Cogprints: No conditions. Results ordered -Date, Title. 2018-01-17T14:22:52ZEPrintshttp://cogprints.org/images/sitelogo.gifhttp://cogprints.org/2015-10-06T12:09:46Z2015-10-06T12:09:46Zhttp://cogprints.org/id/eprint/9956This item is in the repository with the URL: http://cogprints.org/id/eprint/99562015-10-06T12:09:46ZTHE SPECIES PROBLEM AND ITS LOGIC: Inescapable Ambiguity and Framework-relativity
For more than fifty years, taxonomists have proposed numerous alternative definitions of species while they searched for a unique, comprehensive, and persuasive definition. This monograph shows that these efforts have been unnecessary, and indeed have provably been a pursuit of a will o' the wisp because they have failed to recognize the theoretical impossibility of what they seek to accomplish. A clear and rigorous understanding of the logic underlying species definition leads both to a recognition of the inescapable ambiguity that affects the definition of species, and to a framework-relative approach to species definition that is logically compelling, i.e., cannot not be accepted without inconsistency. An appendix reflects upon the conclusions reached, applying them in an intellectually whimsical taxonomic thought experiment that conjectures the possibility of an emerging new human species.Dr. Steven Bartlettsbartlet@willamette.edu2017-02-18T20:30:22Z2017-02-18T20:30:22Zhttp://cogprints.org/id/eprint/9812This item is in the repository with the URL: http://cogprints.org/id/eprint/98122017-02-18T20:30:22ZA Theory of General Reduction of Gene-Expression
Manifesting as Autism (1993 with 2014 revisions of presentation)This paper was originally written for a very different audience around 25 years ago, since when a great deal has changed both in autism research and in the wider world. Thus there was no mention of mercury (of which I knew almost nothing at the time) or of the autism increase (of which no-one else knew much either back then). And also I have become much more experienced in writing than back then. And paper-printed journals were very hostile to “excessive” length such that at least one paragraph got rather more squashed than I am happy to see it now.
So for these reasons I am making some minor changes to the writing, which do not change the actual content or meaning but which make for a better reading experience. For the convenience of cynics I will list all those changes at the end. In addition I am adding in some update notes in the text, indicated thus: [2014 Update: blah blah...]Robin P Clarkerpclarke[at]autismcauses.info2014-02-25T12:39:56Z2014-02-25T12:39:56Zhttp://cogprints.org/id/eprint/9132This item is in the repository with the URL: http://cogprints.org/id/eprint/91322014-02-25T12:39:56ZAutism spectrum disorders: A relational causeJones and Klin (1) showed that newborns who will later develop autism spectrum disorders (ASDs) pay normal attention to eyes, but that attention declines from 2-6 months. This shows, they say, how 'initial genotypic vulnerabilities' cause ASDs. Their results suggest, however, that ASDs are caused by insufficient practice of early eye-contact.Dr Maxson J McDowellmaxmcdowell@jungny.com2012-04-25T12:29:38Z2012-04-25T12:29:38Zhttp://cogprints.org/id/eprint/8149This item is in the repository with the URL: http://cogprints.org/id/eprint/81492012-04-25T12:29:38ZCategory of Metabolic-Replication Systems
in Biology and MedicineMetabolic-repair models, or (M,R)-systems were introduced in Relational Biology by Robert Rosen. Subsequently, Rosen represented such (M,R)-systems (or simply MRs) in terms of categories of sets, deliberately selected without any structure other than the discrete topology of sets. Theoreticians of life’s origins postulated that Life on Earth has begun with the simplest possible organism, called the primordial. Mathematicians interested in biology attempted to answer this important question of the minimal living organism by defining the functional relations that would have made life possible in such a minimal system- a grandad and grandma of all living organisms on Earth.Prof.Dr. I.C. Baianuibaianu@illinois.edu2012-04-25T12:30:10Z2012-04-25T12:30:10Zhttp://cogprints.org/id/eprint/8144This item is in the repository with the URL: http://cogprints.org/id/eprint/81442012-04-25T12:30:10ZQuantum Genetics and Quantum Automata Models of Quantum-Molecular Selection Processes Involved in the Evolution of Organisms and Species Previous theoretical or general approaches (Rosen, 1960; Shcherbik and Buchatsky, 2007) to the problems of Quantum Genetics and Molecular Evolution are considered in this article from the point of view of Quantum Automata Theory first published by the author in 1971 (Baianu,1971a, b) , and further developed in several recent articles (Baianu, 1977, 1983, 1987, 2004, 2011).The representation of genomes and Interactome networks in categories of many-valued logic LMn –algebras that are naturally transformed during biological evolution, or evolve through interactions with the environment provide a new insight into the mechanisms of molecular evolution, as well as organismal evolution, in terms of sequences of quantum automata. Phenotypic changes are expressed only when certain environmentally-induced quantum-molecular changes are coupled with an internal re-structuring of major submodules of the genome and Interactome networks related to cell cycling and cell growth. Contrary to the commonly held view of `standard’ Darwinist models of evolution, the evolution of organisms and species occurs through coupled multi-molecular transformations induced not only by the environment but actually realized through internal re-organizations of genome and interactome networks. The biological, evolutionary processes involve certain epigenetic transformations that are responsible for phenotypic expression of the genome and Interactome transformations initiated at the quantum-molecular level. It can thus be said that only quantum genetics can provide correct explanations of evolutionary processes that are initiated at the quantum—multi-molecular levels and propagate to the higher levels of organismal and species evolution. Biological evolution should be therefore regarded as a multi-scale process which is initiated by underlying quantum (coupled) multi-molecular transformations of the genomic and interactomic networks, followed by specific phenotypic transformations at the level of organism and the variable biogroupoids associated with the evolution of species which are essential to the survival of the species. The theoretical framework introduced in this article also paves the way to a Quantitative Biology approach to biological evolution at the quantum-molecular, as well as at the organismal and species levels. This is quite a substantial modification of the `established’ modern Darwinist, and also of several so-called `molecular evolution’ theories.Professor I.C. Baianu, ibaianu@illinois.edu2017-02-18T20:23:42Z2017-02-18T20:23:42Zhttp://cogprints.org/id/eprint/9649This item is in the repository with the URL: http://cogprints.org/id/eprint/96492017-02-18T20:23:42ZUner Tan Syndrome: Review and Emergence of Human Quadrupedalism in Self-Organization, Attarctors and evolutionary PerspectivesUner Tan syndrome, discovered in 2005 by Dr. Tan, in Southern Turkey, mainly consists of habitual quadrupedal locomotioni impaired intelligence, and dysarthric or no speech, with or without (rarely) cerebello-vermial hypoplasia and mildly simplified cortical gyri.
This syndrome may be considered wthin the framework of the nonprogressive autosomal recessive cerebellar ataxias, associated with various genetic mutations (genetic heterogeneity). This is a unique condition among disequilibrium syndrome, Cayman ataxia, and Joubert syndrome.
From the viewpoint of dynamical systems theory, there may be not a single factor including a ganetic code that predetermines the emergence of human quıadrupedalism, seen for instance in Uner Tan syndrome. Rather it may involve self-organization process, consisting of many decentralized and local interactions among neuronal, genetic, and environmental subsystems. Prof. Dr. Uner Tanunertan37@yahoo.comProf. Dr. Yusuf TamamProf. Dr. Sibel KaracaProf. Dr. Meliha TanMeliha_Tan@yahoo.com2011-12-16T00:58:48Z2011-12-16T00:58:48Zhttp://cogprints.org/id/eprint/7739This item is in the repository with the URL: http://cogprints.org/id/eprint/77392011-12-16T00:58:48ZNonlinear Models of Neural and Genetic Network Dynamics:
Natural Transformations of Łukasiewicz Logic LM-Algebras in a Łukasiewicz-Topos as Representations of Neural Network Development and Neoplastic Transformations
A categorical and Łukasiewicz-Topos framework for Algebraic Logic models of nonlinear dynamics in complex functional systems such as Neural Networks, Cell Genome and Interactome Networks is introduced. Łukasiewicz Algebraic Logic models of both neural and genetic networks and signaling pathways in cells are formulated in terms of nonlinear 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/transfer functions is extended to a Łukasiewicz Topos with an N-valued Łukasiewicz Algebraic Logic subobject classifier description that represents non-random and nonlinear network activities as well as their transformations in developmental processes and carcinogenesis.
Professor I.C. Baianuibaianu@illinois.edu2011-12-16T00:11:24Z2011-12-16T00:11:24Zhttp://cogprints.org/id/eprint/7708This item is in the repository with the URL: http://cogprints.org/id/eprint/77082011-12-16T00:11:24ZCan Internalism and Externalism be Reconciled in a Biological Epistemology of Language?This paper is an attempt at exploring the possibility of reconciling the two interpretations of biolinguistics which have been recently projected by Koster(Biolinguistics 3(1):61–92, 2009). The two interpretations—trivial and nontrivial—can be roughly construed as non-internalist and internalist conceptions of biolinguistics respectively. The internalist approach boils down to a conception of language where language as a mental grammar in the form of I-language grows and functions like a biological organ. On the other hand, under such a construal consistent with Koster’s (Biolinguistics 3(1):61-92, 2009), the non-internalist version does not necessarily have to be externalist in nature; rather it is a matter of mutual reinforcement of biology and culture under the rubric of a co-evolutionary dynamics. Here it will be argued that the apparent dichotomy between these two conceptions of biolinguistics can perhaps be resolved if we have a richer synthesis that accounts for both internalism and non-internalism.Prakash Mondalmndlprksh@yahoo.co.in2011-12-16T00:58:01Z2011-12-16T00:58:01Zhttp://cogprints.org/id/eprint/7740This item is in the repository with the URL: http://cogprints.org/id/eprint/77402011-12-16T00:58:01ZEarly Diagnosis of Alzheimer's Disease by NIRF Spectroscopy
and Nuclear Medicine
Novel approaches to Early Diagnosis of Alzheimer's Disease by NIRF Spectroscopy and Nuclear Medicine are presented and related cognitive, as well as molecular and cellular, models are critically evaluated.
Prof.Dr. I.C. Baianuibaianu@illinois.edu2011-12-16T00:04:45Z2011-12-16T00:04:45Zhttp://cogprints.org/id/eprint/7736This item is in the repository with the URL: http://cogprints.org/id/eprint/77362011-12-16T00:04:45ZComplexity, Emergent Systems and Complex Biological Systems:
Complex Systems Theory and Biodynamics. [Edited book by I.C. Baianu, with listed contributors (2011)]An overview is presented of System dynamics, the study of the behaviour of complex systems, Dynamical system in mathematics Dynamic programming in computer science and control theory, Complex systems biology, Neurodynamics and Psychodynamics.
Prof. Dr I.C. Baianu2013-11-18T21:00:21Z2013-11-18T21:00:21Zhttp://cogprints.org/id/eprint/9124This item is in the repository with the URL: http://cogprints.org/id/eprint/91242013-11-18T21:00:21ZAutism’s direct cause? Failure of infant-mother eye contact in a complex adaptive system This paper shows that an experimental hypothesis is plausible and merits testing. In brief the hypothesis is that autism begins with a failure in early learning and that changing the environment of early learning would dramatically change its incidence. Strong statistical evidence supporting this hypothesis was published by Waldman et al. (2008) but this evidence has largely been ignored, perhaps because it challenges prevalent beliefs about autism.
This paper also suggests that the current epidemic of autism is serious enough, and intellectually mysterious enough, to merit attention from a wider community of cognitive scientists: new ideas are needed. A confirmation of this paper’s hypothesis would have interesting implications for cognitive science. Doctor Maxson J McDowellmaxmcdowell@jungny.com2011-01-11T03:27:22Z2011-03-11T08:57:50Zhttp://cogprints.org/id/eprint/7168This item is in the repository with the URL: http://cogprints.org/id/eprint/71682011-01-11T03:27:22ZEye-contact and complex dynamic systems: an hypothesis on autism’s direct cause and a clinical study addressing prevention.
Estimates of autism’s incidence increased 5-10 fold in ten years, an increase which cannot be genetic. Though many mutations are associated with autism, no mutation seems directly to cause autism. We need to find the direct cause. Complexity science provides a new paradigm - confirmed in biology by extensive hard data. Both the body and the personality are complex dynamic systems which spontaneously self-organize from simple dynamic systems. Autism may therefore be caused by the failure of a simple dynamic system.
We know that infants who cannot track their mother’s face often become autistic, that eye-contact initiates intersubjectivity which is blocked in autism, and that the infant-mother pair seems designed to promote eye-contact, as does the eye’s appearance. This author earlier proposed that failure of eye-contact might directly cause autism and that early non-maternal childcare, including television/video, would therefore be statistically linked to autism.
Waldman et al. (2008; 2006) recently proved that autism is strongly linked to precipitation (indoor activity) and to the introduction of cable. The most plausible explanation? Early exposure to television/video is linked to autism. Furthermore a normal developmental cascade (blocked in autism) has been deciphered: (a) Infant-mother eye-contact triggers increased maternal attention. (b) Early maternal attention permanently increases not only baseline vasopressin but also that oxytocin release which is triggered by subsequent maternal attention. (c) Vasopressin and oxytocin promote face recognition, gazing-at-the-eyes, emotion recognition, and social bonding.
The eye-contact hypothesis suggests a clinical study addressing prevention: recruit prospective parents who agree to curtail television/video/computer/wi-fi in their families; measure autism’s incidence in their children.
Dr Maxson J. McDowellmaxmcdowell@jungny.com2011-12-16T00:04:40Z2011-12-16T00:04:40Zhttp://cogprints.org/id/eprint/7754This item is in the repository with the URL: http://cogprints.org/id/eprint/77542011-12-16T00:04:40ZCategorical 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.
KEYWORDS: Emergence of Life and Human Consciousness;
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.
Prof. Dr. I.C. Baianuibaianu@illinois.eduProf. Dr. James F. Glazebrookjfglazebrook@eiu.edu2011-12-16T00:58:12Z2011-12-16T00:58:12Zhttp://cogprints.org/id/eprint/7751This item is in the repository with the URL: http://cogprints.org/id/eprint/77512011-12-16T00:58:12ZŁukasiewicz-Moisil Many-Valued Logic Algebra of Highly-Complex SystemsA novel approach to self-organizing, highly-complex systems (HCS), such as living organisms and artificial intelligent systems (AIs), is presented which is relevant to Cognition, Medical Bioinformatics and Computational Neuroscience. Quantum Automata (QAs) were defined in our previous work as generalized, probabilistic automata with quantum state spaces (Baianu, 1971). Their next-state functions operate through transitions between quantum states defined by the quantum equations of motion in the Schroedinger representation, with both initial and boundary conditions in space-time. Such quantum automata operate with a quantum logic, or Q-logic, significantly different from either Boolean or Łukasiewicz many-valued logic. A new theorem is proposed which states that the category of quantum automata and automata--homomorphisms has both limits and colimits. Therefore, both categories of quantum automata and classical automata (sequential machines) are bicomplete. A second new theorem establishes that the standard automata category is a subcategory of the quantum automata category. The quantum automata category has a faithful representation in the category of Generalized (M,R)--Systems which are open, dynamic biosystem networks with defined biological relations that represent physiological functions of primordial organisms, single cells and higher organisms.Professor I.C. Baianuibaianu@illinois.eduProfessor George Georgescugeorgescu@funinf.cs.unibuc.roProfessor James F. Glazebrookjfglazebrook@eiu.edu2010-07-29T01:44:29Z2011-03-11T08:57:38Zhttp://cogprints.org/id/eprint/6898This item is in the repository with the URL: http://cogprints.org/id/eprint/68982010-07-29T01:44:29ZUniqueness, Self belonging and Intercourse in NatureThis manuscript has ensued from my past studies in biochemistry (PhD, CUNY 1986) and my current endeavors in graduate study in philosophy and anthropology. The current research project began during my period as a graduate student in biochemistry with a professor of classical genetics comment that DNA was unique in the physical world. The paradox presented to relate this notion to existing natural law lead me to evolve and communicate a view that the world itself is a special case of a general case that has no relevant physical existence. I also hope to have presented a description of a situation that connects history, human behavior, the process and symbolisms of science, cause and effect to a holism of form, philosophy, mathematics, shape, and motionDr. Marvin/E. Kirshkirsh2152000@yahoo.com2010-06-06T14:35:14Z2011-03-11T08:57:37Zhttp://cogprints.org/id/eprint/6853This item is in the repository with the URL: http://cogprints.org/id/eprint/68532010-06-06T14:35:14ZNested ontology and causal options: A paradigm for consciousnessA brain charged with guiding its body through a complex and lively world from a position of solitary confinement inside its opaque skull faces a set of functional problems whose solution may account for the existence and nature of consciousness. An analysis of the more general and basic of these problems, sensory as well as motor, suggests the utility of implementing a high-level mutual interface between sensory target selection, motor action selection, and motivational ranking of needs at a late stage in the run-up to the brain’s decision about the very next action to take. The three selection processes are subject to a number of mutual dependencies such that a regimen of constraint satisfaction among them would yield gains in behavioral efficiency. The logistics of implementing such a regimen can be simplified by casting the interface in a particular nested, analog format. It would host a running synthetic summary of the rest of the brain’s interpretive labors, reflecting best estimates of the veridical current state of world, body, and needs for purposes of real-time decision making. Detailed scrutiny of the design requirements for such a mechanism discloses that it would be functionally partitioned in a way that defines a conscious mode of operation. Moreover, the design of the mechanism mandates a specific departure from veridicality at a point that makes its functional format match the assumptions of naive realism. Consciousness itself thus introduces a significant, though not insuperable, psychological obstacle to the development of a veridical account of its nature.Dr. Bjorn Merkergyr694c@tninet.se2011-12-16T00:59:06Z2011-12-16T00:59:06Zhttp://cogprints.org/id/eprint/7756This item is in the repository with the URL: http://cogprints.org/id/eprint/77562011-12-16T00:59:06ZOncogenomics and Cancer InteractomicsAn overview of translational, human oncogenomics, transcriptomics and cancer interactomic networks is presented together with basic concepts and potential, new applications to Oncology and Integrative Cancer Biology. Novel translational oncogenomics research is rapidly expanding through the application of advanced technology, research findings and computational tools/models to both pharmaceutical and clinical problems. A self-contained presentation is adopted that covers both fundamental concepts and the most recent biomedical, as well as clinical, applications. Sample analyses in recent clinical studies have shown that gene expression data can be employed to distinguish between tumor types as well as to predict outcomes. Potentially important applications of such results are individualized human cancer therapies or, in general, ‘personalized medicine’. Several cancer detection techniques are currently under development both in the direction of improved detection sensitivity and increased time resolution of cellular events, with the limits of single molecule detection and picosecond time resolution already reached. The urgency for the complete mapping of a human cancer interactome with the help of such novel, high-efficiency / low-cost and ultra-sensitive techniques is also pointed out.Prof. Dr I.C. Baianuibaianu@illinois.edu2010-10-18T11:00:45Z2011-03-11T08:57:45Zhttp://cogprints.org/id/eprint/7048This item is in the repository with the URL: http://cogprints.org/id/eprint/70482010-10-18T11:00:45ZOctologyThe manuscript describes a new sciencific discipline called Octology, which should unify morphogenetic linguistics and neurobiology to investigate the development of the words, cognition and behavior.Dr. Andrej Poleevandrejpoleev@yahoo.com2009-11-14T11:34:42Z2011-03-11T08:57:32Zhttp://cogprints.org/id/eprint/6698This item is in the repository with the URL: http://cogprints.org/id/eprint/66982009-11-14T11:34:42ZNatural Variation and Neuromechanical SystemsNatural variation plays an important but subtle and often ignored role in neuromechanical systems. This is especially important when designing for living or hybrid systems
which involve a biological or self-assembling component. Accounting for natural variation can be accomplished by taking a population phenomics approach to modeling and analyzing such systems. I will advocate the position that noise in neuromechanical systems is partially represented by natural variation inherent in user physiology. Furthermore, this noise can be augmentative in systems that couple physiological systems with technology. There are several tools and approaches that can be borrowed from computational biology to characterize the populations of users as they interact with the technology. In addition to transplanted approaches, the potential of natural variation can be understood as having a range of effects on both the individual's physiology and function of the living/hybrid system over time. Finally, accounting for natural variation can be put to good use in human-machine system design, as three prescriptions for exploiting variation in design are proposed.Bradly Aliceafreejumper@yahoo.com2009-10-15T22:51:21Z2011-03-11T08:57:29Zhttp://cogprints.org/id/eprint/6655This item is in the repository with the URL: http://cogprints.org/id/eprint/66552009-10-15T22:51:21ZThe meaning of life in a developing universeThe evolution of life on Earth has produced an organism that is beginning to model and understand its own evolution and the possible future evolution of life in the universe. These models and associated evidence show that evolution on Earth has a trajectory. The scale over which living processes are organized cooperatively has increased progressively, as has its evolvability. Recent theoretical advances raise the possibility that this trajectory is itself part of a wider developmental process. According to these theories, the developmental process has been shaped by a yet larger evolutionary dynamic that involves the reproduction of universes. This evolutionary dynamic has tuned the key parameters of the universe to increase the likelihood that life will emerge and produce outcomes that are successful in the larger process (e.g. a key outcome may be to produce life and intelligence that intentionally reproduces the universe and tunes the parameters of ‘offspring’ universes). Theory suggests that when life emerges on a planet, it moves along this trajectory of its own accord. However, at a particular point evolution will continue to advance only if organisms emerge that decide to advance the developmental process intentionally. The organisms must be prepared to make this commitment even though the ultimate nature and destination of the process is uncertain, and may forever remain unknown. Organisms that complete this transition to intentional evolution will drive the further development of life and intelligence in the universe. Humanity’s increasing understanding of the evolution of life in the universe is rapidly bringing it to the threshold of this major evolutionary transition.John E Stewartjes999@tpg.com.au2009-09-07T10:17:27Z2011-03-11T08:57:24Zhttp://cogprints.org/id/eprint/6605This item is in the repository with the URL: http://cogprints.org/id/eprint/66052009-09-07T10:17:27ZThe phenomenon of biological evolution: 19th century misconceptionScientists still think that biological evolution is driven by the process named natural selection. Perhaps this 19th century notion was indeed a revolutionary idea at the time when it has been introduced. However, now it seems that natural selection hypothesis most probably is wrong. It does not explain, above all, why biological organization arise in the course of evolution. I show, on a rather abstract level of consideration, that exists another explanation why this intriguing phenomenon - life evolution - take place. Here it is argued that biological organization is solely a product of self-replication.Mr Dalius Balciunasdbalciunas@post.skynet.lt2009-07-06T09:43:13Z2011-03-11T08:57:23Zhttp://cogprints.org/id/eprint/6576This item is in the repository with the URL: http://cogprints.org/id/eprint/65762009-07-06T09:43:13ZDegenerate neutrality creates evolvable fitness landscapesUnderstanding how systems can be designed to be evolvable is fundamental to research in optimization, evolution, and complex systems science. Many researchers have thus recognized the importance of evolvability, i.e. the ability to find new variants of higher fitness, in the fields of biological evolution and evolutionary computation. Recent studies by Ciliberti et al (Proc. Nat. Acad. Sci., 2007) and Wagner (Proc. R. Soc. B., 2008) propose a potentially important link between the robustness and the evolvability of a system. In particular, it has been suggested that robustness may actually lead to the emergence of evolvability. Here we study two design principles, redundancy and degeneracy, for achieving robustness and we show that they have a dramatically different impact on the evolvability of the system. In particular, purely redundant systems are found to have very little evolvability while systems with degeneracy, i.e. distributed robustness, can be orders of magnitude more evolvable. These results offer insights into the general principles for achieving evolvability and may prove to be an important step forward in the pursuit of evolvable representations in evolutionary computation. Dr James M Whitacrejwhitacre79@yahoo.comDr Axel Bender2009-07-02T01:51:39Z2011-03-11T08:57:22Zhttp://cogprints.org/id/eprint/6551This item is in the repository with the URL: http://cogprints.org/id/eprint/65512009-07-02T01:51:39ZComplexity, BioComplexity, the Connectionist Conjecture and Ontology of Complexity
This paper develops and integrates major ideas and concepts on complexity and biocomplexity - the connectionist conjecture, universal ontology of complexity, irreducible complexity of totality & inherent randomness, perpetual evolution of information, emergence of criticality and equivalence of symmetry & complexity. This paper introduces the Connectionist Conjecture which states that the one and only representation of Totality is the connectionist one i.e. in terms of nodes and edges. This paper also introduces an idea of Universal Ontology of Complexity and develops concepts in that direction. The paper also develops ideas and concepts on the perpetual evolution of information, irreducibility and computability of totality, all in the context of the Connectionist Conjecture. The paper indicates that the control and communication are the prime functionals that are responsible for the symmetry and complexity of complex phenomenon. The paper takes the stand that the phenomenon of life (including its evolution) is probably the nearest to what we can describe with the term “complexity”. The paper also assumes that signaling and communication within the living world and of the living world with the environment creates the connectionist structure of the biocomplexity. With life and its evolution as the substrate, the paper develops ideas towards the ontology of complexity. The paper introduces new complexity theoretic interpretations of fundamental biomolecular parameters. The paper also develops ideas on the methodology to determine the complexity of “true” complex phenomena.
