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The Logic of Chance: The Nature and Origin of Biological Evolution [Hardcover]

Eugene V. Koonin
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Aug. 31 2011 0132542498 978-0132542494 1

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.

 

"Koonin's account of viral and pre-eukaryotic evolution is undoubtedly up-to-date. His "mega views" of evolution (given what was said above) and his cosmological musings, on the other hand, are interesting reading." Summing Up: Recommended

Reprinted with permission from CHOICE, copyright by the American Library Association.

 


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From the 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

About the Author

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).


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1 of 2 people found the following review helpful
By John Kwok TOP 100 REVIEWER
Format:Hardcover
Having heard Eugene Koonin speak on the origins of eukaryotes at Rockefeller University back in May, 2008, I had high expectations for this book. In "The Logic of Chance: The Nature and Origin of Biological Evolution", Koonin argues that biological evolution is a "stochastic process based on historical contingency, constrained by requirements for maintaining cell organization and modulated by adaptation." To a considerable degree, I believe Koonin is right, since we find echoes of this in several decades of Stephen Jay Gould's scientific and popular writings, and in recent interest in creating an Extended Modern Synthesis that does realize the stochastic nature of biological evolution. However, Koonin doesn't make a compelling argument, since it is drowned out by his substantial emphasis - dare we say bias - toward understanding evolutionary processes primarily at the cellular level, with surprisingly few references with respect to organismal biology. It is compounded further by his suggestion that we treat his book as an introduction to understanding biological evolution from the perspective of molecular biology, but most of his reasoning seems more concerned with issues pertaining to the origin of life and the taxonomic affinities of various single-celled organisms, from viruses and bacteria to prokaryotes, than in discussing in great depth, major concepts in evolutionary biology. Regrettably, while "The Logic of Chance" was written to convey Koonin and others' work to a more general audience, it reads more like an introductory textbook in an advanced molecular biology course; those of us trained primarily in organismal biology will find this a difficult, often tedious, read. Read more ›
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Amazon.com: 4.0 out of 5 stars  24 reviews
11 of 12 people found the following review helpful
4.0 out of 5 stars Heavy but very thought provoking read Sept. 19 2011
By Alex Samaras - Published on Amazon.com
Format:Kindle Edition|Verified Purchase
This book is targeted at the experts but can be understood well enough by knowledgeable amateurs with some background in genomics (even unofficial; mine comes from my hobby of reading research papers because I am fascinated with biology). Having already read a good number of Dr. Koonin's papers as well as several others referenced in the book helped.

Anyway, this was a fascinating, thought-provoking read, though it was also rather difficult. Koonin's writing style, which serves him quite well in academic papers, doesn't translate extremely well to a full length book. For the sake of comparison, because both books seem to be targeted at a similar level crowd, it is not as readable as "The Extended Phenotype" by Richard Dawkins.

However, the ideas are fascinating, and this book seems to be an excellent overview of modern genomics research and what it tells us about what we understand and misunderstand about evolution. I certainly learned a lot about these topics as well as directions that future research will be taking. While I was less than impressed with some of the conclusions near the end (for example, the appeal to MWO and weak Anthropic Principal seemed to me to be a cop-out and at best should be a hypothesis of last resort).

However, I am not an expert, just an interested knowledgeable amateur, so I am not in the best position to judge Dr. Koonin's interpretations of the various data and research. But, whether his interpretations are spot on or not, they are certainly quite thought provoking, and will certainly serve science by creating discussion and lying groundwork for real testable hypotheses of all of the topics of genomics and evolution he discussed.

If you are very interested in biology, genetics, genomics, and evolution, you will want to read this book.
10 of 12 people found the following review helpful
5.0 out of 5 stars Challenging and fascinating Oct. 2 2011
By Michael Blyth - Published on Amazon.com
Format:Hardcover|Verified Purchase
In the preface to this book, the author writes that he set out with the desire to write a popular book along the lines of A Brief History of Time but on the subject of evolution. He soon recognized that the book "refused to be written that way" and became much more scientific and specialized. This is quite true. I am not a biologist but a physician, so I have had a fair number of biology courses, but much of this book was at about the limit of my ability to absorb, or even beyond. You probably won't get very far without a basic understanding of molecular biology: chromosomes, genes, DNA, tRNA, mRNA, transcription, translation, replication, ribosomes, operons, introns, splicing, and so on. On the other hand, if you have that background and some basic understanding with the concepts of biological evolution, you'll probably do fine with the book; little else is required--no math or biochemistry, for example. So be sure to take advantage of the "Look Inside" feature before you buy.

