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Book Review: The Logic of Chance 44

Posted by samzenpus
from the read-all-about-it dept.
eldavojohn writes "The Logic of Chance: The Nature and Origin of Biological Evolution is a comprehensive snapshot of the latest research of biological evolution. The text is written by Eugene V. Koonin, an editor for a journal and researcher at NCBI. The book, although lacking in foundational knowledge and often foregoing explanation of research, presents a comprehensive and well-referenced view of modern evolutionary research. It is heavily laden with acronyms and jargon specific to biology and evolution. As a result, reading it requires either prior knowledge or a high tolerance for looking up these advanced topics with the reward of it being an extremely eye opening and enjoyable read worthy of your time." Keep reading for the rest of eldavojohn's review.
The Logic of Chance: The Nature and Origin of Biological Evolution
author Eugene V. Koonin
pages 516
publisher FT Press Science
rating 7/10
reviewer eldavojohn
ISBN 978-0132542494
summary An outline of a fundamentally new evolutionary synthesis reflecting key advances in genomics, systems biology and biological physics.
First off, my background is primarily in computer science although I took courses in bioinformatics in my undergrad and have maintained an interest in evolution since evolutionary and genetic algorithms were supposed to revolutionize computer science when I was in school. Unfortunately, my lack of biology caused the text to be extremely tedious (so much googling) for some chapters while my strong statistical background made other chapters very much enjoyable. For most readers this presents a large barrier of entry. When the author discusses neural networks being used to categorize prokaryotic genes, it may be insufficient to the reader to understand what that means. As a result, this book's audience is a relatively small set of people: 1) biology graduates with strong statistical knowledge or 2) someone willing to work very hard to understand advanced terms and concepts in both fields. Please proceed knowing that a biologist's review of this same book could very well sound entirely different from mine. Also, Koonin wastes very few words in this book, the text is dense and if you are unable to complete reading this review due to jargon there is a low chance you'll be able to tolerate it in the book. To sample some of this book, there is a short PDF containing chapter one or Google Books offering the first 147 pages at the time of this writing — you will see that this review barely scratches the surface of what is covered in this information-dense book.

Secondly, I will preface my review of the technical aspects of this book with my reason for giving it a score of 7 out of 10. The introduction to this book sets very lofty goals. One of them being the hope that this book does for evolution what A Brief History of Time did for physics. That is a seriously tall order and gave me correspondingly high hopes for this book. Koonin, unfortunately, is a very gifted writer and is unafraid of using exceedingly complex sentences such as this gem from page 117 (deliberately taken out of context):

"It has been known for years that a widespread form of global regulation in bacteria is mediated by cAMP, with the participation of diverse adenylate cyclases (a striking case of NOGD); numerous proteins containing cAMP sensors, such as the GAF domain; and the CRP, FNR, and other transcription regulators, also containing cAMP-binding domains."

That sentence is typical of Koonin's writing — lengthy and intricately peppered with many acronyms (only one of which had been described well enough for me earlier in the text). Of course, that paragraph comes with a reference to a paper (like almost all of the paragraphs in this book) from 2010 by Seshasayee so the reader is free to seek external resources if these sentences are daunting.

Considering all of this, I read A Brief History of Time in high school and, despite not having had a physics course yet, learned a lot from it. I attribute that, mostly, to the fact that the sentences are simple and straightforward. Not only that but A Brief History of Time did a great job of building upward from the foundational mechanics of physics while somehow remaining refreshingly brief. This is not the case in The Logic of Chance but I will rush to the book's defense somewhat on that charge. Prior to having read this book, I would have stated my desire that the text start from the basics and work its way up. After reading this book and understanding this field better than I ever have, I now agree that the subject matter of evolution would demand quite the epic tome to accomplish such a feat. I do hope to see future versions of this book with more concise and clear sentences as well as more fundamental concepts explained. If I could have begged Koonin to add one thing to this book, it would be a glossary in the back spanning many hundreds of pages for ignorant readers like myself. Right now this book is for graduate students and academia whereas A Brief History of Time could almost be consumed by anyone who made it through the public school system.

