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| Editorial | |
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| Codes and Evolution | |
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| Codes of Biosequences | |
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| Introduction | |
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| Hierarchy of the Codes | |
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| DNA Level Codes | |
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| RNA Level Codes | |
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| Codes of Protein Sequences | |
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| Fast Adaptation Code | |
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| The Codes of Evolutionary Past | |
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| Superposition of the Codes and Interactions Between Them | |
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| Is That All? | |
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| References | |
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| The Mechanisms of Evolution: Natural Selection and Natural Conventions | |
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| Introduction | |
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| The Organic Codes | |
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| The First Major Transition: The Origin of Genes | |
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| The Second Major Transition: The Origin of Proteins | |
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| The Fingerprints of the Organic Codes | |
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| The Splicing Codes | |
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| The Signal Transduction Codes | |
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| The Cytoskeleton Codes | |
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| The Compartment Codes | |
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| The Sequence Codes | |
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| A Stream of Codes | |
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| The Mechanisms of Evolution | |
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| The Molecular Mechanisms | |
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| Copying and Coding | |
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| Different Mechanisms at Different Levels | |
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| Natural Selection and Natural Conventions | |
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| Codes and Macroevolution | |
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| The Contribution of the Codes | |
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| The Contribution of Natural Selection | |
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| Common Descent | |
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| Conclusion | |
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| References | |
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| The Genetic Code | |
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| Catalytic Propensity of Amino Acids and the Origins of the Genetic Code and Proteins | |
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| Introduction | |
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| Catalytic Propensity of Amino Acids and Organization of the Genetic Code | |
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| The Anticodon Hairpin as the Ancient Adaptor | |
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| Towards the Appearance of Proteins | |
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| Towards an Experimental Test of the CCH Hypothesis with Catalytically Important Amino Acids | |
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| References | |
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| Why the Genetic Code Originated: Implications for the Origin of Protein Synthesis | |
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| Introduction | |
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| Peptidyl-tRNA-like Molecules were the Centre of Protocell Catalysis and the Fulcrum for the Origin of the Genetic Code | |
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| The First 'Messengers RNAs' Codified Successions of Interactions Between Different Peptide-RNAs | |
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| The Birth of the First mRNA | |
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| A Prediction of the Model | |
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| Conclusions | |
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| References | |
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| Self-Referential Formation of the Genetic System | |
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| Introduction | |
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| The Biotic World | |
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| Strings and Folding | |
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| Hydropathy and Cohesiveness | |
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| Networks and Stability | |
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| The Ribonucleoprotein (RNP) World and Prebiotic Chemistry | |
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| The Coded Biotic World | |
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| Hypotheses of Early Translation | |
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| The Self-Referential Model | |
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| The Pools of Reactants: tRNAs and Amino Acids | |
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| Stages in the Formation of the Coding System | |
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| The tRNA Dimers Orient the Entire Process | |
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| Processes Forming the Code | |
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| Amino Acid Coding | |
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| The Palindromic Triplets and Pairs | |
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| Steps in the Coding at Each Box | |
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| Proteins Organized the Code | |
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| Stages Indicated by the Hydropathy Correlation | |
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| Selection in the Regionalization of Attributes | |
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| Protein Structure and Nucleic Acid-Binding | |
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| Protein Stability and Nonspecific Punctuation | |
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| Specific Punctuation | |
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| Nucleic Acid-Binding | |
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| Protein Conformations | |
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| Amino Acid Biosynthesis and Possible Precodes at the Core of the Matrix | |
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| Biosynthesis of Gly and Ser Driven by Stage 1 Protein Synthesis | |
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| The Proteic Synthetases | |
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| The Atypical Acylation Systems | |
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| Regionalization and Plasticity of the Synthetases | |
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| Specificity and Timing the Entrance of Synthetases | |
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| Evolutionary Code Variants and the Hierarchy of Codes | |
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| Discussion | |
