The theoretical biology movement originating in Britain in the early 1930’s and the biosemiotics movement which took off in Europe in the 1980’s have much in common. They are both committed to replacing the neo-Darwinian synthesis, and they have both invoked theories of signs to this end. Yet, while there has been some mutual appreciation and influence, particularly in the cases of Howard Pattee, René Thom, Kalevi Kull, Anton Markoš and Stuart Kauffman, for the most part, these movements have (...) developed independently of each other. Focussing on morphogenesis understood as vegetative semiosis, in this paper I will argue that the ideas of these movements are commensurate. Furthermore, synthesising them would enable us to see life processes as proto-narratives. Doing so will involve synthesising biohermeneutics, Peircian biosemiotics with Waddington’s theoretical biology and Piagetian genetic structuralism, and this, I claim, would strengthen the challenge of these traditions to mainstream biology. At the same time, this should contribute to overcoming the opposition between the sciences and the humanities, developing a broader tradition of Schellingian thought which involves developing the humanities and then demanding of the physical and biological sciences that they are consistent with and can make intelligible the emergence of humans as conceived by the humanities. (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 idea behind this special theme journal issue was to continue the work we have started with the INBIOSA initiative (www.inbiosa.eu) and our small inter-disciplinary scientific community. The result of this EU funded project was a white paper (Simeonov et al., 2012a) defining a new direction for future research in theoretical biology we called Integral Biomathics and a volume (Simeonov et al., 2012b) with contributions from two workshops and our first international conference in this field in 2011. The initial (...) impulse for this effort was given a year earlier by a publication of one of the guest editors of this issue (Simeonov, 2010) in this journal. This time we wish to provide a broader forum and more space to elaborate in detail some of the most interesting concepts we have encountered in our discussions, as well as to invite some new contributions of particular interest in the field. Another goal we had in mind was to collect and review as many provocative perspectives as possible on the same key topic we are interested before making a decision to follow a more focused notion that would lead to a funded research program. Therefore we welcomed the generous suggestion of Professor Denis Noble, FRS, who is also editor of this journal to prepare a special theme issue entitled: “Can biology create a profoundly new mathematics and computation?” It has taken a while to invite and collect the contributions. Most of them had a couple of revision cycles and adjustments after having been thoroughly discussed with colleagues, incl. the editors of this issue. We think that the result we have obtained at the end is a satisfactory one, since we succeeded to integrate a diversity of original, but sometimes controversial and mutually excluding concepts organized within chapters of a self-contained volume. The task of compiling all this was not easy at all. Despite our efforts to position the articles of different authors and themes in a way allowing their easy comprehension and relation to each other within the individual chapters, some of them still require a sort of introduction to dissolve possible ambiguities. This is what we are going to do in the following few paragraphs with the hope that the reader (and some of the authors) would excuse our failures. (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)

In the contemporary philosophy of mind and consciousness studies, views such as panpsychism or theories of universal consciousness, have enjoyed a recent renaissance of metaphysical speculations in Western philosophy. Its similarities with Eastern philosophical traditions went not unnoticed. However, the potential contribution that the evolutionary cosmology of the Indian poet, mystic and philosopher Sri Aurobindo can offer to these ontologies, remains largely unknown or unexplored. Here, consciousness, mind, life, matter and evolution are interpreted in an extended metaphysical framework, uniting Western (...) and Eastern traditions inside a modern philosophical system where materialism, panpsychism, cosmopsychism and philosophical idealism are not seen as irreconcilable exclusives, but different points of view that can be reconciled in a synthesis of knowledge, as envisioned from higher states of consciousness. This integral view of reality offers a conceptual platform that can complement and incorporate current theoretical approaches in modern philosophy, where their present internal inconsistencies do not emerge, and can be suggestive for scientists as well, especially in the fields of biology and physical sciences. (shrink)

The study of biodiversity spans many disciplines and includes data pertaining to species distributions and abundances, genetic sequences, trait measurements, and ecological niches, complemented by information on collection and measurement protocols. A review of the current landscape of metadata standards and ontologies in biodiversity science suggests that existing standards such as the Darwin Core terminology are inadequate for describing biodiversity data in a semantically meaningful and computationally useful way. Existing ontologies, such as the Gene Ontology and others in the Open (...) Biological and Biomedical Ontologies (OBO) Foundry library, provide a semantic structure but lack many of the necessary terms to describe biodiversity data in all its dimensions. In this paper, we describe the motivation for and ongoing development of a new Biological Collections Ontology, the Environment Ontology, and the Population and Community Ontology. These ontologies share the aim of improving data aggregation and integration across the biodiversity domain and can be used to describe physical samples and sampling processes (for example, collection, extraction, and preservation techniques), as well as biodiversity observations that involve no physical sampling. Together they encompass studies of: 1) individual organisms, including voucher specimens from ecological studies and museum specimens, 2) bulk or environmental samples (e.g., gut contents, soil, water) that include DNA, other molecules, and potentially many organisms, especially microbes, and 3) survey-based ecological observations. We discuss how these ontologies can be applied to biodiversity use cases that span genetic, organismal, and ecosystem levels of organization. We argue that if adopted as a standard and rigorously applied and enriched by the biodiversity community, these ontologies would significantly reduce barriers to data discovery, integration, and exchange among biodiversity resources and researchers. (shrink)

Defending Robert Rosen’s claim that in every confrontation between physics and biology it is physics that has always had to give ground, it is shown that many of the most important advances in mathematics and physics over the last two centuries have followed from Schelling’s demand for a new physics that could make the emergence of life intelligible. Consequently, while reductionism prevails in biology, many biophysicists are resolutely anti-reductionist. This history is used to identify (...) and defend a fragmented but progressive tradition of anti-reductionist biomathematics. It is shown that the mathematicoephysico echemical morphology research program, the biosemiotics movement, and the relational biology of Rosen, although they have developed independently of each other, are built on and advance this antireductionist tradition of thought. It is suggested that understanding this history and its relationship to the broader history of post-Newtonian science could provide guidance for and justify both the integration of these strands and radically new work in post-reductionist biomathematics. (shrink)

To understand the mind and its place in Nature is one of the great intellectual challenges of our time, a challenge that is both scientific and philosophical. How does cognition influence an animal's behaviour? What are its neural underpinnings? How is the inner life of a human being constituted? What are the neural underpinnings of the conscious condition? Embodiment and the Inner Life approaches each of these questions from a scientific standpoint. But it contends that, before we can make progress (...) on them, we have to give up the habit of thinking metaphysically, a habit that creates a fog of philosophical confusion. From this post-reflective point of view, the book argues for an intimate relationship between cognition, sensorimotor embodiment, and the integrative character of the conscious condition. Drawing on insights from psychology, neuroscience, and dynamical systems, it proposes an empirical theory of this three-way relationship whose principles, not being tied to the contingencies of biology or physics, are applicable to the whole space of possible minds in which humans and other animals are included. Embodiment and the Inner Life is one of very few books that provides a properly joined-up theory of consciousness, and will be essential reading for all psychologists, philosophers, and neuroscientists with an interest in the enduring puzzle of consciousness. (shrink)

In the present essay I suggest that the main reason why history failed to develop societies in harmony with Nature, including our internal nature as well, is that we failed to evaluate the exact basis of the factor ultimately governing our thoughts. We failed to realise that it is the worldview that ultimately governs our thoughts and through our thoughts, our actions. In this work I consider the ultimate foundations of philosophy, science, religion, and art, pointing out that they were (...) and can be again in harmony with each other if their ultimate tasks are specified. I specify here the first task of philosophy as considering the philosophical significance of the ultimate principles of physics, biology and man/society. These ultimate principles are in direct connection with the ultimate questions of religion. I show that the fundamental nature of art makes it able to perceive the ultimate destination of mankind and the Universe, the world-to-be. I propose that philosophy, religion and art together are able to supply us with an inter-subjective picture of the world-process, including the inter-subjective picture of the future of mankind and the Universe. Care is taken to enlighten the possible role of values in founding scientific research in the frame of present wide-ranging discussions. The result is found that universal values of respect for existence, life and reason represent the inevitable basis of science. The exact foundations of a new, integral worldview are outlined, involving the worldprocess-picture, Nature-picture, images of man, society, self, history and manipulation. A list of our common tasks for founding the Integral Culture is proposed. (shrink)

Why is listening to sad music pleasurable? Eerola et al. convincingly argue that we should adopt an integrative framework — encompassing biological, psycho-social, and cultural levels of explanation — to answer this question. I agree. The authors have done a great service in providing the outline of such an integrative account. But in their otherwise rich discussion of the psycho-social level of engagements with sad music, they say little about the phenomenology of such experiences — including features that may help (...) shed further light on this question. I suggest that emerging enactive perspectives on music and emotion can offer some useful resources. (shrink)

Many biologists and philosophers have worried that importing models of reasoning from the physical sciences obscures our understanding of reasoning in the life sciences. In this paper we discuss one example that partially validates this concern: part-whole reductive explanations. Biology and physics tend to incorporate different models of temporality in part-whole reductive explanations. This results from differential emphases on compositional and causal facets of reductive explanations, which have not been distinguished reliably in prior philosophical analyses. Keeping these two (...) facets distinct facilitates the identifi cation of two further aspects of reductive explanation: intrinsicality and fundamentality. Our account provides resources for discriminating between different types of reductive explanation and suggests a new approach to comprehending similarities and differences in the explanatory reasoning found in biology and physics. (shrink)

MEMS is a structural technology, an example of the design and development of sophisticated, well integrated electronics systems and mechanical devices utilizing single-stage manufacturing techniques . Techniques for making the MEMS enables the components and equipment with performance and increased production are combined with the advantages of the ordinary, such as reducing the size of the physical volume, weight and cost and providing a basis for the production of non-manufacturing methods, the other is the reality of internal order Technology (...) MEMS and its micro-machining techniques are well versed in its application to an unprecedented range of MEMS devices over previous dependent fields (for example Biology and Microelectronics) These agents make MEMS far more comprehensive than IC microchips technology . (shrink)

