Science and Reason

Sunday, November 28, 2010

Selected readings 11/28/10

Interesting reading and news items.

Please leave some comments that indicate which articles you find most interesting or that identify topics you would like to read about, and I will try to include more articles of a similar nature in the future

These items are also bookmarked at my Diigo account.

Bad seeds, bad science, and fairly black cats?: Geneticists have failed to remind the public what the word “genetic” actually means. Heritability implies that gene and environment work, or might be persuaded to work, together. Why, after all, are taxpayers spending money on the double helix if there is no hope of an environmental intervention—a drug, a change in lifestyle, or cancer surgery after the early diagnosis of a somatic mutation—to help those at risk from what they inherit? Everyone in the trade knows this although they fail to mention it except to their first-year undergraduate classes. Transcripts of their lectures should be sent out with every press release. [The Lancet, 10/23/10]
Cancer’s little helpers: No one would have predicted a decade ago that these microRNAs, as the hairpins are called, were involved in cancer, because no one even knew that they existed in people. Mere snippets of RNA — DNA’s underappreciated cousin — these micromolecules are about 22 chemical letters long. But their size belies their power. [Science News, 8/28/10]
Hogan’s holometer: Testing the hypothesis of a holographic universe: In 2008, Fermilab particle astrophysicist Craig Hogan made waves with a mind-boggling proposition: The 3D universe in which we appear to live is no more than a hologram. Now he is building the most precise clock of all time to directly measure whether our reality is an illusion. [Symmetry Breaking, 10/20/10]
The Brain That Changed Everything: When a surgeon cut into Henry Molaison's skull to treat him for epilepsy, he inadvertently created the most important brain-research subject of our time — a man who could no longer remember, who taught us everything we know about memory. Six decades later, another daring researcher is cutting into Henry's brain. Another revolution in brain science is about to begin. [Esquire, 10/25/10]
How Big is the Unobservable Universe?: Based on what we currently think about inflation, this means that the Universe is at least 10^(1030) times the size of our observable Universe! And good luck living long enough to even write that number down. ... All that we know, see, and observe is just one tiny region that slid down that hill fast enough to end inflation, but most of it just keeps on inflating forever and ever. [Starts with a Bang!, 10/27/10]
Revealing the galaxy’s dark side: “In our paper, we discussed a number of astrophysical possibilities for the origin of the signal, including a population of pulsars, cosmic ray interactions and emission from our galaxy's supermassive black hole,” notes Hooper. “And in the end, no combination of any astrophysical sources could give us the signal we’re seeing,” he adds. “Eventually we just got fed up and concluded there doesn’t seem to be a way to explain the signal except for one thing — we tried dark matter and it fit beautifully without any special bells or whistles.” [Science News, 11/20/10]
When Muons Collide: A new type of particle collider known as a muon collider considered a wild idea a decade ago is winning over skeptics as scientists find solutions to the machine's many technological challenges. [Symmetry, 10/1/10]
We all need (a little bit of) sex: Sex costs amazing amounts of time and energy. Just take birds of paradise touting their tails, stags jousting with their antlers or singles spending their weekends in loud and sweaty bars. Is sex really worth all the effort that we, sexual species, collectively put into it? [Scientific American, 11/2/10]
Glia: The new frontier in brain science: Glia, in contrast to neurons, are brain cells that do not generate electrical impulses, and there are a lot of them—85 percent of the cells in the brain. Yet, these cells have been largely neglected for 100 years. I call this new frontier of neuroscience "The Other Brain," because we are only now beginning to explore it. The new findings are expanding our concept of information processing in the brain. They are leading rapidly to new treatments for diseases ranging from spinal cord injury to brain cancer to chronic pain, and Alzheimer's disease. [Scientific American, 11/4/10]
Extra neutrino flavor could be bitter end to Standard Model: What seems to have caught everyone's attention is the suggestion that this might be evidence of what are called sterile neutrinos. Although regular neutrinos barely interact with matter, sterile neutrinos can only interact via gravity, which (if they exist) is what has allowed them to escape our detection to date. Since they'd also be heavier than the regular neutrinos, they would make good dark matter candidates. [Nobel Intent, 11/2/10]
The Neanderthal Romeo and Human Juliet hypothesis: Scientists have had trouble reconciling data from analyses of human mitochondrial DNA and the male Y chromosome. Analyses of human mitochondrial DNA indicate that we all share a common female ancestor 170,000 years ago. Analyses of the Y chromosome indicate that we share a common male ancestor 59,000 years ago. How can we account for the idea that our common grandmother is 111,000 years older than our common grandfather? [Neuroanthropology, 10/26/10]
An idle brain may be the self's workshop: As neuroscientists study the idle brain, some believe they are exploring a central mystery in human psychology: where and how our concept of "self" is created, maintained, altered and renewed. After all, though our minds may wander when in this mode, they rarely wander far from ourselves, as Mrazek's mealtime introspection makes plain. [Los Angeles Times, 8/30/10]
Determining 500th Alien Planet Will Be a Tricky Task: At NASA's last count, astronomers had confirmed the discovery of 494 planets around alien suns. There are signs of dozens more, if not hundreds, but it will take time to weed out which of the detections are actual worlds and which are merely false alarms. [Space.com, 11/11/10]
Tracking Viruses Back in Time: How long have viruses been around? No one knows. Scientists at Portland State University have begun taking the first steps toward answering this question. [Astrobiology, 9/6/10]
Can a 1960s Approach Unify Gravity with the Rest of Physics?: In July mathematicians and physicists met at the Banff International Research Station in Alberta, Canada, to discuss a return to the golden age of particle physics. They were harking back to the 1960s, when physicist Murray Gell-Mann realized that elementary particles could be grouped according to their masses, charges and other properties, falling into patterns that matched complex symmetrical mathematical structures known as Lie groups. [Scientific American, 9/7/10]
Neuroscience: Settling the great glia debate: The consequences of this 'gliotransmission' could be profound. The human brain contains roughly equal numbers of glia and neurons (about 85 billion of each), and any given astrocyte can make as many as 30,000 connections with cells around it. If glia are involved in signalling, processing in the brain turns out to be an order of magnitude more complex than previously expected, says Andrea Volterra, who studies astrocytes at the University of Lausanne in Switzerland. Neuroscientists, who have long focused on the neuron, he says, would have to revise everything. [Nature News, 11/10/10]
This Is Your Brain on Metaphors: Symbols, metaphors, analogies, parables, synecdoche, figures of speech: we understand them. We understand that a captain wants more than just hands when he orders all of them on deck. We understand that Kafka’s “Metamorphosis” isn’t really about a cockroach. If we are of a certain theological ilk, we see bread and wine intertwined with body and blood. We grasp that the right piece of cloth can represent a nation and its values, and that setting fire to such a flag is a highly charged act. [New York Times, 11/14/10]
Tree or ring: the origin of complex cells: All complex life belongs to a single group called the eukaryotes, whose members, from humans to amoebas, share a common ancestry. Their cells are distinguished by having several internal compartments, including the nucleus, which shelters their precious DNA, and the mitochondria, which provide them with power. [Not Exactly Rocket Science, 9/12/10]
I am virus – animal genomes contain more fossil viruses than ever expected: Your closest fossils are inside you, scattered throughout your genome. They are the remains of ancient viruses, which shoved their genes among those of our ancestors. There they remained, turning into genetic fossils that still lurk in our genomes to this day. [Not Exactly Rocket Science, 11/18/10]
Effective Field Theory: "Effective field theory" is a technical term within quantum field theory, but it is associated with a more informal notion of extremely wide applicability. Namely: if we imagine dividing the world into "what happens at very short, microscopic distances" and "what happens at longer, macroscopic distances," then it is possible to consistently describe the macroscopic world without referring to (or even understanding) the microscopic world. [Cosmic Variance, 11/25/10]
Meet a superpartner at the LHC: Of the many ideas for new physics that can be tested at the Large Hadron Collider (LHC), supersymmetry is one of the most promising. The theory proposes that each fundamental fermion particle has a heavier bosonic superpartner (and vice versa for each fundamental boson) and by doing so, offers an extension of the standard model of particle physics that fixes many of its problems. None of the known particles appear to be superpartners, however, which leads to the daunting conclusion that if supersymmetry is correct, there are more than twice as many fundamental particles as we thought, but we have only been left with the lightest partners; that is, supersymmetry is broken. [Physics, 11/22/10]
Mafia Wars: An increasing amount of data is showing that the cellular battle between pathogens and hosts needs much more than a simple military metaphor to describe it—think undercover infiltration, front organizations, and forced suicide. [The Scientist, 6/1/10]