I also sympathize with Koonin's herculean task because modern evolutionary studies seem relatively young compared to other fields like particle physics. As a result, Koonin must (and does) concede in some sections that there still exists largely debated theories. These debates often concern things about which we may never know the absolute truth like the branching factor of a tree of evolution on Earth some indeterminable time ago. As more and more prokaryotes and eukaryotes are added to their statistical algorithms, this may become clearer and yield revelations like the genetic makeup of the last eukaryotic common ancestor (LECA) and free this text of many pages devoted to questions surrounding such origins of life. But for now Koonin must tediously cover all his bases to introduce such things to the reader.

The book starts off by establishing the fundamentals of evolution up until the consolidation of Modern Synthesis. This includes purifying selection, drift, draft, fitness landscapes, etc until Darwinian Evolution was combined with genetics. At this point, the substrate of evolution (the genome) lead to evolutionary genomics. In particular Koonin concentrates on the statistics applied at the molecular level including distance methods, maximum parsimony, maximum likelihood, Bayesian inference and a similar analysis of phylogenetic methods. Koonin establishes early on that evolutionary research can no longer rely merely on phenotypic effects but rather there is a vast array of concrete changes happening at a molecular level.

The book moves on into comparative genomics and discusses extensively the intricate differences between the genomes of viruses, bacteria, archaea and eukaryota. Koonin exhaustively compares these groups through statistics and lays a brief foundation of relationships between genes. From this point on the book is heavily infested with the terminology of homologous, orthologous and paralogous genes. In addition to those the author discusses In-/Out-paralogous, co-orthologous and groups of orthologous (COG) genes. For people unfamiliar with this world, bookmarking and referring to Box 3-1 on page 56 is strongly advised. For the layperson, I believe an expansion of such a graphic would be a great addition to this book. Inside this part, the book also covers a simple but often misunderstood core piece of evolution and that is that evolution has the basic elementary events at the level of gene and genome evolution: substitution, deletion/loss, insertion, recombination/HGT and duplication. Over and over on Slashdot, I see comments that indicate a confusion or perception of evolution being one big monolithic thing. Koonin obviously reads or even studies a lot of other academic fields and tries to explain "the gene universe" as a space-time where there are a few dense clusters of core genes represented in most genomes but most of that space-time is occupied by a huge number of increasingly sparse "nebulae" consisting of rare genes. The author says of this universe: "This organization of the gene universe is distinctly fractal--that is, it appears at all scales of evolutionary distances."

As if that wasn't enough to prove that a definitive phenome narrative (what I alluded to earlier as desired) would be a bad idea, the next section moves on to systems biology and a heavier statistical look at genomics. Beyond the gene status (present or not present) exist two classes of variables: intensive evolutionary variables and extensive phenomic variables. At this point, we're not even talking about tangible things like eye or hair color but rather the underlying mechanisms to those sorts of things like proteins and how they are folded. Everywhere Koonin uses italics, the reader should pay special attention as I found these to be the most interesting key points (example: "Highly expressed genes evolve slowly"). In defining the nature of the evolutionary process, the author covers important concepts like fitness graphs that contain multiple local maxima to demonstrate how non-optimal progressions can occur. Furthermore this section makes it clear that adaptation is not the be-all end-all of evolution. The extensive discussion of the quantifiable properties of genome architecture, functioning and evolution are defined more so by non-adaptive, stochastic processes. Here (and in many later sections) Koonin attempts to use metaphors like Jacob's tinkering and ratchets to help the reader understand these complex concepts but I felt that these metaphors were still so far abstracted that the text could use anything linking these processes to tangible observations in organisms. Again I cannot hold this as a flaw for, after reading the book, it's clear that such a request would be viewed as sophomoric and evidence that I am unable to progress past The Origin of the Species (this book's key objective).

