It is outlined the possibility to extend the quantum formalism in relation to the requirements of the general systems theory. It can be done by using a quantum semantics arising from the deep logical structure of quantum theory. It is so possible taking into account the logical openness relationship between observer and system. We are going to show how considering the truth-values of quantum propositions within the context of the fuzzy sets is here more useful for (...) systemics. In conclusion we propose an example of formal quantum coherence. (shrink)

This chapter introduces a research-based conceptual framework for the study of the inner psychosocial reality of business enterprises. It is called the Inner Organizational Ecosystem Approach (IOEA). This model is systemic in nature, and it defines the basic features of small and medium-size enterprises, such as elements, structures, borders, social actors, organizational climate, processes and resources. Further, it also covers the dynamics of psychosocial reality, processes, emergent qualities and the higher-order subsystems of the overall organizational ecosystem, including the global business (...) environment, which is understood as a macro-system where all the individual organizational ecosystems co-exist. In the applied part of the chapter, cognitive changes emerging within systemic leadership training are defined. Participation in systemic training causes changes in the cognitive processing of reality, more specifically improvements in layer-based framing, relativistic contextual orientation, temporality drift and meaning generation. All of these changes are components of the systemic mind, which is a concept newly proposed and defined by the present study. The systemic mind is a living matrix that is extremely open to acquiring new skills and new patterns of thinking, analyzing and meaning generation. It is processual and it can be considered as an ongoing process of continuous absorption of new cognitive patterns. Both the Inner Organizational Ecosystem Approach and the concept of the systemic mind provide a new theoretical background for empirical investigation in the fields of systemic and systems psychology, complexity psychology, organizational psychology, economic anthropology and the social anthropology of work. (shrink)

In this paper the central ideas and history of the theory of complex systems are described. It is shown how this theory lends itself to different interpretations and, correspondingly, to different political conclusions.

A new advanced systems theory concerning the emergent nature of the Social, Consciousness, and Life based on Mathematics and Physical Analogies is presented. This meta-theory concerns the distance between the emergent levels of these phenomena and their ultra-efficacious nature. The theory is based on the distinction between Systems and Meta-systems (organized Openscape environments). We first realize that we can understand the difference between the System and the Meta-system in terms of the relationship between a (...) ‘Whole greater than the sum of the parts’ and a ‘Whole less than the sum of its parts’, i.e., a whole full of holes (like a sponge) that provide niches for systems in the environment. Once we understand this distinction and clarify the nature of the unusual organization of the Meta-system, then it is possible to understand that there is a third possibility which is a whole exactly equal to the sum of its parts that is only supervenient like perfect numbers. In fact, there are three kinds of Special System corresponding to the perfect, amicable, and sociable aliquot numbers. These are all equal to the sum of their parts but with different degrees of differing and deferring in what Jacques Derrida calls “differance”. All other numbers are either excessive (systemic) or deficient (metasystemic) in this regard. The Special Systems are based on various mathematical analogies and some physical analogies. But the most important of the mathematical analogies are the hypercomplex algebras, which include the Complex Numbers, Quaternions, and Octonions, with the Sedenions corresponding to the Emergent Meta-system. However, other analogies are the Hopf fibrations between hyperspheres of various dimensions, nonorientable surfaces, soliton solutions, etc. These Special Systems have a long history within the tradition since they can be traced back to the imaginary cities of Plato. The Emergent Meta-system is a higher order global structure that includes the System with the three Special Systems as a cycle. An example of this from our tradition is in the Monadology of Gottfried Wilhelm von Leibniz. There is a conjunctive relationship between the System schema and the Special Systems that produce the Meta-system schema cycle. The Special Systems are a meta-model for the relationship between the emergent levels of Consciousness (Dissipative Ordering based on the theory of negative entropy of Prigogine), Living (Autopoietic Symbiotic based on the theory of Maturana and Varela), and Social (Reflexive based on the theory of John O’Malley and Barry Sandywell). These different special systems are related to the various existenitals identified by Martin Heidegger in Being and Time and various temporal reference frames identified by Richard M. Pico. We also relate the special systems to morphodynamic and teleodynamic systems of Terrence Deacon in Incomplete Nature to which we add sociodynamic systems to complete the series of Special Systems. (shrink)

Considers that in ecosystem, landscape and global ecology, an energetics reading of ecological systems is an expression of a cybernetic, systemic and holistic approach. In ecosystem ecology, the Odumian paradigm emphasizes the concept of emergence, but it has not been accompanied by the creation of a method that fully respects the complexity of the objects studied. In landscape ecology, although the emergentist, multi-level, triadic methodology of J.K. Feibleman and D.T. Campbell has gained acceptance, the importance of emergent properties is (...) still undervalued. In global ecology, the Gaia hypothesis is an expression of an organicist metaphor, while the emergentist terminology used is incongruent with the underlying physicalist cybernetics. More generally, an analytico-additional methodology and the reduction of the properties of ecosystems to the laws of physical chemistry render purely formal any assertion about the emergentist and holistic nature of the ecological systems studied. (shrink)

Since the nineteen fifties many social theorists, religion specialists, and theologians have turned to general systems theory for insight into the nature of religion and its expressions. As an interdisciplinary perspective introduced by the biologist Ludwig von Bertalanffy and developed by the philosopher Ervin Laszlo and others, systems theory seeks common patterns of organization throughout the natural and cultural worlds. Because of its high level of generality, expressed in the relational principles of integration, adaptation, emergence, (...) and hierarchy, systems theory attempts to transcend artificial boundaries separating the sciences and the humanities. Advocates have claimed its value in interpreting a broad range of religious phenomena, including Christian theology and ethics, and Buddhist metaphysics and meditation. ;Religious studies has long struggled to integrate the competing contributions of the social sciences and phenomenology. A mediating proposal came in 1968 with Robert Bellah's cybernetic-systems theory of religion . An account of the common origins of systems theory and religious studies in nineteenth century thought , and a survey of representative literature between 1950 and 1985 , introduce a critique if specific methodological issues. ;The problem of functionalism is reinterpreted in terms of the adaptive self-regulation of open systems, and illustrated by three cybernetic theories of religion . The problem of historicism is reinterpreted in terms of the emergent self-organization of open systems, and illustrated by Talcott Parsons' action theory of religion and the theories of religious evolution of Bellah and D. T. Campbell . Reductionism is reconceived as the heuristic relationship of theoretical constructs in a hierarchy of open systems, and illustrated by theological conceptions of nature and meaning . ;In conclusion, the systems principle of integration is applied to the problems of personalism and pluralism, and illustrated in the personality theories of Bertalanffy, Koestler, Laszlo, and others. A systems theory of religious consciousness is shown to encompass the findings of religious studies broadly conceived: phenomenology and hermeneutics, social scientific theory, history of religions, philosophy of religion, and systematic theology. (shrink)

The term gestalt, when used in the context of general systems theory, assumes the value of “systemic touchstone”, namely a figure of reference useful to categorize the properties or qualities of a set of systems. Typical gestalts used, e.g., in biology, are those based on anatomical or physiological characteristics, which correspond respectively to architectural and organizational design choices in natural and artificial systems. In this paper we discuss three gestalts of general systems (...) class='Hi'>theory: behavior, organization, and substance, which refer respectively to the works of Wiener, Boulding, and Leibniz. Our major focus here is the system introduced by the latter. Through a discussion of some of the elements of the Leibnitian System, and by means of several novel interpretations of those elements in terms of today’s computer science, we highlight the debt that contemporary research still has with this Giant among the giant scholars of the past. (shrink)

