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The Logic of Chance: The Nature and Origin of Biological Evolution
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 Recommended Reprinted with permission from CHOICE, copyright by the American Library Association.
529 pages, Kindle Edition
First published June 16, 2011
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Displaying 1 - 18 of 18 reviews
March 25, 2012
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").
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").
January 16, 2012
Fascinating, But Flawed, Argument Emphasizing Biological Evolution's Stochastic Nature
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.
(Reposted from my 2011 Amazon review)
There are several serious flaws which reduce this book's potential usefulness to colleagues and to those in the scientifically literate public who may be familiar with Koonin's research. He offers rather fleeting discussions of exaptation and phylogenetic systematics (cladistics), omitting some of the key published scientific literature, beginning with the classic punctuated equilibrium paper co-authored by Niles Eldredge and Stephen Jay Gould. For example, in Chapter One, I find it odd that he cites the Gould and Lewontin paper "The Spandrels of San Marco", without referencing both it and another, more important, paper on the concept of exaptation, that was co-written by Gould and Elisabeth Vrba, published a few years later in the journal Paleobiology. Nor does he discuss cladistics, assuming that readers are familiar with its terminology (which is an unrealistic expectation for a book that is meant for a more general, science-literate audience). More worrisome is his acceptance of the anthropic principle, to which he devotes an entire appendix, since that falls within the realm more of metaphysical speculation, than of science, even if there are some cosmologists who think that the anthropic principle does explain much with regards to the present physical properties of the universe. Regrettably, "The Logic of Chance" is a most unsatisfying work of popular scientific literature, and one that is suited not for a general audience, including those in the sciences, but maybe, most appropriately, only those who are most familiar with Koonin's research.
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.
(Reposted from my 2011 Amazon review)
There are several serious flaws which reduce this book's potential usefulness to colleagues and to those in the scientifically literate public who may be familiar with Koonin's research. He offers rather fleeting discussions of exaptation and phylogenetic systematics (cladistics), omitting some of the key published scientific literature, beginning with the classic punctuated equilibrium paper co-authored by Niles Eldredge and Stephen Jay Gould. For example, in Chapter One, I find it odd that he cites the Gould and Lewontin paper "The Spandrels of San Marco", without referencing both it and another, more important, paper on the concept of exaptation, that was co-written by Gould and Elisabeth Vrba, published a few years later in the journal Paleobiology. Nor does he discuss cladistics, assuming that readers are familiar with its terminology (which is an unrealistic expectation for a book that is meant for a more general, science-literate audience). More worrisome is his acceptance of the anthropic principle, to which he devotes an entire appendix, since that falls within the realm more of metaphysical speculation, than of science, even if there are some cosmologists who think that the anthropic principle does explain much with regards to the present physical properties of the universe. Regrettably, "The Logic of Chance" is a most unsatisfying work of popular scientific literature, and one that is suited not for a general audience, including those in the sciences, but maybe, most appropriately, only those who are most familiar with Koonin's research.
November 14, 2011
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)
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)
December 18, 2023
This is an important book on the topic of evolutionary biology. Recommended for those who are really interested in this topic. The ideas are totally relevant to this day (writing in 2023), but it must be noted that the research has moved a great deal since the book was written (but if a reader is interested in the topics of evolutionary biology, eukaryogenesis, and the origin of life - then this reader knows which parts have been updated by the time of reading). For me, reading was also difficult because the book gets quite technical at times. But it is still readable for a layperson, which I am, and enjoyable.
March 14, 2012
This is an impressively written book, and I found it quite interesting for the most part. Note that it's a lengthy volume - the hardcover is 528 pages - although the references and other material at the end take up about 20% of that. I actually read the Kindle version which I downloaded during a limited time free Amazon offer that I was alerted to by Jerry Coyne's blog (website).
A lot of the material is rather dense - you'd have to be a biologist to completely understand everything Koonin covers here - but the writing is good enough that a layman can at least follow the thread of his arguments. However, although the arguments sound reasonable while wading through them, in a few cases I found myself wondering at the end: “so what?” But I’m not an evolutionary biologist so I could have missed the significance of what he’s said in these cases.
