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)

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)

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)

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)

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)

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)

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. Three general, main claims are advanced here. This new taxonomy can be useful in describing learning and communication. It avoids some problems that the natural/non-natural information distinction faces. 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)

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)

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)

What is the relationship between information and representation? Dating back at least to Dretske, 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)

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)

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)

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)

A new approach to landscape ecology involves the application of the eco-field hypothesis and the General Theory of Resources. In this study, we describe the putative eco-field of bark beetles as a spatial configuration with a specific meaning-carrier for every organism-resource interaction. Bark beetles are insects with key roles in matter and energy cycles in coniferous forests, which cause significant changes to forestry landscapes when outbreaks occur. Bark beetles are guided towards host trees by the recognition of semiotic signals using (...) a specific eco-field. These signals mainly comprise a group of scents, which are called the odourtope. Their interactions with other organisms occur by sharing relevant information from the eco-field networks in the forest ecosystem. The eco-field networks modulate the expansion of the realized semiotic niche of the bark beetle towards the potential semiotic niche. Moreover, the niche construction process can be initiated by interchanging signals among species living in the same place, where these signals allow the exploitation of the required resources. If different organisms are interdependent on signals in eco-field networks, then this process may result in the establishment of mutualistic relationships. This is an example of how evolutionary processes are initiated by the recognition of signals in a network of eco-fields. (shrink)

In this chapter we examine the relationship between biological information, the key biological concept of specificity, and recent philosophical work on causation. We begin by showing how talk of information in the molecular biosciences grew out of efforts to understand the sources of biological specificity. We then introduce the idea of ‘causal specificity’ from recent work on causation in philosophy, and our own, information theoretic measure of causal specificity. Biological specificity, we argue, is simple the causal specificity of certain biological (...) processes. This, we suggest, means that causal relationships in biology are ‘informational’ relationships simply when they are highly specific relationships. Biological information can be identified with the storage, transmission and exercise of biological specificity. It has been argued that causal relationships should not be regarded as informational relationship unless they are ‘arbitrary’. We argue that, whilst arbitrariness is an important feature of many causal relationships in living systems, it should not be used in this way to delimit biological information. Finally, we argue that biological specificity, and hence biological information, is not confined to nucleic acids but distributed among a wide range of entities and processes. (shrink)

We describe an approach to measuring biological information where ‘information’ is understood in the sense found in Francis Crick’s foundational contributions to molecular biology. Genes contain information in this sense, but so do epigenetic factors, as many biologists have recognized. The term ‘epigenetic’ is ambiguous, and we introduce a distinction between epigenetic and exogenetic inheritance to clarify one aspect of this ambiguity. These three heredity systems play complementary roles in supplying information for development. -/- We then consider the evolutionary significance (...) of the three inheritance systems. Whilst the genetic inheritance system was the key innovation in the evolution of heredity, in modern organisms the three systems each play important and complementary roles in heredity and evolution. -/- Our focus in the earlier part of the paper is on ‘proximate biology’, where information is a substantial causal factor that causes organisms to develop and causes offspring to resemble their parents. But much philosophical work has focused on information in ‘ultimate biology’. Ultimate information is a way of talking about the evolutionary design of the mechanisms of development and inheritance. We conclude by clarifying the relationship between the two. Ultimate information is not a causal factor that acts in development or heredity, but it can help to explain the evolution of proximate information, which is. (shrink)

This book tackles the most difficult and profound open questions about life and its origins from an information-based perspective.

The concepts of the origin of the genetic code and the definitions of life changed dramatically after the RNA world hypothesis. Main narratives in molecular biology and genetics such as the “central dogma,” “one gene one protein” and “non-coding DNA is junk” were falsified meanwhile. RNA moved from the transition intermediate molecule into centre stage. Additionally the abundance of empirical data concerning nonrandom genetic change operators such as the variety of mobile genetic elements, persistent viruses and defectives do not fit (...) with the dominant narrative of error replication events (mutations) as being the main driving forces creating genetic novelty and diversity. The reductionistic and mechanistic views on physico-chemical properties of the genetic code are no longer convincing as appropriate descriptions of the abundance of non-random genetic content operators which are active in natural genetic engineering and natural genome editing. (shrink)

This article interprets Jakob von Uexkull’s understanding of different beings’ Innenwelt, Gegenwelt, and umwelt through Deleuzian insights of multiplicity, context, and particularity. This Deleuzian interpolation into Uexkull’s insights acknowledges the absence of a unitary ‘human’ view of nature, recognizing instead that plural viewpoints of cultures, subgroups and individuals understand and interpret natural signs variously not just because of ideology but because of physiology and contrastive fundamental ways of accessing the world. Recent formative research in comparative neurobiology suggests that universal anthropological (...) claims of cross-cultural semiotic similarity are incorrect.Interpreting biosemiotics as the investigation of apprehending the Innenwelt of radically different others (species), such semiotic understandings themselves are not necessarily generalizable between different members of the same species in a group, same-species groups in different natural cultural contexts, or even (as with humans) the same animal at different points of time (based on new understandings, patterns, or events of meaning altering interpretations of self and events). Conjoining Deleuze’s insights of the complexity of multiplicity with Uexkull’s scientific-imaginative system of comprehending other creatures’ ways of understanding their world offers an increased self-reflexivity regarding the simultaneous levels of actual semiotic activity for biosemiotic inquiry. (shrink)

