Preface xv
Selection of Publications xix
Introduction xxiii
Part 1. From Gene to Species: Variability, Randomness and Stability 1
Chapter 1. The Emergence of Life: Some Notes on the Origin of Biological Information 3
Antonio LAZCANO
1.1. Acknowledgments 12
1.2. Bibliography 12
Chapter 2. Fluctuating RNA 17
Giuseppe ZACCAI, Marie-Christine MAUREL and Ada YONATH
2.1. The ribosome 17
2.2. Ribosome dynamics 18
2.3. Primitive RNA, ribozymes and viroids 20
2.4. The proto-ribosome 21
2.5. Bibliography 22
Chapter 3. Artificial Darwinian Evolution of Nucleic Acids 23
Frédéric DUCONGÉ
3.1. Refresher on Darwin's theory of evolution 23
3.2. The molecular mechanisms of evolution 24
3.3. Molecular evolution external to the being 25
3.4. Imagery of molecular evolution 26
3.5. Conclusion 27
3.6. Acknowledgments 27
3.7. Bibliography 27
Chapter 4. Information and Epigenetics 29
András PÁLDI
4.1. Bibliography 34
Chapter 5. Molecular Forces and Motion in the Transmission of Information in Biology 37
Giuseppe ZACCAI
5.1. The dynamics-function hypothesis 37
5.2. From thermodynamics to molecular forces 38
5.3. Like the devil, biology is in the details 39
5.4. The guitar in the river: theoretical MD 40
5.5. Experimental MD 40
5.6. Measuring average MD in whole cells 41
5.7. Dynamics response to stress 41
5.8. Conclusion: evolution "is obliged" to select dynamics 42
5.9. Bibliography 42
Chapter 6. Decline and Contingency, Bases of Biological Evolution 45
Bernard DUJON
6.1. Introduction 45
6.2. Too many genes in the genomes 46
6.3. Parasitism and symbiosis 48
6.4. Asexual eukaryotes 49
6.5. Yeasts 50
6.6. Conclusion 52
6.7. Bibliography 52
Chapter 7. Conservation, Co-evolution and Dynamics: From Sequence to Function 55
Alessandra CARBONE
7.1. Introduction 55
7.2. Reverse engineering: from the protein described in a single dimension to its 3D properties 56
7.3. Before any modeling, the geometric and physical properties, the behavior and history of proteins are characterized 57
7.3.1. Proteins are dynamic objects 57
7.3.2. Proteins have a history 57
7.3.3. Some proteins share the same evolutionary history 57
7.4. Chance and selection govern the generation of observed sequences 58
7.5. Conservation and interaction sites of proteins 59
7.6. Co-evolution: identification of contacts that can occur at different moments in the lifetime of a protein 60
7.7. Co-evolution used to reconstruct protein-protein interaction networks in viruses 61
7.8. Molecular modeling of several partners used to reconstruct protein-protein interaction networks for prokaryotic and eukaryotic organisms 63
7.9. Dynamics and function 64
7.10. Conclusions 64
7.11. Acknowledgments 65
7.12. Bibliography 65
Chapter 8. Localization of the Morphodynamic Information in Amniote Formation 69
Vincent FLEURY
8.1. Introduction 69
8.2. Schematic view of an amniote 70
8.3. Mechanism of amniote formation 74
8.4. Additional features 77
8.5. Discussion and conclusion 78
8.6. Bibliography 79
Chapter 9. From the Century of the Gene to that of the Organism: Introduction to New Theoretical Perspectives 81
Maël MONTÉVIL, Giuseppe LONGO and Ana SOTO
9.1. Introduction 81
9.2. Philosophical positions 87
9.3. From the inert to the living 87
9.4. Cell theory: a starting point toward a theory of organisms 88
9.5. The founding principles: from entanglement to integration? 89
9.5.1. Genealogy of the three proposed principles: the default state, the principle of organization and the principle of variation 89
9.5.2. How to organize these principles into a coherent ensemble? 90
9.6. Conclusion 92
9.7. Acknowledgments 94
9.8. Bibliography 94
Chapter 10. The Game of Survival, Chance and Complexity 99
Philippe KOURILSKY
10.1. Introduction 99
10.2. Complex systems 100
10.2.1. Definition 100
10.2.2. How to evaluate the complexity of a system? 102
10.2.3. The notion of robustness 102
10.3. Chance and robustness in living organisms 103
10.3.1. The system of natural defenses in living organisms 103
10.3.2. Natural defenses and robustness 103
10.3.3. Natural defenses, chance and hazards 104
10.4. Evolution and chance 105
10.4.1. On the links between robustness and evolution 105
10.4.2. On human evolution 106
10.5. Conclusion: the logic of the living 107