Attempts to ‘naturalize’ phenomenology challenge both traditional phenomenology and traditional approaches to cognitive science. They challenge Edmund Husserl’s rejection of naturalism and his attempt to establish phenomenology as a foundational transcendental discipline, and they challenge efforts to explain cognition through mainstream science. While appearing to be a retreat from the bold claims made for phenomenology, it is really its triumph. Naturalized phenomenology is spearheading a successful challenge to the heritage of Cartesian dualism. This converges with the reaction against Cartesian thought (...) within science itself. Descartes divided the universe between res cogitans, thinking substances, and res extensa, the mechanical world. The latter won with Newton and we have, in most of objective science since, literally lost our mind, hence our humanity. Despite Darwin, biologists remain children of Newton, and dream of a grand theory that is epistemologically complete and would allow lawful entailment of the evolution of the biosphere. This dream is no longer tenable. We now have to recognize that science and scientists are within and part of the world we are striving to comprehend, as proponents of endophysics have argued, and that physics, biology and mathematics have to be reconceived accordingly. Interpreting quantum mechanics from this perspective is shown to both illuminate conscious experience and reveal new paths for its further development. In biology we must now justify the use of the word “function”. As we shall see, we cannot prestate the ever new biological functions that arise and constitute the very phase space of evolution. Hence, we cannot mathematize the detailed becoming of the biosphere, nor write differential equations for functional variables we do not know ahead of time, nor integrate those equations, so no laws “entail” evolution. The dream of a grand theory fails. In place of entailing laws, a post-entailing law explanatory framework is proposed in which Actuals arise in evolution that constitute new boundary conditions that are enabling constraints that create new, typically unprestatable, Adjacent Possible opportunities for further evolution, in which new Actuals arise, in a persistent becoming. Evolution flows into a typically unprestatable succession of Adjacent Possibles. Given the concept of function, the concept of functional closure of an organism making a living in its world, becomes central. Implications for patterns in evolution include historical reconstruction, and statistical laws such as the distribution of extinction events, or species per genus, and the use of formal cause, not efficient cause, laws. (shrink)

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

Philosophy of biology is often said to have emerged in the last third of the twentieth century. Prior to this time, it has been alleged that the only authors who engaged philosophically with the life sciences were either logical empiricists who sought to impose the explanatory ideals of the physical sciences onto biology, or vitalists who invoked mystical agencies in an attempt to ward off the threat of physicochemical reduction. These schools paid little attention to actual biological science, (...) and as a result philosophy of biology languished in a state of futility for much of the twentieth century. The situation, we are told, only began to change in the late 1960s and early 1970s, when a new generation of researchers began to focus on problems internal to biology, leading to the consolidation of the discipline. In this paper we challenge this widely accepted narrative of the history of philosophy of biology. We do so by arguing that the most important tradition within early twentieth-century philosophy of biology was neither logical empiricism nor vitalism, but the organicist movement that flourished between the First and Second World Wars. We show that the organicist corpus is thematically and methodologically continuous with the contemporary literature in order to discredit the view that early work in the philosophy of biology was unproductive, and we emphasize the desirability of integrating the historical and contemporary conversations into a single, unified discourse. (shrink)

"Living systems are cognitive systems, and living as a process is a process of cognition." -H.R. Maturana, The Biology of Cognition (1970/1980) Just as the cell has gradually come to be understood as a highly regulated and unctionally integrated whole, so too is the biosphere now recognized as a finely balanced ecological whole in which local disturbances can create world-wide climatic catastrophe. The oversimplified ideas of biology that characterized the field in its immature beginning led to the (...) theories of a progressive cumulative development or evolution to explain the present state of Nature. However, today, a more mature understanding of biology has brought with it the realization that Nature can not be the product of a gradual development, based only on the reductionist principles of chemistry and physics. In an ideal situation, where there are no strong interactions with the environment, isolated and purified chemicals may react in a mechanically simple manner, but in a living organism there are no isolated molecules. Everything within the cell interacts with everything else. The constituents of a cell are produced by the cell as much as they produce the cell itself. As the German philosopher Immanuel Kant understood, the unique judgment that allows us to identify a living organism as distinct from non-living matter, is that a living organism is both the cause and effect of itself. Thus, the life of a cell, as much as the life of the biosphere, can only be properly understood as an integrated organic whole. (shrink)

The nature of “the self” has been one of the central problems in philosophy and more recently in neuroscience. This raises various questions: Can we attribute a self to animals? Do animals and humans share certain aspects of their core selves, yielding a trans-species concept of self? What are the neural processes that underlie a possible trans-species concept of self? What are the developmental aspects and do they result in various levels of self-representation? Drawing on recent literature from both human (...) and animal research, we suggest a trans-species concept of self that is based upon what has been called a “core-self” which can be described by self-related processing as a specific mode of interaction between organism and environment. When we refer to specific neural networks, we will here refer to the underlying system as the “core-SELF.” The core-SELF provides primordial neural coordinates that represent organisms as living creatures—at the lowest level this elaborates interoceptive states along with raw emotional feelings while higher medial cortical levels facilitate affective-cognitive integration . Developmentally, SRP allows stimuli from the environment to be related and linked to organismic needs, signaled and processed within core-self structures within subcorical-cortical midline structures that provide the foundation for epigenetic emergence of ecologically framed, higher idiographic forms of selfhood across different individuals within a species. These functions ultimately operate as a coordinated network. We postulate that core SRP operates automatically, is deeply affective, and is developmentally and epigenetically connected to sensory-motor and higher cognitive abilities. This core-self is mediated by SCMS, embedded in visceral and instinctual representations of the body that are well integrated with basic attentional, emotional and motivational functions that are apparently shared between humans, non-human mammals, and perhaps in a proto-SELF form, other vertebrates. Such a trans-species concept of organismic coherence is thoroughly biological and affective at the lowest levels of a complex neural network, and culturally and ecologically molded at higher levels of neural processing. It allows organisms to selectively adapt to and integrate with physical and social environments. Such a psychobiologically universal, but environmentally diversified, concept may promote novel trans-species studies of the core-self across mammalian species. (shrink)

The human attempts to access, measure and organize physical phenomena have led to a manifold construction of mathematical and physical spaces. We will survey the evolution of geometries from Euclid to the Algebraic Geometry of the 20th century. The role of Persian/Arabic Algebra in this transition and its Western symbolic development is emphasized. In this relation, we will also discuss changes in the ontological attitudes toward mathematics and its applications. Historically, the encounter of geometric and algebraic perspectives enriched the mathematical (...) practices and their foundations. Yet, the collapse of Euclidean certitudes, of over 2300 years, and the crisis in the mathematical analysis of the 19th century, led to the exclusion of “geometric judgments” from the foundations of Mathematics. After the success and the limits of the logico-formal analysis, it is necessary to broaden our foundational tools and re-examine the interactions with natural sciences. In particular, the way the geometric and algebraic approaches organize knowledge is analyzed as a cross-disciplinary and cross-cultural issue and will be examined in Mathematical Physics and Biology. We finally discuss how the current notions of mathematical (phase) “space” should be revisited for the purposes of life sciences. (shrink)

Seminal work intended to found a new field of integrative Noetic Science is summarized. Until now the philosophy of Biological Mechanism has ruled medicine and psychology. Penrose claims, AA scientific world-view which does not profoundly come to terms with the problem of conscious mind can have no serious pretensions of completeness@. A noetic action principle synonymous with the historic concept of élan vital is introduced as the basis of a Continuous State Conscious Universe (CSCU). The least unit of CSCU superspace (...) defines Awareness as a fundamental physical quantity like charge in electrodynamics. This cosmological context reveals the origin of complexity in self-organized living-systems wherein the physical basis of qualia is formalized. The dynamics of this teleological action principle, mediated by a unitary noetic field pervading all biochemical species, optimizes the state of well-being through homeostasis and provides the fundamental basis for developing a Moral Psychology. (shrink)

This paper presents a unified theory of reality, which integrates two interdependent frameworks: Cellular Primary Consciousness Theory (CPCT) and Open and Closed Systems Theory (OCST). Although CPCT and OCST can each stand as individual theories, they are, in this work, combined to form a cohesive explanation of both the mechanics and purpose of the universe. CPCT posits that consciousness is a fundamental aspect of all life, extending to even the simplest cells, rather than being an emergent property exclusive to complex (...) neural systems. Drawing upon evidence from quantum mechanics, cell biology, and systems theory, CPCT challenges traditional views on the origins of consciousness by suggesting that awareness is a universal property present from the cellular level. OCST, which forms the second component of this unified theory, examines the nature of the universe as a closed system subject to the laws of entropy. This theory explores how the universe is moving toward maximum entropy, where meaning and contrasts dissolve. However, beyond this closed system lies the realm of an open system—a domain of infinite potential that transcends the dualities and limitations of the physical universe. This open system offers a philosophical explanation for existence and the possibility of eternal meaning. Together, these two theories provide a novel and cohesive framework that addresses both the mechanics of consciousness and the ultimate purpose of the universe. The integration of CPCT and OCST bridges scientific evidence from quantum biology and systems theory with philosophical explorations of existence, presenting a comprehensive vision of reality as both a closed physical system and an open metaphysical one. This unified theory encourages a reexamination of our place in the cosmos, suggesting that beyond the observable universe lies an infinite realm of potential where consciousness and meaning endure. (shrink)

This paper explores the nature of hate, forgiveness, and interconnectedness in human relationships. Hatred often arises from conflicts with personal expectations but can be transformed into forgiveness by adopting an impersonal, holistic perspective. Drawing on evolutionary theory, psychological insights, and Buddhist philosophy, the paper argues that forgiveness is essential for individual mental well-being and societal harmony. The Buddhist concept of “two arrows” illustrates that while pain is unavoidable, suffering stems from emotional reactions and can be mitigated. Embracing the interconnected nature (...) of events allows individuals to transcend psychological suffering and cultivate compassion. Forgiveness, distinct from condoning or forgetting, is a profound process of healing and self-liberation with significant implications for mental and physical health. By integrating philosophical and psychological perspectives, the paper highlights forgiveness as a biological and psychological necessity, improving mental health, life satisfaction, and fostering both personal and communalistic harmony. (shrink)

