Slashdot Mirror

bonch writes "Researches at Northwestern University have developed an inexpensive solar cell intended to solve the problems of current solar cell designs, such as high cost, low efficiency, and toxic production materials (abstract). Based on the Grätzel cell, the new cell uses millions of light-absorbing nanoparticles and delivers the highest conversion efficiency reported for a dye-sensitized solar cell."

An anonymous reader writes "A man with one clock knows what time it is, goes the old saw, a man with two is never sure. Imagine the confusion, then, experienced by a doctor with dozens. Julian Goldman is an anaesthetist at Massachusetts General Hospital in Boston. After beginning to administer blood-thinning medication during an urgent neurological procedure in 2005, Mr Goldman noticed that the EMR had recorded him checking the level of clotting 22 minutes earlier. As a result, four hospitals in the northeast had their medical devices checked, and found that on average they were off by 24 minutes. The easy solution that devices could have used since 1985? NTP."

MistrX writes with a tidbit about what the Cassini probe is up to nowadays. From the article: "NASA's Cassini spacecraft made its closest approach to Saturn's tiny moon Methone as part of a trajectory that will take it on a close flyby of another of Saturn's moons, Titan. The Titan flyby will put the spacecraft in an orbit around Saturn that is inclined, or tilted, relative to the plane of the planet's equator. The flyby of Methone took place on May 20 at a distance of about 1,200 miles (1,900 kilometers). It was Cassini's closest flyby of the 2-mile-wide (3-kilometer-wide) moon. The best previous Cassini images were taken on June 8, 2005, at a distance of about 140,000 miles (225,000 kilometers), and they barely resolved this object."

First time accepted submitter n7ytd writes "The Register has a piece today about overcoming one of the biggest challenges to migrating to cloud-based storage: how to get all that data onto the service provider's disks. With all of the enterprisey interweb solutions available, the oldest answer is still the right one: ship them your disks. Remember: 'Never underestimate the bandwidth of a station wagon full of tapes hurtling down the highway.'"

Hugh Pickens writes "Michael Grynbaum writes that 40,000 ultra-Orthodox Jewish men filed through the gates of Citi Field to discuss the dangers of the Internet. For the attendees, many of whom said they came at the instructions of their rabbis, it was a chance to hear about a moral topic considered gravely important in the Hasidic community: the potential problems that can stem from access to pornography and other explicit content on the uncensored, often incendiary Web. Schlomo Cohen, 24, said he came to Citi Field because the rally was a good way to remind his community to keep temptation at bay. 'Desires are out there,' said Cohen. 'We have to learn how to control ourselves.' The rally was sponsored by a rabbinical group, Ichud Hakehillos Letohar Hamachane, that is linked to a software company that sells Internet filtering software to Orthodox Jews. Those in attendance were handed fliers that advertised services like a 'kosher GPS App' for iPhone and Android phones, which helps users locate synagogues and kosher restaurants. 'No one here is a Luddite who denies the manifold benefits that technology has brought to mankind as a whole,' says Eytan Kobre, spokesman for the event. 'But at a certain point, a mature, thinking individual stops and says, "I've got to make a cost-benefit analysis [of] what ways it is enriching my life, [and] in what ways it is undermining it."'"

Fluffeh writes "Around a year ago, a person working for the ABC in Australia with the highest levels of access to systems got caught with his fingers on the CPU cycles. The staffer had installed Bitcoin mining software on the systems used by the Australian broadcaster. While the story made a bit of a splash at the time, it was finally announced today that the staffer hadn't been sacked, but was merely being disciplined by his manager and having his access to systems restricted. All the stories seem a little vague as to what he actually installed, however — on one side he installed the software on a public facing webserver, and the ABC itself admits, 'As this software was for a short time embedded within pages on the ABC website, visitors to these pages may have been exposed to the Bitcoin software,' and 'the Coalition (current Opposition Parties) was planning on quizzing the ABC further about the issue, including filing a request for the code that would have been downloaded to users' machines,' but on the other side there is no mention of the staffer trying to seed a Bitcoin mining botnet through the site, just that mining software had been installed."

Lasrick writes "Benjamin Loehrke describes the rather odd definitions of what is a 'tactical' nuclear weapon and what isn't. 'There is enough ambiguity surrounding the capabilities of tactical and strategic nuclear weapons to render the term "tactical" all but useless for arms control purposes. As the United States and Russia pursue new arms control treaties, they should drop the tactical distinction and limit the total number of all nuclear weapons — strategic, tactical, or other.'"

Lasrick writes "Benjamin Loehrke describes the rather odd definitions of what is a 'tactical' nuclear weapon and what isn't. 'There is enough ambiguity surrounding the capabilities of tactical and strategic nuclear weapons to render the term "tactical" all but useless for arms control purposes. As the United States and Russia pursue new arms control treaties, they should drop the tactical distinction and limit the total number of all nuclear weapons — strategic, tactical, or other.'"