Koonin then moves on to the prokaryotic world and examines their genes and operons while paying special attention to an odd case: cyanobacteria. Most importantly in the prokaryotic domain, extensive comparative genomics has revealed a concept called horizontal gene transfer (HGT). I was personally hoping that Koonin would seize upon this novel concept and its importance in bacterial antibiotic resistance and how bacteria can evolve to dissolve novel compounds. For better or for worse, Koonin sticks to the pure purpose of this book and extensively covers important HGT discoveries like the convergence of protein sequences in similar groups of bacteria and archaea. Some selfish genes rely so heavily on horizontal mobility that they are dubbed "mobilomes" and Koonin discusses their aspects extensively. Darwin's Tree of Life concept was a very small eukaryotic part of the big picture that Koonin tries to re-invent as the "Forest of Life" or "Web of Life" (considering HGT). A whole chapter is devoted to discussing its properties and graphically visualizing its structure based on extensive surveys and what we know today.

From there the author discusses the origins of eukaryotes, Last Eukaryotic Common Ancestor (LECA), the branching factor of its evolution, its relative distance to the point of symbiogenesis in proposed evolutionary trees and the many competing theories about that tree. This section of the book spends considerable time examining the inferred origins of basic eukaryotic cell functioning and also discusses at length the archaeal roots of elaborate systems with the exception of the mitochondrion. This chapter also looks at the perplexing features of introns in eukaryotic genes. Koonin then tackles the misconceptions and abuses of the word complexity in all aspects of evolution. He applies information theory to the genetic code and notes that "information (entropy) tells us very little about the meaningful information content or complexity of a genomic sequence." It is then suggested that a new way to compute entropy and complexity is to examine the alignment of orthologous sequences instead of single sequences. For people interested in information theory, chapter eight is the most fruitful where Koonin proposes a computable formula for biological (evolutionary) information density. Like Claude Shannon's ability to infer many important aspects of communication, Koonin's modifications allow us to calculate that perceptually complex organisms possess more "entropic" genomes while perceptually less complex organisms like bacteria have the tightly packed and information dense "informational" genomes. After establishing these studies in information theory, Koonin is able to argue that neutrality of mutations that are fixed during evolution is the null hypothesis for all molecular evolutionary theories. All of this aids the author in discussing why evolution progressed passed single celled organisms that already had 1,000 to 1,500 genes to larger sets of genes in multicelled organisms.

Chapter nine tackles the modalities of Darwinian, Larmarckian and Wrightean evolutionary theories. This chapter improves upon the simplistic triad of heredity-variance-selection that defines Modern Synthesis by showing that the relationship between population size and environmental stress determines which of the three modalities is expressed the most in evolution while at the same time observing the importance of entropy (noise) at all levels of transmission. Koonin shows that by combining very well known molecular mechanisms we can achieve a complex scenario like Jean-Bapteste Lamarck's proposed modality of evolution. The text gives viruses the same treatment which, despite my assumption that they would be easier to analyze, appear to have many of the same complexities that prokaryotes and eukaryotes have. Possibly even more so given the effects of the Red Queen Hypothesis and all of the counterdefense genomes in some viruses. Furthermore the cellular empire and virus empires have two-way exchanges of genes. The truth is we know very little about the virus world — considering its size and history — and the author postulates that viromes in unknown and unstudied viruses consist largely of uncharacterized "dark matter" (again, borrowing terms from cosmologists).

Koonin then approaches the next logical step backwards: the last universal common ancestor (LUCA). He starts by listing the arguments that cellular life indeed had a common ancestor and looks at competing theories (for example cell organization complexity versus genetic complexity leading to different models of varying degrees of cellularity). In chapter twelve, Koonin covers the topic that is often the hardest to imagine — the origin of life. This is interesting and particularly difficult because the translation system itself at some point evolved. Interestingly enough, these 60 protein-coding genes and ~40 structural RNA genes are the only complex ensemble of genes that are conserved across all extant cellular life forms. So, of course, the point in the evolutionary tree where this had developed is discussed as well as the Darwin-Eigen cycle. The latter requiring a system of a far greater complexity in order to be started. So the author begins examining the proposition that over time and due to their catalytic properties ribozymes lead to processive synthesis of peptides (long enough to be the first proteins). After discussing the eleven stages this would have to encompass, the author discusses the existing skepticism of models that try to explain how replication and transcription came about. This chapter also tackles geochemical and chemical propositions on the origin of life — something that has been discussed on Slashdot before. This research centers on networks of inorganic compartments consisting of catalytic surfaces with gradients of heat and acidity that could have supported primordial organic chemistry.