The quest for a unified “Theory of Everything” that explains the fundamental nature of the universe has long been a holy grail for scientists and philosophers, dating back to the ancient Greeks’ search for Arche. -/- So far, the mainstream of research on A Theory of Everything primarily focuses on the lifeless phenomena and laws of physics while ignores the realm of biology. However, a fundamentally different approach to the ToE has been put forward, presenting a viable alternative (...) to address the challenge of a Theory of Everything. This approach does not seek the ultimate “building block” but rather aims to uncover the intangible rules that fundamentally govern everything in the universe, seeking their universality across the vast spectrum, from the minute subatomic world to the mega mass cosmic world and the magical biological world. -/- To address the challenge, a set of the fundamental interrelationships is introduced and represented by a model, the Fundamental Interrelationships Model. This model cohesively represents these fundamental interrelationships, including serial-parallel relationships, transition of state, critical point, continuation-discontinuation, convergence-divergence, contraction-expansion, singularity-plurality, commonality-difference, similarity, symmetry-asymmetry, periodicity, dynamics-stability, order-disorder, limitation-without limitation, hierarchical structure, and cohesive interconnectedness. These interrelationships, found in nature, can be interpreted as the fundamental laws of physics. -/- Built on the foundation of the Fundamental Interrelationships Model, a collection of the well-established laws of physics and theories are represented and unified, including Newton’s three laws of motion, the four laws of thermodynamics, Einstein’s space-time relationship, Heisenberg’s uncertainty principle, Noether’s theorem, Schrodinger’s wave function collapse, chaos theory and complexity theory. The list continues to grow… Based on this model, a groundbreaking research has, for the first time, put forward a new hypothesis that unifies the Big Bang theory with the evolutionary theory, published in a book in 2022. This research unequivocally demonstrates that the evolution of life also follows the fundamental laws of physics, marking a significant stride toward addressing the longstanding challenge of a comprehensive Theory of Everything. -/- Subsequent studies reveal that the evolution of life (including the evolution of multicellularity), embryonic development, evolution of society (civilisation), and the evolution of the universe all adhere to these fundamental interrelationships. These events are specific expressions of the underlying principles of the Fundamental Interrelationships Model. -/- Ultimately, as a truly all-encompassing theory, the Theory of Everything should not only incorporate non-biological events and the laws of physics but also extend to all facets of life. Thus, unlike most existing candidates, the Fundamental Interrelationships Model offers a comprehensive framework, encompassing both non-biological and living phenomena. Therefore, any hypothesis failing to integrate biology and sociology shouldn’t be considered a comprehensive Theory of Everything -/- This article and the subsequent ones are the abstracts derived from the book, Behind Civilisation/civilization (multiple editions), which represents the culmination of decades of research. The book offers a more comprehensive exploration of how fundamental interrelationships govern all aspect of the universe. -/- . (shrink)

As the title, The Entangled State of God and Humanity suggests, this lecture dispenses with the pre-Copernican, patriarchal, anthropomorphic image of God while presenting a case for a third millennium theology illuminated by insights from archetypal depth psychology, quantum physics, neuroscience and evolutionary biology. It attempts to smash the conceptual barriers between science and religion and in so doing, it may contribute to a Copernican revolution which reconciles both perspectives which have been apparently irreconcilable opposites since the sixteenth (...) century. The published work of C.G. Jung, Wolfgang Pauli, David Bohm and Teilhard de Chardin outline a process whereby matter evolves in increasing complexity from sub-atomic particles to the human brain and the emergence of a reflective consciousness leading to a noosphere evolving towards an Omega point. The noosphere is the envelope of consciousness and meaning superimposed upon the biosphere a concept central to the evolutionary thought of visionary Jesuit palaeontologist Pierre Teilhard de Chardin (The Phenomenon of Man). -/- His central ideas, like those of Jung with his archetypes, in particular that of the Self, provide intimations of a numinous principle implicit in cosmology and the discovery that in and through humanity, evolution becomes not only conscious of itself but also directed and purposive. Although in Jung’s conception it was a “late-born offspring of the unconscious soul”, consciousness has become the mirror which the universe has evolved to reflect upon itself and in which its very existence is revealed. Without consciousness, the universe would not know itself. The implication for process theology is that God and humanity are in an entangled state so that the evolution of God cannot be separated from that of humankind. -/- A process (Incarnational) theology inseminated by the theory of evolution is one in which humankind completes the individuation of God towards the wholeness represented for instance in cosmic mandala symbols (Jung, Collected Works, vol. 11). Jung believed that God needs humankind to become conscious, whole and complete, a thesis explored in my book The Individuation of God: Integrating Science and Religion (Wilmette, IL: Chiron Publications 2012). This process theology like that implicit in the work of Teilhard de Chardin, is panentheistic so that God is immanent in nature though not identical with it (Atmanspacher: 2014: 284). (shrink)

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

Is integrative biology a good idea, or even possible? There has been much interest lately in the unifica- tion of biology and the integration of traditionally separate disciplines such as molecular and develop- mental biology on one hand, and ecology and evolutionary biology on the other. In this paper I ask if and under what circumstances such integration of efforts actually makes sense. I develop by example an analogy with Aristotle’s famous four “causes” that one can (...) investigate concerning any object or phenomenon: material (what something is made of), formal (what distinguishes that particular object from others), efficient (how was the object made) and final (why was the object made). The example is provided by ongoing research on different aspects of flowering time in the model system Arabidop- sis, a small weed belonging to the mustard family. I show that understanding how flowering time is controlled is an epistemologically different sort of question from why and how it evolved, and that the two research agendas can be pursued largely independently of each other. Toward the end, I propose that the real goal of integrative biology is to understand the boundary layers between levels of biologi- cal analysis, something to which modern philosophy of science can contribute significantly. (shrink)

Integration sustainability outcomes give attention to construction ecology in the design review of urban environments to comply with Earth’s System that is composed of integral parts of the (i.e., physical, chemical and biological components). Naturally, exchange patterns of industrial ecology have consistent and periodic cycles to preserve energy flows and materials in Earth’s System. When engineering topology is affecting internal and external processes in system networks, it postulated the valence of the first-level spatial outcome (i.e., project compatibility success). These instrumentalities (...) are dependent on relating the second-level outcome (i.e., participant security satisfaction). The construction ecology-based topology (i.e., as feedback energy system) flows from biotic and abiotic resources in the entire Earth’s ecosystems. These spatial outcomes are providing an innovation, as entails a wide range of interactions to state, regulate and feedback “topology” to flow as “interdisciplinary equilibrium” of ecosystems. The interrelation dynamics of ecosystems are performing a process in a certain location within an appropriate time for characterizing their unique structure in “equilibrium patterns”, such as biosphere and collecting a composite structure of many distributed feedback flows. These interdisciplinary systems regulate their dynamics within complex structures. These dynamic mechanisms of the ecosystem regulate physical and chemical properties to enable a gradual and prolonged incremental pattern to develop a stable structure. The engineering topology of construction ecology for integration sustainability outcomes offers an interesting tool for ecologists and engineers in the simulation paradigm as an initial form of development structure within compatible computer software. This approach argues from ecology, resource savings, static load design, financial other pragmatic reasons, while an artistic/architectural perspective, these are not decisive. The paper described an attempt to unify analytic and analogical spatial modeling in developing urban environments as a relational setting, using optimization software and applied as an example of integrated industrial ecology where the construction process is based on a topology optimization approach. (shrink)

Full applicability of physics to human biology does not necessarily imply that one can uncover a comprehensive, algorithmic correlation between physical brain states and corresponding mental states. The argument takes into account that information processing is finite in principle in a finite world. Presumbly the brain-mind-relation cannot be resolved in all essential aspects, particularly when high degrees of abstraction or self-analytical processes are involved. Our conjecture plausibly unifies the universal validity of physics and a logical limitation of (...) human thought, and it does not regard consciousness -the most basic human experience - as a marginal phenomenon. (shrink)

We characterize a type of functional explanation that addresses why a homologous trait originating deep in the evolutionary history of a group remains widespread and largely unchanged across the group’s lineages. We argue that biologists regularly provide this type of explanation when they attribute conserved functions to phenotypic and genetic traits. The concept of conserved function applies broadly to many biological domains, and we illustrate its importance using examples of molecular sequence alignments at the intersection of evolution and cell (...) class='Hi'>biology. We use these examples to show how the study of conserved functions can integrate knowledge of a trait’s causal effects on fitness and its history of natural selection without invoking adaptation. We also show how conserved function provides a novel basis for addressing objections against evolutionary functions raised by Robert Cummins. (shrink)

How the universe came to be what it is now is a key philosophical question. The hypothesis that it came from nothing or śūnya (as proposed by Stephen Hawking, among others) proves to be dissembling, since the quantum vacuum can hardly be considered a void (śūnya). In modern science, it is generally assumed that matter existed before the universe came to be. Modern science hypothesizes that the manifestation of life on earth is nothing but a mere increment in the complexity (...) of matter – and hence is an outcome of evolution of matter (chemical evolution) following the Big Bang. After the manifestation of life, modern science believed that chemical evolution transformed itself into biological evolution, which then had caused the entire biodiversity on our planet. In the framework of materialism, the major attention is to find general organizational laws stimulated by physical sciences, ignoring the uniqueness of life. The main goal of materialism is to reduce consciousness to natural processes, which in turn can be translated into the language of math, physics, and chemistry. Following this approach, scientists have made several attempts to deny the living organism of its veracity as an immortal soul, in favor of genes, molecules, atoms, and so on. However, advancement in various fields of biology has repeatedly given rise to questions against such a denial and has supplied more and more evidence against the completely misleading ideological imposition that living entities are particular states of matter. In the recent past, however, the realization has arisen that cognitive nature of life at all levels has begun presenting significant challenges to the views of materialism in biology and has created a more receptive environment for the soul hypothesis (Shanta BN. Commun Integr Biol 8(5):e1085138, 2015). Therefore, instead of adjudicating different aprioristic claims, the development of an authentic theory of origin of life and universe needs both proper scientific knowledge and the appropriate tools of philosophical analysis of life. This talk will highlight the uniqueness of biological systems that offers a considerable challenge to the mainstream materialism and proposes the Vedāntic philosophical view as a viable alternative for development of a theory worthy of origin of life and universe. (shrink)