Mr. Debaprasad Mukherjeebiodeb@gmail.com2009-04-06T01:10:06Z2011-03-11T08:57:20Zhttp://cogprints.org/id/eprint/6407This item is in the repository with the URL: http://cogprints.org/id/eprint/64072009-04-06T01:10:06ZGene expression and its discontents: Developmental disorders as dysfunctions of epigenetic cognitionReductionist treatments of the epigenetic regulation of gene expression suffer the same mereological and sufficiency fallacies that haunt both contemporary systems biology and neural network models of high order cognition. Shifting perspective from the massively parallel space of gene matrix interactions to the grammar/syntax of the time series of developmentally expressed phenotypes using a cognitive paradigm permits import of techniques from statistical physics via the homology between information source uncertainty and free energy density. This produces a broad spectrum of 'coevolutionary' probability models of development and its pathologies in which epigenetic regulation and the effects of embedding environment are analogous to a tunable enzyme catalyst. A cognitive paradigm naturally incorporates memory, leading directly to models of epigenetic inheritance, as affected by environmental exposures, in the largest sense. Understanding gene expression, development, and their dysfunctions will require data analysis tools considerably more sophisticated than the present crop of simplistic models abducted from neural network studies or stochastic chemical reaction theory.Rodrick Wallacewallace@pi.cpmc.columbia.edu2009-02-13T01:14:50Z2011-03-11T08:57:18Zhttp://cogprints.org/id/eprint/6342This item is in the repository with the URL: http://cogprints.org/id/eprint/63422009-02-13T01:14:50ZGene Expression and its Discontents: Developmental disorders as dysfunctions of epigenetic cognitionSystems biology presently suffers the same mereological and sufficiency fallacies that haunt neural network models of high order cognition. Shifting perspective from the massively parallel space of gene matrix interactions to the grammar/syntax of the time series of expressed phenotypes using a cognitive paradigm permits import of techniques from statistical physics via the homology between information source uncertainty and free energy density. This produces a broad spectrum of possible statistical models of development and its pathologies in which epigenetic regulation and the effects of embedding environment are analogous to a tunable enzyme catalyst. A cognitive paradigm naturally incorporates memory, leading directly to models of epigenetic inheritance, as affected by environmental exposures, in the largest sense. Understanding gene expression, development, and their dysfunctions will require data analysis tools considerably more sophisticated than the present crop of simplistic models abducted from neural network studies or stochastic chemical reaction theory.Rodrick Wallacewallace@pi.cpmc.columbia.edu2008-07-13T11:03:39Z2011-03-11T08:57:09Zhttp://cogprints.org/id/eprint/6123This item is in the repository with the URL: http://cogprints.org/id/eprint/61232008-07-13T11:03:39Z“Io sono evoluto e quello è un uomo di Neanderthal”:
Un’analisi linguistica cognitivista del concetto di evoluzione“Evoluzione” è una parola usata ormai frequentemente dall’uomo comune nonché in tutte le discipline, umanistiche e scientifiche. Culturalmente radicata, è diventata una metafora potente. Una definizione corrente è “sviluppo lento e graduale; svolgimento da una forma a un’altra, generalmente più completa e perfetta” (Garzanti). In questi termini non si parla soltanto dell’evoluzione biologica dell’uomo, ma anche dell’evoluzione del linguaggio, della società, della cognizione umana – a prescindere da un’effettiva conoscenza delle teorie evoluzionistiche.
L’evoluzione, in quanto teoria biologica, rimanda quasi automaticamente alla teoria di Darwin, il quale, tuttavia, ha usato il termine solo una volta, nel paragrafo finale del suo celeberrimo L’origine delle specie (1859). Nel concetto di evoluzione è comunemente implicato il passaggio da una specie “primitiva” ad una specie “progredita”, più avanzata o sofisticata e strutturalmente più complessa. Nei suoi scritti, Darwin preferiva parlare di “discendenza con modificazioni” anziché di “evoluzione”, termine usato invece da Bonnet (1762) nella sua teoria dell’homunculus, proprio perché portatore della valenza semantica di “progresso”, non presente nella teoria che Darwin proponeva. Infatti, per quest’ultimo “evoluzione” ha più a che fare con il cambiamento (x --> y) che con il progresso (x --> x+1). L’idea che il concetto di evoluzione abbia a che fare con quello di progresso è in realtà posteriore: nell’accezione più comune del termine è presente l’idea di una temporalità lineare, nella quale l’hic et nunc è visto come la massima compiutezza dello sviluppo, della complessità e della “modernità”, e il passato è visto da un punto di vista situato in un setting storico del presente (antropo-, etno-, euro-, ego-centrico etc), in un’opposizione binaria tra “adesso” e “allora”, tra “noi” e “loro”, tra “progredito” e “primitivo”. Eppure l’evoluzione, in senso stretto, non è teleologica e non c’è un “avanti” o un “indietro”, c’è solo un cambiamento causato dall’adattamento nell’ecosistema in cui l’essere storico si trova. Evoluzione non è necessariamente sinonimo di ottimizzazione (chi può dire che la “prossima generazione” sarà migliore?).
La mia ipotesi è che questa metafora (linguaggio) influenza il nostro modo di concepire e ragionare circa un oggetto (pensiero). Anticipando qualche dato, mi avvalgo delle discipline linguistiche, nell’ambito delle quali si parla dell’evoluzione non solo del linguaggio, ma anche della lingua. Ad esempio l’idea che una lingua sia meno complessa sintatticamente, come nel caso della lingua dei Pirahã del Sudamerica, ha generato il giudizio di “primitivismo” nei confronti del popolo che la parla da parte soprattutto di alcuni filochomskyiani e altri1. In altre scienze sociali, alcune manifestazioni culturali, come l’arte, vengono intese come “primitive” o “moderne”, oppure si parla di evoluzione di generi letterari. La dimostrazione forse più eclatante di questo antropocentrismo riguarda il problema del genere Homo, in cui l’avvento dell’Uomo Anatomicamente Moderno si fa coincidere con la nascita della cultura, utilizzando un doppio standard di modernità, visto che Neandertal fu probabilmente molto più simile a noi di quanto si tende a pensare2.
L’utilizzo dell’idea di evoluzione come metafora può essere estremamente potente nell’ambiente accademico, ma occorre prestare attenzione alle sue possibili implicazioni. Il mio intento è quello di analizzare questa metafora usata comunemente all’interno delle varie discipline dal punto di vista della linguistica cognitiva (frames e metafore concettuali), mettendo in evidenza come il concetto target eredita delle implicazioni che emergono a causa delle qualità proprie del concetto source, per dimostrare che il modo in cui avviene il framing del concetto condiziona sovente la metodologia di studio, nonché la tassonomia applicata all’oggetto studiato. Vito Evolaevola@unipa.it2010-10-18T11:06:02Z2011-03-11T08:57:45Zhttp://cogprints.org/id/eprint/7033This item is in the repository with the URL: http://cogprints.org/id/eprint/70332010-10-18T11:06:02ZConcepts of Human Physiology in Ayurveda‘Human Physiology’, or the study of functional aspects of human body, is designated by the term ‘Śarīra Vicaya’ in Ayurvedic literature. The word ‘Vicaya’ means the special or detailed knowledge. Detailed knowledge of normal human body i.e., ‘Śarīra’, is considered helpful in understanding the factors influencing the health. Though most of the
basic concepts of human physiology explained in Ayurveda are strikingly similar to the concepts of modern physiology, some concepts like ‘Ātmā’, ‘Manas’ and ‘Prakrti’ are unique
to Ayurveda. Understanding of Physiology in Ayurveda should start with the understanding of innumerable minute individual living units called ‘Śarīra Paramānus’ or ‘Anu Srotāmsi’. These units are now known as cells. A group of such functionally and structurally similar units is called a ‘Dhātu’. These ‘Dhātus’ are almost equivalent to the tissues. Seven such ‘Dhātus’ have been enumerated. Similarly, the individual systems in the body have been
designated by the term ‘Sthūla Srotāmsi’ and thirteen such ‘Srotāmsi’ have been described by Caraka. ‘Annavaha Stotas’, for example, stands equivalent to the digestive system and ‘Rasavaha Srotas’ to the cardio vascular system. Apart from these, the functioning of individual systems has also been described in a considerably detailed manner. Cardiovascular system as a closed circuit, role of liver in the functioning of hemopoietic system, functional significance of brain in the neural mechanisms, basics of digestion and metabolism and basics of immunity ‐ are some such topics worth mentioning. Theory of ‘Tridosha’ is another important theory of physiology. This represents the various reciprocally
functioning homeostatic mechanisms at various levels of organization. The state of equilibrium among these ‘Doshas’ is responsible for maintenance of health. Three ‘Doshas’ –
i.e., ‘Vāta’, ‘Pitta’ and ‘Kapha’ in general, represent neural, endocrine and immune mechanisms respectively and form the basis of neuro‐ immuno‐ endocrinology.Dr. Kishor Patwardhanpatwardhan.kishor@gmail.com2007-10-12T16:39:07Z2011-03-11T08:56:58Zhttp://cogprints.org/id/eprint/5743This item is in the repository with the URL: http://cogprints.org/id/eprint/57432007-10-12T16:39:07ZNational Trends on Agricultural Crops Production: Cluster AnalysisStaring from descriptive data on crop production and cultivated area at national level during on fifteen years, the aim of this study is to reveal the trends on crops cultivation. The cluster analysis reveals linkages between crops classes as well as between different crops, which can be partly assigned to crops rotation. Time series analysis reveals dramatically reducing of production of some crops, such as flax, hemp, and sugar beet, and increasing of production, such at sunflower, and increasing of productivity, such at potatoes and field vegetables.Dr. Lorentz JÄNTSCHIlori@academicdirect.orgDr. Sorana D. BOLBOACAsbolboaca@umfcluj.roCarmen E, STOENOIUcarmen@j.academicdirect.ro2007-09-12Z2011-03-11T08:56:57Zhttp://cogprints.org/id/eprint/5711This item is in the repository with the URL: http://cogprints.org/id/eprint/57112007-09-12ZSlowness and Sparseness Lead to Place, Head-Direction, and Spatial-View CellsWe present a model for the self-organized formation of place cells, head-direction cells, and spatial-view cells in the hippocampal formation based on unsupervised learning on quasi-natural visual stimuli. The model comprises a hierarchy of Slow Feature Analysis (SFA) nodes, which were recently shown to reproduce many properties of complex cells in the early visual system. The system extracts a distributed grid-like representation of position and orientation, which is transcoded into a localized place-field, head-direction, or view representation, by sparse coding. The type of cells that develops depends solely on the relevant input statistics, i.e., the movement pattern of the simulated animal. The numerical simulations are complemented by a mathematical analysis that allows us to accurately predict the output of the top SFA layerMathias FranziusHenning SprekelerProf. Dr. Laurenz Wiskott2007-10-22T10:40:41Z2011-03-11T08:56:59Zhttp://cogprints.org/id/eprint/5779This item is in the repository with the URL: http://cogprints.org/id/eprint/57792007-10-22T10:40:41ZAutonomy: a review and a reappraisalIn the field of artificial life there is no agreement on what defines ‘autonomy’. This makes it difficult to measure progress made towards understanding as well as engineering autonomous systems. Here, we review the diversity of approaches and categorize them by introducing a conceptual distinction between behavioral and constitutive autonomy. Differences in the autonomy of artificial and biological agents tend to be marginalized for the former and treated as absolute for the latter. We argue that with this distinction the apparent opposition can be resolved.Mr Tom Froeset.froese@gmail.comMr Nathaniel Virgon.d.virgo@sussex.ac.ukMr Eduardo Izquierdoe.j.izquierdo@sussex.ac.uk2007-06-07Z2011-03-11T08:56:51Zhttp://cogprints.org/id/eprint/5584This item is in the repository with the URL: http://cogprints.org/id/eprint/55842007-06-07ZCultural evolution entails (creativity entails (concept combination entails quantum structure))The theory of natural selection cannot describe how early life evolved, in part because acquired characteristics are passed on through horizontal exchange. It has been proposed that culture, like life, began with the emergence of autopoietic form, thus its evolution too cannot be described by natural selection. The evolution of autopoietic form can be described using a framework referred to as Context-driven Actualization of Potential (CAP), which grew out of a generalization of the formalisms of quantum mechanics, and encompasses nondeterministic as well as deterministic change of state. The autopoietic structure that evolves through culture is the mind, or more accurately the conceptual network that yields an individual's internal model of the world. A branch of CAP research referred to as the state-context-property (SCOP) formalism provides a mathematical framework for reconciling the stability of conceptual structure with its susceptibility to context-driven change. The combination of two or more concepts (an extreme case of contextual influence), as occurs in insight, is modeled as a state of entanglement. Theoretical and empirical findings are presented that challenge assumptions underlying virtually all of cognitive science, such as the notion of spreading activation and the assumption that cognitive processes can be described with a Kolmogorovian probability model.Dr. Liane M. Gabora2008-03-10T14:49:25Z2011-03-11T08:57:05Zhttp://cogprints.org/id/eprint/5962This item is in the repository with the URL: http://cogprints.org/id/eprint/59622008-03-10T14:49:25ZEpigenetic and Cultural Evolution are non-DarwinianThe argument that heritable epigenetic change plays a distinct role in evolution would be strengthened through recognition that it is what bootstrapped the origin and early evolution of life, and like behavioral and symbolic change, is non-Darwinian. The mathematics of natural selection, a population-level process, is limited to replication with negligible individual-level change, i.e. that uses a self-assembly code.Dr. L. M. Gaboraliane.gabora@ubc.ca2006-12-22Z2011-03-11T08:56:45Zhttp://cogprints.org/id/eprint/5329This item is in the repository with the URL: http://cogprints.org/id/eprint/53292006-12-22ZEVIDENCE FOR "UNER TAN SYNDROME" AS A HUMAN MODEL FOR REVERSE EVOLUTION“Uner Tan Syndrome” was further studied in a second family. There was no cerebellar atrophy, except a mild vermial atrophy in MRI scans of the affected individuals. This is not, however, the pathogenesis of the “Uner Tan Syndrome”, since in the first and second families there were bipedal men exhibiting very similar MRI scans. The second family may also be considered a live model for reverse evolution in human beings. The present work provided evidence for a reverse evolution: (i) quadrupedality; (ii) primitive mental abilities including language; (iii) curved fingers during wrist-walking of the quadrupedal woman; (iv) arm to leg ratios being close to those of the human-like apes. The quadrupedal individuals were raised in separate places, so that they could not imitate each other, excluding the socio-cultural factors contributing to the habitual quadrupedal gait. The results are consistent with the single gene theory, suggesting a single gene controlling multiple behavioral traits, and the psychomotor theory, and a co-evolution of the human mind, an emergent property of the motor system expressed by human language.Prof. Dr. Uner Tan2006-12-12Z2011-03-11T08:56:43Zhttp://cogprints.org/id/eprint/5281This item is in the repository with the URL: http://cogprints.org/id/eprint/52812006-12-12ZSlowness: An Objective for Spike-Timing-Dependent Plasticity?Slow Feature Analysis (SFA) is an efficient algorithm for
learning input-output functions that extract the most slowly varying features from a quickly varying signal. It
has been successfully applied to the unsupervised learning
of translation-, rotation-, and other invariances in a
model of the visual system, to the learning of complex cell
receptive fields, and, combined with a sparseness
objective, to the self-organized formation of place cells
in a model of the hippocampus.
In order to arrive at a biologically more plausible implementation of this learning rule, we consider analytically how SFA could be realized in simple linear continuous and spiking model neurons. It turns out that for the continuous model neuron SFA can be implemented by means of a modified version of standard Hebbian learning. In this framework we provide a connection to the trace learning rule for invariance learning. We then show that for Poisson neurons spike-timing-dependent plasticity (STDP) with a specific learning window can learn the same weight distribution as SFA. Surprisingly, we find that the appropriate learning rule reproduces the typical STDP learning window. The shape as well as the timescale are in good agreement with what has been measured experimentally. This offers a completely novel interpretation for the functional role of spike-timing-dependent plasticity in physiological neurons. Henning SprekelerChristian MichaelisLaurenz Wiskott2006-08-01Z2011-03-11T08:56:33Zhttp://cogprints.org/id/eprint/5038This item is in the repository with the URL: http://cogprints.org/id/eprint/50382006-08-01ZSelf-Replication and Self-Assembly for ManufacturingIt has been argued that a central objective of nanotechnology is to make
products inexpensively, and that self-replication is an effective approach
to very low-cost manufacturing. The research presented here is intended to
be a step towards this vision. We describe a computational simulation of
nanoscale machines floating in a virtual liquid. The machines can bond
together to form strands (chains) that self-replicate and self-assemble
into user-specified meshes. There are four types of machines and the
sequence of machine types in a strand determines the shape of the mesh
they will build. A strand may be in an unfolded state, in which the bonds
are straight, or in a folded state, in which the bond angles depend on the
types of machines. By choosing the sequence of machine types in a strand,
the user can specify a variety of polygonal shapes. A simulation typically
begins with an initial unfolded seed strand in a soup of unbonded machines.
The seed strand replicates by bonding with free machines in the soup. The
child strands fold into the encoded polygonal shape, and then the polygons
drift together and bond to form a mesh. We demonstrate that a variety of
polygonal meshes can be manufactured in the simulation, by simply changing
the sequence of machine types in the seed.Robert EwaschukPeter D. Turney21752007-12-22T02:50:44Z2011-03-11T08:57:02Zhttp://cogprints.org/id/eprint/5884This item is in the repository with the URL: http://cogprints.org/id/eprint/58842007-12-22T02:50:44ZThe Theory of Brain-Sign: A Physical Alternative to ConsciousnessConsciousness and the mind are prescientific concepts that begin with Greek theorizing. They suppose human rationality and reasoning placed in the human head by God, who structured the universe he created with the same kind of underlying characteristics. Descartes’ development of the model included scientific objectivity by placing the mind outside the physical universe. In its failure under evidential scrutiny and without physical explanation, this model is destined for terminal decline. Instead, a genuine biological and physical function for the brain phenomenon can be developed. This is the theory of brain-sign. It accepts the causality of the brain as its physical characteristics, already under scientific scrutiny. What is needed is a new neurophysiological language that specifies the relation of the structure and operation of the brain to organismic action in the world. Still what is lacking is an account of how neurophysiologies in different organisms communicate on unpredictable dynamic tasks. It is this evolved capacity that has emerged as brain-sign. Thus rather than mentality being an inner epistemological parallel world suddenly appearing in the head, brain-sign, as the neural sign of the causal status of the brain capable of being held adequately in common, facilitates the communicative medium of otherwise isolated organisms. The biogenesis of the phenomenon thus emerges directly from the account of the physical brain, and functions as a monistic feature of organisms in the physical world. This new paradigm offers disciplinary compatibility, and genuine development in behavioral and brain sciences. Philip Clapson2006-04-08Z2011-03-11T08:56:20Zhttp://cogprints.org/id/eprint/4743This item is in the repository with the URL: http://cogprints.org/id/eprint/47432006-04-08ZDigit-Type Mechanisms in Cell Differentiation Process: a Theoretical StudyAccording to inductive conception, the interference of neighboring cells causes a production of broken spatial symmetry in an initially homogenous system (cell differentiation process) during embryo development. A concentration gradient of a specific substance (morphogen), which serves as an analog-type control signal, is proposed as an agent to provide this process. It is known fact, that genes’ activity are of a discreet-type (digit) and, therefore, cell differentiation mechanism based on the control digit-type signals in comparison with the analog-type signals is more or less probable.
A model presented here simulates the cell differentiation process. The model is based on the assumption that only the digit-type interactions take place between adjacent cells (not analog-type interactions that are typical for the concentration gradient field). Within model assumptions, the genes’ interaction algorithms and boundary condition are postulated.
Under the model assumptions, the cell differentiation process starts with the homogeneous blastula formation and comprises three consecutive stages. 1) The loop-like inhomogeneous cell formation development and corresponding set of the self-blocking genes activation - the set of the asymmetric pattern genes governs the process. 2) The line-type inhomogeneous cell formations, with their origins at different cells of the loop-type formation, development and corresponding self-blocking genes activation - the sets of the symmetric pattern genes govern the process. 3) The variety of the function genes activation in the complex inhomogeneous cell formation - the sets of the self-blocking genes govern the process. Under model assumptions the multi level tree-type inhomogeneous cell structures creation is possible. The number of the pattern genes limits the complexity of the inhomogeneous structure. According to the model, in order to provide the further blastula development process, the concentration gradient fields may appear after the initial stages of the cell differentiation process.
As simulated by the model, results qualitatively coincide with some of the experimental facts.
Yaroslav Strokovskyy2006-12-12Z2011-03-11T08:56:43Zhttp://cogprints.org/id/eprint/5296This item is in the repository with the URL: http://cogprints.org/id/eprint/52962006-12-12ZCultural evolution developing its own rules: The rise of conservatism and persuasion
In the human sciences, cultural evolution is often viewed as an autonomous process free of genetic influence. A question that follows is, If culture is not influenced by genes, can it take any path? Employing a simple mathematical model of cultural transmission in which individuals may copy each other's traits, we show that cultural evolution favors individuals who are weakly influenced by others and able to influence others. The model suggests that the cultural evolution of rules of cultural transmission tends to create populations that evolve rapidly toward conservatism, and that bias in cultural transmission may result purely from cultural dynamics. Freedom from genetic influence is not freedom to take any direction.
Stefano GhirlandaMagnus EnquistMayuko Nakamaru2006-09-08Z2011-03-11T08:56:35Zhttp://cogprints.org/id/eprint/5129This item is in the repository with the URL: http://cogprints.org/id/eprint/51292006-09-08ZMetastability, Criticality and Phase Transitions in brain and its ModelsThis essay extends the previously deposited paper "Oscillations, Metastability and Phase Transitions" to incorporate the theory of Self-organizing Criticality. The twin concepts of Scaling and Universality of the theory of nonequilibrium phase transitions is applied to the role of reentrant activity in neural circuits of cerebral cortex and subcortical neural structures.MD Gerhard Werner2006-05-25Z2011-03-11T08:56:24Zhttp://cogprints.org/id/eprint/4873This item is in the repository with the URL: http://cogprints.org/id/eprint/48732006-05-25ZOscillations, metastability and phase transitions in brain and models of cognition Neuroscience is being practiced in many different forms and at many different organizational levels of the Nervous System. Which of these levels and associated conceptual frameworks is most informative for elucidating the association of neural processes with processes of Cognition is an empirical question and subject to pragmatic validation. In this essay, I select the framework of Dynamic System Theory. Several investigators have applied in recent years tools and concepts of this theory to interpretation of observational data, and for designing neuronal models of cognitive functions. I will first trace the essentials of conceptual development and hypotheses separately for discerning observational tests and criteria for functional realism and conceptual plausibility of the alternatives they offer. I will then show that the statistical mechanics of phase transitions in brain activity, and some of its models, provides a new and possibly revealing perspective on brain events in cognition.