The term “Complex Systems Biology” was introduced a few years ago [Kaneko, 2006] and, although not yet of widespread use, it seems particularly well suited to indicate an approach to biology which is well rooted in complex systems science. Although broad generalizations are always dangerous, it is safe to state that mainstream biology has been largely dominated by a gene-centric view in the last decades, due to the success of molecular biology. So the one gene - one trait (...) approch, which has often proved to be effective, has been extended to cover even complex traits. This simplifying view has been appropriately criticized, and the movement called systems biology has taken off. Systems biology [Noble, 2006] emphasizes the presence of several feedback loops in biological systems, which severely limit the range of validity of explanations based upon linear causal chains (e.g. gene → behaviour). Mathematical modelling is one the favourite tools of systems biologists to analyze the possible effects of competing negative and positive feedback loops which can be observed at several levels (from molecules to organelles, cells, tissues, organs, organisms, ecosystems). Systems biology is by now a well-established field, as it can be inferred by the rapid growth in number of conferences and journals devoted to it, as well as by the existence of several grants and funded projects.Systems biology is mainly focused upon the description of specific biological items, like for example specific organisms, or specific organs in a class of animals, or specific genetic-metabolic circuits. It therefore leaves open the issue of the search for general principles of biological organization, which apply to all living beings or to at least to broad classes. We know indeed that there are some principles of this kind, biological evolution being the most famous one. The theory of cellular organization also qualifies as a general principle. But the main focus of biological research has been that of studying specific cases, with some reluctance to accept (and perhaps a limited interest for) broad generalizations. This may however change, and this is indeed the challenge of complex systems biology: looking for general principles in biological systems, in the spirit of complex systems science which searches for similar features and behaviours in various kinds of systems. The hope to find such general principles appears well founded, and I will show in Section 2 that there are indeed data which provide support to this claim. Besides data, there are also general ideas and models concerning the way in which biological systems work. The strategy, in this case, is that of introducing simplified models of biological organisms or processes, and to look for their generic properties: this term, borrowed from statistical physics, is used for those properties which are shared by a wide class of systems. In order to model these properties, the most effective approach has been so far that of using ensembles of systems, where each member can be different from another one, and to look for those properties which are widespread. This approach was introduced many years ago [Kauffman, 1971] in modelling gene regulatory networks. At that time one had very few information about the way in which the expression of a given gene affects that of other genes, apart from the fact that this influence is real and can be studied in few selected cases (like e.g. the lactose metabolism in E. coli). Today, after many years of triumphs of molecular biology, much more has been discovered, however the possibility of describing a complete map of gene-gene interactions in a moderately complex organism is still out of reach. Therefore the goal of fully describing a network of interacting genes in a real organism could not be (and still cannot be) achieved. But a different approach has proven very fruitful, that of asking what are the typical properties of such a set of interacting genes. Making some plausible hypotheses and introducing some simplifying assumptions, Kauffman was able to address some important problems. In particular, he drew attention to the fact that a dynamical system of interacting genes displays selforganizing properties which explain some key aspects of life, most notably the existence of a limited number of cellular types in every multicellular organism (these numbers are of the order of a few hundreds, while the number of theoretically possible types, absent interactions, would be much much larger than the number of protons in the universe). In section 3 I will describe the ensemble based approach in the context of gene regulatory networks, and I will show that it can describe some important experimental data. Finally, in section 4 I will discuss some methodological aspects. (shrink)

The aim of this paper is to describe and analyze the epistemological justification of a proposal initially made by the biomathematician Robert Rosen in 1958. In this theoretical proposal, Rosen suggests using the mathematical concept of “category” and the correlative concept of “natural equivalence” in mathematical modeling applied to living beings. Our questions are the following: According to Rosen, to what extent does the mathematical notion of category give access to more “natural” formalisms in the modeling of living (...) beings? Is the so -called “naturalness” of some kinds of equivalences (which the mathematical notion of category makes it possible to generalize and to put at the forefront) analogous to the naturalness of living systems? Rosen appears to answer “yes” and to ground this transfer of the concept of “natural equivalence” in biology on such an analogy. But this hypothesis, although fertile, remains debatable. Finally, this paper makes a brief account of the later evolution of Rosen’s arguments about this topic. In particular, it sheds light on the new role played by the notion of “category” in his more recent objections to the computational models that have pervaded almost every domain of biology since the 1990s. (shrink)

The following article was written to honour Johan Buitendag’s contribution to the discipline of eco-theology. Assuming an interdisciplinary stance, eco-theology in general and his work, in particular, is observed from the position of legal theory and sociology. As such, eco-theology is not assessed on theological grounds but is treated interdisciplinary through comparison with environmental law. More specifically, the project of eco-theology is shown to share certain characteristics with the nascent subdiscipline of Earth systems law within environmental law. (...) It is argued that one of the most important of these is the use of norms as an ecological strategy. This is understandable as both the religious and legal systems rely on the norm form to a lesser or greater extent. However, in the legal sociology of systems theory, the shortcomings of norms have been eloquently argued. This article thus posits the limits of norms to eco-theology and Earth systems law as a challenge deserving attention. However, social systems theory has its shortcomings, and a preliminary line of flight away from this challenge is suggested in the shape of Agamben’s description of the monastic form-of-life, where life and norm overlap so intensely that suggestions of a new worldview gain plausibility. (shrink)

Information and Meaning are present everywhere around us and within ourselves. Specific studies have been implemented in order to link information and meaning: - Semiotics - Phenomenology - Analytic Philosophy - Psychology No general coverage is available for the notion of meaning. We propose to complement this lack by a systemic approach to meaning generation.

Information and Meaning are present everywhere around us and within ourselves. Specific studies have been implemented in order to link information and meaning: - Semiotics - Phenomenology - Analytic Philosophy - Psychology No general coverage is available for the notion of meaning. We propose to complement this lack by a systemic approach to meaning generation.

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)

Information and Meaning are present everywhere around us and within ourselves. Specific studies have been implemented in order to link information and meaning: - Semiotics - Phenomenology - Analytic Philosophy - Psychology No general coverage is available for the notion of meaning. We propose to complement this lack by a systemic approach to meaning generation.

Easy to understand philosophy papers in all areas. Table of contents: Three Short Philosophy Papers on Human Freedom The Paradox of Religions Institutions Different Perspectives on Religious Belief: O’Reilly v. Dawkins. v. James v. Clifford Schopenhauer on Suicide Schopenhauer’s Fractal Conception of Reality Theodore Roszak’s Views on Bicameral Consciousness Philosophy Exam Questions and Answers Locke, Aristotle and Kant on Virtue Logic Lecture for Erika Kant’s Ethics Van Cleve on Epistemic Circularity Plato’s Theory of Forms Can we trust our senses? (...) Yes we can Descartes on What He Believes Himself to Be The Role of Values in Science Modern Science Kant’s Moral Philosophy Plato’s Republic as Pol Potist Bureaucracy Schopenhauer on Human Suffering Bertrand Russell on the Value of Philosophy The Philosophical Value of Uncertainty Logic Homework: Theorems and Models Searle vs. Turing on the Imitation Game Hume, Frankfurt, and Holbach on Personal Freedom Manifesto of the University of Wisconsin, Madison Secular Society Michael’s Analysis of the Limits of Civil Protections Bentham and Mill on Different Types of Pleasure Set Theory Homework Aristotle on Virtue Nagel On the Hard Problem Wittgenstein on Language and Thought Camus and Schopenhauer on the Meaning of Life Camus’ Hero as Rebel without a Cause My Little Finger: Camus’ Absurdism Illustrated Are Late-term Abortions Ethical? Does Mathematics Assume the Truth of Platonism? The Self-defeating Nature of Utilitarianism and Consequentialism Generally What is The Good Life? Bentham and Mill regarding types of pleasures Kant’s Moral Philosophy Five Short Papers on Mind-body Dualism Tracy Latimer’s Father had the Right to Kill Her: Towards a doctrine of generalized self-defense Arguments Concerning God and Morality Goldman, Rousseau and von Hayek on the Ideal State J.S Mill on Liberty and Personal Freedom A Kantian Analysis of a Borderline Date-rape Situation Living Well as Flourishing: Aristotle’s Conception of the Good Life Three Essays on Medical Ethics: Answers to Exam Questions on Elective Amputation, Vaccination, and Informed Consent Hobbes, Marx, Rousseau, Nietzsche: Their Central Themes De Tocqueville on Egoism Mill vs. Hobbes on Liberty Exam-Essays on the Moral Systems of Mill, Bentham, and Kant Kant’s Moral System Aristotle on Virtue Plato’s Cave Allegory An Ethical Quandary Superorganisms The Tuskegee Experiment A Rawlsian Analysis Why Moore’s Proof of an External World Fails A Defense of Nagel’s Argument Against Materialism A Utilitarian Analysis of a Case of Theft The Paradox of the Self-aware Wretch: An Analysis of Pascal’s Moral Philosophy Jean-Paul Sartre: Decline and Fall of a Marxist Sell-out A One Page Proof of Plato’s Theory of Forms Plato’s Republic as Pol Potist Bureaucracy The problem of the one and the many Four Short Essays on Truth and Knowledge What is ‘the Good Life?’ The Ontological Argument Different Political Philosophies: Plato, Locke, Madison, Rousseau, Hayek, and Mill on the State What do I know with certainty? Skepticism about skepticism Neuroscience and Freewill Operant Conditioning What makes us special? Are Late-term Abortions Ethical? No Two Papers on Epistemology: Gettier and Bostrom Examination Nietzsche on Punishment God’s Foreknowledge and Moral Responsibility . (shrink)

