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Codes of Life The Rules of Macroevolution

ISBN-10: 1402063393

ISBN-13: 9781402063398

Edition: 2008

Authors: Marcello Barbieri

List price: $279.99
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Description:

Building on a range of disciplines ??? from biology and anthropology to philosophy and linguistics ??? this book draws on the expertise of leading names in the study of organic, mental and cultural codes brought together by the emerging discipline of biosemiotics. The book??'s 18 chapters present a range of experimental evidence which suggests that the genetic code was only the first in a long series of organic codes, and that it has been the appearance of new codes ??? organic, mental and cultural ??? that paved the way for the major transitions in the history of life. While the existence of many organic codes has been proposed since the 1980s, this volume represents the first multi-authored attempt to deal with the range of codes relevant to life, and to reveal the ubiquitous role of coding mechanisms in both organic and mental evolution. This creates the conditions for a synthesis of biology and linguistics that finally overcomes the old divide between nature and culture. The book will appeal to all those interested in the origins and evolution of life, including biologists (from molecular and cellular biologists to evolutionary and developmental biologists), ecologists, anthropologists, psychologists, philosophers of science, linguists, and researchers interested in the history of science, the origins of life, artificial life and intelligence, and information theory and communication technology.
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Book details

List price: $279.99
Copyright year: 2008
Publisher: Springer
Publication date: 11/7/2007
Binding: Hardcover
Pages: 440
Size: 6.00" wide x 9.25" long x 1.00" tall
Weight: 1.980
Language: English

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