New submitter closer2it writes with news of interface changes in Windows 8. From the article: "Microsoft has revealed that it has made some big changes to its desktop UI for Windows 8, which includes moving away from Aero Glass — the UI first introduced with Vista. According to the company, this means visual changes that include 'flattening surfaces, removing reflections, and scaling back distracting gradients.' Despite all of these changes with the interface, the company doesn't appear to be worried about the issue of 'learnability.' Instead, Microsoft believes that with a little help it won't take long for users to adapt to the new operating system."

First time accepted submitter ourlovecanlastforeve writes "Those of you still hanging on to Jaguar and Land Rover as the last vestiges of the truly British automobile in the States may find yourselves grasping at straws as Chery announces a nearly two billion dollar joint effort with the auto brand to move production to Changsu in China." Anyone still hanging on to that idea might also be interested to learn that Jaguar and Land Rover are subsidiaries of India's Tata, maker of the low-priced Nano.

benrothke writes "Elementary Information Security, based on its title, weight and page length, I assumed was filled with mindless screen shots of elementary information security topics, written with a large font, in order to jack up the page count. Such an approach is typical of far too many security books. With that, if there ever was a misnomer of title, Elementary Information Security is it." Read below for the rest of Ben's review Elementary Information Security author Richard E. Smith pages 800 publisher Jones & Bartlett Learning rating 10/10 reviewer Ben Rothke ISBN 978-1449648206 summary Information security magnum opus For anyone looking for a comprehensive information security reference guide - Elementary Information Security is it. While the title may say elementary, for the reader who spends the time and effort to complete the book, they will come out with a complete overview of every significant information security topic.

The book is in fact a textbook meant to introduce the reader to the topic of information security. But it has enough content to be of value to everyone; security notices or experienced professional.

Author Richard Smith notes that if you want to get a solid understanding of information security technology, you have to look closely at the underlying strengths and weakness of information technology itself, which requires a background in computer architecture, operating systems and computing networking.

With that, Elementary Information Security is a tour de force that covers every information security topic, large and small. The book also provides a relevant overview of the peripheral topics that are embedded into information security.

In 17 chapters covering over 800 pages, the book is well organized and progressively gets more complex. Two large chapters of the book are freely available online, with chapter 3 here and chapter 9 here. The early chapters focus on the fundamentals of computers and networking, and the core aspects of information security. The chapters progress in complexity and deal with distributed systems and more complex security topics. The mid-chapters deal with cryptography, starting with an introduction to the topic, into more complex topics and scenarios. One is hard-pressed to find an information security topic not covered in the book.

Chapter 1 is on Security from the Ground Up and lays the groundwork for what security is. Various topics around risk are detailed; such as identifying, prioritizing and assessing risks.

Chapter 2 is on Controlling a Compute rand reviews the underlying architecture around computers.

For some people, much of their learning about information security is based on rote memorization. In the book, Smith eschews this and each chapter closes with a glossary of topics, and penetrating questions. There are also problem definitions which detail practical situations with the hope that the reader can create and adequate security solution. The reader who spends extra time reviewing the questions will find that it will significantly help in their mastering the myriad topics.

The goal of the questions and exercises is to make the knowledge real. Some of the exercises include watching movies with computer security related topics such as The Falcon and the Snowman, Crimson Tide, and others. For example, in The Falcon and the Snowman, the author asks the reader to identify two types of security measure that would have helped prevent theft of the crypto keys. In Crimson Tide, it asks the reader to consider the missile launch procedures portrayed in the film and asks if it is possible for a single person to launch a nuclear missile. Another scenario is that under what circumstances a recipient should accept an unauthenticated message. It also asks the reader to give an example of a circumstance in which accepting an unauthenticated message would yield the wrong result.

The book is not meant as a For Dummies guide to the topic, and it assumes a college-level comprehension of relevant mathematical concepts. Note though that the requisite math is detailed in the sections on encryption and cryptography.

The book is also the first textbook certified by the NSA to comply with the NSTISSI 4011 standard, which is the federal training standard for information security professionals. The author notes on his blog that in order to gain that certification, he had to map each topic required by the standard to the information as it appears in the textbook.

Given the value of the book, (ISC) should consider using this title as a reference for their CISSP certification. With all of the CISSP preparation guides available, even the Official (ISC)2 Guide to the CISSP CBK, one is hard pressed to find a comprehensive all-embracing security reference such as this. Some may even want to simply use this book as their definitive CISSP study guide.

For those looking for a single encyclopedic reference on information security, they should look no further than Elementary Information Security. Richard Smith has written a magnum opus on the topic, which will be of value for years to come.

Ben Rothke is the author of Computer Security: 20 Things Every Employee Should Know.

You can purchase Elementary Information Security from amazon.com. Slashdot welcomes readers' book reviews -- to see your own review here, read the book review guidelines, then visit the submission page.

benrothke writes "Elementary Information Security, based on its title, weight and page length, I assumed was filled with mindless screen shots of elementary information security topics, written with a large font, in order to jack up the page count. Such an approach is typical of far too many security books. With that, if there ever was a misnomer of title, Elementary Information Security is it." Read below for the rest of Ben's review Elementary Information Security author Richard E. Smith pages 800 publisher Jones & Bartlett Learning rating 10/10 reviewer Ben Rothke ISBN 978-1449648206 summary Information security magnum opus For anyone looking for a comprehensive information security reference guide - Elementary Information Security is it. While the title may say elementary, for the reader who spends the time and effort to complete the book, they will come out with a complete overview of every significant information security topic.