Information and meaning are present everywhere around us and within ourselves. Specific studies have been implemented to link information and meaning (Linguistic, Biosemiotic, Psychology, Psychiatry, Cognition, Artificial Intelligence... ). No general coverage is available for the notion of meaning. We propose to complement this lack by a system approach to meaning generation in an evolutionary background. That short paper is a summary of the system approach where a Meaning Generator System (MGS) based on internal constraint satisfaction has been introduced. (...) The MGS can be used for animals (with “stay alive” related constraints), for humans (with “look for happiness” type constraints) and for artificial agents with programmed constraints. Definitions for agency and autonomy are made available based on internal constraint satisfaction. Usage of the MGS with the Turing Test shows why today computers cannot think like humans do. The MGS also allows to introduces evolutionary scenarios for cognition, intentionality and self-consciousness, with an entry point to a human specific anxiety. Continuations are proposed. (shrink)

Au milieu des années 1970, de nombreuses théories alternatives de la gravité ont été confirmées par des expériences au niveau du système solaire, mais pas au niveau cosmologique. En 1974, Joseph Taylor et Russell Hulse ont découvert le pulsar binaire , dont les impulsions extrêmement stables ont été surveillées par radiotélescope, permettant une mesure précise des paramètres astrophysiques. En 1978, le taux de changement de la période orbitale du système a été mesuré, ce qui a été confirmé par la relativité (...) générale mais pas par la plupart des théories alternatives. DOI: 10.13140/RG.2.2.30141.69606. (shrink)

The present article is an attempt to give - in the frame of the theory of the organism - environment system - a new interpretation to the role of efferent influences on receptor activity and to the functions of senses in the formation of knowledge. It is argued, on the basis of experimental evidence and theoretical considerations, that the senses are not transmitters of environmental information, but they create a direct connection between the organism and the environment, which makes (...) the development of a dynamic living system, the organism - environment system, possible. In this connection process the efferent influences on receptor activity are of particular significance, because with their help the receptors may be adjusted in relation to the parts of the environment which are most important in the achievement of behavioral results. Perception is the process of joining of new parts of the environment to the organism - environment system ; thus, the formation of knowledge by perception is based on reorganization of the organism - environment system, and not on transmission of information from the environment. With the help of the efferent influences on receptors each organism creates its own peculiar world which is simultaneously subjective and objective. The present considerations have far reaching influences as well on experimental work in neurophysiology and psychology of perception as on philosophical considerations of knowledge formation. (shrink)

Elsevier, the world's leading provider of science and health information, published an academic/scientific textbook about a new mathematical discovery discovered in a near-death experience (NDE) that matches the dynamics of living and life-like (social) systems and has applications in general systems theory, universal systems modelling, human clinical molecular genetics modelling, medical informatics, astrobiology, education and other areas of study. This article is about Lynnclaire Dennis and how she brought back perhaps the greatest scientific discovery (...) ever from a NDE. The Mereon Matrix's sequential process generates a coherent link to living and non-living systems whether they are physical, mathematical, philosophical, or social. (shrink)

This paper centers on the implicit metaphysics beyond the Theory of Relativity and the Principle of Indeterminacy – two revolutionary theories that have changed 20th Century Physics – using the perspective of Husserlian Transcedental Phenomenology. Albert Einstein (1879-1955) and Werner Heisenberg (1901-1976) abolished the theoretical framework of Classical (Galilean- Newtonian) physics that has been complemented, strengthened by Cartesian metaphysics. Rene Descartes (1596- 1850) introduced a separation between subject and object (as two different and self- enclosed substances) while Galileo and (...) Newton did the “mathematization” of the world. Newtonian physics, however, had an inexplicable postulate of absolute space and absolute time – a kind of geometrical framework, independent of all matter, for the explication of locality and acceleration. Thus, Cartesian modern metaphysics and Galilean- Newtonian physics go hand in hand, resulting to socio- ethical problems, materialism and environmental destruction. Einstein got rid of the Newtonian absolutes and was able to provide a new foundation for our notions of space and time: the four (4) dimensional space- time; simultaneity and the constancy of velocity of light, and the relativity of all systems of reference. Heisenberg, following the theory of quanta of Max Planck, told us of our inability to know sub- atomic phenomena and thus, blurring the line between the Cartesian separation of object and subject, hence, initiating the crisis of the foundations of Classical Physics. But the real crisis, according to Edmund Husserl (1859-1930) is that Modern (Classical) Science had “idealized” the world, severing nature from what he calls the Lebenswelt (life- world), the world that is simply there even before it has been reduced to mere mathematical- logical equations. Husserl thus, aims to establish a new science that returns to the “pre- scientific” and “non- mathematized” world of rich and complex phenomena: phenomena as they “appear to human consciousness”. To overcome the Cartesian equation of subject vs. object (man versus environment), Husserl brackets the external reality of Newtonian Science (epoché = to put in brackets, to suspend judgment) and emphasizes (1) the meaning of “world” different from the “world” of Classical Physics, (2) the intentionality of consciousness (L. in + tendere = to tend towards, to be essentially related to or connected to) which means that even before any scientific- logical description of the external reality, there is always a relation already between consciousness and an external reality. The world is the equiprimordial existence of consciousness and of external reality. My paper aims to look at this new science of the pre- idealized phenomena started by Husserl (a science of phenomena as they appear to conscious, human, lived experience, hence he calls it phenomenology), centering on the life- world and the intentionality of consciousness, as providing a new way of looking at ourselves and the world, in short, as providing a new metaphysics (as an antidote to Cartesian metaphysics) that grounds the revolutionary findings of Einstein and Heisenberg. The environmental destruction, technocracy, socio- ethical problems in the modern world are all rooted in this Galilean- Newtonian- Cartesian interpretation of the relationship between humans and the world after the crumbling of European Medieval Ages. Friedrich Nietzsche (1844-1900) comments that the modern world is going toward a nihilism (L. nihil = nothingness) at the turn of the century. Now, after two World Wars and the dropping of Atomic bomb, the capitalism and imperialism on the one hand, and on the other hand the poverty, hunger of the non- industrialized countries alongside destruction of nature (i.e., global warming), Nietzsche might be correct: unless humanity changes the way it looks at humanity and the kosmos. The works of Einstein, Heisenberg and Husserl seem to be pointing the way for us humans to escape nihilism by a “great existential transformation.” What these thinkers of post- modernity (after Cartesian/ Newtonian/ Galilean modernity) point to are: a) a new therapeutic way of looking at ourselves and our world (metaphysics) and b) a new and corrective notion of “rationality” (different from the objectivist, mathematico- logical way of thinking). This paper is divided into four parts: 1) A summary of Classical Physics and a short history of Quantum Theory 2) Einstein’s Special and General Relativity and Heisenberg’s Indeterminacy Principle 3) Husserl’s discussion of the Crisis of Europe, the life- world and intentionality of consciousness 4) A Metaphysics of Relativity and Indeterminacy and a Corrective notion of Rationality in Husserl’s Phenomenology . (shrink)

Modern life sciences research is increasingly relying on artificial intelligence (AI) approaches to model biological systems, primarily centered around the use of machine learning (ML) models. Although ML is undeniably useful for identifying patterns in large, complex data sets, its widespread application in biological sciences represents a significant deviation from traditional methods of scientific inquiry. As such, the interplay between these models and scientific understanding in biology is a topic with important implications for the future of scientific research, yet (...) it is a subject that has received little attention. Here, we draw from an epistemological toolkit to contextualize recent applications of ML in biological sciences under modern philosophical theories of understanding, identifying general principles that can guide the design and application of ML systems to model biological phenomena and advance scientific knowledge. We propose that conceptions of scientific understanding as information compression, qualitative intelligibility, and dependency relation modelling provide a useful framework for interpreting ML-mediated understanding of biological systems. Through a detailed analysis of two key application areas of ML in modern biological research – protein structure prediction and single cell RNA-sequencing – we explore how these features have thus far enabled ML systems to advance scientific understanding of their target phenomena, how they may guide the development of future ML models, and the key obstacles that remain in preventing ML from achieving its potential as a tool for biological discovery. Consideration of the epistemological features of ML applications in biology will improve the prospects of these methods to solve important problems and advance scientific understanding of living systems. (shrink)

In this paper, I present a general theory of topological explanations, and illustrate its fruitfulness by showing how it accounts for explanatory asymmetry. My argument is developed in three steps. In the first step, I show what it is for some topological property A to explain some physical or dynamical property B. Based on that, I derive three key criteria of successful topological explanations: a criterion concerning the facticity of topological explanations, i.e. what makes it true of a (...) particular system; a criterion for describing counterfactual dependencies in two explanatory modes, i.e. the vertical and the horizontal; and, finally, a third perspectival one that tells us when to use the vertical and when to use the horizontal mode. In the second step, I show how this general theory of topological explanations accounts for explanatory asymmetry in both the vertical and horizontal explanatory modes. Finally, in the third step, I argue that this theory is universally applicable across biological sciences, which helps to unify essential concepts of biological networks. (shrink)