This collection of articles was written over the last 10 years and the most important and longest within the last year. Also I have edited them to bring them up to date (2016). The copyright page has the date of this first edition and new editions will be noted there as I edit old articles or add new ones. All the articles are about human behavior (as are all articles by anyone about anything), and so about the limitations of having (...) a recent monkey ancestry (8 million years or much less depending on viewpoint) and manifest words and deeds within the framework of our innate psychology as presented in the table of intentionality. As famous evolutionist Richard Leakey says, it is critical to keep in mind not that we evolved from apes, but that in every important way, we are apes. If everyone was given a real understanding of this (i.e., human ecology and psychology) in school, maybe civilization would have a chance. -/- In my view these articles and reviews have many novel and highly useful elements, in that they use my own version of the recently (ca. 1980’s) developed dual systems view of our brain and behavior to lay out a logical system of rationality (personality, psychology, mind, language, behavior, thought, reasoning, reality etc.) that is sorely lacking in the behavioral sciences (psychology, philosophy, literature, politics, anthropology, history, economics, sociology etc.). The philosophy centers around the two writers I have found the most important, Ludwig Wittgenstein and John Searle, whose ideas I combine and extend within the dual system (two systems of thought) framework that has proven so useful in recent thinking and reasoning research. As I note, there is in my view essentially complete overlap between philosophy, in the strict sense of the enduring questions that concern the academic discipline, and the descriptive psychology of higher order thought (behavior). Once one has grasped Wittgenstein’s insight that there is only the issue of how the language game is to be played, one determines the Conditions of Satisfaction (what makes a statement true or satisfied etc.) and that is the end of the discussion. -/- Now that I think I understand how the games work I have mostly lost interest in philosophy, which of course is how Wittgenstein said it should be. But since they are the result of our innate psychology, or as Wittgenstein put, it due to the lack of perspicuity of language, the problems run throughout all human discourse, so there is endless need for philosophical analysis, not only in the ‘human sciences’ of philosophy, sociology, anthropology, political science, psychology, history, literature, religion, etc., but in the ‘hard sciences’ of physics, mathematics, and biology. It is universal to mix the language game questions with the real scientific ones as to what the empirical facts are. Scientism is ever present and the master has laid it before us long ago, i.e., Wittgenstein (hereafter W) beginning principally with the Blue and Brown Books in the early 1930’s. -/- "Philosophers constantly see the method of science before their eyes and are irresistibly tempted to ask and answer questions in the way science does. This tendency is the real source of metaphysics and leads the philosopher into complete darkness." (BBB p18) -/- Nevertheless, a real understanding of Wittgenstein’s work, and hence of how our psychology functions, is only beginning to spread in the second decade of the 21st century, due especially to P.M.S. Hacker (hereafter H) and Daniele Moyal-Sharrock (hereafter DMS),but also to many others, some of the more prominent of whom I mention in the articles. -/- When I read ‘On Certainty’ a few years ago I characterized it in an Amazon review as the Foundation Stone of Philosophy and Psychology and the most basic document for understanding behavior, and about the same time DMS was writing articles noting that it had solved the millennia old epistemological problem of how we can know anything for certain. I realized that W was the first one to grasp what is now characterized as the two systems or dual systems of thought, and I generated a dual systems (S1 and S2) terminology which I found to be very powerful in describing behavior. I took the small table that John Searle (hereafter S) had been using, expanded it greatly, and found later that it integrated perfectly with the framework being used by various current workers in thinking and reasoning research. -/- Since they were published individually, I have tried to make the book reviews and articles stand by themselves, insofar as possible, and this accounts for the repetition of various sections, notably the table and its explanation. I start with a short article that presents the table of intentionality and briefly describes its terminology and background. Next, is by far the longest article, which attempts a survey of the work of W and S as it relates to the table and so to an understanding or description (not explanation as W insisted) of behavior. -/- The key to everything about us is biology, and it is obliviousness to it that leads millions of smart educated people like Obama, Chomsky, Clinton and the Pope to espouse suicidal utopian ideals that inexorably lead straight to Hell On Earth. As W noted, it is what is always before our eyes that is the hardest to see. We live in the world of conscious deliberative linguistic System 2, but it is unconscious, automatic reflexive System 1 that rules. This is Searle’s The Phenomenological Illusion (TPI), Pinker’s Blank Slate and Tooby and Cosmides Standard Social Science Model. Democracy and equality are wonderful ideals, but without strict controls, selfishness and stupidity gain the upper hand and soon destroy any nation and any world that adopts them. The monkey mind steeply discounts the future, and so we sell our children’s heritage for temporary comforts. -/- The astute may wonder why we cannot see System 1 at work, but it is clearly counterproductive for an animal to be thinking about or second guessing every action, and in any case there is no time for the slow, massively integrated System 2 to be involved in the constant stream of split second ‘decisions’ we must make. As W noted, our ‘thoughts’ (T1 or the thoughts of System 1) must lead directly to actions. It is my contention that the table of intentionality (rationality, mind, thought, language, personality etc.) that features prominently here describes more or less accurately, or at least serves an heuristic for how we think and behave, and so it encompasses not merely philosophy and psychology but everything else (history, literature, mathematics, politics etc.). Note especially that intentionality and rationality as I (along with Searle, Wittgenstein and others) view it,includes both conscious deliberative System 2 and unconscious automated System 1 actions or reflexes. -/- Thus all the articles, like all behavior, are intimately connected if one knows how to look at them. As I note, The Phenomenological Illusion (oblivion to our automated System 1) is universal and extends not merely throughout philosophy but throughout life. I am sure that Chomsky, Obama, Zuckerberg and the Pope would be incredulous if told that they suffer from the same problem as Hegel, Husserl and Heidegger, but it’s clearly true. While the phenomenologists only wasted a lot of people’s time, they are wasting the earth. -/- My writings are available in updated versions as paperbacks and Kindles on Amazon. -/- Talking Monkeys: Philosophy, Psychology, Science, Religion and Politics on a Doomed Planet - Articles and Reviews 2006-2017 (2017) ASIN B071HVC7YP. -/- The Logical Structure of Philosophy, Psychology, Mind and Language in Ludwig Wittgenstein and John Searle--Articles and Reviews 2006-2016 (2017) ASIN B071P1RP1B. -/- Suicidal Utopian Delusions in the 21st century: Philosophy, Human Nature and the Collapse of Civilization - Articles and Reviews 2006-2017 (2017) 2nd printing with corrections (Feb 2018) ASIN B0711R5LGX -/- Suicide by Democracy: an Obituary for America and the World (2018) ASIN B07CQVWV9C . (shrink)

