The codes of life : the rules of macroevolution

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.

Author Notes

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.

Reviews 1

Choice Review

Biosemiotics purports to be a new synthesis of existing theories and compilations of theories addressing evolutionary bases. Barbieri (Univ. of Ferrara, Italy) has asked a group of researchers to present their ideas on a wide-ranging set of notions about change and stability. Many of the ideas offer excellent backgrounds and intriguing positions. To assimilate this material is daunting, and to correlate each of 18 essays is virtually impossible. This work offers an impressive array of facts and speculations, extremely stimulating in origin and execution. This is not a collection to explore easily. The book contains four parts, with an abstract at the beginning of each article. Even if one is not interested in the idea of biosemiotics as a discipline, the articles are generally well done with good bibliographies, and they will be useful to many researchers. This book and subsequent volumes in the series present a fresh look at a discipline that has been at the forefront of biological thought in recent years. The reader is left to integrate the material, a worthy intellectual challenge indeed. Summing Up: Recommended. Graduate students and researchers/faculty. F. W. Yow emeritus, Kenyon College

Marcello BarbieriEdward N. TrifonovMarcello BarbieriAdam Kun and Sandor Pongor and Ferenc Jordan and Eors SzathmaryMassimo Di GiulioRomeu Cardoso Guimaraes and Carlos Henrique and Costa Moreira and Savio Torres de FariasDiego L. GonzalezVladimir shCherbakMario GimonaNadir M. MaraldiHans-Joachim GabiusYair NeumanMarcella FariaEors SzathmaryStephen J. CowleySean O NuallainAlessandro E.P. VillaDiego L. GonzalezMark Reybrouck