The present article is an attempt to bring together the development of mental activity and consciousness in the framework of the organism-environment theory (Jarvilehto, 1998a, 1998b, 1999); the main question is how the development of mental activity and consciousness can be formulated if the starting point is not the separation of man and environment as in traditional cognitive psychology, but a unitary organism-environment system. According to the present formulation, mental activity is conceived as activity of the whole organism-environment system (...) and connected to the general development of life as a specific form of an organism-environment system comprising neurons. The advent of consciousness is regarded as a result of co-operation of such organism-environment systems. Consciousness is based on co-operation for the achievement of common results, and shared by the co-operating individuals (general consciousness), although each individual also makes it concrete from the perspective of his/her own body in the act of participation in common results (personal consciousness). Language is the means of formation of the co-operative system in the achievement of common results, and it is suggested that the use of language is related more to the type of co-operative system and intended common results than to any symbolic representation of the world. It is claimed that on this basis it is possible to develop psychology which takes seriously the concepts of mental activity and consciousness in the description of human action, but does not reduce these concepts either to biological or social factors. The present formulation should be regarded more as a conceptual outline than as a full-blown theory. (shrink)

The relation between mental processes and brain activity is studied from the point of view of the theory of the organism-environment system. It is argued that the systemic point of view leads to a new kind of definition of the primary tasks of neurophysiology and to a new understanding of the traditional neurophysiological concepts. Neurophysiology is restored to its place as a part of biology: its task is the study of neurons as living units, not as computer chips. (...) Neurons are living units which are organised as metabolic systems in connection with other neurons; they are not units which would carry out some psychological functions or maintain states which are typical only of the whole organism-environment system. Psychological processes, on the other hand, are processes always comprising the whole organism-environment system. (shrink)

For millennia, knowledge has eluded a precise definition. The industrialization of knowledge (IoK) and the associated proliferation of the so-called knowledge communities in the last few decades caused this state of affairs to deteriorate, namely by creating a trio composed of data, knowledge, and information (DIK) that is not unlike the aporia of the trinity in philosophy. This calls for a general theory of knowledge (ToK) that can work as a foundation for a science of knowledge (SoK) and (...) additionally distinguishes knowledge from both data and information. In this paper, I attempt to sketch this generality via the establishing of both knowledge structures and knowledge systems that can then be adopted/adapted by the diverse communities for the respective knowledge technologies and practices. This is achieved by means of a formal–indeed, mathematical–approach to epistemological matters a.k.a. formal epistemology. The corresponding application focus is on knowledge systems implementable as computer programs. (shrink)

The question of whether there are laws of nature in ecology has developed substantially in the last 20 years. Many have attempted to rehabilitate ecology’s lawlike status through establishing that ecology possesses laws that robustly appear across many different ecological systems. I argue that there is still something missing, which explains why so many have been skeptical of ecology’s lawlike status. Community ecology has struggled to establish what I call a General Unificatory Theory. The lack of a (...) GUT causes problems for explanation as there are no guidelines for how to integrate the lower-level mathematical and causal models into a larger theory of how ecological assemblages are formed. I turn to a promising modern attempt to provide a unified higher-level explanation in ecology, presented by ecologist Mark Vellend, and advocate for philosophical engagement with its prospects for aiding ecological explanation. (shrink)

Reconstructability analysis (RA) decomposes wholes, namely data in the form either of set theoretic relations or multivariate probability distributions, into parts, namely relations or distributions involving subsets of variables. Data is modeled and compressed by variable-based decomposition, by more general state-based decomposition, or by the use of latent variables. Models, which specify the interdependencies among the variables, are selected to minimize error and complexity.

What is the class of possible semiotic systems? What kinds of systems could count as such systems? The human mind is naturally considered the prototypical semiotic system. During years of research in semiotics the class has been broadened to include i.e. living systems like animals, or even plants. It is suggested in the literature on artificial intelligence that artificial agents are typical examples of symbol-processing entities. It also seems that semiotic processes are in fact cognitive (...) processes. In consequence, it is natural to ask the question about the relation between semiotic studies and research on artificial cognitive systems within cognitive science. Consequently, my main question concerns the problem of inclusion or exclusion from the semiotic spectrum at least some artificial systems. I would like to consider some arguments against the possibility of artificial semiotic systems and I will try to repeal them. Then I will present an existing natural-language using agent of the SNePS system and interpret it in terms of Peircean theory of signs. I would like also to show that some properties of semiotic systems in Peircean sense could be also found in a discussed artificial system. Finally, I will have some remarks on the status of semiotics in general. (shrink)

A generalized information theory is proposed as a natural extension of Shannon's information theory. It proposes that information comes from forecasts. The more precise and the more unexpected a forecast is, the more information it conveys. If subjective forecast always conforms with objective facts then the generalized information measure will be equivalent to Shannon's information measure. The generalized communication model is consistent with K. R. Popper's model of knowledge evolution. The mathematical foundations of the new information theory, (...) the generalized communication model , information measures for semantic information and sensory information, and the coding meanings of generalized entropy and generalized mutual information are introduced. Assessments and optimizations of pattern recognition, predictions, and detection with the generalized information criterion are discussed. For economization of communication, a revised version of rate-distortion theory: rate-of-keeping-precision theory, which is a theory for datum compression and also a theory for matching an objective channels with the subjective understanding of information receivers, is proposed. Applications include stock market forecasting and video image presentation. (shrink)

The machine conception of the organism (MCO) is one of the most pervasive notions in modern biology. However, it has not yet received much attention by philosophers of biology. The MCO has its origins in Cartesian natural philosophy, and it is based on the metaphorical redescription of the organism as a machine. In this paper I argue that although organisms and machines resemble each other in some basic respects, they are actually very different kinds of systems. I submit that (...) the most significant difference between organisms and machines is that the former are intrinsically purposive whereas the latter are extrinsically purposive. Using this distinction as a starting point, I discuss a wide range of dissimilarities between organisms and machines that collectively lay bare the inadequacy of the MCO as a general theory of living systems. To account for the MCO’s prevalence in biology, I distinguish between its theoretical, heuristic, and rhetorical functions. I explain why the MCO is valuable when it is employed heuristically but not theoretically, and finally I illustrate the serious problems that arise from the rhetorical appeal to the MCO. (shrink)

Entanglement is one of the most striking features of quantum mechanics, and yet it is not specifically quantum. More specific to quantum mechanics is the connection between entanglement and thermodynamics, which leads to an identification between entropies and measures of pure state entanglement. Here we search for the roots of this connection, investigating the relation between entanglement and thermodynamics in the framework of general probabilistic theories. We first address the question whether an entangled state can be transformed into another (...) by means of local operations and classical communication. Under two operational requirements, we prove a general version of the Lo-Popescu theorem, which lies at the foundations of the theory of pure-state entanglement. We then consider a resource theory of purity where free operations are random reversible transformations, modelling the scenario where an agent has limited control over the dynamics of a closed system. Our key result is a duality between the resource theory of entanglement and the resource theory of purity, valid for every physical theory where all processes arise from pure states and reversible interactions at the fundamental level. As an application of the main result, we establish a one-to-one correspondence between entropies and measures of pure bipartite entanglement and exploit it to define entanglement measures in the general probabilistic framework. In addition, we show a duality between the task of information erasure and the task of entanglement generation, whereby the existence of entropy sinks (systems that can absorb arbitrary amounts of information) becomes equivalent to the existence of entanglement sources (correlated systems from which arbitrary amounts of entanglement can be extracted). (shrink)

Context: The majority of contemporary enactivist work is influenced by the philosophical biology of Hans Jonas. Jonas credits all living organisms with experience that involves particular “existential” structures: nascent forms of concern for self-preservation and desire for objects and outcomes that promote well-being. We argue that Jonas’s attitude towards living systems involves a problematic anthropomorphism that threatens to place enactivism at odds with cognitive science, and undermine its legitimate aims to become a new paradigm for scientific investigation (...) and understanding of the mind. Problem: Enactivism needs to address the tension between its Jonasian influences and its aspirations to become a new paradigm for cognitive science. By relying on Jonasian phenomenology, contemporary enactivism obscures alternative ways in which phenomenology can be more smoothly integrated with cognitive science. Method: We outline the historical relationship between enactivism and phenomenology, and explain why anthropomorphism is problematic for a research program that aspires to become a new paradigm for cognitive science. We examine the roots of Jonas’s existential interpretation of biological facts, and describe how and why Jonas himself understood his project as founded on an anthropomorphic assumption that is incompatible with a crucial methodological assumption of scientific enquiry: the prohibition of unexplained natural purposes. We describe the way in which phenomenology can be integrated into Maturana’s autopoietic theory, and use this as an example of how an alternative, non-anthropomorphic science of the biological roots of cognition might proceed. Results: Our analysis reveals a crucial tension between Jonas’s influence on enactivism and enactivism’s paradigmatic aspirations. This suggests the possibility of, and need to investigate, other ways of integrating phenomenology with cognitive science that do not succumb to this tension. Implications: In light of this, enactivists should either eliminate the Jonasian inference from properties of our human experience to properties of the experience of all living organisms, or articulate an alternative conception of scientific enquiry that can tolerate the anthropomorphism this inference entails. The Maturanian view we present in the article’s final section constitutes a possible framework within which enactivist tools and concepts can be used to understand cognition and phenomenology, and that does not involve a problematic anthropomorphism. Constructivist content: Any constructivist approach that aims for integration with current scientific practice must either avoid the type of anthropomorphic inference on which Jonas bases his work, or specify a new conception of scientific enquiry that renders anthropomorphism unproblematic. (shrink)

