From Gene to Species: Variability, Randomness and Stability -- The Emergence of Life: Some Notes on the Origin of Biological Information / Acknowledgments -- Bibliography -- Fluctuating RNA / The ribosome -- Ribosome dynamics -- Primitive RNA, ribozymes and viroids -- The proto-ribosome -- Bibliography -- Artificial Darwinian Evolution of Nucleic Acids / Refresher on Darwin's theory of evolution -- The molecular mechanisms of evolution -- Molecular evolution external to the being -- Imagery of molecular evolution -- Conclusion -- Acknowledgments -- Bibliography -- Information and Epigenetics / Bibliography -- Molecular Forces and Motion in the Transmission of Information in Biology / The dynamics-function hypothesis -- From thermodynamics to molecular forces -- Like the devil, biology is in the details -- The guitar in the river: theoretical MD -- Experimental MD -- Measuring average MD in whole cells -- Dynamics response to stress -- Conclusion: evolution "is obliged" to select dynamics -- Bibliography -- Decline and Contingency, Bases of Biological Evolution / Introduction -- Too many genes in the genomes -- Parasitism and symbiosis -- Asexual eukaryotes -- Yeasts -- Conclusion -- Bibliography -- Conservation, Co-evolution and Dynamics: From Sequence to Function / Introduction -- Reverse engineering: from the protein described in a single dimension to its 3D properties -- Before any modeling, the geometric and physical properties, the behavior and history of proteins are characterized -- Proteins are dynamic objects -- Proteins have a history -- Some proteins share the same evolutionary history -- Chance and selection govern the generation of observed sequences -- Conservation and interaction sites of proteins -- Co-evolution: identification of contacts that can occur at different moments in the lifetime of a protein -- Co-evolution used to reconstruct protein-protein interaction networks in viruses -- Molecular modeling of several partners used to reconstruct protein-protein interaction networks for prokaryotic and eukaryotic organisms -- Dynamics and function -- Conclusions -- Acknowledgments -- Bibliography -- Localization of the Morphodynamic Information in Amniote Formation / Introduction -- Schematic view of an amniote -- Mechanism of amniote formation -- Additional features -- Discussion and conclusion -- Bibliography -- From the Century of the Gene to that of the Organism: Introduction to New Theoretical Perspectives / Introduction -- Philosophical positions -- From the inert to the living -- Cell theory: a starting point toward a theory of organisms -- The founding principles: from entanglement to integration? -- Genealogy of the three proposed principles: the default state, the principle of organization and the principle of variation -- How to organize these principles into a coherent ensemble? -- Conclusion -- Acknowledgments -- Bibliography -- The Game of Survival, Chance and Complexity / Introduction -- Complex systems -- Definition -- How to evaluate the complexity of a system? -- The notion of robustness -- Chance and robustness in living organisms -- The system of natural defenses in living organisms -- Natural defenses and robustness -- Natural defenses, chance and hazards -- Evolution and chance -- On the links between robustness and evolution -- On human evolution -- Conclusion: the logic of the living -- Bibliography -- Life from the Origins to Homo sapiens / Setting the scene -- The conquest of solid earth by the vertebrates -- A few insights on evolution -- The horse -- Eagle and vulture -- The cetaceans -- The Red Queen -- The spotted hyena -- Primates and humans -- Plankton Chronicles and the Tara Expeditions / Plankton -- Plankton and climate -- The Tara Oceans expedition -- Bibliography -- The Living Species is Not a Natural Kind but an Intellectual Construction / Introduction -- Two ways to study evolution: genealogy versus phylogeny -- Three main families of concepts of species -- Reconciling the different concepts: pragmatism or essentialism? -- The species and the taxon name -- The nature of species: a salutatory philosophical exercise -- Bibliography -- The Boxes and their Content: What to Do with Invariants in Biology? / Natural history -- Natural history and evolution -- The species -- The grade -- Genetic information -- The body plan -- On the misuse of convergences -- Conclusion -- Bibliography -- Probability, Sense and Evolution (Promenade) / Introduction -- Difficult dialogue -- Knowledge and big data -- The probabilities -- A few striking examples -- Pagerank -- Decoding -- Reconstitution of preferences -- Correspondence between genotype and phenotype -- Phylogeny -- Automatic recognition -- Autopilot -- Imitation of styles -- And all the rest -- The MCMC method -- Neural networks -- A few questions -- Do we understand? -- Describing convergence -- Geometrizing -- Varied questions -- Bibliography -- Program and Life: Individuation and Interaction -- Towards an Algorithmic Approach to Life Sciences / Prologue -- Matter, energy, waves and information -- Medical imaging -- The simulation of the living -- Computer modeling and its levels of abstraction -- The role of embedded computing -- Other subjects -- But is all this without danger? -- The importance of training

