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.
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.
eldavojohn writes: Agricultural biotechnology company Monsanto is now at the receiving end of a lawsuit from representatives of anyone who lived in the small town of Nitro, WV from 1949 on. This suit alleges that Monsanto spread chemical toxins all over town — most notably the carcinogenic dioxins. The plant in question produced herbicide 2,4,5-T which was used in Vietnam as an ingredient for "Agent Orange." From the article, 'Originally the suit called for Monsanto to both monitor people's health and clean up polluted property. The court rejected the property claims last year, leaving just the medical monitoring.' Strange that the suit is only allowed to address the symptom and not the root cause.
eldavojohn writes: In the grand scheme of things, antibiotics are a very temporary solution to aid humans in combating bacteria. Bacterial resistance to said antibiotics is an increasing fear and DARPA's "Rapidly Adaptable Nanotherapeutics" solicitation reveals they're interested in a more permanent solution as modifying the genes of harmless bacteria can result in powerful bioweapons. Like siRNA, DARPA is hoping for more nanomolecules that can specifically target cells and deliver medicine to them anywhere in the body. Most amazing about this proposal is that it's aimed at small businesses and hopes to turn a process that takes decades to study a new antibiotic into a few weeks to manufacture nanomedicine to specifically target bacteria.
eldavojohn writes: Wuhan University researchers working with the National Research Council of Canada and the Center for Functional Genomics at the University at Albany have announced that they have genetically modified rice to produce a medically useful protein chemically identical to human serum albumin. This protein is used to treat burns, traumatic shock and liver disease at a global demand rate of 500 tons each year. Normally this would be extracted from blood donations but now you can just grow rice and extract it at a rate of 2.75 grams of protein per kilogram of rice. After testing on rats with liver cirrhosis, the same response was shown as the protein from blood. This is important for China after a spike in demand and lack of supply lead to fake albumin medicine flowing through Chinese hospitals. Worried about these GMO crops cross pollinating regular crops? The researchers referred to a study indicating "a very low frequency (0.04-0.80%) of pollen-mediated gene flow between genetically modified (GM) rice and adjacent non-GM plants." Nature has a slightly more detailed article with a reference to the peer review publication.
eldavojohn writes: Standford's OpenSim software is a human motion modeling package that is currently making the rounds at museums where 'visitors walk across a pressure-sensitive floor and are presented at the other side with color-coded print outs of their weight distribution, identifying even slight imbalances that might be putting undue stress on their limbs and joints.' This project can also help with planning surgery. The work of Scott L. Delp, Frank C. Anderson, Allison S. Arnold, Peter Loan, Ayman Habib, Chand T. John, Eran Guendelman, and Darryl G. Thelen has been published in IEEE Transactions on Biomedical Engineering (note that this is a different effort from the virtual world of the same name). Although Standford's press release says it is now open source, I cannot find what license they are using nor can I access their SVN browser after registering.
eldavojohn writes: Bovines rejoice, rinderpest has been eradicated worldwide. The rinderpest virus has plagued Europe, Africa and Asia for centuries causing indirect famine in countries as hundreds of millions of cattle fell victim. This is the first time in recorded history that humankind has completely eradicated an animal disease.
eldavojohn writes: Several news outlets are reporting that a universal flu vaccine breakthrough has been made by Oxford scientists. The pain of matching yearly strains, the threat of swine flu and future threats of all new strains of influenza have taken a blow today. The vaccine works by 'differs from traditional treatments by targeting proteins inside the flu virus rather than proteins on the flu's external coat.' Such proteins are less likely to mutate between strains. These initial tests involved 11 people and there is call for a larger trail size.
eldavojohn writes: From the Institute of Public and Environmental Affairs in China, a report with a disturbing video titled "The Other Side of Apple" has been released that alleges Apple's supply chain rests atop a variety of recurring unaddressed employee health issues. The IPE video seems to indicate that N-Hexane causes respiratory and illnesses in workers — even nerve damage. The video claims 49 Wintek employees in Suzhou City had been treated at the time of filming, many of which end up tens of thousands of dollars in irreversible debt due to recurring illness. The report itself at this time is only in Chinese but can be found here. Additionally IPE released a 2010 report of all companies involvement in ethical supply chain issues that heralded Hewlett Packard, British Telecom, Alcatel-Lucent, Vodafone, Samsung, Toshiba and Sharp for taking positive steps but chastised Apple, Nokia, Sony, LG, Ericsson and Sing Tel for remaining inactive. If what the report indicates is true, Apple has done little to remedy the health issues associated with its clean room solvent (N-hexane) use reported back in May. IPE has also started issuing reports on heavy metal pollution by companies in China.
eldavojohn writes: I was home for the holidays and my father claimed that the well water has gotten worse in quality. About fifteen years ago we had been advised that our well was unfit for drinking due to sulfates and nitrogen from runoff and that we should no longer be drinking it unless we enjoyed permanent diarrhea (giardia). So since then my parents have been stocking jugs of purified water (and there was a noticeable difference in digestion after that point). Recently an ADM ethanol plant has opened up nearby that has started processing corn ethanol. My father is convinced that the water quality is getting worse and worse but when he contacts the DNR and EPA they don't take him seriously (he's already been told not to drink it). Like any government fearin' American, he's now convinced they're on the payroll over at ADM so I started investigating online water drinking tests and I'm quite out of my element here with many questions. If someone was refining corn into ethanol, what byproducts might be found in the drinking water? Sulfates? Heavy metals? How could you discern that stuff from runoff from farm fertilizer? Which tests available from which company (there are seemingly thousands) are priced reasonably that will provide good data on this? Are there certifications that companies hold that would give them legal weight should my dad find evidence of increasing destruction of the water? If I sent my dad to the local college, would this be a reasonable request for their chemistry department? Has anyone had any experience monitoring water quality and, if so, how frequently should this be tested to establish a trend in quality? If aquifers have already been ruined, do companies still have the same pollution requirements they have for untainted drinking water? I have no clue if my father is correct but he claims he can't even make a cup of coffee from the tap now without spending awhile on the throne. I'd like to give him advice on how to do his own measurements and either confirm or refute his suspicions.
eldavojohn writes: Wouldn't it be great if periwinkle cured cancer? Well, it doesn't — at least not in its natural form. That didn't stop a few MIT chemists who found that metabolically engineering them creates new cancer fighting drugs like an alkaloid called vinblastine. As any farmer sued by Monsanto will tell you, genetically modifying plants is so 1990s but in this case the article explains how they tricked out periwinkle roots by genetically modifying how the plant created proteins and then controlling what it is fed. The team hopes to expand on this research to create even more novel compounds like tweaking venblastine — in addition to amplifying the yield of said proteins, enzymes and alkaloids. First pesticides and now medicine, what's next for our GMO leafy friends? Terraforming other planets? Or will we be hoisted by our own petard as GMO kudzu becomes Skynet?