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Life Sciences, Information Sciences


Life Sciences, Information Sciences


1. Aufl.

von: Thierry Gaudin, Dominique Lacroix, Marie-Christine Maurel, Jean-Charles Pomerol

144,99 €

Verlag: Wiley
Format: EPUB
Veröffentl.: 15.03.2018
ISBN/EAN: 9781119516606
Sprache: englisch
Anzahl Seiten: 400

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Beschreibungen

<p>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.</p> <p>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.</p> <p>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.</p>
<p>Preface xv</p> <p>Selection of Publications xix</p> <p>Introduction xxiii</p> <p><b>Part 1. From Gene to Species: Variability, Randomness and Stability 1</b></p> <p><b>Chapter 1. The Emergence of Life: Some Notes on the Origin of Biological Information 3<br /></b><i>Antonio LAZCANO</i></p> <p>1.1. Acknowledgments 12</p> <p>1.2. Bibliography 12</p> <p><b>Chapter 2. Fluctuating RNA 17<br /></b><i>Giuseppe ZACCAI, Marie-Christine MAUREL and Ada YONATH</i></p> <p>2.1. The ribosome 17</p> <p>2.2. Ribosome dynamics 18</p> <p>2.3. Primitive RNA, ribozymes and viroids  20</p> <p>2.4. The proto-ribosome 21</p> <p>2.5. Bibliography 22</p> <p><b>Chapter 3. Artificial Darwinian Evolution of Nucleic Acids  23<br /></b><i>Frédéric DUCONGÉ</i></p> <p>3.1. Refresher on Darwin’s theory of evolution 23</p> <p>3.2. The molecular mechanisms of evolution  24</p> <p>3.3. Molecular evolution external to the being 25</p> <p>3.4. Imagery of molecular evolution 26</p> <p>3.5. Conclusion 27</p> <p>3.6. Acknowledgments 27</p> <p>3.7. Bibliography 27</p> <p><b>Chapter 4. Information and Epigenetics 29<br /></b><i>András PÁLDI</i></p> <p>4.1. Bibliography 34</p> <p><b>Chapter 5. Molecular Forces and Motion in the Transmission of Information in Biology 37<br /></b><i>Giuseppe ZACCAI</i></p> <p>5.1. The dynamics–function hypothesis  37</p> <p>5.2. From thermodynamics to molecular forces 38</p> <p>5.3. Like the devil, biology is in the details 39</p> <p>5.4. The guitar in the river: theoretical MD 40</p> <p>5.5. Experimental MD 40</p> <p>5.6. Measuring average MD in whole cells 41</p> <p>5.7. Dynamics response to stress 41</p> <p>5.8. Conclusion: evolution “is obliged” to select dynamics 42</p> <p>5.9. Bibliography 42</p> <p><b>Chapter 6. Decline and Contingency, Bases of Biological Evolution 45<br /></b><i>Bernard DUJON</i></p> <p>6.1. Introduction 45</p> <p>6.2. Too many genes in the genomes 46</p> <p>6.3. Parasitism and symbiosis 48</p> <p>6.4. Asexual eukaryotes 49</p> <p>6.5. Yeasts 50</p> <p>6.6. Conclusion 52</p> <p>6.7. Bibliography 52</p> <p><b>Chapter 7. Conservation, Co-evolution and Dynamics: From Sequence to Function 55<br /></b><i>Alessandra CARBONE</i></p> <p>7.1. Introduction 55</p> <p>7.2. Reverse engineering: from the protein described in a single dimension to its 3D properties 56</p> <p>7.3. Before any modeling, the geometric and physical properties, the behavior and history of proteins are characterized 57</p> <p>7.3.1. Proteins are dynamic objects 57</p> <p>7.3.2. Proteins have a history 57</p> <p>7.3.3. Some proteins share the same evolutionary history 57</p> <p>7.4. Chance and selection govern the generation of observed sequences 58</p> <p>7.5. Conservation and interaction sites of proteins 59</p> <p>7.6. Co-evolution: identification of contacts that can occur at different moments in the lifetime of a protein 60</p> <p>7.7. Co-evolution used to reconstruct protein–protein interaction networks in viruses 61</p> <p>7.8. Molecular modeling of several partners used to reconstruct protein–protein interaction networks for prokaryotic and eukaryotic organisms 63</p> <p>7.9. Dynamics and function 64</p> <p>7.10. Conclusions 64</p> <p>7.11. Acknowledgments 65</p> <p>7.12. Bibliography 65</p> <p><b>Chapter 8. Localization of the Morphodynamic Information in Amniote Formation 69<br /></b><i>Vincent FLEURY</i></p> <p>8.1. Introduction 69</p> <p>8.2. Schematic view of an amniote  70</p> <p>8.3. Mechanism of amniote formation 74</p> <p>8.4. Additional features 77</p> <p>8.5. Discussion and conclusion 78</p> <p>8.6. Bibliography 79</p> <p><b>Chapter 9. From the Century of the Gene to that of the Organism: Introduction to New Theoretical</b> <b>Perspectives 81<br /></b><i>Maël MONTÉVIL, Giuseppe LONGO and Ana SOTO</i></p> <p>9.1. Introduction 81</p> <p>9.2. Philosophical positions 87</p> <p>9.3. From the inert to the living 87</p> <p>9.4. Cell theory: a starting point toward a theory of organisms  88</p> <p>9.5. The founding principles: from entanglement to integration?  