Basically, his aim is to convince readers that what we've read about evolution by natural selection in the likes of Darwin, Dawkins, etc., is not all there is to know about the process. If you're interested in evolution, you're probably already aware of this - but Koonin goes into the details of why this is the case, and there's a lot of in depth discussion of genome evolution, viruses, horizontal gene transfer, biological complexity, and the origin of eukaryotes. He also touches on epigenetics and Lamarckian evolution, and at the end, the origin of life. These topics are no doubt vitally important in understanding evolution in viruses, archaea and other microscopic organisms, and in understanding what happened "in the beginning" of life on earth, but less important for explaining the diversity we see in the small subset that's nevertheless the most obvious to us: animals and plants.
In conclusion, this book did add somewhat to my layman’s understanding of evolution, although a less wordy volume might have been able to do the same.
A lot of the material is rather dense - you'd have to be a biologist to completely understand everything Koonin covers here - but the writing is good enough that a layman can at least follow the thread of his arguments. However, although the arguments sound reasonable while wading through them, in a few cases I found myself wondering at the end: “so what?” But I’m not an evolutionary biologist so I could have missed the significance of what he’s said in these cases.
Basically, his aim is to convince readers that what we've read about evolution by natural selection in the likes of Darwin, Dawkins, etc., is not all there is to know about the process. If you're interested in evolution, you're probably already aware of this - but Koonin goes into the details of why this is the case, and there's a lot of in depth discussion of genome evolution, viruses, horizontal gene transfer, biological complexity, and the origin of eukaryotes. He also touches on epigenetics and Lamarckian evolution, and at the end, the origin of life. These topics are no doubt vitally important in understanding evolution in viruses, archaea and other microscopic organisms, and in understanding what happened "in the beginning" of life on earth, but less important for explaining the diversity we see in the small subset that's nevertheless the most obvious to us: animals and plants.
In conclusion, this book did add somewhat to my layman’s understanding of evolution, although a less wordy volume might have been able to do the same.
December 7, 2014
Exicting book. Explains new bioinformatic approach of the evolution.
August 10, 2017
Очень сложная книга для небиологов, даже в обнимку с википедией было очень трудно читать. Но оч. интересная, попробую перечитать года через два.
January 24, 2022
In this quite technical book, Eugene Koonin explores how the ideas from the Modern Synthesis have changed in the light of genomic data.
Natural selection is but one evolutionary force that shapes genomes. To a large extent, neutral processes such as genetic drift and draft define evolution. He emphasizes the population genetic model of Lynch which focuses on effective population size (Ne). When Ne is large, selection is the dominant force. When Ne is small, drift becomes the most important factor. All lineages pass through several bottleneck phases where drift (and thus chance) plays a crucial role.
Darwin focused on random variation leading to infinitesimally small changes. However, this is only one class of variation. Nearly neutral variation is not “seen” by selection but does play an important role, such as the construction of nearly neutral networks that form the basis of evolvability. Non-gradualist variation includes gene and genome duplications, gene loss, and horizontal gene transfer.
Moreover, given the rampant exchange of genetic material between prokaryotes the Tree of Life can be better represented as a Web of Life.
Detailed chapters on the origin of Eukaryotes and the origin of life in general highlight the role of viruses and the importance of unique events in evolution. He also provides a radical alternative for the origin of life, namely the Anthropic Chemical Evolution (ACE) model. Given that there are an infinite number of universes, it is inevitable that life should emerge in some of them. We just happen to live in a universe where this happened (i.e. the Anthropic Principle). He argues that a complex replication-translation systems could have come about by chance, after which biological evolution took hold. Perhaps a bit farfetched, but interesting to contemplate.
A thought-provoking read which gave me a new perspective on evolution.
Natural selection is but one evolutionary force that shapes genomes. To a large extent, neutral processes such as genetic drift and draft define evolution. He emphasizes the population genetic model of Lynch which focuses on effective population size (Ne). When Ne is large, selection is the dominant force. When Ne is small, drift becomes the most important factor. All lineages pass through several bottleneck phases where drift (and thus chance) plays a crucial role.
Darwin focused on random variation leading to infinitesimally small changes. However, this is only one class of variation. Nearly neutral variation is not “seen” by selection but does play an important role, such as the construction of nearly neutral networks that form the basis of evolvability. Non-gradualist variation includes gene and genome duplications, gene loss, and horizontal gene transfer.