MD Gerhard Werner2007-06-07Z2011-03-11T08:56:51Zhttp://cogprints.org/id/eprint/5583This item is in the repository with the URL: http://cogprints.org/id/eprint/55832007-06-07ZSelf-other organization: Why early life did not evolve through natural selectionThe improbability of a spontaneously generated self-assembling molecule has suggested that life began with a set of simpler, collectively replicating elements, such as an enclosed autocatalytic set of polymers (or protocell). Since replication occurs without a self-assembly code, acquired characteristics are inherited. Moreover, there is no strict distinction between alive and dead; one can only infer that a protocell was alive if it replicates. These features of early life render natural selection inapplicable to the description of its change-of-state because they defy its underlying assumptions. Moreover, natural selection describes only randomly generated novelty; it cannot describe the emergence of form at the interface between organism and environment. Self-organization is also inadequate because it is restricted to interactions amongst parts; it too cannot account for context-driven change. A modified version of selection theory or self-organization would not work because the description of change-of-state through interaction with an incompletely specified context has a completely different mathematical structure, i.e. entails a non-Kolmogorovian probability model. It is proposed that the evolution of early life is appropriately described as lineage transformation through context-driven actualization of potential (CAP), with self-organized change-of-state being a special case of no contextual influence, and competitive exclusion of less fit individuals through a selection-like process possibly (but not necessarily) playing a secondary role. It is argued that natural selection played an important role in evolution only after genetically mediated replication was established.
Dr. Liane M. Gabora2006-11-07Z2011-03-11T08:56:42Zhttp://cogprints.org/id/eprint/5251This item is in the repository with the URL: http://cogprints.org/id/eprint/52512006-11-07ZSymbols are not uniquely humanModern semiotics is a branch of logics that formally defines symbol-based communication. In recent years, the semiotic classification of signs has been invoked to support the notion that symbols are uniquely human. Here we show that alarm-calls such as those used by African vervet monkeys (Cercopithecus aethiops), logically satisfy the semiotic definition of symbol. We also show that the acquisition of vocal symbols in vervet monkeys can be successfully simulated by a computer program based on minimal semiotic and neurobiological constraints. The simulations indicate that learning depends on the tutor-predator ratio, and that apprentice-generated auditory mistakes in vocal symbol interpretation have little effect on the learning rates of apprentices (up to 80% of mistakes are tolerated). In contrast, just 10% of apprentice-generated visual mistakes in predator identification will prevent any vocal symbol to be correctly associated with a predator call in a stable manner. Tutor unreliability was also deleterious to vocal symbol learning: a mere 5% of “lying” tutors were able to completely disrupt symbol learning, invariably leading to the acquisition of incorrect associations by apprentices. Our investigation corroborates the existence of vocal symbols in a non-human species, and indicates that symbolic competence emerges spontaneously from classical associative learning mechanisms when the conditioned stimuli are self-generated, arbitrary and socially efficacious. We propose that more exclusive properties of human language, such as syntax, may derive from the evolution of higher-order domains for neural association, more removed from both the sensory input and the motor output, able to support the gradual complexification of grammatical categories into syntax.Sidarta RibeiroAngelo LoulaIvan AraújoRicardo GudwinJoao Queiroz2005-07-06Z2011-03-11T08:56:07Zhttp://cogprints.org/id/eprint/4432This item is in the repository with the URL: http://cogprints.org/id/eprint/44322005-07-06ZSingle-Neuron Theory of Consciousness By most accounts, the mind arises from the integrated activity of large populations of neurons distributed across multiple brain regions. A contrasting model is presented in the present paper that places the mind/brain interface not at the whole brain level but at the level of single neurons. Specifically, it is proposed that each neuron in the nervous system is independently conscious, with conscious content corresponding to the spatial pattern of a portion of that neuron's dendritic electrical activity. For most neurons, such as those in the hypothalamus or posterior sensory cortices, the conscious activity would be assumed to be simple and unable to directly affect the organism's macroscopic conscious behavior. For a subpopulation of layer 5 pyramidal neurons in the lateral prefrontal cortices, however, an arrangement is proposed to be present such that, at any given moment: i) the spatial pattern of electrical activity in a portion of the dendritic tree of each neuron in the subpopulation individually manifests a complexity and diversity sufficient to account for the complexity and diversity of conscious experience; ii) the dendritic trees of the neurons in the subpopulation all contain similar spatial electrical patterns; iii) the spatial electrical pattern in the dendritic tree of each neuron interacts nonlinearly with the remaining ambient dendritic electrical activity to determine the neuron's overall axonal response; iv) the dendritic spatial pattern is reexpressed at the population level by the spatial pattern exhibited by a synchronously firing subgroup of the conscious neurons, thereby providing a mechanism by which conscious activity at the neuronal level can influence overall behavior. The resulting scheme is one in which conscious behavior appears to be the product of a single macroscopic mind, but is actually the integrated output of a chorus of minds, each associated with a different neuron.Steven Sevush2005-02-26Z2011-03-11T08:55:51Zhttp://cogprints.org/id/eprint/4110This item is in the repository with the URL: http://cogprints.org/id/eprint/41102005-02-26ZSelf-Replicating Strands that Self-Assemble into User-Specified MeshesIt has been argued that a central objective of nanotechnology is to make
products inexpensively, and that self-replication is an effective approach to
very low-cost manufacturing. The research presented here is intended to be a
step towards this vision. In previous work (JohnnyVon 1.0), we simulated
machines that bonded together to form self-replicating strands. There were two
types of machines (called types 0 and 1), which enabled strands to encode
arbitrary bit strings. However, the information encoded in the strands had no
functional role in the simulation. The information was replicated without being
interpreted, which was a significant limitation for potential manufacturing
applications. In the current work (JohnnyVon 2.0), the information in a strand
is interpreted as instructions for assembling a polygonal mesh. There are now
four types of machines and the information encoded in a strand determines how
it folds. A strand may be in an unfolded state, in which the bonds are straight
(although they flex slightly due to virtual forces acting on the machines), or
in a folded state, in which the bond angles depend on the types of machines. By
choosing the sequence of machine types in a strand, the user can specify a
variety of polygonal shapes. A simulation typically begins with an initial
unfolded seed strand in a soup of unbonded machines. The seed strand replicates
by bonding with free machines in the soup. The child strands fold into the
encoded polygonal shape, and then the polygons drift together and bond to form
a mesh. We demonstrate that a variety of polygonal meshes can be manufactured
in the simulation, by simply changing the sequence of machine types in the
seed.Robert EwaschukPeter Turney21752005-12-19Z2011-03-11T08:56:14Zhttp://cogprints.org/id/eprint/4647This item is in the repository with the URL: http://cogprints.org/id/eprint/46472005-12-19ZCreative thought as a non-Darwinian evolutionary processSelection theory requires multiple, distinct, simultaneously-actualized states. In cognition, each thought or cognitive state changes the 'selection pressure' against which the next is evaluated; they are not simultaneously selected amongst. Creative thought is more a matter of honing in a vague idea through redescribing successive iterations of it from different real or imagined perspectives; in other words, actualizing potential through exposure to different contexts. It has been proven that the mathematical description of contextual change of state introduces a non-Kolmogorovian probability distribution, and a classical formalism such as selection theory cannot be used. This paper argues that creative thought evolves not through a Darwinian process, but a process of context-driven actualization of potential.Dr. Liane M. Gabora2006-05-25Z2011-03-11T08:56:24Zhttp://cogprints.org/id/eprint/4876This item is in the repository with the URL: http://cogprints.org/id/eprint/48762006-05-25ZDifferent Neurons Population Distribution correlates with Topologic-Temporal Dynamic Acoustic Information FlowIt is reported a great variety of functional actions of GABA in auditory system. Although many studies reports the presence and distribution of GABA receptors; nevertheless, the studies about the inhibitory GABA-dependent neurons distribution in the Inferior Culliculus are scarce. We are interested in studies on the role played by GABAergic neurons in the acoustic information transmission in the Central Nucleus of Inferior Culliculus. The existence and distribution of GABAergic neurons in CNIC, could give us understandings on how the inhibitory actions of neurotransmitters are participating in ways which the information flow is spatial-temporal associated with the firing synchrony in each isofrequency region. And with these results, we could achieve some insights over the emergence of certain mind properties from neurons dynamic interactions.Walter RiofriocoldriverLuis Angel Aguilar2005-02-22Z2011-03-11T08:55:51Zhttp://cogprints.org/id/eprint/4107This item is in the repository with the URL: http://cogprints.org/id/eprint/41072005-02-22ZThe Self-Organization of Speech SoundsThe speech code is a vehicle of language: it defines
a set of forms used by a community to carry information.
Such a code is necessary to support the linguistic
interactions that allow humans to communicate.
How then may a speech code be formed prior to the
existence of linguistic interactions?
Moreover, the human speech code is discrete and compositional,
shared by all the individuals of a community but different
across communities, and phoneme inventories are characterized by
statistical regularities. How can a speech code with these properties form?
We try to approach these questions in the paper,
using the ``methodology of the artificial''. We
build a society of artificial agents, and detail a mechanism that
shows the formation of a discrete speech code without pre-supposing
the existence of linguistic capacities or of coordinated interactions.
The mechanism is based on a low-level model of
sensory-motor interactions. We show that the integration of certain very
simple and non language-specific neural devices
leads to the formation of a speech code that
has properties similar to the human speech code.
This result relies on the self-organizing properties of a generic
coupling between perception and production
within agents, and on the interactions between agents.
The artificial system helps us to develop better intuitions on how speech
might have appeared, by showing how self-organization
might have helped natural selection to find speech.
Pierre-Yves Oudeyer2004-11-06Z2011-03-11T08:55:43Zhttp://cogprints.org/id/eprint/3915This item is in the repository with the URL: http://cogprints.org/id/eprint/39152004-11-06ZFour basic symmetry types in the universal 7-cluster
structure of 143 complete bacterial genomic sequencesCoding information is the main source of heterogeneity
(non-randomness) in the sequences of bacterial genomes. This
information can be naturally modeled by analysing cluster structures in the ``in-phase'' triplet distributions of relatively short genomic fragments (200-400bp). We found a universal 7-cluster structure in all 143 completely sequenced bacterial genomes available in Genbank in August 2004, and explained its properties.
The 7-cluster structure is responsible for the main part of sequence heterogeneity in bacterial genomes. In this sense, our 7 clusters is the basic model of bacterial genome sequence. We demonstrated that there are four basic ``pure'' types of this model, observed in nature: ``parallel triangles'', ``perpendicular triangles'',
degenerated case and the flower-like type. We show that codon usage of bacterial genomes is a multi-linear function of their genomic G+C-content with high accuracy (more precisely, by two similar functions, one for eubacterial genomes and the other one for archaea).
All 143 cluster animated 3D-scatters are collected in a database and is made available on our web-site:
http://www.ihes.fr/~zinovyev/7clusters
The finding can be readily introduced into any software for gene prediction, sequence alignment or bacterial genomes classification.
A.N. GorbanT.G. PopovaA.Yu. Zinovyev2004-10-22Z2011-03-11T08:55:42Zhttp://cogprints.org/id/eprint/3891This item is in the repository with the URL: http://cogprints.org/id/eprint/38912004-10-22ZSingle-Neuron Theory of ConsciousnessA theory is outlined that shifts the presumed locus of mind/brain interaction from the whole brain level to that of single neurons. Neuroanatomical and neurophysiological evidence is offered in support of the existence of single neurons that may individually receive dendritic input of sufficient complexity and diversity to account for the full content of conscious experience, and of an arrangement in which the output of multiple such neurons summate to achieve amplification of the individually emitted messages. An ultramicroscopic extension of the theory is suggested as a way of moving forward on the philosophically difficult aspects of the mind/brain problem.Steven Sevush2004-11-06Z2011-03-11T08:55:43Zhttp://cogprints.org/id/eprint/3926This item is in the repository with the URL: http://cogprints.org/id/eprint/39262004-11-06ZWhat about physiology?This is an essay which tries to locate physiology among other disciplines studying life and its place in the world.Andres Soosaar2009-06-16T19:27:26Z2011-03-11T08:57:22Zhttp://cogprints.org/id/eprint/6456This item is in the repository with the URL: http://cogprints.org/id/eprint/64562009-06-16T19:27:26ZCortex, countercurrent context, and dimensional integration of lifetime memoryThe correlation between relative neocortex size and longevity in mammals encourages a search for a cortical function specifically related to the life-span. A candidate in the domain of permanent and cumulative memory storage is proposed and explored in relation to basic aspects of cortical organization. The pattern of cortico-cortical connectivity between functionally specialized areas and the laminar organization of that connectivity converges on a globally coherent representational space in which contextual embedding of information emerges as an obligatory feature of cortical function. This brings a powerful mode of inductive knowledge within reach of mammalian adaptations, a mode which combines item specificity with classificatory generality. Its neural implementation is proposed to depend on an obligatory interaction between the oppositely directed feedforward and feedback currents of cortical activity, in countercurrent fashion. Direct interaction of the two streams along their cortex-wide local interface supports a scheme of "contextual capture" for information storage responsible for the lifelong cumulative growth of a uniquely cortical form of memory termed "personal history." This approach to cortical function helps elucidate key features of cortical organization as well as cognitive aspects of mammalian life history strategies.Dr. Bjorn Merkergyr694c@tninet.se2005-02-26Z2011-03-11T08:55:51Zhttp://cogprints.org/id/eprint/4109This item is in the repository with the URL: http://cogprints.org/id/eprint/41092005-02-26ZTowards a Model of Life and CognitionWhat should be the ontology of the world such that life and cognition are possible? In this essay, I undertake to outline an alternative ontological foundation which makes biological and cognitive phenomena possible. The foundation is built by defining a model, which is presented in the form of a description of a hypothetical but a logically possible world with a defined ontological base.
Biology rests today on quite a few not so well connected foundations: molecular biology based on the genetic dogma; evolutionary biology based on neo-Darwinian model; ecology based on systems view; developmental biology by morphogenetic models; connectionist models for neurophysiology and cognitive biology; pervasive teleonomic
explanations for the goal-directed behavior across the discipline; etc. Can there be an underlying connecting theme or a model which could make these seemingly disparate domains interconnected? I shall atempt to answer this question.
By following the semantic view of scientific theories, I tend to believe that the models employed by the present physical sciences are not rich enough to capture biological (and some of the non-biological) systems. A richer theory that could capture biological reality could also capture physical and chemical phenomena as limiting cases, but
not vice versa.Nagarjuna G.Nagarjuna G.2006-05-30Z2011-03-11T08:56:26Zhttp://cogprints.org/id/eprint/4895This item is in the repository with the URL: http://cogprints.org/id/eprint/48952006-05-30ZTowards a Model of Life and CognitionThis essay argues for an alternative scientific foundation for accounting complex phenomena like life, cognition and evolution. The approach taken to the problem is neither reductionism, not emergentism (holism), but a third alternative called assimilationism. The analysis based on the alternative foundation indicated some counter intuitive implications like: chemical reactions can happen independent of heat under idealized conditions; all systems, including non-living, counteract perturbations to exist; non-living systems are more open than the living.
Outline: There are abundant building blocks that are systems but not atoms, which perturb each other. The building blocks are heterogenous (have different functional interfaces). There are mainly two kinds interactions: identity preserving (IP) and identity transforming (IT) interactions. Given only IP interactions the system would reach high entropy --- first tendency. Given only IT interactions the system would reach a crystalline state --- second tendency. The actual world is a function of these two tendencies. All beings (living as well as non-living) are open, and their adaptation in an environment is an expression of their invertibility of the two tendencies. Living beings are part of a special dialogically invertible space made by amphipathic agents like water molecules on the one hand and agents with multiple interfaces like biomolecules with possibilities of interacting among their own functional interfaces on the other. This space makes possible for a dialogical opposition of the two tendencies: distribution and collection of energy. Thus, living being is described to be a neither-nor-state, between the two extremes. The characteristic of this space is to maintain the state by replacement, reproduction, recycling or feedback. The abundance of little loops produce highly efficient work cycles, minimizing external energy dependence. A self-reproducing network of such beings manages to engulf a process and a counter process within the network of a being, to counteract the two `deadly' tendencies. A living being is capable of displaying behavioral changes without undergoing change in identity. Thus, living beings are interpreted to be more closed than non-living, for they can neither resist nor repair interactions. And this logic continues to operate recursively to explain physiology, epigenesis, evolution, adaptation, complexity, autonomy and cognition.
The initial cognitive base of a living being is rooted in the invertibility of the perturbations from the environment. It is hypothesized that this repairing process itself becomes the difference, and the processes that are induced in turn within the system generate a differentiation of difference, which is defined as knowledge. However, this knowledge is implicit, and cannot account for conscious cognition, which is explicit.
Nagarjuna G.Nagarjuna G.2004-07-06Z2011-03-11T08:55:38Zhttp://cogprints.org/id/eprint/3703This item is in the repository with the URL: http://cogprints.org/id/eprint/37032004-07-06ZComplex Systems Analysis of Arrested Neural Cell Differentiation during Development and Analogous Cell Cycling Models in Carcinogenesis
A new approach to the modular, complex systems analysis of nonlinear dynamics of arrested neural cell Differentiation--induced cell proliferation during organismic development and the analogous cell cycling network transformations involved in carcinogenesis is proposed. Neural tissue arrested differentiation that induces cell proliferation during perturbed development and Carcinogenesis are complex processes that involve dynamically inter-connected biomolecules in the intercellular, membrane, cytosolic, nuclear and nucleolar compartments. Such 'dynamically inter-connected' biomolecules form numerous inter-related pathways referred to as 'molecular networks'. One such family of signaling pathways contains the cell cyclins. Cyclins are proteins that link several critical pro-apoptotic and other cell cycling/division components, including the tumor suppressor gene TP53 and its product, the Thomsen-Friedenreich antigen (T antigen), Rb, mdm2, c-Myc, p21, p27, Bax, Bad and Bcl-2, which play major roles in various neoplastic transformations of many tissues. The novel theoretical analysis presented here is based on recently published studies of arrested cell differentiation that normally leads to neural system formation during early developmental stages; the perturbed development may involve cyclin signaling and cell cycling responsible for rapidly induced cell proliferation without differentiation into neural cells in such experimental studies; special emphasis in this modular model is placed upon the roles of cyclins D1 and E, and does suggest novel clinical trials as well as rational therapies of cancer through re-establishment of cell cycling inhibition in metastatic cancer cells. Cyclins are proteins that are often over-expressed in cancerous cells (Dobashi et al., 2004). They may also be over-expressed in cells whose differentiation is arrested during the early stages of organismic development, leading to increased cell proliferation instead of differentiation into specialized tissues such as those forming the neural system. Cyclin-dependent kinases (CDK), their respective cyclins, and inhibitors of CDKs (CKIs) were identified as instrumental components of the cell cycle-regulating machinery. In mammalian cells the complexes of cyclins D1, D2, D3, A and E with CDKs are considered motors that drive cells to enter and pass through the “S” phase. Cell cycle regulation is a critical mechanism governing cell division and proliferation, and it is finely regulated by the interaction of cyclins with CDKs and CKIs, among other molecules (Morgan et al., 1995). A categorical and Topos framework for Łukasiewicz Algebraic Logic models of nonlinear dynamics in complex functional genomes and cell interactomes is also proposed. Łukasiewicz Algebraic Logic models of genetic networks and signaling pathways in cells are formulated in terms of nonlinear 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 varying 'next-state' functions is extended in a Łukasiewicz-Topos with an n-valued Łukasiewicz Algebraic Logic subobject classifier description that represents non-random and nonlinear network activities as well as their transformations in developmental processes and carcinogenesis.
Important aspects of Cell Cycling, the Control of Cell Division,and the Neoplastic Transformation in Carcinogenesis are being considered and subjected to algebraic-logico- relational, and computer-aided investigations. The essential roles of various levels of
c-Myc, p27 quasi-complete inhibition/blocking, TP53 and/or p53 inactivation, as well as the perpetual hTERT activation of Telomerase biosynthesis are pointed out as key conditions for Malignant Cell transformations and partial re-differentiation leading to various types of cancer such as lung, breast,skin, prostate and colon. Rational Clinical trials, Individualized Medicine and the potential for optimized Radio-, Chemo-, Gene-, and Immuno- therapies of Cancers are suggested on the basis of integrated complex systems biology modeling of oncogenesis, coupled with extensive genomic/proteomic and interactomic High-throughput/high-sensitivity measurements of identified, sorted cell lines that are being isolated from malignant tumors of patients undergoing clinical trials with adjuvant signaling drug therapies. The implications of the cyclin model for abnormal neural development during early development are being considered in this model that may lead to explanations of subsequent cognitive changes associated with abnormal neural cell differentiation in environmentally-affected embryos. This new model may also be relevant to detecting the onset of senescing neuron transformations in Alzheimer's and related diseases of the human brain in ageing populations at risk.
Professor I.C. Baianuicb1M.S. V Prisecaru2004-07-06Z2011-03-11T08:55:37Zhttp://cogprints.org/id/eprint/3697This item is in the repository with the URL: http://cogprints.org/id/eprint/36972004-07-06ZQuantum Genetics in terms of Quantum Reversible Automata and
Quantum Computation of Genetic Codes and Reverse Transcription
The concepts of quantum automata and quantum computation are studied in the context of quantum genetics and genetic networks with nonlinear dynamics. In previous publications (Baianu,1971a, b) the formal concept of quantum automaton and quantum computation, respectively, were introduced and their possible implications for genetic processes and metabolic activities in living cells and organisms were considered. This was followed by a report on quantum and abstract, symbolic computation based on the theory of categories, functors and natural transformations (Baianu,1971b; 1977; 1987; 2004; Baianu et al, 2004). The notions of topological semigroup, quantum automaton, or quantum computer, were then suggested with a view to their potential applications to the analogous simulation of biological systems, and especially genetic activities and nonlinear dynamics in genetic networks. Further, detailed studies of nonlinear dynamics in genetic networks were carried out in categories of n-valued, Łukasiewicz Logic Algebras that showed significant dissimilarities (Baianu, 1977; 2004a; Baianu et al, 2004b) from Boolean models of human neural networks (McCullough and Pitts, 1943). Molecular models in terms of categories, functors and natural transformations were then formulated for uni-molecular chemical transformations, multi-molecular chemical and biochemical transformations (Baianu, 1983, 1987, 2004a). Previous applications of computer modeling, classical automata theory, and relational biology to molecular biology, oncogenesis and medicine were extensively reviewed and several important conclusions were reached regarding both the potential and limitations of the computation-assisted modeling of biological systems, and especially complex organisms such as Homo sapiens sapiens (Baianu,1987). Novel approaches to solving the realization problems of Relational Biology models in Complex System Biology are introduced in terms of natural transformations between functors of such molecular categories. Several applications of such natural transformations of functors were then presented to protein biosynthesis, embryogenesis and nuclear transplant experiments. Topoi of Łukasiewicz Logic Algebras and Intuitionistic Logic (Heyting) Algebras are being considered for modeling nonlinear dynamics and cognitive processes in complex neural networks that are present in the human brain, as well as stochastic modeling of genetic networks in Łukasiewicz Logic Algebras.
Professor I.C. Baianuicb12004-07-06Z2011-03-11T08:55:37Zhttp://cogprints.org/id/eprint/3701This item is in the repository with the URL: http://cogprints.org/id/eprint/37012004-07-06ZŁukasiewicz-Topos Models of Neural Networks, Cell Genome and Interactome Nonlinear Dynamic Models
A categorical and Łukasiewicz-Topos framework for Algebraic Logic models of nonlinear dynamics in complex functional systems such as Neural Networks, Cell Genome and Interactome Networks is introduced. Łukasiewicz Algebraic Logic models of both neural and genetic networks and signaling pathways in cells are formulated in terms of nonlinear 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 Topos with an n-valued Łukasiewicz Algebraic Logic subobject classifier description that represents non-random and nonlinear network activities as well as their transformations in developmental processes and carcinogenesis.