10.6. Bibliography 108
Chapter 11. Life from the Origins to Homo sapiens 109
Jean FOURTAUX
11.1. Setting the scene 109
11.2. The conquest of solid earth by the vertebrates 110
11.3. A few insights on evolution 111
11.3.1. The horse 112
11.3.2. Eagle and vulture 112
11.3.3. The cetaceans 112
11.3.4. The Red Queen 112
11.3.5. The spotted hyena 112
11.4. Primates and humans 113
Chapter 12. Plankton Chronicles and the Tara Expeditions 117
Christian SARDET
12.1. Plankton 117
12.2. Plankton and climate 118
12.3. The Tara Oceans expedition 121
12.4. Bibliography 123
Chapter 13. The Living Species is Not a Natural Kind but an Intellectual Construction 125
Philippe GRANDCOLAS
13.1. Introduction 125
13.2. Two ways to study evolution: genealogy versus phylogeny 126
13.3. Three main families of concepts of species 128
13.4. Reconciling the different concepts: pragmatism or essentialism? 130
13.5. The species and the taxon name 131
13.6. The nature of species: a salutatory philosophical exercise 132
13.7. Bibliography 135
Chapter 14. The Boxes and their Content: What to Do with Invariants in Biology? 139
Guillaume LECOINTRE
14.1. Natural history 139
14.2. Natural history and evolution 141
14.3. The species 142
14.4. The grade 146
14.5. Genetic information 146
14.6. The body plan 148
14.7. On the misuse of convergences 149
14.8. Conclusion 151
14.9. Bibliography 151
Chapter 15. Probability, Sense and Evolution (Promenade) 153
Cédric VILLANI
15.1. Introduction 153
15.2. Difficult dialogue 154
15.3. Knowledge and big data 155
15.4. The probabilities 156
15.5. A few striking examples 157
15.5.1. Pagerank 157
15.5.2. Decoding 157
15.5.3. Reconstitution of preferences 157
15.5.4. Correspondence between genotype and phenotype 158
15.5.5. Phylogeny 158
15.5.6. Automatic recognition 160
15.5.7. Autopilot 160
15.5.8. Imitation of styles 160
15.5.9. And all the rest 160
15.6. The MCMC method 160
15.7. Neural networks 162
15.8. A few questions 164
15.8.1. Do we understand? 164
15.8.2. Describing convergence 165
15.8.3. Geometrizing 166
15.8.4. Varied questions 166
15.9. Bibliography 167
Part 2. Program and Life: Individuation and Interaction 169
Chapter 16. Towards an Algorithmic Approach to Life Sciences 171
Gérard BERRY
16.1. Prologue 171
16.2. Matter, energy, waves and information 172
16.3. Medical imaging 173
16.4. The simulation of the living 175
16.5. Computer modeling and its levels of abstraction 176
16.6. The role of embedded computing 178
16.7. Other subjects 179
16.8. But is all this without danger? 180
16.9. The importance of training 182
Chapter 17. Where Does the Notion of Function Come From? 183
Heinz WISMANN
Chapter 18. The Contribution of Artificial Life to Theoretical Biology 191
Hugues BERSINI
18.1. Introduction 191
18.2. Support to pedagogy 192
18.3. Food for thought: a philosophy in software form 193
18.4. Conclusions: royal life, falsifiable modeling 198
18.5. Bibliography 199
Chapter 19. Biochemical Programs and Analog-Digital Mixed Algorithms in the Cell 201
François FAGES and Guillaume LE GULUDEC
19.1. Introduction 201
19.2. Biochemical programs 202
19.2.1. Syntax 202
19.2.2. Semantics 203
19.2.3. Example of MAPK signaling networks 203
19.3. Behavioral logical specifications 205
19.4. Analog specifications 206
19.4.1. Computability and analog complexity theory . 206
19.4.2. Computability and biochemical algorithmic complexity 208
19.4.3. GPAC biochemical compilation 210
19.4.4. Analog-digital converter compared to MAPK 211
19.5. Biochemical compilation of sequentiality and cell cycle 212
19.6. Discussion 213
19.7. Bibliography 214
Chapter 20. From Computational Physics to the Origins of Life 217
A. Marco SAITTA
20.1. Prebiotic emergence of the basic bricks of life 217
20.2. Computational approaches and simulations in chemistry 219
20.3. Computational approaches and simulations in prebiotic chemistry 220
20.4. New challenges in modeling: reaction networks 222
20.5. At the frontiers of modeling in prebiotic chemistry: topological approaches 224
20.6. Conclusion and perspectives 227
20.7. Bibliography 227
Chapter 21. Computing and the Temptation of Babel 231
Kavé SALAMATIAN
21.1. Introduction 232
