Life Sciences, Information Sciences

Developed from presentations given at the Cerisy SVSI (Sciences de la vie, sciences de l’information) conference held in 2016, this book presents a broad overview of thought and research at the intersection of life sciences and information sciences. The contributors to this edited volume explore life and information on an equal footing, with each considered as crucial to the other. In the first part of the book, the relation of life and information in the functioning of genes, at both the phylogenetic and ontogenetic levels, is articulated and the common understanding of DNA as code is problematized from a range of perspectives. The second part of the book homes in on the algorithmic nature of information, questioning the fit between life and automaton and the accompanying division between individualization and invariance. Consisting of both philosophical speculation and ethological research, the explorations in this book are a timely intervention into prevailing understandings of the relation between information and life.

Table of Contents:
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