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Dec 26

2010: The year in which …

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Reported by Adam Mann in Nature News, published online 22 December 2010 | Nature 468, 1014-1016 (2010) | doi:10.1038/4681014a

Natural disasters pummelled Earth

In a year marked by environmental disasters, Pakistan was perhaps hardest hit, as a flood affected an estimated 20 million people.Reuters/A. Soomro

In January, a magnitude- 7.0 earthquake struck Haiti — the most violent such event to strike the impoverished nation in a century. An estimated 230,000 people died and a further 1 million were left homeless. Other earthquakes, including a magnitude-8.8 quake in Chile in February and a magnitude 7.1 in New Zealand in September, also caused widespread damage, but smaller death tolls. Ash from the eruption of volcano Eyjafjallajökull in Iceland grounded commercial flights across Europe for a week in April, stranding thousands of travellers (see ‘Quotes of the year’). And unusually intense rains related to the La Niña cooling of the Pacific Ocean flooded one-fifth of Pakistan and affected an estimated 20 million people. The weather pattern was also implicated in a drought in Russia as the country experienced the hottest summer in its recorded history, unleashing hundreds of deadly wildfires.

Ancient kissing cousins were found

Two reports suggested that modern man carries genes from extinct branches of the human family tree. The question of whether Neanderthals, which went extinct about 30,000 years ago, ever mated with humans had been hotly debated, but evidence had been sparse. Even the sequencing of the Neanderthal genome in 2009 provided no definitive evidence. On 7 May, researchers announced the results of a genetic analysis of nearly 2,000 people from around the world, which yielded signs of gene flow between Neanderthals and Homo sapiens around the time that modern humans first migrated out of Africa some 50,000–60,000 years ago. Evidence of more recent mixing appears in this issue of Nature. A genome extracted from a 30,000–50,000 year-old finger bone found in a Siberian cave not only attests to the existence of another hominin group, but suggests that the group interbred with a particular band of human migrants that were ancestors of today’s Melanesians (see pages 1012, 1044 & 1053).

Doctors gained new weapons against HIV

In July, researchers revealed that an antiretroviral microbicide gel cut HIV infection by up to 54% in women who used it regularly. The findings, which came from a study of about 900 South African women at high risk of infection, gave hope to those seeking to bring down the rate of HIV infection in sub-Saharan Africa, where the majority of new cases occur. Another breakthrough came in November, when a study of nearly 2,500 men showed that the antiretroviral drug Truvada is an effective preventative measure. Among men who have sex with men, those who took the drug consistently lowered their risk of acquiring the virus by 73%.

Scientists unveiled a synthetic genome

In a bold step towards designer life, researchers at the J. Craig Venter Institute in Rockville, Maryland, announced on 20 May that an artificial genome inserted into a bacterium had successfully commandeered the cell and commenced replication. Using the genome from the bacterium Mycoplasma mycoides as a blueprint, Daniel Gibson and his colleagues at the institute assembled their synthetic genome in a yeast cell and transplanted it into the closely related species Mycoplasma capricolum. Although the 1.1-million-base-pair sequence was a near duplicate of M. mycoides, it included four special ‘watermark sequences’ to distinguish it from the original, as well as a hidden code that, once deciphered, included a website address and several famous quotes. Some researchers considered the move to be a significant advance over conventional genetic engineering, although others argued that scientists are a long way from being able to design and construct novel bacteria from scratch. If the technology advances sufficiently, many hope that artificial life can be used for a variety of tasks, including carbon sequestration, biofuel production or the clean-up of chemicals.