The book is in fact a textbook meant to introduce the reader to the topic of information security. But it has enough content to be of value to everyone; security notices or experienced professional.

Author Richard Smith notes that if you want to get a solid understanding of information security technology, you have to look closely at the underlying strengths and weakness of information technology itself, which requires a background in computer architecture, operating systems and computing networking.

With that, Elementary Information Security is a tour de force that covers every information security topic, large and small. The book also provides a relevant overview of the peripheral topics that are embedded into information security.

In 17 chapters covering over 800 pages, the book is well organized and progressively gets more complex. Two large chapters of the book are freely available online, with chapter 3 here and chapter 9 here. The early chapters focus on the fundamentals of computers and networking, and the core aspects of information security. The chapters progress in complexity and deal with distributed systems and more complex security topics. The mid-chapters deal with cryptography, starting with an introduction to the topic, into more complex topics and scenarios. One is hard-pressed to find an information security topic not covered in the book.

Chapter 1 is on Security from the Ground Up and lays the groundwork for what security is. Various topics around risk are detailed; such as identifying, prioritizing and assessing risks.

Chapter 2 is on Controlling a Compute rand reviews the underlying architecture around computers.

For some people, much of their learning about information security is based on rote memorization. In the book, Smith eschews this and each chapter closes with a glossary of topics, and penetrating questions. There are also problem definitions which detail practical situations with the hope that the reader can create and adequate security solution. The reader who spends extra time reviewing the questions will find that it will significantly help in their mastering the myriad topics.

The goal of the questions and exercises is to make the knowledge real. Some of the exercises include watching movies with computer security related topics such as The Falcon and the Snowman, Crimson Tide, and others. For example, in The Falcon and the Snowman, the author asks the reader to identify two types of security measure that would have helped prevent theft of the crypto keys. In Crimson Tide, it asks the reader to consider the missile launch procedures portrayed in the film and asks if it is possible for a single person to launch a nuclear missile. Another scenario is that under what circumstances a recipient should accept an unauthenticated message. It also asks the reader to give an example of a circumstance in which accepting an unauthenticated message would yield the wrong result.

The book is not meant as a For Dummies guide to the topic, and it assumes a college-level comprehension of relevant mathematical concepts. Note though that the requisite math is detailed in the sections on encryption and cryptography.

The book is also the first textbook certified by the NSA to comply with the NSTISSI 4011 standard, which is the federal training standard for information security professionals. The author notes on his blog that in order to gain that certification, he had to map each topic required by the standard to the information as it appears in the textbook.

Given the value of the book, (ISC) should consider using this title as a reference for their CISSP certification. With all of the CISSP preparation guides available, even the Official (ISC)2 Guide to the CISSP CBK, one is hard pressed to find a comprehensive all-embracing security reference such as this. Some may even want to simply use this book as their definitive CISSP study guide.

For those looking for a single encyclopedic reference on information security, they should look no further than Elementary Information Security. Richard Smith has written a magnum opus on the topic, which will be of value for years to come.

Ben Rothke is the author of Computer Security: 20 Things Every Employee Should Know.

You can purchase Elementary Information Security from amazon.com. Slashdot welcomes readers' book reviews -- to see your own review here, read the book review guidelines, then visit the submission page.

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

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

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

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

CowboyRobot writes "Ward Cunningham developed the first wiki, wrote the Fit test framework, is the co-inventor of CRC cards, and is now promoting the concept of technical debt. He recently won the Dr. Dobb's Excellence in Programming Award and was interviewed by that publication. 'The creator of the Wiki dishes on the Wiki, Wikipedia's policies, OO design, technical debt, CoffeeScript and Perl, how to survive as a veteran programmer, and doing the simplest thing that could possibly work.' Cunningham is given the chance to explain his philosophy of coding: 'I like the picture and I like the look of the code. It's only 40 lines, but every line carried some careful thought. There was a learning curve there that surprised me because the programs looked short. The most rewarding work I've done this year is digging through that code and understanding what it does and understanding what it didn't do, and how to approach the problem.'"

New submitter slashbill writes "MIT's working on a way to measure network capacity. Seems no one really knows how much data their network can handle. Makes you wonder about how then do you calculate expense when building out capacity? From the article: 'Recently, one of the most intriguing developments in information theory has been a different kind of coding, called network coding, in which the question is how to encode information in order to maximize the capacity of a network as a whole. For information theorists, it was natural to ask how these two types of coding might be combined: If you want to both minimize error and maximize capacity, which kind of coding do you apply where, and when do you do the decoding?'" This is a synopsis of the first of two papers on the topic.