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Sunday, October 24, 2010

Selected readings 10/24/10

The New Nu News!: There could be an extra, "sterile" neutrino out there, although cosmology places tight restrictions on that. There could be a fundamental difference between neutrinos and anti-neutrinos, which we don't (at present) understand at all. Or there could be some physics that's completely off the radar that explains this, but it looks like the good ol' standard model (and the simplest modifications to it) is woefully inadequate to explain what we're seeing. [Starts with a Bang, 9/27/10]
Primordial Magnetic Field May Permeate the Universe: Two physicists attempting to overcome some unexpected fuzziness in images of distant, supermassive black holes say they have found yet another potential big bang vestige: an extremely weak magnetic field that stretches across the universe. If scientists confirm the finding, it could help reveal the origins of magnetism in the cosmos. [ScienceNOW, 9/24/10]
The Itch of Curiosity: Curiosity is one of those personality traits that gets short scientific shrift. It strikes me as a really important mental habit - how many successful people are utterly incurious? - but it's also extremely imprecise. What does it mean to be interested in seemingly irrelevant ideas? And how can we measure that interest? While we've analyzed raw intelligence to death - scientists are even beginning to unravel the anatomy of IQ - our curiosity about the world remains mostly a mystery. [Wired, 8/3/10]
The Personality Paradox: There's an interesting new paper in Biological Psychiatry on the genetic variations underlying human personality. The study relied on a standard inventory of temperaments - novelty-seeking, harm avoidance, reward dependence and persistence - as measured in 5,117 Australian adults. What did the scientists find? Mostly nothing. The vast genetic search came up empty. [Wired, 8/9/10]
The Worm In Your Brain: So our cortex turns out to be a lot older than previously thought. The common ancestor of us and ragworms–a wormy creature that lived 600 million years ago–not only had a brain, but had an ur-cortex. And it probably used that ur-cortex to learn about its world–most likely learning about the odors it sniffed. That animal’s descendants diverged into different forms, and the ur-cortex changed along the way. Yet they still used many of the same genes their ancestor did long ago. [The Loom, 9/3/10]
Mapping the Brain on a Massive Scale: A massive new project to scan the brains of 1,200 volunteers could finally give scientists a picture of the neural architecture of the human brain and help them understand the causes of certain neurological and psychological diseases. The National Institutes of Health announced $40 million in funding this month for the five-year effort, dubbed the Human Connectome Project. Scientists will use new imaging technologies, some still under development, to create both structural and functional maps of the human brain. [Technology Review, 9/28/10]
Recipes For Limb Renewal: Bioengineers continue to refine prosthetic limbs, but they still can’t replicate the entire constellation of capabilities provided by flesh and blood. So a few determined scientists are pursuing a different solution: They are seeking the recipe for regrowing a missing limb. [Chemical & Engineering News, 8/2/10]
If low serotonin levels aren't responsible for depression, what is?: While traditional antidepressants do increase neurogenesis and relieve depression symptoms in some animal models, others show that neurogenesis and antidepressant behaviours are unrelated. Much of this debate comes down to the fact that we don't yet have a real understanding of neurogenesis, how it works, and how it is controlled both in normal brains and in the presence of antidepressants. Until we know, finding a truly effective antidepressant may remain out of reach. So while the monoamine/serotonin hypothesis for depression may be out, neurogenesis needs to step it up a little to make it in. [guardian.co.uk, 9/28/10]
A New Way to Make Stem Cells: A Harvard researcher has developed a way to make pluripotent stem cells that solves several of the major impediments to using them to treat human diseases. Derrick Rossi, an assistant professor at Harvard Medical School, created pluripotent stem cells--which can turn into virtually any other type of cell in the body--from non-stem cells without using viruses to tinker with a cell's genome, as conventional methods do. This means that Rossi's method could be substantially safer for treating disease. [Technology Review, 10/1/10]
Alien World Tour: The Exoplanets Around Star Gliese 581: The announcement Wednesday (Sept. 29) of two newfound alien planets circling the star Gliese 581 adds to the nearby solar system's intrigue, further cementing its status as a top candidate to harbor extraterrestrial life. One of the two newly discovered planets, known as Gliese 581g, is a small, Earth-like world that likely lies within its star's habitable zone - the just-right range of distances that allow liquid water to exist. Astronomers have now detected six planets orbiting Gliese 581, the most known to circle any star beyond our own sun. [Space.com, 9/29/10]
If There's Life on Alien Planet Gliese 581g, How Do We Find It?: After spending decades searching for alien planets capable of harboring life, astronomers may have found one. So how can they check to see if life actually exists on this alien world? ... One of the planet's discoverers said in a briefing yesterday that "the chances of life on this planet are 100 percent." To determine if this is true, researchers will have to scrutinize Gliese 581g from afar, searching its atmosphere for certain telltale molecules. But it might be a while before they have the tools to do this properly. [Space.com, 9/30,10]
Astronomer Seeks ET Machines: If we ever do receive a message from outer space, we’ll want to know what kind of aliens sent it. SETI researcher Seth Shostak says we shouldn’t expect them to be anything like us – in fact, they might not be biological at all, but instead, extraterrestrial machines. [Astrobiology Magazine, 10/1/10]
The Gates of Immortality: Why do cells allow some mistakes to accumulate? If evolution is such a powerful process-one that finds solutions to all manner of problems-how could there be processes or problems that can't be fixed? [The Scientist, 10/1/10]
The One True Path?: Niswender and Galli are elucidating a molecular link between mental illness and problems with how the body processes sugars. That link is part of the complex series of events that make up the insulin-signaling pathway, a crucial mechanism by which the pancreatic hormone insulin directs the transport and storage of glucose in virtually every cell type in the body. This is only one of a recent rash of discoveries about how insulin is also intricately involved in many disease processes, including the growth of cancer cells and defects in bone mass regulation. [The Scientist, 10/1/10]
A new source of CP violation?: Abazov et al. report an unexpectedly large value of the same-sign dimuon charge asymmetry. This means that they see pairs of positive muons, μ+μ+, among the debris of their proton-antiproton collisions more often than they see pairs of negative muons, μ-μ-. The key point is that their measurement violates CP symmetry, which relates the behavior of matter and antimatter particles. [Physics, 8/16/10]
Hagfish Analysis Opens Major Gap in Tree of Life: Since the 1970s, many evolutionary biologists have considered an eel-like, deep-sea-dwelling creature called the hagfish to be the closest extant relative of a last common ancestor for all backboned creatures. That made the hagfish a stand-in for a transitional species between invertebrates and higher animals, spanning a leap as dramatic as any in evolutionary history. But a new family tree based on high-powered molecular analysis lumps hagfish together with lampreys, a jawless fish that’s primitive, but very much a vertebrate. [Wired, 10/19/10]
On a quest to map the brain’s hidden territory: On a recent morning, Wedeen pulled up images created with the new technology, in which the lakes of white were crisscrossed by colorful, ropy bundles of fibers, revealing an elegant, three-dimensional architecture. Looking more like art than anatomy, these strands form the connections in the brain — the “connectome.’’ They are neural highways crucial for brain function, including thoughts, movements, and sensations. [The Boston Globe, 10/11/10]
The origin of complex life – it was all about energy: According to a new hypothesis, put forward by Nick Lane and Bill Martin, we are all natural-born gas-guzzlers. Our very existence, and that of every animal, plant and fungus, depended on an ancient partnership, forged a few billion years ago, which gave our ancestors access to unparalleled supplies of energy and allowed them to escape from the shackles of simplicity. [Not Exactly Rocket Science, 10/20/10]
The Fuel Of Evolution: Within the cells of humans and all other modern creatures are lots of tiny mitochondria, which may have been the key to the evolution of complex multicellular life billions of years ago. [InsideScience.org, 10/22/10]
Geologists revisit the Great Oxygenation Event: Why did oxygen levels spike 2.5 billion years ago, and how much oxygen was there in the atmosphere really? Why are banded iron formations made of layers only a few centimeters thick, and why did they stop forming so abruptly? If the oceans were oxygenated 2.5 billion years ago, why did multicellular life delay its appearance for another 2 billion years? And did all these changes really take place at pretty much the same time everywhere on Earth? [Physorg.com, 8/19/10]
Mirror Mirror On The Wall: Every one of the four forces of Nature we know of - gravity, electromagnetism, the weak force, and the nuclear force - all originate from slight variations of this narrative. Gauge symmetries are the origins of all the forces of Nature. For example, gravity arises from a gauge symmetry in 3D: a sphere of a gauge with its hand pointing in any direction in the full three dimensional span of space. [Schrödinger's Dog, 10/22/10]
Gravity Up Close: Scientists know how gravity works at big distances -- the inter-planetary or inter-stellar range -- but does it work the same way at the inter-atomic range? A variety of tabletop experiments are trying to explore this issue. Already some theorists say that a departure from conventional gravity behavior could hint at the existence of extra dimensions. [InsideScience.org, 10/13/10]
Cracks In The Universe: Physicists are hot on the trail of one of strangest theorized structures in the universe. A team of researchers have announced what they think are the first indirect observations of ancient cosmic strings, bizarre objects thought to have contributed to the arrangement of objects throughout the universe. [InsideScience.org, 10/11/10]

