Slashdot Mirror

Fluffeh writes "A researcher has found and published a way to tune into an RSA SecurID Token. Once a few easy steps are followed, anyone can generate the exact numbers shown on the token. The method relies on finding the seed that is used to generate the numbers in a way that seems random. Once it is known, it can be used to generate the exact numbers displayed on the targeted Token. The technique, described on Thursday by a senior security analyst at a firm called SensePost, has important implications for the safekeeping of the tokens. An estimated 40 million people use these to access confidential data belonging to government agencies, military contractors, and corporations. Scrutiny of the widely used two-factor authentication system has grown since last year, when RSA revealed that intruders on its networks stole sensitive SecurID information that could be used to reduce its security. Defense contractor Lockheed Martin later confirmed that a separate attack on its systems was aided by the theft of the RSA data."

zacharye writes with news of the end of the regulatory saga that was Google acquiring Motorola Mobility. From the article: "In line with earlier reports, Google on Tuesday finalized its acquisition of Motorola Mobility. The $12.5 billion merger was approved by regulators in China on Monday after having been given the green light by the United States Department of Justice this past February. Chinese regulators did stipulate terms for its approval, however, namely that Google must continue to make Android open-source and freely available. Former Motorola Mobility CEO Sanjay Jha has stepped down and Google's Dennis Woodside will replace him as chief executive..."

zacharye writes with news of the end of the regulatory saga that was Google acquiring Motorola Mobility. From the article: "In line with earlier reports, Google on Tuesday finalized its acquisition of Motorola Mobility. The $12.5 billion merger was approved by regulators in China on Monday after having been given the green light by the United States Department of Justice this past February. Chinese regulators did stipulate terms for its approval, however, namely that Google must continue to make Android open-source and freely available. Former Motorola Mobility CEO Sanjay Jha has stepped down and Google's Dennis Woodside will replace him as chief executive..."

zacharye writes with an excerpt from BGR: "The new 'six strikes' anti-piracy policy soon to be implemented by a number of major Internet service providers in the United States will reportedly stumble out of the gate. The policy, which is set to be adopted by Comcast, Cablevision, Verizon, Time Warner Cable, and other ISPs, will see action taken against users caught downloading pirated files in six steps, ultimately resulting in bandwidth throttling or even service suspensions. The system responsible for managing the new policy may not be ready on schedule, however, and the targeted launch date of July 12th may slip back as a result..."

Fluffeh writes "The EU has accused Google of abusing its dominant position in advertising to benefit its own advertising services at the expense of competitors. In a twist however, rather than initiating formal proceedings, the EU has given Google a chance to settle the whole matter without much fuss. They outlined four changes that Google can make that will put it firmly back in the good graces of the EU. Google has been given 'a matter of weeks' to propose remedies to the four issues — which all tie in with how search results are displayed, their format and their portability to other platforms. This matter has come before the EU based on complaints by a few small companies and Microsoft." The four issues: Displaying results to their own services specially, use of user reviews from other sites in search results, Advertising "...agreements result in de facto exclusivity requiring them to obtain all or most of their requirements of search advertisements from Google," and concerns that Google is imposing "...contractual restrictions on software developers which prevent them from offering tools that allow the seamless transfer of search advertising campaigns across AdWords and other platforms..."

An anonymous reader writes "Emacsy is 'a Guile library that provides Emacs-like facilities — keymaps, minibuffer, tab completion, recordable macros, and major/minor modes — for applications natively.' However, to my eyes, it looks more like an attempt to revive the development style done on Symbolics Lisp Machines that survives to some extent in Emacs. Might be a boon to Emacs users, but where's a comparable VIM alternative?" The skeptic in me asks what benefit this would have over just using libguile directly, and how it fits in with efforts to port Emacs itself to Guile and things like Englightenment's pluggable event loop. The example code seems to imply Emacs-like APIs will be used (despite not intending to replace parts of Emacs), even when better alternatives exist. Some of the proposed components seem orthogonal to existing interface toolkits; others seem to compete with components provided by various Free desktop environments.