21.2. The role of information technologies 233
21.3. On conflicts of rationality and more specifically on rationality in biology 236
21.4. Information and its role in biology 239
21.5. Conclusion 241
21.6. Acknowledgments 241
21.7. Bibliography 241
Chapter 22. Big Data, Knowledge and Biology 243
Giuseppe LONGO and Maël MONTÉVIL
22.1. Introduction 243
22.2. Big databases, prediction and chance 245
22.3. Bibliography 247
Chapter 23. Natural Language, Formal Language and the Description of the Living World 249
Régine VIGNES LEBBE
23.1. Introduction 249
23.2. Describing the living world 250
23.2.1. The objects in the description of the living world 250
23.2.2. Describing specimens 251
23.2.3. Describing taxa 252
23.3. Formal language 253
23.3.1. Semantic step 253
23.3.2. The characters: several concepts 254
23.3.3. Structured computerization of knowledge 255
23.4. Conclusion 256
23.5. Bibliography 257
Chapter 24. Vital Individuation and Morphogenetic Information 259
Vincent BONTEMS
24.1. Introduction 259
24.2. The theory of vital individuation 261
24.3. Lamarck's ghost 263
24.4. DNA and its transductions 266
24.5. Schrödinger's flower 269
Chapter 25. How to Account for Interspecies Socio-cultural Phenomena? An Evolutionist and Interactionist Model 273
Dominique GUILLO
25.1. The difficult dialogue between social sciences and life sciences 273
25.2. The empire of the principle of identity in theories of society and culture 274
25.3. A field of neglected social and cultural phenomena 276
25.4. Linking social sciences and life sciences 279
25.5. Bibliography 281
Chapter 26. Life: A Simplex Whirlwind between Matter, Energy and Information 283
Jean-Claude BARREY
26.1. Introduction 283
26.2. The Craig-Lorenz principle, traditional base of animal and human behavior 284
26.3. The formulations incompatible with modern systemic biology 284
26.4. Lorenz's principle reformulated based on current biological data 287
26.5. Ethosociological interpretation of the reformulated principle 287
26.5.1. Ontogenesis, sociogenesis and phylogenesis 287
26.6. Regulating societies through economy: ethoeconomy 289
26.7. The bioethological stages of a social evolution 292
26.8. Conclusion 293
26.9. Bibliography 293
Chapter 27. Nutritional Interactions through the Living: from Individuals to Societies and Beyond 295
Mathieu LIHOREAU
27.1. The living: a complex nutritional system 295
27.2. Nutrition at the individual level 296
27.3. Nutrition at the collective level 297
27.3.1. Mass migrations 298
27.3.2. Collective decisions 299
27.3.3. Parental care 299
27.3.4. Cooperative foraging 300
27.3.5. Division of labor 300
27.3.6. Interactions between species 301
27.4. Toward a multilevel theory of nutrition? 302
27.5. Bibliography 303
Chapter 28. Epigenetic Regulation of Protein Biosynthesis by Scale Resonance: Study of the Reduction of ESCA Effects on Vines in Field Applications - Summary 2016 305
Pedro FERRANDIZ, Michel DUHAMEL and Joël STERNHEIMER
28.1. Introduction 305
28.2. Materials and methods 307
28.3. 2003-2011 results 308
28.4. Results 2012 310
28.5. Results 2013 311
28.6. Results 2014 312
28.7. Results 2015 313
28.8. Results 2016 314
28.9. Conclusions 315
Chapter 29. Quantum and Multiverse Inflation 317
Michel CASSÉ
29.1. Copernican and anti-Copernican revolutions 318
29.2. Selection criteria for the number of dimensions of space and time 318
29.3. Why is time monodimensional? 320
29.4. The bones of the void 320
29.5. The buzz effect of inflation 322
29.6. The eye hears and recognizes the fundamental and harmonic 325
Chapter 30. Reontologization of the World and of Life 329
Jean-Gabriel GANASCIA
30.1. Philosophy of information 329
30.2. Method and levels of abstraction 330
30.3. "Inforgs" and infosphere 332
30.4. Originality of the infosphere 333
30.5. Reontologization 335
30.6. Ethics of information 336
30.7. Bibliography 337
Chapter 31. Redesigning Life, a Serious and Credible Research Agenda? 339
Bernadette BENSAUDE VINCENT
31.1. Introduction 339
31.2. Favorite metaphors 341
31.3. Inappropriate metaphors 343
31.4. Ethical challenges and metaphysics 345
31.5. Bibliography 347
Chapter 32. Transhumanism and the Future of Negation 349
Jean-Michel BESNIER
List of Authors 359
Index 363