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Tuesday, September 28, 2010

Selected readings 9/28/10

Convincing a Young Scientist that Dark Matter Exists: So I was in favor of dark matter, but I wasn't entirely convinced. I wanted a "smoking gun" piece of evidence for dark matter. Something that was an entirely new prediction that we could look for -- much like that 1919 eclipse was for general relativity -- and decide whether dark matter predicts what we're going to see. [Starts with a Bang, 6/24/10]
How blind to change are you?: This failure to notice what should be very apparent is something we unconsciously experience every day as our brains filter the barrage of visual information which we are flooded with. And apparently it has a name; it is called change blindness. [BBC News, 6/11/10]
New data suggest a lighter Higgs: New data offer evidence that the heft of the Higgs particle lies somewhere in the low end of the range being probed by particle colliders on two continents. The results also hint that the particle’s mass may be consistent with supersymmetry, a theory that gives every particle in the standard model of physics a much heavier partner. [Science News, 7/26/10]
Jellyfish eye genes suggest a common origin for animal eyes: Jellyfish may seem like simple blobs but some have surprisingly sophisticated features, including eyes. These are often just light-sensitive pits but species like the root-arm medusa have complex ‘camera’ eyes, with a lens that focuses light onto a retina. Not only are these organs superficially similar to ours, they’re also constructed from the same genetic building blocks. [Not Exactly Rocket Science, 7/27/10]
Astronomy and particle physics race to replace Standard Model: If energy issues seem to be attracting the attention of a lot of physicists, the Large Hadron Collider seems to be drawing the attention of many of the rest of them, including people in fields like cosmology, which deals with items on the opposite end of the size scale. In turn, the people working on the LHC and other particle detectors are carefully paying attention to the latest astronomy results, hoping they'll put limits on the properties and identities of the zoo of theoretical particles that need to be considered. [Nobel Intent, 7/28/10]
Genetics tells tall tales: Studies scanning the genomes of tens of thousands of individuals for gene variants associated with height have come up short: around 50 variants have been identified, but together they account for only 5% or so of height's heritability. ... This heritability may not be missing — it may simply be buried deeper than previously thought, in a multitude of genetic variants that have tiny effects individually. [Nature News, 6/20/10]
Dark matter eldorado: Observations confirm that a faint group of stars in the Milky Way’s backyard has the highest density of dark matter — the invisible material thought to account for 83 percent of the mass of the universe — of any galaxy known. [Science News, 7/30/10]
Searching through the LHC data flood for dark matter: Although the Standard Model has needed some minor tweaking to deal with recent observations, Gross said that there are three major issues that suggests it's due for a major overhaul. One of these is that we have convincing evidence that dark matter exists, and comes in the form of particles that are heavy and stable to at least the life of the Universe. Unfortunately, the Standard Model provides nothing that meets these requirements. [Nobel Intent, 8/1/10]
Two New Paths to the Dream: Regeneration: Animals like newts and zebra fish can regenerate limbs, fins, even part of the heart. If only people could do the same, amputees might grow new limbs and stricken hearts be coaxed to repair themselves. But humans have very little regenerative capacity, probably because of an evolutionary trade-off: suppressing cell growth reduced the risk of cancer, enabling humans to live longer. A person can renew his liver to some extent, and regrow a fingertip while very young, but not much more. [New York Times, 8/5/10]
Sponge genes surprise: A complete genetic catalog of the sponge Amphimedon queenslandica suggests that the first animals already had a complex kit of genetic tools at their disposal. Sponges harbor between 18,000 and 30,000 genes — roughly the same number as humans, fruit flies, roundworms and other animals. [Science News, 8/4/10]
Plentiful and Potential Planets: Two planet-hunting telescopes - CoRoT and Kepler - are keeping astronomers hard at work cataloging far-distant planets that orbit other stars in our galaxy. The search for distant planets is essential for astrobiologists who are hunting for habitable, Earth-like worlds beyond our solar system. [Physorg.com, 6/23/10]
World’s Most Intense X-Ray Laser Takes First Shots: The world’s most intense X-ray laser may soon be the fastest strobe-light camera ever. Two of the laser’s first experiments show the device will be able to take snapshots of single molecules in motion — without destroying them first. [Wired Science, 6/30/10]
The origin of life: putting chemistry inside a cell: In Szostak's view, interesting chemistry is easy. He also said that Darwinian evolution also makes things easy, since it's possible to take what you've got and radically improve it. So what's bugging him these days is the transition in between the two. How do you move from interesting chemistry to something that can evolve? He's doing this by trying to engineer a system that can make the transition. [Nobel Intent, 6/28/10]
Why weather != climate: the engine behind climate models: In this article I take a look at climate modeling and in particular why the comment "They can't predict the weather, therefore climate models are not good" is just plain wrong. It represents a fundamental misunderstanding of what climate modelers are trying to achieve, what is achievable and why the weather is unpredictable. [Nobel Intent, 7/9/10]
Does Your Language Shape How You Think?: The habits of mind that our culture has instilled in us from infancy shape our orientation to the world and our emotional responses to the objects we encounter, and their consequences probably go far beyond what has been experimentally demonstrated so far; they may also have a marked impact on our beliefs, values and ideologies. We may not know as yet how to measure these consequences directly or how to assess their contribution to cultural or political misunderstandings. But as a first step toward understanding one another, we can do better than pretending we all think the same. [New York Times, 8/26/10]
Stem Cell Biology and Its Complications: Stem cell biology turned out to be more complicated than they anticipated. Besides the stem cells from embryos, there are so-called adult stem cells found in all tissues but with limited potential because they can only turn into cells from their tissue of origin. And there are these newer cells made by reprogramming mature cells. [New York Times, 8/24/10]
Scientists Square Off on Evolutionary Value of Helping Relatives: For the past 46 years, biologists have used Dr. Hamilton’s theory to make sense of how animal societies evolve. They’ve even applied it to the evolution of our own species. But in the latest issue of the journal Nature, a team of prominent evolutionary biologists at Harvard try to demolish the theory. [New York Times, 8/30/10]
Think You're Operating on Free Will? Think Again: There may be few things more fundamental to human identity than the belief that people are rational individuals whose behavior is determined by conscious choices. But recently psychologists have compiled an impressive body of research that shows how deeply our decisions and behavior are influenced by unconscious thought, and how greatly those thoughts are swayed by stimuli beyond our immediate comprehension. [Time, 7/2/10]
Forget What You Know About Good Study Habits: In recent years, cognitive scientists have shown that a few simple techniques can reliably improve what matters most: how much a student learns from studying. The findings can help anyone, from a fourth grader doing long division to a retiree taking on a new language. But they directly contradict much of the common wisdom about good study habits, and they have not caught on. [New York Times, 9/6/10]
Gene networks underlie disease?: An international group of researchers have developed a novel method for identifying entire networks of genes and their association to disease, providing a more accurate picture of the genetic risks associated with specific diseases than single genes can provide. [The Scientist, 9/8/10]
Collider gets yet more exotic 'to-do' list: As if the Large Hadron Collider (LHC) didn't have enough to look for. It is already charged with hunting for the fabled Higgs boson, extra dimensions and supersymmetry, but physicists are now adding even more elaborate phenomena to its shopping list — including vanishing dimensions that could explain the accelerating expansion of the Universe. Some argue that signs of new and exotic physics could show up in the LHC far sooner than expected. [Nature News, 7/20/10]
Under Pressure: The Search for a Stress Vaccine: Chronic stress, it turns out, is an extremely dangerous condition. ... While stress doesn’t cause any single disease — in fact, the causal link between stress and ulcers has been largely disproved — it makes most diseases significantly worse. The list of ailments connected to stress is staggeringly diverse and includes everything from the common cold and lower-back pain to Alzheimer’s disease, major depressive disorder, and heart attack. [Wired Magazine, 7/28/10]
Why some memories stick: A study published in Science this week indicates that reactivating neural patterns over and over again may etch items into the memory. People find it easier to recall things if material is presented repeatedly at well-spaced intervals rather than all at once. For example, you're more likely to remember a face that you've seen on multiple occasions over a few days than one that you've seen once in one long period. One reason that a face linked to many different contexts — such as school, work and home — is easier to recognize than one that is associated with just one setting, such as a party, could be that there are multiple ways to access the memory. This idea, called the encoding variability hypothesis, was proposed by psychologists about 40 years ago. [Nature News, 9/9/10]
DNA 'Volume Knobs' May Be Associated With Obesity: When it comes to our expanding waistlines, we usually blame either diet or genes. But a new study fingers a third culprit: chemicals that attach to DNA and change its function. A survey of millions of these modifications has uncovered a handful associated with body mass index, a measure of height and weight. [Science Now, 9/15/10]
Astronomy and particle physics race to replace Standard Model: If energy issues seem to be attracting the attention of a lot of physicists, the Large Hadron Collider seems to be drawing the attention of many of the rest of them, including people in fields like cosmology, which deals with items on the opposite end of the size scale. In turn, the people working on the LHC and other particle detectors are carefully paying attention to the latest astronomy results, hoping they'll put limits on the properties and identities of the zoo of theoretical particles that need to be considered. [Nobel Intent, 7/28/10]
Sizing Up Consciousness by Its Bits: Consciousness, Dr. Tononi says, is nothing more than integrated information. Information theorists measure the amount of information in a computer file or a cellphone call in bits, and Dr. Tononi argues that we could, in theory, measure consciousness in bits as well. When we are wide awake, our consciousness contains more bits than when we are asleep. [New York Times, 9/20/10]
Translating Stories of Life Forms Etched in Stone: The Ediacaran fossils tell us that Darwin was being too generous. Our earliest animal ancestor probably had no head, tail, or sexual organs, and lay immobile on the sea floor like a door mat. [New York Times, 7/26/10]

