meanings. Cognition is system dependent. Contrary to approaches on meaning generation based on psychology or linguistics, the MGS approach is not based on human mind. We want to avoid the circularity of taking human mind as a starting point. Free will and self-consciousness participate to the management of human meanings. They do not exist for animals or robots. Staying alive is a constraint that we share with animals. Robots ignore that constraint. We first use the MGS for animals with “stay alive” and “group life” constraints. The analysis of meaning and cognition in animals is however limited by our un-complete understanding of the nature of life (the question of final causes). Extending the analysis of meaning generation and cognition to humans is complex and has some true limitations as the nature of human mind is a mystery for today science and philosophy. The natures of our feelings, free will or self-consciousness are unknown. Approaches to identify human constraints are however possible, where the MGS can highlight some openings [3, 4]. Modeling meaning management in artificial agents is rather straightforward with the MGS. We, the designers, know the agents and the constraints. The derived nature of constraints, meaning and cognition is however to be highlighted. We define a meaningful representation of an item for an agent as being the networks of meanings relative to the item for the agent, with the action scenarios involving the item. Such meaningful representations embed the agents in their environments and are far from the GOFAI type of representations. Cognition, meanings and representations exist by and for the agents. We finish by summarizing the points presented here and highlight possible continuations . [1] “Information and Meaning” [2] “Introduction to a systemic theory of meaning” [3] “Computation on Information, Meaning and Representations. An Evolutionary Approach” [4] “Proposal for a shared evolutionary nature of language and consciousness”. (shrink)

In this paper, we use the Meaning Generator System (MGS) presented at Gathering in Biosemiotics 2 [1] to analyse the evolution of meaningful information generation through different steps of the evolution of life. Taking as a starting point the usage of MGS for vital constraint satisfaction in basic life (paramecium), we develop its application for more complex living elements up to the case of non-human primate. The thread we follow is relative to the identification of new constraints that can appear (...) through evolution of life, and correspondingly participate to generation of new types of meaningful information. We show that beside the complexification of vital constraints to be satisfied, and in addition to the corresponding enrichment of their satisfaction processes, there is a step in evolution that naturally introduces some specific new constraint in living elements. This step is the one corresponding to the performance of self-representation. Self-representation appeared in evolution at the level of non-human primates. We present the content of self-representation and show that it has a direct consequence on the living element in terms of a new type of constraint to be satisfied. We show that this new constraint participates to the generation of a new set of meaningful information via the MGS, and that the satisfaction of the constraint introduces some natural formulation of emotion generation during the evolution of life. [1]. (shrink)

The presentation proposes to complement an existing development on meaning generation for animals, humans and artificial agents by looking at what could have existed at pre-biotic times and what could be a post-human meaning generation. The core of the approach is based on an existing model for meaning generation: the Meaning Generator System (MGS). The MGS is part of an agent submitted to an internal constraint. The MGS generates a meaning when it receives an information that has a connection with (...) the constraint. The generated meaning is used by the agent to implement an action (physical, biological or mental) aimed at satisfying the constraint. The action can be in or out the agent. The purpose of the presentation is to widen the MGS approach in order to reach a coverage for information, constraint and meaning from a pre-biotic level to a possible post-human one. We present the MGS for animals, humans and artificial agents with the corresponding constraints. We then look at what could have been a constraint at a pre-biotic far from thermodynamic equilibrium level. At the other end of the spectrum we look at a possible post-human status with an evolution of a ‘limit anxiety’ human constraint and also with AAs submitted to animal or human type constraints. Such approach links information science with physics, evolution, anthropology, semiotics and human mind. Continuations are proposed. (shrink)

The relations between life and cogntion have been addressed through different perspectives [Stewart 1996, Boden 2001, Bourgine and Stewart 2004, van Duijn & all 2006, Di Paolo 2009]. We would like here to address that subject by relating life to cognition through a process of meaning generation. Life emerged on earth as a far from thermodynamic equilibrium performance that had to maintain herself. Life is charactertized by a ‘stay alive’ constraint that has to be satisfied (such constraint can be included (...) in the constraint of being able to maintain far from equilibrium thermodynamic conditions [Bickhard 2011]). The local ‘stay alive‘ constraint has to be satisfied in an environment containing elements potentially supportive or harmfull. A key activity for the living entity is to characterize these elements in terms of meaningfulness relatively to the ‘stay alive’ constraint. This process can be modeled with an existing tool where a system submitted to an internal constraint generates meaningful information characterizing elements of the environment: the Meaning Generator System (MGS) [Menant, 2003, 2014 a]. In a few words: when a system submitted to an internal constraint receives from the environment an information that has a connection with the constraint it generates a meaning usable for the implementation of an action satisfying the constraint.The generated meaning is the connection existing between the received information and the constraint. The MGS models this process and interfaces to the action implementation for constraint satisfaction The meaning is generated by and for the system. The MGS grounds meaning generation in constraint satisfaction and links the living entity to her environment in a relational process. A simple example is with a paramecium close to a drop of acid. The paramecium which is submitted to a ‘stay alive’ constraint will move away from the acid area. The received information ‘presence of acid’ generates the meaning ‘acid not compatible with the ‘stay alive’ constraint‘ which triggers the moving away action (that example is close to Varela’s bacteria swimming up a sugar gradient. What the MGS brings in addition is a modeling of the significance of the chemical gradient for the organism). The action implemented to satisfy the constraint modifies the environment and the received information, establishing an interactive process linking the living entity to her environment. During its evolution animal life has elaborated new constraints (like ‘live group life’) and new functions enriching meaning generation and action scenarios. As a result the build up of meaningful representations has improved the constraint satisfaction processes of animals, embedding them in their environments in relational and interactive terms [Menant, 2011]. Cognition can be defined by proposing that ‘a system is cognitive if and only if sensory inputs serve to trigger actions in a specific way, so as to satisfy a viability constraint’ [Bourgine, Stewart 2004]. Cognition can also be considered as exemplifying a ‘vital criterion of responsiveness’ [Boden, 2001 ]. Consequently the MGS can be positioned as an elementary and generic version of animal cognition. For animal life, meaning generation for internal constraint satisfaction links life and cognition in a relational and interactive process. Cognition for human life is more complex as new performances have to be taken into account like self-consciousness and free-will. Meaning generation at human level is a challenging subject as human constraints are not clearly understood [Menant, 2011]. Many research activities are in process looking for some understanding of human mind [Philpapers]. One area of investigation is an evolutionary approach to self-consciousness using meaning generation where anxiety limitation comes up as a generic human constraint [Menant, 2014 b]. Assuming that we can have clear enough an understanding of some human constraints, we can look at the MGS for partly extending to humans the link between life and cognition that has been established for animals. So overall, we can consider that the MGS approach makes available an evolutionary link between life and cognition for animals, and partly for humans. A characteristic of the proposed system approach to meaning generation is the possibility to use it for any type of agent, be it organic (with intrinsic constraints ) or artificial (with derived constraints). Such characterization of agents through meaning generation can be used to discriminate artificial itelligence from human intelligence (see the MGS usage to support Searle’s chinese room argument [Menant, 2013]). On a more general basis, the proposed system approach can positions the MGS as a simple model for an internal source of normativity. It’s usage as a simple building block allows a bottom-up modeling for normativity in the sensorimotor approach. The ‘stay alive’ constraint could also be taken as a starting point for an evolutionary grounding of sensorimotor norms ‘in the biological normativity of the agent as a whole’ [Di Paolo & all 2014]. The proposed presentation will develop the points summarized here above and position them relatively to the autopoietic and enactive approaches. Several possible continuations will also be highlighted. (shrink)