Organisms actively compete for environmental resources. They assess their surroundings, estimate how much energy they need for particular goals, and then realize the optimum variant. They take measures to control certain environmental resources. They perceive themselves and can distinguish between “self” and “non-self.” Current empirical data on all domains of life indicate that unicellular organisms such as bacteria, archaea, giant viruses, and protozoa as well as multicellular organisms such as animals, fungi, and plants coordinate and organize their essential life functions (...) through signaling processes. Signaling allows for real life coordination and organization and is a communicative action in which speciesspecific behavioral patterns and sign repertoires are used. Cells, tissues, organs, and organisms that communicate share several key levels that are essential to all life forms and which serve as a uniform tool for investigating biocommunication. (shrink)

According to the proponents of Developmental Systems Theory and the Causal Parity Thesis, the privileging of the genome as “first among equals” with respect to the development of phenotypic traits is more a reflection of our own heuristic prejudice than of ontology - the underlying causal structures responsible for that specified development no more single out the genome as primary than they do other broadly “environmental” factors. Parting with the methodology of the popular responses to the Thesis, this paper offers (...) a novel criterion for ‘causal primacy’, one that is grounded in the ontology of the unique causal role of dispositional properties. This paper argues that, if the genome is conceptualised as realising dispositional properties that are “directed toward” phenotypic traits, the parity of ‘causal roles’ between genetic and extra-genetic factors is no longer apparent, and further, that the causal primacy of the genome is both plausible and defensible. (shrink)

The rapidly increasing interest in the quantum properties of living matter stimulates a discussion of the fundamental properties of life as well as quantum mechanics. In this discussion often concepts are used that originate in philosophy and ask for a philosophical analysis. In the present work the classic philosophical tradition based on Aristotle and Aquinas is employed which surprisingly is able to shed light on important aspects. Especially one could mention the high degree of unity in living objects and the (...) occurrence of thorough qualitative changes. The latter are outside the scope of classical physics where changes are restricted to geometrical rearrangement of microscopic particles. A challenging approach is used in the philosophical analysis as the empirical evidence is not taken from everyday life but from 20th century science (quantum mechanics) and recent results in the field of quantum biology. In the discussion it is argued that quantum entanglement is possibly related to the occurrence of life. Finally it is recommended that scientists and philosophers should be open for dialogue that could enrich both. Scientists could redirect their investigation, as paradigm shifts like the one originating from philosophical evaluation of quantum mechanics give new insight about the relation between the whole en the parts. Whereas philosophers could use scientific results as a consistency check for their philosophical framework for understanding reality. (shrink)

Manfred Eigen extended Erwin Schroedinger’s concept of “life is physics and chemistry” through the introduction of information theory and cybernetic systems theory into “life is physics and chemistry and information.” Based on this assumption, Eigen developed the concepts of quasispecies and hypercycles, which have been dominant in molecular biology and virology ever since. He insisted that the genetic code is not just used metaphorically: it represents a real natural language.However, the basics of scientific knowledge changed dramatically within the second half (...) of the 20th century.Unfortunately, Eigen ignored the results of the philosophy of science discourse on essential features of natural languages and codes: a natural language or code emerges from populations of living agents that communicate. This contribution will look at some of the highlights of this historical development and the results relevant for biological theories about life. (shrink)

Ethological theories usually attribute semantic content to animal signals. To account for this fact, many biologists and philosophers appeal to some version of teleosemantics. However, this picture has recently came under attack: while mainstream teleosemantics assumes that representational systems must cooperate, some biologists and philosophers argue that in certain cases signaling can evolve within systems lacking common interest. In this paper I defend the standard view from this objection.

What are the functional units of the brain? If the function of the brain is to process information-carrying signals, then the functional units will be the senders and receivers of those signals. Neurons have been the default candidate, with action potentials as the signals. But there are alternatives: synapses fit the action potential picture more cleanly, and glial activities (e.g., in astrocytes) might also be characterized as signaling. Are synapses or nonneuronal cells better candidates to play the role of functional (...) units? Will informational signaling still be the best model for brain function if we move beyond the neuron doctrine? (shrink)

Research in archaeology and anthropology on the evolution of modern patterns of human behavior often makes use of general theories of signs, usually derived from semiotics. Recent work generalizing David Lewis’ 1969 model of signaling provides a better theory of signs than those currently in use. This approach is based on the coevolution of behaviors of sign production and sign interpretation. I discuss these models and then look at applications to human prehistoric behavior, focusing on body ornamentation, tools, and other (...) artifacts. (shrink)