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

Proceedings of the ECCS 2005 satellite workshop: embracing complexity in design - Paris 17 November 2005

Embracing complexity in design is one of the critical issues and challenges of the 21st century. As the realization grows that design activities and artefacts display properties associated with complex adaptive systems, so grows the need to use complexity concepts and methods to understand these properties and inform the design of better artifacts. It is a great challenge because complexity science represents an epistemological and methodological swift that promises a holistic approach in the understanding and operational support of design. But design is also a major contributor in complexity research. Design science is concerned with problems that are fundamental in the sciences in general and complexity sciences in particular. For instance, design has been perceived and studied as a ubiquitous activity inherent in every human activity, as the art of generating hypotheses, as a type of experiment, or as a creative co-evolutionary process. Design science and its established approaches and practices can be a great source for advancement and innovation in complexity science. These proceedings are the result of a workshop organized as part of the activities of a UK government AHRB/EPSRC funded research cluster called Embracing Complexity in Design (www.complexityanddesign.net) and the European Conference in Complex Systems (complexsystems.lri.fr). Embracing complexity in design is one of the critical issues and challenges of the 21st century. As the realization grows that design activities and artefacts display properties associated with complex adaptive systems, so grows the need to use complexity concepts and methods to understand these properties and inform the design of better artifacts. It is a great challenge because complexity science represents an epistemological and methodological swift that promises a holistic approach in the understanding and operational support of design. But design is also a major contributor in complexity research. Design science is concerned with problems that are fundamental in the sciences in general and complexity sciences in particular. For instance, design has been perceived and studied as a ubiquitous activity inherent in every human activity, as the art of generating hypotheses, as a type of experiment, or as a creative co-evolutionary process. Design science and its established approaches and practices can be a great source for advancement and innovation in complexity science. These proceedings are the result of a workshop organized as part of the activities of a UK government AHRB/EPSRC funded research cluster called Embracing Complexity in Design (www.complexityanddesign.net) and the European Conference in Complex Systems (complexsystems.lri.fr)

Computer-aided exploration of architectural design spaces: a digital sketchbook

Het ontwerpproces van architecten vormt vaak geen lineair pad van ontwerpopgave tot eindresultaat, maar wordt veeleer gekenmerkt door exploratie of het doorzoeken van meerdere alternatieven in een (conceptuele) ontwerpruimte. Dit proces wordt in de praktijk vaak ondersteund door manueel schetsen, waarbij de ontwerpers schetsboek kan gelezen worden als een reeks exploraties. Dit soort interactie met de ontwerpruimte wordt in veel mindere mate ondersteund door hedendaagse computerondersteunde ontwerpsystemen. De metafoor van een digitaal schetsboek, waarbij menselijke exploratie wordt versterkt door de (reken)kracht van een computer, is het centrale onderzoeksthema van dit proefschrift. Hoewel het opzet van een ontwerpruimte op het eerste gezicht schatplichtig lijkt aan het onderzoeksveld van de artificiële intelligentie (AI), wordt het ontwerpen hier ruimer geïnterpreteerd dan het oplossen van problemen. Als onderzoeksmethodologie worden vormengrammatica’s ingezet, die enerzijds nauw aanleunen bij de AI en een formeel raamwerk bieden voor de exploratie van ontwerpruimtes, maar tegelijkertijd ook weerstand bieden tegen de AI en een vorm van visueel denken en ambiguïteit toelaten. De twee bijhorende onderzoeksvragen zijn hoe deze vormengrammatica’s digitaal kunnen worden gerepresenteerd, en op welke manier de ontwerper-computer interactie kan gebeuren. De resultaten van deze twee onderzoeksvragen vormen de basis van een nieuw hulpmiddel voor architecten: het digitaal schetsboek

Rules for Making: Kinematic Design, Shape and Structure

The thesis examines the role of making rules, within the creative exploration of kinematic design spaces. As a process of searching within a conceptual space, creative exploration can be described using rules. When applied to design, this model for creativity affords the application of computational techniques. In shape grammars, shape rules for ‘seeing’ and ‘doing’ apply a descriptive approach to the visual recognition, composition and modification of pictorial representations. This formalism can provide generative specifications and reveal the synthetic reasoning underlying iterative trajectories of design development. Making rules extend this approach to the tactile-visual representations of physical models and prototypes. When instantiating design representations within the material world, actions to construct and alter descriptions are grounded in material algebras. This thesis has a focus in Kinematics, where physical models provide a synthetic alternative to analytic techniques for modelling motions. In this context, making rules describe how to construct designs, make alterations, and manipulate models. Kinematic connections afford variable spatial relations between kinematic parts, and rules for physically manipulating models elicit their motions. Single closed-loop kinematic chains with full cycle mobility provide case studies for experimenting with making rules in design exploration, using both physical models and abstract geometric descriptions. An existing design creates a point of entry, where rules then afford the exploration of a surrounding kinematic design space. Applying alterations and transformations to physical models can identify the boundaries within which kinematic properties are preserved. The experimental cases inform theoretical development of exploratory making, with special reference to the variable spatial relations in kinematic designs and the integration of visual and tactile sensing. The main conclusion is that: as making rules construct models, rules are abstracted into schema by comparing properties of similar designs. The schema explain the results of exploration, initiating new explorations and new designs