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Sunday, July 25, 2010

Selected readings 7/25/10

The Muon Guys: On the Hunt for New Physics: The experiment will search for a phenomenon so incredibly rare that, according to the Standard Model of physics, humans could never build a machine sensitive enough to actually see it. Which is exactly why scientists want to build this experiment. Mu2e is on the hunt for new physics. [Symmetry Magazine, 6/1/10]
SLAC’s new X-ray laser peels and cores atoms: The first published scientific results from the world’s most powerful hard X-ray laser, located at the Department of Energy’s SLAC National Accelerator Laboratory, show its unique ability to control the behaviors of individual electrons within simple atoms and molecules by stripping them away, one by one—in some cases creating hollow atoms. [Symmetry Breaking, 7/2/10]
Antiaging protein also boosts learning and memory: Aging and wisdom are supposed to go together, but it turns out that a molecule that prevents one may actually play a role in the other. Researchers have discovered a new role for the famous antiaging protein SIRT1. It not only fends off aging, but also aids in learning and memory, a new study published online July 11 in Nature shows. [Science News, 7/12/10]
Galaxies weigh in on neutrinos: Neutrinos are infamously lightweight particles that are near impossible to detect, let alone place on a scale. Yet our most basic model for understanding the symmetries of matter and particles rests on an accurate measure of the neutrino masses. Over the past decade, observational cosmology has taken a leading position in providing an upper bound on these masses. Now, in a paper appearing in Physical Review Letters, Shaun Thomas, Filipe Abdalla, and Ofer Lahav at University College London in the UK predict that the total neutrino mass, summed over the three neutrino families, is smaller than 0.28 eV—the tightest upper bound yet. Their prediction is based on a new mapping of the distribution of density of surrounding galaxies. [Physics, 7/12/10]
Neutrino quick-change artist caught in the act: Physicists have for the first time found direct evidence that a neutrino, a ghostly elementary particle that barely interacts with matter, morphs from one type into another. The finding provides additional support for the notion that neutrinos have mass, a property that requires an explanation beyond the realm of the standard model of particle physics. [Science News, 6/1/10]
Magic quantum wand does not vanish hard math: They conclude that NP-complete problems are just as hard on an adiabatic quantum computer as on a classical computer. And, since earlier work showed the equivalence between different variants of quantum computers, that pretty much shuts down the possibility of any quantum computer helping with NP-complete problems. [Nobel Intent, 6/3/10]
An unpaleontological lament for lost molecules and shattered cells and the cruelty of time: These were almost certainly colonial organisms that took advantage of the higher concentration of oxygen to build denser mats on top of the sea floor. They probably weren't true multi-cellular organisms; they were a step up from a colony of bacteria that you might see growing on a petri dish, but with additional molecular features that permitted greater coordination and the development of more elaborate spatial patterning. [Pharyngula, 7/15/10]
Cosmology forum: Is dark energy really a mystery?: The Universe is expanding. And the expansion seems to be speeding up. To account for that acceleration, a mysterious factor, 'dark energy', is often invoked. A contrary opinion — that this factor isn't at all mysterious — is here given voice, along with counter-arguments against that view. [Nature, 7/14/10]
How to read a genome-wide association study: As any avid follower of genomics or medical genetics knows, genome-wide association studies (GWAS) have been the dominant tool used by complex disease genetics researchers in the last five years. There’s a very active debate in the field about whether GWAS have revolutionized our understanding of disease genetics or whether they were a waste of money for little tangible gain. [Genomes Unzipped, 7/18/10]
Brain's bubble wrap may be lots more: They have long been dismissed as the brain’s Bubble Wrap, packing material to protect precious cells that do the real work of the mind. But glial cells — the name literally means “glue’’ — are now being radically recast as neuroscientists explore the role they play in disease and challenge longstanding notions about how the brain works. [Boston Globe, 5/31/10]
Collider gets yet more exotic 'to-do' list: As if the Large Hadron Collider (LHC) didn't have enough to look for. It is already charged with hunting for the fabled Higgs boson, extra dimensions and supersymmetry, but physicists are now adding even more elaborate phenomena to its shopping list — including vanishing dimensions that could explain the accelerating expansion of the Universe. Some argue that signs of new and exotic physics could show up in the LHC far sooner than expected. [Nature News, 7/20/10]
Shock and Age: The accumulation of misfolded protein marks the accrual of years as the body ages. Could heat shock proteins be used to reduce the effects of aging and diminish the risk of disease by untangling improperly folded proteins? [The Scientist, 6/1/10]
Quantum mechanics flummoxes physicists again: Weihs and colleagues aimed a source of single photons (which, like electrons, exhibit wave–particle duality) at a mask containing various open and closed combinations of three slits. The authors fired photons repeatedly through the mask, while building a probability distribution of photons arriving on a detector beyond it. From the probabilities of each combination, they could calculate a crucial interference term, which would highlight any three-path interference. [Nature News, 7/22/10]

