The desire to understand the mathematics of living systems is increasing. The widely held presupposition that the mathematics developed for modeling of physical systems as continuous functions can be extended to the discrete chemical reactions of genetic systems is viewed with skepticism. The skepticism is grounded in the issue of scientific invariance and the role of the International System of Units in representing the realities of the apodictic sciences. Various formal logics contribute to the theories of biochemistry and molecular (...) class='Hi'>biology and genetics. Various paths of extension are invoked in these formal logics in order to express the information of biological apodicticism. Symbolizing the appropriate notations for invariant relations and for biological extensions of relations is fundamental to the exact generating functions of discrete algebraic biology. Aspects of philosophical perspectives of the relation scientific number systems are contrasted. The deep distinction between physical motion and biological motion is expressed in terms the roles of Aristotelian causes. The interior motion within perplex numbers is contrasted with the exterior motion of physical systems. The need for a new mathematics for biology is suggested. (shrink)

Whereas women are sure of their biological maternity, men can never be fully certain of paternity and instead need to rely on indirect cues to assess whether they are likely to be father of their putative children. According to the psychological literature, men commonly use the information on the resemblance of offspring to self as an indicator of genetic relatedness. It seems, however, that in the absence of such a resemblance, similarity between a mother and a child might be important, (...) because a man has additional reason to doubt his own biological paternity when the child is dissimilar to his partner. This assumption has been verified in two empirical studies. (shrink)

A novel algebraic structure of the genetic code is proposed. Here, the principal partitions of the genetic code table were obtained as equivalent classes of quotient spaces of the genetic code vector space over the Galois field of the four DNA bases. The new algebraic structure shows strong connections among algebraic relationships, codon assignment and physicochemical properties of amino acids. Moreover, a distance function defined between the codon binary representations in the vector space was demonstrated to have (...) a linear behavior respect to physical variables such as the mean of amino acids interaction energies in proteins. It was also noticed that the distance between wild type and mutant codons approach to smaller values in mutational variants of four genes, i.e., human phenylalanine hydroxylase, human β-globin, HIV-1 protease and HIV-1 reverse transcriptase. These results strongly suggest that deterministic rules must be involved in the genetic code origin. (shrink)

A categorical, higher dimensional algebra and generalized topos framework for Łukasiewicz–Moisil Algebraic–Logic models of non-linear dynamics in complex functional genomes and cell interactomes is proposed. Łukasiewicz–Moisil Algebraic–Logic models of neural, genetic and neoplastic cell networks, as well as signaling pathways in cells are formulated in terms of non-linear dynamic systems with n-state components that allow for the generalization of previous logical models of both genetic activities and neural networks. An algebraic formulation of variable ‘next-state functions’ is extended (...) to a Łukasiewicz–Moisil Topos with an n-valued Łukasiewicz–Moisil Algebraic Logic subobject classifier description that represents non-random and non-linear network activities as well as their transformations in developmental processes and carcinogenesis. The unification of the theories of organismic sets, molecular sets and Robert Rosen’s (M,R)-systems is also considered here in terms of natural transformations of organismal structures which generate higher dimensional algebras based on consistent axioms, thus avoiding well known logical paradoxes occurring with sets. Quantum bionetworks, such as quantum neural nets and quantum genetic networks, are also discussed and their underlying, non-commutative quantum logics are considered in the context of an emerging Quantum Relational Biology. (shrink)

A categorical, higher dimensional algebra and generalized topos framework for Łukasiewicz–Moisil Algebraic–Logic models of non-linear dynamics in complex functional genomes and cell interactomes is proposed. Łukasiewicz–Moisil Algebraic–Logic models of neural, genetic and neoplastic cell networks, as well as signaling pathways in cells are formulated in terms of non-linear dynamic systems with n-state components that allow for the generalization of previous logical models of both genetic activities and neural networks. An algebraic formulation of variable ‘next-state functions’ is extended (...) to a Łukasiewicz–Moisil Topos with an n-valued Łukasiewicz–Moisil Algebraic Logic subobject classifier description that represents non-random and non-linear network activities as well as their transformations in developmental processes and carcinogenesis. The unification of the theories of organismic sets, molecular sets and Robert Rosen’s (M,R)-systems is also considered here in terms of natural transformations of organismal structures which generate higher dimensional algebras based on consistent axioms, thus avoiding well known logical paradoxes occurring with sets. Quantum bionetworks, such as quantum neural nets and quantum genetic networks, are also discussed and their underlying, non-commutative quantum logics are considered in the context of an emerging Quantum Relational Biology. (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)

Fundamental properties of N-valued logics are compared and eleven theorems are presented for their Logic Algebras, including Łukasiewicz–Moisil Logic Algebras represented in terms of categories and functors. For example, the Fundamental Logic Adjunction Theorem allows one to transfer certain universal, or global, properties of the Category of Boolean Algebras,, (which are well-understood) to the more general category \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$${\cal L}$$\end{document}Mn of Łukasiewicz–Moisil Algebras. Furthermore, the relationships of LMn-algebras to other many-valued logical structures, (...) such as the n-valued Post, MV and Heyting logic algebras, are investigated and several pertinent theorems are derived. Applications of Łukasiewicz–Moisil Algebras to biological problems, such as nonlinear dynamics of genetic networks – that were previously reported – are also briefly noted here, and finally, probabilities are precisely defined over LMn-algebras with an eye to immediate, possible applications in biostatistics. (shrink)

