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...

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Bibliographic Details
Corporate Author:	Colloque de Cerisy Cerisy-la-Salle, France
Other Authors:	Gaudin, Thierry (Editor), Lacroix, Dominique (Editor), Maurel, Marie-Christine (Editor), Pomerol, Jean-Charles (Editor)
Format:	Conference Proceeding eBook
Language:	English
Published:	London, UK : Hoboken, NJ : ISTE Ltd ; John Wiley and Sons, Inc., 2018.
Series:	Information systems, web and pervasive computing series.
Subjects:	Life sciences > Congresses. Information science > Congresses. Life sciences. Biological Science Disciplines Information Science Congress
Online Access:	Connect to the full text of this electronic book

Table of Contents:

Note continued: ch. 25 How to Account for Interspecies Socio-cultural Phenomena? An Evolutionist and Interactionist Model / Dominique Guillo
25.1. The difficult dialogue between social sciences and life sciences
25.2. The empire of the principle of identity in theories of society and culture
25.3. A field of neglected social and cultural phenomena
25.4. Linking social sciences and life sciences
25.5. Bibliography
ch. 26 Life: A Simplex Whirlwind between Matter, Energy and Information / Jean-Claude Barrey
26.1. Introduction
26.2. The Craig-Lorenz principle, traditional base of animal and human behavior
26.3. The formulations incompatible with modern systemic biology
26.4. Lorenz's principle reformulated based on current biological data
26.5. Ethosociological interpretation of the reformulated principle
26.5.1. Ontogenesis, sociogenesis and phylogenesis
26.6. Regulating societies through economy: ethoeconomy
26.7. The bioethological stages of a social evolution
26.8. Conclusion
26.9. Bibliography
ch. 27 Nutritional Interactions through the Living: from Individuals to Societies and Beyond / Mathieu Lihoreau
27.1. The living: a complex nutritional system
27.2. Nutrition at the individual level
27.3. Nutrition at the collective level
27.3.1. Mass migrations
27.3.2. Collective decisions
27.3.3. Parental care
27.3.4. Cooperative foraging
27.3.5. Division of labor
27.3.6. Interactions between species
27.4. Toward a multilevel theory of nutrition?
27.5. Bibliography
ch. 28 Epigenetic Regulation of Protein Biosynthesis by Scale Resonance: Study of the Reduction of ESCA Effects on Vines in Field Applications
Summary 2016 / Joel Sternheimer
28.1. Introduction
28.2. Materials and methods
28.3. 2003
2011 results
28.4. Results 2012
28.5. Results 2013
28.6. Results 2014
28.7. Results 2015
28.8. Results 2016
28.9. Conclusions
ch. 29 Quantum and Multiverse Inflation / Michel Casse
29.1. Copernican and anti-Copernican revolutions
29.2. Selection criteria for the number of dimensions of space and time
29.3. Why is time monodimensional?
29.4. The bones of the void
29.5. The buzz effect of inflation
29.6. The eye hears and recognizes the fundamental and harmonic
ch. 30 Reontologization of the World and of Life / Jean-Gabriel Ganascia
30.1. Philosophy of information
30.2. Method and levels of abstraction
30.3. Inforgs and infosphere
30.4. Originality of the infosphere
30.5. Reontologization
30.6. Ethics of information
30.7. Bibliography
ch. 31 Redesigning Life, a Serious and Credible Research Agenda? / Bernadette Bensaude Vincent
31.1. Introduction
31.2. Favorite metaphors
31.3. Inappropriate metaphors
31.4. Ethical challenges and metaphysics
31.5. Bibliography
ch. 32 Transhumanism and the Future of Negation / Jean-Michel Besnier.