This paper studies a formalisation of intuitionistic logic by Negri and von Plato which has general introduction and elimination rules. The philosophical importance of the system is expounded. Definitions of ‘maximal formula’, ‘segment’ and ‘maximal segment’ suitable to the system are formulated and corresponding reduction procedures for maximal formulas and permutative reduction procedures for maximal segments given. Alternatives to the main method used are also considered. It is shown that deductions in the system convert into normal form and that (...) deductions in normal form have the subformula property. (shrink)

ABSTRACT The individual-community relationship has always been one of the most fundamental topics of social sciences. In sociology, this is known as the micro-macro relationship while in economics it refers to the processes, through which, individual actions lead to macroeconomic phenomena. Based on philosophical discourse and systems theory, many sociologists even use the term "emergence" in their understanding of micro-macro relationship, which refers to collective phenomena that are created by the cooperation of individuals, but cannot be reduced to (...) individual actions. "Emergence" theories attempt to explain the nature of society as a complex system by examining how individuals and their relationships lead to the creation of integrated and macro-social phenomena such as markets, educational systems, cultural beliefs, and shared social practices. As a prelude to activity, every researcher has to answer the question from the methodological point of view, how is it possible to study the behavior of social groups and how can we gain knowledge about the laws related to social groups? Anyone who deals with humanities and social sciences or any reality and phenomenon that affects human beings, inevitably deals with the reality that is emerging. In fact, emergence occurs when one level of reality emerges radically from another level. Examples of emergent levels of reality include how the mind emerges from the body; or the way society emerges from human beings. Therefore, when there is an emerging factor, different scientific disciplines should be used, because it is inevitable to talk about social affairs, psychology and neurobiology, as well as physical and even chemical. -/- INTRODUCTION Since its beginning in the 19th century, sociology has faced the fundamental question of what a social phenomena stands for? At a glance, sociologists deal with the study of social groups, collective behavior, institutions, social structures, social networks, and social dynamics, and ultimately all such phenomena are composed of individuals. Therefore, social phenomena seem to have no independent ontological status, and in this case, sociology is ultimately about reducible individuals. Different approaches about the micro-macro relationship, using the concept of "emergence", argue that although collective phenomena are created by individuals, they cannot be reduced to individual action. The term "emergence" is used to distinguish "emergent results" from " Procedural results". Results are called Procedural that can only be calculated by adding or subtracting the causes that act together. On the contrary, they are emergent outcomes that are qualitatively novel compared to the causes from which they originate. An example of such emergent results is mental characteristics that emerge from neural processes, but are not considered among the characteristics of neural processes of components - which are their origin. Philosophical debates about emergentism and reductionism focus on the mind-brain relationship, but as many philosophers have noted, they can be generalized to apply to any hierarchical set of features. The cognitive revolution reactivated a 19th century controversy between theorists of Identity and dualism. The theorists of Identity believe in reductionist materialism and elimination of metaphysics, according to which the mind is nothing more than the biological, while the dualists believe that the mind and the brain are distinct from each other. Emergence has been considered as a third way between the theories of Identity and dualism. -/- METHODOLOGY Interdisciplinarity Is fundamentally indicated by the dominance of open systems as well as social and emerging systems at different levels. Therefore, as long as we are facing a new emergentism, there will necessarily be different fields and an interdisciplinary method. The commonality of social sciences and cognitive sciences on the issue of emergence provides the possibility of interaction and exchange of concepts between these two for deeper research. Therefore, in this research, apart from the concepts of Subvenience and downward causation, we have used multiple realization and wildly disjunctive, which are used to explain the emerging concept in cognitive sciences, including neurobiology, psychology, and philosophy. For analytical and interdisciplinary approaches, after examining the concepts of subvenience, and wildly disjunctive, Individualistic and collectivist emergentism have been reviewed. And then their adequacy is criticized and evaluated in meeting strong emergence conditions. -/- FINDINGS Philosophers of the mind have been able to define the conditions of irreducibility and downward causation, which are essential for strong emergence, by using the principle of subvenience with the help of multiple realization and wildly disjunctive principles. Therefore, by definition, emergentist individualism suffers from the problem of how to explain downward causality and irreducibility, and emergentist collectivism faces the challenge of reification. The analysis of the challenges facing the two methodological approaches of individualism and collectivism leads us to three unresolved issues about the emerging phenomenon, which are realism, downward causality, and mechanism. Despite the differences in the stances of these two approaches regarding the aforementioned triple problems, individualists and collectivists both agree that some social characteristics are reducible; and some others are irreducible due to their complexity, the determination of which, depends on the case study of the mechanism of emergence of each social characteristic. -/- CONCLUSION An emergence that is consistent with reductionism is called a weak emergence. And strong emergence includes the principle of irreducibility and downward causality. According to strong emergence, the characteristics of social phenomena have downward causal power, which cannot be reduced to the causal forces. The principle of subvenience, together with multiple realization and wildly disjunctive, can provide the conditions of irreducibility and downward causality, which are essential conditions of strong emergence. Based on the philosophical analysis of two methodological approaches, individualist and collectivist, it can be concluded that emergentist individualism suffers from the problem of how to explain downward causality and irreducibility, and reification collectivism faces the challenge of reification. The analysis of the problems faced by these two approaches leads us to three unresolved issues, which are realism, downward causality, and mechanism. individualist emergentists acknowledge the existence of emergent social characteristics, but despite this, they believe that these characteristics are not real but merely analytical constructs that require explanation based on individuals and their mutual actions. But collectivists argue that emergentism yields a categorical ontology and supports social realism. They accept the dependence of social characteristics on individuals, but claim that social entities and structures are ontologically independent. Individualists and collectivists both agree that some social characteristics are reducible; and others are irreducible due to their complexity; and the only way to recognize this is to engage in empirical studies of the mechanisms and temporal processes of "emergence" that create social characteristics. -/- NOVELTY The newness of this compact article is as follows: a) Presenting an interdisciplinary approach using the analysis of philosophy of cognitive sciences, including the philosophy of mind, neurobiology and psychology to formulate the issue of social emergence; b) Criticizing individualist and collectivist methodological approaches to the issue of social emergence and explaining the sufficiency and shortcomings of both in providing weak and strong emerging conditions; c) Explaining and categorizing the challenges facing methodological approaches in explaining the phenomenon of social emergence, in three categories: realism, downward causality, and mechanism. BIBLIOGRAPHY Beckermann, A., Flohr, H., & Kim, J. (eds.) (1992). Emergence or reduction? Essays on the prospects of nonreductive physicalism. Berlin: Walter de Gruyter. Bhaskar, R. (1979). The possibility of Naturalism. New York: Routledge. Bhaskar, R., Danermark, B. & Price, L. (2018). Interdisciplinarity and wellbeing: A critical realist general theory of interdisciplinarity. London and New York: Routledge. Blau, P.M. (1981). Introduction: diverse views of social structure and their common denominator. In Blau, P.M. & Merton, R.K. (eds.), Continuity in Structural Inquiry (pp. 1–23). Beverly Hills: Sage. Blau, P.M. (1987). Microprocess and macrostructure. In K.S. Cook (ed.), Social Exchange Theory (pp. 83–100). Newbury Park, CA: Sage. Brooks, R.A., & Maes, P. (eds). (1994). Artificial life IV; proceedings of the Fourth International Workshop on the Synthesis and Simulation of Living Systems. Cambridge, Mass: MIT Press. Clark, A. (1997). Being there: Putting brain, body, and world together again. Cambridge, Mass.: MIT Press. Coleman, J. S. (1987). Microfoundations and macrosocial behavior. In: J. C. Alexander, B. Giesen, R. Munch, & Neil J. Smelser (Eds.). The Micro-Macro Link (pp. 153–73). Berkeley: University of California. Coleman, J. S. (1990). Foundations of social theory. Cambridge, MA: Harvard University Press. Elster, J. (1985). Making sense of Marx. New York: Cambridge University Press. Fodor, J.A. (1974). Special sciences (Or: The disunity of science as a working hypothesis). Synthese, 28(2), 97–115. Fodor, J.A. (1989). Making mind matter more. Philosophical Topics, 17, 59-79. Giddens, A. (1984). The constitution of society: Outline of the theory of structuration. Berkeley: University of California Press. Hempel, C.G. (1965). Aspects of scientific explanation and other essays in the philosophy of science. New York: The Free Press. Horgan, T. (1993). From supervenience to superdupervenience: meeting the demands of a material world. Mind, 102, 555-586. Humphreys, P. (1997). How properties emerge”. Philosophy of Science, 64, 1-17. Kim, J. (1999). Making sense of emergence. Philosophical Studies, 95, 3–36. Kincaid, H. (1997). Individualism and the unity of science. New York: Rowman & Littlefield. Lewis, D.K. (1986). The plurality of worlds. Oxford: Oxford University Press. Nigel, G., & Conte, R. (eds.) (1995). Artificial societies; The computer simulation of social life. London: UCL Press. O’Connor, T. (1994). Emergent properties. American Philosophical Quarterly, 31, 91-104. Popper, K.R. (1968). Conjectures and refutations: The Growth of Scientific Knowledge. New York: Harper & Row. Sawyer, R. K. (2001). Emergence in sociology: contemporary philosophy of mind and some implications for sociological theory. American Journal of Sociology, 107, 551-585. Sawyer, R. K. (2004). The mechanisms of emergence. Philosophy of the Social Sciences, 34, 260–282. Sawyer, R. K. (2005). Social emergence: societies as complex systems. Cambridge: Cambridge University Press. Sawyer, R.K. (2003). Nonreductive individualism: Part 2, Social causation. Philosophy of the Social Sciences, 33, 203–224. Winch, P. (1993). The idea of a social science and its relation to philosophy‭ (SAMT, Trans.). Tehran, Iran: SAMT. (shrink)