Fluffeh writes "In Australia, we have the right to record TV and play it back at a later date; we also have the right to transcode from one format to another, so anyone with a media server can legally back up their entire DVD collection and watch it without all those annoying warnings and unskippable content — as long as we don't break encryption (please stop laughing!). Optus, Australia's second largest Telco, has been raising ire though with the new TV Now service they are offering and Big Media is having a hissy fit. The service does the recording on behalf of the customer. Seems like a no-brainer right? Let the customer do what they are allowed to legally do at home, but charge them for it. Everybody wins! Not according to Sports Broadcasters, who made this statement when Optus said they would appeal their recent loss in an Australian Court to the highest court in the land: 'They are a disgusting organization who is acting reprehensibly again and now putting more uncertainty into sports and broadcast rights going forward I'm really disappointed and disgusted in the comments of their CEO overnight.' Is this yet another case of Big Media clutching at an outdated business model, or should consumers be content with just doing their own work?"

Hugh Pickens writes "Tim Heffernan writes that when 'The Fifty,' as it's known in company circles, broke down three years ago, there was talk of retiring it for good. Instead, Alcoa decided to overhaul their 50,000-ton, 6-story high forging press, now scheduled to resume service early this year. 'What sets the Fifty apart is its extraordinary scale,' writes Heffernan. 'Its 14 major structural components, cast in ductile iron, weigh as much as 250 tons each; those yard-thick steel bolts are also 78 feet long; all told, the machine weighs 16 million pounds, and when activated its eight main hydraulic cylinders deliver up to 50,000 tons of compressive force.' The Fifty could bench-press the battleship Iowa, with 860 tons to spare, but it's the Fifty's amazing precision — its tolerances are measured in thousandths of an inch—that gives it such far-reaching utility. Every manned US military aircraft now flying uses parts forged by the Fifty, as does every commercial aircraft made by Airbus and Boeing making the Jet Age possible. 'On a plane, a pound of weight saved is a pound of thrust gained—or a pound of lift, or a pound of cargo,' writes Heffernan. 'Without the ultra-strong, ultra-light components that only forging can produce, they'd all be pushing much smaller envelopes.' The now-forgotten Heavy Press Program (PDF), inaugurated in 1950 and completed in 1957, resulted in four presses (including the Fifty) and six extruders — giant toothpaste tubes squeezing out long, complex metal structures such as wing ribs and missile bodies. 'Today, America lacks the ability to make anything like the Heavy Press Program machines,' concludes Heffernan, adding that 'The Fifty' will be supplying bulkheads through 2034 for the Joint Strike Fighter. 'Big machines are the product of big visions, and they make big visions real. How about a Heavy Fusion Program?'"

ananyo writes, quoting Nature: "The development of retinal implants has been dogged by problems of unwieldiness since the first implantable stimulator for vision restoration was developed in 1968. Now researchers have come up with a solution that overcomes many of the problems by the use of special glasses that fire infrared signals into the eye and onto an implanted array of silicon photodiodes. The system, tested in rats, simplifies what needs to be implanted and both transmits visual data and power directly to the implants, eliminating the need for any bulky external power source (abstract)."

Hugh Pickens writes "Katherine Ellison reports in the Atlantic that a group of high school students is suing the federal government in U.S. District Court claiming the risks of climate change — dangerous storms, heat waves, rising sea levels, and food-supply disruptions — will threaten their generation absent a major turnabout in global energy policy. 'I think a lot of young people realize that this is an urgent time, and that we're not going to solve this problem just by riding our bikes more,' says 18-year-old Alec Loorz, one of the plaintiffs represented, pro bono, by the Burlingame, California, law firm of former U.S. Republican congressman Paul 'Pete' McCloskey. While skeptics may view the case as little more than a publicity stunt, its implications have been serious enough to attract the time and resources of major industry leaders." (Read more, below.) Pickens continues: "Last month, Judge Wilkins granted a motion to intervene in the case by the National Association of Manufacturers who says the plaintiffs lack standing because their injuries are too speculative and not likely to be reduced by the relief sought. 'At issue is whether a small group of individuals and environmental organizations can dictate through private tort litigation the economic, energy, and environmental policies of the entire nation,' wrote NAM spokesman Jeff Ostermeyer. The plaintiffs contend that they have standing to sue under the 'public trust doctrine,' a legal theory that in past years has helped protect waterways and wildlife. While the adults continue their argument, Loorz says kids his age are much more worried about climate change than many of their parents might imagine. "

Qbertino writes "I'm in my early 40s, and after a little more than 10 years of web, scripting and software development as a freelancer and some gigs as a regular, full-time employee, I'm seriously considering giving my IT career a boost by getting a degree. I'm your regular 1980s computer kid and made a career switch to IT during the dot-bomb days. I have quite a bit of programming and project experience, but no degree. I find myself hitting somewhat of a glass ceiling (with maybe a little age discrimination thrown in there). Since I'm in Germany, degrees count for a lot (70% of IT staff have a degree) so getting one seems fitting and a nice addition to my portfolio. However, I'm pondering wether I should go for Computer Science or Business Informatics. I'd like to move into Project Management or Technical Account Management, which causes my dilemma: CS gives me the pro credibility and proves my knowledge with low-level and technical stuff, and I'd be honing my C/C++ and *nix skills. Business Informatics would teach me some bean-counting skills; I'd be doing modelling, ERP with Java or .NET all day. It would give me some BA cred, but I'd lose karma with the T-shirt wearing crew and the decision-makers in that camp. I'm leaning toward Business Informatics because I suspect that's where the money is, but I'm not quite sure wether a classic CS degree wouldn't still be better — even if I'm wearing a suit. Any suggestions?"