Machine generated contents note: pt. 1 From Gene to Species: Variability, Randomness and Stability
ch. 1 The Emergence of Life: Some Notes on the Origin of Biological Information / Antonio Lazcano
1.1. Acknowledgments
1.2. Bibliography
ch. 2 Fluctuating RNA / Ada yonath
2.1. The ribosome
2.2. Ribosome dynamics
2.3. Primitive RNA, ribozymes and viroids
2.4. The proto-ribosome
2.5. Bibliography
ch. 3 Artificial Darwinian Evolution of Nucleic Acids / Frederic duconge
3.1. Refresher on Darwin's theory of evolution
3.2. The molecular mechanisms of evolution
3.3. Molecular evolution external to the being
3.4. Imagery of molecular evolution
3.5. Conclusion
3.6. Acknowledgments
3.7. Bibliography
ch. 4 Information and Epigenetics / Andras Paldi
4.1. Bibliography
ch. 5 Molecular Forces and Motion in the Transmission of Information in Biology / Giuseppe Zaccai
5.1. The dynamics-function hypothesis
5.2. From thermodynamics to molecular forces
5.3. Like the devil, biology is in the details
5.4. The guitar in the river: theoretical MD
5.5. Experimental MD
5.6. Measuring average MD in whole cells
5.7. Dynamics response to stress
5.8. Conclusion: evolution is obliged to select dynamics
5.9. Bibliography
ch. 6 Decline and Contingency, Bases of Biological Evolution / Bernard Dujon
6.1. Introduction
6.2. Too many genes in the genomes
6.3. Parasitism and symbiosis
6.4. Asexual eukaryotes
6.5. Yeasts
6.6. Conclusion
6.7. Bibliography
ch. 7 Conservation, Co-evolution and Dynamics: From Sequence to Function / Alessandra Carbone
7.1. Introduction
7.2. Reverse engineering: from the protein described in a single dimension to its 3D properties
7.3. Before any modeling, the geometric and physical properties, the behavior and history of proteins are characterized
7.3.1. Proteins are dynamic objects
7.3.2. Proteins have a history
7.3.3. Some proteins share the same evolutionary history
7.4. Chance and selection govern the generation of observed sequences
7.5. Conservation and interaction sites of proteins
7.6. Co-evolution: identification of contacts that can occur at different moments in the lifetime of a protein
7.7. Co-evolution used to reconstruct protein-protein interaction networks in viruses
7.8. Molecular modeling of several partners used to reconstruct protein-protein interaction networks for prokaryotic and eukaryotic organisms
7.9. Dynamics and function
7.10. Conclusions
7.11. Acknowledgments
7.12. Bibliography
ch. 8 Localization of the Morphodynamic Information in Amniote Formation / Vincent Fleury
8.1. Introduction
8.2. Schematic view of an amniote
8.3. Mechanism of amniote formation
8.4. Additional features
8.5. Discussion and conclusion
8.6. Bibliography
ch. 9 From the Century of the Gene to that of the Organism: Introduction to New Theoretical Perspectives / Ana Soto
9.1. Introduction
9.2. Philosophical positions
9.3. From the inert to the living
9.4. Cell theory: a starting point toward a theory of organisms
9.5. The founding principles: from entanglement to integration?
9.5.1. Genealogy of the three proposed principles: the default state, the principle of organization and the principle of variation
9.5.2. How to organize these principles into a coherent ensemble?
9.6. Conclusion
9.7. Acknowledgments
9.8. Bibliography
ch. 10 The Game of Survival, Chance and Complexity / Philippe Kourilsky
10.1. Introduction
10.2. Complex systems
10.2.1. Definition
10.2.2. How to evaluate the complexity of a system?
10.2.3. The notion of robustness
10.3. Chance and robustness in living organisms
10.3.1. The system of natural defenses in living organisms
10.3.2. Natural defenses and robustness
10.3.3. Natural defenses, chance and hazards
10.4. Evolution and chance
10.4.1. On the links between robustness and evolution
10.4.2. On human evolution
10.5. Conclusion: the logic of the living
10.6. Bibliography
ch. 11 Life from the Origins to Homo sapiens / Jean Fourtaux
11.1. Setting the scene
11.2. The conquest of solid earth by the vertebrates
11.3. A few insights on evolution
11.3.1. The horse
11.3.2. Eagle and vulture
11.3.3. The cetaceans
11.3.4. The Red Queen
11.3.5. The spotted hyena
11.4. Primates and humans
ch. 12 Plankton Chronicles and the Tara Expeditions / Christian Sardet
12.1. Plankton
12.2. Plankton and climate
12.3. The Tara Oceans expedition
12.4. Bibliography
ch. 13 The Living Species is Not a Natural Kind but an Intellectual Construction / Philippe Grandcolas