The book ends with a chapter devoted to reiterating topics as well as asking important questions like whether or not another biological evolution model is necessary/feasible as well as caution against logic like the progress fallacy or criticizing a concept like "the selfish gene" because it sounds "undignified." Though these are tempting arguments because of their simplicity, they have proven fruitless. A diagram on page 412 reminds us just how complex the flow of genetic material is between the virus empire and the cellular empire.

There are two appendices to this book and, perhaps because they use a softer language, they were much more accessible to me yet posed more questions than answers. Appendix A concentrates on the philosophy of postmodernism, the infeasibility of synthesis and the distrust of metanarratives. The author argues that any paradigm presented must include oversimplification and that we merely replace them with better metanarratives. It is also important to ask these questions about the current paradigms for without them we would never have come up with drift, draft and various neutral ratchets to improve old models. Koonin references Hawking and Mlodinow with the concept of model-dependent realism which stresses that scientists merely construct models that are in turn swapped out for better models given how well they explain data and predict the outcomes of experiments. Lastly Koonin refers to Popper's famous falsification paradigm and his subsequent position on how invaluable evolution is purely on the grounds that it arms us to model and understand specific experiments. The second appendix deals with roughly estimating the probability of life arising given inflationary cosmology. I know this back of the envelope math has become popular given recent discoveries of exoplanets in the news but I felt the few references to the "many worlds in one" model deserved to be placed in a separate book. Nevertheless, Koonin covers both the strong and weak forms of the anthropic principle and looks at the connotations they hold for evolution.

The references at the end of this book are extensive — 38 pages of two line references. It should probably be mentioned that Koonin's references to his own work consist of two of these pages although at no point did it sound like he was unfairly proffering his theories over others. At certain points I had to wonder whether or not I was reading a lightly adjusted abstract from a peer reviewed paper or a book. This is most evident in one of the figures of an appendix on page 437 that reads "This is a formulation of the 'weak' anthropic principle adopted for the context of this paper." Since it is a graphic and in the appendix, it's forgivable but caused me to wonder if the rest of the book couldn't be more seamlessly tied together with transitionary language for novices like myself. Amazingly, I found maybe one grammatical error and no typos in this book which was a refreshing experience for a first edition. Also, this is one of the best bound books I've had the pleasure of reading, its spine has held up to hours of laying it flat open while I googled for a better understanding. While $50 is pricey, the book is built to last and this $10 premium over the kindle edition is worth it if you must hold a physical copy of a book. It saddened me to be reminded that some states struggle with including the core concepts of Darwinian evolution anywhere in their K-12 curriculum. And should those students desire to break new ground in this modern field, texts like The Logic of Chance are that much further away from them.

You can purchase The Logic of Chance: The Nature and Origin of Biological Evolution from amazon.com. Slashdot welcomes readers' book reviews — to see your own review here, read the book review guidelines, then visit the submission page

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Book Review: The Logic of Chance

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  • by thoughtsatthemoment (1687848) on Wednesday May 16, 2012 @04:52PM (#40021579) Journal
    I don't mind looking up for new words but if you ask me to look up for jargon then I am quite sure the author doesn't know how to communicate or doesn't have much to communicate to begin with.
    • unfamiliar jargon = new words (and phrases)

      Someone learning English might think, for example, that the english jargon "looking up for new words" would suggest skygazing for vocabulary.

      • Someone who knows English would surely be aware that the phrasal verb "look up" takes a direct object, so such an interpretation would be correct.

    • by eldavojohn (898314) * <eldavojohn&gmail,com> on Wednesday May 16, 2012 @04:59PM (#40021643) Journal

      I don't mind looking up for new words but if you ask me to look up for jargon then I am quite sure the author doesn't know how to communicate or doesn't have much to communicate to begin with.

      I tipped off Eugene Koonin about this review on Slashdot. He read it and corrected me saying:

      I will make one comment only: this is a scientific book not a book of popular science, therefore it simply cannot be judged by the standards of 'Brief History of Time' (quite apart from the obvious distinction between Hawking and mere mortals)

      All fields have their super overloaded terms that journals have weighted with baggage so they can have physically short sentences with each other and know the terminology. So I don't think your statement is very fair. I think this book is a must have for any serious biologist but it was probably unfair of me to try and approach it from completely outside that realm.