We extend the comparatively simple processes of group symmetry-breaking in physical systems to groupoid/equivalence class phase transitions characterizing adiabatically, piecewise stationary, information transmission in prebiotic, biological, and social phenomena: High vs. Low probability paths $$\rightarrow$$ Interior and Exterior Interact $$\rightarrow$$ Multiple Interacting Tunable Workspaces Application to nonstationary processes seems possible via generalizations of the symmetry algebra, for example, to semigroupoids. The dynamic probability models explored here can be transformed into statistical tools for the analysis of real-time and other data across (...) a spectrum of important disciplines confronted by biological and other forms of cognition and their dysfunctions. (shrink)

This rare publication continues an exploratory journey in relational biology, a study of biology in terms of the organization of networked connections in living systems. It builds on the author's two earlier monographs which looked at the epistemology of life and the ontogeny of life. Here the emphasis is on the intangibility of life, that the real nature of living systems is conveyed not by their tangible material basis but by their intangible inherent processes. Relational biology is (...) the approach that hails 'function dictates structure'; it is mathematics decoded into biological realizations. Therefore, the work begins with a concise introduction to category theory, equiping the reader with the mathematical metalanguage of relation biology. The book is organized around three parts: Part I is a comprehensive study of the most important functor in relational biology, the power set functor. The author lays the set-theoretic foundations of the functorial connections in relational biology, exploring relations, mappings, and set-valued mappings. In Part II, Natural Law receives a new mathematical formulation founded on two axioms: 'Everything is a set.' and 'Every process is a set-valued mapping.' The reader sees how Metabolism-Repair networks, equipped with set-valued processors, expand their role from models of biological entities to generic models of all natural systems. Part III expounds the various shades of invertibility in general, and the inversion of encoding to decoding in particular. A plethora of mathematical and biological examples illustrate the category-theoretic concepts of equivalence and adjunction. This book's algebraic approach to biological models will appeal to researchers and graduate students in mathematics, biology, and the philosophy of science. (shrink)

Most contemporary chemists consider quantum mechanics to be the foundational theory of their discipline, although few of the calculations that a strict reduction would seem to require have ever been produced. In this essay I discuss contemporary algebraic and diagrammatic representations of molecular systems derived from quantum mechanical models, specifically configuration interaction wavefunctions for ab initio calculations and molecular orbital energy diagrams. My aim is to suggest that recent dissatisfaction with reductive accounts of chemical theory may stem from both (...) the inability of standard accounts of reduction to incorporate the diverse forms of representation found in chemical practice and our philosophical predilection to analyze all connections between theories in terms of logical reduction. (shrink)

We present a method for rejecting competing models from noisy time-course data that does not rely on parameter inference. First we characterize ordinary differential equation models in only measurable variables using differential-algebra elimination. This procedure gives input-output equations, which serve as invariants for time series data. We develop a model comparison test using linear algebra and statistics to reject incorrect models from their invariants. This algorithm exploits the dynamic properties that are encoded in the structure of the model equations without (...) recourse to parameter values, and, in this sense, the approach is parameter-free. We demonstrate this method by discriminating between different models from mathematical biology. (shrink)

Fundamental properties of N-valued logics are compared and eleven theorems are presented for their Logic Algebras, including Łukasiewicz–Moisil Logic Algebras represented in terms of categories and functors. For example, the Fundamental Logic Adjunction Theorem allows one to transfer certain universal, or global, properties of the Category of Boolean Algebras,, (which are well-understood) to the more general category \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$${\cal L}$$\end{document}Mn of Łukasiewicz–Moisil Algebras. Furthermore, the relationships of LMn-algebras to other many-valued logical structures, (...) such as the n-valued Post, MV and Heyting logic algebras, are investigated and several pertinent theorems are derived. Applications of Łukasiewicz–Moisil Algebras to biological problems, such as nonlinear dynamics of genetic networks – that were previously reported – are also briefly noted here, and finally, probabilities are precisely defined over LMn-algebras with an eye to immediate, possible applications in biostatistics. (shrink)

Complex Systems Biology approaches are here considered from the viewpoint of Robert Rosen’s (M,R)-systems, Relational Biology and Quantum theory, as well as from the standpoint of computer modeling. Realizability and Entailment of (M,R)-systems are two key aspects that relate the abstract, mathematical world of organizational structure introduced by Rosen to the various physicochemical structures of complex biological systems. Their importance for understanding biological function and life itself, as well as for designing new strategies for treating diseases such as (...) cancers, is pointed out. The roles played by multiple metastable states in the “continuous uphill flow of Life” supported through internal bioenergetic processes that are coupled to essential inflows are also discussed in relation to dynamic realizations of (M,R)-systems. Furthermore, the roles played by the underlying, many-valued, quantum logics and symbolic computations for ultra-complex biological systems are also briefly discussed. (shrink)

A novel conceptual framework is introduced for the Complexity Levels Theory in a Categorical Ontology of Space and Time. This conceptual and formal construction is intended for ontological studies of Emergent Biosystems, Super-complex Dynamics, Evolution and Human Consciousness. A claim is defended concerning the universal representation of an item’s essence in categorical terms. As an essential example, relational structures of living organisms are well represented by applying the important categorical concept of natural transformations to biomolecular reactions and relational structures that (...) emerge from the latter in living systems. Thus, several relational theories of living systems can be represented by natural transformations of organismic, relational structures. The ascent of man and other living organisms through adaptation, is viewed in novel categorical terms, such as variable biogroupoid representations of evolving species. Such precise but flexible evolutionary concepts will allow the further development of the unifying theme of local-to-global approaches to highly complex systems in order to represent novel patterns of relations that emerge in super- and ultra-complex systems in terms of compositions of local procedures. Solutions to such local-to-global problems in highly complex systems with ‘broken symmetry’ might be possible to be reached with the help of higher homotopy theorems in algebraic topology such as the generalized van Kampen theorems (HHvKT). Categories of many-valued, Łukasiewicz-Moisil (LM) logic algebras provide useful concepts for representing the intrinsic dynamic ‘asymmetry’ of genetic networks in organismic development and evolution, as well as to derive novel results for (non-commutative) Quantum Logics. Furthermore, as recently pointed out by Baianu and Poli (Theory and applications of ontology, vol 1. Springer, Berlin, in press), LM-logic algebras may also provide the appropriate framework for future developments of the ontological theory of levels with its complex/entangled/intertwined ramifications in psychology, sociology and ecology. As shown in the preceding two papers in this issue, a paradigm shift towards non-commutative, or non-Abelian, theories of highly complex dynamics—which is presently unfolding in physics, mathematics, life and cognitive sciences—may be implemented through realizations of higher dimensional algebras in neurosciences and psychology, as well as in human genomics, bioinformatics and interactomics. (shrink)