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Tuesday, July 13, 2010

Selected readings 7/13/10

A Decade Later, Genetic Map Yields Few New Cures: Ten years after President Bill Clinton announced that the first draft of the human genome was complete, medicine has yet to see any large part of the promised benefits. For biologists, the genome has yielded one insightful surprise after another. But the primary goal of the $3 billion Human Genome Project — to ferret out the genetic roots of common diseases like cancer and Alzheimer’s and then generate treatments — remains largely elusive. Indeed, after 10 years of effort, geneticists are almost back to square one in knowing where to look for the roots of common disease. [New York Times, 6/12/10]
How Our Brains Make Memories: His ideas are unconventional within neuroscience, and they have caused researchers to reconsider some of their most basic assumptions about how memory works. In short, Nader believes that the very act of remembering can change our memories. [Smithsonian Magazine, 4/19/10]
Writing Circuits on Graphene: Graphene, an atom-thick carbon sheet, is a promising replacement for silicon in electronic circuits, since it transports electrons much faster. IBM researchers have already made transistors, the building blocks of electronic circuits, with graphene that work 10 times faster than their silicon counterparts. [Technology Review, 6/15/10]
Rare Gene Glitch a Clue to Genomics Mystery: Common diseases have largely resisted genomic analysis, leaving scientists unable to explain genetic underpinnings of diseases that clearly have a hereditary component. These analyses have focused on mutations that are relatively widespread and easy to see. It took new tools to notice mutations like those just found in the SIAE gene, which cause immune cells to go haywire during autoimmune disease. They were detected by ultra high-resolution analysis of a sort rarely used in genomics. [Wired, 6/16/10]
Test Supports Universal Common Ancestor for All Life: One researcher put the basic biological assumption of a single common ancestor to the test--and found that advanced genetic analysis and sophisticated statistics back up Darwin's age-old proposition. [Scientific American, 5/13/10]
Frozen methane, from the gulf oil spill to climate change: At the conditions in which they form, methane is a gas, water a liquid. Somehow, they come together to form a solid. The key to understanding why is the small size and nonpolar (hydrophobic) nature of methane. [Nobel Intent, 5/11/10]
New evidence for quantum Darwinism found in quantum dots: Physicists have found new evidence that supports the theory of quantum Darwinism, the idea that the transition from the quantum to the classical world occurs due to a quantum form of natural selection. By explaining how the classical world emerges from the quantum world, quantum Darwinism could shed light on one of the most challenging questions in physics of the past century. [Physorg.com, 5/10/10]
I.B.M.'s Supercomputer to Challenge 'Jeopardy!' Champions: For the last three years, I.B.M. scientists have been developing what they expect will be the world’s most advanced “question answering” machine, able to understand a question posed in everyday human elocution — “natural language,” as computer scientists call it — and respond with a precise, factual answer. In other words, it must do more than what search engines like Google and Bing do, which is merely point to a document where you might find the answer. It has to pluck out the correct answer itself. [New York Times, 6/14/10]
New Nicaraguan sign language shows how language affects thought: NSL is not a direct translation of Spanish – it is a language in its own right, complete with its own grammar and vocabulary. Its child inventors created it naturally by combining and adding to gestures that they had used at home. Gradually, the language became more regular, more complex and faster. Ever since, NSL has been a goldmine for scientists, providing an unparalleled opportunity to study the emergence of a new language. And in a new study led by Jennie Pyers from Wellesley College, it even tells us how language shapes our thought. [Not Exactly Rocket Science, 6/22/10]
Hunt for genetic causes of diseases narrows targets: The falling cost of genome sequencing has kicked off a new phase in the search for the genetic underpinnings of complex diseases such as asthma, diabetes and autism. [Nature News, 5/18/10]
Researchers tweak fMRIs to map the brain's wiring schematic: Researchers were able to limit the firing of nerve cells to a specific individual type, and show that these triggered normal-looking fMRI signals in rats. Not only does this place fMRI on a firmer empirical footing, the technique allowed the researchers to track networks of connected nerves within the brain. [Nobel Intent, 5/17/10]
Fermi's Tevatron finds another bias against antimatter: Over the last couple of decades, a few cases of what are called C-P violations have been identified. These are cases where a particle decay that should, in theory, produce equal amounts of antimatter and matter, doesn't. These few instances, however, don't occur with sufficient frequency to explain why the Universe has its current abundance of regular matter. That has kept physicists looking and, this morning, Fermilab announced that research performed in its Tevatron accelerator has provided strong evidence for another C-P violation. [Nobel Intent, 5/18/10]
Man-Made Genetic Instructions Yield Living Cells for the First Time: The first microbe to live entirely by genetic code synthesized by humans has started proliferating at a lab in the J. Craig Venter Institute (JCVI). Venter and his colleagues used a synthetic genome—the genetic instruction set for life—to build and operate a new, synthetic strain of Mycoplasma mycoides bacteria. [Scientific American, 5/20/10]
Synthetic genome resets biotech goals: Synthetic biology is a field with an audacious but ultimately utilitarian goal: to redesign the building blocks of life to serve the needs of humanity. It is also an endeavour that challenges clear-cut definitions of natural versus artificial life. [Nature News, 5/26/10]
Primordial Gravitational Waves Provide a Test of Cosmological Theories: Ripples in the fabric of spacetime could someday provide observational evidence for the goings-on in the earliest instants of the universe, revealing high-energy processes that currently remain opaque to even the largest particle colliders. [Scientific American, 5/21/10]
Neutrino experiments sow seeds of possible revolution: Neutrinos are the big nothings of subatomic physics. Nearly massless and lacking an electric charge, these ghostly particles interact so weakly with other types of matter that more than 50 trillion of them pass unimpeded through a person’s body each second. Yet recent preliminary findings from two experiments hint that neutrinos may be opening a window on a hidden world of subatomic particles and forces. [Science News, 6/25/10]