After years of accusations of creating a 'chilled work environment,' Nuclear Regulatory Commission Chairman Gregory Jaczko resigned this morning (PDF). His largest achievement was perhaps killing the Yucca Mountain waste repository, and he oversaw the certification of the AP1000 reactor. It is unknown whether a new chairman will be appointed from within the NRC. Quoting the Washington Post: "The reason for his resignation is unclear. He is stepping down before the release of a second inspector general report rumored to be into allegations of Mr. Jaczko's misconduct. NRC spokesman Eliot Brenner told The Washington Times that the report had no impact on the timing of Mr. Jaczko's resignation announcement. Mr. Jaczko's statement was vague, saying that it 'is the appropriate time to continue my efforts to ensure public safety in a different forum. This is the right time to pass along the public safety torch to a new chairman...' While his statement did not specifically touch on the embarrassing revelations of his tyrannical approach to the job or its impact on NRC staff, he did sound a defiant note by claiming the NRC was 'one of the best places to work in the federal government throughout my tenure.'" Today also marks the start of the annual nuclear industry conference.

After years of accusations of creating a 'chilled work environment,' Nuclear Regulatory Commission Chairman Gregory Jaczko resigned this morning (PDF). His largest achievement was perhaps killing the Yucca Mountain waste repository, and he oversaw the certification of the AP1000 reactor. It is unknown whether a new chairman will be appointed from within the NRC. Quoting the Washington Post: "The reason for his resignation is unclear. He is stepping down before the release of a second inspector general report rumored to be into allegations of Mr. Jaczko's misconduct. NRC spokesman Eliot Brenner told The Washington Times that the report had no impact on the timing of Mr. Jaczko's resignation announcement. Mr. Jaczko's statement was vague, saying that it 'is the appropriate time to continue my efforts to ensure public safety in a different forum. This is the right time to pass along the public safety torch to a new chairman...' While his statement did not specifically touch on the embarrassing revelations of his tyrannical approach to the job or its impact on NRC staff, he did sound a defiant note by claiming the NRC was 'one of the best places to work in the federal government throughout my tenure.'" Today also marks the start of the annual nuclear industry conference.

parallel_prankster writes "New York Times reports that a judge in New Jersey has sentenced Dharun Ravi to 30 days in jail Monday for using a webcam to spy on his Rutgers University roommate having sex with a man, in a case that galvanized concern about suicide among gay teenagers but also prompted debate about the use of laws against hate crimes. The case drew wide attention because his roommate, Tyler Clementi, jumped to his death from the George Washington Bridge in September 2010, a few days after learning of the spying. A jury convicted Mr. Ravi in March of all 15 counts against him, which included invasion of privacy and bias intimidation. The relatively light sentence — he faced up to 10 years in prison — surprised many who were watching the hearing, as it came after the judge spent several minutes criticizing Mr. Ravi's behavior."

quantr writes "The Supreme Court has declined to hear Joel Tenenbaum's appeal. A jury in 2009 ordered Tenenbaum, of Providence, R.I., to pay $675,000 for illegally downloading and sharing 30 songs. A federal judge called the penalty constitutionally excessive, but the 1st U.S. Circuit Court of Appeals reinstated it at the request of the Recording Industry Association of America. Tenenbaum's attorney, Harvard law professor Charles Nesson, said he's disappointed the high court won't hear the case. But he said the 1st Circuit instructed a judge to consider reducing the award without deciding any constitutional challenge. Nesson said 'Tenenbaum is just entering the job market and can't pay the penalty.'"

First time accepted submitter gtirloni writes "Just days after wrapping up the biggest initial public offering in Silicon Valley history, shares of Facebook slumped 6% and tumbled below their issue price on Monday, a troubling signal for the newly-public social network. Facebook broke below its $38-a-share issue IPO price in the wake of a highly-anticipated offering that raised more than $16 billion, the second-largest domestic IPO after Visa's 2008 debut. Shares of Facebook were recently off 6.44% to $35.72."

TheGift73 writes "Last week, longtime chief Howard Schmidt stepped down. He's been replaced by Michael Daniel, who's been in the Office of Management and Budget's national security division for 17 years. What does that mean for the future of the cybersecurity issue? Probably that we can expect his knowledge of the intelligence community to play a part in not just tracking down hackers, but determining the lines that need to be crossed with future SOPA-like bills. So while this sounds like a relatively nondescript appointment, Daniel will almost definitely be a major player the next time someone comes for your internet."

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."

jrepin writes with news of today's release (here's Linus's announcement) of Linux 3.4: "This release includes several Btrfs updates: metadata blocks bigger than 4KB, much better metadata performance, better error handling and better recovery tools. There are other features: a new X32 ABI which allows to run in 64 bit mode with 32 bit pointers; several updates to the GPU drivers: early modesetting of Nvidia Geforce 600 'Kepler', support of AMD RadeonHD 7xxx and AMD Trinity APU series, and support of Intel Medfield graphics; support of x86 cpu driver autoprobing, a device-mapper target that stores cryptographic hashes of blocks to check for intrusions, another target to use external read-only devices as origin source of a thin provisioned LVM volume, several perf improvements such as GTK2 report GUI and a new 'Yama' security module."