New submitter IdleThoughts writes "Sometimes it takes a long time to spark a revolution. Long the ugly duckling of programming languages, iOS' Objective-C passed C# in the 'TIOBE Programming Community Index this month and seems on a trajectory to overtake C++ in the next few. It was invented in the early 1980s by Brad Cox and Tom Love, with the idea of creating 'Software Integrated Circuits' and heavily influenced by Smalltalk — yet another legacy from Xerox PARC, along with desktop GUIs, ethernet and laser printers. It was adopted early on by Steve Jobs' NeXTStep, the grand-daddy of all that is now OS X. It had to wait, however, for the mobile device revolution to have its day, being ideally suited to the limited resources on portable devices. It's still being actively developed by Apple and others, sporting the new automatic reference counting and static analysis in the Clang compiler. It turns out it has supported dynamic patching of code in applications all along. What more surprises does this venerable language have up its sleeve?"

New submitter IdleThoughts writes "Sometimes it takes a long time to spark a revolution. Long the ugly duckling of programming languages, iOS' Objective-C passed C# in the 'TIOBE Programming Community Index this month and seems on a trajectory to overtake C++ in the next few. It was invented in the early 1980s by Brad Cox and Tom Love, with the idea of creating 'Software Integrated Circuits' and heavily influenced by Smalltalk — yet another legacy from Xerox PARC, along with desktop GUIs, ethernet and laser printers. It was adopted early on by Steve Jobs' NeXTStep, the grand-daddy of all that is now OS X. It had to wait, however, for the mobile device revolution to have its day, being ideally suited to the limited resources on portable devices. It's still being actively developed by Apple and others, sporting the new automatic reference counting and static analysis in the Clang compiler. It turns out it has supported dynamic patching of code in applications all along. What more surprises does this venerable language have up its sleeve?"

New submitter IdleThoughts writes "Sometimes it takes a long time to spark a revolution. Long the ugly duckling of programming languages, iOS' Objective-C passed C# in the 'TIOBE Programming Community Index this month and seems on a trajectory to overtake C++ in the next few. It was invented in the early 1980s by Brad Cox and Tom Love, with the idea of creating 'Software Integrated Circuits' and heavily influenced by Smalltalk — yet another legacy from Xerox PARC, along with desktop GUIs, ethernet and laser printers. It was adopted early on by Steve Jobs' NeXTStep, the grand-daddy of all that is now OS X. It had to wait, however, for the mobile device revolution to have its day, being ideally suited to the limited resources on portable devices. It's still being actively developed by Apple and others, sporting the new automatic reference counting and static analysis in the Clang compiler. It turns out it has supported dynamic patching of code in applications all along. What more surprises does this venerable language have up its sleeve?"

New submitter IdleThoughts writes "Sometimes it takes a long time to spark a revolution. Long the ugly duckling of programming languages, iOS' Objective-C passed C# in the 'TIOBE Programming Community Index this month and seems on a trajectory to overtake C++ in the next few. It was invented in the early 1980s by Brad Cox and Tom Love, with the idea of creating 'Software Integrated Circuits' and heavily influenced by Smalltalk — yet another legacy from Xerox PARC, along with desktop GUIs, ethernet and laser printers. It was adopted early on by Steve Jobs' NeXTStep, the grand-daddy of all that is now OS X. It had to wait, however, for the mobile device revolution to have its day, being ideally suited to the limited resources on portable devices. It's still being actively developed by Apple and others, sporting the new automatic reference counting and static analysis in the Clang compiler. It turns out it has supported dynamic patching of code in applications all along. What more surprises does this venerable language have up its sleeve?"

An anonymous reader writes with news that the European Space Agency has lost contact with its Envisat environmental satellite mere weeks after celebrating a full decade in orbit. Engineers have spent the last month trying to re-establish contact, and will continue to do so for another two months. "With ten sophisticated sensors, Envisat has observed and monitored Earth’s land, atmosphere, oceans and ice caps during its ten-year lifetime, delivering over a thousand terabytes of data. An estimated 2500 scientific publications so far have been based on this information, furthering our knowledge of the planet." The ESA was hoping Envisat would stay operational for another two years, until Sentinel satellites from the Global Monitoring for Environment and Security initiative became operational.

ananyo writes "Scientists can now add a 'dwarf mammoth' to the list of biological oxymorons that includes the jumbo shrimp and pygmy whale. Studies of fossils discovered last year on the island of Crete in the Mediterranean Sea reveal that an extinct species once thought to be a diminutive elephant was actually the smallest mammoth known to have existed — which, as an adult, stood no taller than a modern newborn elephant (abstract). The species is the most extreme example of insular dwarfism yet found in mammoths."