X-Ray Laser Resurrects a Laboratory No Longer in the Vanguard: In the first experiments conducted at the SLAC National Accelerator Laboratory in Menlo Park, Calif., since its outdated particle accelerator was converted into the world's brightest X-ray laser, scientists managed to create what they called hollow atoms, giving just a preview of the kind of science expected to be done there. [New York Times, 7/5/10]
SETI Redux: Joining the Galactic Club: David Schwartzman, a biogeochemist at Howard University in Washington D.C., explains why he thinks the aliens are out there, despite the fact that the search for extraterrestrial intelligence (SETI) has only found silence. He also outlines what we need to do for planet Earth to be initiated into the Galactic Club. [Physorg.com, 5/24/10]
Dark Matter May Be Building Up Inside the Sun: The sun could be a net for dark matter, a new study suggests. If dark matter happens to take a certain specific form, it could build up in our nearest star and alter how heat moves inside it in a way that would be observable from Earth. [Wired, 7/9/10]

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Sunday, June 13, 2010

Selected readings 6/13/10

Anticipating the first steps beyond the Standard Model: Physicists’ knowledge of elementary particles is encapsulated in the Standard Model of particle physics, which currently describes almost everything we’ve seen. Yet there is compelling evidence that the Standard Model cannot be the complete description of nature. For example, despite all of its successes, the Standard Model describes only 20 percent of the mass of the Universe. Eighty percent of the mass is known as “dark matter,” which we have never directly observed and know next to nothing about. [Symmetry Breaking, 6/3/10]
Could DZero result point to multiple Higgses?: What caused the DZero result’s large deviation from Standard Model predictions is just as earth-shaking a mystery. The answer could point to the completion of the Standard Model, missing only the theorized Higgs boson particle, or the creation of a new story line for a host of new particles in the saga of how matter in the universe behaves. In their quest for a full explanation, scientists debate whether they are simply missing a chapter in the Standard Model or if they need a sequel that goes beyond the model, potentially including extra dimensions or a theory called supersymmetry that would double the number of known particles. [Symmetry Breaking, 6/4/10]
What is a "law of physics," anyway?: Why should nature be governed by laws? Why should those laws be expressible in terms of mathematics? Why should they be formulated within space and time? These were the questions posed at a fascinating workshop two weeks ago at the Perimeter Institute, the sequel to a workshop held at Arizona State University in December 2008. ... The bottom line is that the organizers had better start planning on more sequels, because the questions seem as intractable as ever. [Scientific American, 6/4/10]
What a shoddy piece of work is man: The human body is certainly no masterpiece of intelligent planning. The eye's retina, for instance, is wired back to front so that the wiring has to pass back through the screen of light receptors, imposing a blind spot. Now John Avise, an evolutionary geneticist at the University of California at Irvine, has catalogued the array of clumsy flaws and inefficiencies at the fundamental level of the genome. His paper ... throws down the gauntlet to advocates of Intelligent design, the pseudo-scientific face of religious creationism. What Intelligent Designer, Avise asks, would make such a botch? [Nature News, 5/3/10]
Illuminating the brain: Now though, advances in a five-year-old field called optogenetics are convincing these scientists to crack open molecular-biology textbooks. Using a hybrid of genetics, virology and optics, the techniques involved enable researchers to instantaneously activate or silence specific groups of neurons within circuits with a precision that electrophysiology and other standard methods do not allow. Systems neuroscientists have longed for such an advance, which allows them their first real opportunity to pick apart the labyrinthine jumble of cell types in a circuit and test what each one does. [Nature News, 5/5/10]
The code within the code: 95% of the human genome is alternatively spliced, and that changes in this process accompany many diseases. But no one knew how to predict which form of a particular gene would be expressed in a given tissue. "The splicing code is a problem that we've been bashing our heads against for years," says Burge. "Now we finally have the technologies we need." [Nature News, 5/5/10]
European and Asian genomes have traces of Neanderthal: The genomes of most modern humans are 1–4% Neanderthal — a result of interbreeding with the close relatives that went extinct 30,000 years ago, according to work by an international group of researchers. [Nature News, 5/6/10]
Linux vs. Genome in Network Challenge: A comparison of the networks formed by genetic code and the Linux operating system has given insight into the fundamental differences between biological and computational programming. The shapes are very dissimilar, reflecting the evolutionary parameters of each process. Biology is driven by random mutations and natural selection. Software is an act of intelligent design. [Wired, 5/5/10]
Complex Life Traced to Ancient Gene Parasites: Mysterious gene structures called introns that help make complex organisms possible are descended from DNA parasites that infested bacteria billions of years ago, according to a new study. ... The findings fit the notion that group II introns flourished in the early Earth’s heat, and were ultimately co-opted into their hosts’ genomes. [Wired, 6/9/10]
The Magical Mystery Tour: Cassini, the first spacecraft to orbit Saturn, has revealed intricate details of the gas giant planet and its moons -- but many mysteries remain. Six years ago, the Cassini spacecraft began orbiting Saturn and taking detailed images of its ring and many moons. While the Cassini-Huygens mission has helped answer questions about this planetary system, it also has revealed new mysteries for scientists to puzzle over. [Physorg.com, 5/5/10]
Peptides may hold 'missing link' to life: Scientists have discovered that simple peptides can organize into bi-layer membranes. The finding suggests a "missing link" between the pre-biotic Earth's chemical inventory and the organizational scaffolding essential to life. [Physorg.com, 5/6/10]
Physicists study how moral behaviour evolved: A statistical-physics-based model may shed light on the age-old question "how can morality take root in a world where everyone is out for themselves?" Computer simulations by an international team of scientists suggest that the answer lies in how people interact with their closest neighbours rather than with the population as a whole. [Physicsworld.com, 5/5/10]