Fluffeh writes "On Friday, a company called SceneTap flipped the on switch enabling cameras installed in around 20 bars to monitor how full the venues are, the mix of men and women, their ages — and to make all this information available live via an iPhone or Android app. Privacy advocates are unimpressed, though, as the only hint that people are being monitored is via tiny stickers on the windows. Beyond academics and policy experts, some San Francisco bar owners that originally partnered with SceneTap have said that they're pulling out and will be taking down the company's cameras. An increasing number of bars still listed on the SceneTap's site are now saying that they're not working with the Chicago startup, including Mr. Smith's, Southpaw, John Colins, and Bar None."

Diggester writes with this news from the Times of India: "Pakistani authorities on Friday further widened the crackdown on websites with blasphemous contents by restricting access to popular social networking website Twitter. Pakistani users were unable to log into Twitter after internet service providers blocked access to the site." The block was prompted by Twitter's refusal to take down messages promoting a cartoon contest to which the Pakistani government objects for its depictions of Muhammad. This end-run falls right in line with the pessimistic reaction from Reporters Without Borders to the Pakistani court decision calling Internet censorship unconstitutional.

theodp writes "A day after taking Facebook public, CEO Mark Zuckerberg changed his Facebook status to 'married' after wedding longtime girlfriend and recent med school grad Priscilla Chan on Saturday. No word if Zuckerberg heeded Donald Trump's prenup advice."

arisvega writes "At a first level (the lowest court level in the Greek judiciary system) an order has been issued (article in Greek, Google translation is fair enough) for a 'plan on behalf of Internet Service Providers regarding he implementation of technological measures to deny access to internet users for webpages through which illegal copies of copyrighted work are being distributed.' The order seems to be general and descriptive, and is a manifestation of the implementation process for an even more general and vague larger-scale EU directive, which is the common source that caused the rulings recently posted on slashdot regarding the UK, the Netherlands and Finland. This appears to be one of the reasons that prompted Anonymous to launch defacing attacks on Greek government websites some three months back."

arisvega writes "At a first level (the lowest court level in the Greek judiciary system) an order has been issued (article in Greek, Google translation is fair enough) for a 'plan on behalf of Internet Service Providers regarding he implementation of technological measures to deny access to internet users for webpages through which illegal copies of copyrighted work are being distributed.' The order seems to be general and descriptive, and is a manifestation of the implementation process for an even more general and vague larger-scale EU directive, which is the common source that caused the rulings recently posted on slashdot regarding the UK, the Netherlands and Finland. This appears to be one of the reasons that prompted Anonymous to launch defacing attacks on Greek government websites some three months back."

arisvega writes "At a first level (the lowest court level in the Greek judiciary system) an order has been issued (article in Greek, Google translation is fair enough) for a 'plan on behalf of Internet Service Providers regarding he implementation of technological measures to deny access to internet users for webpages through which illegal copies of copyrighted work are being distributed.' The order seems to be general and descriptive, and is a manifestation of the implementation process for an even more general and vague larger-scale EU directive, which is the common source that caused the rulings recently posted on slashdot regarding the UK, the Netherlands and Finland. This appears to be one of the reasons that prompted Anonymous to launch defacing attacks on Greek government websites some three months back."

This morning's nixed launch of SpaceX's Dragon capsule to the ISS with the company's Falcon booster was an exciting thing to be on hand for, despite the (literally) last-second halt. Shuttle launches used to cause miles of traffic backups extending well outside the gates of NASA's Cape Canaveral launch facilities; for all the buzz around the first private launch to the ISS, today's launch attempt was much more sparsely attended. In a small set of bleachers set up near the massive countdown clock, there were a few dozen enthusiasts and reporters aiming their cameras and binoculars at the launch site on the horizon. They counted down in time with the clock, and — just like NASA's own announcer — reached all the way to "liftoff." There was a brief flash as the engines ignited, but it died as fast as it appeared. It took only a few seconds for the crowd to realize that it was all over for today's shot. While the company's representatives remain upbeat, pointing out that the software worked as intended to stop a launch before anomalies turn into catastrophes, most of those on hand to see what they'd hoped to be a historic launch were a bit glum as they walked back to the parking lot and the press area — especially the ones who can't stay until the next try. I'm sticking around the area until the next scheduled launch window; hopefully next time the fates (and engines) will align.

