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Submission + - Terrible advice from a great scientist

Submitted by Shipud
Shipud writes: E.O. Wilson is the renowned father of sociobiology, a professor (emeritus) at Harvard, two time pulitzer prize winner, and a popularizer of science. In a recent article in the Wall Street Journal, Wilson provides controversial advice to aspiring young scientists. Wilson claims that math literacy is not essential, and that scientific models in biology, intuitively generated, can later be formalized by a specialized statistician. One blogger calls out Wilson on his article, arguing that knowing mathematics is essential to generating models, and that lacking what Darwin called the "extra sense" is essentially limiting to any scientist.
Biotech

Submission + - A new genetic code found (bytesizebio.net)

Submitted by Shipud
Shipud writes: A group from Oak Ridge National Laboratory, Yale University and the Joint Genome Institute have isolated single cells of otherwise elusive and unculturable SR1 bacteria and sequenced their genomes. They found that SR1 deviate from the genetic code in a way previously unknown: what codes for "stop making proteins" in most organisms, is used differently in SR1, to actually continue making them. This study shows the power of a new technology, single-cell DNA sequencing, to reveal genetic information. SR1 bacteria are found in our mouths, and are suspected to cause periodontitis.
Open Source

Submission + - What does it actually cost to publish a scientific paper? (nature.com)

Submitted by ananyo
ananyo writes: Nature has published an investigation into the real costs of publishing research after delving into the secretive, murky world of science publishing. Few publishers (open access or otherwise-including Nature Publishing Group) would reveal their profit margins, but they've pieced together a picture of how much it really costs to publish a paper by talking to analysts and insiders.
Quoting from the piece: "The costs of research publishing can be much lower than people think,” agrees Peter Binfield, co-founder of one of the newest open-access journals, PeerJ, and formerly a publisher at PLoS. But publishers of subscription journals insist that such views are misguided — born of a failure to appreciate the value they add to the papers they publish, and to the research community as a whole. They say that their commercial operations are in fact quite efficient, so that if a switch to open-access publishing led scientists to drive down fees by choosing cheaper journals, it would undermine important values such as editorial quality." There's also a comment piece by three open access advocates setting out what they think needs to happen next to push forward the movement as well as a piece arguing that "Objections to the Creative Commons attribution license are straw men raised by parties who want open access to be as closed as possible."
Privacy

Submission + - Raytheon's Riot program mines social network data for intelligence agencies (guardian.co.uk)

Submitted by Shipud
Shipud writes: Raytheon has secretly developed software capable of tracking people's movements and predicting future behaviour by mining data from social networking websites according to this story from The Guardian.

An "extreme-scale analytics" system created by Raytheon, the world's fifth largest defence contractor, can gather vast amounts of information about people from websites including Facebook, Twitter and Foursquare.

Raytheon says it has not sold the software – named Riot, or Rapid Information Overlay Technology – to any clients. But the company has acknowledged the technology was shared with US government and industry as part of a joint research and development effort, in 2010, to help build a national security system capable of analysing "trillions of entities" from cyberspace.

The power of Riot to harness popular websites for surveillance offers a rare insight into controversial techniques that have attracted interest from intelligence and national security agencies, at the same time prompting civil liberties and online privacy concerns.
Biotech

Submission + - Did viruses evolve from an extinct domain of life? (bytesizebio.net)

Submitted by Shipud
Shipud writes: A study was recently published by a group from the University of Illinois, Urbana-Champaign . The authors analyzed the structures of proteins found in the genomes of organisms from the three domains of life. Those domains are eukarya which includes all plant, animals, fungi and some microbes; bacteria, and archaea which is a group of single-celled microorganisms distinct from eukarya and bacteria. The researchers also included a group of viruses known as NCLDVs (Nucelocyptoplasmic Large DNA viruses), Their conclusion is these viruses may have evolved from a, now extinct, fourth domain of life. Viruses are not considered to be alive, or even to have a place on the universal tree of life, by most researchers. So their claim has far-reaching consequences in our understanding of the origins of life.
Biotech

Submission + - International challenge to computationally interpret protein function (muohio.edu)

Submitted by Shipud
Shipud writes: We live in the post-genomic era, when DNA sequence data is growing exponentially. However, for most of the genes that we identify, we have no idea of their biological functions. They are like words in a foreign language, waiting to be deciphered. The Critical Assessment of Function Annotation, or CAFA, is a new community-wide experiment to assess the performance of the multitude of computational methods developed by research groups worldwide to help channel the flood of data from genome research to deduce the function of proteins.