There is an increasing agreement in the cognitive sciences community that our sensations are closely related to our actions. Our actions impact our sensations from the environment and the knowledge we have of it. Cognition is grounded in sensori-motor coordination. In the perspective of implementing such a performance in artificial systems, there is a need for a model of sensori-motor coordination. We propose here such a model as based on the generation of meaningful information by a system submitted to a (...) constraint [1]. Systems and agents have constraints to satisfy which are related to their nature (stay alive for an organism, avoid obstacle for a robot, …). We propose here to use an existing meaning generation process where a system submitted to a constraint generates a meaningful information (a meaning) when it receives an information that has a connection with the constraint [2]. The generated meaning is precisely the connection existing between the received information and the constraint of the system. The generated meaning is used to trigger an action that will satisfy the constraint. The generated meaning links the system to its environment. A Meaning Generator System (MGS) has been introduced as a building block for higher level systems (agents). The MGS allows to link sensation and action through the satisfaction of the constraint of the system/agent. We use the MGS in a model which is based on constraint satisfaction for sensori-motor coordination in agents, be they organic or artificial. The meaning is generated by and for the agent that hosts the MGS. Such approach makes possible an addressing of the concept of autonomy through the intrinsic or artificial nature of the constraint to be satisfied (organisms with intrinsic constraints/autonomy, artificial systems with artificial constraints/autonomy). The systemic nature of the MGS also allows to position the groundings of the generated meaning as being in or out of the MGS, and correspondingly identify the constructivist and objectivist components of the generated meaning. The approach presented here makes available a sensori-motor coordination by meaning generation through constraint satisfaction with groundings of the generated meaning. (shrink)

Several authors have used the notion of causal specificity in order to defend non-parity about genetic causes (Waters 2007, Woodward 2010, Weber 2017, forthcoming). Non-parity in this context is the idea that DNA and some other biomolecules that are often described as information-bearers by biologists play a unique role in life processes, an idea that has been challenged by Developmental Systems Theory (e.g., Oyama 2000). Indeed, it has proven to be quite difficult to state clearly what the alleged special role (...) of genetic causes consists in. In this paper, I show that the set of biomolecules that are normally considered to be information-bearers (DNA, mRNA) can be shown to be the most specific causes of protein primary structure, provided that causal specificity is measured over a relevant space of biological possibilities, disregarding physical as well as logically possible states of the causal variables. (shrink)

To explore how molecules became signs I will ask: “What sort of process is necessary and sufficient to treat a molecule as a sign?” This requires focusing on the interpreting system and its interpretive competence. To avoid assuming any properties that need to be explained I develop what I consider to be a simplest possible molecular model system which only assumes known physics and chemistry but nevertheless exemplifies the interpretive properties of interest. Three progressively more complex variants of this model (...) of interpretive competence are developed that roughly parallel an icon-index-symbol hierarchic scaffolding logic. The implication of this analysis is a reversal of the current dogma of molecular and evolutionary biology which treats molecules like DNA and RNA as the original sources of biological information. Instead I argue that the structural characteristics of these molecules have provided semiotic affordances that the interpretive dynamics of viruses and cells have taken advantage of. These molecules are not the source of biological information but are instead semiotic artifacts onto which dynamical functional constraints have been progressively offloaded during the course of evolution. (shrink)

In spite of being ubiquitous in life sciences, the concept of information is harshly criticized. Uses of the concept other than those derived from Shannon's theory are denounced as pernicious metaphors. We perform a computational experiment to explore whether Shannon's information is adequate to describe the uses of said concept in commonplace scientific practice. Our results show that semantic sequences do not have unique complexity values different from the value of meaningless sequences. This result suggests that quantitative theoretical frameworks do (...) not account fully for the complex phenomenon that the term “information” refers to. We propose a restructuring of the concept into two related, but independent notions, and conclude that a complete theory of biological information must account completely not only for both notions, but also for the relationship between them. (shrink)

Forty-two years ago, Capra published “The Tao of Physics” (Capra, 1975). In this book (page 17) he writes: “The exploration of the atomic and subatomic world in the twentieth century has …. necessitated a radical revision of many of our basic concepts” and that, unlike ‘classical’ physics, the sub-atomic and quantum “modern physics” shows resonances with Eastern thoughts and “leads us to a view of the world which is very similar to the views held by mystics of all ages and (...) traditions.“ This article stresses an analogous situation in biology with respect to a new theoretical approach for studying living systems, Integral Biomathics (IB), which also exhibits some resonances with Eastern thought. Stepping on earlier research in cybernetics1 and theoretical biology,2 IB has been developed since 2011 by over 100 scientists from a number of disciplines who have been exploring a substantial set of theoretical frameworks. From that effort, the need for a robust core model utilizing advanced mathematics and computation adequate for understanding the behavior of organisms as dynamic wholes was identified. At this end, the authors of this article have proposed WLIMES (Ehresmann and Simeonov, 2012), a formal theory for modeling living systems integrating both the Memory Evolutive Systems (Ehresmann and Vanbremeersch, 2007) and the Wandering Logic Intelligence (Simeonov, 2002b). Its principles will be recalled here with respect to their resonances to Eastern thought. (shrink)