schliz writes "The Australian software patent system could be used by open source developers to ensure their inventions remain available to the community, a conference organized by intellectual property authority IP Australia heard this week According to Australian inventor Ric Richardson, whose company came out on top of a multi-million dollar settlement with Microsoft in March, a world without software patents would be 'open slather for anybody who can just go faster than the next person.' Software developer Ben Sturmfels, whose 2010 anti-software-patent petition won the support of open source community members such as Jonathan Oxer, Andrew Tridgell, and software freedom activist Richard Stallman, disagreed."

schliz writes "The Australian software patent system could be used by open source developers to ensure their inventions remain available to the community, a conference organized by intellectual property authority IP Australia heard this week According to Australian inventor Ric Richardson, whose company came out on top of a multi-million dollar settlement with Microsoft in March, a world without software patents would be 'open slather for anybody who can just go faster than the next person.' Software developer Ben Sturmfels, whose 2010 anti-software-patent petition won the support of open source community members such as Jonathan Oxer, Andrew Tridgell, and software freedom activist Richard Stallman, disagreed."

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.

First time accepted submitter ixarux writes "India is at a crucial crossroad at the moment. Internet censorship laws are getting stricter as it begins to ban file-sharing and video-sharing websites. It started with Indian courts allowing censorship of Google, Facebook, etc. It has now gone one step ahead and decided to ask ISPs to block file-sharing sites. It is the movie industry which is again at the forefront of this. Anonymous retaliated, and targeted the websites of various Indian government websites in protest. What India lacks at this crucial juncture are debates in the public domain about this and citizens actually organizing protests as seen in the West."

jbrodkin writes "The U.S. International Trade Commission today ordered an import ban on Motorola Mobility Android products, agreeing with Microsoft that the devices infringe a Microsoft patent on 'generating meeting requests' from a mobile device. The import ban stems from a December ruling that the Motorola Atrix, Droid, and Xoom (among 18 total devices) infringed the patent, which Microsoft says is related to Exchange ActiveSync technology. Today, the ITC said in a 'final determination of violation' (PDF) that 'the appropriate form of relief in this investigation is a limited exclusion order prohibiting the unlicensed entry for consumption of mobile devices, associated software and components thereof covered by ... United States Patent No. 6,370,566 and that are manufactured abroad by or on behalf of, or imported by or on behalf of, Motorola.' Motorola (which is being acquired by Google) was the last major Android device maker not to pay off Microsoft in a patent licensing deal. Microsoft has already responded to the decision, saying it hopes Motorola will now reconsider."

jbrodkin writes "The U.S. International Trade Commission today ordered an import ban on Motorola Mobility Android products, agreeing with Microsoft that the devices infringe a Microsoft patent on 'generating meeting requests' from a mobile device. The import ban stems from a December ruling that the Motorola Atrix, Droid, and Xoom (among 18 total devices) infringed the patent, which Microsoft says is related to Exchange ActiveSync technology. Today, the ITC said in a 'final determination of violation' (PDF) that 'the appropriate form of relief in this investigation is a limited exclusion order prohibiting the unlicensed entry for consumption of mobile devices, associated software and components thereof covered by ... United States Patent No. 6,370,566 and that are manufactured abroad by or on behalf of, or imported by or on behalf of, Motorola.' Motorola (which is being acquired by Google) was the last major Android device maker not to pay off Microsoft in a patent licensing deal. Microsoft has already responded to the decision, saying it hopes Motorola will now reconsider."

An anonymous reader writes "The folks at Facebook may be focusing on their IPO today, but a complaint filed in federal court has given them something else to think about. The filing consolidates 21 separate but similar cases and alleges Facebook invaded users privacy by tracking their browsing behavior even after they had logged out of the site. The claim seeks $15 billion in damages. 'If the claimants are successful in their case against Facebook, they could prevent Menlo Park from collecting the huge amount of data it collects about its users to serve ads back to them. Like the previous lawsuits, Facebook is once again being accused of violating the Federal Wiretap Act, which provides statutory damages per user of $100 per day per violation, up to a maximum per user of $10,000. The complaint also asserts claims under the Computer Fraud and Abuse Act, the Stored Communications Act, various California Statutes and California common law.'"