Editorial	p. v
Part 1 Codes and Evolution
Chapter 1 Codes of Biosequences	p. 3
1 Introduction	p. 3
2 Hierarchy of the Codes	p. 5
2.1 DNA Level Codes	p. 6
2.2 RNA Level Codes	p. 7
2.3 Codes of Protein Sequences	p. 7
2.4 Fast Adaptation Code	p. 8
2.5 The Codes of Evolutionary Past	p. 9
3 Superposition of the Codes and Interactions Between Them	p. 10
4 Is That All?	p. 11
References	p. 12
Chapter 2 The Mechanisms of Evolution: Natural Selection and Natural Conventions	p. 15
Introduction	p. 16
Part 1 The Organic Codes	p. 17
1 The First Major Transition: The Origin of Genes	p. 17
2 The Second Major Transition: The Origin of Proteins	p. 18
3 The Fingerprints of the Organic Codes	p. 19
4 The Splicing Codes	p. 20
5 The Signal Transduction Codes	p. 21
6 The Cytoskeleton Codes	p. 22
7 The Compartment Codes	p. 23
8 The Sequence Codes	p. 24
9 A Stream of Codes	p. 25
Part 2 The Mechanisms of Evolution	p. 26
1 The Molecular Mechanisms	p. 26
2 Copying and Coding	p. 27
3 Different Mechanisms at Different Levels	p. 28
4 Natural Selection and Natural Conventions	p. 29
5 Codes and Macroevolution	p. 29
6 The Contribution of the Codes	p. 30
7 The Contribution of Natural Selection	p. 32
8 Common Descent	p. 32
9 Conclusion	p. 33
References	p. 34
Part 2 The Genetic Code
Chapter 3 Catalytic Propensity of Amino Acids and the Origins of the Genetic Code and Proteins	p. 39
1 Introduction	p. 39
2 Catalytic Propensity of Amino Acids and Organization of the Genetic Code	p. 43
3 The Anticodon Hairpin as the Ancient Adaptor	p. 48
4 Towards the Appearance of Proteins	p. 51
5 Towards an Experimental Test of the CCH Hypothesis with Catalytically Important Amino Acids	p. 55
References	p. 56
Chapter 4 Why the Genetic Code Originated: Implications for the Origin of Protein Synthesis	p. 59
1 Introduction	p. 59
2 Peptidyl-tRNA-like Molecules were the Centre of Protocell Catalysis and the Fulcrum for the Origin of the Genetic Code	p. 60
3 The First 'Messengers RNAs' Codified Successions of Interactions Between Different Peptide-RNAs	p. 61
4 The Birth of the First mRNA	p. 63
5 A Prediction of the Model	p. 66
6 Conclusions	p. 66
References	p. 66
Chapter 5 Self-Referential Formation of the Genetic System	p. 69
1 Introduction	p. 70
2 The Biotic World	p. 70
2.1 Strings and Folding	p. 70
2.2 Hydropathy and Cohesiveness	p. 71
2.3 Networks and Stability	p. 71
2.4 The Ribonucleoprotein (RNP) World and Prebiotic Chemistry	p. 72
3 The Coded Biotic World	p. 73
3.1 Hypotheses of Early Translation	p. 75
4 The Self-Referential Model	p. 76
4.1 The Pools of Reactants: tRNAs and Amino Acids	p. 78
4.2 Stages in the Formation of the Coding System	p. 78
4.3 The tRNA Dimers Orient the Entire Process	p. 83
4.4 Processes Forming the Code	p. 84
4.5 Amino Acid Coding	p. 84
4.6 The Palindromic Triplets and Pairs	p. 85
4.7 Steps in the Coding at Each Box	p. 86
4.8 Proteins Organized the Code	p. 86
4.9 Stages Indicated by the Hydropathy Correlation	p. 86
4.10 Selection in the Regionalization of Attributes	p. 88
4.11 Protein Structure and Nucleic Acid-Binding	p. 88
4.12 Protein Stability and Nonspecific Punctuation	p. 89
4.13 Specific Punctuation	p. 90
4.14 Nucleic Acid-Binding	p. 92
4.15 Protein Conformations	p. 92
4.16 Amino Acid Biosynthesis and Possible Precodes at the Core of the Matrix	p. 92
4.17 Biosynthesis of Gly and Ser Driven by Stage 1 Protein Synthesis	p. 94
5 The Proteic Synthetases	p. 94
5.1 The Atypical Acylation Systems	p. 97
5.2 Regionalization and Plasticity of the Synthetases	p. 97
5.3 Specificity and Timing the Entrance of Synthetases	p. 98
6 Evolutionary Code Variants and the Hierarchy of Codes	p. 99
7 Discussion	p. 100
7.1 The Systemic Concept of the Gene	p. 100
