Selected readings 5/8/10

Interesting reading and news items.

These items are also bookmarked at my Diigo account.

The Search for Genes Leads to Unexpected Places

Dr. Marcotte and his colleagues have discovered hundreds of other genes involved in human disorders by looking at distantly related species. They have found genes associated with deafness in plants, for example, and genes associated with breast cancer in nematode worms. [New York Times, 4/26/10]

Are we there yet?

Years of effort and roughly 10,000 people have made the Large Hadron Collider the most powerful particle accelerator in the world. This collaborative feat of technology promises to change the way we understand the universe. Now the world is watching, waiting to see what so much effort will yield. Even at an initial collision energy of 7 trillion electronvolts-half its full capacity-the LHC is in a position to make important discoveries. [Symmetry, 4/1/10]

Moving beyond silicon to break the MegaHertz barrier

We're rapidly closing in on a decade since the first desktop processors cleared the 3GHz mark, but in a stunning break from earlier progress, the clock speed of the top processors has stayed roughly in the same neighborhood since. Meanwhile, the feature shrinks that have at least added additional processing cores to the hardware are edging up to the limits of photolithography technology. [Nobel Intent, 3/26/10]

How huge particle detectors actually detect tiny particles

The detectors in colliders like the Large Hadron Collider and Relativistic Heavy Ion Collider work by looking at some of the items that come rocketing out of the collisions, producing the sort of traces shown here. Given that data, it's possible for physicists to work their way backwards in order to figure out what went on in the collision itself. [Nobel Intent, 3/29/10]

The software brains behind the particle colliders

In the instant that its detectors register the events associated with a collision, the challenges move from the hardware realm into software, as the LHC will literally produce more data than we can possibly handle. We have to figure out what to hang on to in real time, and send it around the globe via dedicated connections that aggregate multiple 10Gbp/s links; those on the receiving end need to safely store it and pursue the sorts of analyses that will hopefully reveal some new physics. [Nobel Intent, 3/30/10]

Lasing Beyond Light

Now, at age 50, the laser has extended its dominion far beyond the realm of light. Physicists have succeeded in building lasers that emit different kinds of waves. Laserlike “hard” X-ray pulses, for example, can freeze atoms in their tracks, providing a ringside view of chemical reactions. And phonon lasers vault the technology out of the electro­magnetic spectrum altogether, creating coherent beams of sound. [Science News, 4/23/10]

Master of the Cell

RNA interference, with its powerful promise of therapy for many diseases, may also act as a master regulator of most-if not all-cellular processes. [The Scientist, 3/29/10]

Obesity: the role of the immune system

Obesity is one symptom of several, which together constitute what is now termed metabolic syndrome. Morbid obesity is also associated with a host of other symptoms including high blood sugar, high blood lipids, insulin resistance and liver disorders. The root causes of which are traced back to excessive food consumption, reduced physical activity and in some cases, genetic predisposition. [Byte Size Biology, 4/25/10]

Evolving a code: A molecular fossil's tale

Every living cell on earth carries a molecular fossil: the ribosome. In a recent paper published in PNAS, researchers from California open the drawer and dust off this ancient molecular machine. The structure of the ribosome seems to provide hints about the origin of that universal feature of life: the genetic code. [Thoughtomics, 4/18/10]

Can Life on Titan Thrive Without Water?

The standard definition of a "habitable world" is a world with liquid water at its surface; the "habitable zone" around a star is defined as that Goldilocks region — not too hot, not too cold — where a watery planet or moon can exist. And then there's Titan. Saturn's giant moon Titan lies about as far from the standard definition of habitable as one can get. The temperature at its surface hovers around 94 degrees Kelvin (minus 179 C, or minus 290 F). At that temperature, water is a rock as hard as granite. And yet many scientists now believe life may have found a way to take hold on Titan. [Space.com, 3/23/10]

Neutrinos: Clues to the Most Energetic Cosmic Rays

“The most energetic cosmic rays are the rarest, and they pose the biggest mystery,” says Spencer Klein of Berkeley Lab’s Nuclear Science Division. He compares the energy of an ultra-high-energy (UHE) cosmic ray to a well-hit tennis ball or a boxer’s punch – all packed into a single atomic nucleus. ... Sources capable of producing such high-energy nuclei have not been clearly identified. One clue to the origin of the highest-energy cosmic rays is the neutrinos they produce when they interact with the very cosmic microwave photons that slow them down. [Berkeley Lab News Center, 4/19/10]

Bizarre models for human diseases

The search for models of human diseases might just have become easier, thanks to a data-mining technique that screens genetic databases to find subtle links to organisms as distant from humans as plants. The new tool integrates information from existing databases that associate gene mutations with observable traits in a range of species, including humans, mice, yeast, worms and plants. And the method identifies genes in the non-human species that are more likely than by chance to contribute to human disease. [Nature News, 3/22/10]