Clifford Algebra: A Case for Geometric and Ontological Unification

Robert Batterman’s ontological insights (2002, 2004, 2005) are apt: Nature abhors singularities. “So should we,” responds the physicist. However, the epistemic assessments of Batterman concerning the matter prove to be less clear, for in the same vein he write that singularities play an essential role in certain classes of physical theories referring to certain types of critical phenomena. I devise a procedure (“methodological fundamentalism”) which exhibits how singularities, at least in principle, may be avoided within the same classes of formalisms discussed by Batterman. I show that we need not accept some divergence between explanation and reduction (Batterman 2002), or between epistemological and ontological fundamentalism (Batterman 2004, 2005). Though I remain sympathetic to the ‘principle of charity’ (Frisch (2005)), which appears to favor a pluralist outlook, I nevertheless call into question some of the forms such pluralist implications take in Robert Batterman’s conclusions. It is difficult to reconcile some of the pluralist assessments that he and some of his contemporaries advocate with what appears to be a countervailing trend in a burgeoning research tradition known as Clifford (or geometric) algebra. In my critical chapters (2 and 3) I use some of the demonstrated formal unity of Clifford algebra to argue that Batterman (2002) equivocates a physical theory’s ontology with its purely mathematical content. Carefully distinguishing the two, and employing Clifford algebraic methods reveals a symmetry between reduction and explanation that Batterman overlooks. I refine this point by indicating that geometric algebraic methods are an active area of research in computational fluid dynamics, and applied in modeling the behavior of droplet-formation appear to instantiate a “methodologically fundamental” approach. I argue in my introductory and concluding chapters that the model of inter-theoretic reduction and explanation offered by Fritz Rohrlich (1988, 1994) provides the best framework for accommodating the burgeoning pluralism in philosophical studies of physics, with the presumed claims of formal unification demonstrated by physicists choices of mathematical formalisms such as Clifford algebra. I show how Batterman’s insights can be reconstructed in Rohrlich’s framework, preserving Batterman’s important philosophical work, minus what I consider are his incorrect conclusions

Computational Modeling, Formal Analysis, and Tools for Systems Biology.

As the amount of biological data in the public domain grows, so does the range of modeling and analysis techniques employed in systems biology. In recent years, a number of theoretical computer science developments have enabled modeling methodology to keep pace. The growing interest in systems biology in executable models and their analysis has necessitated the borrowing of terms and methods from computer science, such as formal analysis, model checking, static analysis, and runtime verification. Here, we discuss the most important and exciting computational methods and tools currently available to systems biologists. We believe that a deeper understanding of the concepts and theory highlighted in this review will produce better software practice, improved investigation of complex biological processes, and even new ideas and better feedback into computer science

Towards a Coherent Theory of Physics and Mathematics

As an approach to a Theory of Everything a framework for developing a coherent theory of mathematics and physics together is described. The main characteristic of such a theory is discussed: the theory must be valid and and sufficiently strong, and it must maximally describe its own validity and sufficient strength. The mathematical logical definition of validity is used, and sufficient strength is seen to be a necessary and useful concept. The requirement of maximal description of its own validity and sufficient strength may be useful to reject candidate coherent theories for which the description is less than maximal. Other aspects of a coherent theory discussed include universal applicability, the relation to the anthropic principle, and possible uniqueness. It is suggested that the basic properties of the physical and mathematical universes are entwined with and emerge with a coherent theory. Support for this includes the indirect reality status of properties of very small or very large far away systems compared to moderate sized nearby systems. Discussion of the necessary physical nature of language includes physical models of language and a proof that the meaning content of expressions of any axiomatizable theory seems to be independent of the algorithmic complexity of the theory. G\"{o}del maps seem to be less useful for a coherent theory than for purely mathematical theories because all symbols and words of any language musthave representations as states of physical systems already in the domain of a coherent theory.Comment: 38 pages, earlier version extensively revised and clarified. Accepted for publication in Foundations of Physic

Dagstuhl News January - December 2000

"Dagstuhl News" is a publication edited especially for the members of the Foundation "Informatikzentrum Schloss Dagstuhl" to thank them for their support. The News give a summary of the scientific work being done in Dagstuhl. Each Dagstuhl Seminar is presented by a small abstract describing the contents and scientific highlights of the seminar as well as the perspectives or challenges of the research topic

Integration of Action and Language Knowledge: A Roadmap for Developmental Robotics

“This material is presented to ensure timely dissemination of scholarly and technical work. Copyright and all rights therein are retained by authors or by other copyright holders. All persons copying this information are expected to adhere to the terms and constraints invoked by each author's copyright. In most cases, these works may not be reposted without the explicit permission of the copyright holder." “Copyright IEEE. Personal use of this material is permitted. However, permission to reprint/republish this material for advertising or promotional purposes or for creating new collective works for resale or redistribution to servers or lists, or to reuse any copyrighted component of this work in other works must be obtained from the IEEE.”This position paper proposes that the study of embodied cognitive agents, such as humanoid robots, can advance our understanding of the cognitive development of complex sensorimotor, linguistic, and social learning skills. This in turn will benefit the design of cognitive robots capable of learning to handle and manipulate objects and tools autonomously, to cooperate and communicate with other robots and humans, and to adapt their abilities to changing internal, environmental, and social conditions. Four key areas of research challenges are discussed, specifically for the issues related to the understanding of: 1) how agents learn and represent compositional actions; 2) how agents learn and represent compositional lexica; 3) the dynamics of social interaction and learning; and 4) how compositional action and language representations are integrated to bootstrap the cognitive system. The review of specific issues and progress in these areas is then translated into a practical roadmap based on a series of milestones. These milestones provide a possible set of cognitive robotics goals and test scenarios, thus acting as a research roadmap for future work on cognitive developmental robotics.Peer reviewe