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| The Systemic Concept of the Gene | |
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| Stability, Abundance and Strings as Driving Forces | |
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| Origins of the Genetic System and of Cells | |
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| Memories for Self-Production | |
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| What is Life | |
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| Information | |
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| References | |
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| The Mathematical Structure of the Genetic Code | |
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| Introduction | |
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| A Biochemical Communication Code Called the 'Standard Genetic Code' | |
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| Specifying the Two Levels of Degeneracy of the Standard Genetic Code | |
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| Degeneracy Distribution | |
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| Codon Distribution | |
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| A Mathematical Description of the Standard Genetic Code | |
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| A Particular Non-Power Number Representation System as a Structural Isomorphism with the Genetic Code Mapping | |
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| A Mathematical Model of the Genetic Code | |
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| Symmetry Properties | |
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| Degeneracy-6 Amino Acids | |
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| The Mathematical Model | |
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| Palindromic Symmetry and the Genetic Code Model | |
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| Parity of Codons | |
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| Rumer's Class | |
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| A Complete Hierarchy of Symmetries Related to the Complement-to-One Binary Operation | |
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| A, G Exchanging Symmetry Involving 16 Codons (Non-Degeneracy-6, -3, and -1 Amino Acids) | |
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| A, G Non-Exchanging Symmetry of 8 Codons Pertaining to the Degeneracy-6 Amino Acids Leucine and Arginine | |
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| A[left and right arrow]G Exchanging Symmetry of 4 Codons Pertaining to the other Degeneracy-6 Amino Acid Serine and Its Palindromically Associated Amino Acid Threonine | |
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| Four Remaining A, G, Ending Codons | |
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| Other Symmetries | |
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| Complement-to-one in the Seventh Position | |
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| Error Control and Dynamical Attractors: A High Level Strategy for the Management of Genetic Information? | |
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| References | |
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| The Arithmetical Origin of the Genetic Code | |
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| Introduction | |
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| A Stony Script and Frozen Accident | |
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| A "Language of Nature" | |
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| Prime Number 037 | |
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| The Genetic Code Itself | |
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| Rumer's Transformation | |
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| Hasegawa's and Miyata's Nucleons | |
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| A Real-life Global Balance | |
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| A Virtual Global Balance | |
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| Arithmetic in Gamow's "Context" | |
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| The Systematization Principle | |
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| The "Egyptian Triangle" | |
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| The Message | |
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| Two 5' Strings | |
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| Two Center Strings | |
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| The Decimalism | |
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| The Formula of the Genetic Code | |
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| Chemistry Obeying Arithmetic | |
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| The Gene Abacus | |
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| Conclusion | |
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| References | |
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| Protein, Lipid, and Sugar Codes | |
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| Protein Linguistics and the Modular Code of the Cytoskeleton | |
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| Introduction | |
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| Protein Linguistics | |
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| Protein Modularity and the Syntactic Units of a Protein Linguistic Grammar | |
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| The Cytoskeleton | |
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| The Cytoskeleton is a Self-Reproducing von Neumann Automaton | |
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| A Modular Code Encapsulated in the Cytoskeleton | |
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| Nature is Structured in a Language-like Fashion | |
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| Conclusions | |
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| References | |
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| A Lipid-based Code in Nuclear Signalling | |
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| Introduction | |
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| Multiple Role of Inositides in Signal Transduction | |
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| Lipid Signal Transduction at the Nucleus | |
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| Clues for the Nuclear Localization of the Inositol Lipid Signalling System | |
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| Nuclear Domains Involved in Inositide Signalling | |
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| Evolution of the Inositide Signalling System | |
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| Towards the Deciphering of the Nuclear Inositol Lipid Signal Transduction Code | |
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| Conclusions | |
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| References | |
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| Biological Information Transfer Beyond the Genetic Code: The Sugar Code | |
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| Introduction | |
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| The Sugar Code: Basic Principles | |
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| The Sugar Code: The Third Dimension | |
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| Lectins: Translators of the Sugar Code | |
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| Principles of Protein-Carbohydrate Recognition | |
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| How to Define Potent Ligand Mimetics | |
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| Conclusions | |
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| References | |