      • by flaming error (1041742) on Wednesday May 16, 2012 @05:04PM (#40021707) Journal

        " it was probably unfair of me to try and approach it from completely outside that realm"

        Unfair to the author perhaps, but not to the general Slashdot community. "The Logic of Chance" sounds like a title that would interest many of us.

        Thanks for your hard work, thanks for sharing it.

      • by Hatta (162192)

        So, the take away message is, "don't give this book to your creationist relations, it won't help"?

        • No, it won't. (Score:4, Insightful)

          by Anonymous Coward on Wednesday May 16, 2012 @05:14PM (#40021807)

          Overcoming superstitions to which one has strong emotional attachments and which one learned when one's mind was young and impressionable requires more than the simple presentation of evidence and reason. It requires that the listener have a very above-average learning aptitude, an unusually adaptable mind capable of making huge shifts of perspective, and of course an authentic interest in Truth for its own sake.

          Needless to say, most people do not have these attributes, and as such spend their entire lives believing (and adamantly defending) whatever made sense to them back when they were children.

          • +1 flattering

          • Re:No, it won't. (Score:4, Insightful)

            by gameboyhippo (827141) on Wednesday May 16, 2012 @05:55PM (#40022207) Journal

            lol... "Christians" like to do that too. That is make generalizations on why a person is an atheist and claim that they have a strong emotional attachment to whatever made sense to them back when they were children. Ah well... (waits for emotional atheist to mod down for disagreeing)

          • by Anonymous Coward

            I've found that one of the most important bits of that equation is that you're willing to be patient and hear the other one out.

            Nobody ever just up-and-relents when it comes to religious superstitions. You can't just convince someone to stop being religious. You can only hope to make them consider the possibility that their superstitions are shaky.

            Then they either reflexively snuff any doubt with a cheap "out" like "well it's just faith", or they decide to be honest with themselves and consider figuring ou

          • by Drethon (1445051)
            I don't think its so much the strong emotional attachments so much as evolution doesn't do much for the fear of death whereas religion does. Could be wrong though...
      • by vlm (69642) on Wednesday May 16, 2012 @05:20PM (#40021865)

        I think this book is a must have for any serious biologist but it was probably unfair of me to try and approach it from completely outside that realm.

        How do you get to be a serious biologist? read books...

        To give a /. analogy I don't think a perl book without all that complicated computer stuff in it would teach me very much, so I wouldn't bother reading it. I've never learned anything from an easy book.

        Good review though. Better than average /. reviews. Write more reviews.

      • by s.petry (762400)

        Just from your review I understood that it was not at all a "regular person" kind of book. Sounds rather interesting, but seems to require a lot of knowledge ahead of reading. I'm sure there are a few /.ers that are genetic specialists and microbiologists that can enjoy.

        • Just from your review I understood that it was not at all a "regular person" kind of book. Sounds rather interesting, but seems to require a lot of knowledge ahead of reading. I'm sure there are a few /.ers that are genetic specialists and microbiologists that can enjoy.

          And high school biology teachers only a background in marine biology and no formal training in genetics, genomics, and molecular biology to the extent presented in the book...

          When this book first came out on Amazon, it was free for a period, and I managed to nab it then. It is an outstanding book, but it IS a long, heavy read (I imagine so, even for the experts, but maybe not). It probably really helped that I had read several of Dr. Koonin's papers over the years and was familiar with his style of writing

      • If you, as outsider, read a programming book, you will encounter terms like Central Processing Unit. You'll probably have no idea what that is and but you can take a wild guess without even looking up at all. You might also encounter a term like "recursive". Here looking up doesn't help as it is not something you can usually see in the physical world. But there is no need to worry. Because that is such a fundamental concept in programming, you'll learn it to such a degree that you start to use it outside of
      • this is a scientific book not a book of popular science, therefore it simply cannot be judged by the standards of 'Brief History of Time' (quite apart from the obvious distinction between Hawking and mere mortals)

        I think he's basically calling you a 'tard.

        Fight fight fight fight fight!

