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E-raamat: Codes of Life: The Rules of Macroevolution

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Edited by Marcello Barbieri

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Sari: Biosemiotics 1
Ilmumisaeg: 26-Oct-2007
Kirjastus: Springer-Verlag New York Inc.
Keel: eng
ISBN-13: 9781402063404

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Formaat: PDF+DRM
Sari: Biosemiotics 1
Ilmumisaeg: 26-Oct-2007
Kirjastus: Springer-Verlag New York Inc.
Keel: eng
ISBN-13: 9781402063404

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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 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.

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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From the reviews:

"Biosemiotics purports to be a new synthesis of existing theories and compilations of theories addressing evolutionary bases. Barbieri has asked a group of researchers to present their ideas on a wide-ranging set of notions about change and stability. This work offers an impressive array of facts and speculations, extremely stimulating in origin and execution. the articles are generally well done with good bibliographies, and they will be useful to many researchers. Summing Up: Recommended. Graduate students and researchers/faculty." (F. W. Yow, CHOICE, Vol. 45 (10), June, 2008)

Editorial

Marcello Barbieri

Part 1 Codes and Evolution

Codes of Biosequences

(12)

Edward N. Trifonov

Introduction

(2)

Hierarchy of the Codes

(5)

DNA Level Codes

(1)

RNA Level Codes

(1)

Codes of Protein Sequences

(1)

Fast Adaptation Code

(1)

The Codes of Evolutionary Past

(1)

Superposition of the Codes and Interactions Between Them

(1)

Is That All?

(4)

References

(3)

The Mechanisms of Evolution: Natural Selection and Natural Conventions

(24)

Marcello Barbieri

Introduction

(1)

Part 1 -- The Organic Codes

(1)

The First Major Transition: The Origin of Genes

(1)

The Second Major Transition: The Origin of Proteins

(1)

The Fingerprints of the Organic Codes

(1)

The Splicing Codes

(1)

The Signal Transduction Codes

(1)

The Cytoskeleton Codes

(1)

The Compartment Codes

(1)

The Sequence Codes

(1)

A Stream of Codes

(1)

Part 2 -- The Mechanisms of Evolution

(1)

The Molecular Mechanisms

(1)

Copying and Coding

(1)

Different Mechanisms at Different Levels

(1)

Natural Selection and Natural Conventions

(1)

Codes and Macroevolution

(1)

The Contribution of the Codes

(2)

The Contribution of Natural Selection

(1)

Common Descent

(1)

Conclusion

(6)

References

(5)

Part 2 The Genetic Code

Catalytic Propensity of Amino Acids and the Origins of the Genetic Code and Proteins

(20)

Adam Kun

Sandor Pongor

Ferenc Jordan

Eors Szathmary

Introduction

(4)

Catalytic Propensity of Amino Acids and Organization of the Genetic Code

(5)

The Anticodon Hairpin as the Ancient Adaptor

(3)

Towards the Appearance of Proteins

(4)

Towards an Experimental Test of the CCH Hypothesis with Catalytically Important Amino Acids

(4)

References

(3)

Why the Genetic Code Originated: Implications for the Origin of Protein Synthesis

(10)

Massimo Di Giulio

Introduction

(1)

Peptidyl-tRNA-like Molecules were the Centre of Protocell Catalysis and the Fulcrum for the Origin of the Genetic Code

(1)

The First `Messengers RNAs' Codified Successions of Interactions Between Different Peptide-RNAs

(2)

The Birth of the First mRNA

(3)

A Prediction of the Model

(1)

Conclusions

(3)

References

(3)

Self-Referential Formation of the Genetic System

(42)

Romeu Cardoso Guimaraes

Carlos Henrique Costa Moreira

Savio Torres de Farias

Introduction

(1)

The Biotic World

(3)

Strings and Folding

(1)

Hydropathy and Cohesiveness

(1)

Networks and Stability

(1)

The Ribonucleoprotein (RNP) World and Prebiotic Chemistry

(1)

The Coded Biotic World

(3)

Hypotheses of Early Translation

(1)

The Self-Referential Model

(18)

The Pools of Reactants: tRNAs and Amino Acids

(1)

Stages in the Formation of the Coding System

(5)

The tRNA Dimers Orient the Entire Process

(1)

Processes Forming the Code

(1)

Amino Acid Coding

(1)

The Palindromic Triplets and Pairs

(1)

Steps in the Coding at Each Box

(1)

Proteins Organized the Code

(1)

Stages Indicated by the Hydropathy Correlation

(2)

Selection in the Regionalization of Attributes

(1)

Protein Structure and Nucleic Acid-Binding

(1)

Protein Stability and Nonspecific Punctuation

(1)

Specific Punctuation

(2)

Nucleic Acid-Binding

(1)

Protein Conformations

(1)

Amino Acid Biosynthesis and Possible Precodes at the Core of the Matrix

(2)

