Chance, Calculation and Life

1 Cover

2 Title Page Series EditorJean-Charles Pomerol

3 Copyright First published 2021 in Great Britain and the United States by ISTE Ltd and John Wiley & Sons, Inc. Apart from any fair dealing for the purposes of research or private study, or criticism or review, as permitted under the Copyright, Designs and Patents Act 1988, this publication may only be reproduced, stored or transmitted, in any form or by any means, with the prior permission in writing of the publishers, or in the case of reprographic reproduction in accordance with the terms and licenses issued by the CLA. Enquiries concerning reproduction outside these terms should be sent to the publishers at the undermentioned address: © ISTE Ltd 2020 ISTE Ltd 27-37 St George’s Road London SW19 4EU UK USA www.iste.co.uk John Wiley & Sons, Inc. 111 River Street Hoboken, NJ 07030 www.wiley.com © ISTE Ltd 2021 The rights of Thierry Gaudin, Marie-Christine Maurel and Jean-Charles Pomerol to be identified as the author of this work have been asserted by them in accordance with the Copyright, Designs and Patents Act 1988. Library of Congress Control Number: 2020952689 British Library Cataloguing-in-Publication Data A CIP record for this book is available from the British Library ISBN 978-1-78630-667-8

4 Preface

5 Introduction

6 PART 1: Randomness in all of its Aspects 1 Classical, Quantum and Biological Randomness as Relative Unpredictability 1.1. Introduction 1.1. Introduction Randomness is everywhere, for better or for worse: vagaries of weather, day-today fluctuations in the stock market, random motions of molecules or random genetic mutations are just a few examples. Random numbers have been used for more than 4,000 years, but they have never been in such high demand than they have in our time. What is the origin of randomness in nature and how does it relate to the only access we have to phenomena, that is, through measurement? How does randomness in nature relate to randomness in sequences of numbers? The theoretical and mathematical analysis of randomness is far from obvious. Moreover, as we will show, it depends on (and is relative to) the particular theory that is being worked on, the intended theoretical framework for the phenomena under investigation. 1.2. Randomness in classical dynamics 1.3. Quantum randomness 1.4. Randomness in biology 1.5. Random sequences: a theory invariant approach 1.6. Classical and quantum randomness revisited 1.7. Conclusion and opening: toward a proper biological randomness 1.8. Acknowledgments 1.9. References 2: In The Name of Chance 2.1. The birth of probabilities and games of chance 2.2. A very brief history of probabilities 2.3. Chance? What chance? 2.4. Prospective possibility 2.5. Appendix: Congruent generators, can prospective chance be periodic? 2.6. References 3 Chance in a Few Languages 3.1. Classical Sanskrit 3.2. Persian and Arabic 3.3. Ancient Greek 3.4. Russian 3.5. Latin 3.6. French 3.7. English 3.8. Dice, chance and the symbolic world 3.9. References 4 The Collective Determinism of Quantum Randomness 4.1. True or false chance 4.2. Chance sneaks into uncertainty 4.3. The world of the infinitely small 4.4. A more figurative example 4.5. Einstein’s act of resistance 4.6. Schrödinger’s cat to neutrino oscillations 4.7. Chance versus the anthropic principle 4.8. And luck in life? 4.9. Chance and freedom 5 Wave-Particle Chaos to the Stability of Living5.1. Introduction 5.2. The chaos of the wave-particle 5.3. The stability of living things 5.4. Conclusion 5.5. Acknowledgments 5.6. References 6 Chance in Cosmology: Random and Turbulent Creation of Multiple Cosmos 6.1. Is quantum cosmology oxymoronic? 6.2. Between two realities – at the entrance and exit – is virtuality 6.3. Who will sing the metamorphoses of this high vacuum? 6.4. Loop lament 6.5. The quantum vacuum exists, Casimir has met it 6.6. The generosity of the quantum vacuum 6.7. Landscapes 6.8. The good works of Inflation 6.9. Sub species aeternitatis 6.10. The smiling vacuum 7 The Chance in Decision: When Neurons Flip a Coin 7.1. A very subjective utility 7.2. A minimum rationality 7.3. There is noise in the choices 7.4. On the volatility of parameters 7.5. When the brain wears rose-tinted glasses 7.6. The neurons that take a vote 7.7. The will to move an index finger 7.8. Free will in debate 7.9. The virtue of chance 7.10. References 8 To Have a Sense of Life: A Poetic Reconnaissance 8.1. References 9 Divine Chance9.1. Thinking by chance 9.2. Chance, need: why choose? 9.3. When chance is not chance 9.4. When chance comes from elsewhere 10 Chance and the Creative Process10.1. Introduction 10.2. Chance 10.3. Creation 10.4. Chance in the artistic creative process 10.5. An art of the present moment 10.6. Conclusion 10.7. References

