Customer Reviews

The Logic of Chance: The Nature and Origin of Biological Evolution (FT Press Science)

5 star:		(6)
4 star:		(5)
3 star:		(1)
2 star:		(1)
1 star:		(1)

 

 

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").

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.

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.

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.

This is a tremendous book. Another reviewer said it's going to be a classic, and perhaps so. However, the author's intention was to write a book suitable for the general public, like Hawkings' "Brief History of Time", and in the introduction, he himself acknowledges that that didn't really work out. In fact, it REALLY didn't work out; the book is extremely hard work for a non-biologist, and perhaps not exactly vanilla yogurt for biologists either. That's not to say a non-biologist can't get a lot out of it, but it's heavy going, and there's a lot that's over my head and will probably remain so.

I approached the book with some initial skepticism, because after all the guy is a Russian, and Russian scientists, especially in life sciences, have been known to believe some odd things that Westerners never heard of or don't give credence to; and the book is so dense and technical for a layman, and has such a vast scope, that I wasn't sure, if it was all nonsense, that I'd be able to tell.

However, after struggling with the book for a while, I've found that everything makes sense eventually, and I've learned a great deal in the process (which continues). I find the arguments convincing once I finally grasp them.

I think maybe Koonin should try writing a much simpler, less comprehensive book or article on the same subject. What makes this book so difficult is not that Koonin can't explain things clearly and simply; he does a great job explaining things like the history of Darwinism and the Modern Synthesis, the anthropic principle, and many, many other such matters. This book covers EVERYTHING, sometimes in excruciating detail, and with enormous numbers of references.

Koonin points out that, while evolution had been observed before, Darwin changed science by presenting a comprehensive, comprehensible, purely naturalistic explanation without recourse to religious or teleological explanations. The theory had obvious gaps and flaws, given that Darwin (and pretty much everyone else) seems not to have known about, or grasped the significance of, Mendel's work on heredity, let alone modern molecular biology. "Darwinism" became rather narrow and rigid, long after Darwin's death, with an insistence that all changes must be gradual and positive. Koonin shows how neutral and even adverse changes can occur with genetic drift (random variation) and genetic draft (mild adverse changes hitchhiking on strongly favorable ones, e.g. the trait for sickle-cell anemia being selected for because it goes along with resistance to malaria).

There are chapters on the origin of eukaryotes, the origin of life, genome complexity and its evolution, the role of random chance in evolution, the Virus World and its evolution,the postmodern state of evolutionary biology, and the cosmological context for all this. None of it is muju-muju or woo-woo; it's all appropriate in my opinion, very well researched, very well explained, and for the most part, very difficult. I'll be learning from this book for a long time.

There was always something a little unsatisfying about the Modern Synthesis (Darwinian survival of the fittest, combined with genetics). Without even being a biologist, one always had a feeling that there was a little more going here.

Koonin shows how much more is going on, and puts it in context. Very difficult, very rewarding, very well worth it, and a really impressive work for original thinking, clear explication, profundity, and an immensely broad scope.

Disclaimer: I am reviewing an advance unproofread copy that I received for free through the Vine program. I'm also reviewing the Kindle edition, which I also got for free.

I was a little concerned from reading the "blurbs" about this book, that it might be misconstrued as some kind of support for creationist attacks on evolution (you can even see this from some other reviews). Indeed some bits in the introductory parts of the book are a bit alarming in this respect, unnecessarily appearing to attack Charles Darwin, or the neo-Darwinist strict adaptationalist modern paradigm. I think the author and/or publishers tried to gin up some non-existent controversy through some exaggerated remarks, to try and generate some sexy press, in this regard.

The exaggerated remarks pointing out that the neo-Darwinist adaptationist paradigm is incomplete are hardly indictments of the "theory of evolution" in general -- indeed, it reminds me more of how Einstein generalized Newton's laws, by filling in details in places, special cases of the very large, very small, or very fast, where Newton's laws break down.

In the case of this book, these special cases are the world of prokaryotes, basically, where things do apparently work a bit differently overall than they do in the world of eukaryotes. In fact later in the book, the author gives us a detailed picture of one important distinction between prokaryotes and eukaryotes, leading to this difference -- HGT (Horizontal Gene Transfer) is a very common and important occurrence, "driving" evolution among prokaryotes where the DNA is not isolated. BUT in eukaryotes, the wall of the nucleus is a barrier that mostly stops HGT. So among prokaryotes with nuclei, the usual adaptationalist paradigm holds, where natural selection is the dominant occurrence and force "driving" evolution.

