State-of-the-art on evolution and reactivity

This report starts by, in Chapter 1, outlining aspects of querying and updating resources on the Web and on the Semantic Web, including the development of query and update languages to be carried out within the Rewerse project. From this outline, it becomes clear that several existing research areas and topics are of interest for this work in Rewerse. In the remainder of this report we further present state of the art surveys in a selection of such areas and topics. More precisely: in Chapter 2 we give an overview of logics for reasoning about state change and updates; Chapter 3 is devoted to briefly describing existing update languages for the Web, and also for updating logic programs; in Chapter 4 event-condition-action rules, both in the context of active database systems and in the context of semistructured data, are surveyed; in Chapter 5 we give an overview of some relevant rule-based agents frameworks

Categorical Ontology of Complex Systems, Meta-Systems and Theory of Levels: The Emergence of Life, Human Consciousness and Society

Single cell interactomics in simpler organisms, as well as somatic cell interactomics in multicellular organisms, involve biomolecular interactions in complex signalling pathways that were recently represented in modular terms by quantum automata with ‘reversible behavior’ representing normal cell cycling and division. Other implications of such quantum automata, modular modeling of signaling pathways and cell differentiation during development are in the fields of neural plasticity and brain development leading to quantum-weave dynamic patterns and specific molecular processes underlying extensive memory, learning, anticipation mechanisms and the emergence of human consciousness during the early brain development in children. Cell interactomics is here represented for the first time as a mixture of ‘classical’ states that determine molecular dynamics subject to Boltzmann statistics and ‘steady-state’, metabolic (multi-stable) manifolds, together with ‘configuration’ spaces of metastable quantum states emerging from complex quantum dynamics of interacting networks of biomolecules, such as proteins and nucleic acids that are now collectively defined as quantum interactomics. On the other hand, the time dependent evolution over several generations of cancer cells --that are generally known to undergo frequent and extensive genetic mutations and, indeed, suffer genomic transformations at the chromosome level (such as extensive chromosomal aberrations found in many colon cancers)-- cannot be correctly represented in the ‘standard’ terms of quantum automaton modules, as the normal somatic cells can. This significant difference at the cancer cell genomic level is therefore reflected in major changes in cancer cell interactomics often from one cancer cell ‘cycle’ to the next, and thus it requires substantial changes in the modeling strategies, mathematical tools and experimental designs aimed at understanding cancer mechanisms. Novel solutions to this important problem in carcinogenesis are proposed and experimental validation procedures are suggested. From a medical research and clinical standpoint, this approach has important consequences for addressing and preventing the development of cancer resistance to medical therapy in ongoing clinical trials involving stage III cancer patients, as well as improving the designs of future clinical trials for cancer treatments.\ud \ud \ud KEYWORDS: Emergence of Life and Human Consciousness;\ud Proteomics; Artificial Intelligence; Complex Systems Dynamics; Quantum Automata models and Quantum Interactomics; quantum-weave dynamic patterns underlying human consciousness; specific molecular processes underlying extensive memory, learning, anticipation mechanisms and human consciousness; emergence of human consciousness during the early brain development in children; Cancer cell ‘cycling’; interacting networks of proteins and nucleic acids; genetic mutations and chromosomal aberrations in cancers, such as colon cancer; development of cancer resistance to therapy; ongoing clinical trials involving stage III cancer patients’ possible improvements of the designs for future clinical trials and cancer treatments. \ud \u

What Are Kinship Terminologies, and Why Do We Care? A Computational Approach to Analyzing Symbolic Domains

Kinship is a fundamental feature and basis of human societies. We describe a set of computational tools and services, the Kinship Algebra Modeler, and the logic that underlies these. These were developed to improve how we understand both the fundamental facts of kinship, and how people use kinship as a resource in their lives. Mathematical formalism applied to cultural concepts is more than an exercise in model building, as it provides a way to represent and explore logical consistency and implications. The logic underlying kinship is explored here through the kin term computations made by users of a terminology when computing the kinship relation one person has to another by referring to a third person for whom each has a kin term relationship. Kinship Algebra Modeler provides a set of tools, services and an architecture to explore kinship terminologies and their properties in an accessible manner

