Contents

Editorial v

Marcello Barbieri

Part 1 Codes and Evolution

Chapter 1 Codes of Biosequences 3

Edward N. Trifonov

1 Introduction 3

2 Hierarchy of the Codes 5

2.1 DNA Level Codes 6

2.2 RNA Level Codes 7

2.3 Codes of Protein Sequences 7

2.4 Fast Adaptation Code 8

2.5 The Codes of Evolutionary Past 9

3 Superposition of the Codes and Interactions

Between Them 10

4 Is That All? 11

References 12

Chapter 2 The Mechanisms of Evolution: Natural Selection and

Natural Conventions 15

Marcello Barbieri

Introduction 16

Part 1 - The Organic Codes 17

1 The First Major Transition: The Origin of Genes 17

2 The Second Major Transition: The Origin of Proteins . . . . 18

3 The Fingerprints of the Organic Codes 19

4 The Splicing Codes 20

5 The Signal Transduction Codes 21

6 The Cytoskeleton Codes 22

7 The Compartment Codes 23

8 The Sequence Codes 24

9 A Stream of Codes 25

Part 2 - The Mechanisms of Evolution 26

1 The Molecular Mechanisms 26

2 Copying and Coding 27

3 Different Mechanisms at Different Levels 28

4 Natural Selection and Natural Conventions 29

5 Codes and Macroevolution 29

6 The Contribution of the Codes 30

7 The Contribution of Natural Selection 32

8 Common Descent 32

9 Conclusion 33

References 34

Part 2 The Genetic Code

Chapter 3 Catalytic Propensity of Amino Acids and the Origins of the Genetic Code and Proteins 39

Ádám Kun, Sándor Pongor, Ferenc Jordán, and Eörs Szathmáry

1 Introduction 39

2 Catalytic Propensity of Amino Acids and Organization of the Genetic Code 43

3 The Anticodon Hairpin as the Ancient Adaptor 48

4 Towards the Appearance of Proteins 51

5 Towards an Experimental Test of the CCH Hypothesis with Catalytically Important Amino Acids 55

References 56

Chapter 4 Why the Genetic Code Originated: Implications for the Origin of Protein Synthesis 59

Massimo Di Giulio

1 Introduction 59

2 Peptidyl-tRNA-like Molecules were the Centre of Protocell Catalysis and the Fulcrum for the Origin of the Genetic Code 60

3 The First 'Messengers RNAs' Codified Successions of Interactions Between Different Peptide-RNAs 61

4 The Birth of the First mRNA 63

5 A Prediction of the Model 66

6 Conclusions 66

References 66

Chapter 5 Self-Referential Formation of the Genetic System 69

Romeu Cardoso Guimaraes, Carlos Henrique Costa Moreira, and Savio Torres de Farias