Addicted to Fat: Overeating May Alter the Brain as Much as Hard Drugs

Like many people, rats are happy to gorge themselves on tasty, high-fat treats. Bacon, sausage, chocolate and even cheesecake quickly became favorites of laboratory rats that recently were given access to these human indulgences-so much so that the animals came to depend on high quantities to feel good, like drug users who need to up their intake to get high. A new study, published online March 28 in Nature Neuroscience, describes these rats' indulgent tribulations, adding to research literature on the how excess food intake can trigger changes in the brain, alterations that seem to create a neurochemical dependency in the eater-or user. [Scientific American, 3/28/10]

Fatty foods can be addictive like crack—at least for rats

Obesity may be a result of a reduced sensitivity to the "rewards" of calorically dense food, fostered by eating too much of the stuff too often, according study published in Nature Neuroscience this week. A group of researchers gave some rats different levels of access to tasty and highly caloric "cafeteria" foods, while training them to respond to aversive stimuli. Rats who had been given the most access to the good stuff ignored any indications of negative consequences and kept right on eating. [Nobel Intent, 3/30/10]

Fast machines, genes and the future of medicine

Some experts say the world is on the cusp of a "golden age" of genomics, when a look at the DNA code will reveal your risk of cancer, diabetes or heart disease, and predict which drugs will work for you. Yet the $3 billion international Human Genome Project, whose first phase was completed a decade ago, has not led to a single blockbuster diagnosis or product. [Reuters, 3/30/10]

Bursting the genomics bubble

For scientists, the Human Genome Project (HGP) might lay the foundation of tomorrow's medicine, with drugs tailored to your genetics. But a venture capitalist would want medical innovations here and now, not decades hence. Nearly ten years after the project's formal completion, there's not much sign of them. [Nature News, 3/31/10]

Human genome at ten: Life is complicated

As sequencing and other new technologies spew forth data, the complexity of biology has seemed to grow by orders of magnitude. Delving into it has been like zooming into a Mandelbrot set — a space that is determined by a simple equation, but that reveals ever more intricate patterns as one peers closer at its boundary. [Nature News, 3/31/10]

The trouble with genes

Scientists were shocked when they found out how few 'old-fashioned' genes we actually have - about the same number as the humble nematode worm (Caenorhabditis elegans). In fact, almost all multicellular creatures with the complexity of a worm or greater have about 20,000 genes. But for Mattick, the death knell of the traditional concept of the gene was triggered by another revolution altogether - that of the digital information age. [Cosmos, 4/12/10]

Genome of a killer

What we call cancer is actually a class of 200 diseases in different tissues, which are all caused by cells that have started to multiply out of control. Most treatments are drastic and invasive, such as chemotherapy and surgery. "Cancer is extremely complex, but we are beginning to understand how this complexity works, in terms of which genes are important," says oncologist Victor Velculescu. [Cosmos, 4/27/10]

10 Years on, ‘The Genome Revolution Is Only Just Beginning’

Almost 10 years after the celebrated completion of the human genome’s first draft, the expected revolution in medicine and research has only partly come to pass. The human genome’s sequencing has profoundly influenced basic research and the refinement of genome-reading tools. But those advances have had only limited medical impacts. [Wired, 3/31/10]

Einstein’s theory fights off challengers

Two new and independent studies have put Einstein’s General Theory of Relativity to the test like never before. These results, made using NASA’s Chandra X-ray Observatory, show Einstein’s theory is still the best game in town. Each team of scientists took advantage of extensive Chandra observations of galaxy clusters, the largest objects in the universe bound together by gravity. One result undercuts a rival gravity model to General Relativity, while the other shows that Einstein’s theory works over a vast range of times and distances across the cosmos. [Symmetry Breaking, 4/15/10]

What are 'mini' black holes?

‘The simplest black holes are objects with a singularity in the centre and that are surrounded by an ‘event horizon’,’ explains Cigdem Issever of Oxford University’s Department of Physics. ‘Once something comes closer to the black hole than the radius of the event horizon, it is not able to leave: even light can’t escape and so the name ‘black hole’ was given to these objects by John Archibald Wheeler back in 1967.’ [Physorg.com, 3/29/10]

A Grand Unified Theory of Artificial Intelligence

In the 1950s and '60s, artificial-intelligence researchers saw themselves as trying to uncover the rules of thought. But those rules turned out to be way more complicated than anyone had imagined. Since then, artificial-intelligence (AI) research has come to rely, instead, on probabilities -- statistical patterns that computers can learn from large sets of training data. [Physorg.com, 3/30/10]

Charting Creativity: Signposts of a Hazy Territory

They hope to figure out precisely which biochemicals, electrical impulses and regions were used when, say, Picasso painted "Guernica," or Louise Nevelson assembled her wooden sculptures. Using M.R.I. technology, researchers are monitoring what goes on inside a person's brain while he or she engages in a creative task. Yet the images of signals flashing across frontal lobes have pushed scientists to re-examine the very way creativity is measured in a laboratory. [New York Times, 5/7/10]

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