TheGift73 writes "By far the most controversial bill discussed in the Queen's speech today has to be the 'Draft Communications Bill' which '...will allow the police and intelligence agencies to collect data on communications, like texts and emails, flexible to changes in technology, such as the Internet. This will apply UK wide.' The Queen's Speech has set out the government's legislative plans for the next year." El Reg has the skinny on the CCDP related parts. From their article: "It's unclear if those 'strict safeguards' mean that a warrant, for example, would be needed before spooks could access such data. The rough proposal appeared to only fuzzily indicate that such protection for British citizens would be provided, however."

udas writes "Two thirds of the world's population, 4 billion people, use cell phones today, and all of them have access to SMS. Groupe Spécial Mobile (GSM), set up in 1982, created the GSM standard, leading to a unified, open, standard-based mobile network. SMS, up to 160 7-bit character messages sent over control channels (when they aren't busy), was part of the original GSM specification itself. The first GSM handsts were approved for sale in May 1992. But it was not until 1996, when pay-as-you-go SIM cards showed up, and the kids got their hands on it, that SMS gained popularity."

Hugh Pickens writes "Dave Lindorff writes in the LA Times that growing numbers of students are discovering their old school is actively blocking them from getting a job or going on to a higher degree by refusing to issue an official transcript. The schools won't send the transcripts to potential employers or graduate admissions office if students are in default on student loans, or in many cases, even if they just fall one or two months behind. It's no accident that they're doing this. It turns out the federal government 'encourages' them to use this draconian tactic, saying that the policy 'has resulted in numerous loan repayments.' It is a strange position for colleges to take, writes Lindorff, since the schools themselves are not owed any money — student loan funds come from private banks or the federal government, and in the case of so-called Stafford loans, schools are not on the hook in any way. They are simply acting as collection agencies, and in fact may get paid for their efforts at collection. 'It's worse than indentured servitude,' says NYU Professor Andrew Ross, who helped organize the Occupy Student Debt movement last fall. 'With indentured servitude, you had to pay in order to work, but then at least you got to work. When universities withhold these transcripts, students who have been indentured by loans are being denied even the ability to work or to finish their education so they can repay their indenture.'"

Hugh Pickens writes "The Telegraph reports that huge plant-eating dinosaurs called sauropods may have produced enough greenhouse gas by breaking wind to alter the Earth's climate. Scientists believe that, just as in cows, methane-producing bacteria aided the digestion of sauropods by fermenting their plant food. 'A simple mathematical model suggests that the microbes living in sauropod dinosaurs may have produced enough methane to have an important effect on the Mesozoic climate,' says study leader Dr Dave Wilkinson. 'Indeed, our calculations suggest that these dinosaurs could have produced more methane than all modern sources — both natural and man-made — put together.' The key factor is the total mass of the animals which included some of the largest animals to walk the Earth, such as Diplodocus, which measured 150 feet and weighed up to 45 tons. Medium-sized sauropods weighed about 20 tons and lived in herds of up to a few tens of individuals per square kilometer so global methane emissions from the animals would have amounted to around 472 million tons per year, the scientists calculated. Sauropods alone may have been responsible for an atmospheric methane concentration of one to two parts per million (ppm), say the scientists and studies have suggested that the Earth was up to 10C (18F) warmer in the Mesozoic Era. ''The Mesozoic trend to sauropod gigantism led to the evolution of immense microbial vats unequaled in modern land animals. Methane was probably important in Mesozoic greenhouse warming. Our simple proof-of-concept model suggests greenhouse warming by sauropod megaherbivores could have been significant in sustaining warm climates.'"

wiredmikey writes "On Wednesday, a remote code execution vulnerability in PHP was accidentally exposed to the Web, prompting fears that it may be used to target vulnerable websites on a massive scale. The bug itself was traced back to 2004, and came to light during a recent CTF competition. 'When PHP is used in a CGI-based setup (such as Apache's mod_cgid), the php-cgi receives a processed query string parameter as command line arguments which allows command-line switches, such as -s, -d or -c to be passed to the php-cgi binary, which can be exploited to disclose source code and obtain arbitrary code execution,' a CERT advisory explains. PHP developers pushed a fix for the flaw, resulting in the release of PHP 5.3.12 and 5.4.2, but as it turns out it didn't actually remove the vulnerability."

ananyo writes "Researchers have used radio waves to remotely activate engineered insulin-producing genes in mice. In the long term, the work could lead to medical procedures in which patients' genes are triggered on demand. The researchers coated iron oxide nanoparticles with antibodies that bind to a modified version of a temperature-sensitive ion channel. They injected these particles into tumors grown under the skins of mice, then heated the nanoparticles with low-frequency radio waves. The nanoparticles heated the ion channel, activating it and allowing calcium to flow into cells. The influx of calcium switched on an engineered calcium-sensitive gene that produces insulin (abstract)."

sunbird writes "As previously covered on Slashdot, on April 18th the FBI seized a server located in a New York colocation facility shared by May First / People Link and Riseup.net. The server, which was operated by the European Counter Network ('ECN'), the oldest independent internet service provider in Europe, was seized in relation to bomb threats sent to the University of Pittsburgh using a Mixmaster anonymous remailer hosted on the server (search warrant). The FBI's action has been criticized by the EFF. Predictably, the threats continued even after the server seizure. On April 24th, the FBI quietly returned the server, without notifying either Mayfirst / People Link or riseup, and were caught on video doing it."

ananyo writes "The head of NASA Ames Research Center may have fallen victim to restrictive arms regulations — just as a US government report recommends changing them to help the space industry. Simon 'Pete' Worden, who recently announced that Mars exploration would be done by private companies, has been accused of giving foreign citizens access to information that falls under the International Traffic in Arms Regulations (ITAR). ITAR has hampered U.S. firms seeking to export satellite technology. The allegations against Worden come just as the new report recommends moving oversight of many commercial satellites and related activities from the State department to the Commerce department, and some fear they could provide lawmakers with reasons to not ease export controls."