The file on this site provides the slides for a lecture given in Hangzhou in May 2018, and the lecture itself is available at the URL beginning 'sms' in the set of links provided in connection with this item. -/- It is commonly assumed that regular physics underpins biology. Here it is proposed, in a synthesis of ideas by various authors, that in reality structures and mechanisms of a biological character underpin the world studied by physicists, in principle supplying detail (...) in the domain that according to regular physics is of an indeterminate character. In regular physics mathematical equations are primary, but this constraint leads to problems with reconciling theory and reality. Biology on the other hand typically does not characterise nature in quantitative terms, instead investigating in detail important complex interrelationships between parts, leading to an understanding of the systems concerned that is in some respects beyond that which prevails in regular physics. It makes contact with quantum physics in various ways, for example in that both involve interactions between observer and observed, an insight that explains what is special about processes involving observation, justifying in the quantum physics context the replacement of the unphysical many-worlds picture by one involving collapse. The link with biology furthermore clarifies Wheeler’s suggestion that a multiplicity of observations can lead to the ‘fabrication of form’, including the insight that this process depends on very specific ‘structures with power’ related to the 'semiotic scaffolding' of the application of sign theory to biology known as biosemiotics. -/- The observer-observed 'circle' of Wheeler and Yardley is a special case of a more general phenomenon, oppositional dynamics, related to the 'intra-action' of Barad's Agential Realism, involving cooperating systems such as mind and matter, abstract and concrete, observer and observed, that preserve their identities while interacting with one another in such a way as to act as a unit. A third system may also be involved, the mediating system of Peirce linking the two together. Such a situation of changing connections and separations may plausibly lead in the future to an understanding of how complex systems are able to evolve to produce 'life, the universe and everything'. -/- (Added 1 July 2018) The general structure proposed here as an alternative to a mathematics-based physics can be usefully characterised by relating it to different disciplines and the specialised concepts utilised therein. In theoretical physics, the test for the correctness of a theory typically involves numerical predictions, corresponding to which theories are expressed in terms of equations, that is to say assertions that two quantities have identical values. Equations have a lesser significance in biology which typically talks in terms of functional mechanisms, dependent for example on details of chemistry and concepts such as genes, natural selection, signals and geometrical or topologically motivated concepts such as the interconnections between systems and the unfolding of DNA. Biosemiotics adds to this the concept of signs and their interpretation, implying novel concepts such as semiotic scaffolding and the semiosphere, code duality, and appreciation of the different types of signs, including symbols and their capacity for abstraction and use in language systems. Circular Theory adds to this picture, as do the ideas of Barad, considerations such as the idea of oppositional dynamics. The proposals in this lecture can be regarded as the idea that concepts such as those deriving from biosemiotics have more general applicability than just conventional biology and may apply, in some circumstances, to nonlinear systems generally, including the domain new to science hypothesised to underlie the phenomena of present-day physics. -/- The task then has to be to restore the mathematical aspect presumed, in this picture, not to be fundamental as it is in conventional theory. Deacon has invoked a complex sequence of evolutionary steps to account for the emergence over time of human language systems, and correspondingly mathematical behaviour can be subsumed under the general evolutionary mechanisms of biosemiotics (cf. also the proposals of Davis and Hersh regarding the nature of mathematics), so that the mathematical behaviour of physical systems is consistent with the proposed scheme. In conclusion, it is suggested that theoretical physicists should cease expecting to find some universal mathematical ‘theory of everything’, and focus instead on understanding in more detail complex systems exhibiting behaviour of a biological character, extending existing understanding. This may in time provide a more fruitful understanding of the natural world than does the regular approach. The essential concepts have an observational basis from both biology and the little-known discipline of cymatics (a discipline concerned with the remarkable patterns that specific waveforms can give rise to), while again computer simulations also offer promise in providing insight into the complex behaviours involved in the above proposals. -/- References -/- Jesper Hoffmeyer, Semiotic Scaffolding of Living Systems. Commens, a Digital Companion to C. S. Peirce (on Commens web site). Terrence Deacon, The Symbolic Species, W.W. Norton & Co. Karen Barad, Meeting the Universe Halfway: Quantum Physics and the Entanglement of Matter and Meaning, Duke University Press. Philip Davis and Reuben Hersh, The Mathematical Experience, Penguin. Ilexa Yardley, Circular Theory. (shrink)

The INBIOSA project brings together a group of experts across many disciplines who believe that science requires a revolutionary transformative step in order to address many of the vexing challenges presented by the world. It is INBIOSA’s purpose to enable the focused collaboration of an interdisciplinary community of original thinkers. This paper sets out the case for support for this effort. The focus of the transformative research program proposal is biology-centric. We admit that biology to date has been more fact-oriented (...) and less theoretical than physics. However, the key leverageable idea is that careful extension of the science of living systems can be more effectively applied to some of our most vexing modern problems than the prevailing scheme, derived from abstractions in physics. While these have some universal application and demonstrate computational advantages, they are not theoretically mandated for the living. A new set of mathematical abstractions derived from biology can now be similarly extended. This is made possible by leveraging new formal tools to understand abstraction and enable computability. [The latter has a much expanded meaning in our context from the one known and used in computer science and biology today, that is "by rote algorithmic means", since it is not known if a living system is computable in this sense (Mossio et al., 2009).] Two major challenges constitute the effort. The first challenge is to design an original general system of abstractions within the biological domain. The initial issue is descriptive leading to the explanatory. There has not yet been a serious formal examination of the abstractions of the biological domain. What is used today is an amalgam; much is inherited from physics (via the bridging abstractions of chemistry) and there are many new abstractions from advances in mathematics (incentivized by the need for more capable computational analyses). Interspersed are abstractions, concepts and underlying assumptions “native” to biology and distinct from the mechanical language of physics and computation as we know them. A pressing agenda should be to single out the most concrete and at the same time the most fundamental process-units in biology and to recruit them into the descriptive domain. Therefore, the first challenge is to build a coherent formal system of abstractions and operations that is truly native to living systems. Nothing will be thrown away, but many common methods will be philosophically recast, just as in physics relativity subsumed and reinterpreted Newtonian mechanics. -/- This step is required because we need a comprehensible, formal system to apply in many domains. Emphasis should be placed on the distinction between multi-perspective analysis and synthesis and on what could be the basic terms or tools needed. The second challenge is relatively simple: the actual application of this set of biology-centric ways and means to cross-disciplinary problems. In its early stages, this will seem to be a “new science”. This White Paper sets out the case of continuing support of Information and Communication Technology (ICT) for transformative research in biology and information processing centered on paradigm changes in the epistemological, ontological, mathematical and computational bases of the science of living systems. Today, curiously, living systems cannot be said to be anything more than dissipative structures organized internally by genetic information. There is not anything substantially different from abiotic systems other than the empirical nature of their robustness. We believe that there are other new and unique properties and patterns comprehensible at this bio-logical level. The report lays out a fundamental set of approaches to articulate these properties and patterns, and is composed as follows. -/- Sections 1 through 4 (preamble, introduction, motivation and major biomathematical problems) are incipient. Section 5 describes the issues affecting Integral Biomathics and Section 6 -- the aspects of the Grand Challenge we face with this project. Section 7 contemplates the effort to formalize a General Theory of Living Systems (GTLS) from what we have today. The goal is to have a formal system, equivalent to that which exists in the physics community. Here we define how to perceive the role of time in biology. Section 8 describes the initial efforts to apply this general theory of living systems in many domains, with special emphasis on crossdisciplinary problems and multiple domains spanning both “hard” and “soft” sciences. The expected result is a coherent collection of integrated mathematical techniques. Section 9 discusses the first two test cases, project proposals, of our approach. They are designed to demonstrate the ability of our approach to address “wicked problems” which span across physics, chemistry, biology, societies and societal dynamics. The solutions require integrated measurable results at multiple levels known as “grand challenges” to existing methods. Finally, Section 10 adheres to an appeal for action, advocating the necessity for further long-term support of the INBIOSA program. -/- The report is concluded with preliminary non-exclusive list of challenging research themes to address, as well as required administrative actions. The efforts described in the ten sections of this White Paper will proceed concurrently. Collectively, they describe a program that can be managed and measured as it progresses. (shrink)