This contribution is an essay of formal philosophy—and more specifically of formal ontology and formal epistemology—applied, respectively, to the philosophy of nature and to the philosophy of sciences, interpreted the former as the ontology and the latter as the epistemology of the modern mathematical, natural, and artificial sciences, the theoretical computer science included. I present the formal philosophy in the framework of the category theory (CT) as an axiomatic metalanguage—in many senses “wider” than set theory (ST)—of mathematics and logic, both (...) of the “extensional” logics of the pure and applied mathematical sciences (=mathematical logic), and the “intensional” modal logics of the philosophical disciplines (=philosophical logic). It is particularly significant in this categorical framework the possibility of extending the operator algebra formalism from (quantum and classical) physics to logic, via the so-called “Boolean algebras with operators” (BAOs), with this extension being the core of our formal ontology. In this context, I discuss the relevance of the algebraic Hopf coproduct and colimit operations, and then of the category of coalgebras in the computations over lattices of quantum numbers in the quantum field theory (QFT), interpreted as the fundamental physics. This coalgebraic formalism is particularly relevant for modeling the notion of the “quantum vacuum foliation” in QFT of dissipative systems, as a foundation of the notion of “complexity” in physics, and “memory” in biological and neural systems, using the powerful “colimit” operators. Finally, I suggest that in the CT logic, the relational semantics of BAOs, applied to the modal coalgebraic relational logic of the “possible worlds” in Kripke’s model theory, is the proper logic of the formal ontology and epistemology of the natural realism, as a formalized philosophy of nature and sciences. (shrink)

Category theory has been proposed as the ultimate algebraic model for biology. We review the Ehresmann–Vanbremeersch theory in the context of other mathematical approaches.

More than any other aspect of the Second Scientific Revolution, the remarkable revitalization or British mathematics and mathematical physics during the first half of the nineteenth century is perhaps the most deserving of the name. While the newly constituted sciences of biology and geology were undergoing their first revolution, as it were, the reform of British mathematics was truly and self-consciously the story of a second coming of age. ‘Discovered by Fermat, cocinnated and rendered analytical by Newton, and enriched (...) by Leibniz with a powerful and comprehensive notation’, wrote the young John Herschel and Charles Babbage of the calculus in 1813, ‘as if the soil of this country [was] unfavourable to its cultivation, it soon drooped and almost faded into neglect; and we now have to re-import the exotic, with nearly a century of foreign improvement, and to render it once more indigenous among us’. (shrink)

We build a topological model, based on intuitionistic logic, for multi-agent biological systems (such as _Physarum polycephalum_, bacterial colonies or any other swarm), reacting to external nourishment stimuli. Our construction follows the topological description of brain activity, where particles (neurons) are activated by an external environment, represented by a topological space _X_ with an open cover \(\{U_i:i\in I\}\). The brain builds the model of this external space via the nerve (trace) of a topological space _X_. Here the body of _Physarum (...) polycephalum_ or a swarm made of networks of tubular structures represents a nerve (trace) of _X_ also which means that _Physarum polycephalum_ or a swarm gains orientation in the space of external stimuli even in the absence of any neural system. The logic of living organisms is based on open subsets of _X_ and thus can be represented by Heyting algebra (i.e. intuitionistically). We also consider the generalisation of the nerve construction to a categorical context, where the category is determined by the network structures of multi-agent biological system. This model can be generalised up to simulating the behaviour of any swarm by means of intuitionistic logic. (shrink)

Biology is seen not merely as a privileged oppressor of women but as a co-victim of masculinist social assumptions. We see feminist critique as one of the normative controls that any scientist must perform whenever analyzing data, and we seek to demonstrate what has happened when this control has not been utilized. Narratives of fertilization and sex determination traditionally have been modeled on the cultural patterns of male/female interaction, leading to gender associations being placed on cells and their components. (...) We also find that when gender biases are controlled, new perceptions of these intracellular and extracellular relationships emerge. (shrink)

In this multidisciplinary book, mathematician Matthew He provides integrative perspectives of algebraic biology, cognitive informatics, and poetic expressions of the human mind. Using classical Pythagorean Theorem and contemporary Category Theory, the proposed matrix models of the human mind connect three domains of the physical space of objective matters, mental space of subjective meanings, and emotional space of bijective modes; draws the connections between neural sparks and idea points, between synapses and idea lines, and between action potentials and frequency (...) curves. (shrink)

Algebraic/topological descriptions of living processes are indispensable to the understanding of both biological and cognitive functions. This paper presents a fundamental algebraic description of living/cognitive processes and exposes its inherent ambiguity. Since ambiguity is forbidden to computation, no computational description can lend insight to inherently ambiguous processes. The impredicativity of these models is not a flaw, but is, rather, their strength. It enables us to reason with ambiguous mathematical representations of ambiguous natural processes. The noncomputability of these structures (...) means computerized simulacra of them are uninformative of their key properties. This leads to the question of how we should reason about them. That question is answered in this paper by presenting an example of such reasoning, the demonstration of a topological strategy for understanding how the fundamental structure can form itself from within itself. (shrink)