7.2 Stability, Abundance and Strings as Driving Forces	p. 102
7.3 Origins of the Genetic System and of Cells	p. 103
7.4 Memories for Self-Production	p. 104
7.5 What is Life	p. 104
7.6 Information	p. 105
References	p. 107
Chapter 6 The Mathematical Structure of the Genetic Code	p. 111
1 Introduction	p. 112
2 A Biochemical Communication Code Called the 'Standard Genetic Code'	p. 115
3 Specifying the Two Levels of Degeneracy of the Standard Genetic Code	p. 118
3.1 Degeneracy Distribution	p. 120
3.2 Codon Distribution	p. 121
4 A Mathematical Description of the Standard Genetic Code	p. 121
4.1 A Particular Non-Power Number Representation System as a Structural Isomorphism with the Genetic Code Mapping	p. 126
5 A Mathematical Model of the Genetic Code	p. 128
5.1 Symmetry Properties	p. 129
5.2 Degeneracy-6 Amino Acids	p. 133
5.3 The Mathematical Model	p. 134
6 Palindromic Symmetry and the Genetic Code Model	p. 135
6.1 Parity of Codons	p. 137
6.2 Rumer's Class	p. 137
7 A Complete Hierarchy of Symmetries Related to the Complement-to-One Binary Operation	p. 140
7.1 A, G Exchanging Symmetry Involving 16 Codons (Non-Degeneracy-6, -3, and -1 Amino Acids)	p. 141
7.2 A, G Non-Exchanging Symmetry of 8 Codons Pertaining to the Degeneracy-6 Amino Acids Leucine and Arginine	p. 141
7.3 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	p. 142
7.4 Four Remaining A, G, Ending Codons	p. 142
7.5 Other Symmetries	p. 143
7.6 Complement-to-one in the Seventh Position	p. 144
8 Error Control and Dynamical Attractors: A High Level Strategy for the Management of Genetic Information?	p. 145
References	p. 150
Chapter 7 The Arithmetical Origin of the Genetic Code	p. 153
1 Introduction	p. 153
2 A Stony Script and Frozen Accident	p. 154
3 A "Language of Nature"	p. 155
4 Prime Number 037	p. 157
5 The Genetic Code Itself	p. 158
6 Rumer's Transformation	p. 160
7 Hasegawa's and Miyata's Nucleons	p. 161
8 A Real-life Global Balance	p. 162
9 A Virtual Global Balance	p. 164
10 Arithmetic in Gamow's "Context"	p. 166
11 The Systematization Principle	p. 169
12 The "Egyptian Triangle"	p. 171
13 The Message	p. 172
13.1 Two 5' Strings	p. 174
13.2 Two Center Strings	p. 174
14 The Decimalism	p. 178
15 The Formula of the Genetic Code	p. 179
16 Chemistry Obeying Arithmetic	p. 180
17 The Gene Abacus	p. 182
18 Conclusion	p. 183
References	p. 184
Part 3 Protein, Lipid, and Sugar Codes
Chapter 8 Protein Linguistics and the Modular Code of the Cytoskeleton	p. 189
1 Introduction	p. 189
2 Protein Linguistics	p. 190
3 Protein Modularity and the Syntactic Units of a Protein Linguistic Grammar	p. 193
4 The Cytoskeleton	p. 195
5 The Cytoskeleton is a Self-Reproducing von Neumann Automaton	p. 198
6 A Modular Code Encapsulated in the Cytoskeleton	p. 199
7 Nature is Structured in a Language-like Fashion	p. 201
8 Conclusions	p. 202
References	p. 203
Chapter 9 A Lipid-based Code in Nuclear Signalling	p. 207
1 Introduction	p. 207
2 Multiple Role of Inositides in Signal Transduction	p. 209
3 Lipid Signal Transduction at the Nucleus	p. 211
4 Clues for the Nuclear Localization of the Inositol Lipid Signalling System	p. 211
5 Nuclear Domains Involved in Inositide Signalling	p. 214
6 Evolution of the Inositide Signalling System	p. 215
7 Towards the Deciphering of the Nuclear Inositol Lipid Signal Transduction Code	p. 217
8 Conclusions	p. 218
References	p. 219
Chapter 10 Biological Information Transfer Beyond the Genetic Code: The Sugar Code	p. 223
1 Introduction	p. 224
2 The Sugar Code: Basic Principles	p. 224
3 The Sugar Code: The Third Dimension	p. 228
3.1 Lectins: Translators of the Sugar Code	p. 230
4 Principles of Protein-Carbohydrate Recognition	p. 234
5 How to Define Potent Ligand Mimetics	p. 236
6 Conclusions	p. 239
References	p. 240