The goal of this paper is to show that the information carried by a structural representation can be decomposed into the information carried by its component parts. In particular, the relations between the components of a structural representation carry quantifiable information about the relations between components of their signifieds. It follows that the information carried by cognitive structural representations, including cognitive maps, can in principle be quantified and decomposed. This is perhaps surprising given that the formal tools of communication theory (...) have typically only been applied to simpler representation-like states without significant structure, such as detectors or indicators. In the final section I consider using computational complexity theory to capture the processing advantages afforded by structural representation. (shrink)

Evoke is a Python library for evolutionary simulations of signalling games. It offers a simple and intuitive API that can be used to analyze arbitrary game-theoretic models, and to easily reproduce and customize well-known results and figures from the literature.

Техника представления информации о внешнем и внутреннем мире постоянно развивается, и сейчас она достигла уровня отображения реальности в многообразных её проявлениях и измерениях, прежде недоступных человеческому восприятию. Язык, текст, фотография, звукозапись, а теперь ещё и техника искусственного интеллекта для моделирования человеческой субъектности и её описания в доступной для человеческого понимания форме, стали эпохальными событиями в теории информации. Однако несмотря на то, что на данном этапе её развития она позволяет оперировать с непрерывно возрастающими объёмами информации, это не приближает её теоретиков к (...) постижению сути того, что определяется как реальность, бытие, и сознание. Но поскольку никакого другого способа достичь этой цели нет, кроме изучения того, как это происходит в процессе восприятия и преобразования информации у живых существ, и в частности, у человека, необходимо разобраться в принципах этого процесса. (shrink)

The concept of regulation pervades biology, for example in models of genetic regulatory networks and the endocrine system. Regulation has a normative opposite, dysregulation, which figures prominently in biomedical models of disease. The use of normative concepts in biology, however, has been thought to present some challenges for the physicalist view of the world, and various resolutions have been proposed. Up to now the problem of biological normativity has been debated largely in connection with the concept of biological information. In (...) this paper we shift focus to the concept of biological regulation, proposing that it provides a promising new approach to these issues. Models of regulatory systems have several features: they are causal, but they do not deal with the energy exchanges and transformations covered by physics and chemistry; further, and entirely connected, regulatory systems can break down, and this is because they and their causal-regulatory properties are dependent on fragile molecular structures. Biological regulatory systems exhibit normativity, because they are not determined by physical and chemical laws, but their close relationship with physical laws and physicalist ontology is transparent. (shrink)

(Back Cover:) « La pensée métaphysique renaîtra demain. Ce sont des savants qui ont le goût et le sens de la pensée conduite jusqu’au terme de ses exigences internes, et des philosophes initiés aux sciences expérimentales qui, en commun, la feront. » L’œuvre de Claude Tresmontant (1925-1997) illustre parfaitement cette recherche de la métaphysique d’un monde en devenir, qui sait écouter et se modeler sur la transformation – la métamorphose – promise à une Création finalisée. Le trait commun aux exposés (...) ici présentés sous forme définitive a été cette recherche autour d’une pensée qui renouvelle de l’intérieur la métaphysique en réalisant le vœu de Bergson qu’elle devienne « auscultatrice », que l’énigme que pose l’homme face à son origine et sa destinée ne soit pas recouverte par une pensée qui se perdrait dans la description des choses ou dans l’esprit de système, mais qui non plus n’irait se recroqueviller sur elle-même, en narrant sa propre expérience subjective sous le mode de la déréliction. Claude Tresmontant a su penser l’être en genèse, et il a cherché à renouveler la question de l’existence de Dieu, en en transformant la problématique en dialogue avec les sciences contemporaines. À ce goût de l’être dont les sciences ont renouvelé l’approche, il a également voulu infuser un « supplément d’âme », en repensant la réalité de la création et l’horizon de la cause finale, toujours à partir de la nature ultimement théologique de la réponse à la question « qu’est-ce que l’homme ? » Contributeurs : Yves Tourenne, Philippe Gagnon, Fabien Revol, Brunor, Frédéric Crouslé, Bertrand Souchard, Emmanuel Gabellieri. Table of Contents: Note Liminaire (Ph. Gagnon) - 7 En quoi la pensée de Claude Tresmontant nous stimule-t-elle encore ? Hommage et critique (Y. Tourenne) - 13 L’imbrication de la preuve de Dieu et de la cosmologie chez Tresmontant représente-t-elle une preuve ? (Ph. Gagnon) - 27 L’usage apologétique de la philosophie de Tresmontant dans les Indices pensables de Brunor (F. Revol) - 49 Réponse à Fabien Revol (Brunor) - 77 Qu’est-ce qui cloche dans la théologie de Claude Tresmontant ? (Fr. Crouslé) - 85 Les métaphysiques principales de Claude Tresmontant : la foi biblique est-elle à part de la raison philosophique grecque ? (B. Souchard) - 109 Maurice Blondel et Claude Tresmontant (E. Gabellieri) - 123 La vision informationnelle de Tresmontant, surtout en référence au problème de l’âme (Ph. Gagnon) - 133. (shrink)

In “An introduction to phytosemiotics”, a masterwork of integration, Kalevi Kull defended Martin Krampen’s notion of phytosemiotics. In doing so, he developed the notion of vegetative semiosis. In a later work, he argued that vegetative semiosis is not a branch of semiotics, and so should not be identified with phytosemiotics. Rather, vegetative semiosis is a basic form of semiosis and the condition for animal semiosis, which in turn is the condition for cultural semiosis. All multi-celled organisms, including plants, animals and (...) humans, are characterized by vegetative semiosis. While clearly influenced by Aristotle (and Thomas Aquinas), this characterization of vegetative semiosis makes it easier to relate biosemiotics to current science, to integrate current science into biosemiotics, and thereby to greatly expand the research potential of biosemiotics. (shrink)