Professor I.C. Baianuicb12006-12-08Z2011-03-11T08:56:43Zhttp://cogprints.org/id/eprint/5283This item is in the repository with the URL: http://cogprints.org/id/eprint/52832006-12-08ZBrain-Sign or The End of ConsciousnessThere is no question that something goes on in the head, which has been called consciousness. But is it consciousness? Over the last fifty years, there has been a concerted attempt to show how consciousness can be physical, of the brain. The diversity of views is characteristic of a Kuhnian pre- normal science revolution: but the revolution has not arrived. This is because the assumption that consciousness exists is wrong. In this paper consciousness (with e.g. its subjective/objective distinction) is characterized as a pre-scientific theory. The biological ontology of the phenomenon is revealed, and its placement in organismic biology explained. The phenomenon will be termed brain-sign, as appropriate to its biological function. The nature of this function completely reconstructs our view of ourselves, and other creatures in which it is manifest. The detail and ramifications cannot be addressed at length in a paper, but a research program is outlined briefly. Philip Clapson2004-07-06Z2011-03-11T08:55:37Zhttp://cogprints.org/id/eprint/3676This item is in the repository with the URL: http://cogprints.org/id/eprint/36762004-07-06ZQuantum Genetics, Quantum Automata and Quantum Computation
The concepts of quantum automata and quantum computation are studied in the context of quantum genetics and genetic networks with nonlinear dynamics. In a previous publication (Baianu,1971a) the formal concept of quantum automaton was introduced and its possible implications for genetic and metabolic activities in living cells and organisms were considered. This was followed by a report on quantum and abstract, symbolic computation based on the theory of categories, functors and natural transformations (Baianu,1971b). The notions of topological semigroup, quantum automaton,or quantum computer, were then suggested with a view to their potential applications to the analogous simulation of biological systems, and especially genetic activities and nonlinear dynamics in genetic networks. Further, detailed studies of nonlinear dynamics in genetic networks were carried out in categories of n-valued, Lukasiewicz Logic Algebras that showed significant dissimilarities (Baianu, 1977) from Bolean models of human neural networks (McCullough and Pitts,1945). Molecular models in terms of categories, functors and natural transformations were then formulated for uni-molecular chemical transformations, multi-molecular chemical and biochemical transformations (Baianu, 1983,2004a). Previous applications of computer modeling, classical automata theory, and relational biology to molecular biology, oncogenesis and medicine were extensively reviewed and several important conclusions were reached regarding both the potential and limitations of the computation-assisted modeling of biological systems, and especially complex organisms such as Homo sapiens sapiens(Baianu,1987). Novel approaches to solving the realization problems of Relational Biology models in Complex System Biology are introduced in terms of natural transformations between functors of such molecular categories. Several applications of such natural transformations of functors were then presented to protein biosynthesis, embryogenesis and nuclear transplant experiments. Other possible realizations in Molecular Biology and Relational Biology of Organisms are here suggested in terms of quantum automata models of Quantum Genetics and Interactomics. Future developments of this novel approach are likely to also include: Fuzzy Relations in Biology and Epigenomics, Relational Biology modeling of Complex Immunological and Hormonal regulatory systems, n-categories and Topoi of Lukasiewicz Logic Algebras and Intuitionistic Logic (Heyting) Algebras for modeling nonlinear dynamics and cognitive processes in complex neural networks that are present in the human brain, as well as stochastic modeling of genetic networks in Lukasiewicz Logic Algebras.
Professor I. C. Baianuicb2004-02-03Z2011-03-11T08:55:28Zhttp://cogprints.org/id/eprint/3418This item is in the repository with the URL: http://cogprints.org/id/eprint/34182004-02-03ZIdeas are not replicators but minds areAn idea is not a replicator because it does not consist of coded self-assembly instructions. It may retain structure as it passes from one individual to another, but does not replicate it. The cultural replicator is not an idea but an associatively-structured network of them that together form an internal model of the world, or worldview. A worldview is a primitive, uncoded replicator, like the autocatalytic sets of polymers widely believed to be the earliest form of life. Primitive replicators generate self-similar structure, but because the process happens in a piecemeal manner, through bottom-up interactions rather than a top-down code, they replicate with low fidelity, and acquired characteristics are inherited. Just as polymers catalyze reactions that generate other polymers, the retrieval of an item from memory can in turn trigger other items, thus cross-linking memories, ideas, and concepts into an integrated conceptual structure. Worldviews evolve idea by idea, largely through social exchange. An idea participates in the evolution of culture by revealing certain aspects of the worldview that generated it, thereby affecting the worldviews of those exposed to it. If an idea influences seemingly unrelated fields this does not mean that separate cultural lineages are contaminating one another, because it is worldviews, not ideas, that are the basic unit of cultural evolution.Dr. Liane Gabora2004-04-07Z2011-03-11T08:55:30Zhttp://cogprints.org/id/eprint/3535This item is in the repository with the URL: http://cogprints.org/id/eprint/35352004-04-07ZTopology of large-scale engineering problem-solving networksThe last few years have led to a series of discoveries that uncovered statistical properties that are common
to a variety of diverse real-world social, information, biological, and technological networks. The goal of the
present paper is to investigate the statistical properties of networks of people engaged in distributed problem
solving and discuss their significance. We show that problem-solving networks have properties ~sparseness,
small world, scaling regimes! that are like those displayed by information, biological, and technological
networks. More importantly, we demonstrate a previously unreported difference between the distribution of
incoming and outgoing links of directed networks. Specifically, the incoming link distributions have sharp
cutoffs that are substantially lower than those of the outgoing link distributions ~sometimes the outgoing
cutoffs are not even present!. This asymmetry can be explained by considering the dynamical interactions that
take place in distributed problem solving and may be related to differences between each actor’s capacity to
process information provided by others and the actor’s capacity to transmit information over the network. We
conjecture that the asymmetric link distribution is likely to hold for other human or nonhuman directed
networks when nodes represent information processing and using elements.Dan BrahaYaneer Bar-Yam2011-05-02T17:19:18Z2011-05-02T17:19:18Zhttp://cogprints.org/id/eprint/7243This item is in the repository with the URL: http://cogprints.org/id/eprint/72432011-05-02T17:19:18ZAutism, Early Narcissistic Injury, and Self Organization: a Role for the Image of the Mother's Eyes?Holland has elucidated the new paradigm of self-organization in complex adaptive systems. This paradigm holds for all living systems, including the personality. In conjunction with the theory of archetypes, self-organization suggests two radical hypotheses, one about early development, the other about the origins of autism. Autism is associated with several medical conditions, with genetic markers, and with infant visual deprivation. None of these factors, however, is either necessary or sufficient to cause autism. It is proposed that each of these factors increases the probability of a primary psychological deficit: failure in the first few weeks to acquire (or retain) the image of the mother’s eyes. These hypotheses were derived from analytic work with patients who have early narcissistic injury and with patients who have mild autistic traits. Both diagnoses may arise from the same initial disturbance: Symington and others have argued that autism is an extreme form of infantile narcissism. Indirect evidence for the image-of-the-eyes hypotheses comes from the evolution of primates, from infant-mother observations, from observations of infant vision, and from experiments on vision in other vertebrates. Byrd recently confirmed that the incidence of autism is increasing dramatically. The image-of-the-eyes hypotheses suggest that this increase may be due to the increased use, in early infancy, of non-maternal childcare including television and video. The search for environmental triggers for autism must be interdisciplinary. This paper makes a timely contribution to that search. Dr Maxson McDowellmaxmcdowell@jungny.com2005-03-27Z2011-03-11T08:55:52Zhttp://cogprints.org/id/eprint/4140This item is in the repository with the URL: http://cogprints.org/id/eprint/41402005-03-27ZComplex-Dynamical Extension of the Fractal Paradigm and Its Applications in Life SciencesComplex-dynamical fractal is a hierarchy of permanently, chaotically changing versions of system structure, obtained as the unreduced, causally probabilistic general solution of arbitrary interaction problem (physics/0305119, physics/9806002). Intrinsic creativity of this extension of usual fractality determines its exponentially high operation efficiency, which underlies many specific functions of living systems, such as autonomous adaptability, "purposeful" development, intelligence and consciousness (at higher complexity levels). We outline in more detail genetic applications of complex-dynamic fractality, demonstrate the dominating role of genome interactions, and show that further progressive development of genetic research, as well as other life-science applications, should be based on the dynamically fractal structure analysis of interaction processes involved. The obtained complex-dynamical fractal of a living organism specifies the intrinsic unification of its interaction dynamics at all levels, from genome structure to higher brain functions. We finally summarise the obtained extension of mathematical concepts and approaches closely related to their biological applications.Andrei Kirilyuk2005-09-08Z2011-03-11T08:56:10Zhttp://cogprints.org/id/eprint/4527This item is in the repository with the URL: http://cogprints.org/id/eprint/45272005-09-08ZComplex-Dynamical Extension of the Fractal Paradigm and Its Applications in Life SciencesComplex-dynamical fractal is a hierarchy of permanently, chaotically changing versions of system structure, obtained as the unreduced, causally probabilistic general solution of arbitrary interaction problem (physics/0305119, physics/9806002). Intrinsic creativity of this extension of usual fractality determines its exponentially high operation efficiency, which underlies many specific functions of living systems, such as autonomous adaptability, "purposeful" development, intelligence and consciousness (at higher complexity levels). We outline in more detail genetic applications of complex-dynamic fractality, demonstrate the dominating role of genome interactions, and show that further progressive development of genetic research, as well as other life-science applications, should be based on the dynamically fractal structure analysis of interaction processes involved. The obtained complex-dynamical fractal of a living organism specifies the intrinsic unification of its interaction dynamics at all levels, from genome structure to higher brain functions. We finally summarise the obtained extension of mathematical concepts and approaches closely related to their biological applications.Andrei Kirilyuk2006-12-12Z2011-03-11T08:56:44Zhttp://cogprints.org/id/eprint/5299This item is in the repository with the URL: http://cogprints.org/id/eprint/52992006-12-12ZThe evolution of brain lateralization: A game theoretical analysis of population structure
In recent years, it has become apparent that behavioural and brain lateralization is the rule rather than the exception among vertebrates. The study of lateralization has been so far the province of neurology and neuropsychology. We show how such research can be integrated with evolutionary biology to more fully understand lateralization. In particular, we address
the fact that, within a species, left- and right-type individuals are often in a definite proportion different from 1/2 (e.g., hand use in humans). We argue that traditional explanations of brain lateralization (that it may avoid costly duplication of neural circuitry and reduce interference between functions) cannot account for this fact, because increased individual efficiency is unre-
lated to the frequency of left- and right-type individuals in a population. A further puzzle is that, if a majority of individuals are of the same type, individual behaviour becomes more predictable to other organisms. Here we
show that alignment of the direction of behavioural asymmetries in a population can arise as an evolutionarily stable strategy (ESS), when individually asymmetrical organisms must coordinate their behaviour with that of other
asymmetrical organisms. Thus, brain and behavioural lateralization, as we know it in humans and other vertebrates, may have evolved under basically
"social" selection pressures.
Stefano GhirlandaGiorgio Vallortigara2008-04-27T16:19:28Z2011-03-11T08:57:06Zhttp://cogprints.org/id/eprint/6012This item is in the repository with the URL: http://cogprints.org/id/eprint/60122008-04-27T16:19:28ZSpin-Mediated Consciousness Theory: Possible Roles of Neural Membrane Nuclear Spin Ensembles and Paramagnetic OxygenA novel theory of consciousness is proposed in this paper. We postulate that consciousness is intrinsically connected to quantum spin since the latter is the origin of quantum effects in both Bohm and Hestenes quantum formulism and a fundamental quantum process associated with the structure of space-time. That is, spin is the “mind-pixel.” The unity of mind is achieved by entanglement of the mind-pixels. Applying these ideas to the particular structures and dynamics of the brain, we theorize that human brain works as follows: Through action potential modulated nuclear spin interactions and paramagnetic O2/NO driven activations, the nuclear spins inside neural membranes and proteins form various entangled quantum states some of which survive decoherence through quantum Zeno effects or in decoherence-free subspaces and then collapse contextually via irreversible and non-computable means producing consciousness and, in turn, the collective spin dynamics associated with said collapses have effects through spin chemistry on classical neural activities thus influencing the neural networks of the brain. Our proposal calls for extension of associative encoding of neural memories to the dynamical structures of neural membranes and proteins. Thus, according our theory, the nuclear spin ensembles are the “mind-screen” with nuclear spins as its pixels, the neural membranes and proteins are the mind-screen and memory matrices, and the biologically available paramagnetic species such as O2 and NO are pixel-activating agents. Together, they form the neural substrates of consciousness. We also present supporting evidence and make important predictions. We stress that our theory is experimentally verifiable with present technologies. Further, experimental realizations of intra-/inter-molecular nuclear spin coherence and entanglement, macroscopic entanglement of spin ensembles and NMR quantum computation, all in room temperatures, strongly suggest the possibility of a spin-mediated mind.Huping Huhupinghu@quantumbrain.orgMaoxin Wu2004-12-30Z2011-03-11T08:55:48Zhttp://cogprints.org/id/eprint/4012This item is in the repository with the URL: http://cogprints.org/id/eprint/40122004-12-30ZWhat is the functional role of adult neurogenesis in the hippocampus? The dentate gyrus is part of the hippocampal memory system and special in
that it generates new neurons throughout life. Here we discuss the
question of what the functional role of these new neurons might be. Our
hypothesis is that they help the dentate gyrus to avoid the problem of
catastrophic interference when adapting to new environments. We assume
that old neurons are rather stable and preserve an optimal encoding
learned for known environments while new neurons are plastic to adapt to
those features that are qualitatively new in a new environment. A simple
network simulation demonstrates that adding new plastic neurons is indeed
a successful strategy for adaptation without catastrophic interference.
Laurenz WiskottMalte J. RaschGerd Kempermann2003-02-06Z2011-03-11T08:55:08Zhttp://cogprints.org/id/eprint/2763This item is in the repository with the URL: http://cogprints.org/id/eprint/27632003-02-06ZChronic infection: punctuated interpenetration and pathogen virulenceWe apply an information dynamics formalism to the Levens and Lewontin vision of biological interpenetration between a 'cognitive condensation' including immune function embedded in social and cultural structure on the one hand, and an established, highly adaptive, parasite population on the other. We iterate the argument, beginning with direct interaction between cognitive condensation and pathogen, then extend the analysis to second order 'mutator' mechanisms inherent both to immune function and to certain forms of rapid pathogen antigenic variability.
The methodology, based on the Large Deviations Program of applied probability, produces synergistic cognitive/adaptive 'learning plateaus' that represent stages of chronic infection, and, for human populations, is able to encompass the fundamental biological reality of culture omitted by other approaches.
We conclude that, for 'evolution machine' pathogens like HIV and malaria, simplistic magic bullet 'medical' drug, vaccine, or behavior modification interventions which do not address the critical context of overall living and working conditions may constitute selection pressures triggering adaptations in life history strategy resulting in marked increase of pathogen virulenceRodrick WallaceNew York State Psychiatric InstituteRobert G. WallaceCity University of New York2003-03-17Z2011-03-11T08:55:14Zhttp://cogprints.org/id/eprint/2836This item is in the repository with the URL: http://cogprints.org/id/eprint/28362003-03-17ZRegulation of Neuromodulator Receptor Efficacy- Implications for Whole-Neuron and Synaptic PlasticityMembrane receptors for neuromodulators (NM) are highly regulated in their distribution and efficacy - a phenomenon which influences the individual cell's response to central signals of NM release.
Even though NM receptor regulation is implicated in the pharmacological action of many drugs, and is also known to be influenced by various environmental factors, its functional consequences and modes of action are not well understood.
In this paper we summarize relevant experimental evidence on NM receptor regulation (specifically dopamine D1 and D2 receptors) in order to explore its significance for neural and synaptic plasticity.
We identify the relevant components of NM receptor regulation (receptor phosphorylation, receptor
trafficking and sensitization of second-messenger pathways)
gained from studies on cultured cells.
Key principles in the regulation and control of short-term plasticity (sensitization) are identified, and a model is presented which employs direct and indirect feedback regulation of receptor efficacy. We also discuss long-term plasticity which involves shifts in receptor sensitivity and loss of responsivity to NM signals.
Finally, we discuss the implications of NM receptor regulation for models
of brain plasticity and memorization.We emphasize that a realistic model of brain plasticity will have to go
beyond Hebbian models of long-term potentiation and depression to include
plasticity in the distribution and efficacy of NM receptors.
Dr. Gabriele Scheler2003-01-03Z2011-03-11T08:55:07Zhttp://cogprints.org/id/eprint/2684This item is in the repository with the URL: http://cogprints.org/id/eprint/26842003-01-03ZSystemic lupus erythematosus in African-American women: immune cognitive modules, autoimmune disease, and pathogenic social hierarchyExamining elevated rates of systemic lupus erythematosus in African-American women from the perspective of the emerging theory of immune cognition suggests the disease constitutes an internalized physiological image of external patterns of psychosocial stress, a 'pathogenic social hierarchy' involving the synergism of racism and gender discrimination. The disorder represents the punctuated resetting of 'normal' immune self-image to a self-attacking 'excited' state, a process formally analogous to models of punctuated equilibrium in evolutionary theory. We speculate that this punctuated onset takes place in the context of an immunological 'cognitive module' similar to what has been proposed by evolutionary psychologists for the human mind. We discuss the broader implications of a high rate of this disorder within a marginalized population, finding it to be a leading indicator for phenomena likely to entrain powerful subgroups into a larger pattern of embedding pathologyRodrick WallaceNew York State Psychiatric Institute2003-01-09Z2011-03-11T08:55:08Zhttp://cogprints.org/id/eprint/2702This item is in the repository with the URL: http://cogprints.org/id/eprint/27022003-01-09ZToward Cultural Oncology: The Evolutionary Information Dynamics of Cancer'Racial' disparities among cancers, particularly of the breast and prostate, are something of a mystery. For the US, in the face of slavery and its sequelae, centuries of interbreeding have greatly leavened genetic differences between 'Blacks' and 'whites', but marked contrasts in disease prevalence and progression persist. 'Adjustment' for socioeconomic status and lifestyle, while statistically accounting for much of the variance in breast cancer, only begs the question of ultimate causality. Here we propose a more basic biological explanation that extends the theory of immune cognition to include elaborate tumor control mechanisms constituting the principal selection pressure acting on pathologically mutating cell clones. The interplay between them occurs in the context of an embedding, highly structured, system of culturally specific psychosocial stress which we find is able to literally write an image of itself onto disease progression. The dynamics are analogous to punctuated equilibrium in simple evolutionary processRodrick WallaceNew York State Psychiatric InstituteDeborah WallaceColumbia UniversityRobert G. WallaceCity University of New York2004-11-29Z2011-03-11T08:55:44Zhttp://cogprints.org/id/eprint/3961This item is in the repository with the URL: http://cogprints.org/id/eprint/39612004-11-29ZApplication of The Method of Elastic Maps In Analysis of Genetic TextsAbstract - Method of elastic maps ( http://cogprints.ecs.soton.ac.uk/archive/00003088/ and
http://cogprints.ecs.soton.ac.uk/archive/00003919/ )
allows us to construct efficiently 1D, 2D and 3D non-linear approximations to the principal manifolds with different topology (piece of plane, sphere, torus etc.) and to project data onto it. We describe the idea of the method and demonstrate its applications in analysis of genetic sequences. The animated 3D-scatters are available on our web-site: http://www.ihes.fr/~zinovyev/7clusters/
We found the universal cluster structure of genetic sequences, and demonstrated the thin structure of these clusters for coding regions. This thin structure is related to different translational efficiency.Alexander N. GorbanAndrey Yu. ZinovyevDonald C. Wunsch2002-09-15Z2011-03-11T08:55:00Zhttp://cogprints.org/id/eprint/2460This item is in the repository with the URL: http://cogprints.org/id/eprint/24602002-09-15ZCan a machine be conscious? How?
A "machine" is any causal physical system, hence we are machines, hence machines can be conscious. The question is: which kinds of machines can be conscious? Chances are that robots that can pass the Turing Test -- completely indistinguishable from us in their behavioral capacities -- can be conscious (i.e. feel), but we can never be sure (because of the "other-minds" problem). And we can never know HOW they have minds, because of the "mind/body" problem. We can only know how they pass the Turing Test, but not how, why or whether that makes them feel.Stevan Harnad632006-12-22Z2015-11-19T23:48:54Zhttp://cogprints.org/id/eprint/5330This item is in the repository with the URL: http://cogprints.org/id/eprint/53302006-12-22ZCan a machine be conscious? How?
A "machine" is any causal physical system, hence we are machines, hence machines can be conscious. The question is: which kinds of machines can be conscious? Chances are that robots that can pass the Turing Test -- completely indistinguishable from us in their behavioral capacities -- can be conscious (i.e. feel), but we can never be sure (because of the "other-minds" problem). And we can never know HOW they have minds, because of the "mind/body" problem. We can only know how they pass the Turing Test, but not how, why or whether that makes them feel.Stevan Harnad632006-12-08Z2011-03-11T08:56:43Zhttp://cogprints.org/id/eprint/5280This item is in the repository with the URL: http://cogprints.org/id/eprint/52802006-12-08ZThe evolution of signal form: Effects of learned versus inherited recognitionOrganisms can learn by individual experience to recognize relevant stimuli
in the environment or they can genetically inherit this ability from their
parents. Here, we ask how these two modes of acquisition affect signal evolution, focusing in particular on the exaggeration and cost of signals. We argue first, that faster learning by individual receivers cannot be a driving force for the evolution of exaggerated and costly signals unless signal senders are related or the same receiver and sender meet repeatedly. We argue instead that biases in receivers’ recognition mechanisms can promote the evolution of costly exaggeration in signals. We provide support for this hypothesis by simulating coevolution between senders and receivers, using artificial neural networks as a model of receivers’ recognition mechanisms. We analyse the joint effects of receiver biases, signal cost and mode of acquisition, investigating the circumstances under which learned recognition gives rise to more exaggerated signals than inherited recognition. We conclude the paper by discussing the relevance of our results to a number of biological scenarios.Masashi KamoStefano GhirlandaMagnus Enquist2003-04-16Z2011-03-11T08:55:15Zhttp://cogprints.org/id/eprint/2888This item is in the repository with the URL: http://cogprints.org/id/eprint/28882003-04-16ZSelf-Replicating Machines in Continuous Space with Virtual PhysicsJohnnyVon is an implementation of self-replicating machines in
continuous two-dimensional space. Two types of particles drift
about in a virtual liquid. The particles are automata with
discrete internal states but continuous external relationships.
Their internal states are governed by finite state machines but
their external relationships are governed by a simulated physics
that includes Brownian motion, viscosity, and spring-like attractive
and repulsive forces. The particles can be assembled into patterns
that can encode arbitrary strings of bits. We demonstrate that, if
an arbitrary "seed" pattern is put in a "soup" of separate individual
particles, the pattern will replicate by assembling the individual
particles into copies of itself. We also show that, given sufficient
time, a soup of separate individual particles will eventually
spontaneously form self-replicating patterns. We discuss the implications
of JohnnyVon for research in nanotechnology, theoretical biology, and
artificial life.Arnold SmithPeter Turney2175Robert Ewaschuk2002-11-12Z2011-03-11T08:55:06Zhttp://cogprints.org/id/eprint/2600This item is in the repository with the URL: http://cogprints.org/id/eprint/26002002-11-12ZBiological limits to reduction in rates of coronary heart disease: a punctuated equilibrium approach to immune cognition, chronic inflammation, and pathogenic social hierarchyOn both empirical and theoretical grounds we find that a particular form of social hierarchy, here characterized as 'pathogenic', can, from the earliest phases of life, exert a formal analog to evolutionary selection pressure, literally writing a permanent image of itself upon immune function as chronic vascular inflammation and its consequences. The staged nature of resulting disease emerges 'naturally' as an analog to punctuated equilibrium in evolutionary theory. Exposure differs according to the social constructs of race, class, and ethnicity, accounting in large measure for observed population-level differences in rates of coronary heart disease affecting industrialized societies. The system of American Apartheid, which enmeshes both majority and minority communities in a construct of pathogenic hierarchy, appears to present a severe biological limit to ultimate possible reductions in rates of coronary heart disease and related disorders for powerful as well as subordinate subgroups.Rodrick WallaceNew York State Psychiatric InstituteDeborah WallaceColumbia UniversityRobert G. WallaceCity University of New York2002-08-15Z2011-03-11T08:54:59Zhttp://cogprints.org/id/eprint/2407This item is in the repository with the URL: http://cogprints.org/id/eprint/24072002-08-15ZCulture and CancerGenetic mechanisms, since they broadly involve information
transmission, should be translatable into information dynamics formalism. From this perspective we reconsider the adaptive mutator, one possible means of 'second order selection' by which a highly structured 'language' of environment and development writes itself onto the variation upon which evolutionary selection and tumorigenesis operate. Our approach uses recent results in the spirit of the Large Deviations Program of applied probability that permit transfer of phase transition approaches from statistical mechanics to information theory, generating evolutionary and developmental punctuation in what we claim to be a highly natural manner.