This collection of articles was written over the last 10 years and edited to bring them up to date (2017). The copyright page has the date of the edition and new editions will be noted there as I edit old articles or add new ones. All the articles are about human behavior (as are all articles by anyone about anything), and so about the limitations of having a recent monkey ancestry (8 million years or much less depending on viewpoint) and (...) manifest words and deeds within the framework of our innate psychology as presented in the table of intentionality. As famous evolutionist Richard Leakey says, it is critical to keep in mind not that we evolved from apes, but that in every important way, we are apes. If everyone was given a real understanding of this (i.e., of human ecology and psychology to actually give them some control over themselves), maybe civilization would have a chance. As things are however the leaders of society have no more grasp of things than their constituents and so collapse into anarchy is inevitable. The first group of articles attempts to give some insight into how we behave that is reasonably free of the theoretical delusions that are universal. In the next group, I show how these insights apply by reviewing some books in philosophy and psychology. Next I review books on science and religion and finally provide reviews and articles showing how understanding of both science and philosophy gives insight into the tragic delusions destroying the world. People believe that society can be saved by science, religion and politics, so I provide some suggestions as to why this is unlikely via short articles and reviews of recent books by well-known writers. It is critical to understand why we behave as we do and so the first section presents articles that try to describe (not explain as Wittgenstein insisted) behavior. I start with a brief review of the logical structure of rationality, which provides some heuristics for the description of language (mind, rationality, personality) and gives some suggestions as to how this relates to the evolution of social behavior. This centers around the two writers I have found the most important in this regard, Ludwig Wittgenstein and John Searle, whose ideas I combine and extend within the dual system (two ii systems of thought) framework that has proven so useful in recent thinking and reasoning research. As I note, there is in my view essentially complete overlap between philosophy, in the strict sense of the enduring questions that concern the academic discipline, and the descriptive psychology of higher order thought (behavior). Once one has grasped Wittgenstein’s insight that there is only the issue of how the language game is to be played, one determines the Conditions of Satisfaction (what makes a statement true or satisfied etc.) and that is the end of the discussion. Since philosophical problems are the result of our innate psychology, or as Wittgenstein put it, due to the lack of perspicuity of language, they run throughout human discourse and behavior, so there is endless need for philosophical analysis, not only in the ‘human sciences’ of philosophy, sociology, anthropology, political science, psychology, history, literature, religion, etc., but in the ‘hard sciences’ of physics, mathematics, and biology. It is universal to mix the language game questions with the real scientific ones as to what the empirical facts are. Scientism is ever present and the master has laid it before us long ago, i.e., Wittgenstein (hereafter W) beginning with the Blue and Brown Books in the early 1930’s. "Philosophers constantly see the method of science before their eyes and are irresistibly tempted to ask and answer questions in the way science does. This tendency is the real source of metaphysics and leads the philosopher into complete darkness." (BBB p18) The key to everything about us is biology, and it is obliviousness to it that leads millions of smart educated people like Obama, Chomsky, Clinton and the Pope to espouse suicidal utopian ideals that inexorably lead straight to Hell on Earth. As W noted, it is what is always before our eyes that is the hardest to see. We live in the world of conscious deliberative linguistic System 2, but it is unconscious, automatic reflexive System 1 that rules. This is the source of the universal blindness described by Searle’s The Phenomenological Illusion (TPI), Pinker’s Blank Slate and Tooby and Cosmides’ Standard Social Science Model. The astute may wonder why we cannot see System 1 at work, but it is clearly counterproductive for an animal to be thinking about or second guessing every action, and in any case, there is no time for the slow, massively integrated System 2 to be involved in the constant stream of split second ‘decisions’ we must make. As W noted, our ‘thoughts’ (T1 or the ‘thoughts’ of System 1) must lead directly to actions. iii It is my contention that the table of intentionality (rationality, mind, thought, language, personality etc.) that features prominently here describes more or less accurately, or at least serves as an heuristic for, how we think and behave, and so it encompasses not merely philosophy and psychology, but everything else (history, literature, mathematics, politics etc.). Note especially that intentionality and rationality as I (along with Searle, Wittgenstein and others) view it, includes both conscious deliberative System 2 and unconscious automated System 1 actions or reflexes. Thus, all the articles, like all behavior, are intimately connected if one knows how to look at them. As I note, The Phenomenological Illusion (oblivion to our automated System 1) is universal and extends not merely throughout philosophy but throughout life. I am sure that Chomsky, Obama, Zuckerberg and the Pope would be incredulous if told that they suffer from the same problem as Hegel, Husserl and Heidegger, (or that that they differ only in degree from drug and sex addicts in being motivated by stimulation of their frontal cortices by the delivery of dopamine (and over 100 other chemicals) via the ventral tegmentum and the nucleus accumbens), but it’s clearly true. While the phenomenologists only wasted a lot of people’s time, they are wasting the earth and their descendant’s futures. Many of the articles describe the ‘digital delusions’, which confuse the language games of System 2 with the automatisms of System 1, and so cannot distinguish biological machines (i.e., people) from other kinds of machines (i.e., computers). The ‘reductionist’ claim is that one can ‘explain’ behavior at a ‘lower’ level, but what actually happens is that one does not explain human behavior but a ‘stand in’ for it. Hence the title of Searle’s classic review of Dennett’s book (“Consciousness Explained”)— “Consciousness Explained Away”. In most contexts ‘reduction’ of higher level emergent behavior to brain functions, biochemistry, or physics is incoherent. Also for ‘reduction’ of chemistry or physics, the path is blocked by chaos and uncertainty. Anything can be ‘represented’ by equations, but when they ‘represent’ higher order behavior, it is not clear (and cannot be made clear) what the ‘results’ mean. Reductionist metaphysics is a joke, but most scientists and philosophers lack the appropriate sense of humor. Other digital delusions are that we will be saved from the pure evil (selfishness) of System 1 by computers/AI/robotics/ nanotech/genetic engineering created by System 2. The No Free Lunch principal tells us there will be serious and possibly fatal consequences. The adventurous may regard this principle as a higher order emergent expression of the Second Law of Thermodynamics. Hi-tech enthusiasts hugely underestimate the problems iv resulting from unrestrained motherhood, and of course it is neither profitable nor politically correct (and now with third world supremacism dominant, not even possible) to be honest about it. The last section describes various versions of the ‘altruism delusion’ that we are selected for cooperation, and that the euphonious ideals of Democracy, Diversity and Equality will lead us into utopia, if we just manage things correctly (the possibility of politics). Again, the No Free Lunch Principle ought to warn us it cannot be true, and we see throughout history and all over the contemporary world, that without strict controls, selfishness and stupidity gain the upper hand and soon destroy any nation that embraces it. In addition, the monkey mind steeply discounts the future, and so we cooperate in selling our descendant’s heritage for temporary comforts, greatly exacerbating the problems. I describe versions of this delusion (i.e., that we are basically ‘friendly’ if just given a chance) as it appears in some recent books on sociology/biology/economics. I end with an essay on the great tragedy playing out in America and the world, which can be seen as a direct result of our evolved psychology manifested as the inexorable machinations of System 1. Our psychology, eminently adaptive and eugenic on the plains of Africa from ca. 6 million years ago, when we split from chimpanzees, to ca. 50,000 years ago, when many of our ancestors left Africa (i.e., in the EEA or Environment of Evolutionary Adaptation), is now maladaptive and dysgenic and the source of our Suicidal Utopian Delusions. So, like all discussions of behavior (philosophy, psychology, sociology, biology, anthropology, politics, law, literature, history, economics, soccer strategies, business meetings, etc.), this book is about evolutionary strategies, selfish genes and inclusive fitness (kin selection). Many accept the delusion that we are selected for cooperation with people generally (group selection or altruism) and not just our immediate relatives (kin selection or inclusive fitness), so I spend some time in the essays of the last section demolishing this fantasy. One thing rarely mentioned by the group selectionists is the fact that, even were ‘group selection’ possible, selfishness is at least as likely (probably far more likely in most contexts) to be group selected for as altruism. Just try to find examples of true altruism in nature –the fact that we can’t (which we know is not possible if we understand evolution) tells us that its apparent presence in humans is an artefact of modern life concealing the facts, and that it can no more be selected for than the tendency to suicide (which in fact it is). One does not really need science or mathematics to grasp this – it is crushingly obvious that an v organism cannot be selected for behavior that decreases the frequency of its own genes in the next generation. One might also benefit from considering a phenomenon never (in my experience) mentioned by group selectionists -- cancer. No group has as much in common as the (originally) genetically identical cells in our own bodies-a 100 trillion cell clone-- but we are all born with thousands and perhaps millions of cells that have already taken the first step on the path to cancer and generate millions to billions of cancer cells in our life. If we did not die of other things first, we (and perhaps all multicellular organisms) would all die of cancer. Only a massive and hugely complex mechanism built into our genome that represses or derepresses trillions of genes in trillions of cells, and kills and creates billions of cells a second, keeps the majority of us alive long enough to reproduce. One might take this to imply that a just, democratic and enduring society for any kind of entity on any planet in any universe is only a dream, and that no being or power could make it otherwise. It is not only ‘the laws’ of physics that are universal and inescapable, or perhaps we should say that inclusive fitness is a law of physics. The great mystic Osho said that the separation of God and Heaven from Earth and Humankind was the most evil idea that ever entered the Human mind. In the 20th century an even more evil notion arose—that humans are born with rights, rather than having to earn privileges. Thus, every day the population increases by 200,000, who must be provided with resources to grow and space to live, and who soon produce another 200,000 etc. And one almost never hears it noted that what they receive must be taken from those already alive. Their lives diminish those already here in both major obvious and countless subtle ways. Every new baby destroys the earth from the moment of conception. There cannot be human rights without human wrongs. It cannot be more obvious, but one will never see the streets full of protesters against motherhood. America and the world are in the process of collapse from excessive population growth, most of it for the last century and now all of it due to 3rd world people. Consumption of resources and the addition of 4 billion more ca. 2100 will collapse industrial civilization and bring about starvation, disease, violence and war on a staggering scale. The earth loses about 2% of it’s topsoil every year, so as it nears 2100, most of it’s food growing capacity will be gone. Billions will die and nuclear war is all but certain. In America, this is being hugely accelerated by massive immigration and immigrant reproduction, combined with abuses made possible by democracy. Depraved human nature inexorably turns the dream of democracy and diversity into a vi nightmare of crime and poverty. China will continue to overwhelm America and the world, as long as it maintains the dictatorship which limits selfishness. The root cause of collapse is the inability of our innate psychology to adapt to the modern world, which leads people to treat unrelated persons as though they had common interests. This, plus ignorance of basic biology and psychology, leads to the social engineering delusions of the partially educated who control democratic societies. Few understand that if you help one person you harm someone else—there is no free lunch and every single item anyone consumes destroys the earth beyond repair. Consequently, social policies everywhere are unsustainable and one by one all societies without stringent controls on selfishness will collapse into anarchy or dictatorship. Without dramatic and immediate changes, there is no hope for preventing the collapse of America, or any country that follows a democratic system. The popular notions supported by the Democratic Party and Third World Supremacists are that Democracy, Diversity, Equality and Social Justice will produce a Utopia in America and the world, but it is clear as crystal that they unavoidably foster selfishness and divisiveness and are producing collapse. Hence my concluding essay “Suicide by Democracy”. The most basic facts, almost never mentioned, are that there are not enough resources in America or the world to lift a significant percentage of the poor out of poverty and keep them there. Even the attempt to do this is already bankrupting America and destroying the world. The earth’s capacity to produce food decreases daily, as does our genetic quality. And now, as always, by far the greatest enemy of the poor is other poor and not the rich. -/- My writings are available as paperbacks and Kindles on Amazon. -/- Talking Monkeys: Philosophy, Psychology, Science, Religion and Politics on a Doomed Planet - Articles and Reviews 2006-2017 (2017) ASIN B071HVC7YP. -/- The Logical Structure of Philosophy, Psychology, Mind and Language in Ludwig Wittgenstein and John Searle--Articles and Reviews 2006-2016 (2017) ASIN B071P1RP1B. -/- Suicidal Utopian Delusions in the 21st century: Philosophy, Human Nature and the Collapse of Civilization - Articles and Reviews 2006-2017 (2017) 2nd printing with corrections (Feb 2018) ASIN B0711R5LGX -/- Suicide by Democracy: an Obituary for America and the World (2018) ASIN B07CQVWV9C -/- . (shrink)

An influential position in the philosophy of biology claims that there are no biological laws, since any apparently biological generalization is either too accidental, fact-like or contingent to be named a law, or is simply reducible to physical laws that regulate electrical and chemical interactions taking place between merely physical systems. In the following I will stress a neglected aspect of the debate that emerges directly from the growing importance of mathematical models of biological phenomena. My main aim is (...) to defend, as well as reinforce, the view that there are indeed laws also in biology, and that their difference in stability, contingency or resilience with respect to physical laws is one of degrees, and not of kind . (shrink)

The paper deals with two central issues in the philosophy of neuroscience and psychiatry, namely those of the nature and the major kinds and types of psychopathological mechanisms. Contrary to a widespread view, I argue that mechanisms are not kinds of systems but kinds of processes unfolding in systems or between systems. More precisely, I argue that psychopathological mechanisms are sets of actions and interactions between brain-systems or circuits as well as between the latter and other systems in one's body (...) and external environment, both physical and social, involved in human psychopathology. According to the kinds of properties of the interacting systems or their component-parts, psychopathological mechanisms may be physical, chemical, biological, psychological, social, or, typically, mixed ones. Furthermore, I focus on two main kinds of psychopathological mechanisms involved in the causation of mental disorders, namely the pathogenetic and pathophysiological ones, stressing the importance of their careful distinction for the integrative understanding of otherwise disparate and apparently incommensurable psychiatric research findings. I illustrate my analysis with an example drawn from contemporary research on the mechanisms of acute psychosis. Finally, I stress the relevance of psychopathological mechanisms to a more scientifi cally-grounded classifi cation of mental disorders. (shrink)

The aim of this paper is to provide a theoretical framework to understand how multicellular systems realize functionally integrated physiological entities by organizing their intercellular space. From a perspective centered on physiology and integration, biological systems are often characterized as organized in such a way that they realize metabolic self-production and self-maintenance. The existence and activity of their components rely on the network they realize and on the continuous management of the exchange of matter and energy with their environment. (...) One of the virtues of the organismic approach focused on organization is that it can provide an understanding of how biological systems are functionally integrated into coherent wholes. Organismic frameworks have been primarily developed by focusing on unicellular life. Multicellularity, however, presents additional challenges to our understanding of biological systems, related to how cells are capable to live together in higher-order entities, in such a way that some of their features and behaviors are constrained and controlled by the system they realize. Whereas most accounts of multicellularity focus on cell differentiation and increase in size as the main elements to understand biological systems at this level of organization, we argue that these factors are insufficient to provide an understanding of how cells are physically and functionally integrated in a coherent system. In this paper, we provide a new theoretical framework to understand multicellularity, capable to overcome these issues. Our thesis is that one of the fundamental theoretical principles to understand multicellularity, which is missing or underdeveloped in current accounts, is the functional organization of the intercellular space. In our view, the capability to be organized in space plays a central role in this context, as it enables (and allows to exploit all the implications of) cell differentiation and increase in size, and even specialized functions such as immunity. We argue that the extracellular matrix plays a crucial active role in this respect, as an evolutionary ancient and specific (non-cellular) control subsystem that contributes as a key actor to the functional specification of the multicellular space and to modulate cell fate and behavior. We also analyze how multicellular systems exert control upon internal movement and communication. Finally, we show how the organization of space is involved in some of the failures of multicellular organization, such as aging and cancer. (shrink)