Uwe Hermann today announced the availability of sigrok, one of the first Open Source logic analyzers. Tired of being tied to Windows and proprietary software with limited features, in late 2010 he began work on flosslogic, which, after discovering Bert Vermeulen was also working on similar software, became sigrok. From the article: "Thus, the goal was to write a portable, GPL'd, software that can talk to many different logic analyzers via modules/plugins, supports many input/output formats, and many different protocol decoders. ... Currently supported hardware includes: Saleae Logic, CWAV USBee SX, Openbench Logic Sniffer (OLS), ZEROPLUS Logic Cube LAP-C, ASIX Sigma/Sigma2, ChronoVu LA8, and others." Their wiki has a list of supported protocols as well. You can grab the source over at SourceForge.

sciencehabit writes "A team of researchers has zoomed in on two spots on the body of the Iceman, a mummified, 5300-year-old hunter found frozen in the Alps in 1991: a shoulder wound found with an embedded arrowhead and a hand lesion resembling a stab wound. The scientists used atomic force microscopy, a visualization method with resolution of less than a nanometer, to scan the wounds for blood residue. They discovered red blood cells — the oldest in the world to be found intact — as well as fibrin, a protein needed for blood to clot. The presence of fibrin indicates that the Iceman, nicknamed Ötzi, didn't die immediately after being wounded."

MrSeb writes with news about a production ready electric-hybrid airplane. From the article: "... The four-passenger carbon fiber aircraft isn't really an electric plane but more of a plug-in hybrid plane, much like the Chevrolet Volt. Whatever it is, the Volta Volare aeronautics company of Portland, Oregon says the plane can travel 300 miles on battery power, then a 1.5-liter gasoline engine engages and extends the plane's range to 1,000 miles. The company sees the plane being attractive for its low cost of operation and its environmental friendliness. Aviation gasoline is typically leaded fuel, which has been gone from motor vehicle fuel since the 1980s. On a 200-mile trip in a comparable four-passenger gas-engine private plane, you'd burn $80 worth of avgas, while the electricity to carry the GT4 200 miles would cost only $20 — nice savings, but perhaps a little inconsequential when the plane itself is expected to cost around $500,000. Testing begins this spring on the Volta Volare GT4."

New submitter drom writes "Google released a key part of their Street View pipeline as open source on Tuesday: Ceres Solver. It's a large-scale nonlinear least squares minimizer. What does that mean? It's a way to fit a model (like expected position of a car) to data (like GPS positions or accelerometers). The library is completely general and works for many problems. It offers state of the art performance for bundle adjustment problems typical in 3D reconstruction, among others."

judgecorp writes "The British Government has announced its plans to handle solar storms. The idea is to improve the resilience of infrastructure, including satellite communications — which the government says will also be useful against the future possibility of electromagnetic pulse (EMP) weapons. From the report: 'National Grid and DECC are building on the work of the Space Environment Impacts Evaluation Group and E3C to analyse the range of impacts of extreme space weather events, with the Carrington Event being adopted as the reasonable worst case. These scientific assessments have enabled National Grid to change the design requirements for its Supergrid transformers, and to increase its reserve holding of transformers. National Grid is currently developing improved monitoring tools with the British Geological Survey (BGS) and installing or reinstalling Geomagnetically Induced Currents (GIC) monitoring devices into its Strategic Asset Management program. The next steps will be for National Grid, in association with BGS and working with E3C, to develop more detailed modelling of severe space weather events including impacts on generator transformers. This will extend and strengthen its analysis on the electricity transmission system completed so far.'"

mcmadman writes "The multi-zone audio player I'm working with uses an almost decade old card/software combo that is prone to crashes and other anomalies. I would like to know if there are open source (read 'free') or other alternatives that would allow multiple simultaneous playlists played through the myriad of audio interfaces out there. The line outs are then plugged into a CobraNet matrix, which handles the distribution of the music/sound to their respective areas. I'm looking at eight channels minimum, timed playlist start/stops, and triggered announcements. So far the only software and hardware I've found are proprietary broadcasting solutions which tend to be a bit heavy on the wallet or meant for home use."

theodp writes "Meet Engineer Doe. A NY Times report has identified Marius Milner as the software engineer at the center of the uproar over a Google project that used Wi-Fi sniffing Google Street View cars to collect e-mail and other personal data from potentially millions of unsuspecting people. Milner, creator of the wardriving software NetStumbler, referred questions to his lawyer. Google declined to comment. A patent search shows the USPTO awarded Google and Milner a patent in June 2011 for protecting Internet users from 'hackers and other ne'er-do-wells [who] may seek to tap into communications on a network.'"

