Life Sciences, Information Sciences

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 xvSelection of Publications xixIntroduction xxiiiPart 1. From Gene to Species: Variability, Randomness and Stability 1Chapter 1. The Emergence of Life: Some Notes on the Origin of Biological Information 3Antonio LAZCANO1.1. Acknowledgments 121.2. Bibliography 12Chapter 2. Fluctuating RNA 17Giuseppe ZACCAI, Marie-Christine MAUREL and Ada YONATH2.1. The ribosome 172.2. Ribosome dynamics 182.3. Primitive RNA, ribozymes and viroids  202.4. The proto-ribosome 212.5. Bibliography 22Chapter 3. Artificial Darwinian Evolution of Nucleic Acids  23Frédéric DUCONGÉ3.1. Refresher on Darwin’s theory of evolution 233.2. The molecular mechanisms of evolution  243.3. Molecular evolution external to the being 253.4. Imagery of molecular evolution 263.5. Conclusion 273.6. Acknowledgments 273.7. Bibliography 27Chapter 4. Information and Epigenetics 29András PÁLDI4.1. Bibliography 34Chapter 5. Molecular Forces and Motion in the Transmission of Information in Biology 37Giuseppe ZACCAI5.1. The dynamics–function hypothesis  375.2. From thermodynamics to molecular forces 385.3. Like the devil, biology is in the details 395.4. The guitar in the river: theoretical MD 405.5. Experimental MD 405.6. Measuring average MD in whole cells 415.7. Dynamics response to stress 415.8. Conclusion: evolution “is obliged” to select dynamics 425.9. Bibliography 42Chapter 6. Decline and Contingency, Bases of Biological Evolution 45Bernard DUJON6.1. Introduction 456.2. Too many genes in the genomes 466.3. Parasitism and symbiosis 486.4. Asexual eukaryotes 496.5. Yeasts 506.6. Conclusion 526.7. Bibliography 52Chapter 7. Conservation, Co-evolution and Dynamics: From Sequence to Function 55Alessandra CARBONE7.1. Introduction 557.2. Reverse engineering: from the protein described in a single dimension to its 3D properties 567.3. Before any modeling, the geometric and physical properties, the behavior and history of proteins are characterized 577.3.1. Proteins are dynamic objects 577.3.2. Proteins have a history 577.3.3. Some proteins share the same evolutionary history 577.4. Chance and selection govern the generation of observed sequences 587.5. Conservation and interaction sites of proteins 597.6. Co-evolution: identification of contacts that can occur at different moments in the lifetime of a protein 607.7. Co-evolution used to reconstruct protein–protein interaction networks in viruses 617.8. Molecular modeling of several partners used to reconstruct protein–protein interaction networks for prokaryotic and eukaryotic organisms 637.9. Dynamics and function 647.10. Conclusions 647.11. Acknowledgments 657.12. Bibliography 65Chapter 8. Localization of the Morphodynamic Information in Amniote Formation 69Vincent FLEURY8.1. Introduction 698.2. Schematic view of an amniote  708.3. Mechanism of amniote formation 748.4. Additional features 778.5. Discussion and conclusion 788.6. Bibliography 79Chapter 9. From the Century of the Gene to that of the Organism: Introduction to New Theoretical Perspectives 81Maël MONTÉVIL, Giuseppe LONGO and Ana SOTO9.1. Introduction 819.2. Philosophical positions 879.3. From the inert to the living 879.4. Cell theory: a starting point toward a theory of organisms  889.5. The founding principles: from entanglement to integration?  899.5.1. Genealogy of the three proposed principles: the default state, the principle of organization and the principle of variation 899.5.2. How to organize these principles into a coherent ensemble?  909.6. Conclusion 929.7. Acknowledgments 949.8. Bibliography 94Chapter 10. The Game of Survival, Chance and Complexity 99Philippe KOURILSKY10.1. Introduction 9910.2. Complex systems 10010.2.1. Definition 10010.2.2. How to evaluate the complexity of a system?  