Biosynthesis of Gly and Ser Driven by Stage 1 Protein Synthesis

(1)

The Proteic Synthetases

(5)

The Atypical Acylation Systems

(1)

Regionalization and Plasticity of the Synthetases

(1)

Specificity and Timing the Entrance of Synthetases

(1)

Evolutionary Code Variants and the Hierarchy of Codes

(1)

Discussion

100

(11)

The Systemic Concept of the Gene

100

(2)

Stability, Abundance and Strings as Driving Forces

102

(1)

Origins of the Genetic System and of Cells

103

(1)

Memories for Self-Production

104

(1)

What is Life

104

(1)

Information

105

(2)

References

107

(4)

The Mathematical Structure of the Genetic Code

111

(42)

Diego L. Gonzalez

Introduction

112

(3)

A Biochemical Communication Code Called the `Standard Genetic Code'

115

(3)

Specifying the Two Levels of Degeneracy of the Standard Genetic Code

118

(3)

Degeneracy Distribution

120

(1)

Codon Distribution

121

(1)

A Mathematical Description of the Standard Genetic Code

121

(7)

A Particular Non-Power Number Representation System as a Structural Isomorphism with the Genetic Code Mapping

126

(2)

A Mathematical Model of the Genetic Code

128

(7)

Symmetry Properties

129

(4)

Degeneracy-6 Amino Acids

133

(1)

The Mathematical Model

134

(1)

Palindromic Symmetry and the Genetic Code Model

135

(5)

Parity of Codons

137

(1)

Rumer's Class

137

(3)

A Complete Hierarchy of Symmetries Related to the Complement-to-One Binary Operation

140

(5)

A, G Exchanging Symmetry Involving Codons (Non-Degeneracy-6, -3, and -1 Amino Acids)

141

(1)

A, G Non-Exchanging Symmetry of 8 Codons Pertaining to the Degeneracy-6 Amino Acids Leucine and Arginine

141

(1)

A↔G Exchanging Symmetry of 4 Codons Pertaining to the other Degeneracy-6 Amino Acid Serine and Its Palindromically Associated Amino Acid Threonine

142

(1)

Four Remaining A, G, Ending Codons

142

(1)

Other Symmetries

143

(1)

Complement-to-one in the Seventh Position

144

(1)

Error Control and Dynamical Attractors: A High Level Strategy for the Management of Genetic Information?

145

(8)

References

150

(3)

The Arithmetical Origin of the Genetic Code

153

(36)

Vladimir shCherbak

Introduction

153

(1)

A Stony Script and Frozen Accident

154

(1)

A ``Language of Nature''

155

(2)

Prime Number 037

157

(1)

The Genetic Code Itself

158

(2)

Rumer's Transformation

160

(1)

Hasegawa's and Miyata's Nucleons

161

(1)

A Real-life Global Balance

162

(2)

A Virtual Global Balance

164

(2)

Arithmetic in Gamow's ``Context''

166

(3)

The Systematization Principle

169

(2)

The ``Egyptian Triangle''

171

(1)

The Message

172

(6)

Two 5' Strings

174

(1)

Two Center Strings

174

(4)

The Decimalism

178

(1)

The Formula of the Genetic Code

179

(1)

Chemistry Obeying Arithmetic

180

(2)

The Gene Abacus

182

(1)

Conclusion

183

(6)

References

184

(5)

Part 3 Protein, Lipid, and Sugar Codes

Protein Linguistics and the Modular Code of the Cytoskeleton

189

(18)

Mario Gimona

Introduction

189

(1)

Protein Linguistics

190

(3)

Protein Modularity and the Syntactic Units of a Protein Linguistic Grammar

193

(2)

The Cytoskeleton

195

(3)

The Cytoskeleton is a Self-Reproducing von Neumann Automaton

198

(1)

A Modular Code Encapsulated in the Cytoskeleton

199

(2)

Nature is Structured in a Language-like Fashion

201

(1)

Conclusions

202

(5)

References

203

(4)

A Lipid-based Code in Nuclear Signalling

207

(16)

Nadir M. Maraldi

Introduction

207

(2)

Multiple Role of Inositides in Signal Transduction

209

(2)

Lipid Signal Transduction at the Nucleus

211

(1)

Clues for the Nuclear Localization of the Inositol Lipid Signalling System

211

(3)

Nuclear Domains Involved in Inositide Signalling

214

(1)

Evolution of the Inositide Signalling System

215

(2)

Towards the Deciphering of the Nuclear Inositol Lipid Signal Transduction Code

217

(1)

Conclusions

218

(5)

References

219

(4)

Biological Information Transfer Beyond the Genetic Code: The Sugar Code

223

(24)

Hans-Joachim Gabius

Introduction

224

(1)

The Sugar Code: Basic Principles

224

(4)

The Sugar Code: The Third Dimension

228

(2)

Lectins: Translators of the Sugar Code

230

(4)

Principles of Protein-Carbohydrate Recognition

234

(2)

How to Define Potent Ligand Mimetics

236

(3)

Conclusions

239

(8)

References

240

(7)

The Immune Self Code: From Correspondence to Complexity

247

(18)

Yair Neuman

Introduction: Codes of Complexity

247

(1)

The Immune Self

248

(1)

The Reductionist Perspective

249

(4)

Putting Complexity into the Picture

253

(1)

Where is the Self?