Harperdog writes "Noah Schactman has a great piece on the Airborne Laser, the ray gun-equipped 747 that became a symbol of wasteful Pentagon weaponeering. Despite sixteen years and billions of dollars in development, the jet could never reliably blast a missile in trials. Now the House Armed Services Committee's Strategic Forces wants the Airborne Laser to be used to defend us against the threat of North Korea's failed missiles."

SchrodingerZ writes "Just in time to miss the 100-year anniversary of the fatal voyage of the Titanic, Australian mining billionaire Clive Palmer announced he has plans to recreate the Titanic, calling it Titanic II. 'It will be every bit as luxurious as the original Titanic but of course it will have state-of-the-art 21st Century technology and the latest navigation and safety systems,' says Palmer. He stated it was to be as close to the original as possible, with some modern adjustments. Its maiden voyage is set for 2016."

New submitter jools33 writes "The BBC has a fascinating story about how a mathematical formula revolutionized the world of finance — and ultimately could have been responsible for its downfall. The Black-Scholes mathematical model, introduced in the '70s, opened up the world of options, futures, and derivatives trading in a way that nothing before or since has accomplished. Its phenomenal success and widespread adoption lead to Myron Scholes winning a Nobel prize in economics. Yet the widespread adoption of the model may have been responsible for the financial crisis of the past few years. It's interesting to ponder how algorithms and formulas that we work on today could fundamentally influence humanity's future."

New submitter ph4cr writes with news that a new particle has been discovered at CERN that confirms theoretical predictions. A pre-print of the academic paper is available at the arXiv (PDF). From the article: "Physicists from the University of Zurich have discovered a previously unknown particle composed of three quarks in the Large Hadron Collider (LHC) particle accelerator. A new baryon could thus be detected for the first time at the LHC. The baryon known as Xi_b^* confirms fundamental assumptions of physics regarding the binding of quarks. ... In the course of proton collisions in the LHC at CERN, physicists Claude Amsler, Vincenzo Chiochia and Ernest Aguiló from the University of Zurich's Physics Institute managed to detect a baryon with one light and two heavy quarks. The particle Xi_b^* comprises one 'up,' one 'strange' and one 'bottom' quark (usb), is electrically neutral and has a spin of 3/2 (1.5). Its mass is comparable to that of a lithium atom. The new discovery means that two of the three baryons predicted in the usb composition by theory have now been observed."

Hugh Pickens writes "AP reports that when a Delta Airlines flight touched down at Midway International Airport in Chicago, the passengers looked out the window to see the jet surrounded by fire trucks, police cars and ambulances. Health officials came through the door wearing facemasks and other protective gear. As it turns out the bedbugs that infest hotels appear to be the source of red marks on a 50-year old Minnesota woman that prompted health officials to quarantine the jet for fear they were dealing with something much more serious: monkeypox. Lise Sievers called her mother during a layover in Detroit and told her that one of the children she visited and is trying to adopt in Uganda had some pus-filled red bumps and also mentioned she had some small bumps of her own, a rash that she suspected was the handiwork of bedbugs. Those two very different bumps — one with pus, one without — got jumbled up in Siever's mother's mind, and she called a hospital near her Indiana home to ask about treatment for her daughter. 'She told them her daughter is on a flight back from Uganda and has some red bumps which are pussing and what should she do to treat them,' says Roger Sievers. 'She was looking for some general advice.' Health officials feared they were looking for monkeypox, a rare and sometimes fatal disease mostly in found in central and western Africa. After the passengers waited on the plane for a couple of hours, officials brought good news. 'They came back down and told my mom it was bed bug bites and they started releasing people.'"

Hugh Pickens writes "AP reports that when a Delta Airlines flight touched down at Midway International Airport in Chicago, the passengers looked out the window to see the jet surrounded by fire trucks, police cars and ambulances. Health officials came through the door wearing facemasks and other protective gear. As it turns out the bedbugs that infest hotels appear to be the source of red marks on a 50-year old Minnesota woman that prompted health officials to quarantine the jet for fear they were dealing with something much more serious: monkeypox. Lise Sievers called her mother during a layover in Detroit and told her that one of the children she visited and is trying to adopt in Uganda had some pus-filled red bumps and also mentioned she had some small bumps of her own, a rash that she suspected was the handiwork of bedbugs. Those two very different bumps — one with pus, one without — got jumbled up in Siever's mother's mind, and she called a hospital near her Indiana home to ask about treatment for her daughter. 'She told them her daughter is on a flight back from Uganda and has some red bumps which are pussing and what should she do to treat them,' says Roger Sievers. 'She was looking for some general advice.' Health officials feared they were looking for monkeypox, a rare and sometimes fatal disease mostly in found in central and western Africa. After the passengers waited on the plane for a couple of hours, officials brought good news. 'They came back down and told my mom it was bed bug bites and they started releasing people.'"