Dr. Rodrick WallaceNew York State Psychiatric InstituteDr. Deborah WallaceMailman School of Public Health, Columbia UniversityDr. Robert WallaceCity University of New York2002-08-31Z2011-03-11T08:54:59Zhttp://cogprints.org/id/eprint/2440This item is in the repository with the URL: http://cogprints.org/id/eprint/24402002-08-31ZJohnnyVon: Self-Replicating Automata in Continuous Two-Dimensional SpaceJohnnyVon is an implementation of self-replicating automata in continuous two-dimensional space. Two types of particles drift about in a virtual liquid. The particles are automata with discrete internal states but continuous external relationships. Their internal states are governed by finite state machines but their external relationships are governed by a simulated physics that includes brownian motion, viscosity, and spring-like attractive and repulsive forces. The particles can be assembled into patterns that can encode arbitrary strings of bits. We demonstrate that, if an arbitrary “seed” pattern is put in a “soup” of separate individual particles, the pattern will replicate by assembling the individual particles into copies of itself. We also show that, given sufficient time, a soup of separate individual particles will eventually spontaneously form self-replicating patterns. We discuss the implications of JohnnyVon for research in nanotechnology, theoretical biology, and artificial life.Arnold SmithPeter Turneypeter.turneyRobert Ewaschuk2003-01-17Z2011-03-11T08:55:08Zhttp://cogprints.org/id/eprint/2721This item is in the repository with the URL: http://cogprints.org/id/eprint/27212003-01-17ZAdaptation in the Corticothalamic Loop: Computational Prospects of Tuning the SensesThe present article discusses computational hypotheses on corticothalamic feedback and modulation of cortical response properties. We have recently proposed the two phenomena to be related, hypothesizing that neuronal velocity preference in the visual cortex is altered by feedback to the lateral geniculate nucleus. We now contrast the common view that response adaptation to stimuli subserves a function of redundancy reduction with the idea that it may enhance cortical representation of objects. Our arguments lead to the concept that the corticothalamic loop is involved in reducing sensory input to behaviorally relevant aspects, a pre-attentive gating.Dr. Ulrich HillenbrandProf. Dr. J. Leo van Hemmen2003-01-09Z2011-03-11T08:55:08Zhttp://cogprints.org/id/eprint/2706This item is in the repository with the URL: http://cogprints.org/id/eprint/27062003-01-09ZApplying Slow Feature Analysis to Image Sequences Yields a Rich Repertoire of Complex Cell PropertiesWe apply Slow Feature Analysis (SFA) to image sequences generated from natural images using a range of spatial transformations. An analysis of the resulting receptive fields shows that they have a rich spectrum of invariances and share many properties with complex and hypercomplex cells of the primary visual cortex. Furthermore, the dependence of the solutions on the statistics of the transformations is investigated.
Pietro BerkesLaurenz Wiskott2002-01-10Z2011-03-11T08:54:52Zhttp://cogprints.org/id/eprint/2008This item is in the repository with the URL: http://cogprints.org/id/eprint/20082002-01-10ZImmune Cognition and Pathogenic Challenge: Sudden and Chronic InfectionWe continue to study the implications of IR Cohen's theory
of immune cognition, in the presence of both sudden and chronic pathogenic challenge, through a mathematical model derived from the Large Deviations Program of applied probability. The analysis makes explicit the linkage between an individual's 'immunocultural condensation' and embedding social or historical structures and processes, in particular power relations between groups. We use methods adapted from the theory of ecosystem resilience to explore the consequences of the sudden 'perturbation' caused by infection in the context of such embedding, and examine a 'stage' model for chronic infection involving multiple phase transitions analogous to 'learning plateaus' in neural networks or 'punctuated equilibria' in adaptive systems.Rodrick Wallace2006-12-03Z2011-03-11T08:56:43Zhttp://cogprints.org/id/eprint/5273This item is in the repository with the URL: http://cogprints.org/id/eprint/52732006-12-03ZIntensity generalisation: physiology and modelling of a neglected topicI briefly review empirical data about the generalisation of acquired behaviour to novel stimuli, showing that variations in stimulus intensity affect behaviour differently from variations in characteristics such as, for instance, visual shape or sound frequency. I argue that such differences can be seen already in how the sense organs react to changes in intensity compared to changes in other stimulus characteristics. I then evaluate a number
of models of generalisation with respect to their ability to reproduce intensity generalisation. I reach three main conclusions. First, realistic stimulus representations, based on knowledge of the sense organs, are necessary to
account for intensity effects. Models employing stimulus representations too remote from the sense organs are unable to reproduce the data. Second, the intuitive notion that generalisation is based on similarities between stimuli, possibly modelled as distances in an appropriate representation space, is difficult to reconcile with data about intensity generalisation. Third, several simple models, in conjunction with realistic stimulus representations, can account for a wide array of generalisation phenomena along both intensity and non-intensity stimulus dimensions. The paper also introduces concepts which may be generally useful to evaluate and compare different models of behaviour.
Stefano Ghirlanda2003-03-12Z2011-03-11T08:55:07Zhttp://cogprints.org/id/eprint/2658This item is in the repository with the URL: http://cogprints.org/id/eprint/26582003-03-12ZPhonemic Coding Might Result From
Sensory-Motor Coupling DynamicsHuman sound systems are invariably phonemically coded. Furthermore,
phoneme inventories follow very particular tendancies. To explain
these phenomena, there existed so far three kinds of approaches :
``Chomskyan''/cognitive innatism, morpho-perceptual innatism
and the more recent approach of ``language as a complex cultural system
which adapts under the pressure of efficient communication''.
The two first approaches are clearly not satisfying, while
the third, even if much more convincing,
makes a lot of speculative assumptions and did not
really bring answers to the question of phonemic coding. We propose
here a new hypothesis based on a low-level model of
sensory-motor interactions. We show that certain very
simple and non language-specific neural devices
allow a population of agents to build signalling systems
without any functional pressure. Moreover, these systems
are phonemically coded. Using a realistic vowel articulatory
synthesizer, we show that the inventories of vowels
have striking similarities with human vowel systems.Pierre-Yves Oudeyer2003-07-23Z2011-03-11T08:55:19Zhttp://cogprints.org/id/eprint/3077This item is in the repository with the URL: http://cogprints.org/id/eprint/30772003-07-23ZSeven clusters in genomic triplet distributions Motivation: In several recent papers new algorithms were proposed for detecting coding regions without requiring learning dataset of already known genes. In this paper we studied cluster structure of several genomes in the space of codon usage. This allowed to interpret some of the results obtained in other studies and propose a simpler method, which is, nevertheless, fully
functional.
Results: Several complete genomic sequences were analyzed, using visualization of tables of triplet counts in a sliding window. The distribution of 64-dimensional vectors of triplet frequencies displays a well-detectable cluster structure. The structure was found to consist of seven clusters, corresponding to protein-coding information in three possible phases in one of the two complementary strands and in the non-coding regions. Awareness of the existence of this structure allows development of methods for the segmentation of sequences into regions with the same coding phase and non-coding regions.
This method may be completely unsupervised or use some external information. Since the method does not need extraction of ORFs, it can be applied even for unassembled genomes. Accuracy calculated on the base-pair level (both sensitivity and specificity) exceeds 90%. This is not worse as compared to such methods as HMM, however, has the advantage to be much simpler and clear.
Prof. Alexander N. GorbanDr. Andrei Yu ZinovyevDr. Tatyana G. Popova2006-12-08Z2011-03-11T08:56:43Zhttp://cogprints.org/id/eprint/5277This item is in the repository with the URL: http://cogprints.org/id/eprint/52772006-12-08ZSpectacular pehnomena and limits to rationality in genetic and cultural evolutionIn studies of both animal and human behaviour, game theory is used as a tool for understanding strategies that appear in interactions between individuals. Game theory focuses on adaptive behaviour, which can be attained only at evolutionary equilibrium. Here we suggest that behaviour appearing during interactions is often outside the scope of such analysis. In many types of interaction, conflicts of interest exist between players, fueling the evolution of manipulative strategies. Such strategies evolve out of equilibrium, commonly appearing as spectacular morphology or behaviour with obscure meaning, to which other players may react in non-adaptive, irrational way approach, and outline the conditions in which evolutionary equilibria cannot be maintained. Evidence from studies of biological interactions seems to support the view that behaviour is often not at equilibrium. This also appears to be the case for many human cultural traits, which have spread rapidly despite the fact that they have a negative influence on reproduction.Magnus EnquistAnthony ArakStefano GhirlandaCarl-Adam Wachtmeister2002-09-29Z2011-03-11T08:55:00Zhttp://cogprints.org/id/eprint/2480This item is in the repository with the URL: http://cogprints.org/id/eprint/24802002-09-29ZSubthreshold dynamics of the neural membrane potential driven by stochastic synaptic inputIn the cerebral cortex, neurons are subject to a continuous bombardment of synaptic inputs originating from the network's background activity. This leads to ongoing, mostly subthreshold membrane dynamics that depends on the statistics of the background activity and of the synapses made on a neuron. Subthreshold membrane polarization is, in turn, a potent modulator of neural responses. The present paper analyzes the subthreshold dynamics of the neural membrane potential driven by synaptic inputs of stationary statistics. Synaptic inputs are considered in linear interaction. The analysis identifies regimes of input statistics which give rise to stationary, fluctuating, oscillatory, and unstable dynamics. In particular, I show that (i) mere noise inputs can drive the membrane potential into sustained, quasiperiodic oscillations (noise-driven oscillations), in the absence of a stimulus-derived, intraneural, or network pacemaker; (ii) adding hyperpolarizing to depolarizing synaptic input can increase neural activity (hyperpolarization-induced activity), in the absence of hyperpolarization-activated currents.Dr. Ulrich Hillenbrand2002-06-21Z2011-03-11T08:54:56Zhttp://cogprints.org/id/eprint/2289This item is in the repository with the URL: http://cogprints.org/id/eprint/22892002-06-21ZWhat is Autonomy?A system is autonomous if it uses its own information to modify itself and its environment to enhance its survival, responding to both environmental and internal stimuli to modify its basic functions to increase its viability. Autonomy is the foundation of functionality, intentionality and meaning. Autonomous systems accommodate the unexpected through self-organizing processes, together with some constraints that maintain autonomy. Early versions of autonomy, such as autopoiesis and closure to efficient cause, made autonomous systems dynamically closed to information. This contrasts with recent work on open systems and information dynamics. On our account, autonomy is a matter of degree depending on the relative organization of the system and system environment interactions. A choice between third person openness and first person closure is not required.John Collier2001-08-15Z2011-03-11T08:54:46Zhttp://cogprints.org/id/eprint/1734This item is in the repository with the URL: http://cogprints.org/id/eprint/17342001-08-15ZThe Cochlear Amplifier is a Surface Acoustic Wave ResonatorA companion paper (Bell, 2001) formulated a model of the cochlea as a surface acoustic wave (SAW) resonator. This supporting paper seeks to give a working account of the sensing elements in the ear and how they operate together to create a SAW resonator. A key feature of any such device is that the interdigital transducers alternate in polarity, an arrangement ideal for launching and detecting surface waves. Translated to the ear, the three rows of outer hair cells (OHCs) are conjectured to be the interdigital transducers. In the simplest (degenerate) SAW resonator, only a single set of three electrodes is required to create resonance between the fingers, a situation presumed to apply in the cochlea, where OHC2 is assumed to respond in antiphase to OHC1 and 3. The antiphasic response is not to displacement, but to intracochlear fluid pressure. An examination of the literature interprets OHCs as responding directly to pressure via their cell bodies, and two populations, with opposite response polarities, are observed. Whether an OHC behaves in one way or the other depends on its membrane potential and turgor pressure, so it is conjectured that OHC1/3 operate at a membrane potential of about 70 mV, whereas in OHC2 it is about 50 mV. At low sound pressure levels, two mechanisms for creating an electrical response in OHCs are identified: one involves the piezoelectric response of the OHC wall to pressure, the other a transient sodium current which acts as a biological transistor to amplify the transducer voltage.Andrew Bell2001-08-16Z2011-03-11T08:54:46Zhttp://cogprints.org/id/eprint/1735This item is in the repository with the URL: http://cogprints.org/id/eprint/17352001-08-16ZHelmholtz's Piano Strings: Reverberation of Ripples on the Tectorial MembraneIn 1857 Helmholtz proposed that the ear contained an array of sympathetic resonators, like piano strings, which served to give the ear its fine frequency discrimination. Since the discovery that most healthy human ears emit faint, pure tones (spontaneous otoacoustic emissions), it has been possible to view these narrowband signals as the continuous ringing of the resonant elements. But what are the elements? It is noteworhty that motile outer hair cells lie in a precise crystal-like array with their sensitive stereocilia in contact with the tectorial membrane, a gelatinous structure with an observed surface tension. This paper therefore speculates that ripples (surface tension waves) on the lower surface of the tectorial membrane propagate to and fro between neighbouring cells. This mechanism defines a surface acoustic wave (SAW) resonator, and relies on the outer hair cells directly sensing intracochlear fluid pressure through their cell bodies; in this way the proposal revisits the resonance theory of hearing. The SAW resonator acts as a regenerative receiver of acoustic energy, a topology which was invoked in 1948 by Gold, who later drew the analogy to an 'underwater piano' to describe the cochlea's problem of how it could vibrate with high Q while immersed in fluid. The proposal also gives a physical description of the cochlear amplifier postulated by Davis in 1983. An active array of resonating cavities driven by outer hair cells can explain spontaneous emissions, the shape of the basilar membrane tuning curve, and evoked emissions, among others, and could relate strongly to music.
At levels above which the cochlear amplifier saturates, ripples on the tectorial membrane can still be identified, this time due to vibration of the tectorial membrane against the sharp vestibular lip. This second putative mechanism provides time delays between initiation of the ripple by acoustic pressure variations and its detection by the inner hair cells, and so represents an alternative way of interpreting the traveling wave.
Thus, by invoking two ways of generating ripples on the tectorial membrane, a comprehensive account of cochlear mechanics can be constructed, unifying a resonance theory (at low levels) with a traveling wave picture (at high levels).
Andrew Bell2001-08-13Z2011-03-11T08:54:46Zhttp://cogprints.org/id/eprint/1731This item is in the repository with the URL: http://cogprints.org/id/eprint/17312001-08-13ZImmune cognition, social justice and asthma: structured stress and the developing immune systemWe explore the implications of IR Cohen's work on immune
cognition for understanding rising rates of asthma morbidity
and mortality in the US. Immune cognition is conjoined with
central nervous system cognition, and with the cognitive
function of the embedding sociocultural networks by which
individuals are acculturated and through which they work with others to meet challenges of threat and opportunity.
Using a mathematical model, we find that externally-
imposed patterns of 'structured stress' can, through their
effect on a child's socioculture, become synergistic with
the development of immune cognition, triggering the persistence of an atopic Th2 phenotype, a necessary precursor to asthma and other immune disease. Reversal of the rising tide of asthma and related chronic diseases in the US thus seems unlikely without a 21st Century version of the earlier Great Urban Reforms which ended the scourge of infectious diseases.Rodrick WallaceMindy FulliloveDeborah Wallace2001-07-02Z2011-03-11T08:54:44Zhttp://cogprints.org/id/eprint/1665This item is in the repository with the URL: http://cogprints.org/id/eprint/16652001-07-02ZVaccine strategy when the smallpox model fails: 1. immune cognition, Malaria and the FulaniWe begin to examine the implications of IR Cohen's work on immune cognition [1-3] for vaccine strategies when simple
elicitation of sterilizing immunity fails, as is the case
for HIV, tuberculosis, and malaria. Cohen's approach takes on a special importance in the context of recent work by Nisbett et al. [4] showing clearly that central nervous system (CNS) cognition is not universal, but rather differs fundamentally for populations having different cultural systems. A growing body of evolutionary anthropology indeed suggests that such effects are inevitable, since culture is as much a part of human biology 'as the enamel on our teeth.' Thus a successful vaccine strategy for use when the smallpox model fails must address a condensation of sociocultural and immune cognition, in the same sense that neuroimmunology and immunogenetics describe the condensation of CNS and genetic 'languages' with immune function. We reinterpret recent studies of African cultural variation in immune response to malaria from this perspective.Rodrick WallaceRobert G Wallace2002-06-16Z2011-03-11T08:54:56Zhttp://cogprints.org/id/eprint/2276This item is in the repository with the URL: http://cogprints.org/id/eprint/22762002-06-16ZThe immune system and other cognitive systemsIn the following pages we propose a theory on cognitive systems and the common strategies of perception, which are at the basis of their function. We demonstrate that these strategies are easily seen to be in place in known cognitive systems such as vision and language. Furthermore we show that taking these strategies into consideration implies a new outlook on immune function calling for a new appraisal of the immune system as a cognitive system.Uri HershbergSol Efroni2002-08-09Z2011-03-11T08:54:59Zhttp://cogprints.org/id/eprint/2394This item is in the repository with the URL: http://cogprints.org/id/eprint/23942002-08-09ZDoes Corticothalamic Feedback Control Cortical Velocity Tuning?The thalamus is the major gate to the cortex and its contribution to cortical receptive field properties is well established. Cortical feedback to the thalamus is, in turn, the anatomically dominant input to relay cells, yet its influence on thalamic processing has been difficult to interpret. For an understanding of complex sensory processing, detailed concepts of the corticothalamic interplay need yet to be established. To study corticogeniculate processing in a model, we draw on various physiological and anatomical data concerning the intrinsic dynamics of geniculate relay neurons, the cortical influence on relay modes, lagged and nonlagged neurons, and the structure of visual cortical receptive fields. In extensive computer simulations we elaborate the novel hypothesis that the visual cortex controls via feedback the temporal response properties of geniculate relay cells in a way that alters the tuning of cortical cells for speed.Dr. Ulrich HillenbrandProf. Dr. J. Leo van Hemmen2001-11-07Z2011-03-11T08:54:48Zhttp://cogprints.org/id/eprint/1800This item is in the repository with the URL: http://cogprints.org/id/eprint/18002001-11-07ZFrequency ratios of SOAEs match the inter-cell spacing of outer hair cells: support for a SAW model of the cochleaA new resonance theory of hearing models the cochlea as a surface acoustic wave (SAW) resonator. This SAW model calls for outer hair cells (OHCs) to respond piezoelectrically to intracochlear fluid pressure, and, via associated electomotility, to generate slowly propagating surface tension waves (ripples) on the undersurface of the overlying tectorial membrane. Because OHCs are combined sensors and effectors, the ripples continue to reverberate between the precisely aligned rows of OHCs in the same way as electromechanical ripples do between the interdigital electrodes of a SAW resonator. The distance OHC1OHC3 is 1 wavelength (360 degrees phase delay). This mechanism is conjectured as providing the positive feedback and gain underlying the cochlear amplifier. Andrew Bell2001-06-06Z2011-03-11T08:54:40Zhttp://cogprints.org/id/eprint/1543This item is in the repository with the URL: http://cogprints.org/id/eprint/15432001-06-06ZImmune cognition and culture: implications for the AIDS vaccineWe examine the implications of IR Cohen's 'cognitive
principle' address of the immune system [1-3] for the HIV
vaccine program. This approach takes on a special
importance in the context of recent work by Nisbett et al.
[4] showing clearly that central nervous system (CNS)
cognition is fundamentally different for populations having
different cultural systems, and in the context of a growing
body of evolutionary anthropology which suggests that such
effects are inevitable, since culture is as much a part of
human biology 'as the enamel on our teeth'.Rodrick Wallace2008-04-27T16:18:52Z2011-03-11T08:57:06Zhttp://cogprints.org/id/eprint/6011This item is in the repository with the URL: http://cogprints.org/id/eprint/60112008-04-27T16:18:52ZMechanism of Anesthetic Action: Oxygen Pathway Perturbation HypothesisThe mechanism of anesthesia is relevant to the neural and biological aspects of cognitive sciences. Although more than 150 years have past since the discovery of general anesthetics, how they precisely work remains a mystery. We propose a novel unitary mechanism of general anesthesia verifiable by experiments. In the proposed mechanism, general anesthetics perturb oxygen pathways in both membranes and oxygen-utilizing proteins such that the availabilities of oxygen to its sites of utilization are reduced which in turn triggers cascading cellular responses through oxygen-sensing mechanisms resulting in general anesthesia. Despite the general assumption that cell membranes are readily permeable to oxygen, exiting publications indicate that these membranes are plausible oxygen transport barriers. The present hypothesis provides a unified framework for explaining phenomena associated with general anesthesia and experimental results on the actions of general anesthetics. If verified by experiments, the proposed mechanism also has other significant medical and biological implications.Huping Huhupinghu@quantumbrain.orgMaoxin Wu2001-08-30Z2011-03-11T08:54:47Zhttp://cogprints.org/id/eprint/1776This item is in the repository with the URL: http://cogprints.org/id/eprint/17762001-08-30ZMeta-Genetic Programming: Co-evolving the Operators of VariationThe standard Genetic Programming approach is augmented by co-evolving the genetic operators. To do this the operators are coded as trees of indefinite length. In order for this technique to work, the language that the operators are defined in must be such that it preserves the variation in the base population. This technique can varied by adding further populations of operators and changing which populations act as operators for others, including itself, thus to provide a framework for a whole set of augmented GP techniques. The technique is tested on the parity problem. The pros and cons of the technique are discussed.Bruce Edmonds2001-05-25Z2011-03-11T08:54:38Zhttp://cogprints.org/id/eprint/1512This item is in the repository with the URL: http://cogprints.org/id/eprint/15122001-05-25ZNonlinear cochlear signal processingThis chapter describes the mechanical function of the
cochlea, or inner ear, the organ that converts signals
from acoustical to neural.
Many cochlear hearing disorders are still not well
understood. If systematic progress is to be made
in improved diagnostics and treatment of these disorders,
a clear understanding of basic principles is essential.
Models of the cochlea are useful because they succinctly
describe auditory perception principles.
Several topics will be reviewed. First, the history of cochlear
models, including extensions that have taken place in recent years.
These models include both macromechanics and micromechanics of the
tectorial membrane and hair cells. This leads to comparisons of the
basilar membrane, hair cell, and neural frequency tuning.
The role of nonlinear mechanics and dynamic range are covered
to help the student understand the importance of modern wideband
dynamic range compression hearing aids.
Hearing loss, loudness recruitment, as well as other important
topics of modern hearing health care, are briefly discussed.
Jont Allen2000-05-31Z2011-03-11T08:53:43Zhttp://cogprints.org/id/eprint/187This item is in the repository with the URL: http://cogprints.org/id/eprint/1872000-05-31ZClosure, Function, Emergence, Semiosis and Life: The Same Idea? Reflections on the Concrete and the Abstract in Theoretical Biology.In this note some epistemological problems in general theories about living systems are considered; in particular, the question of hidden connections between different areas of experience, such as folk biology and scientific biology, and hidden connections between central concepts of theoretical biology, such as function, semiosis, closure and life.Claus Emmeche2000-05-24Z2011-03-11T08:53:43Zhttp://cogprints.org/id/eprint/186This item is in the repository with the URL: http://cogprints.org/id/eprint/1862000-05-24ZThe Underwater Piano: Revival of the Resonance Theory of HearingIn 1857 Helmholtz proposed that the ear contained an array of sympathetic resonators, like piano strings, which served to give the ear its fine frequency discrimination. Since the discovery that most healthy human ears emit faint, pure tones (spontaneous otoacoustic emissions), it has been possible to view these narrowband signals as the continuous ringing of the resonant elements. But what are the elements? We note that motile outer hair cells lie in a precise crystal-like array with their sensitive stereocilia in contact with the gelatinous tectorial membrane. This paper therefore proposes that ripples on the surface of the tectorial membrane propagate to and fro between neighbouring cells. The resulting array of active resonators accounts for spontaneous emissions, the shape of the ears tuning curve, cochlear echoes, and could relate strongly to music. By identifying the resonating elements that eluded Helmholtz, this hypothesis revives the resonance theory of hearing, displaced this century by the traveling wave picture, and locates the regenerative receiver invoked by Gold in 1948.Andrew Bell2000-08-08Z2011-03-11T08:54:22Zhttp://cogprints.org/id/eprint/924This item is in the repository with the URL: http://cogprints.org/id/eprint/9242000-08-08ZCoherence in a coupled network: Implication for brain functionIn many body systems, constituents interact with each other,
forming a recursive pattern of mutual interaction and giving rise
to many interesting phenomena. Based upon concepts of the modern
many body theory, a model for a generic many body system is
developed. A novel approach is used to investigate the general
features in such a system. An interesting phase transition in the
system is found. Possible link to brain dynamics is discussed. It
is shown how some of the basic brain processes, such as learning
and memory, find therein a natural explanation.