254

(3)

Codes and Context

257

(3)

Codes of Complexity

260

(5)

References

262

(3)

Signal Transduction Codes and Cell Fate

265

(22)

Marcella Faria

Signal Transduction as a Recognition Science

266

(1)

A Census of Cell Senses

267

(5)

Levels of Organization and Signal Transduction Codes

272

(6)

Polysemic Signs, Degenerated Codes, Selected Meanings

278

(9)

References

282

(5)

Part 4 Neural, Mental, and Cultural Codes

Towards an Understanding of Language Origins

287

(32)

Eors Szathmary

Introduction

287

(5)

Genetic Background of Language

292

(4)

Brain and Language

296

(2)

Brain Epigenesis and Gene-language Co-evolution

298

(3)

Selective Scenarios for the Origin of Language

301

(5)

A Possible Modelling Approach

306

(13)

Evolutionary Neurogenetic Algorithm

307

(2)

Simulation of Brain Development

309

(1)

Benchmars Tasks: Game Theory

310

(2)

Outlook

312

(1)

References

313

(6)

The Codes of Language: Turtles All the Way Up?

319

(28)

Stephen J. Cowley

The Language Stance

319

(1)

Coding

320

(6)

Language-Behaviour versus Morse Code

322

(2)

Challenges to Constructed Process Models

324

(2)

From Wordings to Dynamic Language

326

(2)

External Adaptors in Language?

328

(3)

Human Symbol Grounding

331

(6)

Below the Skin

334

(3)

Artefactual Selves?

337

(3)

Turtles All the Way Up?

340

(7)

References

342

(5)

Code and Context in Gene Expression, Cognition, and Consciousness

347

(10)

Sean O Nuallain

Introduction

348

(1)

Gene Expression and Linguistic Behaviour

349

(2)

Cognition

351

(2)

Code and Context in Consciousness and Intersubjectivity

353

(2)

Conclusion

355

(2)

References

355

(2)

Neural Coding in the Neuroheuristic Perspective

357

(22)

Alessandro E.P. Villa

Prolegomenon

358

(1)

The Neuroheuristic Paradigm

358

(4)

The Coding Paradox

362

(3)

Spatio-Temporal Patterns of Neural Activity

365

(3)

The Neural Catastrophe

368

(6)

Postlude

374

(5)

References

375

(4)

Error Detection and Correction Codes

379

(16)

Diego L. Gonzalez

Introduction

379

(1)

Number Representation Systems

380

(2)

Information Theory, Redundancy, and Error Correction

382

(8)

The Shannon Theorem

384

(1)

Parity Based Error Detection/Correction Methods

385

(5)

Other Error Detection/Correction Methods, Genetic and Neural Systems, and a Nonlinear Dynamics Approach for Biological Information Processing

390

(5)

References

393

(2)

The Musical Code between Nature and Nurture: Ecosemiotic and Neurobiological Claims

395

(40)

Mark Reybrouck

Introduction

395

(1)

Dealing with Music: Towards an Operational Approach

396

(2)

Musical Sense-making and the Concept of Code

398

(12)

Universals of Perception, Cognition, and Emotion

399

(3)

Universals in music: Do they Exist?

402

(3)

Primary and Secondary Code

405

(2)

The Concept of Coding

407

(2)

Coding and Representation

409

(1)

Principles of Perceptual Organisation: Steps and Levels of Processing

410

(9)

Levels of Processing

411

(2)

Nativism and the Wired-in Circuitry

413

(1)

Arousal, Emotion, and Feeling

414

(4)

The Role of Cognitive Penetration

418

(1)

Psychobiology and the Mind-Brain Relationship

419

(3)

Psychophysics and Psychophysical Elements

420

(1)

Psychobiology and its Major Claims

421

(1)

The Neurobiological Approach

422

(5)

Brain and Mind: Towards a New Phrenology

422

(2)

Neural Plasticity and the Role of Adaptation

424

(1)

Structural and Functional Adaptations

425

(2)

Conclusion

427

(8)

References

428

(7)

Index

435

Marcello Barbieri is Professor of Embryology at the University of Ferrara, Italy, president of the Italian Association for Theoretical Biology, Editor-in-Chief of the Journal of Biosemiotics, and Co-Editor of the Springer book series in Biosemiotics.

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