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.

medv4380 writes "38 Studios, run by Curt Schilling, is having a hard time paying its bills and employees. The gaming community hasn't been happy with the company since the issue with an Online Pass for Single Player Content, which we discussed previously. Now, 38 Studios has bounced a check intended as a payment on its $75 million loan from the state of Rhode Island. If the company defaults, Rhode Island taxpayers will have to cover the loan and interest, which could total nearly $100 million."

Sparrowvsrevolution writes "On Thursday, the House Judiciary Committee held a hearing to discuss a proposed bill to limit location tracking of electronic devices without a warrant — what it's calling the Geolocational Privacy and Surveillance Act, or the GPS Act. Ahead of that hearing, University of Pennsylvania computer science professor Matt Blaze submitted written testimony (PDF) telling Congress that phone carriers, as well as the law enforcement agencies with which they share data, can now use phones' proximity to cell towers and other sources of cellular data to track their location as precisely or even more precisely than they can with global positioning satellites. Thanks to the growing density of cell towers and the proliferation of devices like picocells and femtocells that transmit cell signals indoors, even GPS-less phones can be tracked with a high degree of precision and can offer data that GPS can't, like the location of someone inside a building or what floor they're on. With the GPS Act, Congress is considering expanding the ban on warrantless tracking of cars with GPS devices that the Supreme Court decided on in January. Blaze's testimony suggests they need to include non-GPS tracking of cell phones in that ban, a measure law enforcement agencies are strongly resisting."

cedarhillbilly writes "In his new book The Geek Manifesto, Mark Henderson 'pleads for citizens who value science to force it onto the mainstream political agenda and other main walks of life.' There are some important questions that need answers: 'Do you have to give up your tech practice to undertake a public role?' Also, 'Is political life (compromise, working by consensus, irrationality) antithetical to the "geek" values?'" The Guardian's coverage sums up the idea nicely: "What I desperately want is a move toward an evidence-based culture in politics. Politicians are free to say: 'I think people on drugs should be punished because drugs are immoral.' That's a moral call, albeit a rather stupid one in my opinion. What they shouldn't do is say: 'I want to reduce drug use, and sending all users to prison is the most cost-effective way to achieve that.' That's not a moral call, it's a factual statement; as such it should be evidence-based, or else the person making it should shut the hell up."

New submitter kimtysirt sends this excerpt from a Bloomberg report about U.S. tariffs for Chinese solar panels: "The U.S. yesterday imposed tariffs of as much as 250 percent on Chinese-made solar cells to aid domestic manufacturers beset by foreign competition, though critics said the decision may end up raising prices and hurting the U.S. renewable energy industry. The U.S. Commerce Department ruled that Chinese manufacturers sold cells in the U.S. at prices below the cost of production and announced preliminary antidumping duties ranging from 31 percent to 250 percent, depending on the manufacturer. China criticized the action, saying the U.S. is hurting itself and cooperation between the world’s two largest economies. The decision is meant to provide a boost to the U.S. solar manufacturing industry, where four companies filed for bankruptcy in the past year."

jfruh writes "Mandriva SA, one of the oldest pure Linux companies still out there, was on the verge of shutting down earlier this year, but escaped by the skin of its teeth. Now, however, the company is punting control of its flagship Linux distribution to its developer community, leaving Mandriva SA's future prospects up in the air. From the blog post: 'This means that the future of the distribution will not be arbitrary[sic] decided by the Mandriva company anymore, but we intend to let the distribution evolve in and under the caring responsibility of the community.'"

jfruh writes "Mandriva SA, one of the oldest pure Linux companies still out there, was on the verge of shutting down earlier this year, but escaped by the skin of its teeth. Now, however, the company is punting control of its flagship Linux distribution to its developer community, leaving Mandriva SA's future prospects up in the air. From the blog post: 'This means that the future of the distribution will not be arbitrary[sic] decided by the Mandriva company anymore, but we intend to let the distribution evolve in and under the caring responsibility of the community.'"

Fluffeh writes "In recent times, it seems many Police Departments believe that recording them doing their work is an act of war with police officers, destroying the tapes, phones or cameras while arresting the folks doing it. But in a surprising twist, the U.S. Justice Department has sent letter (PDF) to attorneys for the Baltimore Police Department — who have been quite heavy handed in enforcing their 'Don't record me bro!' mantra. The letter contains an awful lot of lawyer babble and lists many court cases and the like, although some sections are surprisingly clear: 'Policies should prohibit officers from destroying recording devices or cameras and deleting recordings or photographs under any circumstances. In addition to violating the First Amendment, police officers violate the core requirements of the Fourteenth Amendment procedural due process clause when they irrevocably deprived individuals of their recordings without first providing notice and an opportunity to object.' There is a lot more and it certainly seems like a firm foothold in the right direction."