Zhen Ye2000-07-04Z2011-03-11T08:53:42Zhttp://cogprints.org/id/eprint/150This item is in the repository with the URL: http://cogprints.org/id/eprint/1502000-07-04ZConstructional Tools as the Origin of Cognitive CapacitiesIt is argued that cognitive capacities can be understood as the outcome of the collective action of a set of agents created by tools that explore possible behaviours and train the agents to behave in such appropriate ways as may be discovered. The coherence of the whole system is assured by a combination of vetting the performance of new agents and dealing appropriately with any faults that the whole system may develop. This picture is shown to account for a range of cognitive capacities, including language.Brian D. Josephson2001-09-13Z2011-03-11T08:54:47Zhttp://cogprints.org/id/eprint/1799This item is in the repository with the URL: http://cogprints.org/id/eprint/17992001-09-13ZA simple model of unbounded evolutionary versatility as a largest-scale trend in organismal evolutionThe idea that there are any large-scale trends in the evolution of biological organisms is highly controversial. It is commonly believed, for example, that there is a large-scale trend in evolution towards increasing complexity, but empirical and theoretical arguments undermine this belief. Natural selection results in organisms that are well adapted to their local environments, but it is not clear how local adaptation can produce a global trend. In this paper, I present a simple computational model, in which local adaptation to a randomly changing environment results in a global trend towards increasing evolutionary versatility. In this model, for evolutionary versatility to increase without bound, the environment must be highly dynamic. The model also shows that unbounded evolutionary versatility implies an accelerating evolutionary pace. I believe that unbounded increase in evolutionary versatility is a large-scale trend in evolution. I discuss some of the testable predictions about organismal evolution that are suggested by the model. Peter Turney2002-08-15Z2011-03-11T08:54:59Zhttp://cogprints.org/id/eprint/2406This item is in the repository with the URL: http://cogprints.org/id/eprint/24062002-08-15ZSpatiotemporal adaptation through corticothalamic loops: A hypothesisThe thalamus is the major gate to the cortex and its control over cortical responses is well established. Cortical feedback to the thalamus is, in turn, the anatomically dominant input to relay cells, yet its influence on thalamic processing has been difficult to interpret. For an understanding of complex sensory processing, detailed concepts of the corticothalamic interplay need yet to be established. Drawing on various physiological and anatomical data, we elaborate the novel hypothesis that the visual cortex controls the spatiotemporal structure of cortical receptive fields via feedback to the lateral geniculate nucleus. Furthermore, we present and analyze a model of corticogeniculate loops that implements this control, and exhibit its ability of object segmentation by statistical motion analysis in the visual field.Dr. Ulrich HillenbrandProf. Dr. J. Leo van Hemmen2003-12-18Z2011-03-11T08:55:25Zhttp://cogprints.org/id/eprint/3320This item is in the repository with the URL: http://cogprints.org/id/eprint/33202003-12-18ZTherapeutic applications of computer models of brain activity for Alzheimer disease. THERAPEUTIC IMPLICATIONS OF COMPUTER MODELS OF BRAIN ACTIVITY FOR ALZHEIMER DISEASE.Prof Wlodzislaw Duch1999-10-11Z2011-03-11T08:53:43Zhttp://cogprints.org/id/eprint/184This item is in the repository with the URL: http://cogprints.org/id/eprint/1841999-10-11ZThe Geometry of Stimulus ControlMany studies, both in ethology and comparative psychology, have shown that animals react to modifications of familiar stimuli. This phenomenon is often referred to as generalisation. Most modifications lead to a decrease in responding, but to certain new stimuli an increase in responding is observed. This holds for both innate and learned behaviour. Here we propose a heuristic approach to stimulus control, or stimulus selection, with the aim of explaining these phenomena. The model has two key elements. First, we choose the receptor level as the fundamental stimulus space. Each stimulus is represented as the pattern of activation it induces in sense organs. Second, in this space we introduce a simple measure of `similarity' between stimuli by calculating how activation patterns overlap. The main advantage we recognise in this approach is that the generalisation of acquired responses emerges from a few simple principles which are grounded in the recognition of how animals actually perceive stimuli. Many traditional problems that face theories of stimulus control (e.g. the Spence-Hull theory of gradient interaction or ethological theories of stimulus summation) do not arise in the present framework. These problems include the amount of generalisation along different dimensions, peak-shift phenomena (with respect to both positive and negative shifts), intensity generalisation, and generalisation after conditioning on two positive stimuliStefano GhirlandaMagnus Enquist2000-07-18Z2011-03-11T08:54:21Zhttp://cogprints.org/id/eprint/877This item is in the repository with the URL: http://cogprints.org/id/eprint/8772000-07-18ZThe Geometry of Stimulus ControlMany studies, both in ethology and comparative psychology, have shown that animals react to modifications of familiar stimuli. This phenomenon is often referred to as generalisation. Most modifications lead to a decrease in responding, but to certain new stimuli an increase in responding is observed. This holds for both innate and learned behaviour. Here we propose a heuristic approach to stimulus control, or stimulus selection, with the aim of explaining these phenomena. The model has two key elements. First, we choose the receptor level as the fundamental stimulus space. Each stimulus is represented as the pattern of activation it induces in sense organs. Second, in this space we introduce a simple measure of `similarity' between stimuli by calculating how activation patterns overlap. The main advantage we recognise in this approach is that the generalisation of acquired responses emerges from a few simple principles which are grounded in the recognition of how animals actually perceive stimuli. Many traditional problems that face theories of stimulus control (e.g. the Spence-Hull theory of gradient interaction or ethological theories of stimulus summation) do not arise in the present framework. These problems include the amount of generalisation along different dimensions, peak-shift phenomena (with respect to both positive and negative shifts), intensity generalisation, and generalisation after conditioning on two positive stimuli.Stefano GhirlandaMagnus Enquist1999-07-16Z2011-03-11T08:53:43Zhttp://cogprints.org/id/eprint/183This item is in the repository with the URL: http://cogprints.org/id/eprint/1831999-07-16ZThe Fifth InfluenceThis article is a theoretical consideration on the role of sensory pleasure and mental joy as optimizers of behavior. It ends with an axiomatic proposal. When they compare the human body to its environment, Philosophers recognise the cosmos as the Large Infinite, and the atomic particles as the Small Infinite. The human brain reaches such a degree of complexity that it may be considered as a third infinite in the universe, a Complex Infinite. It follows that any force capable of moving such an infinite deserves a place among the forces of the universe. Physicists have recognized four forces, the gravitational, the electromagnetic, the weak, and the strong nuclear force. Forces are defined in four dimentions (reversible or not in time) and it is postulated that these forces are valid and applicable everywhere. Pleasure and displeasure, the affective axis of consciousness, can move the infinitely complex into action and no human brain can avoid the trend to maximize its pleasure. Therefore, we suggest, axiomatically, that the affective capability of consciousness operates in a way similar to the four forces of the Physics, i.e. influences the behavior of conscious agents in a way similar to the way the four forces influence masses and particles. However, since a mental phenomenon is dimensioneless we propose to call the affective capability of consciousness the fifth influence rather than the fifth force.Michel CabanacRemi A. CabanacHarold T. Hammel1999-07-14Z2011-03-11T08:53:40Zhttp://cogprints.org/id/eprint/106This item is in the repository with the URL: http://cogprints.org/id/eprint/1061999-07-14ZThe Future of Research on Electroreception and Electrocommunication.Besides the rounding out of presently active areas, six are selected for predictions of marked advance. (1) Most discoveries will be in cellular componentry and molecular mechanisms for one or another class of receptors or central pathways. (2) More major taxa will be found with electroreceptive species, possibly birds, reptiles or invertebrates, representing independent evolutionary "inventions". (3) Electric organs with weak and episodic electric discharges will be found in new taxa; first, among siluriforms. (4) New examples are expected, like lampreys, where synchronized muscle action potentials add up to voltages in the range of weakly electric fish. Some of these will look like intermediates in the evolution of electric organs. (5) Ethological significance will be found for a variety of known physiological features. Exs.: uranoscopids, skates and weakly electric catfish with episodic electric discharges of unknown role; electroreceptive ability of some of the diverse group having Lorenzinian-type ampullae (besides elasmobranchs) including lampreys, chimaeras, lungfish, sturgeons, paddlefish, and salamanders; gymnotiform and mormyrid detection of capacitive component of impedance. (6) The organization of some higher functions in the cerebellum and forebrain will gradually come to light.Theodore H. Bullock2002-10-09Z2011-03-11T08:55:03Zhttp://cogprints.org/id/eprint/2499This item is in the repository with the URL: http://cogprints.org/id/eprint/24992002-10-09ZIncreasing Evolvability Considered as a Large-Scale Trend in EvolutionEvolvability is the capacity to evolve. This paper introduces a simple computational model of evolvability and demonstrates that, under certain conditions, evolvability can increase indefinitely, even when there is no direct selection for evolvability. The model shows that increasing evolvability implies an accelerating evolutionary pace. It is suggested that the conditions for indefinitely increasing evolvability are satisfied in biological and cultural evolution. We claim that increasing evolvability is a large-scale trend in evolution. This hypothesis leads to testable predictions about biological and cultural evolution. Peter Turney1999-07-14Z2011-03-11T08:53:52Zhttp://cogprints.org/id/eprint/388This item is in the repository with the URL: http://cogprints.org/id/eprint/3881999-07-14ZSubjekt und Selbstmodell. Die Perspektivität phänomenalen Bewußtseins vor dem Hintergrund einer naturalistischen Theorie mentaler RepräsentationThis book contains a representationalist theory of self-consciousness and of the phenomenal first-person perspective. It draws on empirical data from the cognitive and neurosciences.Thomas K. Metzinger2004-04-28Z2011-03-11T08:55:31Zhttp://cogprints.org/id/eprint/3579This item is in the repository with the URL: http://cogprints.org/id/eprint/35792004-04-28ZTaking the trivial doctrine seriously: Functionalism, eliminativism, and materialism
Gold & Stoljar's characterization of the trivial doctrine and of its relationships with the radical one misses some differences that may be crucial. The radical doctrine can be read as a derivative of the computational version of functionalism that provides the backbone of current cognitive science and is fundamentally uninterested in biology: both doctrines are fundamentally wrong. The synthesis between neurobiology and psychology requires instead that minds be viewed as ontologically primitive, that is, as material properties of functioning bodies. G&S's characterization of the trivial doctrine should therefore be correspondingly modified.
Maurizio Tirassa2000-02-09Z2011-03-11T08:53:41Zhttp://cogprints.org/id/eprint/139This item is in the repository with the URL: http://cogprints.org/id/eprint/1392000-02-09ZThe theory of the organism-environment system: III. Role of efferent influences on receptors in the formation of knowledge.The present article is an attempt to give - in the frame of the theory of the organism-environment system (Jarvilehto 1998a) - a new interpretation to the role of efferent influences on receptor activity and to the functions of senses in the formation of knowledge. It is argued, on the basis of experimental evidence and theoretical considerations, that the senses are not transmitters of environmental information, but they create a direct connection between the organism and the environment, which makes the development of a dynamic living system, the organism-environment system, possible. In this connection process the efferent influences on receptor activity are of particular significance, because with their help the receptors may be adjusted in relation to the parts of the environment which are most important in the achievement of behavioral results. Perception is the process of joining of new parts of the environment to the organism-environment system; thus, the formation of knowledge by perception is based on reorganization (widening and differentiation) of the organism-environment system, and not on transmission of information from the environment. With the help of the efferent influences on receptors each organism creates its own peculiar world which is simultaneously subjective and objective. The present considerations have far reaching influences as well on experimental work in neurophysiology and psychology of perception as on philosophical considerations of knowledge formation.Timo Jarvilehto1999-01-10Z2011-03-11T08:54:17Zhttp://cogprints.org/id/eprint/785This item is in the repository with the URL: http://cogprints.org/id/eprint/7851999-01-10ZResponse to BullerBuller recently posted a critique of evolutionary psychology (reproduced below). Although I disagree with many of his assertions, this is the most credible attempt to critique evolutionary psychology that I have encountered. Bullers arguments regarding improper motivational inferences from evolutionary psychological explanations are largely correct--such inferences are indeed erroneous. Furthermore, the mistakes he identifies have been made by some prominent evolutionists including, apparently, W. D. Hamilton (Symons, personal communication). However, most evolutionary psychologists are not saying what he claims they are saying. Buller wishes to find evolutionary psychology trapped in Freudian quicksand so that he can rescue it. Instead, it is he who must hoist himself from the bog using the theoretical rigging created by evolutionary psychologists over the last two decades, including, most prominently, Don Symons, a primary target of his essay.Edward H. Hagen1998-08-27Z2011-03-11T08:53:43Zhttp://cogprints.org/id/eprint/172This item is in the repository with the URL: http://cogprints.org/id/eprint/1721998-08-27ZThe Secrets of FacesThis is a comment on an article by Perrett et al., on the same issue of Nature, investigating face perception. With computer graphics, Perrett and colleagues have produced exaggerated male and female faces, and asked people to rate them with respect to femininity or masculinity, and personality traits such as intelligence, emotionality and so on. The key question is: what informations do faces (and sexual signals in general) convey? One view, supported by Perrett and colleagues, is that all aspects of sexual signals convey important information about partner quality. We suggest instead that the interaction between the signal and the receiver's nervous system can result in the evolution of sexual traits not linked to partner quality.Magnus EnquistStefano Ghirlanda1998-08-06Z2011-03-11T08:53:38Zhttp://cogprints.org/id/eprint/57This item is in the repository with the URL: http://cogprints.org/id/eprint/571998-08-06ZFrom Neurons to Brain: Adaptive Self-Wiring of NeuronsDuring embryonic morpho-genesis, a collection of individual neurons turns into a functioning network with unique capabilities. Only recently has this most staggering example of emergent process in the natural world, began to be studied. Here we propose a navigational strategy for neurites growth cones, based on sophisticated chemical signaling. We further propose that the embryonic environment (the neurons and the glia cells) acts as an excitable media in which concentric and spiral chemical waves are formed. Together with the navigation strategy, the chemical waves provide a mechanism for communication, regulation, and control required for the adaptive self-wiring of neurons.Ronen SegevEshel Ben-Jacob1998-11-28Z2011-03-11T08:53:51Zhttp://cogprints.org/id/eprint/369This item is in the repository with the URL: http://cogprints.org/id/eprint/3691998-11-28Z"Funda-Mentality": is the conscious mind subtly linked to a basic level of the universe?Age-old battle lines over the puzzling nature of mental experience are shaping a modern resurgence in the study of consciousness. On one side are the long-dominant "physicalists" who view consciousness as an emergent property of the brain's neural networks. On the alternative, rebellious side are those who see a necessary added ingredient: proto-conscious experience intrinsic to reality, perhaps understandable through modern physics (panpsychists, pan-experientialists, "funda-mentalists"). It is argued here that the physicalist premise alone is unable to solve completely the difficult issues of consciousness and that to do so will require supplemental panpsychist/pan-experiential philosophy expressed in modern physics. In one scheme proto-conscious experience is a basic property of physical reality accessible to a quantum process associated with brain activity. The proposed process is Roger Penrose's "objective reduction" (OR), a self-organizing "collapse" of the quantum wave function related to instability at the most basic level of space-time geometry. In the Penrose- Hameroff model of "orchestrated objective reduction" (Orch OR), OR quantum computation occurs in cytoskeletal microtubules within the brain's neurons. The basic thesis is that consciousness involves brain activities coupled to a self-organizing ripples in fundamental reality.Stuart R. Hameroff1998-06-22Z2011-03-11T08:54:12Zhttp://cogprints.org/id/eprint/695This item is in the repository with the URL: http://cogprints.org/id/eprint/6951998-06-22ZThe evolution of what?There is now a huge amount of interest in consciousness among scientists as well as philosophers, yet there is so much confusion and ambiguity in the claims and counter-claims that it is hard to tell whether any progress is being made. This ``position paper'' suggests that we can make progress by temporarily putting to one side questions about what consciousness is or which animals or machines have it or how it evolved. Instead we should focus on questions about the sorts of architectures that are possible for behaving systems and ask what sorts of capabilities, states and processes, might be supported by different sorts of architectures. We can then ask which organisms and machines have which sorts of architectures. This combines the standpoint of philosopher, biologist and engineer. If we can find a general theory of the variety of possible architectures (a characterisation of ``design space'') and the variety of environments, tasks and roles to which such architectures are well suited (a characterisation of ``niche space'') we may be able to use such a theory as a basis for formulating new more precisely defined concepts with which to articulate less ambiguous questions about the space of possible minds. For instance our initially ill-defined concept (``consciousness'') might split into a collection of more precisely defined concepts which can be used to ask unambiguous questions with definite answers. As a first step this paper explores a collection of conjectures regarding architectures and their evolution. In particular we explore architectures involving a combination of coexisting architectural levels including: (a) reactive mechanisms which evolved very early, (b) deliberative mechanisms which evolved later in response to pressures on information processing resources and (c) meta-management mechanisms that can explicitly inspect evaluate and modify some of the contents of various internal information structures. It is conjectured that in response to the needs of these layers, perceptual and action subsystems also developed layers, and also that an ``alarm'' system which initially existed only within the reactive layer may have become increasingly sophisticated and extensive as its inputs and outputs were linked to the newer layers. Processes involving the meta-management layer in the architecture could explain the origin of the notion of ``qualia''. Processes involving the ``alarm'' mechanism and mechanisms concerned with resource limits in the second and third layers gives us an explanation of three main forms of emotion, helping to account for some of the ambiguities which have bedevilled the study of emotion. Further theoretical and practical benefits may come from further work based on this design-based approach to consciousness. A deeper longer term implication is the possibility of a new science investigating laws governing possible trajectories in design space and niche space, as these form parts of high order feedback loops in the biosphere.Aaron Sloman1998-10-19Z2011-03-11T08:53:51Zhttp://cogprints.org/id/eprint/362This item is in the repository with the URL: http://cogprints.org/id/eprint/3621998-10-19ZTHE THEORY OF THE ORGANISM-ENVIRONMENT SYSTEM: I. DESCRIPTION OF THE THEORYThe theory of the organism-environment system starts with the proposition that in any functional sense organism and environment are inseparable and form only one unitary system. The organism cannot exist without the environment and the environment has descriptive properties only if it is connected to the organism. Although for practical purposes we do separate organism and environment, this common-sense starting point leads in psychological theory to problems which cannot be solved. Therefore, separation of organism and environment cannot be the basis of any scientific explanation of human behavior. The theory leads to a reinterpretation of basic problems in many fields of inquiry and makes possible the definition of mental phenomena without their reduction either to neural or biological activity or to separate mental functions. According to the theory, mental activity is activity of the whole organism-environment system, and the traditional psychological concepts describe only different aspects of organisation of this system. Therefore, mental activity cannot be separated from the nervous system, but the nervous system is only one part of the organismenvironment system. This problem will be dealt with in detail in the second part of the article.Timo Jarvilehto1998-10-20Z2011-03-11T08:53:51Zhttp://cogprints.org/id/eprint/365This item is in the repository with the URL: http://cogprints.org/id/eprint/3651998-10-20ZTHE THEORY OF THE ORGANISM-ENVIRONMENT SYSTEM: II. SIGNIFICANCE OF NERVOUS ACTIVITY IN THE ORGANISM-ENVIRONMENT SYSTEMThe relation between mental processes and brain activity is studied from the point of view of the theory of the organism-environment system. It is argued that the systemic point of view leads to a new kind of definition of the primary tasks of neurophysiology and to a new understanding of the traditional neurophysiological concepts. Neurophysiology is restored to its place as a part of biology: its task is the study of neurons as living units, not as computer chips. Neurons are living units which are organised as metabolic systems in connection with other neurons; they are not units which would carry out some psychological functions or maintain states which are typical only of the whole organism-environment system. Psychological processes, on the other hand, are processes always comprising the whole organism-environment system.Timo Jarvilehto1998-06-22Z2011-03-11T08:53:49Zhttp://cogprints.org/id/eprint/333This item is in the repository with the URL: http://cogprints.org/id/eprint/3331998-06-22ZSupervenience and ImplementationHow can a virtual machine X be implemented in a physical machine Y? We know the answer as far as compilers, editors, theorem-provers, operating systems are concerned, at least insofar as we know how to produce these implemented virtual machines, and no mysteries are involved. This paper is about extrapolating from that knowledge to the implementation of minds in brains. By linking the philosopher's concept of supervenience to the engineer's concept of implementation, we can illuminate both. In particular, by showing how virtual machines can be implemented in causally complete physical machines, and still have causal powers, we remove some philosophical problems about how mental processes can be real and can have real effects in the world even if the underlying physical implementation has no causal gaps. This requires a theory of ontological levels.Aaron Sloman2005-02-16Z2011-03-11T08:55:51Zhttp://cogprints.org/id/eprint/4095This item is in the repository with the URL: http://cogprints.org/id/eprint/40952005-02-16ZActivation of G protein-coupled receptors entails cysteine modulation of agonist bindingThe increase of the affinity of agonists with an increase in pH and experiments using thiol-specific reagents indicate that G protein-coupled receptors contain an ionizable cysteine residue at the ligand binding site. Since treatment of receptors with reducing agents produces functional activation and potentiates agonist stimulation, it is likely that this free sulfhydryl modulates receptor activation. We have derived a two-state acid-base model for cysteine modulation of ligand binding which leads to a description of ligand efficacy. We have shown that pH-dependent binding of agonists is closely correlated with measurements of ligand efficacy at the 5-HT2A receptor. In general, efficacy is determined by the preference of a ligand for the base of the receptor. Efficacy may also be described in thermodynamic terms as the coupling free energy involving a ligand and the acid and base states of the receptor. Molecular modeling of the third transmembrane domain of the 5-HT2A receptor, which contains a conserved cysteine, shows that efficacy is determined by the difference between the electrostatic interaction energies of a ligand with the acid and base forms of the receptor model. The difference in interaction energy between the two forms of cysteine makes the largest contribution to this electrostatic interaction energy difference. Therefore, the cysteine makes the largest contribution to ligand efficacy. Using this approach, we can distinquish between the efficacies of agonists with varying molecular structures and account for the differences between the properties of agonists and antagonists.Lester A. RubensteinRichard G. Lanzara1998-12-02Z2011-03-11T08:53:43Zhttp://cogprints.org/id/eprint/181This item is in the repository with the URL: http://cogprints.org/id/eprint/1811998-12-02ZBook review of Allen & Bekoff (1997) on Cognitive EthologyIn this review of Allen & Bekoff's Species of Mind (1997), underlying theoretical assumptions of cognitive ethology are examined from a biological and philosophical viewpoint. In particular, the aim of the book to constitute a foundational concept for cognitive ethology is addressed. The ambiguity of theory-of-mind approaches in animal cognition is discussed as a major problem for causal explanations in behavioural biology.W.H. Dittrich1998-07-09Z2011-03-11T08:54:13Zhttp://cogprints.org/id/eprint/717This item is in the repository with the URL: http://cogprints.org/id/eprint/7171998-07-09ZDamasio, Descartes, Alarms and Meta-managementThis paper discusses some of the requirements for the control architecture of an intelligent human-like agent with multiple independent dynamically changing motives in a dynamically changing only partly predictable world. The architecture proposed includes a combination of reactive, deliberative and meta-management mechanisms along with one or more global ``alarm'' systems. The engineering design requirements are discussed in relation our evolutionary history, evidence of brain function and recent theories of Damasio and others about the relationships between intelligence and emotions. (The paper was completed in haste for a deadline and I forgot to explain why Descartes was in the title. See Damasio 1994.)A. Sloman2006-12-08Z2011-03-11T08:56:43Zhttp://cogprints.org/id/eprint/5278This item is in the repository with the URL: http://cogprints.org/id/eprint/52782006-12-08ZDiscrete conventional signalling of a continuous variableIn aggressive interactions, animals often use a discrete set of signals,
while the properties being signalled are likely to be continuous, for example
fighting ability or value of victory. Here we investigate a particular model
of fighting which allows for conventional signalling of subjective resource
value to occur. The result shows that neither perfect nor no signalling are
evolutionarily stable strategies (ESSs) in the model. Instead, we find ESSs in
which partial information is communicated, with discrete displays signalling
a range of values rather than a precise one. The result also indicates that
communication should be more precise in conflicts over small resources.