It's important to note the subtitle, "The Nature and Origin of Biological Evolution." This is not a chronicle of evolution, but a rather detailed (for a layperson) look at mechanisms of evolution, mostly at the genetic level, along with some reasoning and speculation about how the whole ball of wax got started.

You should also be aware that the "highest" organisms considered in any detail are the earliest, single-cell eukaryotes. Animals are, after all, only "a single, relatively small, tight group of eukaryotes" while bacteria and viruses are the most numerous and successful organisms on earth. Virtually the entire book is based on the evolution of bacteria, archaea, and viruses, though occasionally animals and plants are mentioned in passing. This is fine, since the purpose of the book is to explore evolution beyond the classical understanding of natural-selection-based, adaptive evolution, and also to probe the earliest origins of life.

I'm not sure what previous reviewer Jim means by "But it will be a classic because it deals handily with nearly every contested area of evolution, neatly demolishing every criticism leveled by creationists. It does this by making positive statements about what is known rather than by arguing against creationism." The book certainly deals with some contested areas, but the contests are among evolutionary biologists and not between creationists and biologists. This book and creationists are not in the same universe of discourse.

A few of the book's interesting points include:

* At least at the "interesting" scale of evolution (up to the origin of eukaryotes), adaptation or positive natural selection is not the major factor in genetic change: "the overall quantifiable characteristics of genome architecture, functioning and evolution are primarily determined by non-adaptive, stochastic processes. Adaptations only modulate these processes."

* Increasing complexity over time is not a measure of some kind of "progress" of evolution, but is due largely to two factors: (1) a random-walk phenomenon in which more complex structures will occur by chance given longer periods of time (2) the natural result when the effective population size is not great enough for purifying selection to eliminate slightly deleterious mutations. "Junk" DNA can accumulate as a result, both requiring and providing the substrate for complexity. Complexity as a "syndrome" of less-numerically-successful lineages coping with junk.

* Viruses as a separate "empire" of life not as a derivative of cellular life. The important role of viruses (and other conceptually-related entities) in evolution especially through horizontal gene transfer.

* The importance of the "Red Queen" arms-race between hosts and parasites (including especially viruses and other selfish elements) in driving genetic change.

* The logical necessity of an "RNA world" as precursor of cellular life. At the same time, the extreme improbability of the whole replication system arising in this universe: a "back of envelope" estimate of the probability of life evolving somewhere in the observable universe in 10 billion years is something like one in 10 to the power 1000. The author resorts to the "many worlds in one" hypothesis in which there are an infinity of infinite universes, so every possible event happens in not only one but an infinite number of them. We're here to observe one of these extremely improbable universes only because, of all these universes, living observers can only exist in the ones where life did arise ("weak anthropic principle").
30 of 41 people found the following review helpful
5.0 out of 5 stars Likely to be a Classic Sept. 7 2011
By Jim - Published on Amazon.com
Format:Kindle Edition|Verified Purchase
I'm not qualified to judge whether there are technical errors, so I will assume that a person who has hundreds of peer-reviewed publications will not have made many mistakes.

I can, however, judge the beauty of the writing and compare it to other classics, such as The Selfish Gene and A Brief History of Time. It compares well, even though it contains numerous diagrams and formulas. It's a bit more technical than those works, but only where it needs to be in order to make its points.

But it will be a classic because it deals handily with nearly every contested area of evolution, neatly demolishing every criticism leveled by creationists. It does this by making positive statements about what is known rather than by arguing against creationism. This is a refreshing change from most books written for a wide audience.

Perhaps its boldest claim is that there has been more progress made in the last ten years than in the previous 150 years.

