Logic of Chance, The

Financial Times
Eugene V. Koonin  
Total pages
August 2011
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Logic of Chance, The
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The Logic of Chance offers a reappraisal and a new synthesis of theories, concepts, and hypotheses on the key aspects of the evolution of life on earth in light of comparative genomics and systems biology. The author presents many specific examples from systems and comparative genomic analysis to begin to build a new, much more detailed, complex, and realistic picture of evolution. The book examines a broad range of topics in evolutionary biology including  the inadequacy of natural selection and adaptation as the only or even the main mode of evolution; the key role of horizontal gene transfer in evolution and the consequent overhaul of the Tree of Life concept;  the central, underappreciated evolutionary importance of viruses; the origin of eukaryotes as a result of endosymbiosis; the concomitant origin of cells and viruses on the primordial earth; universal dependences between genomic and molecular-phenomic variables; and the evolving landscape of constraints that shape the evolution of genomes and molecular phenomes.


A scholarly critique of our current understanding of biological evolution and how life radiated from its origins.

  • A broad overview of the current state of evolutionary biology.
  • Presents theoretical models and original hypotheses that may help to answer key problems in evolution.
  • Offers a more multidisciplinary perspective of evolutionary biology, integrating quantitative, mathematical, and systems approaches.

Table of Contents

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

Back Cover

An Outline of a Fundamentally New Evolutionary Synthesis Reflecting Key Advances in Genomics, Systems Biology, and Biological Physics


In this ambitious book, Eugene V. Koonin illuminates the gamut of randomness and regularity that is at the heart of life. Pointing the way beyond Modern Synthesis, Koonin brings together new data and concepts in an attempt to achieve a far deeper understanding of the interplay between chance and necessity that drives biological evolution. He explains evolution as a stochastic process based on historical contingency, constrained by requirements for maintaining cell organization and modulated by adaptation. To support his argument, he weaves together multiple conceptual threads: genomic comparisons that illuminate ancestral forms; new insights into pattern, process, and contingency in evolution; advances in the study of gene expression, protein abundance, and other phenotypic molecular characteristics; application of statistical physics to the study of the evolution of genes and genomes; and new perspectives on probability now emerging from modern cosmology.


The Logic of Chance shows why these insights make the twentieth-century scientific consensus about evolution appear outdated and incomplete and outlines a fundamentally new approach: one that is challenging, sometimes controversial, and always firmly rooted in hard science. Coverage includes

  • Understanding the forces and patterns of evolution
  • Surprising evolutionary reconstructions arising from the comparison of complete genomes
  • Is there a tree of life--or a forest?
  • How complex eukaryotes arose: tantalizing hints about one of evolutionary biology’s key enigmas
  • Biological complexity and entropy: evolutionary lessons from Kolmogorov, Shannon, and Boltzmann
  • Robustness, evolvability, and the creative role of noise in evolution
  • The Last Universal Common Ancestor, cell origins, and the primordial gene pool
  • The key role of viruses and the virus-cell arms race in evolution
  • Life’s origin: estimating the probability of “unique events” in the context of modern cosmology


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).