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Sunday, June 06, 2010

Selected readings 6/6/10

Einstein (Still) Rules The Universe: The pair of independent studies each used observations from NASA's Chandra X-ray Observatory to test Einstein's theory of General Relativity, and to study the properties of gravity on cosmic scales. Both demonstrated that Einstein's theory continues to hold true almost a century after it was first published. [Space.com, 4/23/10]
Listening for the 'birth cries' of black holes: We're talking about the astronomical stuff of nightmares - gargantuan explosions that rip apart giant stars to create black holes. Artist's impression of jets emerging from a dying starThese events are detected in space every few days thanks to Nasa's Swift observatory. The spacecraft sits above the Earth hunting for gamma-ray bursts (GRBs), the intensely bright but fleeting flashes of very high-energy radiation that can sweep our way from all points in the sky.
[BBC News, 4/20/10]
Hubble's role in search for aliens: The powerful vision of the Hubble Telescope - which turns 20 this week - has expanded our cosmic horizons and brought into sharper focus a new set of mysteries about the universe that is our home. To those whose science is gleaned from the media, astronomy may seem to be on a roll. And it is. [BBC News, 4/22/10]
Revealing the True Solar Corona: A total solar eclipse—the Moon blocking out the entire body of the Sun—actually reveals great detail of the Sun’s structure. When the blinding brilliance of the Sun is obscured, this allows its more tenuous surrounding features—its corona—to come into view. Investigating the corona may seem straightforward, but it requires an understanding beyond seeing, imaging and modeling. [American Scientist, 5/1/10]
Convincing the Public to Accept New Medical Guidelines: A $1.1 billion provision in the federal stimulus package aims to address the issue by providing funds for comparative effectiveness research to find the most effective treatments for common conditions. But these efforts are bound to face resistance when they challenge existing beliefs. As Nieman and countless other researchers have learned, new evidence often meets with dismay or even outrage when it shifts recommendations away from popular practices or debunks widely held beliefs. [Miller-McCune Online, 4/20/10]
Terra Incognita: The essential question is not whether you do or don't believe in a fundamental theory of everything. The essential question is what is a good and promising way to expand what is known. You can believe in flying spaghetti monsters, reincarnation, or a theory of everything: if it helps you with your research, by all means, go ahead, just don't put your believes in the abstract of your paper. [Backreaction, 5/21/10]
Protons not as “strange” as expected: The G-Zero collaboration proposed a precisely tuned survey for ephemeral particles that appear only briefly inside matter. Specifically, they wanted to measure the effect of strange particles in the proton, the sub-atomic particle found deep inside the nucleus of every atom in our universe. [Symmetry Breaking, 4/27/10]
Signs of dark matter may point to mirror matter candidate: Mirror matter would interact very weakly with ordinary matter. For this reason, some physicists have speculated that mirror particles could be candidates for dark matter. Even though mirror matter would produce light, we would not see it, and it would be very difficult to detect. [Physorg.com, 4/27/10]
Earth's Climate Used to Weigh Chances of Alien Life: Greenhouse gases have a bad reputation because of the role they're playing in global warming on Earth today. However, scientists say we also owe our lives to greenhouse gases because they might have allowed life to take hold in the first place. A new study of how these and other climate conditions have affected the origin and evolution of life on Earth could provide clues to understanding how climates on alien planets might affect their potential life. [Space.com, 6/3/10]
Evidence grows for tetraquarks: The existence of a new form of matter called a tetraquark has been given further support by the re-analysis of an experiment that has baffled particle physicists for the past two years. [Physicsworld.com, 4/27/10]
The cancer genome challenge: In the past two years, labs around the world have teamed up to sequence the DNA from thousands of tumours along with healthy cells from the same individuals. Roughly 75 cancer genomes have been sequenced to some extent and published; researchers expect to have several hundred completed sequences by the end of the year. [Nature News, 4/14/10]
Biomarker Studies Could Realize Goal of More Effective and Personalized Cancer Medicine: Biological and genomic studies are showing that most types of cancer are not single diseases, but rather complex disorders with distinct causes. Take breast cancer, for example: "When we say 'breast cancer', we're probably lumping 15 different diseases into that category," says co-author Joseph Nevins.... Subtle differences in the tumors' genomes and genetic expression are what make drugs work in certain patients and not in others. [Scientific American, 4/26/10]