I suspect it will be criticized for concluding that the origin of life might have been a one in a zillion long shot, and invoking multiple universes to beat the odds. This is presented as speculation, not fact, but it will be quote-mined by ID advocates. Correction, it already has been.
14 of 19 people found the following review helpful
5.0 out of 5 stars Tremendous analysis of mathematical basis of chance for advanced student - not for beginners in evolutionary science Sept. 16 2011
By Joel Avrunin - Published on Amazon.com
Format:Hardcover|Vine Customer Review of Free Product
Evolution is obviously a popular topic today, and the science is moving so fast that a book older than 10 years likely contains outdated information. One topic of recent interest has been mathematical difficulties in the probabilities and direction of evolution as clasically understood. In my own mind, I often liken Darwin to Lord Kelvin. Lord Kelvin was correct that the world was far older than 6000 years, but his estimate of 20-400 million years based on estimates of the cooling of the Earth seems laughable by our standards today. Even during his own day geologists could marvel as the scientific rigor of his calculations, but still say that something seemed wrong with a world of a mere 400 millions years. Kelvin used good science, but not all of the science, missing the role radioactivity played in the cooling of the Earth.

Darwin is like Kelvin, in that he got the rough idea, but the details would take further scientific understanding. Kelvin was saved by the advanceds in astronomy and chemistry, but deeper insight into Darwin's ideas would take much more research.

In his comprehensive new book, "The Logic of Chance", Eugene Koonin starts with an excellent overview of the history of evolutionary theory. For instance, Darwin did not known about genetics and he did not know about viruses and bacteria or eukaryotes. When he thought of irreducible complexity, he thought of the eye, not the multi-protein clotting process or the bacterial flagella. Darwin could only observe gross physical features, and the subtleties of the engine of evolution were invisible to him. Koonin also notes that Darwin wasn't even the first to observe the change of species over time. Writings from Greek and Indian sources present what we might now call evolution, and Darwin was also preceded by Lamarck, Lyell, and others.

Koonin establishes that what made Darwin unique was that he brought together many of these ideas into one framework (entirely rationalist, survival of the fittest, and speciation) and created the most compelling presentation ever seen.

One problem plaguing evolutionary science compared to cosmology (something more accepted) is the difficulty of experimentation. Whereas cosmologists have their theories supported by physicists performing experiments, biologists have more difficulty replicating or observing speciation. Indeed, Koonin's primary contention, which could be well misunderstood, is that we really have not understood much of the engine of evolution until recently. Koonin's book presents several diversions from the classical notion of the "Tree of Life", where we think of linear progression, one ancestor begetting 2 different lineages, etc. True evolution is far more complex that the "ascent of man" image or progression of horses. As creationists would object, these are stories that fit our fossil record, but not science.

Koonin brings mathematics and analysis to the process of evolution, showing how random chance combines with survival of the fittest, and demolishes the classical notion of evolution as striving towards greater complexity or improvement. Indeed, he shows through numerous examples how the complexity of evolution makes modeling immensely difficult. One particular noteworthy image is the 3-d surface plot of a "fitness landscape" showing how certain maxima can increase fitness, but random chance can move from one peak to another. There is no tree of life, no strive towards complexity. There is a random forest with localized maxima of fitness where species will land, with no direction in particular.

I recommend this book as you advance in your study of evolution and crave a mathematical understanding of just how the evolutionary process can function.

I do not recommend this book if you are just starting to learn about Evolution. The first chapter is a great overview, but the reader will jump the track after that. I read books on cosmology all the time, and yet my background in physics and math was not quite enough to make the biology easy to follow. I struggled through it and you likely will as well. If you a religious person looking to understand evolution and creationism, I recommend "Finding Darwin's God" by Kenneth Miller or "The Challenge of Creation" by Rabbi Slifkin. For a modern overview of evolutionary science without the religion (or religion bashing), I recommend "Evolution is True" by Jerry Coyne and "Written in Stone" by Brian Switek.

5 stars for a tremendous addition to the library of evolutionary science, and a necessary one for the mathematical mind struggling to understand the nature of chance and how it relates to evolutionary science.
2 of 2 people found the following review helpful
5.0 out of 5 stars State of the art book on evolutionary biology Jan. 23 2012
By Clyde M. Wisham Jr. - Published on Amazon.com
Format:Kindle Edition|Verified Purchase
This is a SOFTA* book on evolutionary biology. Professional and complete, it covers not only the most up-to-date aspects, but also has several good chapters detailing the history and development of evolutionary theory. However, be warned, there is no baby talk in this book. You will have to take on complex subjects (including some mathematics and analysis) and specialized terminology to get the most from this book. (I must admit I struggled at points. Good for the brain!)
I read the eBook version. However, biologists or paleontologists or any who are serious students of evolutionary biology, should probably get the hardback version because the tables and charts do not display well in the mobi [= Kindle] format.
(*State of the art)
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