In the substance of the book it is obviously just a very detailed, up to date, thorough, and wonderful investigation through many aspects of molecular genomics. Also the title of the book is well chosen, because it seems that now we do have more and more real data from the molecular level, the grand story of evolution is a kind of story of molecular chance being modulated by various larger forces, leading to some kind of emergent "logic of chance"....

The early chapters of the book do present a lot of very detailed, very well documented/footnoted material, on how evolution among prokaryotes does have a strong "web" like structure rather than a strict "tree" structure, because HGT (Horizontal Gene Transfer) is turning out to be an even more fundamental force driving evolution, among prokaryotes, than strict adaptation is. But that's hardly an indictment of Darwin, or of adaptation as the most successful paradigm ever theorized, for evolution at the level of multi-cellular organisms, or even single-celled eukaryotes!

This is fascinating new stuff, for me at least. And it is pretty technical, so it is hard to follow sometimes. But I still am fascinated by it and I am able to understand enough to (I think) get the main points.

Since this is not a work of fiction, it's probably OK to leak some spoilers? (and other reviews have already done so) -- for instance, (apologies for my mis-translating into crude layman terminology here) it seems that the molecular genomic evidence strongly suggests that eukaryotes (including us humans) may have their origins in some kind of complex ancestor of some Archaea type prokaryotes (with a large genome, subsequently lost in its more modern Archaea prokaryote descendants, yet still lacking a nucleus or mitochondria etc.), which may have captured some kind of Bacterial type prokaryote (the genomic evidence is apparently fairly conclusive as to the family of bacteria that was the predecessor of mitochondria-type organelles inside eukaryotes), tried to eat it I guess :-) but resulted in endosymbiosis, where the resultant creature (and this may even have only happened once, as the rarest of rare events) was a chimera with things on the inside and things on the outside, which eventually had descendants that led to the Least Eukaryotic Common Ancestor ....

The only observation I can make about the Kindle edition is that for the most part it is well-formatted and easy to read, except for the images and diagrams. For them, I turn to the printed edition. But I do have the original Kindle 1, which is less capable at rendering images & stuff like that, so if you have a newer Kindle, they may look better on yours?

But overall I definitely recommend this book for anyone who has enough of a general science background to be able to read this level of technical stuff, and who is interested in evolution and genetics and wants to learn about the current situation (2011), of theories built from data obtained through molecular genomics, large-scale cross-species analyses and comparisons of genomes, etc. across archaea, bacteria, and all manner of eukaryotes.

Logic of Chance, The Nature and Origin of Biological Evolution

By Eugene V. Koonin

Due to some comments I have received on this review previously, I thought I should make a few things a bit more clear concerning this review. As for bias, I don't hide my bias, recognizing my biases is the only thing that helps me keep an open mind, which though it is critical, and skeptical, is in fact still open. That said, while I myself remain skeptical concerning evolution, my skepticism has been fostered and nourished reading atheistic and agnostic philosophers such as Thomas Nagel,The Last Word and Karl Popper,The Myth of the Framework: In Defence of Science and Rationality, whom the author of this book himself enjoys and respects, writing a great critique concerning Popper's contributions to science in Appendix A. The book in question further piqued that skepticism. Yet,I am not one who finds belief in Evolution to be completely incompatible with Christianity. I say that because I know many Christians who have held or do hold to evolutionary beliefs. I also say that because my faith is not so much in creation, as it is in a man, known to have existed, who claimed to be God, who died, and left an empty tomb after three days according to all historical documents concerning the matter biblical and extra biblical, whose self purported reason for coming in the first place was to forgive sins,for more on that read Tractatus Logico-Theologicus, Revised Edition, "Religion on Trial, Or "Jesus - God and Man (scm classics). Whereas my faith would be refuted by the bones of Christ, 1 Cor. 15, even if evolution were to be true, I'd be forced ask why that tomb is empty, and the only rational explanation accounting for the evidence, is in fact the resurrection.