89</p> <p>9.5.1. Genealogy of the three proposed principles: the default state, the principle of organization and the principle of variation 89</p> <p>9.5.2. How to organize these principles into a coherent ensemble?  90</p> <p>9.6. Conclusion 92</p> <p>9.7. Acknowledgments 94</p> <p>9.8. Bibliography 94</p> <p><b>Chapter 10. The Game of Survival, Chance and Complexity 99<br /></b><i>Philippe KOURILSKY</i></p> <p>10.1. Introduction 99</p> <p>10.2. Complex systems 100</p> <p>10.2.1. Definition 100</p> <p>10.2.2. How to evaluate the complexity of a system?  102</p> <p>10.2.3. The notion of robustness  102</p> <p>10.3. Chance and robustness in living organisms 103</p> <p>10.3.1. The system of natural defenses in living organisms 103</p> <p>10.3.2. Natural defenses and robustness 103</p> <p>10.3.3. Natural defenses, chance and hazards 104</p> <p>10.4. Evolution and chance 105</p> <p>10.4.1. On the links between robustness and evolution 105</p> <p>10.4.2. On human evolution 106</p> <p>10.5. Conclusion: the logic of the living 107</p> <p>10.6. Bibliography 108</p> <p><b>Chapter 11. Life from the Origins to Homo sapiens 109<br /></b><i>Jean FOURTAUX</i></p> <p>11.1. Setting the scene 109</p> <p>11.2. The conquest of solid earth by the vertebrates 110</p> <p>11.3. A few insights on evolution  111</p> <p>11.3.1. The horse 112</p> <p>11.3.2. Eagle and vulture 112</p> <p>11.3.3. The cetaceans 112</p> <p>11.3.4. The Red Queen 112</p> <p>11.3.5. The spotted hyena 112</p> <p>11.4. Primates and humans 113</p> <p><b>Chapter 12. Plankton Chronicles and the Tara Expeditions  117<br /></b><i>Christian SARDET</i></p> <p>12.1. Plankton 117</p> <p>12.2. Plankton and climate 118</p> <p>12.3. The Tara Oceans expedition  121</p> <p>12.4. Bibliography 123</p> <p><b>Chapter 13. The Living Species is Not a Natural Kind but an Intellectual Construction 125<br /></b><i>Philippe GRANDCOLAS</i></p> <p>13.1. Introduction 125</p> <p>13.2. Two ways to study evolution: genealogy versus phylogeny  126</p> <p>13.3. Three main families of concepts of species 128</p> <p>13.4. Reconciling the different concepts: pragmatism or essentialism? 130</p> <p>13.5. The species and the taxon name 131</p> <p>13.6. The nature of species: a salutatory philosophical exercise  132</p> <p>13.7. Bibliography 135</p> <p><b>Chapter 14. The Boxes and their Content: What to Do with Invariants in Biology? 139<br /></b><i>Guillaume LECOINTRE</i></p> <p>14.1. Natural history 139</p> <p>14.2. Natural history and evolution 141</p> <p>14.3. The species 142</p> <p>14.4. The grade 146</p> <p>14.5. Genetic information 146</p> <p>14.6. The body plan 148</p> <p>14.7. On the misuse of convergences 149</p> <p>14.8. Conclusion 151</p> <p>14.9. Bibliography 151</p> <p><b>Chapter 15. Probability, Sense and Evolution (Promenade)  153<br /></b><i>Cédric VILLANI</i></p> <p>15.1. Introduction 153</p> <p>15.2. Difficult dialogue 154</p> <p>15.3. Knowledge and big data 155</p> <p>15.4. The probabilities 156</p> <p>15.5. A few striking examples 157</p> <p>15.5.1. Pagerank 157</p> <p>15.5.2. Decoding 157</p> <p>15.5.3. Reconstitution of preferences  157</p> <p>15.5.4. Correspondence between genotype and phenotype 158</p> <p>15.5.5. Phylogeny 158</p> <p>15.5.6. Automatic recognition 160</p> <p>15.5.7. Autopilot 160</p> <p>15.5.8. Imitation of styles 160</p> <p>15.5.9. And all the rest 160</p> <p>15.6. The MCMC method 160</p> <p>15.7. Neural networks 162</p> <p>15.8. A few questions 164</p> <p>15.8.1. Do we understand? 