This edited volume of 13 new essays aims to turn past discussions of natural kinds on their head. Instead of presenting a metaphysical view of kinds based largely on an unempirical vantage point, it pursues questions of kindedness which take the use of kinds and activities of kinding in practice as significant in the articulation of them as kinds. The book brings philosophical study of current and historical episodes and case studies from various scientific disciplines to bear on natural kinds (...) as traditionally conceived of within metaphysics. Focusing on these practices reveals the different knowledge-producing activities of kinding and processes involved in natural kind use, generation, and discovery. -/- Specialists in their field, the esteemed group of contributors use diverse empirically responsive approaches to explore the nature of kindhood. This groundbreaking volume presents detailed case studies that exemplify kinding in use. Newly written for this volume, each chapter engages with the activities of kinding across a variety of disciplines. Chapter topics include the nature of kinds, kindhood, kinding, and kind-making in linguistics, chemical classification, neuroscience, gene and protein classification, colour theory in applied mathematics, homology in comparative biology, sex and gender identity theory, memory research, race, extended cognition, symbolic algebra, cartography, and geographic information science. -/- The volume seeks to open up an as-yet unexplored area within the emerging field of philosophy of science in practice, and constitutes a valuable addition to the disciplines of philosophy and history of science, technology, engineering, and mathematics. -/- Contributions from a diverse group of established and junior scholars in the fields of Philosophy and History and Philosophy of Science including Hasok Chang, Jordi Cat, Sally Haslanger, Joyce C. Havstad, Catherine Kendig, Bernhard Nickel, Josipa Petrunic, Samuli Pöyhönen, Thomas A. C. Reydon, Quayshawn Spencer, Jackie Sullivan, Michael Wheeler, and Rasmus Grønfeldt Winther. (shrink)

An algebraic interpretation of multigraph networks is introduced in relation to conscious experience, brain and body. These multigraphs have the ability to merge by an associative binary operator \(\odot \), accounting for biological composition. We also study a mathematical formulation of splitting layers, resulting in a formal analysis of the transition from conscious to non-conscious activity. From this construction, we recover core structures for conscious experience, dynamical content and causal constraints that conscious interactions may impose. An important result is (...) the prediction of structural topological changes after conscious interactions. These results may inspire further use of formal mathematics to describe and predict new features of conscious experience while aligning well with formal tries to mathematize phenomenology, phenomenological tradition and applications to artificial consciousness. (shrink)

Humans are standouts in their propensity to trade. More specially, the kind of trading found in humans—featuring the exchange of many different goods and services with many different others, for the mutual benefit of all the involved parties—far exceeds anything that is found in any other creature. However, a number of important questions about this propensity remain open. First, it is not clear exactly what makes this propensity so different in the human case from that of other animals. Second, it (...) is not clear why other animals did not acquire this propensity to the extent that humans did. Third, it is not clear what explains the fact that the extent to which humans engage in trade is culturally highly variable. The paper argues that at the heart of the human-animal divergence in this propensity is the particular socio-cultural environment in which humans evolved. This has led them to sometimes, but not always, acquire the cognitive technology (writing, algebra, tallying devices, money, etc.) to support a sophisticated disposition and capacity for reciprocal cooperation, and deep and wide concepts of property and exchange value. (shrink)

An overview of the following three related papers in this issue presents the Emergence of Highly Complex Systems such as living organisms, man, society and the human mind from the viewpoint of the current Ontological Theory of Levels. The ontology of spacetime structures in the Universe is discussed beginning with the quantum level; then, the striking emergence of the higher levels of reality is examined from a categorical—relational and logical viewpoint. The ontological problems and methodology aspects discussed in the first (...) two papers are followed by a rigorous paper based on Category Theory, Algebraic Topology and Logic that provides a conceptual and mathematical basis for a Categorical Ontology Theory of Levels. The essential links and relationships between the following three papers of this issue are pointed out, and further possible developments are being considered. (shrink)

This collection of 38 papers gives a cross-section of ongoing research in philosophy of science and philosophical logic. The papers, written by active researchers in the field and published here for the first time, are drawn from around 650 papers that were contributed to the 9th International Congress of Logic, Methodology and Philosophy of Science in Uppsala, Sweden, 1991. Some of the speakers whose contributions attracted special interest were invited to contribute their papers to this volume. A few papers appear (...) here more or less as they were presented at the Congress, whereas others are expansions or elaborations of the talks given. There is one section with five papers on philosophical logic. The other papers deal with many different aspects of philosophy of science, including general methodological questions, problems of probability, induction and decision theory, and ethics of science and technology, as well as foundational problems about particular sciences. Five special sections are concerned with logic, mathematics and computer science, the physical sciences, the biological sciences, cognitive science, and linguistics, respectively. Finally, there is one section on the history of logic, methodology and philosophy of science. The book will be of interest to philosophers of science and logicians, as well as to all researchers interested in the foundations of their disciplines. (shrink)