State-of-the-art on evolution and reactivity

This report starts by, in Chapter 1, outlining aspects of querying and updating resources on the Web and on the Semantic Web, including the development of query and update languages to be carried out within the Rewerse project. From this outline, it becomes clear that several existing research areas and topics are of interest for this work in Rewerse. In the remainder of this report we further present state of the art surveys in a selection of such areas and topics. More precisely: in Chapter 2 we give an overview of logics for reasoning about state change and updates; Chapter 3 is devoted to briefly describing existing update languages for the Web, and also for updating logic programs; in Chapter 4 event-condition-action rules, both in the context of active database systems and in the context of semistructured data, are surveyed; in Chapter 5 we give an overview of some relevant rule-based agents frameworks

The Post‐Modern Transcendental of Language in Science and Philosophy

In this chapter I discuss the deep mutations occurring today in our society and in our culture, the natural and mathematical sciences included, from the standpoint of the “transcendental of language”, and of the primacy of language over knowledge. That is, from the standpoint of the “completion of the linguistic turn” in the foundations of logic and mathematics using Peirce’s algebra of relations. This evolved during the last century till the development of the Category Theory as universal language for mathematics, in many senses wider than set theory. Therefore, starting from the fundamental M. Stone’s representation theorem for Boolean algebras, computer scientists developed a coalgebraic first-order semantics defined on Stone’s spaces, for Boolean algebras, till arriving to the definition of a non-Turing paradigm of coalgebraic universality in computation. Independently, theoretical physicists developed a coalgebraic modelling of dissipative quantum systems in quantum field theory, interpreted as a thermo-field dynamics. The deep connection between these two coalgebraic constructions is the fact that the topologies of Stone spaces in computer science are the same of the C*-algebras of quantum physics. This allows the development of a new class of quantum computers based on coalgebras. This suggests also an intriguing explanation of why one of the most successful experimental applications of this coalgebraic modelling of dissipative quantum systems is just in cognitive neuroscience

A Formal Model for Trust in Dynamic Networks

We propose a formal model of trust informed by the Global Computing scenario and focusing on the aspects of trust formation, evolution, and propagation. The model is based on a novel notion of trust structures which, building on concepts from trust management and domain theory, feature at the same time a trust and an information partial order

From Simple to Complex and Ultra-complex Systems:\ud A Paradigm Shift Towards Non-Abelian Systems Dynamics

Atoms, molecules, organisms distinguish layers of reality because of the causal links that govern their behavior, both horizontally (atom-atom, molecule-molecule, organism-organism) and vertically (atom-molecule-organism). This is the first intuition of the theory of levels. Even if the further development of the theory will require imposing a number of qualifications to this initial intuition, the idea of a series of entities organized on different levels of complexity will prove correct. Living systems as well as social systems and the human mind present features remarkably different from those characterizing non-living, simple physical and chemical systems. We propose that super-complexity requires at least four different categorical frameworks, provided by the theories of levels of reality, chronotopoids, (generalized) interactions, and anticipation

From Simple to Complex and Ultra-complex Systems:\ud A Paradigm Shift Towards Non-Abelian Systems Dynamics

Atoms, molecules, organisms distinguish layers of reality because of the causal links that govern their behavior, both horizontally (atom-atom, molecule-molecule, organism-organism) and vertically (atom-molecule-organism). This is the first intuition of the theory of levels. Even if the further development of the theory will require imposing a number of qualifications to this initial intuition, the idea of a series of entities organized on different levels of complexity will prove correct. Living systems as well as social systems and the human mind present features remarkably different from those characterizing non-living, simple physical and chemical systems. We propose that super-complexity requires at least four different categorical frameworks, provided by the theories of levels of reality, chronotopoids, (generalized) interactions, and anticipation