1 Introduction 70

2 The Biotic World 70

2.1 Strings and Folding 70

2.2 Hydropathy and Cohesiveness 71

2.3 Networks and Stability 71

2.4 The Ribonucleoprotein (RNP) World and Prebiotic Chemistry 72

3 The Coded Biotic World 73

3.1 Hypotheses of Early Translation 75

4 The Self-Referential Model 76

4.1 The Pools of Reactants: tRNAs and Amino Acids 78

4.2 Stages in the Formation of the Coding System . . . . 78

4.3 The tRNA Dimers Orient the Entire Process 83

4.4 Processes Forming the Code 84

4.5 Amino Acid Coding 84

4.6 The Palindromic Triplets and Pairs 85

4.7 Steps in the Coding at Each Box 86

4.8 Proteins Organized the Code 86

4.9 Stages Indicated by the Hydropathy Correlation . . . 86

4.10 Selection in the Regionalization of Attributes 88

4.11 Protein Structure and Nucleic Acid-Binding 88

4.12 Protein Stability and Nonspecific Punctuation . . . . 89

4.13 Specific Punctuation 90

4.14 Nucleic Acid-Binding 92

4.15 Protein Conformations 92

4.16 Amino Acid Biosynthesis and Possible

Precodes at the Core of the Matrix 92

4.17 Biosynthesis of Gly and Ser Driven by Stage 1 Protein Synthesis 94

5 The Proteic Synthetases 94

5.1 The Atypical Acylation Systems 97

5.2 Regionalization and Plasticity of the Synthetases . . 97

5.3 Specificity and Timing the Entrance of Synthetases 98

6 Evolutionary Code Variants and the Hierarchy of Codes . . 99

7 Discussion 100

7.1 The Systemic Concept of the Gene 100

7.2 Stability, Abundance and Strings as

Driving Forces 102

7.3 Origins of the Genetic System and of Cells 103

7.4 Memories for Self-Production 104

7.5 What is Life 104

7.6 Information 105

References 107

Chapter 6 The Mathematical Structure of the Genetic Code 111

Diego L. Gonzalez

1 Introduction 112

2 A Biochemical Communication Code Called the 'Standard Genetic Code' 115

3 Specifying the Two Levels of Degeneracy of the Standard Genetic Code 118

3.1 Degeneracy Distribution 120

3.2 Codon Distribution 121

4 A Mathematical Description of the Standard

Genetic Code 121

4.1 A Particular Non-Power Number Representation System as a Structural Isomorphism with the Genetic Code Mapping 126

5 A Mathematical Model of the Genetic Code 128

5.1 Symmetry Properties 129

5.2 Degeneracy-6 Amino Acids 133

5.3 The Mathematical Model 134

6 Palindromic Symmetry and the Genetic

Code Model 135

6.1 Parity of Codons 137

6.2 Rumer's Class 137

7 A Complete Hierarchy of Symmetries Related to the Complement-to-One Binary Operation 140

7.1 A, G Exchanging Symmetry Involving

Amino Acids) 141

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

Leucine and Arginine 141

7.3 AoG Exchanging Symmetry of 4 Codons Pertaining to the other Degeneracy-6 Amino Acid Serine and Its Palindromically Associated

Amino Acid Threonine 142

7.4 Four Remaining A, G, Ending Codons 142

7.5 Other Symmetries 143

7.6 Complement-to-one in the Seventh Position 144

8 Error Control and Dynamical Attractors: A High Level Strategy for the Management of Genetic Information? 145

References 150

Chapter 7 The Arithmetical Origin of the Genetic Code 153

Vladimir sftCherbak

1 Introduction 153

2 A Stony Script and Frozen Accident 154

3 A "Language of Nature" 155

4 Prime Number 037 157

5 The Genetic Code Itself 158

6 Rumer's Transformation 160

7 Hasegawa's and Miyata's Nucleons 161

8 A Real-life Global Balance 162

9 A Virtual Global Balance 164

10 Arithmetic in Gamow's "Context" 166

11 The Systematization Principle 169

12 The "Egyptian Triangle" 171

13 The Message 172

13.1 Two 5' Strings 174

13.2 Two Center Strings 174

14 The Decimalism 178

15 The Formula of the Genetic Code 179

16 Chemistry Obeying Arithmetic 180

17 The Gene Abacus 182

18 Conclusion 183

References 184

Part 3 Protein, Lipid, and Sugar Codes

Chapter 8 Protein Linguistics and the Modular Code of the Cytoskeleton 189

Mario Gimona

1 Introduction 189

2 Protein Linguistics 190

3 Protein Modularity and the Syntactic Units of a Protein Linguistic Grammar 193

4 The Cytoskeleton 195

5 The Cytoskeleton is a Self-Reproducing von Neumann Automaton 198

6 A Modular Code Encapsulated in the Cytoskeleton 199

7 Nature is Structured in a Language-like Fashion 201

8 Conclusions 202

References 203

Chapter 9 A Lipid-based Code in Nuclear Signalling 207

Nadir M. Maraldi

1 Introduction 207

2 Multiple Role of Inositides in Signal Transduction 209

3 Lipid Signal Transduction at the Nucleus 211

4 Clues for the Nuclear Localization of the Inositol Lipid Signalling System 211

5 Nuclear Domains Involved in Inositide Signalling 214

6 Evolution of the Inositide Signalling System 215

7 Towards the Deciphering of the Nuclear Inositol

Lipid Signal Transduction Code 217

8 Conclusions 218

References 219

Chapter 10 Biological Information Transfer Beyond the Genetic Code: The Sugar Code 223