164</p> <p>15.8.2. Describing convergence  165</p> <p>15.8.3. Geometrizing 166</p> <p>15.8.4. Varied questions 166</p> <p>15.9. Bibliography 167</p> <p><b>Part 2. Program and Life: Individuation and Interaction  169</b></p> <p><b>Chapter 16. Towards an Algorithmic Approach to Life Sciences 171<br /></b><i>Gérard BERRY</i></p> <p>16.1. Prologue 171</p> <p>16.2. Matter, energy, waves and information  172</p> <p>16.3. Medical imaging 173</p> <p>16.4. The simulation of the living  175</p> <p>16.5. Computer modeling and its levels of abstraction 176</p> <p>16.6. The role of embedded computing  178</p> <p>16.7. Other subjects 179</p> <p>16.8. But is all this without danger? 180</p> <p>16.9. The importance of training 182</p> <p><b>Chapter 17. Where Does the Notion of Function Come From?  183<br /></b><i>Heinz WISMANN</i></p> <p><b>Chapter 18. The Contribution of Artificial Life to Theoretical Biology 191<br /></b><i>Hugues BERSINI</i></p> <p>18.1. Introduction 191</p> <p>18.2. Support to pedagogy 192</p> <p>18.3. Food for thought: a philosophy in software form 193</p> <p>18.4. Conclusions: royal life, falsifiable modeling 198</p> <p>18.5. Bibliography 199</p> <p><b>Chapter 19. Biochemical Programs and Analog-Digital Mixed Algorithms in the Cell  201<br /></b><i>François FAGES and Guillaume LE GULUDEC</i></p> <p>19.1. Introduction 201</p> <p>19.2. Biochemical programs 202</p> <p>19.2.1. Syntax 202</p> <p>19.2.2. Semantics 203</p> <p>19.2.3. Example of MAPK signaling networks 203</p> <p>19.3. Behavioral logical specifications  205</p> <p>19.4. Analog specifications 206</p> <p>19.4.1. Computability and analog complexity theory . 206</p> <p>19.4.2. Computability and biochemical algorithmic complexity  208</p> <p>19.4.3. GPAC biochemical compilation 210</p> <p>19.4.4. Analog–digital converter compared to MAPK  211</p> <p>19.5. Biochemical compilation of sequentiality and cell cycle  212</p> <p>19.6. Discussion 213</p> <p>19.7. Bibliography 214</p> <p><b>Chapter 20. From Computational Physics to the Origins of Life 217<br /></b><i>A. Marco SAITTA</i></p> <p>20.1. Prebiotic emergence of the basic bricks of life 217</p> <p>20.2. Computational approaches and simulations in chemistry  219</p> <p>20.3. Computational approaches and simulations in prebiotic chemistry 220</p> <p>20.4. New challenges in modeling: reaction networks 222</p> <p>20.5. At the frontiers of modeling in prebiotic chemistry: topological approaches 224</p> <p>20.6. Conclusion and perspectives  227</p> <p>20.7. Bibliography 227</p> <p><b>Chapter 21. Computing and the Temptation of Babel 231<br /></b><i>Kavé SALAMATIAN</i></p> <p>21.1. Introduction 232</p> <p>21.2. The role of information technologies 233</p> <p>21.3. On conflicts of rationality and more specifically on rationality in biology 236</p> <p>21.4. Information and its role in biology 239</p> <p>21.5. Conclusion 241</p> <p>21.6. Acknowledgments 241</p> <p>21.7. Bibliography 241</p> <p><b>Chapter 22. Big Data, Knowledge and Biology 243<br /></b><i>Giuseppe LONGO and Maël MONTÉVIL</i></p> <p>22.1. Introduction 243</p> <p>22.2. Big databases, prediction and chance 245</p> <p>22.3. Bibliography 247</p> <p><b>Chapter 23. Natural Language, Formal Language and the Description of the Living World  249<br /></b><i>Régine VIGNES LEBBE</i></p> <p>23.1. Introduction 249</p> <p>23.2. Describing the living world 250</p> <p>23.2.1. The objects in the description of the living world 250</p> <p>23.2.2. Describing specimens 251</p> <p>23.2.3. Describing taxa 252</p> <p>23.3. Formal language 253</p> <p>23.3.1. Semantic step 253</p> <p>23.3.2. The characters: several concepts 254</p> <p>23.3.3. Structured computerization of knowledge  255</p> <p>23.4. Conclusion 256</p> <p>23.5. Bibliography 257</p> <p><b>Chapter 24. Vital Individuation and Morphogenetic Information 259<br /></b><i>Vincent BONTEMS</i></p> <p>24.1. Introduction 259</p> <p>24.2. The theory of vital individuation  261</p> <p>24.3. Lamarck’s ghost 263</p> <p>24.4. DNA and