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

Stone-type representations and dualities for varieties of bisemilattices

In this article we will focus our attention on the variety of distributive bisemilattices and some linguistic expansions thereof: bounded, De Morgan, and involutive bisemilattices. After extending Balbes' representation theorem to bounded, De Morgan, and involutive bisemilattices, we make use of Hartonas-Dunn duality and introduce the categories of 2spaces and 2spaces$^{\star}$. The categories of 2spaces and 2spaces$^{\star}$ will play with respect to the categories of distributive bisemilattices and De Morgan bisemilattices, respectively, a role analogous to the category of Stone spaces with respect to the category of Boolean algebras. Actually, the aim of this work is to show that these categories are, in fact, dually equivalent

A New Penta-valued Logic Based Knowledge Representation

In this paper a knowledge representation model are proposed, FP5, which combine the ideas from fuzzy sets and penta-valued logic. FP5 represents imprecise properties whose accomplished degree is undefined, contradictory or indeterminate for some objects. Basic operations of conjunction, disjunction and negation are introduced. Relations to other representation models like fuzzy sets, intuitionistic, paraconsistent and bipolar fuzzy sets are discussed.Comment: The 12th International Conference Information Processing and Management of Uncertainty in Knowledge-Based Systems, June 22-27, 2008, Malaga, Spai

Towards ontology interoperability through conceptual groundings

Abstract. The widespread use of ontologies raises the need to resolve heterogeneities between distinct conceptualisations in order to support interoperability. The aim of ontology mapping is, to establish formal relations between a set of knowledge entities which represent the same or a similar meaning in distinct ontologies. Whereas the symbolic approach of established SW representation standards – based on first-order logic and syllogistic reasoning – does not implicitly represent similarity relationships, the ontology mapping task strongly relies on identifying semantic similarities. However, while concept representations across distinct ontologies hardly equal another, manually or even semi-automatically identifying similarity relationships is costly. Conceptual Spaces (CS) enable the representation of concepts as vector spaces which implicitly carry similarity information. But CS provide neither an implicit representational mechanism nor a means to represent arbitrary relations between concepts or instances. In order to overcome these issues, we propose a hybrid knowledge representation approach which extends first-order logic ontologies with a conceptual grounding through a set of CS-based representations. Consequently, semantic similarity between instances – represented as members in CS – is indicated by means of distance metrics. Hence, automatic similarity-detection between instances across distinct ontologies is supported in order to facilitate ontology mapping

Exploiting conceptual spaces for ontology integration

The widespread use of ontologies raises the need to integrate distinct conceptualisations. Whereas the symbolic approach of established representation standards – based on first-order logic (FOL) and syllogistic reasoning – does not implicitly represent semantic similarities, ontology mapping addresses this problem by aiming at establishing formal relations between a set of knowledge entities which represent the same or a similar meaning in distinct ontologies. However, manually or semi-automatically identifying similarity relationships is costly. Hence, we argue, that representational facilities are required which enable to implicitly represent similarities. Whereas Conceptual Spaces (CS) address similarity computation through the representation of concepts as vector spaces, CS rovide neither an implicit representational mechanism nor a means to represent arbitrary relations between concepts or instances. In order to overcome these issues, we propose a hybrid knowledge representation approach which extends FOL-based ontologies with a conceptual grounding through a set of CS-based representations. Consequently, semantic similarity between instances – represented as members in CS – is indicated by means of distance metrics. Hence, automatic similarity detection across distinct ontologies is supported in order to facilitate ontology integration

Using the event calculus for tracking the normative state of contracts

In this work, we have been principally concerned with the representation of contracts so that their normative state may be tracked in an automated fashion over their deployment lifetime. The normative state of a contract, at a particular time, is the aggregation of instances of normative relations that hold between contract parties at that time, plus the current values of contract variables. The effects of contract events on the normative state of a contract are specified using an XML formalisation of the Event Calculus, called ecXML. We use an example mail service agreement from the domain of web services to ground the discussion of our work. We give a characterisation of the agreement according to the normative concepts of: obligation, power and permission, and show how the ecXML representation may be used to track the state of the agreement, according to a narrative of contract events. We also give a description of a state tracking architecture, and a contract deployment tool, both of which have been implemented in the course of our work.

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