Generalized Quantum Theory seeks to explain and predict quantum-like phenomena in areas usually outside the scope of quantum physics, such as biology and psychology. It draws on fundamental theories and uses the algebraic formalism of quantum theory that is used in the study of observable physical matter such as photons, electrons, etc. In contrast to quantum theory proper, GQT is a very generalized form that does not allow for the full application of formalism. For instance neither a commutator, (...) such as Planck’s constant, nor any additive operations are defined, which precludes the usage of a full Hilbert-space formalism. But it is a formalized phenomenological theory that is applicable whenever the core element of a quantum theory needs to be captured, namely in the presence of incompatible or non-commuting operations. As a consequence, it also predicts nonlocal, generalized entanglement correlations in systems other than proper quantum systems. In this paper we summarize the specific scientific evidence relating to the quantum-like mental, behavioral and physiological nonlocal correlations. Such non-local, generalized entanglement correlations are expected, both in space and time, between subsystems of a larger system, whenever observables pertaining to the global system are incompatible or complementary to observables pertaining to subsystems, as predicted by GQT. The result is a coherent explanation of a significant amount of controversial and seemingly weird occurrences that cannot be explained by classical physical laws. This review also offers a new perspective of the human mind’s potential. (shrink)

Computer analysis of biological systems, using approaches such as metabolic control analysis is common. A typical example is a language like Herbert Sauro's SCAMP (Sauro & Fell, 1991), which allows simulations of enzyme systems, and calculation of control coefficients and elasticities. However such systems are motivated by the underlying biochemical theory and often have limitations as programming languages which mean that they can only be applied to particular classes of problems.ABPL (a biochemical programming language) extends these ideas by adding all (...) the facilities of a fully-fledged programming language, together with some of the capabilities of a modern computer algebra system. Syntactically it derives from the programming language LISP, while the underlying functionality is that of iMAP, the successor to SCAMP. (shrink)

The brain displays both the anatomical features of a vast amount of interconnected topological mappings as well as the functional features of a nonlinear, metastable system at the edge of chaos, equipped with a phase space where mental random walks tend towards lower energetic basins. Nevertheless, with the exception of some advanced neuro-anatomic descriptions and present-day connectomic research, very few studies have been addressing the topological path of a brain embedded or embodied in its external and internal environment. Herein, by (...) using new formal tools derived from algebraic topology, we provide an account of the metastable brain, based on the neuro-scientific model of Operational Architectonics of brain-mind functioning. We introduce a “topodynamic” description that shows how the relationships among the countless intertwined spatio-temporal levels of brain functioning can be assessed in terms of projections and mappings that take place on abstract structures, equipped with different dimensions, curvatures and energetic constraints. Such a topodynamical approach, apart from providing a biologically plausible model of brain function that can be operationalized, is also able to tackle the issue of a long-standing dichotomy: it throws indeed a bridge between the subjective, immediate datum of the naïve complex of sensations and mentations and the objective, quantitative, data extracted from experimental neuro-scientific procedures. Importantly, it opens the door to a series of new predictions and future directions of advancement for neuroscientific research. (shrink)

This volume contains ten papers that have been collected by the Canadian Society for History and Philosophy of Mathematics/Société canadienne d’histoire et de philosophie des mathématiques. It showcases rigorously-reviewed contemporary scholarship on an interesting variety of topics in the history and philosophy of mathematics from the seventeenth century to the modern era. -/- The volume begins with an exposition of the life and work of Professor Bolesław Sobociński. It then moves on to cover a collection of topics about twentieth-century philosophy (...) of mathematics, including Fred Sommers’s creation of Traditional Formal Logic and Alexander Grothendieck’s work as a starting point for discussing analogies between commutative algebra and algebraic geometry. Continuing the focus on the philosophy of mathematics, the next selections discuss the mathematization of biology and address the study of numerical cognition. The volume then moves to discussing various aspects of mathematics education, including Charles Davies’s early book on the teaching of mathematics and the use of Gaussian Lemniscates in the classroom. A collection of papers on the history of mathematics in the nineteenth century closes out the volume, presenting a discussion of Gauss’s “Allgemeine Theorie des Erdmagnetismus” and a comparison of the geometric works of Desargues and La Hire. Written by leading scholars in the field, these papers are accessible not only to mathematicians and students of the history and philosophy of mathematics, but also to anyone with a general interest in mathematics. (shrink)

Rosen's modelling relations constitute a conceptual schema for the understanding of the bidirectional process of correspondence between natural systems and formal symbolic systems. The notion of formal systems used in this study refers to information structures constructed as algebraic rings of observable attributes of natural systems, in which the notion of observable signifies a physical attribute that, in principle, can be measured. Due to the fact that modelling relations are bidirectional by construction, they admit a precise categorical formulation in (...) terms of the category-theoretic syntactic language of adjoint functors, representing the inverse processes of information encoding/decoding via adjunctions. As an application, we construct a topological modelling schema of complex systems. The crucial distinguishing requirement between simple and complex systems in this schema is reflected with respect to their rings of observables by the property of global commutativity. The global information structure representing the behaviour of a complex system is modelled functorially in terms of its spectrum functor. An exact modelling relation is obtained by means of a complex encoding/decoding adjunction restricted to an equivalence between the category of complex information structures and the category of sheaves over a base category of partial or local information carriers equipped with an appropriate topology. (shrink)