Everything you think you know about Evolution is wrong. That's the basic message of the book, which in fact still argues for evolution. Koonin set out to write a book of popular science explaining the current state of affairs in evolution, and the new theories being proposed. He admits himself, though, that the book fails to be popular. It is readable enough, but in some sections the reading gets a bit heavy and involved. A nice corrective to this, aside from Dictionaries and other internet resources, is that each chapter ends with a synopsis that is generally very readable, and overall the book is quite enjoyable. I do imagine that he will perhaps upset many with the honesty with which he approaches the subject, and perhaps some of his bluntness. He is a committed materialist, and even more committed to belief in evolution, but he is honest in showing that currently science just does not have all the answers and perhaps never will, as to how evolution has occurred. He is certain though, that it has not happened the way most everyone has been taught and conceives of it as happening. Scrapping the "Modern Synthesis" which most of us were taught in high school and even intro courses to biology in college, he argues for a "post modern synthesis".

In the first two chapters of this book, and the intro, he argues that Darwinian Evolution and all that it relied on needs to be relegated to the "venerable museum halls where it belongs, so that we can explore the paradigm shift that has happened with the "post modern view of life." Indeed, the so-called "Tree of Life," pan-adaptationism" etc, are all shown to be wrong throughout the rest of the book. Even the concept that evolution is a process from simple to more complex life forms is thrown on the scrap heap of discarded scientific theories. For instance on page 399, and 261 he unabashedly states that there is no trend towards complexity in evolution. One begins to ask then, what is even left of the idea of evolution? Indeed, he spends a whole chapter talking about the streamlining of plants and insects, an "evolution" from complex to simple, what he calls on pg. 177 "reductive evolution."

To his credit, he doesn't try to shy away from the problem of the origin of life. He maintains that problems here cannot be overstated. He does not like the idea of "irreducible complexity" and sees intelligent design as malicious nonsense ( pg 498), and would rather like to use the term "purported or apparent irreducibility of complex structures" but is at pains to find solutions to these problems, neither having any readily available, or even a concept of how one might find a remedy. (Pg. 377) After a long discussion of possible alternatives he hangs his hat on a theory known as MWO or Many worlds in one, maintaining that a multiverse guarantees that somewhere, somehow this might happen. Yet I keep wondering to myself, if there is an infinite chance that something will happen, there is an equally infinite chance that nothing will happen, and you are back at ground zero wondering why there is something rather than nothing. Perhaps it is better for science to contemplate what is rather than why there is an is. And that strikes me as another peculiarity of this book. On pg. 250 You have the curious opening to his synopsis stating that the emergence of complexity is a problem. One wonders why this complexity has to be a problem, and not just a fact? It's only a problem because it doesn't fit with preconceived notions with which Koonin is approaching the information.

In the end, one can see why even Atheist Philosophers like Thomas Nagel, remain unconvinced by the propositions of Evolutionary theory. Yet Nagel shares a disposition with Koonin, that is comfortable maintaining his atheism, and waiting for an alternative explanation, to why there is something. And that is more or less what this book is about. Koonin readily admits a concise Metanarrative concerning evolution is impossible (pg. 422 A point he reiterates elsewhere, (pg.418.). This book is not about replacing the metanarratives of Darwin and the Modern Synthesis, but rather about ideas and concepts (pg 410). Yet, one wonders then if evolution as a theory isn't dying a death of a thousand qualifications, indeed if it hasn't already. When Koonin is done, you begin to think "evolution" is no longer even a workable theory, but a concept in want of a theory, a theory its proponents are desperately trying to find.

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)

Evolution, it is a heated topic in today's classrooms. With many states mandating that they also teach Creationism, or emphasize that evolution is nothing more than a theory. In this book Eugene Koonin takes a look at biological evolution, the evolution at a cellular level, at a level that we can't see with the naked eye; a level that is important for all life. In this highly technical work, Dr. Koonin follows the path of biological evolution. From the days of Darwin, through Modern Synthesis, to the modern Genome project; where they can actually look at individual species genes and follow the path of said genes.

The history of evolution is handled in two well written chapters, he has to spend time on this topic; but he does not want it to distract him from his larger goal. The majority of the book is split up by different types of organisms, virus, and the search for the common ancestor, which sounds like a fools search. This book is not written for the lay person, it is written for scientists. It is meant to further the scientific debate. Dr. Koonin does a good job, and hopefully he will spark some debate within the scientific community.

This is detailed. It is rather scholastic, not for the layman. It is rampacked with diagrams and related charts.

I would not say that it solved the delimna of chance but it sure showed that there are many factors involved, and in some instance we cannot figure it all out.

It is a great book if you are into detail.