13.1. Introduction
13.2. Two ways to study evolution: genealogy versus phylogeny
13.3. Three main families of concepts of species
13.4. Reconciling the different concepts: pragmatism or essentialism?
13.5. The species and the taxon name
13.6. The nature of species: a salutatory philosophical exercise
13.7. Bibliography
ch. 14 The Boxes and their Content: What to Do with Invariants in Biology? / Guillaume Lecointre
14.1. Natural history
14.2. Natural history and evolution
14.3. The species
14.4. The grade
14.5. Genetic information
14.6. The body plan
14.7. On the misuse of convergences
14.8. Conclusion
14.9. Bibliography
ch. 15 Probability, Sense and Evolution (Promenade) / Cedric Villani
15.1. Introduction
15.2. Difficult dialogue
15.3. Knowledge and big data
15.4. The probabilities
15.5. A few striking examples
15.5.1. Pagerank
15.5.2. Decoding
15.5.3. Reconstitution of preferences
15.5.4. Correspondence between genotype and phenotype
15.5.5. Phylogeny
15.5.6. Automatic recognition
15.5.7. Autopilot
15.5.8. Imitation of styles
15.5.9. And all the rest
15.6. The MCMC method
15.7. Neural networks
15.8. A few questions
15.8.1. Do we understand?
15.8.2. Describing convergence
15.8.3. Geometrizing
15.8.4. Varied questions
15.9. Bibliography
pt. 2 Program and Life: Individuation and Interaction
ch. 16 Towards an Algorithmic Approach to Life Sciences / Gerard Berry
16.1. Prologue
16.2. Matter, energy, waves and information
16.3. Medical imaging
16.4. The simulation of the living
16.5. Computer modeling and its levels of abstraction
16.6. The role of embedded computing
16.7. Other subjects
16.8. But is all this without danger?
16.9. The importance of training
ch. 17 Where Does the Notion of Function Come From? / Heinz Wismann
ch. 18 The Contribution of Artificial Life to Theoretical Biology / Hugues Bersini
18.1. Introduction
18.2. Support to pedagogy
18.3. Food for thought: a philosophy in software form
18.4. Conclusions: royal life, falsifiable modeling
18.5. Bibliography
ch. 19 Biochemical Programs and Analog-Digital Mixed Algorithms in the Cell / Guillaume Le Guludec
19.1. Introduction
19.2. Biochemical programs
19.2.1. Syntax
19.2.2. Semantics
19.2.3. Example of MAPK signaling networks
19.3. Behavioral logical specifications
19.4. Analog specifications
19.4.1. Computability and analog complexity theory
19.4.2. Computability and biochemical algorithmic complexity
19.4.3. GPAC biochemical compilation
19.4.4. Analog-digital converter compared to MAPK
19.5. Biochemical compilation of sequentiality and cell cycle
19.6. Discussion
19.7. Bibliography
ch. 20 From Computational Physics to the Origins of Life / A. Marco Saitta
20.1. Prebiotic emergence of the basic bricks of life
20.2. Computational approaches and simulations in chemistry
20.3. Computational approaches and simulations in prebiotic chemistry
20.4. New challenges in modeling: reaction networks
20.5. At the frontiers of modeling in prebiotic chemistry: topological approaches
20.6. Conclusion and perspectives
20.7. Bibliography
ch.
21 Computing and the Temptation of Babel / Kave Salamatian
21.1. Introduction
21.2. The role of information technologies
21.3. On conflicts of rationality and more specifically on rationality in biology
21.4. Information and its role in biology
21.5. Conclusion
21.6. Acknowledgments
21.7. Bibliography
ch. 22 Big Data, Knowledge and Biology / Mael Montevil
22.1. Introduction
22.2. Big databases, prediction and chance
22.3. Bibliography
ch. 23 Natural Language, Formal Language and the Description of the Living World / Regine Vignes Lebbe
23.1. Introduction
23.2. Describing the living world
23.2.1. The objects in the description of the living world
23.2.2. Describing specimens
23.2.3. Describing taxa
23.3. Formal language
23.3.1. Semantic step
23.3.2. The characters: several concepts
23.3.3. Structured computerization of knowledge
23.4. Conclusion
23.5. Bibliography
ch. 24 Vital Individuation and Morphogenetic Information / Vincent Bontems
24.1. Introduction
24.2. The theory of vital individuation
24.3. Lamarck's ghost
24.4. DNA and its transductions
24.5. Schrodinger's flower