This book (in German) on "Physics, life and mind" is on the physical foundations of modern biology. The basic features of living systems, reproduction, mutation and metabolism, can be explained in terms of molecular processes involving nucleic acids as genetic material, and proteins as catalysts. The generation of structure and form in each generation results from spatiotemporal gene regulation in conjunction with the de novo formation of spatial order in which interplays of activation and inhibition play a crucial (...) part. Brain functions can be understood in terms of information processing in neural networks. Fundamental limitations of explanations of biological phenomena on the basis of physics are expected for the relation between neural and mental states, which may not be fully decodable by finite procedures. A complete algorithmic theory of the human mind encompassing all, including self-referential, aspects appears to be impossible even in principle, not only in practice. The range and limitations of explanations of life on the basis of physical laws and processes reflect the scope and limits of science in general. In contrast to the notions in circulation in the 19th century, modern science is open at the metatheoretical level to different philosophical, cultural and religious interpretations of man and the universe. -/- . (shrink)

Precision medicine and molecular systems medicine (MSM) are highly utilized and successful approaches to improve understanding, diagnosis, and treatment of many diseases from bench-to-bedside. Especially in the COVID-19 pandemic, molecular techniques and biotechnological innovation have proven to be of utmost importance for rapid developments in disease diagnostics and treatment, including DNA and RNA sequencing technology, treatment with drugs and natural products and vaccine development. The COVID-19 crisis, however, has also demonstrated the need for systemic thinking and transdisciplinarity and the (...) limits of MSM: the neglect of the bio-psycho-social systemic nature of humans and their context as the object of individual therapeutic and population-oriented interventions. COVID-19 illustrates how a medical problem requires a transdisciplinary approach in epidemiology, pathology, internal medicine, public health, environmental medicine, and socio-economic modeling. Regarding the need for conceptual integration of these different kinds of knowledge we suggest the application of general system theory (GST). This approach endorses an organism-centered view on health and disease, which according to Ludwig von Bertalanffy who was the founder of GST, we call Organismal Systems Medicine (OSM). We argue that systems science offers wider applications in the field of pathology and can contribute to an integrative systems medicine by (i) integration of evidence across functional and structural differentially scaled subsystems, (ii) conceptualization of complex multilevel systems, and (iii) suggesting mechanisms and non-linear relationships underlying the observed phenomena. We underline these points with a proposal on multi-level systems pathology including neurophysiology, endocrinology, immune system, genetics, and general metabolism. An integration of these areas is necessary to understand excess mortality rates and polypharmacological treatments. In the pandemic era this multi-level systems pathology is most important to assess potential vaccines, their effectiveness, short-, and long-time adverse effects. We further argue that these conceptual frameworks are not only valid in the COVID-19 era but also important to be integrated in a medicinal curriculum. (shrink)

This paper discusses the epistemic status of biology from the standpoint of the systemic approach to living systems based on the notion of biological autonomy. This approach aims to provide an understanding of the distinctive character of biological systems and this paper analyses its theoretical and epistemological dimensions. The paper argues that, considered from this perspective, biological systems are examples of emergent phenomena, that the biological domain exhibits special features with respect to other domains, and that (...) biology as a discipline employs some core concepts, such as teleology, function, regulation among others, that are irreducible to those employed in physics and chemistry. It addresses the claim made by Jacques Monod that biology as a science is marginal. It argues that biology is general insofar as it constitutes a paradigmatic example of complexity science, both in terms of how it defines the theoretical object of study and of the epistemology and heuristics employed. As such, biology may provide lessons that can be applied more widely to develop an epistemology of complex systems. (shrink)

Far from being indiscriminately critical of the ideas he associated with the morality system, Bernard Williams offered vindicatory explanations of its crucial building blocks, such as the moral/non-moral distinction, the idea of obligation, the voluntary/involuntary distinction, and the practice of blame. The rationale for these concessive moves, I argue, is that understanding what these ideas do for us when they are not in the service of the system is just as important to leading us out of the system as the (...) critique of that system. I then show how regarding the aspiration to shelter life from luck as the system’s organizing ambition explains why the system elaborates and combines these building blocks in the way it does. Finally, I argue that the ultimate problem with the resulting construction is its frictionless purity. It robs valuable concepts of their grip on the world we live in, and, by insisting on purity from contingency, threatens to issue in nihilism about value and scepticism about agency. (shrink)

Ideal theory in social and political philosophy generally works to hide philosophical theories’ complicity in sustaining the structural violence and maintenance of white supremacy that are foundational to settler colonial societies. While non-ideal theory can provide a corrective to some of ideal theory’s intended omissions, it can also work to conceal the same systems of violence that ideal theory does, especially when framed primarily as a response to ideal theory. This article takes a decolonial (...) approach to exploring the limitations of non-ideal theory in its ability to respond to and redress the continuing harms done to Indigenous peoples by settler colonialism, including by outlining non-ideal theory’s relationship to a colonial politics of recognition. (shrink)

The way, in which quantum information can unify quantum mechanics (and therefore the standard model) and general relativity, is investigated. Quantum information is defined as the generalization of the concept of information as to the choice among infinite sets of alternatives. Relevantly, the axiom of choice is necessary in general. The unit of quantum information, a qubit is interpreted as a relevant elementary choice among an infinite set of alternatives generalizing that of a bit. The invariance to the (...) axiom of choice shared by quantum mechanics is introduced: It constitutes quantum information as the relation of any state unorderable in principle (e.g. any coherent quantum state before measurement) and the same state already well-ordered (e.g. the well-ordered statistical ensemble of the measurement of the quantum system at issue). This allows of equating the classical and quantum time correspondingly as the well-ordering of any physical quantity or quantities and their coherent superposition. That equating is interpretable as the isomorphism of Minkowski space and Hilbert space. Quantum information is the structure interpretable in both ways and thus underlying their unification. Its deformation is representable correspondingly as gravitation in the deformed pseudo-Riemannian space of general relativity and the entanglement of two or more quantum systems. The standard model studies a single quantum system and thus privileges a single reference frame turning out to be inertial for the generalized symmetry [U(1)]X[SU(2)]X[SU(3)] “gauging” the standard model. As the standard model refers to a single quantum system, it is necessarily linear and thus the corresponding privileged reference frame is necessary inertial. The Higgs mechanism U(1) → [U(1)]X[SU(2)] confirmed enough already experimentally describes exactly the choice of the initial position of a privileged reference frame as the corresponding breaking of the symmetry. The standard model defines ‘mass at rest’ linearly and absolutely, but general relativity non-linearly and relatively. The “Big Bang” hypothesis is additional interpreting that position as that of the “Big Bang”. It serves also in order to reconcile the linear standard model in the singularity of the “Big Bang” with the observed nonlinearity of the further expansion of the universe described very well by general relativity. Quantum information links the standard model and general relativity in another way by mediation of entanglement. The linearity and absoluteness of the former and the nonlinearity and relativeness of the latter can be considered as the relation of a whole and the same whole divided into parts entangled in general. (shrink)

The paper seeks to make a contribution towards a better understanding of the current global political unrest. It argues that this unrest reflects ongoing tensions between hierarchical and non-hierarchical interactions. It also argues that the opposition between hierarchical and non-hierarchical interactions is not ontological but rather is rooted in the way we approach reality and is, therefore, subject to our control. The tendency to exclude the process of construction from our frame of vision is characteristic for the view of reality (...) that is dominant in our civilization. Contemporary theoretical perspectives that include, but are not limited to, systems theory, complexity theory, theory of self-organization, emergence theory and autopoiesis have much to offer in addressing and resolving this problem. The paper outlines some general organizing principles that should be part of this solution. (shrink)