Chapter 11 The Immune Self Code: From Correspondence to Complexity	p. 247
1 Introduction: Codes of Complexity	p. 247
2 The Immune Self	p. 248
3 The Reductionist Perspective	p. 249
4 Putting Complexity into the Picture	p. 253
5 Where is the Self?	p. 254
6 Codes and Context	p. 257
7 Codes of Complexity	p. 260
References	p. 262
Chapter 12 Signal Transduction Codes and Cell Fate	p. 265
1 Signal Transduction as a Recognition Science	p. 266
2 A Census of Cell Senses	p. 267
3 Levels of Organization and Signal Transduction Codes	p. 272
4 Polysemic Signs, Degenerated Codes, Selected Meanings	p. 278
References	p. 282
Part 4 Neural, Mental, and Cultural Codes
Chapter 13 Towards an Understanding of Language Origins	p. 287
1 Introduction	p. 287
2 Genetic Background of Language	p. 292
3 Brain and Language	p. 296
4 Brain Epigenesis and Gene-language Co-evolution	p. 298
5 Selective Scenarios for the Origin of Language	p. 301
6 A Possible Modelling Approach	p. 306
6.1 Evolutionary Neurogenetic Algorithm	p. 307
6.2 Simulation of Brain Development	p. 309
6.3 Benchmars Tasks: Game Theory	p. 310
6.4 Outlook	p. 312
References	p. 313
Chapter 14 The Codes of Language: Turtles All the Way Up?	p. 319
1 The Language Stance	p. 319
2 Coding	p. 320
2.1 Language-Behaviour versus Morse Code	p. 322
2.2 Challenges to Constructed Process Models	p. 324
3 From Wordings to Dynamic Language	p. 326
4 External Adaptors in Language?	p. 328
5 Human Symbol Grounding	p. 331
5.1 Below the Skin	p. 334
6 Artefactual Selves?	p. 337
7 Turtles All the Way Up?	p. 340
References	p. 342
Chapter 15 Code and Context in Gene Expression, Cognition, and Consciousness	p. 347
1 Introduction	p. 348
2 Gene Expression and Linguistic Behaviour	p. 349
3 Cognition	p. 351
4 Code and Context in Consciousness and Intersubjectivity	p. 353
5 Conclusion	p. 355
References	p. 355
Chapter 16 Neural Coding in the Neuroheuristic Perspective	p. 357
1 Prolegomenon	p. 358
2 The Neuroheuristic Paradigm	p. 358
3 The Coding Paradox	p. 362
4 Spatio-Temporal Patterns of Neural Activity	p. 365
5 The Neural Catastrophe	p. 368
6 Postlude	p. 374
References	p. 375
Chapter 17 Error Detection and Correction Codes	p. 379
1 Introduction	p. 379
2 Number Representation Systems	p. 380
3 Information Theory, Redundancy, and Error Correction	p. 382
3.1 The Shannon Theorem	p. 384
3.2 Parity Based Error Detection/Correction Methods	p. 385
4 Other Error Detection/Correction Methods, Genetic and Neural Systems, and a Nonlinear Dynamics Approach for Biological Information Processing	p. 390
References	p. 393
Chapter 18 The Musical Code between Nature and Nurture: Ecosemiotic and Neurobiological Claims	p. 395
1 Introduction	p. 395
2 Dealing with Music: Towards an Operational Approach	p. 396
3 Musical Sense-making and the Concept of Code	p. 398
3.1 Universals of Perception, Cognition, and Emotion	p. 399
3.2 Universals in music: Do they Exist?	p. 402
3.3 Primary and Secondary Code	p. 405
3.4 The Concept of Coding	p. 407
3.5 Coding and Representation	p. 409
4 Principles of Perceptual Organisation: Steps and Levels of Processing	p. 410
4.1 Levels of Processing	p. 411
4.2 Nativism and the Wired-in Circuitry	p. 413
4.3 Arousal, Emotion, and Feeling	p. 414
4.4 The Role of Cognitive Penetration	p. 418
5 Psychobiology and the Mind-Brain Relationship	p. 419
5.1 Psychophysics and Psychophysical Elements	p. 420
5.2 Psychobiology and its Major Claims	p. 421
6 The Neurobiological Approach	p. 422
6.1 Brain and Mind: Towards a New Phrenology	p. 422
6.2 Neural Plasticity and the Role of Adaptation	p. 424
6.3 Structural and Functional Adaptations	p. 425
7 Conclusion	p. 427
References	p. 428
Index	p. 435

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