An original quantum foundations concept of a deep learning computational Universe is introduced. The fundamental information of the Universe (or Triuniverse)is postulated to evolve about itself in a Red, Green and Blue (RGB) tricoloured stable self-mutuality in three information processing loops. The colour is a non-optical information label. The information processing loops form a feedback-reinforced deep learning macrocycle with trefoil knot topology. Fundamental information processing is driven by ψ-Epistemic Drive, the Natural appetite for information selected for advantageous knowledge. From its (...) substrate of Mathematics, the knotted information processing loops determine emergent Physics and thence the evolution of super-emergent Life (biological and artificial intelligence). RGB-tricoloured information is processed in sequence in an Elemental feedback loop (R), then an Operational feedback loop (G), then a Structural feedback loop (B) and back to an Elemental feedback loop (R), and so on around the trefoil in deep learning macrocycles. It is postulated that hierarchical information correspondence from Mathematics through Physics to Life is mapped and conserved within each colour. The substrate of Mathematics has RGB-tricoloured feedback loops which are respectively Algebra (R), Algorithms (G) and Geometry (B). In Mathematics, the trefoil macrocycle is Algebraic Algorithmic Geometry and its correlation system is a Tensor Neural Knot Network enabling Qutrit Entanglement. Emergent Physics has corresponding RGB-tricoloured feedback loops of Quantum Mechanics (R), Quantum Deep Learning (G) and Quantum Geometrodynamics(B). In Physics, the trefoil macrocycle is Quantum Intelligent Geometrodynamics and its correlation system is Quantum Darwinism. Super-emergent Life has corresponding RGB-tricoloured loops of Variation (R), Selection (G) and Heredity (B). In the evolution of Life, the trefoil macrocycle is Variational Selective Heredity and its correlation ecosystem is Darwin’s ecologically “Entangled Bank”. (shrink)

The defining characteristics anticipated for any prospective psychophysically neutral language are explored in this essay through the analysis and comparison of two previous approaches. The idea of a psychophysically neutral language was first articulated byWolfgang Pauli in the context of the dual-aspect theory of mind and matter that he developed with C.G. Jung. The first approach discussed is George Spencer Brown's Laws of Form. An overview is given, followed by a review of the critical responses and extensions of the work, (...) particularly Francisco Varela's attempt to use it to formalize biological autopoiesis and Louis Kaufman's development of Brownian algebra. The mathematical basis of Spencer Brown's calculus and its philosophical assumptions and implications are then investigated. The second approach discussed is Marie-Louise von Franz's Number and Time, an investigation of number archetypes through which she continued the inquiry begun by Jung and Pauli. The central tenets of her work are summarized and critically evaluated, and a comparison with Spencer Brown's work is carried out. Finally, implications are drawn for any future attempt to formulate a psychophysically neutral language. (shrink)

In lieu of an abstract, here is a brief excerpt of the content:Reviewed by:Handbook of Cognitive Mathematics ed. by Marcel DanesiNathan HaydonMarcel Danesi (Ed) Handbook of Cognitive Mathematics Cham, Switzerland: Springer International, 2022, vii + 1383, including indexFor one acquainted with C.S. Peirce, it is hard to see Springer's recent Handbook of Cognitive Mathematics (editor: Marcel Danesi) through none other than a Peircean lens. Short for the cognitive science of mathematics, such a modern, scientific pursuit into the nature and study (...) of mathematical practice would no doubt be found agreeable to Peirce. The fact that references to Peirce appear often throughout the Handbook is a welcome find, with Peirce's ideas being a key subject of half a dozen chapters, and where a reader of any other chapter may well find further connections to Peirce's ideas. After spending time with the Handbook, it is clear that cognitive mathematics has not only embraced some of Pierce's ideas but may be at an important forefront of Peirce studies. In the end, the field may well be an area a Peircean should pay attention to.The book itself is pitched as a reference volume to the field (p. v) with the necessary background to familiarize oneself with the aims and results. The connection to cognitive science may call to mind detailed cognitive models [Ch. 10–14], theories on the origins of numeracy and other theories behind the biological and evolutionary requirements of mathematical thought [Ch.15–18], and the like. These are all present. But a key theme of the Handbook is to situate mathematics not just within more traditional 'cognitive' faculties and the more formal, i.e. algebraic, presentations of mathematics, but also to place mathematics within other human faculties and practices, from the arts to language [Ch. 19–22], within education and learning more broadly [Ch. 23–26], and in relation to the significant, though at first perhaps less quantitative parts of mathematics, like the use of metaphor, gesture, analogy, [End Page 243] abstraction, as well as further cultural and ethnographic considerations [Ch. 5–8]. The Handbook has explicitly taken a broader, more interdisciplinary approach (p. vi–vii) towards the scientific aspects of mathematical practice—choosing to regulate the study not by antecedently drawn opinions about what mathematics is (or has traditionally been taken to be) but by what future quantifiable and diverse study may come to bear on the practice and have to say about those engaging in it.This broad interdisciplinarity has a pragmatist ring, where theory cannot so easily be separated from the normative, social, and, more generally, the more thoroughly human aspects that we encounter and employ when we engage in it. Two further commitments of cognitive mathematics steer us even closer towards Peirce's views. The first—going back, for example, to Lakoff and Núñez's Where Mathematics Comes From (2000), which is taken to be a key early work in shaping the field—is that mathematics is taken to be a language like any other and as such must be learned and situated within our other cognitive faculties (p. vi, Ch. 4). The second—and largely, one imagines, following from a concern for seeing how mathematics is actually practiced—is that mathematics is essentially diagrammatic, involving as it does experimenting in diagrams and employing other signs (one may think here even of the mathematician sketching equations or geometric figures on a sheet of paper). What is perhaps initially most noteworthy about Peirce's philosophy of mathematics is his early concern for both these aspects of the practice.The book (more like a tome of over 1300 pages) is too large to be covered here in all its aspects, hence the review will focus on those aspects a Peircean or Pragmatist may find of interest. In particular, this review focuses on several of the themes above—situating mathematics more broadly within our everyday (cognitive) lives, the necessarily diagrammatic, fallible, and creative aspects of the practice, and, finally, what these aspects may have to say about Peirce's philosophy more generally, particularly with respect to (scientific) inquiry.A Peircean reader may well begin with Pietarinen's "Pragmaticism as Philosophy of Cognitive Mathematics" [Ch. 39] and "Peirce on Mathematical... (shrink)