The current technoscientific progress has led to a sectorization in the philosophy of science. Today the philosophy of science isn't is informal interested in studying old problems about the general characteristics of scientific practice. The interest of the philosopher of science is the study of concepts, problems and riddles of particular disciplines. Then, within this progress of philosophy of science, neuroscientific research stands out, because it invades issues traditionally addressed by the humanities, such as the nature of consciousness, action, (...) knowledge, normativity, etc. As a result, the new area of interdisciplinary study of neuroscience and philosophy arises: neurophilosophy. This emerging area applies neuroscientific concepts to traditional philosophical questions, limiting their responses to neuroscientific revelations about nervous systems. Neurophilosophy research focuses on problems related to the indirect nature of mind and brain, computational or representative analysis of brain process, relationships between psychological and neuroscientific research, adequate adaptations of physical and philosophical concepts in neuroscience and the place of cognitive functions. Now, the temporal representation of conscious experience and the types of the neural architecture to represent objects in time have aroused scientific interest. Under these interests, we focus on the studies on the temporary triadic structure of phenomenological consciousness in Dan Lloyd and Rick Grush. From Grush’s studies, the importance of Kantian ideas for cognitive neuroscience emerges, due to the active way in which Kant conceived space and time as forms of intuition, within which the mind interprets its experience. Under this perspective, the theoretical arguments of Dennett-Kinsbourne and Eagleman-Sejnowski represent winks in the direction of Kant-Husserl within the neuroscientific goal while considering that the contents provided by the mind included space, objects and perception of causal relationships. Then, theories of cognitive neuroscience are beginning to suggest that these elements are also, as Kant argued, interpretative elaborations provided by mind / brain, and not only content received from outside. In other words, current cognitive neuroscientific theories try to pass from its Humean phase to a Kantian phase. So, the challenge has been to explain that these elements are provided by the mind and the world itself, and how they have the content they have come from. These are lacking in current studies. Filling this gap helps to involve the analysis of the scientist’s experience in his theoretical attitude. In this sense, an investigation under the Kantian-Husserlian approach that involves pure intuitions a priori with the experience of the scientific and neuroscientific concepts represents a ground-breaking. At present, a neurophilosophical study about this does not exist. In this sense, one feasible proposal for research would be based on the application of neuroscientific results of Moser-Britt to philosophical problems of foundational notions in relativistic physics: space, time, space-time, field, etc., under the Kantian-Husserlian approach, which allows to demonstrate the multidisciplinary link between neurophilosophy and physics. This represents a ground-breaking area in current interests in scientific research, with a positive impact in the field of neuroscience, and contributing to the study of abstraction emphasizing the importance of Kant’s Copernican turn and Husserl’s phenomenological ideas in the construction of physical theories. -/- . (shrink)

There is a deeply entrenched view in philosophy and physics, the closed systems view, according to which isolated systems are conceived of as fundamental. On this view, when a system is under the influence of its environment this is described in terms of a coupling between it and a separate system which taken together are isolated. We argue against this view, and in favor of the alternative open systems view, for which systems interacting with their environment (...) are conceived of as fundamental, and the environment's influence is represented via the dynamical equations that govern the system's evolution. Taking quantum theories of closed and open systems as our case study, and considering three alternative notions of fundamentality: (i) ontic fundamentality, (ii) epistemic fundamentality, and (iii) explanatory fundamentality, we argue that the open systems view is fundamental, and that this has important implications for the philosophy of physics, the philosophy of science, and for metaphysics. (shrink)

It is argued that those who defend the Everett, or ‘many-worlds’, interpretation of quantum mechanics should embrace what we call the general quantum theory of open systems (GT) as the proper framework in which to conduct foundational and philosophical investigations in quantum physics. GT is a wider dynamical framework than its alternative, standard quantum theory (ST). This is true even though GT makes no modifications to the quantum formalism. GT rather takes a different view, what we (...) call the open systems view, of the formalism; i.e., in GT, the dynamics of systems whose physical states are fundamentally represented by density operators are represented as fundamentally open as specified by an in general non-unitary dynamical map. This includes, in principle, the dynamics of the universe as a whole. We argue that the more general dynamics describable in GT can be physically motivated, that there is as much prima facie empirical support for GT as there is for ST, and that GT could be fully in the spirit of the Everett interpretation—that there might, in short, be little reason for an Everettian not to embrace the more general theoretical landscape that GT allows one to explore. (shrink)

This work addresses a broad range of questions which belong to four fields: computation theory, general philosophy of science, philosophy of cognitive science, and philosophy of mind. Dynamical system theory provides the framework for a unified treatment of these questions. ;The main goal of this dissertation is to propose a new view of the aims and methods of cognitive science--the dynamical approach . According to this view, the object of cognitive science is a particular set of dynamical (...) systems, which I call "cognitive systems". The goal of a cognitive study is to specify a dynamical model of a cognitive system, and then use this model to produce a detailed account of the specific cognitive abilities of that system. The dynamical approach does not limit a-priori the form of the dynamical models which cognitive science may consider. In particular, this approach is compatible with both computational and connectionist modeling, for both computational systems and connectionist networks are special types of dynamical systems. ;To substantiate these methodological claims about cognitive science, I deal first with two questions in two different fields: What is a computational system? What is a dynamical explanation of a deterministic process? ;Intuitively, a computational system is a deterministic system which evolves in discrete time steps, and which can be described in an effective way. In chapter 1, I give a formal definition of this concept which employs the notions of isomorphism between dynamical systems, and of Turing computable function. In chapter 2, I propose a more comprehensive analysis which is based on a natural generalization of the concept of Turing machine. ;The goal of chapter 3 is to develop a theory of the dynamical explanation of a deterministic process. By a "dynamical explanation" I mean the specification of a dynamical model of the system or process which we want to explain. I start from the analysis of a specific type of explanandum--dynamical phenomena--and I then use this analysis to shed light on the general form of a dynamical explanation. Finally, I analyze the structure of those theories which generate explanations of this form, namely dynamical theories. (shrink)

In this article we present an advanced version of Dual-PECCS, a cognitively-inspired knowledge representation and reasoning system aimed at extending the capabilities of artificial systems in conceptual categorization tasks. It combines different sorts of common-sense categorization (prototypical and exemplars-based categorization) with standard monotonic categorization procedures. These different types of inferential procedures are reconciled according to the tenets coming from the dual process theory of reasoning. On the other hand, from a representational perspective, the system relies on the hypothesis (...) of conceptual structures represented as heterogeneous proxytypes. Dual-PECCS has been experimentally assessed in a task of conceptual categorization where a target concept illustrated by a simple common-sense linguistic description had to be identified by resorting to a mix of categorization strategies, and its output has been compared to human responses. The obtained results suggest that our approach can be beneficial to improve the representational and reasoning conceptual capabilities of standard cognitive artificial systems, and –in addition– that it may be plausibly applied to different general computational models of cognition. The current version of the system, in fact, extends our previous work, in that Dual-PECCS is now integrated and tested into two cognitive architectures, ACT-R and CLARION, implementing different assumptions on the underlying invariant structures governing human cognition. Such integration allowed us to extend our previous evaluation. (shrink)

The biological sciences study (bio)complex living systems. Research directed at the mechanistic explanation of the "live" state truly requires a pluralist research program, i.e. BioComplexity research. The program should apply multiple intra-level and inter-level theories and methodologies. We substantiate this thesis with analysis of BioComplexity: metabolic and modular control analysis of metabolic pathways, emergence of oscillations, and the analysis of the functioning of glycolysis.

Every year, hundreds of patients in England die whilst waiting for a kidney transplant, and this is evidence that the current system of altruistic-based donation is not sufficient to address the shortage of kidneys available for transplant. To address this problem, we propose a monopsony system whereby kidney donors can opt-in to receive financial compensation, whilst still preserving the right of individuals to donate without receiving any compensation. A monopsony system describes a market structure where there is only one ‘buyer’—in (...) this case the National Health Service. By doing so, several hundred lives could be saved each year in England, wait times for a kidney transplant could be significantly reduced, and it would lessen the burden on dialysis services. Furthermore, compensation would help alleviate the common disincentives to living kidney donation, such as its potential associated health and psychological costs, and it would also help to increase awareness of living kidney donation. The proposed system would also result in significant cost savings that could then be redirected towards preventing kidney disease and reducing health disparities. While concerns about exploitation, coercion, and the ‘crowding out’ of altruistic donors exist, we believe that careful implementation can mitigate these issues. Therefore, we recommend piloting financial compensation for living kidney donors at a transplant centre in England. (shrink)