The Logic of Chance

Preface: Toward a postmodern synthesis of evolutionary biology vii Chapter 1: The fundamentals of evolution: Darwin and Modern Synthesis 1 Chapter 2: From Modern Synthesis to evolutionary genomics: Multiple processes and patterns of evolution 21 Chapter 3: Comparative genomics: Evolving genomescapes 49 Chapter 4: Genomics, systems biology, and universals of evolution: Genome evolution as a phenomenon of statistical physics 81 Chapter 5: The web genomics of the prokaryotic world: Vertical and horizontal flows of genes, the mobilome, and the dynamic pangenomes 105 Chapter 6: The phylogenetic forest and the quest for the elusive Tree of Life in the age of genomics 145 Chapter 7: The origins of eukaryotes: Endosymbiosis, the strange story of introns, and the ultimate importance of unique events in evolution 171 Chapter 8: The non-adaptive null hypothesis of genome evolution and origins of biological complexity 225 Chapter 9: The Darwinian, Lamarckian, and Wrightean modalities of evolution, robustness, evolvability, and the creative role of noise in evolution 257 Chapter 10: The Virus World and its evolution 293 Chapter 11: The Last Universal Common Ancestor, the origin of cells, and the primordial gene pool 329 Chapter 12: Origin of life: The emergence of translation, replication, metabolism, and membranes--the biological, geochemical, and cosmological perspectives 351 Chapter 13: The postmodern state of evolutionary biology 397 Appendix A: Postmodernist philosophy, metanarratives, and the nature and goals of the scientific endeavor 421 Appendix B: Evolution of the cosmos and life: Eternal inflation, "many worlds in one," anthropic selection, and a rough estimate of the probability of the origin of life 431 References 439 Endnotes 479 Acknowledgments 495 About the author 497 Index 499

Eugene V. Koonin is a Senior Investigator at the National Center for Biotechnology Information (National Library of Medicine, National Institutes of Health), as well as the Editor-in-Chief of the journal Biology Direct. Dr. Koonin's group performs research in many areas of evolutionary genomics, with a special emphasis on whole-genome approaches to the study of major transitions in life's evolution, such as the origin of eukaryotes, the evolution of eukaryotic gene structure, the origin and evolution of different classes of viruses, and evolutionary systems biology. Dr. Koonin is the author of more than 600 scientific articles and a previous book Sequence--Evolution--Function: Computational Approaches in Comparative Genomics (with Michael Galperin [2002] New York: Springer).