The fracture in the emerging discipline of biosemiotics when the code biologist Marcello Barbieri claimed that Peircian biosemiotics is not genuine science raises anew the question: What is science? When it comes to radically new approaches in science, there is no simple answer to this question, because if successful, these new approaches change what is understood to be science. This is what Galileo, Darwin and Einstein did to science, and with quantum theory, opposing interpretations are not merely about what theory (...) is right, but what is real science. Peirce's work, as he acknowledged, is really a continuation of efforts of Schelling to challenge the heritage of Newtonian science for the very good reason that the deep assumptions of Newtonian science had made sentient life, human consciousness and free will unintelligible, the condition for there being science. Pointing out the need for such a revolution in science has not succeeded as a defence of Peircian biosemiotics, however. In this paper, I will defend the scientific credentials of Peircian biosemiotics by relating it to the theoretical biology of the bio-mathematician, Robert Rosen. Rosen's relational biology, focusing on anticipatory systems and giving a place to final causes, should also be seen as a rigorous development of the Schellingian project to conceive nature in such a way that the emergence of sentient life, mind and science are intelligible. Rosen has made a very strong case for the characterization of his ideas as a real advance not only in science, but in how science should be understood, and I will argue that it is possible to provide a strong defence of Peircian biosemiotics as science through Rosen's defence of relational biology. In the process, I will show how biosemiotics can and should become a crucial component of anticipatory systems theory. (shrink)

There are two fundamentally distinct kinds of biological theorizing. "Formal biology" focuses on the relations, captured in formal laws, among mathematically abstracted properties of abstract objects. Population genetics and theoretical mathematical ecology, which are cases of formal biology, thus share methods and goals with theoretical physics. "Compositional biology," on the other hand, is concerned with articulating the concrete structure, mechanisms, and function, through developmental and evolutionary time, of material parts and wholes. Molecular genetics, biochemistry, developmental (...) class='Hi'>biology, and physiology, which are examples of compositional biology, are in serious need of philosophical attention. For example, the very concept of a "part" is understudied in both philosophy of biology and philosophy of science. ;My dissertation is an attempt to clarify the distinction between formal biology and compositional biology and, in so doing, provide a clear philosophical analysis, with case studies, of compositional biology. Given the social, economic, and medical importance of compositional biology, understanding it is urgent. For my investigation, I draw on the philosophical fields of metaphysics and epistemology, as well as philosophy of biology and philosophy of science. I suggest new ways of thinking about some classic philosophy of science issues, such as modeling, laws of nature, abstraction, explanation, and confirmation. I hint at the relevance of my study of two kinds of biological theorizing to debates concerning the disunity of science. (shrink)

For two reasons, physics occupies a preeminent position among the sciences. On the one hand, due to its recognized position as a fundamental science, and on the other hand, due to the characteristic of its obvious certainty of knowledge. For both reasons it is regarded as the paradigm of scientificity par excellence. With its focus on the issue of epistemic certainty, philosophy of science follows in the footsteps of classical epistemology, and this is also the basis of its 'judicial' (...) pretension vis-à-vis physics. Whereas physics is in a strong competitive relationship to philosophy and epistemology with respect to its position as a fundamental science - even on the subject of cognition, as the pretension of 'reductionism' shows. It is the thematic focus on epistemic certainty itself, however, that becomes the root of a profound epistemological misunderstanding of physics. The reason for this is twofold: first, the idea of epistemic certainty as a criterion of 'demarcation' between physics and metaphysics obscures the view of the much deeper heuristic differences between the two kinds of knowledge. The second, related, reason is that epistemology does not ask the question of the reason for the epistemic certainty of physics; instead, it sets itself the task of 'legitimating' physical knowledge, and this, crucially, with reference to the interpretation of the process of cognition. Thus, as a matter of course, all epistemological assumptions about this process – including the common descriptive understanding of knowledge and its ontological premises – flow into the interpretation of physics as a science. Consequently, this undertaking is not only doubtful from the ground up, because it presupposes for its meaningfulness nothing less than certainty of knowledge concerning (the interpretation of) the process of knowledge, thereby relying on mere convictions; moreover, by projecting the descriptive, 'metaphysical' concept of knowledge onto physics, it leads to unsolvable epistemological problems and corresponding resignative conclusions concerning the claim of knowledge of physics. In other words, epistemology itself builds, due to its basic assumptions, a major obstacle for an adequate understanding of physics. Physics' cross-object, deconstructive approach to knowledge implies a completely different, non-descriptive understanding of its concepts, with consequences that extend far beyond itself due to its status as a basic science. (shrink)

Since the world is full of indeterminacy, the Neutrosophics found their place into contemporary research. We now introduce for the first time the notions of Neutrosophic Crisp Sets and Neutrosophic Topology on Crisp Sets. We develop the 2012 notion of Neutrosophic Topological Spaces and give many practical examples. Neutrosophic Science means development and applications of Neutrosophic Logic, Set, Measure, Integral, Probability etc., and their applications in any field. It is possible to define the neutrosophic measure and consequently the neutrosophic integral (...) and neutrosophic probability in many ways, because there are various types of indeterminacies, depending on the problem we need to solve. Indeterminacy is different from randomness. Indeterminacy can be caused by physical space, materials and type of construction, by items involved in the space, or by other factors. In 1965 [51], Zadeh generalized the concept of crisp set by introducing the concept of fuzzy set, corresponding to the situation in which there is no precisely defined set;there are increasing applications in various fields, including probability, artificial intelligence, control systems, biology and economics. Thus, developments in abstract mathematics using the idea of fuzzy sets possess sound footing. In accordance, fuzzy topological spaces were introduced by Chang [12] and Lowen [33]. After the development of fuzzy sets, much attention has been paid to the generalization of basic concepts of classical topology to fuzzy sets and accordingly developing a theory of fuzzy topology [1-58]. In 1983, the intuitionistic fuzzy set was introduced by K. Atanassov [55, 56, 57] as a generalization of the fuzzy set, beyond the degree of membership and the degree of non-membership of each element. In 1999 and 2002, Smarandache [71, 72, 73, 74] defined the notion of Neutrosophic Sets, which is a generalization of Zadeh’s fuzzy set and Atanassov's intuitionistic fuzzy set. Some neutrosophic concepts have been investigated by Salama et al. [61-70]. Forwarding the study of neutrosophic sets, this book consists of seven chapters, targeting to:  generalize the previous studies in [1-59], and[91-94] so to define the neutrosopic crisp set and neutrosophic set concepts;  discuss their main properties; A. A. Salama & Florentin Smarandache  introduce and study some concepts of neutrosophic crisp and neutrosophic topological spaces and deduce their properties;  deduce many types of functions and give the relationships between different neutrosophic topological spaces, which helps to build new properties of neutrosophic topological spaces;  stress once more the importance of Neutrosophic Ideal as a nontrivial extension of neutrosophic set and neutrosophic logic [71, 72, 73, 74];  propose applications on computer sciences by using neutrosophic sets. (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)

Symmetries play a major role in physics, in particular since the work by E. Noether and H. Weyl in the first half of last century. Herein, we briefly review their role by recalling how symmetry changes allow to conceptually move from classical to relativistic and quantum physics. We then introduce our ongoing theoretical analysis in biology and show that symmetries play a radically different role in this discipline, when compared to those in current physics. By this (...) comparison, we stress that symmetries must be understood in relation to conservation and stability properties, as represented in the theories. We posit that the dynamics of biological organisms, in their various levels of organization, are not just processes, but permanent (extended, in our terminology) critical transitions and, thus, symmetry changes. Within the limits of a relative structural stability (or interval of viability), variability is at the core of these transitions. (shrink)

Where humans can manipulate and integrate the information they receive in subtle and ever changing ways from context to context, computers need structured and context-free background information of a sort which ontologies can help to provide. A domain ontology captures the stable, highly general and commonly accepted core knowledge for an application domain. The domain at issue here is that of the life sciences, in particular molecular biology and bioinformatics. Contemporary life science research includes components drawn from physics, (...) chemistry, mathematics, medicine and many other areas, and all of these dimensions, as well as fundamental philosophical issues, must be taken into account in the construction of a domain ontology. Here we describe the basic features of domain ontologies in the life sciences and show how they can be used. (shrink)

In a recent forum article, Dan Needleman and Jan Brugues argue that, despite the astonishing advances in cell biology, a fundamental understanding of even the most well-studied subcellular biological processes is lacking. This lack of understanding is evidenced by our inability to make precise predictions of subcellular and cellular behaviors. They suggest that to achieve such an under- standing, we need to apply a combination of quantitative experiments with new theoretical concepts and determine the physical principles of subcellular biological (...) organization. We discuss these issues and suggest that, besides biophysics, we need strong theoretical inputs from biocommunication theory in order to understand all the core agents of the cellular life and subcellular organization. (shrink)

Schröedinger’s question “what is life?” was a real challenge for the scientific community and this still remains as an opened question, because in spite of the important advances in various scientific branches like philosophy, biology, chemistry and physics,, each of them assesses life from its particular point of view to explain the life’ characteristic features, so not a coherent and well structured general model of life was reported. In this paper life is approached from informational perspective, starting from (...) earlier Draganeacu's philosophic concepts, showing that actually life is structured by matter and information. Therefore, it is analyzed carbon-matter properties on the basis of which the living structures are composed, giving rise not only of a considerable number of carbon-based compounds, but serving now beside silicon, as an useful material for micro/nanostructure applications. Such specific properties refers to the high ability of carbon to associate/dissociate in chemical reactions regulated/facilitated by informational (Bit unit) YES/NO bistable mechanisms to form macro/small molecules with complementary properties, reactive info-functional pathways of transduction, relaying, amplification, integration, spreading, modulation, activation and positive/negative feedback reactions, like in the informational microelectronic/microsystems circuits. It is argued that the negentropy invoked earlier in Schrödinger's analysis is a consequence of informational-assisted structuration/organization of the cell and human organism. From the analysis of inter/intra-communication mechanisms in the cell and comparing with the outcomes described by the Informational Model of Human Body, it is deduced that, the living organisms operate on the basis of three main streaming circuits assuring the living functions: (1) the metabolic matter-related circuit; (2) the operative informational circuit; (3) the epigenetic informational circuit for the gradual integration of information in the central informational structure – DNA. It is founded on these bases the Informational Model of the Living Structures, and the Informational System of the Living Structures (ISLS), with similar functions on the entire living scale size, from unitary to multicellular living structures, composed by seven informational systems, namely [CASI (center of acquisition and storing of information), CDC (center of decision and command), IRSS (info-reactive sentient system), MIS (maintenance info-system), GTS (genetic transmission system), IGG (info-genetic generator) and IC (info-connection)]ISLS, and are identified the specific functions of each of them. The living structures operate thus like self-“polarized" bipolar info-matter informational devices by means of the stand-by metabolic matter-related circuit, and react/respond to the external/internal informational stimuli, which modulate their functionality, returning an external reaction signal (“attitude"), for adaptation and survival. (shrink)