Signalling strategies can exist in fighting because of the common interest
in avoiding injuries, but communication is likely to be limited because of
the fundamental conflict over the resource. Our results reflect a compromise
between these two factors. Data allowing for a thorough test of the model are lacking; however, existing data seem consistent with the obtained theoretical results.Magnus EnquistStefano GhirlandaPete L. Hurd1999-05-08Z2011-03-11T08:53:39Zhttp://cogprints.org/id/eprint/84This item is in the repository with the URL: http://cogprints.org/id/eprint/841999-05-08ZMixing Memory and Desire: Want and Will in Neural ModelingValues are critical for intelligent behavior, since values determine interests, and interests determine relevance. Therefore we address relevance and its role in intelligent behavior in animals and machines. Animals avoid exhaustive enumeration of possibilities by focusing on relevant aspects of the environment, which emerge into the (cognitive) foreground, while suppressing irrelevant aspects, which submerge into the background. Nevertheless, the background is not invisible, and aspects of it can pop into the foreground if background processing deems them potentially relevant. Essential to these ideas are questions of how contexts are switched, which defines cognitive/behavioral episodes, and how new contexts are created, which allows the efficiency of foreground/background processing to be extended to new behaviors and cognitive domains. Next we consider mathematical characterizations of the foreground/background distinction, which we treat as a dynamic separation of the concrete space into (approximately) orthogonal subspaces, which are processed differently. Background processing is characterized by large receptive fields which project into a space of relatively low dimension to accomplish rough categorization of a novel stimulus and its approximate location. Such background processing is partly innate and partly learned, and we discuss possible correlational (Hebbian) learning mechanisms. Foreground processing is characterized by small receptive fields which project into a space of comparatively high dimension to accomplish precise categorization and localization of the stimuli relevant to the context. We also consider mathematical models of valences and affordances, which are an aspect of the foreground. Cells processing foregound information have no fixed meaning (i.e., their meaning is contextual), so it is necessary to explain how the processing accomplished by foreground neurons can be made relative to the context. Thus we consider the properties of several simple mathematical models of how the contextual representation controls foreground processing. We show how simple correlational processes accomplish the contextual separation of foreground from background on the basis of differential reinforcement. That is, these processes account for the contextual separation of the concrete space into disjoint subspaces corresponding to the foreground and background. Since an episode may comprise the activation of several contexts (at varying levels of activity) we consider models, suggested by quantum mechanics, of foreground processing in superposition. That is, the contextual state may be a weighted superposition of several pure contexts, with a corresponding superposition of the foreground representations and the processes operating on them. This leads us to a consideration of the nature and origin of contexts. Although some contexts are innate, many are learned. We discuss a mathematical model of contexts which allows a context to split into several contexts, agglutinate from several contexts, or to constellate out of relatively acontextual processing. Finally, we consider the acontextual processing which occurs when the current context is no longer relevant, and may trigger the switch to another context or the formation of a new context. We relate this to the situation known as "breakdown" in phenomenology.Bruce J. MacLennan1998-06-15Z2011-03-11T08:53:38Zhttp://cogprints.org/id/eprint/38This item is in the repository with the URL: http://cogprints.org/id/eprint/381998-06-15ZNew method for analyzing the synchronization of synaptic input and spike output in neural systemsWe present a new technique for analyzing the probability distribution of output spikes for the integrate and fire model. Using this method we investigate models with arbitrary synaptic response functions and the results, which are compared with numerical simulations, are exact in the limit of a large number of small amplitude inputs. We apply this method to the synchronization problem, in which the relationship between the spread in arrival times of the inputs (the temporal jitter of the synaptic input) and the resultant spread in the times at which the output spikes are generated (output jitter) is analyzed. The results indicate that the ratio of the output jitter to the input jitter is consistently less than one and that it decreases for increasing numbers of inputs, in agreement with earlier studies. We identify the variation in the spike generating thresholds of the neurons and the variation in the number of active inputs as being important factors that determine the timing jitter in layered networks, in addition to those identified previously.Anthony N. BurkittGraeme M. Clark2002-03-07Z2011-03-11T08:54:54Zhttp://cogprints.org/id/eprint/2119This item is in the repository with the URL: http://cogprints.org/id/eprint/21192002-03-07ZPhototaxic foraging of the archaepaddler, a hypothetical deep-sea speciesAn autonomous agent (animat, hypothetical animal), called the (archae) paddler, is simulated in sufficient detail to regard its simulated aquatic locomotion (paddling) as physically possible. The paddler is supposed to be a model of an animal that might exist, although it is perfectly possible to view it as a model of a robot that might be built. The agent is assumed to navigate in a simulated deep-sea environment, where it hunts autoluminescent prey. It uses a biologically inspired phototaxic foraging-strategy, while paddling in a layer just above the bottom. The advantage of this living space is that the navigation problem is essentially two-dimensional. Moreover, the deep-sea environment is physically simple (and hence easier to simulate): no significant currents, constant temperature, completely dark. A foraging performance metric is developed that circumvents the necessity to solve the travelling salesman problem. A parametric simulation study then quantifies the influence of habitat factors, such as the density of prey, and the body-geometry (e.g. placement, direction and directional selectivity of the eyes) on foraging success. Adequate performance proves to require a specific body-% geometry adapted to the habitat characteristics. In general performance degrades smoothly for modest changes of the geometric and habitat parameters, indicating that we work in a stable region of 'design space'. The parameters have to strike a compromise between on the one hand the ability to 'fixate' an attractive target, and on the other hand to 'see' as many targets at the same time as possible. One important conclusion is that simple reflex-based navigation can be surprisingly efficient. In the second place, performance in a global task (foraging) depends strongly on local parameters like visual direction-tuning, position of the eyes and paddles, etc. Behaviour and habitat 'mould' the body, and the body-geometry strongly influences performance. The resulting platform enables further testing of foraging strategies, or vision and locomotion theories stemming either from biology or from robotics.
R.J.V. BertinW.A. van de Grind1998-06-22Z2011-03-11T08:54:12Zhttp://cogprints.org/id/eprint/694This item is in the repository with the URL: http://cogprints.org/id/eprint/6941998-06-22ZThe ``Semantics'' of Evolution: Trajectories and Trade-offs in Design Space and Niche SpaceThis paper attempts to characterise a unifying overview of the practice of software engineers, AI designers, developers of evolutionary forms of computation, designers of adaptive systems, etc. The topic overlaps with theoretical biology, developmental psychology and perhaps some aspects of social theory. Just as much of theoretical computer science follows the lead of engineering intuitions and tries to formalise them, there are also some important emerging high level cross disciplinary ideas about natural information processing architectures and evolutionary mechanisms and that can perhaps be unified and formalised in the future. There is some speculation about the evolution of human cognitive architectures and consciousness.Aaron Sloman1998-09-30Z2011-03-11T08:53:43Zhttp://cogprints.org/id/eprint/179This item is in the repository with the URL: http://cogprints.org/id/eprint/1791998-09-30ZThe Common Denominator of Conscious States: Implications for the Biology of ConsciousnessIn order to distinguish the conscious state itself from its aspects and contents we need an answer to the question "if there is something it is like to be conscious, what is it?" A succinct answer to this question is provided in the form of a common denominator of all conscious states. This characterization of the conscious state has implications for the systematic study of consciousness through its bearing on a number of concrete issues connected with the nature of consciousness and its relation to the biology of brains and their evolution. These are discussed with a view to delineating the characteristics of consciousness, suggesting the primary functional role of consciousness in the total economy of brain functions, and exploring the tractability of the problem of consciousness from the standpoint of ordinary science. 1997Bjorn H. Merker1999-01-27Z2011-03-11T08:54:17Zhttp://cogprints.org/id/eprint/794This item is in the repository with the URL: http://cogprints.org/id/eprint/7941999-01-27ZThe Origin and Evolution of Culture and CreativityLike the information patterns that evolve through biological processes, mental representations, or memes, evolve through adaptive exploration and transformation of an information space through variation, selection, and transmission. Since unlike genes, memes do not come packaged with instructions for their replication, our brains do it for them, strategically, guided by a fitness landscape that reflects both internal drives and a worldview that is continually updated through meme assimilation. This paper presents a model for how an individual becomes a meme-evolving agent via the emergence of an autocatalytic network of sparse, distributed memories, and discusses implications for complex, creative thought processes and why they are unique to humans. Memetics can do more than account for the spread of catchy tunes; it can pave the way for the kind of overarching framework for the humanities that the first form of evolution has provided for the biological sciences.L. Gabora1998-04-28Z2011-03-11T08:53:56Zhttp://cogprints.org/id/eprint/437This item is in the repository with the URL: http://cogprints.org/id/eprint/4371998-04-28ZModeling dynamic receptive field changes produced by intracortical microstimulationIntracortical microstimulation (ICMS) of a localized site in the somatosensory cortex of rats and monkeys for 2-6 hours produces a large increase in the cortical representation of the skin region represented by the ICMS-site neurons before ICMS, with very little effect on the ICMS-site neuron's RF location, RF size, and responsiveness (Recanzone et al., 1992). The "EXIN" (afferent excitatory and lateral inhibitory) learning rules (Marshall, 1995) are used to model RF changes during ICMS. The EXIN model produces reorganization of RF topography similar to that observed experimentally. The possible role of inhibitory learning in producing the effects of ICMS is studied by simulating the EXIN model with only lateral inhibitory learning. The model also produces an increase in the cortical representation of the skin region represented by the ICMS-site RF. ICMS is compared to artificial scotoma conditioning (Pettet & Gilbert, 1992) and retinal lesions (Darian-Smith & Gilbert, 1995), and it is suggested that lateral inhibitory learning may be a general principle of cortical plasticity.G.J. KalarickalJ.A. Marshall2001-05-09Z2011-03-11T08:54:38Zhttp://cogprints.org/id/eprint/1487This item is in the repository with the URL: http://cogprints.org/id/eprint/14872001-05-09ZThe Coherence Definition of ConsciousnessI will focus in this essay on a riddle that in my view is central to the consciousness issue: How does the mind or brain create the unity we perceive out of the diversity that we know is there? I contend this is a technical issue, not a philosophical one, although its resolution will have profound philosophical repercussions, and although we have at present little more than the philosophical method to attack it.Christoph von der Malsburg1998-05-25Z2011-03-11T08:53:42Zhttp://cogprints.org/id/eprint/168This item is in the repository with the URL: http://cogprints.org/id/eprint/1681998-05-25ZEpistemic Autonomy in Models of Living SystemsThis paper discusses epistemological consequences of embodied AI for Artificial Life models. The importance of robotic systems for ALife lies in the fact that they are not purely formal models and thus have to address issues of semantic adaptation and epistemic autonomy, which means the system's own ability to decide upon the validity of measurements. Epistemic autonomy in artificial systems is a difficult problem that poses foundational questions. The proposal is to concentrate on biological transformations of epistemological questions that have lead to the development of modern ethology. Such an approach has proven to be useful in the design of control systems for behavior-based robots. It leads to a better understanding of modern ontological conceptions as well as a reacknowledgement of finality in the description and design of autonomous systems.Erich Prem2002-03-07Z2011-03-11T08:54:54Zhttp://cogprints.org/id/eprint/2118This item is in the repository with the URL: http://cogprints.org/id/eprint/21182002-03-07ZThe influence of light/dark adaptation and lateral inhibition on phototaxic foraging. A hypothetical-animal study.Vision did not arise and evolve to just "see" things, but rather to act on and interact with the habitat. Thus it might be misleading to study vision without its natural coupling to vital action. Here we investigate this problem in a simulation study of the simplest kind of visually-guided foraging by a species of 2D hypothetical animal called the (diurnal) paddler. In a previous study, we developed a hypothetical animal called the archaepaddler, which used positive phototaxis to forage for autoluminescent prey in a totally dark environment (the deep-sea). Here we discuss possible visual mechanisms that allow (diurnal) paddlers to live in shallower water, foraging for light-reflecting prey in ambient light. The modification consists of two stages. In the first stage Weber adaptation compresses the retinal illumination into an acceptable range of neural firing frequencies. In the second stage highpass filtering with lateral inhibition separates background responses from foreground responses. We report on a number of parameter-studies conducted with the foraging diurnal paddler, in which the influence of dark/light adaptation and lateral inhibition on foreground/background segregation and foraging performance ("fitness") are quantified. It is shown that the paddler can survive adequately for a substantial range of parameters that compromises between discarding as much unwanted visual (background) information as possible, whilst retaining as much information on potential prey as possible. Parameter values that optimise purely visual performance like foreground/background segregation are not always optimal for foraging performance and vice versa. This shows that studies of vision might indeed require more serious consideration of the goals of vision and the ethogram of the studied organisms than has been customary.
R.J.V. BertinW.A. van de Grind1998-07-18Z2011-03-11T08:53:38Zhttp://cogprints.org/id/eprint/53This item is in the repository with the URL: http://cogprints.org/id/eprint/531998-07-18ZDevelopmental changes in the alpha response systemEvoked and event-related brain potentials (ERPs) may be regarded as originating from the reorganization of the spontaneous EEG rhythms. The main objective of the present research was to study the alpha responses in 6-11 year-old children to determine whether the ability to reorganize alpha activity after external stimulation demonstrates developmental changes that could reflect variations in information processing with increased age. A total of 50 children aged 6-11 years, divided into 5 age groups, and 10 young adults were assessed in a passive and an oddball condition. Alpha responses in the passive and non-target ERPs at Fz, Cz and Pz were analyzed to assess quantitatively the repeatability (phase-locking) of the evoked alpha oscillations. The alpha responses in 6-11 year-old children were different from those in adults: (1) Adults had significantly lower amplitude and stronger phase-locking than children; (2) Adults had maximal alpha amplitudes and phase-locking over the vertex, whereas children displayed maximal responses over the parietal site; (3) The phase-locking of eldest (10-11 year-old) children was as strong as in adults. These findings indicate that the alpha response system is functionally involved in 6-11 year-old children, though its development is not complete at the age of 11, and the magnitude and the phase-locking parameters may relate to different functional aspects of the alpha response system. Thus, younger children do produce alpha responses during information processing, but are not able to engage this system as strongly as older children and adults.Juliana YordanovaVasil Kolev2000-09-05Z2011-03-11T08:54:23Zhttp://cogprints.org/id/eprint/954This item is in the repository with the URL: http://cogprints.org/id/eprint/9542000-09-05ZAre interactions between different time-scales a characteristic of complexity?A self-organized complex natural system, such as a biological, a neural or a social system, is characterized by the fact that its dynamics is generated by a network of competitive regulations, each one acting as a 'simple system' (in the Newtonian sense) at a given level of complexity and with its own time-scale. A dialectics dependent on specific structural temporal constraints is established between them, punctuated by local fractures imposing a change of strategy. Such systems are capable of anticipation and adaptation thanks to the development of a memory.
The Memory Evolutive Systems (MES) defined by Ehresmann and Vanbremeersch in a series of papers since 1986 represent a mathematical model for such systems, based on the Theory of categories. This model takes into account the above properties, and it allows to study the problem of emergence; an analysis of causality attributions shows that MES satisfy the definition given by Rosen for an 'organism'.
Jean-Paul VanbremeerschJerry ChandlerAndree Ehresmann1998-06-22Z2011-03-11T08:53:58Zhttp://cogprints.org/id/eprint/470This item is in the repository with the URL: http://cogprints.org/id/eprint/4701998-06-22ZRetrieval properties of attractor neural networks that obey Dale's law using a self-consistent signal-to-noise analysisThe recently proposed self-consistent signal-to-noise analysis is applied to a current--rate dynamics attractor network of excitatory neurons with a Hebbian synaptic matrix. The effect of inhibitory interneurons is included by a term modeling their effective inhibition that depends upon both the level of activity of the excitatory neurons and the stored patterns. The low rate attractor structure is identified, and at low loading the network retrieves single patterns with uniform low rates without errors, and is stable to the admixture of additional patterns. The self-consistent signal-to-noise method enables the analysis of the network properties with an extensive number of patterns, and the results are compared with simulations. The method allows the identification of the fixed point structure of networks for which there is no Lyapanov function, and hence for which mean-field techniques cannot be used. This analysis is shown to provide a powerful and straightforward way to analyse the properties of networks with neuronal specificity, low spike rates and synaptic noise, as well as incorporating the effects of random asymmetric synaptic dilution and limited analog synaptic depth in a natural way. The simulations show that the network properties are very robust both to errors in the stimulus and to the stimulus strength and duration.Anthony N. Burkitt2001-05-09Z2011-03-11T08:54:38Zhttp://cogprints.org/id/eprint/1486This item is in the repository with the URL: http://cogprints.org/id/eprint/14862001-05-09ZBinding in Models of Perception and Brain
FunctionThe development of the issue of binding as fundamental to neural dynamics has made possible recent advances in the modeling of difficult problems of perception and brain function. Among them is perceptual segmentation, invariant pattern recognition and one-shot learning. Also, longer-term conceptual developments that have led to this success are reviewed.Christoph von der Malsburg2001-09-23Z2011-03-11T08:54:44Zhttp://cogprints.org/id/eprint/1659This item is in the repository with the URL: http://cogprints.org/id/eprint/16592001-09-23ZContrasting Two Representations of Emergence of Cellular DynamicsThe organization of molecular and biological dynamics of a single cell is contrasted in terms of two general theories:
1. Memory Evolutive Systems (MES) which present a mathematical model, based on category theory, for evolving self-organized hierarchical systems and have been developed in a series of papers by Ehresmann and Vanbremeersch since 1987; and
2. the C8 hypothesis of Chandler (1991-92) which proposes specific methods of enumerating complexity.
Both theories give account of the hierarchical conformation of the cell and of its growth relying on a sequence of events during which manifestations of biological strategies emerge from exchanges with the environment and internal assemblies or disassemblies of higher complex structures. They indicate how a balanced cellular flow is achieved through the interactions among a net of overlapping cyclic internal communications channels. If a conflict arises, the biological coherence is restored by accelerating, delaying or inhibiting some of the cycles, thus explaining the simultaneous plasticity and bounded stability of a cell. The potential melding of these two theories to create applications describing the organization of evolutionary systems is being explored.
Jerry ChandlerAndrée EhresmannJeanPaul Vanbremeersch2001-05-09Z2011-03-11T08:54:38Zhttp://cogprints.org/id/eprint/1485This item is in the repository with the URL: http://cogprints.org/id/eprint/14852001-05-09ZFace Recognition and Gender DeterminationThe system presented here is a specialized version of a general object recognition system. Images of faces are represented as graphs, labeled with topographical information and local templates. Different poses are represented by different graphs. New graphs of faces are generated by an elastic graph matching procedure comparing the new face with a set of precomputed graphs: the "general face knowledge". The final phase of the matching process can be used to generate composite images of faces and to determine certain features represented in the general face knowledge, such as gender or the presence of glasses or a beard. The graphs can be compared by a similarity function which makes the system efficient in recognizing faces.Laurenz WiskottJean-Marc FellousNorbert KrügerChristoph von der Malsburg1999-01-22Z2011-03-11T08:54:02Zhttp://cogprints.org/id/eprint/531This item is in the repository with the URL: http://cogprints.org/id/eprint/5311999-01-22ZMeme and Variations: A Computational Model of Cultural EvolutionThis paper describes a computational model of how ideas, or memes, evolve through the processes of variation, selection, and replication. Every iteration, each neural-network based agent in an artificial society has the opportunity to acquire a new meme, either through 1) INNOVATION, by mutating a previously-learned meme, or 2) IMITATION, by copying a meme performed by a neighbor. Imitation, mental simulation, and using past experience to bias mutation all increase the rate at which fitter memes evolve. Memes at epistatic loci converged more slowly than memes at over- or underdominant loci. The higher the ratio of innovation to imitation, the greater the meme diversity, and the higher the fitness of the fittest meme. Optimization is fastest for the society as a whole with an innovation to imitation ratio of 2:1, but diversity is comprimized.L. Gabora1999-07-22Z2011-03-11T08:53:40Zhttp://cogprints.org/id/eprint/110This item is in the repository with the URL: http://cogprints.org/id/eprint/1101999-07-22ZNeural Integration at the Mesoscopic Level: the Advent of some Ideas in the Last Half CenturyHistory seen by a professional historian, based only on the documented record, always incomplete and liable to bias, can be unreliable. Modern history seen by a protagonist must surely be among the most unreliable. My only excuse for this effort is that I was invited by the relevant Society committee. My reason for accepting is that I feel even the fragmentary part of neuroscience I can speak about is a human drama, romantic and exciting, and a flood on which we are floating, unable to dump the baggage of past biases. Our points of view, priorities, and positions on all the controversial issues and even the well established, noncontroversial ones, are not as rational as we would like to think but are strongly conditioned by where we came from. I will depend mainly on selected vignettes of the way things looked when I was a student, a young postdoctoral fellow and an Assistant Professor, to compare with the way they look to me or to others now, in each of half a dozen mesoscopic domains. I mean by mesoscopic domains the middle levels - those in between the most basic subcellular or molecular and the higher levels of learning and cognition. The half dozen domains constitute of course, anything but a representative fraction of neuroscience. I believe, however, that they add up to a nontrivial segment of the big picture with respect to the integrative aspects of our science. Most of the fronts that grew into today's popular branches of our science are not represented but a small set of particular interest and probability of further surprises.Theodore H. Bullock1999-09-02Z2011-03-11T08:53:52Zhttp://cogprints.org/id/eprint/392This item is in the repository with the URL: http://cogprints.org/id/eprint/3921999-09-02ZReview of Jaegwon Kim, Supervenience and Mind"Adaptation properties," as individuated according to evolutionary biology, cannot be reduced to physical properties of the token items that have the adaptation properties. This causes serious if not fatal trouble for several of Kim's crucial theses: the Causal Individuation of Kinds, Weak Supervenience, Alexander's Dictum, the synchronicity thesis (that all psychological kinds supervene on the contemporaneous physical states of the organism), the Correlation Thesis, and indeed his Restricted Correlation Thesis. All these theses are strongly individualist, in the sense of entailing that all a thing's properties are determined by its own physical properties and relations, contrary to many properties in biology and psychology.John F. Post2005-02-16Z2011-03-11T08:55:51Zhttp://cogprints.org/id/eprint/4094This item is in the repository with the URL: http://cogprints.org/id/eprint/40942005-02-16ZWeber's Law Modeled by the Mathematical Description of a Beam BalanceA beam balance is analyzed as a model that describes Weber's law. The mathematical derivations of the torques on a beam balance produce a description that is strictly compatible with that law. The natural relationship of the beam balance model to Weber's law provides for an intuitive understanding of the relationship of Weber's law to sensory and receptor systems. Additionally, this model may offer a simple way to compute perturbations that result from unequal effects on coupled steady state systems. A practical outgrowth from this work is that a relatively simple mathematical description models sensory phenomena and may aid in the understanding of sensory and receptor systems.Richard G. Lanzara1998-09-29Z2011-03-11T08:53:43Zhttp://cogprints.org/id/eprint/178This item is in the repository with the URL: http://cogprints.org/id/eprint/1781998-09-29ZIs the monkeys' world scientifically impenetrable?Cheney & Seyfarth (C&S) argue for a hybrid approach which 'place (empiricistic findings) tentatively within the framework of a more mentalistic approach'(p.9). The book is an important contribution to clarify the value and limits of the intentional approach in interpreting monkey behaviour, particularly C&S's excellent field work with vervets. But, unintentionally, it also demonstrates that cognitive science is more a perspective than a scientific discipline. In order to illustrate this, I shall consider the following topics: evolution of intelligence, concept formation, philosophy of scienceWinand Dittrich2002-02-09Z2011-03-11T08:54:53Zhttp://cogprints.org/id/eprint/2075This item is in the repository with the URL: http://cogprints.org/id/eprint/20752002-02-09ZSemantics and Communication for Memory Evolutive SystemsIn a series of preceding papers, the authors have developed the theory of Memory Evolutive Systems which represents a mathematical model (based on Category theory) for natural open self-organizing systems, such as biological, sociological or neural systems. In these systems, the dynamics is modulated by the cooperative or/and competitive interactions between the global system and a net of internal more or less specialized Centers of Regulation (CR) with a differential access to a central hierarchical Memory. Each CR operates at its own complexity level and time-scale, but their strategies are competitive, whence a 'dialectics between heterogeneous CRs which is at the root of higher order cognition.