Where Does the Notion of Function Come From? / The Contribution of Artificial Life to Theoretical Biology / Introduction -- Support to pedagogy -- Food for thought: a philosophy in software form -- Conclusions: royal life, falsifiable modeling -- Bibliography -- Biochemical Programs and Analog-Digital Mixed Algorithms in the Cell / Introduction -- Biochemical programs -- Syntax -- Semantics -- Example of MAPK signaling networks -- Behavioral logical specifications -- Analog specifications -- Computability and analog complexity theory -- Computability and biochemical algorithmic complexity -- GPAC biochemical compilation -- Analog-digital converter compared to MAPK -- Biochemical compilation of sequentiality and cell cycle -- Discussion -- Bibliography -- From Computational Physics to the Origins of Life / Prebiotic emergence of the basic bricks of life -- Computational approaches and simulations in chemistry -- Computational approaches and simulations in prebiotic chemistry -- New challenges in modeling: reaction networks -- At the frontiers of modeling in prebiotic chemistry: topological approaches -- Conclusion and perspectives -- Bibliography -- Computing and the Temptation of Babel / Introduction -- The role of information technologies -- On conflicts of rationality and more specifically on rationality in biology -- Information and its role in biology -- Conclusion -- Acknowledgments -- Bibliography -- Big Data, Knowledge and Biology / Introduction -- Big databases, prediction and chance -- Bibliography -- Natural Language, Formal Language and the Description of the Living World / Introduction -- Describing the living world -- The objects in the description of the living world -- Describing specimens -- Describing taxa -- Formal language -- Semantic step -- The characters: several concepts -- Structured computerization of knowledge -- Conclusion -- Bibliography -- Vital Individuation and Morphogenetic Information / Introduction -- The theory of vital individuation -- Lamarck's ghost -- DNA and its transductions -- Schrodinger's flower -- How to Account for Interspecies Socio-cultural Phenomena? An Evolutionist and Interactionist Model / The difficult dialogue between social sciences and life sciences -- The empire of the principle of identity in theories of society and culture -- A field of neglected social and cultural phenomena -- Linking social sciences and life sciences -- Bibliography -- Life: A Simplex Whirlwind between Matter, Energy and Information / Introduction -- The Craig-Lorenz principle, traditional base of animal and human behavior -- The formulations incompatible with modern systemic biology -- Lorenz's principle reformulated based on current biological data -- Ethosociological interpretation of the reformulated principle -- Ontogenesis, sociogenesis and phylogenesis -- Regulating societies through economy: ethoeconomy -- The bioethological stages of a social evolution -- Conclusion -- Bibliography -- Nutritional Interactions through the Living: from Individuals to Societies and Beyond / The living: a complex nutritional system -- Nutrition at the individual level -- Nutrition at the collective level -- Mass migrations -- Collective decisions -- Parental care -- Cooperative foraging -- Division of labor -- Interactions between species -- Toward a multilevel theory of nutrition? -- Bibliography -- Epigenetic Regulation of Protein Biosynthesis by Scale Resonance: Study of the Reduction of ESCA Effects on Vines in Field Applications -- Summary 2016 / Introduction -- Materials and methods -- 2003 -- 2011 results -- Results 2012 -- Results 2013 -- Results 2014 -- Results 2015 -- Results 2016 -- Conclusions -- Quantum and Multiverse Inflation / Copernican and anti-Copernican revolutions -- Selection criteria for the number of dimensions of space and time -- Why is time monodimensional? -- The bones of the void -- The buzz effect of inflation -- The eye hears and recognizes the fundamental and harmonic -- Reontologization of the World and of Life / Philosophy of information -- Method and levels of abstraction -- "Inforgs" and infosphere -- Originality of the infosphere -- Reontologization -- Ethics of information -- Bibliography -- Redesigning Life, a Serious and Credible Research Agenda? / Introduction -- Favorite metaphors -- Inappropriate metaphors -- Ethical challenges and metaphysics -- Bibliography -- Transhumanism and the Future of Negation