In this book I show that science suffers from a damaging but rarely noticed methodological disease, which I call rationalistic neurosis. It is not just the natural sciences which suffer from this condition. The contagion has spread to the social sciences, to philosophy, to the humanities more generally, and to education. The whole academic enterprise, indeed, suffers from versions of the disease. It has extraordinarily damaging long-term consequences. For it has the effect of preventing us from developing traditions and institutions (...) of learning rationally devoted to helping us learn how to make progress towards a wiser, more civilized world. On our fragile earth, overcrowded, fraught with injustice, inequality and conflict, menaced by unprecedented and terrifying technological and industrial means for change and destruction, we urgently need to acquire a little more wisdom and civilization if we are to avoid repeating horrors of the kind suffered by so many during the 20th century (and already suffered by many in the first few years of the 21st century). We can ill afford to have in our hands instruments of learning botched and bungled from the standpoint of helping us learn how to live more wisely. It may seem scarcely credible that something as important as our institutions of learning can suffer from wholesale, structural defects. Why has this not been noticed before? Why have not armies of scientists and scholars appreciated the point and, long ago, put the matter right? The answer will emerge as my argument unfolds. I will show that one of the most damaging features of rationalistic neurosis is that it has built-in methodological and institutional mechanisms which effectively conceal that anything is wrong. But there is also an immediately obvious reason: specialization, and the resulting fragmentation of academia, has resulted in a situation in which hardly anyone takes responsibility for the overall ideals, the overall aims and methods, of academic inquiry. Academics, these days, are specialists, furiously trying to keep abreast of developments in their own specialist fields. They have no time, and no inducement, to lift their eyes from their particular disciplines, and look at the whole endeavour. Science has long been under attack, at least since the Romantic movement. Blake objected to “Single vision & Newton’s sleep” and declared that “Art is the Tree of Life... Science is the Tree of Death”. Keats lamented that science will “clip an Angel’s wings” and “unweave a rainbow”. Whereas the Enlightenment had valued science and reason as tools for the liberation of humanity, Romanticism found science and reason oppressive and destructive, and instead valued art, imagination, inspiration, individual genius, emotional and motivational honesty rather than careful attention to objective fact. Much subsequent opposition to science stems from, or echoes, the Romantic opposition of Blake, Wordsworth, Keats and many others. There is the movement Isaiah Berlin has described as the “Counter-Enlightenment” (Berlin, 1979, ch. 1). There is existentialism, with its denunciation of the tyranny of reason, its passionate affirmation of the value and centrality of irrationality in human life, from Dostoevsky, Kierkegaard and Nietzsche to Heidegger and Sartre (see, for example, Barrett, 1962). There is the attack on Enlightenment ideals concerning science and reason undertaken by the Frankfurt school, by postmodernists and others, from Horkheimer and Adorno to Lyotard, Foucault, Habermas, Derrida, MacIntyre and Rorty (see Gascardi, 1999). The soul-destroying consequences of valuing science and reason too highly is a persistent theme in literature: it is to be found in the works of writers such as D.H. Lawrence, Doris Lessing, Max Frisch, Y. Zamyatin. There is persistent opposition to modern science and technology, and to scientific rationality, often associated with the Romantic wing of the green movement, and given expression in such popular books as Marcuse’s One Dimensional Man, Roszak’s Where the Wasteland Ends, Berman’s The Reenchantment of the World and Appleyard’s Understanding the Present. There is the feminist critique of science and conceptions of science: see, for example, Fox Keller (1984) and Harding (1986). And there are the corrosive implications of the so-called “strong programme” in the sociology of knowledge, and of the work of social constructivist historians of science, which depict scientific knowledge as a belief system alongside many other such conflicting systems, having no more right to claim to constitute knowledge of the truth than these rivals, the scientific view of the world being no more than an elaborate myth, a social construct (see Barnes and Bloor, 1981; Bloor, 1991; Barnes, Bloor and Henry, 1996; Shapin and Schaffer, 1985; Shapin, 1994; Pickering, 1984; Latour, 1987). This latter literature has provoked a counter-attack by scientists, historians and philosophers of science seeking to defend science and traditional conceptions of scientific rationality: see Gross and Levitt (1994), Gross, Levitt and Lewis (1996), and Koertge (1998). This debate between critics and defenders of science came abruptly to public attention with the publication of Alan Sokal’s brilliant hoax article ‘Transgressing the boundaries’ in a special issue of the cultural studies journal Social Text in 1996 entitled Science Wars: see Sokal and Bricmont (1998). What does this book have to contribute, given the above avalanche of criticism of science? The criticisms of science developed in this book are diametrically opposed to the above, in so far as the above criticisms oppose scientific rationality, seek to diminish or restrict its influence, or hold that it is unattainable. My central point is that we suffer, not from too much scientific rationality, but from not enough. What is generally taken to constitute scientific rationality is actually nothing of the kind. It is rationalistic neurosis, a characteristic, influential and damaging kind of irrationality masquerading as rationality. Science is damaged by being trapped within a widely upheld but severely defective philosophy of science; free science from this defective philosophy, provide it with a more intellectually rigorous philosophy, and it will flourish in both intellectual and humanitarian terms. And more generally, as we shall see, academic inquiry as a whole is damaged by being trapped within an intellectually defective philosophy of inquiry; free it from this defective philosophy, from its rationalistic neurosis, and it will flourish in intellectual and human terms. It is not reason that is damaging, but defective pretensions to reason — rationalistic neurosis —masquerading as reason. Thus what I seek to do here is the exact opposite of what all those who oppose science and scientific rationality do. I shall argue that Reason, the authentic article, arrived at by generalizing the progress-achieving methods of science, can have profoundly liberating and enriching consequences for all worthwhile, problematic aspects of life, and thus deserves to enter into every aspect of life. The bare bones of the argument of this book can be stated quite simply like this. Science cannot proceed without making the substantial metaphysical assumption that the universe is physically comprehensible (to some extent at least). But this conflicts with the orthodox view that in science everything is assessed impartially with respect to evidence, nothing being permanently assumed independently of evidence. So the metaphysical assumption of comprehensibility is repressed. Science pretends that no such assumption is made. But this damages science. For the assumption is substantial, influential and highly problematic. It needs to be made explicit within science so that it can be critically scrutinized, so that alternatives can be developed and considered. Pretending the assumption is not being made undermines the intellectual rigour of science, its intellectual value and success. And it does not stop there. For science also makes value assumptions. Quite properly, science is concerned to discover that which is of value. New factual knowledge devoid of all value (whether intellectual or practical) does not contribute to science. But the orthodox view of science holds that values have no place within science. As in the case of metaphysics, here too, science pretends that values have no role to play within the intellectual domain of science. And this damages science. For values are, if anything, even more influential and problematic than metaphysics (in influencing the direction of research). Here too, values need to be made explicit within science so that they can be scrutinized, so that alternatives can be developed and assessed. Pretending that values play no role within the intellectual domain damages science; both the intellectual and the practical aspects of science are adversely affected. Science fails to pursue those avenues of research that lie in the best interests of humanity. And it goes further. Science is pursued in a social, cultural, economic and political context. It is a part of various social, economic and political projects which seek to achieve diverse human objectives. But the idea that science is an integral part of humanitarian or political enterprises with political ends clashes, once again, with the official view of science that the aim of science is to improve factual knowledge. The political objectives of science are repressed. And, once again, this damages science. For, of course, the political objectives of science, like all our political objectives, are profoundly problematic. These need to be made explicit so that they can be scrutinized, so that alternatives can be developed and considered. The pretence that science does not have this political dimension once again undermines the intellectual rigour of science, and its human value. It lays science open to becoming a part of economic, corporate and political enterprises that are not in the best interests of humanity. The upshot of the line of argument just indicated is that we need to bring about a revolution in the aims and methods of science, and of academic inquiry more generally. Natural science needs to change; its relationship with the rest of academic inquiry, with social inquiry and the humanities, needs to change; and most importantly and dramatically, academic inquiry as a whole needs to change. The basic task of the academic enterprise needs to become to help humanity learn how to tackle its problems of living in more cooperatively rational ways than at present. We need to put the intellectual tasks of articulating our problems of living, and proposing and critically assessing possible solutions, possible and actual actions, at the heart of academic inquiry. The basic task needs to be to help humanity learn a bit more wisdom – wisdom being the capacity to realize what is of value in life, for oneself and others, wisdom including knowledge and technological know-how, but much else besides. Natural science, despite its flaws, has massively increased our knowledge and technological know-how. This in turn has led to a massive and sometimes terrifying increase in our power to act. Often this unprecedented power to act is used for human good, as in medicine or agriculture. But it is also used to cause harm, whether unintentionally (initially at least) as when industrialization and modern agriculture lead to global warming, destruction of natural habitats and rapid extinction of species, or intentionally, as when the technology of war is used by governments and terrorists to maim and kill. Before the advent of modern science, when we lacked the means to do too much damage to ourselves and the planet, lack of wisdom did not matter too much. Now, with our unprecedented powers to act, bequeathed to us by science, lack of wisdom has become a menace. This is the crisis behind all the other current global crises: science without wisdom. In these circumstances, to continue to pursue knowledge and technological know-how dissociated from a more fundamental quest for wisdom can only deepen the crisis. As a matter of urgency, we need to free science and academia of their neuroses; we need to bring about a revolution in the academic enterprise so that the basic aim becomes to promote wisdom by intellectual and educational means. At present science and the humanities betray both reason and humanity. The argument of this book, which I have just summarized, begins with a discussion of the philosophical and methodological problems that beset theoretical physics. At once, many of those who are concerned about moral, political and environmental issues that plague our world today, will feel impatient. What have the methodological problems of theoretical physics to do with third world poverty, war and the threat of war, pollution, extinction of species, the menace of conventional, chemical, biological and nuclear armaments? I can only plead with such a reader: patience. The root cause of the sickness of our times does indeed lie, I claim, with a methodological sickness of natural science or, even more specifically, of physical science. What makes the modern world so utterly different from all previous ages is our possession of modern science and technology. This is the instrument that has changed the conditions of human life almost beyond all recognition, and put unprecedented, and sometimes terrifying, powers into our hands. One should not dismiss out of hand the suggestion that a part of our problem may lie with this instrument, this engine, of rapid change. We see, here, too, the way in which intellectual specialization, referred to above, has effectively concealed from view the nature and extent of the problem that confronts us. The argument that I shall develop in what follows begins with physics, with problems concerning the aims and methods of physics. But it then leaps to social science, to philosophy, to the humanities, to education, to psychotherapy, and to politics: in the end there is scarcely an aspect of modern life that is not touched and, potentially, affected by the argument. How many academic experts are prepared to follow, to take seriously, an argument that ranges so recklessly across such a wide range of academic disciplines? How many non-academic non-experts? But just this is what the argument and message of this book requires. I hope that the reader will endure with patience the somewhat esoteric discussion concerning the aims and methods of physics pursued in chapter one. This may not seem to have anything much to do with the urgent problems of our times, but it does. This is in part how the intellectual disaster I seek to expose in this book conceals itself from view: it buries itself in the obscure, recondite field of the philosophy of physics. Those who devote their lives to the philosophy of physics are, by and large, too myopic to see how their specialized field of study has anything to do with the great and dreadful humanitarian problems and disasters of our age; and those who are above all concerned with these humanitarian disasters have no time at all for abstruse issues concerning the aims and methods of physics. And so the connection is never made. As it happens, the methodological neurosis of physics, with which we begin in chapter one, is actually a quite simple matter to grasp. It does not require any real knowledge of physics to understand. Indeed, physicists and philosophers of physics are much more likely to find the argument difficult to follow than are non-experts. We non-scientists can stand back and see the whole wood; scientists, trained to think in terms of the current orthodox conception of science, trapped in the thickets of research, will find this much harder to do. In an attempt to take this peculiar circumstance into account, I have arranged the exposition as follows. In chapter one I give a simple exposition of the case for declaring natural science to suffer from what I call "rationalistic neurosis"; this avoids all technicalities, and goes straight to the heart of the matter. In the appendix I tackle a host of more technical objections that may be made to the elementary argument of chapter one. So, those experts in the fields of the philosophy of physics and philosophy of science who find the argument of chapter one naïve and unconvincing, should consult the appendix before tossing the book away in disgust. I write in the hope that there will be a few who will not dismiss out of hand the suggestion that the question of how we are to go about learning how to live in wiser and more civilized ways might have something to learn from scientific learning, and will take the trouble to pursue the line of argument traced out in this book. I write in the hope that these few will grasp just how desperate our situation is, how urgent the need to change the status quo, and will do everything in their power to alert others to the need to heal the methodological sickness from which our institutions and traditions of learning at present suffer. To begin with, we need a campaigning organization, modelled perhaps on "Friends of the Earth", which might be called something like "Friends of Wisdom". (shrink)