10210.2.3. The notion of robustness  10210.3. Chance and robustness in living organisms 10310.3.1. The system of natural defenses in living organisms 10310.3.2. Natural defenses and robustness 10310.3.3. Natural defenses, chance and hazards 10410.4. Evolution and chance 10510.4.1. On the links between robustness and evolution 10510.4.2. On human evolution 10610.5. Conclusion: the logic of the living 10710.6. Bibliography 108Chapter 11. Life from the Origins to Homo sapiens 109Jean FOURTAUX11.1. Setting the scene 10911.2. The conquest of solid earth by the vertebrates 11011.3. A few insights on evolution  11111.3.1. The horse 11211.3.2. Eagle and vulture 11211.3.3. The cetaceans 11211.3.4. The Red Queen 11211.3.5. The spotted hyena 11211.4. Primates and humans 113Chapter 12. Plankton Chronicles and the Tara Expeditions  117Christian SARDET12.1. Plankton 11712.2. Plankton and climate 11812.3. The Tara Oceans expedition  12112.4. Bibliography 123Chapter 13. The Living Species is Not a Natural Kind but an Intellectual Construction 125Philippe GRANDCOLAS13.1. Introduction 12513.2. Two ways to study evolution: genealogy versus phylogeny  12613.3. Three main families of concepts of species 12813.4. Reconciling the different concepts: pragmatism or essentialism? 13013.5. The species and the taxon name 13113.6. The nature of species: a salutatory philosophical exercise  13213.7. Bibliography 135Chapter 14. The Boxes and their Content: What to Do with Invariants in Biology? 139Guillaume LECOINTRE14.1. Natural history 13914.2. Natural history and evolution 14114.3. The species 14214.4. The grade 14614.5. Genetic information 14614.6. The body plan 14814.7. On the misuse of convergences 14914.8. Conclusion 15114.9. Bibliography 151Chapter 15. Probability, Sense and Evolution (Promenade)  153Cédric VILLANI15.1. Introduction 15315.2. Difficult dialogue 15415.3. Knowledge and big data 15515.4. The probabilities 15615.5. A few striking examples 15715.5.1. Pagerank 15715.5.2. Decoding 15715.5.3. Reconstitution of preferences  15715.5.4. Correspondence between genotype and phenotype 15815.5.5. Phylogeny 15815.5.6. Automatic recognition 16015.5.7. Autopilot 16015.5.8. Imitation of styles 16015.5.9. And all the rest 16015.6. The MCMC method 16015.7. Neural networks 16215.8. A few questions 16415.8.1. Do we understand? 16415.8.2. Describing convergence  16515.8.3. Geometrizing 16615.8.4. Varied questions 16615.9. Bibliography 167Part 2. Program and Life: Individuation and Interaction  169Chapter 16. Towards an Algorithmic Approach to Life Sciences 171Gérard BERRY16.1. Prologue 17116.2. Matter, energy, waves and information  17216.3. Medical imaging 17316.4. The simulation of the living  17516.5. Computer modeling and its levels of abstraction 17616.6. The role of embedded computing  17816.7. Other subjects 17916.8. But is all this without danger? 18016.9. The importance of training 182Chapter 17. Where Does the Notion of Function Come From?  183Heinz WISMANNChapter 18. The Contribution of Artificial Life to Theoretical Biology 191Hugues BERSINI18.1. Introduction 19118.2. Support to pedagogy 19218.3. Food for thought: a philosophy in software form 19318.4. Conclusions: royal life, falsifiable modeling 19818.5. Bibliography 199Chapter 19. Biochemical Programs and Analog-Digital Mixed Algorithms in the Cell  201François FAGES and Guillaume LE GULUDEC19.1. Introduction 20119.2. Biochemical programs 20219.2.1. Syntax 20219.2.2. Semantics 20319.2.3. Example of MAPK signaling networks 20319.3. Behavioral logical specifications  20519.4. Analog specifications 20619.4.1. Computability and analog complexity theory . 20619.4.2. Computability and biochemical algorithmic complexity  20819.4.3. GPAC biochemical compilation 21019.4.4. Analog–digital converter compared to MAPK  21119.5. Biochemical compilation of sequentiality and cell cycle  21219.6. Discussion 21319.7. Bibliography 214Chapter 20. From Computational Physics to the Origins of Life 217A. Marco SAITTA20.1. Prebiotic emergence of the basic bricks of life 21720.2. Computational approaches and simulations in chemistry  21920.3. Computational approaches and simulations in prebiotic chemistry 22020.4. New challenges in modeling: reaction networks 22220.5. At the frontiers of modeling in prebiotic chemistry: topological approaches 22420.6. Conclusion and perspectives  22720.7. Bibliography 227Chapter 21. Computing and the Temptation of Babel 231Kavé SALAMATIAN21.1. Introduction 