Over the last fifteen years, an ambitious explanatory framework has been proposed to unify explanations across biology and cognitive science. Active inference, whose most famous tenet is the free energy principle, has inspired excitement and confusion in equal measure. Here, we lay the ground for proper critical analysis of active inference, in three ways. First, we give simplified versions of its core mathematical models. Second, we outline the historical development of active inference and its relationship to other theoretical approaches. Third, (...) we describe three different kinds of claim -- labelled mathematical, empirical and general -- routinely made by proponents of the framework, and suggest dialectical links between them. Overall, we aim to increase philosophical understanding of active inference so that it may be more readily evaluated. -/- This the final submitted version of the Introduction to the Topical Collection "The Free Energy Principle: From Biology to Cognition", forthcoming in Biology & Philosophy. (shrink)

The field of the philosophy of biology is flourishing in its aim to evaluate and rethink the view inherited from the previous century ---the Modern Synthesis. Different research areas and theories have come to the fore in the last decades in order to account for different biological phenomena that, in the first instance, fall beyond the explanatory scope of the Modern Synthesis. This thesis is anchored and motivated by this revolt in the philosophy of biology. -/- The central target in (...) this context is the possibility of naturalizing teleology, a classical nightmare for the history of biology itself. This requires, principally, understanding the causes of teleological explanations without assuming an unfashioned backward causation of sorts. As the riddles of teleological explanations are about their temporal dimension, I analyze different temporal scales of biological processes: evolutionary, developmental, and physiological. -/- The first one is the one defended in the context of the Modern Synthesis. As expected, one of the aims of this thesis is to evaluate the adequacy of an evolutionary account of teleological explanation. The scrutiny is negative. Evolutionary explanations in the context of the Modern Synthesis lack the necessary causal roots to naturalize teleology. Concerning the physiological scale, a long tradition pushed up by Kant and the organicist movement in the 20th century allows us to better understand how teleological explanations can be naturalized in physiological process. The key notions in this temporal scale are self-organization and the recursive, looped character of physiological process. While the physiological scale may be suitably accounted by contemporaries views, such as Autonomous Systems Theory, different central teleological phenomena remain unexplained from a purely physiological perspective. In particular, different issues concerning the (adaptive) construction of organism ---such as plasticity, robustness, variation, novelty, inheritance--- deserve an ontogenetic analysis. -/- The principal aim of this thesis is to provide a theory of teleological development that falls beyond the Modern Synthesis' framework and is prompted by different insights from the history of biology. I call it Agential Teleosemantics. It rests on two central pillars. First, that developmental processes, beyond any gene-centered stance, can be understood in informational terms; i.e. developmental processes are about the interaction of developmental resources conveying biological information. The second ingredient is agentivity, namely the idea that development is regulated by an agentive system according to the adaptiveness of the phenotypic outcomes produced. The role of agency in Agential Teleosemantic is equivalent to the role of genes in the Modern Synthesis: it is responsible for explaining the order and the adaptive complexity in the living realm. -/- The second target of this thesis regards the possibility of naturalizing intentional explanations in cognitive science. The central project involved in such an aim is known as teleosemantics. Classical teleosemantics however is etiological: it explains the teleofunctions of representational systems in terms of evolutionary processes. The different disputes in the contemporary philosophy of biology provide two insights to analyze teleosemantics in cognitive science. First, the challenges against the Modern Synthesis must be extended to the evolutionary approach of etiological teleosemantics. Second, as Agential Teleosemantics suggests an alternative source for teleofunctions ---ontogeny, I offer an attempt to integrate Agential Teleosemantics into cognitive science in order to provide an alternative teleosemantic project to understand intentional explanations in cognitive science. (shrink)

There is a deep-seated neopositivist view which regards the language of science as a neutral medium of communication, radically different from indirect symbolic forms of discourse characteristic of arts and humanities. But naturalists, like poets and social scientists, also draw on the dominant images in their culture to organize their thoughts and simplify complex concepts. By conceptualizing one thing in terms of another, metaphors in science not only aid mutual communication between researchers but also structure their understanding of experience and (...) reality. Too transparent to be noticed and critically analyzed within the framework of science itself, metaphors act as lenses, making selected aspects of complex phenomena visible to study and investigation (Reynolds 2018). By linking two seemingly unrelated ideas, for example, those of a machine and DNA replication, metaphors establish new interactions of meaning evoking shared associated connotations between these interacting concepts (Black 1962). This, in turn, may not only transform the perception of a target domain but also open up new prospects for experimental and interpretative avenues. Understanding Metaphors by Andrew Reynolds draws on this vision of metaphors as indispensable tools of scientific thinking to elucidate their role in the life sciences. (shrink)

In all kinds of implementations of computing, whether technological or biological, some material carrier for the information exists, so in real-world implementations, the propagation speed of information cannot exceed the speed of its carrier. Because of this limitation, one must also consider the transfer time between computing units for any implementation. We need a different mathematical method to consider this limitation: classic mathematics can only describe infinitely fast and small computing system implementations. The difference between mathematical handling methods leads to (...) different descriptions of the computing features of the systems. The proposed handling also explains why biological implementations can have lifelong learning and technological ones cannot. Our conclusion about learning matches published experimental evidence, both in biological and technological computing. (shrink)

In this article we offer a two-part commentary on Bolton and Gillett’s reconceptualization of Engel’s biopsychosocial model. In the first section we present a conceptual and historical assessment of the biopsychosocial model that differs from the analysis by Bolton and Gillett. Specifically, we point out that Engel in his vision of the biopsychosocial model was less concerned with the ontological possibility and nature of psychosocial causes, and more concerned with psychosocial influences in the form of illness interpretation and presentation, sick (...) role, seeking or rejection of care, the doctor-patient therapeutic relationship, and role of personality factors and family relationships in recovery from illness, etc. On the basis of this assessment, we then question Bolton and Gillett’s restricted focus on accounting for biopsychosocial causal interactions. The second section compares Bolton and Gillett’s account with a recent enactivist account of mental disorder that tackles similar conceptual problems of causal interactions. Bolton and Gillett’s utilize elements of the 4E cognition, but they combine these proto-ideas with an information-processing paradigm. Given their explicit endorsement of 4E approaches to mind and cognition, we illustrate some key ways in which a more fleshed out enactive account, particularly one that doesn’t rely on notions of information-processing, differs from the account proposed by Bolton and Gillett. (shrink)

