17,317 research outputs found
Categorical Ontology of Complex Systems, Meta-Systems and Theory of Levels: The Emergence of Life, Human Consciousness and Society
Single cell interactomics in simpler organisms, as well as somatic cell interactomics in multicellular organisms, involve biomolecular interactions in complex signalling pathways that were recently represented in modular terms by quantum automata with âreversible behaviorâ 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 âclassicalâ states that determine molecular dynamics subject to Boltzmann statistics and âsteady-stateâ, metabolic (multi-stable) manifolds, together with âconfigurationâ 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 âstandardâ 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 âcycleâ to the next, and thus it requires substantial changes in the modeling strategies, mathematical tools and experimental designs aimed at understanding cancer mechanisms. Novel solutions to this important problem in carcinogenesis are proposed and experimental validation procedures are suggested. From a medical research and clinical standpoint, this approach has important consequences for addressing and preventing the development of cancer resistance to medical therapy in ongoing clinical trials involving stage III cancer patients, as well as improving the designs of future clinical trials for cancer treatments.\ud
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KEYWORDS: Emergence of Life and Human Consciousness;\ud
Proteomics; Artificial Intelligence; Complex Systems Dynamics; Quantum Automata models and Quantum Interactomics; quantum-weave dynamic patterns underlying human consciousness; specific molecular processes underlying extensive memory, learning, anticipation mechanisms and human consciousness; emergence of human consciousness during the early brain development in children; Cancer cell âcyclingâ; 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 patientsâ possible improvements of the designs for future clinical trials and cancer treatments. \ud
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The Nature of the Chemical Process. 1. Symmetry Evolution - Revised Information Theory, Similarity Principle and Ugly Symmetry
Three laws of information theory have been proposed. Labeling by introducing
nonsymmetry and formatting by introducing symmetry are defined. The function L
(L=lnw, w is the number of microstates, or the sum of entropy and information,
L=S+I) of the universe is a constant (the first law of information theory). The
entropy S of the universe tends toward a maximum (the second law law of
information theory). For a perfect symmetric static structure, the information
is zero and the static entropy is the maximum (the third law law of information
theory). Based on the Gibbs inequality and the second law of the revised
information theory we have proved the similarity principle (a continuous higher
similarity-higher entropy relation after the rejection of the Gibbs paradox)
and proved the Curie-Rosen symmetry principle (a higher symmetry-higher
stability relation) as a special case of the similarity principle. Some
examples in chemical physics have been given. Spontaneous processes of all
kinds of molecular interaction, phase separation and phase transition,
including symmetry breaking and the densest molecular packing and
crystallization, are all driven by information minimization or symmetry
maximization. The evolution of the universe in general and evolution of life in
particular can be quantitatively considered as a series of symmetry breaking
processes. The two empirical rules - similarity rule and complementarity rule -
have been given a theoretical foundation. All kinds of periodicity in space and
time are symmetries and contribute to the stability. Symmetry is beautiful
because it renders stability. However, symmetry is in principle ugly because it
is associated with information loss.Comment: 29 pages, 14 figure
The face, beauty, and symmetry: Perceiving asymmetry in beautiful faces
The relationship between bilateral facial symmetry and beauty remains to be clarified. Here, straight head-on photographs of âbeautifulâ faces from the collections of professional modeling agencies were selected. First, beauty ratings were obtained for these faces. Then, the authors created symmetrical left-left and right-right composites of the beautiful faces and asked a new group of subjects to choose the most attractive pair member. âSameâ responses were allowed. No difference between the left-left and right-right composites was revealed but significant differences were obtained between âsameâ and the left-left or right-right. These results show that subjects detected asymmetry in beauty and suggest that very beautiful faces can be functionally asymmetrical
Orientational Harmonic Model for Illusory Boundary Formation in Biological Vision
An extension to the Boundary Contour System model is proposed to account for boundary completion through vertices with arbitrary numbers of orientations, in a manner consistent with psychophysical observartions, by way of harmonic resonance in a neural architecture
From Simple to Complex and Ultra-complex Systems:\ud A Paradigm Shift Towards Non-Abelian Systems Dynamics
Atoms, molecules, organisms distinguish layers of reality because of the causal links that govern their behavior, both horizontally (atom-atom, molecule-molecule, organism-organism) and vertically (atom-molecule-organism). This is the first intuition of the theory of levels. Even if the further development of the theory will require imposing a number of qualifications to this initial intuition, the idea of a series of entities organized on different levels of complexity will prove correct. Living systems as well as social systems and the human mind present features remarkably different from those characterizing non-living, simple physical and chemical systems. We propose that super-complexity requires at least four different categorical frameworks, provided by the theories of levels of reality, chronotopoids, (generalized) interactions, and anticipation
From Simple to Complex and Ultra-complex Systems:\ud A Paradigm Shift Towards Non-Abelian Systems Dynamics
Atoms, molecules, organisms distinguish layers of reality because of the causal links that govern their behavior, both horizontally (atom-atom, molecule-molecule, organism-organism) and vertically (atom-molecule-organism). This is the first intuition of the theory of levels. Even if the further development of the theory will require imposing a number of qualifications to this initial intuition, the idea of a series of entities organized on different levels of complexity will prove correct. Living systems as well as social systems and the human mind present features remarkably different from those characterizing non-living, simple physical and chemical systems. We propose that super-complexity requires at least four different categorical frameworks, provided by the theories of levels of reality, chronotopoids, (generalized) interactions, and anticipation
Automated Identification and Classification of Stereochemistry: Chirality and Double Bond Stereoisomerism
Stereoisomers have the same molecular formula and the same atom connectivity
and their existence can be related to the presence of different
three-dimensional arrangements. Stereoisomerism is of great importance in many
different fields since the molecular properties and biological effects of the
stereoisomers are often significantly different. Most drugs for example, are
often composed of a single stereoisomer of a compound, and while one of them
may have therapeutic effects on the body, another may be toxic. A challenging
task is the automatic detection of stereoisomers using line input
specifications such as SMILES or InChI since it requires information about
group theory (to distinguish stereoisomers using mathematical information about
its symmetry), topology and geometry of the molecule. There are several
software packages that include modules to handle stereochemistry, especially
the ones to name a chemical structure and/or view, edit and generate chemical
structure diagrams. However, there is a lack of software capable of
automatically analyzing a molecule represented as a graph and generate a
classification of the type of isomerism present in a given atom or bond.
Considering the importance of stereoisomerism when comparing chemical
structures, this report describes a computer program for analyzing and
processing steric information contained in a chemical structure represented as
a molecular graph and providing as output a binary classification of the isomer
type based on the recommended conventions. Due to the complexity of the
underlying issue, specification of stereochemical information is currently
limited to explicit stereochemistry and to the two most common types of
stereochemistry caused by asymmetry around carbon atoms: chiral atom and double
bond. A Webtool to automatically identify and classify stereochemistry is
available at http://nams.lasige.di.fc.ul.pt/tools.ph
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