its transductions 266</p> <p>24.5. Schrödinger’s flower 269</p> <p><b>Chapter 25. How to Account for Interspecies Socio-cultural Phenomena? An Evolutionist and</b> <b>Interactionist Model 273<br /></b><i>Dominique GUILLO</i></p> <p>25.1. The difficult dialogue between social sciences and life sciences  273</p> <p>25.2. The empire of the principle of identity in theories of society and culture 274</p> <p>25.3. A field of neglected social and cultural phenomena 276</p> <p>25.4. Linking social sciences and life sciences 279</p> <p>25.5. Bibliography 281</p> <p><b>Chapter 26. Life: A Simplex Whirlwind between Matter, Energy and Information 283<br /></b><i>Jean-Claude BARREY</i></p> <p>26.1. Introduction 283</p> <p>26.2. The Craig–Lorenz principle, traditional base of animal and human behavior 284</p> <p>26.3. The formulations incompatible with modern systemic biology  284</p> <p>26.4. Lorenz’s principle reformulated based on current biological data 287</p> <p>26.5. Ethosociological interpretation of the reformulated principle 287</p> <p>26.5.1. Ontogenesis, sociogenesis and phylogenesis 287</p> <p>26.6. Regulating societies through economy: ethoeconomy 289</p> <p>26.7. The bioethological stages of a social evolution 292</p> <p>26.8. Conclusion 293</p> <p>26.9. Bibliography 293</p> <p><b>Chapter 27. Nutritional Interactions through the Living: from Individuals to Societies and Beyond 295<br /></b><i>Mathieu LIHOREAU</i></p> <p>27.1. The living: a complex nutritional system 295</p> <p>27.2. Nutrition at the individual level 296</p> <p>27.3. Nutrition at the collective level 297</p> <p>27.3.1. Mass migrations 298</p> <p>27.3.2. Collective decisions 299</p> <p>27.3.3. Parental care 299</p> <p>27.3.4. Cooperative foraging 300</p> <p>27.3.5. Division of labor 300</p> <p>27.3.6. Interactions between species  301</p> <p>27.4. Toward a multilevel theory of nutrition? 302</p> <p>27.5. Bibliography 303</p> <p><b>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<br /></b><i>Pedro FERRANDIZ, Michel DUHAMEL and Joël STERNHEIMER</i></p> <p>28.1. Introduction 305</p> <p>28.2. Materials and methods 307</p> <p>28.3. 2003–2011 results 308</p> <p>28.4. Results 2012 310</p> <p>28.5. Results 2013 311</p> <p>28.6. Results 2014 312</p> <p>28.7. Results 2015 313</p> <p>28.8. Results 2016 314</p> <p>28.9. Conclusions 315</p> <p><b>Chapter 29. Quantum and Multiverse Inflation 317<br /></b><i>Michel CASSÉ</i></p> <p>29.1. Copernican and anti-Copernican revolutions 318</p> <p>29.2. Selection criteria for the number of dimensions of space and time 318</p> <p>29.3. Why is time monodimensional? 320</p> <p>29.4. The bones of the void 320</p> <p>29.5. The buzz effect of inflation 322</p> <p>29.6. The eye hears and recognizes the fundamental and harmonic 325</p> <p><b>Chapter 30. Reontologization of the World and of Life 329<br /></b><i>Jean-Gabriel GANASCIA</i></p> <p>30.1. Philosophy of information 329</p> <p>30.2. Method and levels of abstraction  330</p> <p>30.3. “Inforgs” and infosphere 332</p> <p>30.4. Originality of the infosphere  333</p> <p>30.5. Reontologization 335</p> <p>30.6. Ethics of information 336</p> <p>30.7. Bibliography 337</p> <p><b>Chapter 31. Redesigning Life, a Serious and Credible Research Agenda? 339<br /></b><i>Bernadette BENSAUDE VINCENT</i></p> <p>31.1. Introduction 339</p> <p>31.2. Favorite metaphors 341</p> <p>31.3. Inappropriate metaphors 343</p> <p>31.4. Ethical challenges and metaphysics 345</p> <p>31.5. Bibliography 347</p> <p><b>Chapter 32. Transhumanism and the Future of Negation  349<br /></b><i>Jean-Michel BESNIER</i></p> <p>List of Authors 359</p> <p>Index 363</p>
<p><b>Thierry Gaudin</b> 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.</p> <p><b>Dominique Lacroix</b> 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.</p> <p><b>Marie-Christine Maurel</b> 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.</p> <p><b>Jean-Charles Pomerol</b> 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.</p>

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