Biological and cognitive sciences rely heavily on the idea of information transmitted between natural events or processes. This paper critically assesses some current philosophical views of natural information and defends a view of natural information as Nomic and Factive. Dretske offered a Factive view of information, and recent work on the topic has tended to reject this aspect of his view in favor of a non-Factive, probabilistic approach. This paper argues that the reasoning behind this move to non-Factivity is flawed (...) and mixes up different problems with Dretske’s original view. I show that one of these problems—strictness—has to do with Nomicity rather than Factivity. The other problem—reference class ambiguity—is not solvable just in terms of a theory of natural information. On the Dretske-inspired view I defend, natural information is Factive and Nomic but is insufficient to determine the cognitive or biological content of a natural process. In sum I present an examination what natural information is and what role it can play in our understanding of living and thinking things. (shrink)

I respond to the 4 commentaries by Awais Aftab & Kristopher Nielsen, Hane Htut Maung, Diane O’Leary and Kathryn Tabb under 3 main headings: “What is the BPSM really?” & Why update it?; “Is our approach foundationally compromised?”, and finally, “Antagonists or fellow travellers?”.

The primary focus of this project is the silent and subvocal speech-recognition interface unveiled in 2018 as an ambulatory device wearable on the neck that detects a myoelectrical signature by electrodes worn on the surface of the face, throat, and neck. These emerge from an alleged “intending to speak” by the wearer silently-saying-something-to-oneself. This inner voice is believed to occur while one reads in silence or mentally talks to oneself. The artifice does not require spoken sounds, opening the mouth, or (...) any explicit or external movement of the lips. The essay then considers such subvocal “speech” as a mode of writing or saying and the interior of the mouth or oral cavity as its writing surface. It briefly revisits discussions of telepathy to recontextualize Heidegger’s warning against enframing language exclusively within calculative technics and physiology, which he suggests is detrimental to Mundarten (mouth-modes of regional dialects). It closes in reconsideration of Husserl’s phenomenology of language and meaning in Ideas as it might apply to subvocal speech-recognition interfaces. It suggests ways by which the electrophysiology that the device detects and deciphers (as an alleged intention of a presumed natural language unspoken vocally or aloud) might supplement Husserl’s insinuation of the Leiblichkeit of language through a self-stamping extraction of an extension of meaning. (shrink)

The free-energy principle states that all systems that minimize their free energy resist a tendency to physical disintegration. Originally proposed to account for perception, learning, and action, the free-energy principle has been applied to the evolution, development, morphology, anatomy and function of the brain, and has been called a postulate, an unfalsifiable principle, a natural law, and an imperative. While it might afford a theoretical foundation for understanding the relationship between environment, life, and mind, its epistemic status is unclear. Also (...) unclear is how the free-energy principle relates to prominent theoretical approaches to life science phenomena, such as organicism and mechanism. This paper clarifies both issues, and identifies limits and prospects for the free-energy principle as a first principle in the life sciences. (shrink)

The author argues that the reductionist illusions of the Modern Synthesis, which Noble criticizes in his target article, are to a large extent resulting from a mere syntactical notion of biological information, neglecting the pragmatic and semantic dimension of information. Although the syntactical notion, introduced by Shannon, has been applied with much success in information theory and computer technologies, it is too narrow to understand biological reality. Biosemiotics can help to clarify the problems identified by Noble, and offers a more (...) adequate biological information concept, which not only may help to overcome these problems in the life sciences, but may also serve to integrate natural-scientific and humanities approaches to life. (shrink)

Theoretical minimal RNA rings are candidate primordial genes evolved for non‐redundant coding of the genetic code's 22 coding signals (one codon per biogenic amino acid, a start and a stop codon) over the shortest possible length: 29520 22‐nucleotide‐long RNA rings solve this min‐max constraint. Numerous RNA ring properties are reminiscent of natural genes. Here we present analyses showing that all RNA rings lack dinucleotide CG (a mutable, chemically instable dinucleotide coding for Arginine), bearing a resemblance to known CG‐depleted genomes. CG (...) in “incomplete” RNA rings (not coding for all coding signals, with only 3–12 nucleotides) gradually decreases towards CG absence in complete, 22‐nucleotide‐long RNA rings. Presumably, feedback loops during RNA ring growth during evolution (when amino acid assignment fixed the genetic code) assigned Arg to codons lacking CG (AGR) to avoid CG. Hence, as a chemical property of base pairs, CG mutability restructured the genetic code, thereby establishing itself as genetically encoded biological information. (shrink)

In The Biopsychosocial Model of Health and Disease, Derek Bolton and Grant Gillett argue that a defensible updated version of the biopsychosocial model requires a metaphysically adequate account of disease causation that can accommodate biological, psychological, and social factors. This present paper offers a philosophical critique of their account of biopsychosocial causation. I argue that their account relies on claims about the normativity and the semantic content of biological information that are metaphysically contentious. Moreover, I suggest that these claims are (...) unnecessary for a defence of biopsychosocial causation, as the roles of multiple and diverse factors in disease causation can be readily accommodated by a more widely accepted and less metaphysically contentious account of causation. I then raise the more general concern that they are misdiagnosing the problem with the traditional version of the biopsychosocial model. The challenge when developing an explanatorily valuable version of the biopsychosocial model, I argue, is not so much providing an adequate account of biopsychosocial causation, but providing an adequate account of causal selection. Finally, I consider how this problem may be solved to arrive at a more explanatorily valuable and clinically useful version of the biopsychosocial model. (shrink)