Philosophers of dispositionalism deny the Humean account of causality in terms of constant conjunction, contiguity, temporal priority and contingency. And some of them go further to explain the causal relation not between events or objects, but between properties, in terms of reciprocity, simultaneity, ubiquity, intentionality and holism. But their exposition seems to remain fragmented even though they try to make use of the notions of intentionality and holim. I would inquire reasons why it is piecemeal, by analysing that they employ (...) these notions of intentionality and holism which has been constructed within the dualistic tradition. If one wants to make the dispositional project to be powerful, she should look for the notions of intentionality and holism which are free of the dualistic traits and which have been constructed in the tradition of naturalism. The concept of integrationality may be a candidate for such a task. This conception was coined in Zhongyong under the name of cheng in that there is nothing without cheng, and was developed in one of Sok-hon Ham's thesis that any entity in the world contains "seed" within it to realize objectives shared by all involved. Humans are privileged and distinct from other natures, but there is continuity between them. An example of the integrationality applied to the case of humans would be that realization of myself and realizations of all others are one and not two. I would summarize notions of "cheng" and "seed" by offering the integrationality thesis, that is, that there is integrationality in any entity like dispositions such that the integrationality is a power to realize the embedded objective of it in the context where it interacts with all others. I would claim that integrationality is a metaphysical basis for a way of human thinking, by arguing that it is a necessary part of presupposition for our understanding of the world without which the world is not intelligible. The notion of integrationality is involved empirically as well as conceptually. Empirically, there are numerous reports from physics, biology and information science, which provide with a clue which may well be taken to show the ubiquitous integrationality. But some conceptual considerations would also indicate necessarily toward the same direction. These would include various theses of ontology, epistemology, disposition, modality, naturalized intentionality, fitting and topics like these. I will investigate some of them in order to justify my claim of this paper. (shrink)

In the past, philosophers, scientists, and even the general opinion, had no problem in accepting the existence of consciousness in the same way as the existence of the physical world. After the advent of Newtonian mechanics, science embraced a complete materialistic conception about reality. Scientists started proposing hypotheses like abiogenesis (origin of first life from accumulation of atoms and molecules) and the Big Bang theory (the explosion theory for explaining the origin of universe). How the universe came to be what (...) it is now is a key philosophical question. The hypothesis that it came from Nothing (as proposed by Stephen Hawking, among others), proves to be dissembling, since the quantum vacuum can hardly be considered a void. In modern science, it is generally assumed that matter existed before the universe came to be. Modern science hypothesizes that the manifestation of life on Earth is nothing but a mere increment in the complexity of matter — and hence is an outcome of evolution of matter (chemical evolution) following the Big Bang. After the manifestation of life, modern science believed that chemical evolution transformed itself into biological evolution, which then had caused the entire biodiversity on our planet. The ontological view of the organism as a complex machine presumes life as just a chance occurrence, without any inner purpose. This approach in science leaves no room for the subjective aspect of consciousness in its attempt to know the world as the relationships among forces, atoms, and molecules. On the other hand, the Vedāntic view states that the origin of everything material and nonmaterial is sentient and absolute (unconditioned). Thus, sentient life is primitive and reproductive of itself – omne vivum ex vivo – life comes from life. This is the scientifically verified law of experience. Life is essentially cognitive and conscious. And, consciousness, which is fundamental, manifests itself in the gradational forms of all sentient and insentient nature. In contrast to the idea of objective evolution of bodies, as envisioned by Darwin and followers, Vedānta advocates the idea of subjective evolution of consciousness as the developing principle of the world. In this paper, an attempt has been made to highlight a few relevant developments supporting a sentient view of life in scientific research, which has caused a paradigm shift in our understanding of life and its origin. (shrink)

Biological evolution is a complex blend of ever changing structural stability, variability and emergence of new phe- notypes, niches, ecosystems. We wish to argue that the evo- lution of life marks the end of a physics world view of law entailed dynamics. Our considerations depend upon dis- cussing the variability of the very ”contexts of life”: the in- teractions between organisms, biological niches and ecosys- tems. These are ever changing, intrinsically indeterminate and even unprestatable: we do not know ahead (...) of time the ”niches” which constitute the boundary conditions on selec- tion. More generally, by the mathematical unprestatability of the ”phase space”, no laws of mo- tion can be formulated for evolution. We call this radical emergence, from life to life. The purpose of this paper is the integration of variation and diversity in a sound concep- tual frame and situate unpredictability at a novel theoretical level, that of the very phase space. Our argument will be carried on in close comparisons with physics and the mathematical constructions of phase spaces in that discipline. The role of symmetries as invariant preserving transformations will allow us to under- stand the nature of physical phase spaces and to stress the differences required for a sound biological theoretizing. In this frame, we discuss the novel notion of ”enablement”. Life lives in a web of enablement and radical emergence. This will restrict causal analyses to differential cases. Mutations or other causal differ- ences will allow us to stress that ”non conservation princi- ples” are at the core of evolution, in contrast to physical dynamics, largely based on conservation principles as sym- metries. Critical transitions, the main locus of symmetry changes in physics, will be discussed, and lead to ”extended criticality” as a conceptual frame for a better understanding of the living state of matter. (shrink)

Although molecular biology, genetics, and related special disciplines represent a large amount of empirical data, a practical method for the evaluation and overview of current knowledge is far from being realized. The main concepts and narratives in these fields have remained nearly the same for decades and the more recent empirical data concerning the role of noncoding RNAs and persistent viruses and their defectives do not fit into this scenario. A more innovative approach such as applied biocommunication theory could (...) translate empirical data into a coherent perspective on the functions within and between biological organisms and arguably lead to a sustainable integrative biology. (shrink)

This review investigates the potential of non-orientable topology as a fundamental framework for understanding the Poincaré conjecture and its implications across various scientific disciplines. Integrating insights from Dokuchaev (2020), Rapoport, Christianto, Chandra, Smarandache (under review), and other pioneering works, this article explores the theoretical foundations linking non-orientable spaces to resolving the Poincaré conjecture and its broader implications in theoretical physics, geology, cosmology, and biology.

In this dissertation I achieve the following: (1) I present motivating criteria for a general comprehensive theory of scientific explanation. I review historical approaches to modeling explanation in light of these criteria. (2) I present New Mechanist Explanation ("NME") as the leading candidate for a contemporary, complete theory of scientific explanation. (3) I present constraints on the applicability of New Mechanism in modeling biology, chemistry, and physics. I argue for the unsuitability of NME as a candidate for a (...) general theory of explanation due to its significant omissions of explanatory content and subsequent incompleteness. (4) I present arguments for the indispensable explanatory power of mathematics in science, noting that much of NME's failures are owed to its poor integration of mathematical explanation as applied to science. (5) I propose a Rational-Relational theory of explanation(“RRE”). I present RRE in detail and demonstrate it as a true working general theory of explanation which best meets the motivating criteria presented in (1). I disambiguate RRE from structural explanation ("SE"). I show that historical models of explanation, including the deductive nomological (DNE) model, statistical relevance ("SRE") model, structural model (SE) and unification model ("UE") may be successfully treated as sub-classes of explanation within the scope of RRE. I provide a rubric for selecting amongst sub-theories of explanation under RRE in the purpose of highlighting particular features of relational explanations. (6) In conclusion, I argue that philosophers of science should move forward using RRE as a general model of scientific explanation as a working alternative to the incomplete model of NME. (shrink)