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 Stochastic 13.1. 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 Chance 14.1. 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
9 Index
List of Illustrations
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