Title Details

Thierry Gaudin is an engineer at MINES ParisTech and holds a doctorate in Information Sciences and Communication from Paris Nanterre University. He is a widely renowned expert in innovation policy and has worked with the OECD, European Commission and the World Bank.

Dominique Lacroix is a web publisher and photographer. After studying Classics at the University of Nice in France, she acquired diverse experience in multimedia. She is a co-founder, with Thierry Gaudin, of the 2100 Foundation.

Marie-Christine Maurel is Professor at Pierre and Marie Curie University (UPMC) and the Muséum National d'Histoire Naturelle in Paris. Her research focuses on the informational and catalytic properties of DNA and RNA and their role in the origin of life.

Jean-Charles Pomerol is a specialist in Decision Support Systems and former project leader for information technology in the Engineering Sciences Department at the CNRS. He was formerly in charge of the Artificial Intelligence laboratory at UPMC, Paris, as well as being the President of UPMC between 2006 and 2011.

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 TheoreticalPerspectives 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 andInteractionist 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