On the basis of previous studies in relational biology and the phenomenological calculus, in my contribution I outline the mathematical foundations of biological perception generally, and visual perception specifically. In this approach, the premise is that objects in nature are not directly accessible, and that real manifestations are projections of these invariant objects. The morphology of observables is mathematically entailed by the duality of projections and projectors in a bilinear algebra that is the phenomenological calculus. The relationships between what (...) is not directly accessible (which can be defined as noumena) and phenomena may be explicated in terms of metabolism and repair, whence a geometric theory of the perceived, the visible in particular, may be formulated in the category-theoretic language of relational biology. (shrink)

Quantum probability (QP) theory can be seen as a type of vector symbolic architecture (VSA): mental states are vectors storing structured information and manipulated using algebraic operations. Furthermore, the operations needed by QP match those in other VSAs. This allows existing biologically realistic neural models to be adapted to provide a mechanistic explanation of the cognitive phenomena described in the target article by Pothos & Busemeyer (P&B).

This thirteenth volume of Collected Papers is an eclectic tome of 88 papers in various fields of sciences, such as astronomy, biology, calculus, economics, education and administration, game theory, geometry, graph theory, information fusion, decision making, instantaneous physics, quantum physics, neutrosophic logic and set, non-Euclidean geometry, number theory, paradoxes, philosophy of science, scientific research methods, statistics, and others, structured in 17 chapters (Neutrosophic Theory and Applications; Neutrosophic Algebra; Fuzzy Soft Sets; Neutrosophic Sets; Hypersoft Sets; Neutrosophic Semigroups; Neutrosophic Graphs; Superhypergraphs; (...) Plithogeny; Information Fusion; Statistics; Decision Making; Extenics; Instantaneous Physics; Paradoxism; Mathematica; Miscellanea), comprising 965 pages, published between 2005-2022 in different scientific journals, by the author alone or in collaboration with the following 110 co-authors (alphabetically ordered) from 26 countries: Abduallah Gamal, Sania Afzal, Firoz Ahmad, Muhammad Akram, Sheriful Alam, Ali Hamza, Ali H. M. Al-Obaidi, Madeleine Al-Tahan, Assia Bakali, Atiqe Ur Rahman, Sukanto Bhattacharya, Bilal Hadjadji, Robert N. Boyd, Willem K.M. Brauers, Umit Cali, Youcef Chibani, Victor Christianto, Chunxin Bo, Shyamal Dalapati, Mario Dalcín, Arup Kumar Das, Elham Davneshvar, Bijan Davvaz, Irfan Deli, Muhammet Deveci, Mamouni Dhar, R. Dhavaseelan, Balasubramanian Elavarasan, Sara Farooq, Haipeng Wang, Ugur Halden, Le Hoang Son, Hongnian Yu, Qays Hatem Imran, Mayas Ismail, Saeid Jafari, Jun Ye, Ilanthenral Kandasamy, W.B. Vasantha Kandasamy, Darjan Karabašević, Abdullah Kargın, Vasilios N. Katsikis, Nour Eldeen M. Khalifa, Madad Khan, M. Khoshnevisan, Tapan Kumar Roy, Pinaki Majumdar, Sreepurna Malakar, Masoud Ghods, Minghao Hu, Mingming Chen, Mohamed Abdel-Basset, Mohamed Talea, Mohammad Hamidi, Mohamed Loey, Mihnea Alexandru Moisescu, Muhammad Ihsan, Muhammad Saeed, Muhammad Shabir, Mumtaz Ali, Muzzamal Sitara, Nassim Abbas, Munazza Naz, Giorgio Nordo, Mani Parimala, Ion Pătrașcu, Gabrijela Popović, K. Porselvi, Surapati Pramanik, D. Preethi, Qiang Guo, Riad K. Al-Hamido, Zahra Rostami, Said Broumi, Saima Anis, Muzafer Saračević, Ganeshsree Selvachandran, Selvaraj Ganesan, Shammya Shananda Saha, Marayanagaraj Shanmugapriya, Songtao Shao, Sori Tjandrah Simbolon, Florentin Smarandache, Predrag S. Stanimirović, Dragiša Stanujkić, Raman Sundareswaran, Mehmet Șahin, Ovidiu-Ilie Șandru, Abdulkadir Șengür, Mohamed Talea, Ferhat Taș, Selçuk Topal, Alptekin Ulutaș, Ramalingam Udhayakumar, Yunita Umniyati, J. Vimala, Luige Vlădăreanu, Ştefan Vlăduţescu, Yaman Akbulut, Yanhui Guo, Yong Deng, You He, Young Bae Jun, Wangtao Yuan, Rong Xia, Xiaohong Zhang, Edmundas Kazimieras Zavadskas, Zayen Azzouz Omar, Xiaohong Zhang, Zhirou Ma.‬‬‬‬‬‬‬‬. (shrink)

Following a previous article published in Biological Theory, in this study we present a mathematical theory for a science of qualities as directly perceived by living organisms, and based on morphological patterns. We address a range of qualitative phenomena as observables of a psychological system seen as an impredicative system. The starting point of our study is the notion that perceptual phenomena are projections of underlying invariants, objects that remain unchanged when transformations of a certain class under consideration are applied. (...) The study develops with the observables, the entailed total order and metric, whence the algebra and the geometry of such a science, presenting a formal phenomenological model for phenomena that are not rigidly Euclidean. We show how non-Euclidean perception can have many useful Euclidean formalizations, as well as locally-homeomorphic-to-Euclidean-space models. The mathematical models we provide are tested on the basis of results from experimental psychology, in particular from the field of color, time, and space perception. (shrink)