Moreover, given the rampant exchange of genetic material between prokaryotes the Tree of Life can be better represented as a Web of Life.
Detailed chapters on the origin of Eukaryotes and the origin of life in general highlight the role of viruses and the importance of unique events in evolution. He also provides a radical alternative for the origin of life, namely the Anthropic Chemical Evolution (ACE) model. Given that there are an infinite number of universes, it is inevitable that life should emerge in some of them. We just happen to live in a universe where this happened (i.e. the Anthropic Principle). He argues that a complex replication-translation systems could have come about by chance, after which biological evolution took hold. Perhaps a bit farfetched, but interesting to contemplate.
A thought-provoking read which gave me a new perspective on evolution.
August 29, 2021
Worth it for probability of life alone
At the very end Koonin puts together an estimate of the probability of life's origin in any given pocket universe in an infinitely expanding metaverse, which (spoiler) is less than 10 to the -1000. To put this in context of ID theory the origin of life greatly exceeds Dembski's cap of 10 to the 150 of probabilistic resources.
How does Koonin get out of this conudrum? Infinite probabilistic resources and the weak anthropic principle. Both of which bring their own set of issues.
The rest of Koonin's book show just how much we have to adjust evolutionary theory to take into account the actual scientific discoveries of this day and age. It would make Darwin spin in his grave!
At the very end Koonin puts together an estimate of the probability of life's origin in any given pocket universe in an infinitely expanding metaverse, which (spoiler) is less than 10 to the -1000. To put this in context of ID theory the origin of life greatly exceeds Dembski's cap of 10 to the 150 of probabilistic resources.
How does Koonin get out of this conudrum? Infinite probabilistic resources and the weak anthropic principle. Both of which bring their own set of issues.
The rest of Koonin's book show just how much we have to adjust evolutionary theory to take into account the actual scientific discoveries of this day and age. It would make Darwin spin in his grave!
June 20, 2020
Excellent and mind-changing book. A bit too hard for pop-science, but for somebody with good background in science -- pleasure to read
November 27, 2020
I read only that which interested me.
December 13, 2016
The book fits uniquely into 2 categories: simultaneously professional and by and large accessible to general public. Unlike many similar popular scientific books, it doesn`t dumb down arguments for reader`s comprehension. Author`s level intelligence is evident in his wording, pleasure to see this clear intellectual style.
Fresh: mr. Koonin is one of the world`s leading biologists, so the info presented is accurate and up-to-date. It sums up, roughly, last 30 years of evolutionary biology. And it turns out it biology can be as interesting and authoritative as physics, but with a feeling of frontier being explored right now(adays) - included. Really it is a detective story. Sometimes too technical for my understanding, but also plenty of material accessible for a 15 year old. It turns out that Tree of Life model I learned at school is already outdated - rather Forest.
Should definitely be one of contemporary must-reads for the educated people. Somewhat provocative is inclusion of multiverse theories from physics to explain the origin of life. That was way too much... well, I accept. Unexpected connection for a biology book.
Fresh: mr. Koonin is one of the world`s leading biologists, so the info presented is accurate and up-to-date. It sums up, roughly, last 30 years of evolutionary biology. And it turns out it biology can be as interesting and authoritative as physics, but with a feeling of frontier being explored right now(adays) - included. Really it is a detective story. Sometimes too technical for my understanding, but also plenty of material accessible for a 15 year old. It turns out that Tree of Life model I learned at school is already outdated - rather Forest.
Should definitely be one of contemporary must-reads for the educated people. Somewhat provocative is inclusion of multiverse theories from physics to explain the origin of life. That was way too much... well, I accept. Unexpected connection for a biology book.
January 7, 2013
Completely changed the way I thought of evolution from a clean, neatly dividing tree into a confusing, seemingly random web of connections that unites everything on the planet. Great read, though can get a little confusing at points with some of the detail
November 15, 2011
Some of the bits are somewhat challenging but very interesting
July 23, 2014
Couldn't finish it. Boring as hell.
abandoned-reads
July 23, 2013BOOK TOO BRAINY. HURT HEAD.
August 31, 2016
Definitely more difficult to read than your standard popular science books on evolution. Nonetheless, it is well worth your time.
April 12, 2013
Technical.
Displaying 1 - 18 of 18 reviews