Hans-Joachim Gabius

1 Introduction 224

2 The Sugar Code: Basic Principles 224

3 The Sugar Code: The Third Dimension 228

3.1 Lectins: Translators of the Sugar Code 230

4 Principles of Protein-Carbohydrate Recognition 234

5 How to Define Potent Ligand Mimetics 236

6 Conclusions 239

References 240

Chapter 11 The Immune Self Code: From Correspondence to Complexity 247

Yair Neuman

1 Introduction: Codes of Complexity 247

2 The Immune Self 248

3 The Reductionist Perspective 249

4 Putting Complexity into the Picture 253

5 Where is the Self? 254

6 Codes and Context 257

7 Codes of Complexity 260

References 262

Chapter 12 Signal Transduction Codes and Cell Fate 265

Marcella Faria

1 Signal Transduction as a Recognition Science 266

2 A Census of Cell Senses 267

3 Levels of Organization and Signal Transduction Codes . . 272

4 Polysemic Signs, Degenerated Codes, Selected Meanings 278 References 282

Part 4 Neural, Mental, and Cultural Codes

Chapter 13 Towards an Understanding of Language Origins 287

Eörs Szathmary

1 Introduction 287

2 Genetic Background of Language 292

3 Brain and Language 296

4 Brain Epigenesis and Gene-language Co-evolution 298

5 Selective Scenarios for the Origin of Language 301

6 A Possible Modelling Approach 306

6.1 Evolutionary Neurogenetic Algorithm 307

6.2 Simulation of Brain Development 309

6.3 Benchmars Tasks: Game Theory 310

6.4 Outlook 312

References 313

Chapter 14 The Codes of Language: Turtles All the Way Up? 319

Stephen J. Cowley

1 The Language Stance 319

2 Coding 320

2.1 Language-Behaviour versus Morse Code 322

2.2 Challenges to Constructed Process Models 324

3 From Wordings to Dynamic Language 326

4 External Adaptors in Language? 328

5 Human Symbol Grounding 331

5.1 Below the Skin 334

6 Artefactual Selves? 337

7 Turtles All the Way Up? 340

References 342

Chapter 15 Code and Context in Gene Expression, Cognition, and Consciousness 347

Sean O Nuallain

1 Introduction 348

2 Gene Expression and Linguistic Behaviour 349

3 Cognition 351

4 Code and Context in Consciousness and Intersubjectivity 353

5 Conclusion 355

References 355

Chapter 16 Neural Coding in the Neuroheuristic Perspective 357

Alessandro E.P. Villa

1 Prolegomenon 358

2 The Neuroheuristic Paradigm 358

3 The Coding Paradox 362

4 Spatio-Temporal Patterns of Neural Activity 365

5 The Neural Catastrophe 368

6 Postlude 374

References 375

Chapter 17 Error Detection and Correction Codes 379

Diego L. Gonzalez

1 Introduction 379

2 Number Representation Systems 380

3 Information Theory, Redundancy, and Error Correction . . 382

3.1 The Shannon Theorem 384

3.2 Parity Based Error Detection/Correction Methods . . 385

4 Other Error Detection/Correction Methods,

Genetic and Neural Systems, and a Nonlinear Dynamics

Approach for Biological Information Processing 390

References 393

Chapter 18 The Musical Code between Nature and Nurture:

Ecosemiotic and Neurobiological Claims 395

Mark Reybrouck

1 Introduction 395

2 Dealing with Music: Towards an Operational

Approach 396

3 Musical Sense-making and the Concept of Code 398

3.1 Universals of Perception, Cognition, and Emotion 399

3.2 Universals in music: Do they Exist? 402

3.3 Primary and Secondary Code 405

3.4 The Concept of Coding 407

3.5 Coding and Representation 409

4 Principles of Perceptual Organisation: Steps and Levels of Processing 410

4.1 Levels of Processing 411

4.2 Nativism and the Wired-in Circuitry 413

4.3 Arousal, Emotion, and Feeling 414

4.4 The Role of Cognitive Penetration 418

5 Psychobiology and the Mind-Brain Relationship 419

5.1 Psychophysics and Psychophysical Elements 420

5.2 Psychobiology and its Major Claims 421

6 The Neurobiological Approach 422

6.1 Brain and Mind: Towards a New Phrenology 422

6.2 Neural Plasticity and the Role of Adaptation 424

6.3 Structural and Functional Adaptations 425

7 Conclusion 427

References 428

Index 435

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