MrSeb writes "Using BrainGate, the world's most advanced brain-computer interface, a woman with quadriplegia has used a mind-controlled robot arm to serve herself coffee — an act she hasn't been able to perform for 15 years. BrainGate, which is being developed by a team of American neuroscientists from Brown and Stanford universities, and is currently undergoing clinical trial, requires a computer chip to be implanted in the motor cortex of the patient, which it then transmits to a computer for processing. Like all brain-computer interfaces, the user must train the software — but once this is done, you simply think of a movement, and the software moves the robot accordingly. Moving forward, the researchers would like to miniaturize the system and make it wireless — at the moment, BrainGate users have a box attached to their head, and they're tethered to a computer — which is OK for robot arm use at home, but obviously doesn't grant much mobility. The work was partly funded by DARPA, with the hope of creating more advanced prosthetics for wounded war veterans." This comes on the heels of a 71-year-old man regaining motor function in his fingers after doctors rewired his nerves to bypass the damaged ones.

eldavojohn writes "Vermont is the first state to ban fracking (hydraulic fracturing), a process that was to revolutionize the United States' position into a major producer of natural gas. New York currently has a moratorium on fracking but it is not yet a statewide ban. Video of the signing indicates the concern over drinking water as the motivation for Vermont's measures (PDF draft of legislation). Slashdot has frequently encountered news debating the safety of such practices."

An anonymous reader writes "After being the victim of a massive Distributed Denial of Service (DDoS) attack by an unknown party, The Pirate Bay has returned. An Anonymous traitor who goes by the name AnonNyre has claimed responsibility for the DDoS attack that kept the site offline for days."

An anonymous reader writes "Sen. Chuck Schumer, D-N.Y., has a status update for Facebook co-founder Eduardo Saverin: Stop attempting to dodge your taxes by renouncing your U.S. citizenship or never come to back to the U.S. again." See this earlier story on Saverin's plan to make the leap out of the U.S. tax system.

Fluffeh writes "A recent study of over 1,000 folks for a paper published in Nature Climate Change has found that the average U.S. citizen is inclined to pay a premium to ensure that by 2035, 80% of U.S. power comes from clean energy. At random, respondents received one of three "technological treatments" or definitions of clean energy that included renewable energy sources alone, renewable sources plus natural gas, and renewable sources plus nuclear power. Delving into the socioeconomics, researchers found that Republicans, Independents, and respondents with no party allegiance were less likely by 25, 13 and 25 percentage points respectively to support a NCES than respondents that identified themselves as Democrats."

mcleland writes "I'm not getting the bandwidth I paid for from my DSL connection. My '3mbps' fluctuates between about 2.7 during the day down to 0.1 or 0.2 in the evening according to speedtest.net. Let's assume DSL is the only viable option for broadband at my house and I can't really move right now (rural area, on north face of the mountain, no cable service, very poor cell coverage). This was discussed 6 years ago, but I'd like to see if there are any current thoughts on whether I'm just stuck or if there is some way to make the ISP hold up its end."

gollum123 writes "As with past technological threats, network executives are closing ranks against a Dish Network device that undermines the broadcast business model. The disruptive technology at hand is an ad-eraser, embedded in new digital video recorders sold by Charles W. Ergen's Dish Network, one of the nation's top distributors of TV programming. Turn it on, and all the ads recorded on most prime-time network shows are automatically skipped, no channel-flipping or fast-forwarding necessary. Some reviewers have already called the feature, called the Auto Hop, a dream come true for consumers. But for broadcasters and advertisers, it is an attack on an entrenched television business model, and it must be strangled, lest it spread elsewhere."

First time accepted submitter Maow writes "Despite a recent story claiming that Canada's Bill C-30, covering internet surveillance, has died a 'lonely' death, the minister responsible claims otherwise. 'Public Safety Minister Vic Toews is denying reports that the Harper government intends to quietly shelve its controversial online surveillance bill, C-30.' Speaking to reporters on Wednesday morning, Toews insisted the legislation was moving ahead. He has previously stated this is the bill that you either support, 'or you stand with the child pornographers.'"

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

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