In recent years the philosophy of information has emerged as an important area of research in philosophy. However, until now information’s philosophical history has been largely overlooked. Information and the History of Philosophy is the first comprehensive investigation of the history of philosophical questions around information, including work from before the Common Era to the twenty-first century. It covers scientific and technology-centred notions of information; views of human information processing, as well as socio-political topics such as the control and use (...) of information in societies. Organised into five parts, nineteen chapters by an international team of contributors cover the following topics and more: Information before 500 CE, including ancient Chinese, Greek and Roman approaches to information Early theories of information processing, sources of information and cognition Information and computation in Leibniz, visualised scientific information, copyright and social reform The nineteenth century, including biological information, knowledge economies, and information’s role in empire and eugenics Recent and contemporary philosophy of information, including racialized information, Shannon information, and the very idea of an information revolution. Information and the History of Philosophy is a landmark publication in this emerging field. As such, it is essential reading for students and researchers in the history of philosophy, philosophy of science and technology, and library and information studies. It is also a valuable resource for those working in subjects such as the history of science, media and communication studies, and intellectual history. (shrink)

Deacon’s target article is a welcome contribution not only on “biological information” but, more generally, on representation in cognitive science. Some kind of explanation and justification for use of the terms “representation” and “interpretant” for primordial autogen system would be helpful. A connection between the notions of “information” and “representation” can be elaborated more in this respect.

The key assumption behind evolutionary epistemology is that animals are active learners or ‘knowers’. In the present study, I updated the concept of natural learning, developed by Henry Plotkin and John Odling-Smee, by expanding it from the animal-only territory to the biosphere-as-a-whole territory. In the new interpretation of natural learning the concept of biological information, guided by Peter Corning’s concept of “control information”, becomes the ‘glue’ holding the organism–environment interactions together. The control information guides biological systems, from bacteria to ecosystems, (...) in the process of natural learning executed by the universal algorithm. This algorithm, summarized by the acronym IGPT (information-gain-process-translate) incorporates natural cognitive methods including sensing/perception, memory, communication, and decision-making. Finally, the biosphere becomes the distributed network of communicative interactions between biological systems termed the interactome. The concept of interactome is based on Gregory Bateson’s natural epistemology known as the “ecology of mind”. Mimicking Bateson’s approach, the interactome may also be designated “physiology of mind”—the principle behind regulating the biosphere homeostasis. (shrink)

There are many different notions of information in logic, epistemology, psychology, biology and cognitive science, which are employed differently in each discipline, often with little overlap. Since our interest here is in biological processes and organisms, we develop a taxonomy of functional information that extends the standard cue/signal distinction (in animal communication theory). Three general, main claims are advanced here. (1) This new taxonomy can be useful in describing learning and communication. (2) It avoids some problems that the natural/non-natural information (...) distinction faces. (3) Functional information is​ ​produced through exploration and stabilisation processes. (shrink)

Starting from a philosophical perspective, which states that the living structures are actually a combination between matter and information, this article presents the results on an analysis of the bipolar information-matter structure of the human organism, distinguishing three fundamental circuits for its survival, which demonstrates and supports this statement, as a base for further development of the informational model of consciousness to a general informational model of the human organism. For this, it was examined the Informational System of the Human (...) Body and its components from the perspective of the physics/information/neurosciences concepts, showing specific functions of each of them, highlighting the correspondence of these centers with brain support areas and with their projections in consciousness, which are: Center of Acquisition and Storing of Information (CASI) reflected in consciousness as memory, Center of Decision and Command (CDC) (decision), Info-Emotional Center (IES) (emotions), Maintenance Informational System (MIS) (personal status), Genetic Transmission System (GTS) (associativity/genetic transmission) and Info Genetic Generator (IGG) related by the body development and inherited behaviors. The Info Connection (IC), detected in consciousness as trust and confidence can explain the Near-Death Experiences (NDEs) and associated phenomena. This connection is antientropic and informational, because from the multitude of uncertain possibilities is selected a certain one, helping/supporting the survival and life. The human body appears therefore as a bipolar structure, connected to two poles: information and matter. It is argued that the survival, which is the main objective of the organism, is complied in three main ways, by means of: (i) the reactive operation for adaptation by attitude; (ii) the info-genetic integration of information by epigenetic processes and genetic transmission of information for species survival, both circuits (i) and (ii) being associated to the information pole; (iii) maintenance of the material body (defined as informed matter) and its functions, associated to the matter pole of the organism. It results therefore that the informational system of the human body is supported by seven informational circuits formed by the neuro-connections between the specific zones of the brain corresponding to the informational subsystems, the cognitive centers, the sensors, transducers and execution (motor/mobile) elements. The fundamental informational circuits assuring the survival are the reactive circuit, expressible by attitude, the epigenetic/genetic circuit, absorbing and codifying information to be transmitted to the next generations, and the metabolic circuit, connected to matter (matter pole). The presented analysis allows to extend the informational modeling of consciousness to an Informational Model of Consciousness and Organism, fully describing the composition/functions of the organism in terms of information/matter and neurosciences concept. (shrink)

The concept of information and its relation to biosemiotics is a major area of contention among biosemioticians. Biosemioticians influenced by von Uexküll, Sebeok, Bateson and Peirce are critical of the way the concept as developed in information science has been applied to biology, while others believe that for biosemiotics to gain acceptance it will have to embrace information science and distance biosemiotics from Peirce’s philosophical work. Here I will defend the influence of Peirce on biosemiotics, arguing that information science and (...) biosemiotics as these were originally formulated are radically opposed research traditions. Failure to appreciate this will undermine the challenge of biosemiotics and other anti-reductionist traditions to mainstream science with its reductionist ambition to explain everything through physics. However, for this challenge to be successful, it will be necessary to respond to criticisms of Peircian ideas, jettisoning ideas that are no longer defensible and integrating ideas allied to his anti-reductionist agenda. Here I will argue that the natural philosophy of Gilbert Simondon, offering a searching critique of the application of the new concept of information and cybernetics to the life and human sciences, provides the means to defend and advance Peirce’s core ideas and thereby defend post-reductionist biosemiotics. (shrink)