7 PART 2: Randomness, Biology and Evolution 11 Epigenetics, DNA and Chromatin Dynamics: Where is the Chance and Where is the Necessity?11.1. Introduction 11.2. Random combinations 11.3. Random alterations 11.4. Beyond the gene 11.5. Epigenetic variation 11.6. Concluding remarks 11.7. Acknowledgments 11.8. References 12 When Acquired Characteristics Become Heritable: The Lesson of Genomes 12.1. Introduction 12.2. Horizontal genetic exchange in prokaryotes 12.3. Two specificities of eukaryotes theoretically oppose horizontal gene transfer 12.4. Criteria for genomic analysis 12.5. Abundance of horizontal transfers in unicellular eukaryotes 12.6. Remarkable horizontal genetic transfers in pluricellular eukaryotes 12.7. Main mechanisms of horizontal genetic transfers 12.8. Introgressions and limits to the concept of species 12.9. Conclusion 12.10. References 13 The Evolutionary Trajectories of Organisms are Not Stochastic13.1. Evolution and stochasticity: a few metaphors 13.2. The Gouldian metaphor of the “replay” of evolution 13.3. The replay of evolution: what happened 13.4. Evolutionary replay experiments 13.5. Phylogenies versus experiments 13.6. Stochasticity, evolution and extinction 13.7. Conclusion 13.8. References 14 Evolution in the Face of Chance14.1. Introduction 14.2. Waddington and the concept of canalization 14.3. A stochastic model of Darwinian evolution 14.4. Numerical results 14.5. Discussion 14.6. Acknowledgments 15 Chance, Contingency and the Origins of Life: Some Historical Issues 15.1. Acknowledgments 15.2. References 16 Chance, Complexity and the Idea of a Universal Ethics 16.1. Cosmic evolution and advances in computation 16.2. Two notions of complexity 16.3. Biological computations 16.4. Energy and emergy 16.5. What we hold onto 16.6. Noah knew this already! 16.7. Create, protect and collect 16.8. An ethics of organized complexity 16.9. Not so easy 16.10. References

8 List of Authors

9 Index

10 End User License Agreement

1 Chapter 2Figure 2.1. Simulated annealing (above) and stochastic gradient (below)

2 Chapter 4Figure 4.1. Radioactive decay curve. For a color version of this figure, see www...Figure 4.2. Diagram of an interference experiment. For a color version of this f...Figure 4.3. Electron interference; each point indicates a particle impactFigure 4.4. Distribution of chance; number of days passed between two successive...

3 Chapter 5Figure 5.1. Image of a bouncing drop inducing a parametric wave around it and sh...Figure 5.2. (a) There is no relationship between the distance to the middle of t...Figure 5.3. Quantification of the trajectories for a macroscopic wave-particle i...Figure 5.4. A squirrel killed by a cat. Individually, it is an unforeseeable cat...Figure 5.5. The collective motion experience, where a sheep trained to move towa...

4 Chapter 6Figure 6.1. Evolution of the universe since the emergence of classical time (the..