Cognitive neuroscience increasingly relies on complex data analysis methods. Researchers in this field come from highly diverse scientific backgrounds, such as psychology, engineering, and medicine. This poses challenges with respect to acquisition of appropriate scientific computing and data analysis skills, as well as communication among researchers with different knowledge and skills sets. Are researchers in cognitive neuroscience adequately equipped to address these challenges? Here, we present evidence from an online survey of methods skills. Respondents (n= 307) mainly comprised students and (...) post-doctoral researchers working in the cognitive neurosciences. Multiple choice questions addressed a variety of basic and fundamental aspects of neuroimaging data analysis, such as signal analysis, linear algebra, and statistics. We analyzed performance with respect to the following factors: undergraduate degree (grouped into Psychology, Methods, and Biology), current researcher status (undergraduate student, PhD student, and post-doctoral researcher), gender, and self-rated expertise levels. Overall accuracy was 72%. Not surprisingly, the Methods group performed best (87%), followed by Biology (73%) and Psychology (66%). Accuracy increased from undergraduate (59%) to PhD (74%) level, but not from PhD to post-doctoral (74%) level. The difference in performance for the Methods vs. non-methods (Psychology/Biology) groups was especially striking for questions related to signal analysis and linear algebra, two areas particularly relevant to neuroimaging research. Self-rated methods expertise was not strongly predictive of performance. The majority of respondents (93%) indicated they would like to receive at least some additional training on the topics covered in this survey. In conclusion, methods skills among junior researchers in cognitive neuroscience can be improved, researchers are aware of this, and there is strong demand for more skills-oriented training opportunities. We hope that this survey will provide an empirical basis for the development of bespoke skills-oriented training programs in cognitive neuroscience institutions. We will provide practical suggestions on how to achieve this. (shrink)

The phenomenological calculus is a relational paradigm for complex systems, closely related in substance and spirit to Robert Rosen’s own approach. Its mathematical language is multilinear algebra. The epistemological exploration continues in this paper, with the expansion of the phenomenological calculus into the realm of anisotropy.

Every university student has his or her nemesis. Biology and social science students anticipate with great apprehension their required statistics course, while many philosophy students live in fear of formal logic. Math anxiety is the common thread uniting all of them. This article argues that since formal logic is an algebra requiring similar kinds of symbol-manipulation skills needed to succeed in a basic mathematics course, then if logic students have math anxiety, this can impede their progress. Further, it argues (...) that math anxiety is primarily caused by and exacerbated by poor instruction. Formal logic instructors who employ effective instructional techniques for reducing it can help their students overcome math anxiety to foster learning. Methods of instruction leading to anxiety reduction and evidence supporting their efficacy are discussed, including co-operative learning, the mastery goal approach, and self-paced learning. None of these methods holds back more advanced students. (shrink)

A synthesis of the two primary theory structures in Robert Rosen’s relational complexity, relational entailment mapping based on category theory as described by Rosen and Louie, and relational holism based on modeling relations, as described by Kineman, provides an integral foundation for relational complexity theory as a natural science and analytical method. Previous incompatibilities between these theory structures are resolved by re-interpreting Aristotle’s four causes, identifying final and formal causes as relations with context. Category theory is applied to introduce contextual (...) entailment algebra needed to complete the synthesis. The modeling relation is represented as a recursive four-cause hierarchy, which is a unit of both whole and part analysis that relates realized and contextual domains of nature as complementary inverse entailments between structure and function. Context is a non-localized domain of distributed potentials for existence, as contrasted with the realized domain of localized interactive and measurable events. Synthesis is achieved by giving modeling relations an algebraic form in category theory and by expanding relational analysis to include contextual entailments. The revised form of analysis is applied and demonstrated to examine Rosen’s M-R diagram, showing that structure–function relations imply adaptive interaction with the environment, and that contextual relations imply three forms of the M-R entailment corresponding with the generally known three forms of life; Archaea, Bacteria, and Eukaryota, which can be represented by their holon diagrams. The result of this synthesis is a consistent foundation for relational science that should have important implications in many disciplines. (shrink)

Monoidal t-norm based logic $\mathbf {MTL}$ is the weakest t-norm based residuated fuzzy logic, which is a $[0,1]$ -valued propositional logical system having a t-norm and its residuum as truth function for conjunction and implication. Monadic fuzzy predicate logic $\mathbf {mMTL\forall }$ that consists of the formulas with unary predicates and just one object variable, is the monadic fragment of fuzzy predicate logic $\mathbf {MTL\forall }$, which is indeed the predicate version of monoidal t-norm based logic $\mathbf {MTL}$. The main (...) aim of this paper is to give an algebraic proof of the completeness theorem for monadic fuzzy predicate logic $\mathbf {mMTL\forall }$ and some of its axiomatic extensions. Firstly, we survey the axiomatic system of monadic algebras for t-norm based residuated fuzzy logic and amend some of them, thus showing that the relationships for these monadic algebras completely inherit those for corresponding algebras. Subsequently, using the equivalence between monadic fuzzy predicate logic $\mathbf {mMTL\forall }$ and S5-like fuzzy modal logic $\mathbf {S5(MTL)}$, we prove that the variety of monadic MTL-algebras is actually the equivalent algebraic semantics of the logic $\mathbf {mMTL\forall }$, giving an algebraic proof of the completeness theorem for this logic via functional monadic MTL-algebras. Finally, we further obtain the completeness theorem of some axiomatic extensions for the logic $\mathbf {mMTL\forall }$, and thus give a major application, namely, proving the strong completeness theorem for monadic fuzzy predicate logic based on involutive monoidal t-norm logic $\mathbf {mIMTL\forall }$ via functional representation of finitely subdirectly irreducible monadic IMTL-algebras. (shrink)