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Monday, May 31, 2010

Selected readings 5/31/10

Seeing Aliens Will Likely Take Centuries: Although our telescopes will likely become good enough to detect signs of life on exoplanets within the next 100 years, it would probably take many centuries before we could ever get a good look at the aliens. "Unfortunately, we are perhaps as far away from seeing aliens with our own eyes as Epicurus was from seeing the first other worlds when, 23 centuries ago, he predicted the existence of these planets," said astrobiologist Jean Schneider at the Paris Observatory at Meudon. [Space.com, 4/29/10]
Only a matter of time, says Frank Drake: The search for extraterrestrial intelligence began in earnest 50 years ago, led by a young American astronomer named Frank Drake - a man, who is still confident we'll eventually find extraterrestrial civilisations. [COSMOS Magazine, 4/7/10]
A review of the Drake Equation: Which is the more shocking proposition: that our galactic neighbourhood is riddled with advanced alien civilisations? Or that we humans are a solitary beacon of intelligent life in a silent universe of almost incomprehensible vastness? Either prospect is enough to keep you awake at night. Yet one of these two statements is likely true. We just don't know which one. [COSMOS Magazine, 4/7/10]
What's up with nanotech?: While nanotechnology — working at a scale that is one-thousandth the width of a human hair — may have faded from the public’s imagination, the field has made substantial progress in recent years, opening new frontiers in electronics, medicine, and materials. [Boston.com, 3/29/10]
Scientist who cloned Dolly the sheep sees revolution in disease treatment in 20 years: The scientist who cloned Dolly the sheep believes that a new approach to the production of stem cells could revolutionise the treatment of inherited diseases such as Parkinson’s and motor neurone disease “within ten to twenty years”. [Times Online, 3/26/10]
Next Big Thing in English: Knowing They Know That You Know: This layered process of figuring out what someone else is thinking — of mind reading — is both a common literary device and an essential survival skill. Why human beings are equipped with this capacity and what particular brain functions enable them to do it are questions that have occupied primarily cognitive psychologists. [New York Times, 3/31/10]
Telescope arrays give fine view of stars: Radio astronomers have relied on interferometry for more than half a century, but optical astronomers have lagged behind. Now, optical interferometry has come of age. [Nature News, 4/7/10]
Protein folding: The dark side of proteins: Almost every human protein has segments that can form amyloids, the sticky aggregates known for their role in disease. Yet cells have evolved some elaborate defences. [Nature News, 4/7/10]
A New Clue to Explain Existence: Physicists at the Fermi National Accelerator Laboratory are reporting that they have discovered a new clue that could help unravel one of the biggest mysteries of cosmology: why the universe is composed of matter and not its evil-twin opposite, antimatter. [New York Times, 5/17/10]
Fermilab scientists find evidence for significant matter-antimatter asymmetry: The dominance of matter that we observe in the universe is possible only if there are differences in the behavior of particles and antiparticles. Although physicists have observed such differences (called “CP violation”) in particle behavior for decades, these known differences are much too small to explain the observed dominance of matter over antimatter in the universe and are fully consistent with the Standard Model. If confirmed by further observations and analysis, the effect seen by DZero physicists could represent another step towards understanding the observed matter dominance by pointing to new physics phenomena beyond what we know today. [SymmetryBreaking, 5/18/10]
How Many Sparks in the Genome?: The first two categories include stretches of DNA that are useful. The second two include stretches that are useless. Now comes the hard part: figuring out just how much of the genome is made up of each. [The Loom, 5/19/10]
Supermassive Black Holes Can Kill Whole Galaxies: Astrophysicists have found that when a supermassive black hole quickly devours gas and dust, it can generate enough radiation to abort all the embryonic stars in the surrounding galaxy. [ScienceNOW, 4/15/10]
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]
Life on Titan: stand well back and hold your nose!: Research by astrobiologist William Bains suggests that if life has evolved on the frozen surface of Saturn's moon, Titan, it would be strange, smelly and explosive compared to life on Earth. [Physorg.com, 4/14/10]
Perhaps a longer lifespan, certainly a longer 'health span': Organisms from yeast to rodents to humans all benefit from cutting calories. In less complex organisms, restricting calories can double or even triple lifespan. It's not yet clear just how much longer calorie restriction might help humans live, but those who practice the strict diet hope to survive past 100 years old. [Physorg.com, 4/15/10]
Hubble Space Telescope clocks up 20 years: It was an instrument that much of the astronomical community didn't want, but times change: to get time now on the Hubble Space Telescope, which is celebrating its 20th anniversary this week, an astronomer usually faces competition from at least 11 other eager scientists. [Nature News, 4/22/10]
Origin of Life Chicken-and-Egg Problem Solved: Scientists have wondered how the first simple, self-replicating chemicals could have formed complex, information-rich genetic structures, when replication was originally such an error-prone process. Every advance would soon be lost to copying errors. According to a new study, the answer may lie in the fundamental nature of those chemicals. The errors may have triggered an automatic shutdown of replication. Such stalling would allow only error-free sequences to be completed, giving them a chance at evolving. [Wired, 4/22/10]
A Skeptic Questions Cancer Genome Projects: Fueled by hundreds of millions of grant dollars, biomedical researchers have begun sequencing the genomes of thousands of tumor samples in the past few years, linking up scores of labs and sequencing centers in a massive effort to identify the genes behind major cancers. But a leading cancer geneticist this week questioned whether this strategy still makes sense. [ScienceInsider, 4/23/10]
Black holes and qubits: While string theory and M-theory have yet to make readily testable predictions in high-energy physics, they could find practical applications in quantum-information theory. [CERN Courier, 5/5/10]
Neutrinos: Clues to the Most Energetic Cosmic Rays: ARIANNA, a proposed array of detectors for capturing the most energetic cosmic rays, is being tested in Antarctica with a prototype station built last December on the Ross Ice Shelf by a Berkeley Lab team. By detecting neutrino-generated signals bounced off the interface of water and ice beneath the shelf, scientists hope to pinpoint the still unidentified sources of ultra-high-energy cosmic rays. [Physorg.com, 4/20/10]
In praise of the Y chromosome: David Page, director of the Whitehead Institute and professor of biology at Massachusetts Institute of Technology, says research indicates the much-maligned Y chromosome plays a more critical role in genetics than previously believed. [Physorg.com, 4/20/10]
The Evolution of the End: Immortality comes with some fairly significant disadvantages. A large complex organism requires a good bit of resources and the environment offers only so many available niches in which organisms of a set design can live. If the landscape is already saturated by unaging oldsters doing their timeless thing, there's little room for new and at least possibly improved models to take the stage. For most organisms, the areas where life is most tenuous is at the ends; both predators and disease take the hardest toll on the very young and the very old. If there are no old, then additional stress could be placed on the newcomers, further cutting turnover in a population. That means little chance for newbies, with their occasional mutations and interesting new combinations of genes. For immortals, evolution runs in slow motion. [Daily Kos, 5/30/10]
The Rise of the Mind: When and where did the cognitive abilities of modern humans arise? It's a big question -- one debated by anthropologists for decades. It's an even bigger question for an undergraduate thesis, but senior Logan Bartram has a leg up on this ambitious project: he helped unearth artifacts that are playing a critical role in shaping our knowledge about human origins. [Physorg.com, 4/22/10]
Airport security: Intent to deceive?: To Honts, the decade since the 11 September attacks has been one of lost opportunity. Calling SPOT an "abject failure", he says that the government would have done better to invest first in basic science, experimentally establishing how people with malintent think and respond during screenings. That work, in turn, could have laid a more solid foundation for effective detection methods. [Nature News, 5/26/10]

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Saturday, May 08, 2010

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]