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| The Immune Self Code: From Correspondence to Complexity | |
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| Introduction: Codes of Complexity | |
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| The Immune Self | |
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| The Reductionist Perspective | |
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| Putting Complexity into the Picture | |
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| Where is the Self? | |
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| Codes and Context | |
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| Codes of Complexity | |
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| References | |
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| Signal Transduction Codes and Cell Fate | |
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| Signal Transduction as a Recognition Science | |
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| A Census of Cell Senses | |
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| Levels of Organization and Signal Transduction Codes | |
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| Polysemic Signs, Degenerated Codes, Selected Meanings | |
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| References | |
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| Neural, Mental, and Cultural Codes | |
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| Towards an Understanding of Language Origins | |
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| Introduction | |
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| Genetic Background of Language | |
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| Brain and Language | |
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| Brain Epigenesis and Gene-language Co-evolution | |
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| Selective Scenarios for the Origin of Language | |
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| A Possible Modelling Approach | |
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| Evolutionary Neurogenetic Algorithm | |
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| Simulation of Brain Development | |
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| Benchmars Tasks: Game Theory | |
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| Outlook | |
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| References | |
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| The Codes of Language: Turtles All the Way Up? | |
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| The Language Stance | |
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| Coding | |
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| Language-Behaviour versus Morse Code | |
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| Challenges to Constructed Process Models | |
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| From Wordings to Dynamic Language | |
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| External Adaptors in Language? | |
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| Human Symbol Grounding | |
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| Below the Skin | |
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| Artefactual Selves? | |
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| Turtles All the Way Up? | |
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| References | |
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| Code and Context in Gene Expression, Cognition, and Consciousness | |
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| Introduction | |
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| Gene Expression and Linguistic Behaviour | |
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| Cognition | |
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| Code and Context in Consciousness and Intersubjectivity | |
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| Conclusion | |
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| References | |
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| Neural Coding in the Neuroheuristic Perspective | |
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| Prolegomenon | |
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| The Neuroheuristic Paradigm | |
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| The Coding Paradox | |
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| Spatio-Temporal Patterns of Neural Activity | |
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| The Neural Catastrophe | |
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| Postlude | |
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| References | |
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| Error Detection and Correction Codes | |
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| Introduction | |
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| Number Representation Systems | |
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| Information Theory, Redundancy, and Error Correction | |
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| The Shannon Theorem | |
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| Parity Based Error Detection/Correction Methods | |
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| Other Error Detection/Correction Methods, Genetic and Neural Systems, and a Nonlinear Dynamics Approach for Biological Information Processing | |
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| References | |
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| The Musical Code between Nature and Nurture: Ecosemiotic and Neurobiological Claims | |
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| Introduction | |
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| Dealing with Music: Towards an Operational Approach | |
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| Musical Sense-making and the Concept of Code | |
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| Universals of Perception, Cognition, and Emotion | |
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| Universals in music: Do they Exist? | |
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| Primary and Secondary Code | |
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| The Concept of Coding | |
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| Coding and Representation | |
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| Principles of Perceptual Organisation: Steps and Levels of Processing | |
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| Levels of Processing | |
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| Nativism and the Wired-in Circuitry | |
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| Arousal, Emotion, and Feeling | |
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| The Role of Cognitive Penetration | |
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| Psychobiology and the Mind-Brain Relationship | |
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| Psychophysics and Psychophysical Elements | |
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| Psychobiology and its Major Claims | |
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| The Neurobiological Approach | |
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| Brain and Mind: Towards a New Phrenology | |
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| Neural Plasticity and the Role of Adaptation | |
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| Structural and Functional Adaptations | |
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| Conclusion | |
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| References | |
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| Index | |