The teleosemantic theory of representational content is held by some philosophers to imply that genes carry semantic information about whole-organism phenotypes. In this paper, I argue that this position is not supported by empirical findings. I focus on one of the most elaborate defenses of this position: Shea’s view that genes represent whole-organism phenotypes. I distinguish between two ways of individuating genes in contemporary biological science as possible vehicles of representational content—as molecular genes and as difference-maker genes. I show that (...) given either of these ways of individuating genes, genes fail to meet conditions which the teleosemantic theory requires an entity to meet if that entity is to qualify as a representational vehicle that represents a whole-organism phenotype. The considerations I present against Shea’s view generalize to other attempts to use the teleosemantic theory in support of the claim that genes represent whole-organism phenotypes. (shrink)

Over the last two decades, network-focused approaches have become highly popular in diverse fields of biology, including neuroscience, ecology, molecular biology and genetics. While the network approach continues to grow very rapidly, some of its conceptual and methodological aspects still require a programmatic foundation. This challenge particularly concerns the question of whether a generalized account of explanatory, organisational and descriptive levels of networks can be applied universally across biological sciences. Consequently, the central focus of this theme issue will be on (...) the definition, motivation and application of key concepts in biological network science, such as levels, hierarchies, and explanatory directionality. A unification will be achieved by formulating norms for delimiting the distinctively network-topological class of explanations that connect general as well as very specific biological research questions. The impact of this theme issue is broad and encompassing, as it is highly interdisciplinary and opens a uniquely normative perspective on the foundational aspects of network-based explanations and modelling. This theme issue is intended to become a landmark publication for practical research as well as funding policy decisions, by unifying network approaches in biological sciences in terms of fundamental concepts and informing the public understanding of the network science. (shrink)

Predictive information is a popular and promising family of information-based theories of biological communication. It is difficult to adjudicate between predictive information-based theories and influence-based theories of biological communication because the same acts seem to count as communicative on both theories. In this paper, I argue that predictive information theories and influence-based theories give importantly different descriptions of deceptive signals in some non-evolutionarily stable communicative systems by citing a novel case observed in nature. Moreover, predictive information gives a counter-intuitive description (...) to the case while some of its rival influence-based theories do not. I argue that there are no clear ways for defenders of predictive information to respond to this apparent problem without sacrificing important virtues of their theory or deflating the difference between the rival views. (shrink)

What is the relationship between information and representation? Dating back at least to Dretske (1981), an influential answer has been that information is a rung on a ladder that gets one to representation. Representation is information, or representation is information plus some other ingredient. In this paper, I argue that this approach oversimplifies the relationship between information and representation. If one takes current probabilistic models of cognition seriously, information is connected to representation in a new way. It enters as a (...) property of the represented content as well as a property of the vehicles that carry that content. This offers a new, conceptually and logically distinct way in which information and representation are intertwined in cognition. (shrink)

Description courte (Électre, 2019) : Une étude d'un des principaux axes de réflexion du philosophe des sciences et de la nature Raymond Ruyer (1902-1987). À la lumière des découvertes de l'embryogenèse et en s'appuyant par ailleurs sur la théorie de l'information, il proposa une interprétation des concepts unificateurs de la cybernétique mécaniste. -/- Short Descriptor (Electre 2019): A study of one of the main axes of reflection of the French philosopher of science and of nature Raymond Ruyer (1902-1987). Relying on (...) the discoveries about embryogenesis, and also with the use of information theory, Ruyer proposed an interpretation of the main unifying concepts of mechanistic cybernetics. -/- Cet ouvrage propose une étude fouillée d'un des principaux axes de réflexion du philosophe des sciences et de la nature français Raymond Ruyer (1902–1987) : la cybernétique. Après avoir proposé une philosophie structuraliste, Ruyer la modifia à la lumière des découvertes de l'embryogenèse, puis il proposa une interprétation des concepts unificateurs de la cybernétique mécaniste. Réfléchissant sur cette dernière et sur la théorie de l'information, en particulier sur l'origine de l'information, il défendit que cette cybernétique n'était qu'une lecture inversée de la vraie cybernétique, qui nous donnerait de lire dans l'expérience même les traces du pouvoir morphogénétique, appréhendé comme un champ axiologique. Dans un texte résumant son propre parcours, Ruyer affirma finalement que la critique de la théorie de l'information « peut donner […] l'espoir d'aboutir à quelque chose comme une nouvelle théologie. » Les idées directrices de Ruyer sont tout particulièrement contextualisées ici à partir de la question du développement des formes en biologie, et de celles de la génétique, de la genèse stochastique de l'ordre, et de l'identification mentale ou physique de l'information. Il se termine en départageant ce qui est théologique et axiologique dans ce projet de métaphysique qui, bien que resté inachevé, n'en représente pas moins le plus impressionnant conçu en France au siècle dernier. – This book offers an in-depth study of one of the main axes in the reflection of French philosopher of science and nature Raymond Ruyer. In a text summarising his own development, Ruyer stated about the philosophical critique of information theory that it "is what can give the most long-lasting hope of getting to something like a new theology." After propounding a structuralist philosophy, and distinguishing between form and structure, to then modify it in the light of discoveries in embryogenesis, Ruyer offered a re-evaluation of the unifying concepts of mechanistic cybernetics. Thinking about it and about information theory, he defended the idea that this cybernetics was in reality an inverted reading of the real one, which would allow us to read in experience itself traces of the morphogenetic power, apprehended as the axiological field. On some transversal points, the development of forms in biology and genetics, the stochastic genesis of order, the identification of information with either psychological and mental, or physical reality, behaviour, and the access to meaning, this work exposes the main ideas of Ruyer while situating them in the context of the breadth of others' contributions. It ends by determining what is theological and axiological in this project for a metaphysics which, although unfinished, is nevertheless the most impressive effort done in France in the last century. – Available on i6doc dot com (ISBN 978-2-930517-56-8 ; pdf 978-2-930517-57-5). (shrink)