The problem tackled in the present paper is the emergence of a Semantics in the MES modeling a cognitive system; it relies on the detection of specific invariances by the CRs that leads to classify objects according to their main attributes, and form new formal units representing their invariance classes. The idea is that a (lower) CR, say E, classifies two objects B and C as having 'the same shape' if they activate the same pattern of its actors; however this classification remains implicit for E itself and it can be apprehended only by a higher Ievel CR which may memorize the invariance class by a higher object, called a 'E-concept'. The concepts with respect to the various CRs form the semantic memory which gives more flexibility in the evaluation, selection and memorization of appropriate strategies, as well as in internal or external communications.
Andrée EhresmannJean-Paul Vanbremeersch1998-11-15Z2011-03-11T08:53:43Zhttp://cogprints.org/id/eprint/180This item is in the repository with the URL: http://cogprints.org/id/eprint/1801998-11-15ZEnhancement of Opioid-Mediated Analgesia: A Solution to the Enigma of PlacentophagiaTwo major consequences of placentophagia, the ingestion of afterbirth materials that occurs usually during mammalian parturition, have been uncovered in the past several years. The first is that increased contact, associated with ingesting placenta and amniotic fluid from the surface of the young, causes an accelerated onset of maternal behavior toward those young. The second, which probably has importance for a broader range of mammalian taxa than the first, is that ingestion of afterbirth materials produces enhancement of ongoing opioid-mediated analgesia. The active substance in placenta and amniotic fluid has been named POEF, for Placental Opioid-Enhancing Factor. Recent research on both consequences is summarized, with particular attention to POEF, the generalizability of the enhancement phenomenon, its locus and mode of action, and its significance for new approaches to the management of pain and addiction.Mark B. Kristal1998-03-20Z2011-03-11T08:54:07Zhttp://cogprints.org/id/eprint/615This item is in the repository with the URL: http://cogprints.org/id/eprint/6151998-03-20ZThe Symbol Grounding ProblemThere has been much discussion recently about the scope and limits of purely symbolic models of the mind and about the proper role of connectionism in cognitive modeling. This paper describes the symbol grounding problem: How can the semantic interpretation of a formal symbol system be made intrinsic to the system, rather than just parasitic on the meanings in our heads? How can the meanings of the meaningless symbol tokens, manipulated solely on the basis of their (arbitrary) shapes, be grounded in anything but other meaningless symbols? The problem is analogous to trying to learn Chinese from a Chinese/Chinese dictionary alone. A candidate solution is sketched: Symbolic representations must be grounded bottom-up in nonsymbolic representations of two kinds: (1) iconic representations, which are analogs of the proximal sensory projections of distal objects and events, and (2) categorical representations, which are learned and innate feature-detectors that pick out the invariant features of object and event categories from their sensory projections. Elementary symbols are the names of these object and event categories, assigned on the basis of their (nonsymbolic) categorical representations. Higher-order (3) symbolic representations, grounded in these elementary symbols, consist of symbol strings describing category membership relations (e.g., An X is a Y that is Z). Connectionism is one natural candidate for the mechanism that learns the invariant features underlying categorical representations, thereby connecting names to the proximal projections of the distal objects they stand for. In this way connectionism can be seen as a complementary component in a hybrid nonsymbolic/symbolic model of the mind, rather than a rival to purely symbolic modeling. Such a hybrid model would not have an autonomous symbolic module, however; the symbolic functions would emerge as an intrinsically dedicated symbol system as a consequence of the bottom-up grounding of categories' names in their sensory representations. Symbol manipulation would be governed not just by the arbitrary shapes of the symbol tokens, but by the nonarbitrary shapes of the icons and category invariants in which they are grounded.Stevan Harnad2003-08-12Z2011-03-11T08:55:19Zhttp://cogprints.org/id/eprint/3106This item is in the repository with the URL: http://cogprints.org/id/eprint/31062003-08-12ZThe Symbol Grounding ProblemThere has been much discussion recently about the scope and limits of purely symbolic models of the mind and about the proper role of connectionism in cognitive modeling. This paper describes the symbol grounding problem: How can the semantic interpretation of a formal symbol system be made intrinsic to the system, rather than just parasitic on the meanings in our heads? How can the meanings of the meaningless symbol tokens, manipulated solely on the basis of their (arbitrary) shapes, be grounded in anything but other meaningless symbols? The problem is analogous to trying to learn Chinese from a Chinese/Chinese dictionary alone. A candidate solution is sketched: Symbolic representations must be grounded bottom-up in nonsymbolic representations of two kinds: (1) iconic representations, which are analogs of the proximal sensory projections of distal objects and events, and (2) categorical representations, which are learned and innate feature-detectors that pick out the invariant features of object and event categories from their sensory projections. Elementary symbols are the names of these object and event categories, assigned on the basis of their (nonsymbolic) categorical representations. Higher-order (3) symbolic representations, grounded in these elementary symbols, consist of symbol strings describing category membership relations (e.g., An X is a Y that is Z). Connectionism is one natural candidate for the mechanism that learns the invariant features underlying categorical representations, thereby connecting names to the proximal projections of the distal objects they stand for. In this way connectionism can be seen as a complementary component in a hybrid nonsymbolic/symbolic model of the mind, rather than a rival to purely symbolic modeling. Such a hybrid model would not have an autonomous symbolic module, however; the symbolic functions would emerge as an intrinsically dedicated symbol system as a consequence of the bottom-up grounding of categories' names in their sensory representations. Symbol manipulation would be governed not just by the arbitrary shapes of the symbol tokens, but by the nonarbitrary shapes of the icons and category invariants in which they are grounded.Stevan Harnad2004-09-07Z2011-03-11T08:55:41Zhttp://cogprints.org/id/eprint/3810This item is in the repository with the URL: http://cogprints.org/id/eprint/38102004-09-07ZQuantum Interactomics and Cancer Molecular Mechanisms 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.
*Communicated to: The Institute of Genomic Biology (currently under construction at UIUC, at 905 S. Goodwin Avenue, Urbana,IL.61801,USA).
KEYWORDS: Cancer cell interactomics; Somatic cell genomics and
Proteomics; current limitations of modular models of carcinogenesis;
Complex quantum 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.
Dr. I.C. Baianuicb2004-07-06Z2011-03-11T08:55:37Zhttp://cogprints.org/id/eprint/3687This item is in the repository with the URL: http://cogprints.org/id/eprint/36872004-07-06ZCOMPUTER MODELS AND AUTOMATA THEORY
IN BIOLOGY AND MEDICINE
The applications of computers to biological and biomedical problem solving go back to the very beginnings of computer science, automata theory [1], and mathematical biology [2]. With the advent of more versatile and powerful computers, biological and biomedical applications of computers have proliferated so rapidly that it would be virtually impossible to compile a comprehensive review of all developments in this field. Limitations of computer simulations in biology have also come under close scrutiny, and claims have been made that biological systems have limited information processing power [3]. Such general conjectures do not, however, deter biologists and biomedical researchers from developing new computer applications in biology and medicine. Microprocessors are being widely employed in biological laboratories both for automatic data acquisition/processing and modeling; one particular area, which is of great biomedical interest, involves fast digital image processing and is already established for routine clinical examinations in radiological and nuclear medicine centers, Powerful techniques for biological research are routinely employing dedicated, on-line microprocessors or array processors; among such techniques are: Fourier-transform nuclear magnetic resonance (NMR), NMR imaging (or tomography),
x-ray tomography, x-ray diffraction, high performance liquid chromatography, differential scanning calorimetry and mass spectrometry. Networking of laboratory microprocessors linked to a central, large memory computer is the next logical step in laboratory automation. Previously unapproachable problems, such as molecular dynamics of solutions, many-body interaction calculations and statistical mechanics of biological processes are all likely to benefit from the increasing access to the new generation of "supercomputers". In view of the large number, diversity and complexity of computer applications in biology and medicine, we could not review in any degree of detail all computer applications in these fields; instead, we shall be selective and focus our discussion on suggestive computer models of biological systems and those fundamental aspects of computer applications that are likely to continue to make an impact on biological and biomedical research. Thus, we shall consider unifying trends in mathematics, mathematical logics and computer science that are relevant to computer modeling of biological and biomedical systems. The latter are pitched at a more formal, abstract level than the applications and, therefore, encompass a number of concepts drawn from the abstract theory of sets and relations, network theory, automata theory, Boolean and n-valued logics, abstract algebra, topology and category theory. The present analysis of relational theories in biology and computer simulation has also inspired a number of new results which are presented here as "Conjectures" since their proofs are too lengthy and too technical to be included in this review. In order to maintain a self-contained presentation-the definitions of the main concepts are given, with the exception of a minimum of simple mathematical concepts.
The purpose of these theoretical sections is to provide the basis for approaching a number of basic biological questions:
(1) What are the essential characteristics of a biological organism as opposed to an automaton?
(2) Are biological systems recursively computable?
(3) What is the structure of the simplest (primordial) organism?
(4) What are the basic structures of neural and genetic networks?
(5) What are the common properties of classes of biological organisms?
(6) Which system representations are adequate for biodynamics?
(7) What is the optimal strategy for modifying an organism through genetic engineering? (8) What is the optimal simulation of a biological system with a digital or analog computer?
(9) What is life?
Professor I. C. Baianuicb2004-07-13Z2011-03-11T08:55:38Zhttp://cogprints.org/id/eprint/3718This item is in the repository with the URL: http://cogprints.org/id/eprint/37182004-07-13ZCOMPUTER SIMULATION AND COMPUTABILITY
OF BIOLOGICAL SYSTEMSThe ability to simulate a biological organism by employing a computer is related to the
ability of the computer to calculate the behavior of such a dynamical system, or the "computability" of the system.* However, the two questions of computability and simulation are not equivalent. Since the question of computability can be given a precise answer in terms of recursive functions, automata theory and dynamical systems, it will be appropriate to consider it first. The more elusive question of adequate simulation of biological systems by a computer will be then addressed and a possible connection between the two answers given will be considered. A conjecture is formulated that suggests the possibility of employing an algebraic-topological, "quantum" computer (Baianu, 1971b)
for analogous and symbolic simulations of biological systems that may include chaotic processes that are not, in genral, either recursively or digitally computable. Depending on the biological network being modelled, such as the Human Genome/Cell Interactome or a trillion-cell Cognitive Neural Network system, the appropriate logical structure for such simulations might be either the Quantum MV-Logic (QMV) discussed in recent publications (Chiara, 2004, and references cited therein)or Lukasiewicz Logic Algebras that were shown to be isomorphic to MV-logic algebras (Georgescu et al, 2001). Professor I.C. BaianuicbMs. H.C. Lin2004-07-06Z2011-03-11T08:55:37Zhttp://cogprints.org/id/eprint/3675This item is in the repository with the URL: http://cogprints.org/id/eprint/36752004-07-06ZNATURAL TRANSFORMATION MODELS IN MOLECULAR BIOLOGYMolecular models in terms of Categories, Functors and Natural Transformations are introduced for unimolecular chemical transformations, multi-molecular chemical and biochemical transformations. Novel approaches to realization of Relational Biology Models of Complex System Biology are introduced in terms of Natural Transformations between Functors of Molecular Categories. Several applications of such natural transformations are then presented to protein biosynthesis, embryogenesis and nuclear transplant experiments. Other possible realizations in Molecular Biology and Relational Biology of Organisms are also suggested. Future developments will include: Fuzzy Relations in Biology; Categories of Lukasiewicz Logic Algebras and Intuitionistic Logic Algebras for Modeling of Complex Neural Network Processes; Stochastic, Genetic Networks in Lukn-Algebras, and Relational Biology Models of Complex Hormonal Controls. Professor Ion Baianuicb2004-10-06Z2011-03-11T08:55:42Zhttp://cogprints.org/id/eprint/3829This item is in the repository with the URL: http://cogprints.org/id/eprint/38292004-10-06ZNATURAL TRANSFORMATIONS OF MULTI-LEVEL ORGANISMAL STRUCTURES REPRESENTED AS ORGANISMIC SUPERCATEGORIES:
I. Generation of Categorical Limits and Colimits during Biological Development and Evolution A current update of our original 1980 publication entitled "Natural Transformations of Organismic Structures" is here presented, along with the original (1980) article. A unifying approach to the realization of Relational Biology models and Complex System Biology was reported in 1980 for the first time in terms of Natural Transformations between Functors of Organismic Supercategories and their generating categorical diagrams. The representation of organismal structures in terms of Organismic-Supercategories, Functors and their Natural Transformations was introduced for the investigation of developmental and evolutionary processes. Several applications of such natural transformations were presented in relation to embryogenesis and evolutionary processes involving natural selection and the emergence of 'optimally designed' organismal structures. Other molecular realizations in Relational Biology and the underlying Molecular Biology of organisms were also discussed. Current developments of this approach to Complex Systems Biology include: Fuzzy Relations in Biological Dynamics and Structural Biology, Categories of Lukasiewicz Logic Algebras as representations of Functional Genomics and Cell Interactomics, and Intuitionistic Logic Algebras in Topoi and Higher-Dimensional Algebras as possible models of the emergence of Human Consciousness through 'long-range' correlations and partially coherent, multi-level Neural Network processes.Dr. Ion Baianuicb2001-05-09Z2011-03-11T08:54:36Zhttp://cogprints.org/id/eprint/1380This item is in the repository with the URL: http://cogprints.org/id/eprint/13802001-05-09ZThe Correlation Theory of Brain FunctionA summary of brain theory is given so far as it is contained within the framework of Localization Theory. Diffculties of this "conventional theory" are traced back to a specific deficiency: there is no way to express relations between active cells (as for instance their representing parts of the same object). A new theory is proposed to cure this deficiency. It introduces a new kind of dynamical control, termed synaptic modulation, according to which synapses switch between a conducting and a non- conducting state. The dynamics of this variable is controlled on a fast time scale by correlations in the temporal fine structure of cellular signals. Furthermore, conventional synaptic plasticity is replaced by a refined version. Synaptic modulation and plasticity form the basis for short-term and long-term memory, respectively. Signal correlations, shaped by the variable network, express structure and relationships within objects. In particular, the figure-ground problem may be solved in this way. Synaptic modulation introduces flexibility into cerebral networks which is necessary to solve the invariance problem. Since momentarily useless connections are deactivated, interference between different memory traces can be reduced, and memory capacity increased, in comparison with conventional associative memory.Christoph von der Malsburg2011-12-16T00:58:34Z2011-12-16T00:58:34Zhttp://cogprints.org/id/eprint/7755This item is in the repository with the URL: http://cogprints.org/id/eprint/77552011-12-16T00:58:34ZNatural Transformations of Organismic StructuresThe mathematical structures underlying the theories of organismic sets, (M, R)-systems and molecular sets are shown to be transformed naturally within the theory of categories and functors. Their natural transformations allow the comparison of distinct entities, as well as the modelling of dynamics in “organismic” structures.Prof. Dr. I. C. Baianuibaianu@illinois.edu2004-10-06Z2011-03-11T08:55:42Zhttp://cogprints.org/id/eprint/3822This item is in the repository with the URL: http://cogprints.org/id/eprint/38222004-10-06ZSTRUCTURAL ORDER AND PARTIAL DISORDER IN BIOLOGICAL SYSTEMS:
Structural "Fuzziness" underlying All Biological FunctionsThe presence of structural order and partial disorder is discussed for several important biological molecules such as DNA, enzymes and proteins, as well as for cellular structures such as nerve myelin. The relationship between structural "fuzziness" and biological function is discussed
as an important aspect of biological complexity and biodynamics. The possible effects of partial disorder on the electron density of states in biological structures are predicted based on known quantum theoretical computations for lattices in solids. Important phenomena such as Anderson delocalization, Hall effect and quantum tunneling are predicted to affect biological function. Novel experiments are being proposed by pulsed lasers, pulsed/FT-NMR and optical/NIR spectroscopy to monitor the effects of structural partial disorder and "fuzziness" on biological function. Novel methods for computer analysis of paracrystalline lattices such as nerve myelin and oriented DNA fibers are also proposed based on molecular models that include partial disorder.
Prof. Dr. I.C. Baianuicb2004-10-06Z2011-03-11T08:55:41Zhttp://cogprints.org/id/eprint/3820This item is in the repository with the URL: http://cogprints.org/id/eprint/38202004-10-06ZSTRUCTURAL ORDER AND PARTIAL DISORDER IN BIOLOGICAL SYSTEMS:
STRUCTURAL "FUZZINESS" UNDERLYING BIOLOGICAL FUNCTIONThe presence of structural order and partial disorder is discussed for several important biological molecules such as DNA, enzymes and proteins, as well as for cellular structures such as nerve myelin. The relationship between structural "fuzziness" and biological function is discussed
as an important aspect of biological complexity and biodynamics. The possible effects of partial disorder on the electron density of states in biological structures is predicted based on known quantum theoretical computations for lattices in solids. Important phenomena such as Anderson delocalization, Hall effect and quantum tunneling are predicted to affect biological function. Novel experiments are being suggested by pulsed lasers, pulsed/FT-NMR and optical/NIR spectroscopy in order to monitor the effects of structural partial disorder and "fuzziness" on biological function. Novel methods for computer analysis of paracrystalline lattices such as nerve myelin and oriented DNA fibers are also being proposed based on molecular models that include partial disorder.
Dr. I.C. Baianuicb2000-07-15Z2011-03-11T08:54:21Zhttp://cogprints.org/id/eprint/863This item is in the repository with the URL: http://cogprints.org/id/eprint/8632000-07-15ZInduction, evolution and accountabilityDISCUSSION PAPER:
HARNAD: Let me just ask a question which everyone else who has been faithfully attending
these sessions is surely burning to ask: If some rules you have described constitute universal
constraints on all languages, yet they are not learned, nor are they somehow logically necessary
a priori, how did language get that way?
CHOMSKY: Well, it seems to me that would be like asking the question how does the heart get
that way? I mean we don't learn to have a heart, we don't learn to have arms rather than wings.
What is interesting to me is that the question should be asked. It seems to be a natural question,
everyone asks it. And we should ask, why people ask it.
My feeling is that if, say, the Martian that I was imagining were to look at earthlings and
investigate them he would have no reason to doubt that language is as much an organ of the
body as the eye or the heart or the liver. It's strictly characteristic of the species, has a highly
intricate structure, developed more or less independently of experience in very specific ways, and
so on. It has all the general properties of an organ of the body.
Why does it seem so strange to us to think in those terms? In other words, why does it seem to us
so strange to us to consider human beings in the mental aspects of their life as we consider any object of the natural world?
Why is it so natural to insist on a dichotomy in accordance with which we treat the physical development of humans as
belonging to the physical world, but not their mental development?
My own feeling is, that what we have here is an inversion of a historical tradition that really ultimately has religious and other
roots. Traditionally it was regarded as impossible, for all sorts of reasons, to study the human soul by the method of science.
Now, what's interesting to me is, precisely within those tendencies in science that tried to be naturalistic, that tried to defend
science against religions, barbarism and so on. Precisely in those branches of science the same curious refusal to deal with the
facts persisted, so that the question you raise seems to pose an overwhelming paradox to an investigator. The problem seems
overwhelming: to explain the growth of this particular mental organ, human language, through the interaction of a genetically
determined system with experience, although analogous questions about other organs do not seem to arise with the same force.
I think the question arises in the case of language exactly as it does in the case of the eye, the heart or the sexual organs (to pick
something that matures long after birth) and so on. There is every reason to suppose that this mental organ, human language,
develops in accordance with its genetically determined characteristics, with some minor modifications that give one language
or another, depending on experience. But than, one would say the same about any bodily organ as far as I can see. Stevan Harnad2011-12-16T00:58:07Z2011-12-16T00:58:07Zhttp://cogprints.org/id/eprint/7753This item is in the repository with the URL: http://cogprints.org/id/eprint/77532011-12-16T00:58:07ZOn Adjoint Dynamical SystemsTransformations of dynamical systems and organismic structures are discussed in terms of adjoint, simple adjoint and weak adjoint functors of organismic supercategories during development and evolution of organisms on markedly different timescales. A representation of nuclear transplants in terms of adjoint functors and a novel interpretation of nuclear transplant experiments is proposed. Three new theorems are proven for adjoint dynamical systems representing multi-potent developing cells and additional results are obtained for weak adjoint systems such as differentiated (specialized) cells.Prof. Dr. I. C. BaianuicbProf.Dr. Dragos Scripcariu2011-12-16T00:58:54Z2011-12-16T00:58:54Zhttp://cogprints.org/id/eprint/7743This item is in the repository with the URL: http://cogprints.org/id/eprint/77432011-12-16T00:58:54ZOrganismic Supercategories: III. Qualitative Dynamics of Systems The representation of biological systems by means of organismic supercategories, developed in previous papers, is further discussed. The different approaches to relational biology, developed by Rashevsky, Rosen and by Baianu and Marinescu, are compared with Qualitative Dynamics of Systems which was initiated by Henri Poincaré (1881). On the basis of this comparison some concrete results concerning dynamics of genetic system, development, fertilization, regeneration, analogies, and oncogenesis are derived.Prof. Dr. I.C. Baianuicb2004-06-19Z2011-03-11T08:55:37Zhttp://cogprints.org/id/eprint/3674This item is in the repository with the URL: http://cogprints.org/id/eprint/36742004-06-19ZOrganismic Supercategories and Qualitative Dynamics of Systems The representation of biological systems by means of organismic supercategories, developed in previous papers, is further discussed. The different approaches to relational biology, developed by Rashevsky, Rosen and by Baianu and Marinescu, are compared with Qualitative Dynamics of Systems which was initiated by Henri Poincaré (1881). On the basis of this comparison some concrete results concerning dynamics of genetic system, development, fertilization, regeneration, analogies, and oncogenesis are derived.Professor I.C. Baianuicb2011-12-16T00:58:58Z2011-12-16T00:58:58Zhttp://cogprints.org/id/eprint/7752This item is in the repository with the URL: http://cogprints.org/id/eprint/77522011-12-16T00:58:58ZOrganismic Supercategores: II. On Multistable Systems
The representation of biological systems in terms of organismic supercategories, introduced in previous papers by Baianu et al. (Bull. Math. Biophysics,30, 625–636;31, 59–70) is further discussed. To state more clearly this representation some new definitions are introduced. Also, some necessary changes in axiomatics are made. The conclusion is reached that any organismic supercategory has at least one superpushout, and this expresses the fact that biological systems are multistable. This way a connection between some results of Rashevsky’s theory of organismic sets and our results becomes obvious.Prof. Dr. I.C. Baianuicb2004-10-06Z2011-12-16T00:59:02Zhttp://cogprints.org/id/eprint/3831This item is in the repository with the URL: http://cogprints.org/id/eprint/38312004-10-06ZOrganismic Supercategories: I. Proposals for a General Unified Theory of Systems- Classical, Quantum, and Complex Biological Systems.
The representation of physical and complex biological systems in terms of organismic supercategories was introduced in 1968 by Baianu and Marinescu in the attached paper which was published in the Bulletin of Mathematical Biophysics, edited by Nicolas Rashevsky. The different approaches to relational biology, developed by Rashevsky, Rosen and by Baianu et al.(1968,1969,1973,1974,1987,2004)were later discussed.
The present paper is an attempt to outline an abstract unitary theory of systems. In the introduction some of the previous abstract representations of systems are discussed. Also a possible connection of abstract representations of systems with a general theory of measure is proposed. Then follow some necessary definitions and authors' proposals for an axiomatic theory of systems. Finally some concrete examples are analyzed in the light of the proposed theory.
An abstract representation of biological systems from the standpoint of the theory of supercategories is presented. The relevance of such representations forG-relational biologies is suggested. In section A the basic concepts of our representation, that is class, system, supercategory and measure are introduced. Section B is concerned with the mathematical representation starting with some axioms and principles which are natural extensions of the current abstract representations in biology. Likewise, some extensions of the principle of adequate design are introduced in section C. Two theorems which present the connection between categories and supercategories are proved. Two other theorems concerning the dynamical behavior of biological and biophysical systems are derived on the basis of the previous considerations. Section D is devoted to a general study of oscillatory behavior in enzymic systems, some general quantitative relations being derived from our representation. Finally, the relevance of these results for a quantum theoretic approach to biology is discussed.
http://www.springerlink.com/content/141l35843506596h/Prof. Dr. I.C. BaianuicbDr. Mircea M. Marinescu