Thirty research groups participated in the first CAFA, presenting a total of 54 algorithms. The results are published in an article in Nature Methods. The researchers participated in blind-test experiments in which they predicted the function of protein sequences for which the functions are already known but haven't yet been made publicly available. Independent assessors then judged their performance. The challenge organizers explain that: 'The accurate annotation of protein function is key to understanding life at the molecular level and has great biochemical and pharmaceutical implications, explain the study authors; however, with its inherent difficulty and expense, experimental characterization of function cannot scale up to accommodate the vast amount of sequence data already available.The computational annotation of protein function has therefore emerged as a problem at the forefront of computational and molecular biology.'
Media

Submission + - A New Concept in Publishing Science (bytesizebio.net)

Submitted by Shipud
Shipud writes: There are three concerns in publising scientific findings: the quality of the venue, the cost, and the distribution. Some journals are open access, but the publication cost ($2000-$4000) can be prohibitive. Those that are behind a paywall generaly have lower costs to get a paper in, but require high subscription fees from university libraries, and are inaccessible to the public. A new journal, PeerJ is trying a new model to be both open-access and cheap. Everything is published under a Creative Commons license, and the authors pay a one-time membership fee entitling them to a certain number of publications per year. O'Reilly media are backing this venture, and Tim O'Reilly is on the board. The quality is assured by a distinguished line of editors, and 10 Nobel laureates on the board of advisors.
Biotech

Submission + - ROSALIND: an addictive bioinformatics learning site (bytesizebio.net)

Submitted by Shipud
Shipud writes: Bioinformatics science which deals with the study of methods for storing, retrieving and analyzing molecular biology data. Byte Size Biology writes about ROSALIND, a cool concept in learning bioinformatics, similar to Project Euler. You are given problems of increasing difficulty to solve. Start with nucleotide counting (trivial) and end with genome assembly (putting it mildly, not so trivial). To solve a problem, you download a sample data set, write your code and debug it. Once you think you are ready, you have a time limit to solve and provide an answer for the actual problem dataset. If you mess up, there is a timed new dataset to download. This thing is coder-addictive. Currently in Beta, but a lot of fun and seems stable.
Programming

Submission + - Can we make accountable research software? (bytesizebio.net) 1

Submitted by Shipud
Shipud writes: This practices of code writing for day-to-day bioinformatic lab research are completely unlike anything software engineers are taught. In fact, they are actually the opposite in many ways, and may horrify you if you come from a classic software-industry development environment. Research coding is not done with the purpose of being robust, or reusable, or long-lived in development and versioning repositories. Upgrades are not provided and the product, such as it is, is definitely not user-friendly for public consumption. It is usually the code’s writer who is the consumer, or in some cases a few others in the lab. In most cases research results are published without the code that was used to generate them. There are no resources in most labs to make that code fir for public consumption. How can this problem be solved?

Submission + - TSA Bodyscanner Fail Video - Now with Surveillance Camera Footage! (wordpress.com)

Submitted by McGruber
McGruber writes: Jonathan Corbett, the subject of the earlier Slashdot Story "The Ineffectiveness of TSA Body Scanners" (http://tech.slashdot.org/story/12/03/07/0329255/the-ineffectiveness-of-tsa-body-scanners), has an update for us.

His video showing him wandering through a nude body scanner with undetected objects is now complete with the feeds from TSA's security cameras at the checkpoint.

Good work Jonathan and thank you TSA for your timely response to his Freedom of Information Law (FOIL) request!
Science

Submission + - Mother's milk trains baby to fight bacteria (bytesizebio.net)

Submitted by Shipud
Shipud writes: It is pretty much common knowledge that mother’s milk is the healthiest food for infants, and that it bestows health benefits upon the baby that formula feeding cannot match. But a recent study of the baby gut metagenome has revealed an unknown benefit: mom's milk enriches a small population of disease causing bacteria in the infant's gut. Just enough to train the infant's immune system, but not enough to cause actual disease. The interesting thing is that the same pathways that enrich the baby's immune system, also help in the development of the gut tissue. An all-around win situation as explained by one of the coauthors.
Books

Submission + - Best Science Fiction/Fantasy for 8 Year Olds 7

Submitted by Jason Levine
Jason Levine writes: My son is 8 years old. I'd love to get him interested in Science Fiction, but most of the books I can think of seem to be targeted to older kids/adults.

Thinking that the length of some novels might be off-putting to him, I read him some of the short stories in Isaac Asimov's "I, Robot". He liked these but I could tell he was having a hard time keeping up. I think the wording of the stories was too advanced and there was too much talking and not enough action. Personally, I love Asimov, but I think much of it just went over his head.

Which science fiction and/or fantasy books would you recommend for an 8 year old? (Either stories he could read himself or that we could read together over the course of a few weeks.)
Music

Submission + - Music evolving by listeners' taste, with a slashdot history (darwintunes.org)

Submitted by Shipud
Shipud writes: A collaboration between a group in Imperial College and Media Interaction group in Japan yielded a really cool website: darwintunes.org. The idea is to apply Darwinian-like selection to music. Starting form a garble, after several generations producing something that is actually melodic and listen-able. The selective force being the appeal of the tune to the listener. From the paper published yesterday in the Proceedings of the National Academy of Sciences: "At any given time, a DarwinTunes population has 100 loops, each of which is 8 s long. Consumers ratethem on a five-point scale (“I can’t stand it” to “I love it”) as they are streamed in random order. When 20 loops have been rated,truncation selection is applied whereby the best 10 loops are paired, recombine, and have two daughters each." Note that in 2009 the creators of darwintunes harnessed the power of slashdot to help "evolve" their site.

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