This article establishes grounds on which attributions of information and encoding in animal signals are warranted. As common interest increases between evolutionary agents, the theoretical approach best suited to describing their interaction shifts from evolutionary game theory to communication theory, which warrants informational language. The take-home positive message is that in cooperative settings, signals can appropriately be described as transmitting encoded information, regardless of the cognitive powers of signalers. The canonical example is the honeybee waggle dance, which is discussed extensively (...) in the second and third sections. The take-home negative message is that signals are not always a consequence of coadaptation. The communication theory approach is just one end of a continuum explored more thoroughly by evolutionary game theory. The fourth and fifth sections explore this wider framework, as well as overturning some widely held misconceptions about information theory. (shrink)

This paper aims to establish several interconnected points. First, a particular interpretation of the mathematical definition of information, known as the causal interpretation, is supported largely by misunderstandings of the engineering context from which it was taken. A better interpretation, which makes the definition and quantification of information relative to the function of its user, is outlined. The first half of the paper is given over to introducing communication theory and its competing interpretations. The second half explores three consequences of (...) the main thesis. First, a popular claim that the quantification of information in a signal is irrelevant for the meaning of that signal is exposed as fallacious. Second, a popular distinction between causal and semantic information is shown to be misleading, and I argue it should be replaced with a related distinction between natural and intentional signs. Finally, I argue that recent empirical work from microbiology and cognitive science drawing on resources of mathematical communication theory is best interpreted by the functional account. Overall, a functional approach is shown to be both theoretically and empirically well-supported. (shrink)

The concept of biological information, and information in general, usually presupposes a purely quantitative view of reality. Even though actualist quantification has an important place in the description of the world, a nominalistic stance that tries to simplify reality in purely actualist terms inevitably runs into inconsistencies; these inconsistencies have been pointed out by the critical assessments of the notion of biological information. Rather than calling for an abandonment of the informational terminology, we try to rethink information as a part (...) of an event, the description of which cannot be exhausted by a physicalist, mechanistic, temporally static view of reality. Reconceptualizing the notion of biological information in terms of a process of interpretation rather than as an informational object allows us to transcend the limitations imposed by an analysis of reality that depends on a fixed, finite structure of outcome. Thus, we argue that measuring biological information is intrinsically problematic. (shrink)

A causal approach to biological information is outlined. There are two aspects to this approach: information as determining a choice between alternative objects and information as determining the construction of a single object. The first aspect has been developed in earlier work to yield a quantitative measure of biological information that can be used to analyze biological networks. This article explores the prospects for a measure based on the second aspect and suggests some applications for such a measure. These two (...) aspects are not suggested to exhaust all the facets of biological information. (shrink)

Path-dependence offers a promising way of understanding the role historicity plays in explanation, namely, how the past states of a process can matter in the explanation of a given outcome. The two main existing accounts of path-dependence have sought to present it either in terms of dynamic landscapes or branching trees. However, the notions of landscape and tree both have serious limitations and have been criticized. The framework of causal networks is both more fundamental and more general that that of (...) landscapes and trees. Within this framework, I propose that historicity in networks should be understood as symmetry breaking. History matters when an asymmetric bias towards an outcome emerges in a causal network. This permits a quantitative measure for how path-dependence can occur in degrees, and offers suggestive insights into how historicity is intertwined both with causal structure and complexity. (shrink)

The idea that development is the expression of information accumulated during evolution and that heredity is the transmission of this information is surprisingly hard to cash out in strict, scientific terms. This paper seeks to do so using the sense of information introduced by Francis Crick in his sequence hypothesis and central dogma of molecular biology. It focuses on Crick's idea of precise determination. This is analysed using an information-theoretic measure of causal specificity. This allows us to reconstruct some of (...) Crick's claims about information in transcription and translation. Crick's approach to information has natural extensions to non-coding regions of DNA, to epigenetic marks, and to the genetic or environmental upstream causes of those epigenetic marks. Epigenetic information cannot be reduced to genetic information. The existence of biological information in epigenetic and exogenetic factors is relevant to evolution as well as to development. (shrink)

The interventionist account of causation offers a criterion to distinguish causes from non-causes. It also aims at defining various desirable properties of causal relationships, such as specificity, proportionality and stability. Here we apply an information-theoretic approach to these properties. We show that the interventionist criterion of causation is formally equivalent to non-zero specificity, and that there are natural, information-theoretic ways to explicate the distinction between potential and actual causal influence. We explicate the idea that the description of causes should be (...) proportional to that of their effects. Then we draw a distinction between two ideas in the existing literature, the range of invariance of a causal relationship and its stability. The range of invariance is related to specificity and range of causal values. Stability concerns the effect of additional variables on the relationship between some focal pair of cause and effect variables. We show how to distinguish and measure the direct influence of background variables on the effect variable, and their influence on the relationship between the focal cause and the effect variable. Finally, we discuss the limitations of the information-theoretic approach, and offer prospects for complementary approaches. (shrink)

The biological human being is an emergent human superorganism consisting of the human organism physiologically integrated with other organisms. The persistence of a superorganism in space and time requires communication among its organisms. This communication occurs through immune processes at the biological boundaries of these organisms. Immune processes also repair disrupted boundaries, with this repair resulting in either health or disease processes depending on how the boundaries are restored. Health, disease, and biological personal identity all emerge from the mode of (...) arrangement of, and communication of biological information among the superorganism’s parts. The study of solid organ transplantation enables the ontology of the biological human being as a superorganism by bringing together the structural and functional boundaries of different organisms in a way that communication can be better understood. By understanding that organ transplant recipients are not just non-transplanted patients with an extra part, but are newly emergent human superorganisms, we can better understand both post-transplant health and disease and target our therapies more effectively. Successful reintegration of the superorganism after disruption may be relevant to many health processes, and therefore to the goals of medicine in general. (shrink)

A fascinating research program in neurophysiology attempts to quantify the amount of information transmitted by single neurons. The claims that emerge from this research raise new philosophical questions about the nature of information. What kind of information is being quantified? Do the resulting quantities describe empirical magnitudes like those found elsewhere in the natural sciences? In this article, it is argued that neural information quantities have a relativisitic character that makes them distinct from the kinds of information typically discussed in (...) the philosophical literature. It is also argued that despite this relativistic character, there are cases in which neural information quantities can be viewed as robustly objective empirical properties. (shrink)