      • David Sloan Wilson's "Evolution For Everyone". He's a group-selectionist in some ways, but don't hold that against him. He really does cover the basics in a way interested but non-technical readers can follow. He makes clear what evolution is, and - equally important these days - what evolution isn't.
    • I don't mind looking up for new words but if you ask me to look up for jargon then I am quite sure the author doesn't know how to communicate or doesn't have much to communicate to begin with.

      Well, then ... good luck learning anything technical, ever.

      Seriously, "jargon" is what people who are scared of big words call vocabulary they don't know yet (and with that attitude, probably never will.) Now, it's true that a lot of writers use obscure words or abbreviations when a common word would do just as well, and generally that's a bad idea. But in any technical field worthy of the name, a lot of the concepts cannot be communicated without using the proper terms. Those who can't deal with this sh

      • If I had to read 'cyclic adenosine mono phosphate' everywhere cAMP is referenced in a molecular biology textbook, a lot more trees would need to be felled. Do we call it jargon when we read 'nut' rather than 'hexaform internally helically threaded rotational compression fixture'? I sympathise with the reviewer, but if you want to understand how evolution works you need to learn a little biochemistry.
        • by xevioso (598654)

          Dude I saw those guys "hexaform internally helically threaded rotational compression fixture" at Bonaroo. They were awesome.

      • by Baloroth (2370816)

        That isn't what jargon means. "Jargon" means terms that are either a) invented by that community for a specific purpose or b) heavily loaded terms with specific meaning within that community (basically, "vocabulary" that is literally meaningless outside that field or has a completely different meaning). The meaning can always be conveyed without recourse to "jargon", it just cannot be done so succinctly (and oftentimes, elegantly). For a book that is only intended to be read by other members of the field, u

      • by notgm (1069012)

        rather large difference in "explaining jargon once, and then using it heavily" vs. "using jargon throughout and never explaining it", which is what the OP doesn't like.

        put it in context, explain it once, and proceed - don't force us to put down the work every three words to go learn something...teach it actively.

    • by tibit (1762298)

      Here's what Feynman told his sister Joan about reading an astronomy text: you read it from the beginning until you get stuck. Then you read again and again, until eventually you'll get to the end. It's uncanny how, eventually, our brain will make up some working definitions for formerly unknown words. They may not be quite correct, but they'll, as if by magic, fit to the text you are reading. That's how I've learned English. I was reading technical texts such as manuals and software UI. Eventually I was goo

    • by tilante (2547392)
      Keep in mind, though, that this is meant to be a textbook for an advanced biology course, not a "general interest" book. The author therefore assumes that readers will have the requisite background and doesn't explain biological jargon, just as the author of a calculus textbook doesn't explain terms from algebra, geometry, etc.
  • by betterunixthanunix (980855) on Wednesday May 16, 2012 @05:01PM (#40021675)
    We all know that this is part of Satan's trick, right?

    http://chick.com/reading/tracts/1079/1079_01.asp [chick.com]
  • I'm confused as to how a book "lacking in foundational knowledge and often foregoing explanation of research" can present "a comprehensive and well-referenced view of modern evolutionary research".

    Don't get me wrong, the book might be terrific, but what an oxymoronic summary (there's some jargon for ya)!

    • by khallow (566160)
      I guess the reviewer was trying to say that you needed some substantial initial understanding of modern evolution in order to use the book as "a comprehensive and well-referenced view of modern evolutionary research".
  • I suspect the evidence, itself, supports both The Logic of Chance and Intelligent Design. Dawkins says this world's biology expresses an appearance of design. I'm not sure why, then, the conclusion of actual design is simply thrown out. If someone pursues Truth and then categorically throws out the other half of the premises because of the philosophical belief that science is the only path to Truth (a statement that cannot be empirically tested), then that person seems to be interested in truth if the concl
    • by tilante (2547392)
      One major problem is that concluding that there was an actual designer simply pushes the problem back a step: where did the designer come from? Opting for a designer requires either acceptance of a miracle ("the designer's existence can't be explained"), an infinite regress ("the designer was designed by a designer-designer, who was designed by a designer-designer-designer, who..."), or brings you back to needing a method for a complex being to arise without a designer.

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