23221.2. The role of information technologies 23321.3. On conflicts of rationality and more specifically on rationality in biology 23621.4. Information and its role in biology 23921.5. Conclusion 24121.6. Acknowledgments 24121.7. Bibliography 241Chapter 22. Big Data, Knowledge and Biology 243Giuseppe LONGO and Maël MONTÉVIL22.1. Introduction 24322.2. Big databases, prediction and chance 24522.3. Bibliography 247Chapter 23. Natural Language, Formal Language and the Description of the Living World  249Régine VIGNES LEBBE23.1. Introduction 24923.2. Describing the living world 25023.2.1. The objects in the description of the living world 25023.2.2. Describing specimens 25123.2.3. Describing taxa 25223.3. Formal language 25323.3.1. Semantic step 25323.3.2. The characters: several concepts 25423.3.3. Structured computerization of knowledge  25523.4. Conclusion 25623.5. Bibliography 257Chapter 24. Vital Individuation and Morphogenetic Information 259Vincent BONTEMS24.1. Introduction 25924.2. The theory of vital individuation  26124.3. Lamarck’s ghost 26324.4. DNA and its transductions 26624.5. Schrödinger’s flower 269Chapter 25. How to Account for Interspecies Socio-cultural Phenomena? An Evolutionist and Interactionist Model 273Dominique GUILLO25.1. The difficult dialogue between social sciences and life sciences  27325.2. The empire of the principle of identity in theories of society and culture 27425.3. A field of neglected social and cultural phenomena 27625.4. Linking social sciences and life sciences 27925.5. Bibliography 281Chapter 26. Life: A Simplex Whirlwind between Matter, Energy and Information 283Jean-Claude BARREY26.1. Introduction 28326.2. The Craig–Lorenz principle, traditional base of animal and human behavior 28426.3. The formulations incompatible with modern systemic biology  28426.4. Lorenz’s principle reformulated based on current biological data 28726.5. Ethosociological interpretation of the reformulated principle 28726.5.1. Ontogenesis, sociogenesis and phylogenesis 28726.6. Regulating societies through economy: ethoeconomy 28926.7. The bioethological stages of a social evolution 29226.8. Conclusion 29326.9. Bibliography 293Chapter 27. Nutritional Interactions through the Living: from Individuals to Societies and Beyond 295Mathieu LIHOREAU27.1. The living: a complex nutritional system 29527.2. Nutrition at the individual level 29627.3. Nutrition at the collective level 29727.3.1. Mass migrations 29827.3.2. Collective decisions 29927.3.3. Parental care 29927.3.4. Cooperative foraging 30027.3.5. Division of labor 30027.3.6. Interactions between species  30127.4. Toward a multilevel theory of nutrition? 30227.5. Bibliography 303Chapter 28. Epigenetic Regulation of Protein Biosynthesis by Scale Resonance: Study of the Reduction of ESCA Effects on Vines in Field Applications – Summary 2016 305Pedro FERRANDIZ, Michel DUHAMEL and Joël STERNHEIMER28.1. Introduction 30528.2. Materials and methods 30728.3. 2003–2011 results 30828.4. Results 2012 31028.5. Results 2013 31128.6. Results 2014 31228.7. Results 2015 31328.8. Results 2016 31428.9. Conclusions 315Chapter 29. Quantum and Multiverse Inflation 317Michel CASSÉ29.1. Copernican and anti-Copernican revolutions 31829.2. Selection criteria for the number of dimensions of space and time 31829.3. Why is time monodimensional? 32029.4. The bones of the void 32029.5. The buzz effect of inflation 32229.6. The eye hears and recognizes the fundamental and harmonic 325Chapter 30. Reontologization of the World and of Life 329Jean-Gabriel GANASCIA30.1. Philosophy of information 32930.2. Method and levels of abstraction  33030.3. “Inforgs” and infosphere 33230.4. Originality of the infosphere  33330.5. Reontologization 33530.6. Ethics of information 33630.7. Bibliography 337Chapter 31. Redesigning Life, a Serious and Credible Research Agenda? 339Bernadette BENSAUDE VINCENT31.1. Introduction 33931.2. Favorite metaphors 34131.3. Inappropriate metaphors 34331.4. Ethical challenges and metaphysics 34531.5. Bibliography 347Chapter 32. Transhumanism and the Future of Negation  349Jean-Michel BESNIERList of Authors 359Index 363