Climate-change policy stalled

Rajendra Pachauri felt the heat in 2010.M. Villagran/Getty Images

Efforts to confront climate change stumbled early on, but finished the year on a positive note. In January, the Intergovernmental Panel on Climate Change, chaired by Rajendra Pachauri, was embarrassed to learn that a 2007 report had erred when it stated that all glaciers in the central and eastern Himalayas could melt by 2035. The claim had not come from peer-reviewed scientific literature, but from a comment by Indian glaciologist Syed Hasnain in a 1999 article in New Scientist, and the mistake provided fodder for climate-change sceptics. Over the summer, three US senators — John Kerry (Democrat, Massachusetts), Joseph Lieberman (Independent, Connecticut) and Lindsey Graham (Republican, South Carolina) — failed to push through a bill that would have instituted a cap-and-trade system for domestic industry’s carbon emissions, even though the House of Representatives had approved a similar bill. The end-of-the-year United Nations Framework Convention on Climate Change meeting in Cancún, Mexico, brought some good news when participants agreed to set a goal of limiting average warming to 2 °C above preindustrial levels. Building on the ultimately unsuccessful Copenhagen Accord from last year, countries also created an international tracking system to report progress on lowering emissions.

Oil gushed into the Gulf of Mexico

On 20 April, an explosion on BP’s Deepwater Horizon oil rig killed 11 workers and precipitated one of the worst oil spills in history. By August, the damaged well had dumped nearly 5 million barrels of oil into the Gulf of Mexico, spewing as much as 62,000 barrels a day at its peak. Engineers capped the well on 15 July, although it was not permanently sealed with cement until 19 September. During the spill, researchers detected large plumes of oil below the water’s surface. In its aftermath, debate continued over where all the oil had gone. An estimate released by the US National Oceanic and Atmospheric Administration, which suggested that about half of the oil had dispersed, dissolved or evaporated, was roundly criticized as too optimistic. Later, researchers discovered a layer of precipitated oil on the sea floor (see page 1024).

Stem-cell research rode a roller coaster

US scientists were jolted on 23 August when federal district court judge Royce Lamberth placed an injunction on federally funded human embryonic stem-cell research. The move also overrode the March 2009 executive order of US President Barack Obama mandating the National Institutes of Health to develop a policy for the approval of new stem-cell lines, which had been prohibited under the administration of George W. Bush. The injunction was to remain in force until Judge Lamberth decided whether the research violates the Dickey–Wicker Amendment, which prohibits the destruction of human embryos in research. But on 9 September, the US Court of Appeals for the District of Columbia Circuit issued a stay on the injunction, allowing federal funding to continue until the court rules on whether Lamberth’s injunction should stand. Some federal stem-cell research resumed, but scientists are braced for more setbacks. Unless federal law is changed, many say the argument will ultimately find its way to the Supreme Court.

Japan’s space agency had a hit and a miss

A Japanese capsule bearing asteroidal dust is recovered in Australia.AP Photo/JAXA

On 16 November, researchers confirmed that micrometre-sized grains found in the Japan Aerospace Exploration Agency’s Hayabusa spacecraft were authentic asteroid dust. The mission, which gently kissed the surface of the Itokawa asteroid twice in November 2005, is the first to retrieve asteroidal material and return it to Earth for study. A month later the agency experienced a setback when its Akatsuki spacecraft failed to enter orbit around Venus, instead sailing past the planet into interplanetary space. Akatsuki, which would have mapped Venus using infrared cameras that can peer beneath its dense cloud layer and search for evidence of recent volcanic activity, will have to orbit the Sun and wait six more years for another try.

Astronomers joined the dark side

In August, US astronomers released the Astro2010 Decadal Survey, a highly influential document that, once every ten years, recommends which astronomy and astrophysics projects NASA, the National Science Foundation and the Department of Energy should fund. Acknowledging the prospect of budget cuts during the economic downturn, the report recommended a few large, expensive projects — such as the US$1.6-billion Wide Field Infrared Survey Telescope (WFIRST), a 1.5-metre space-based instrument that could investigate dark energy, the mysterious phenomenon that is causing the expansion of the Universe to accelerate. But November brought unwelcome news: a report commissioned by Senator Barbara Mikulski (Democrat, Maryland) concluded that the 6.5-metre James Webb Space Telescope, successor to the Hubble, would come in at least $1.5 billion over budget and would be delayed for more than a year. This implicit expected drain on NASA’s budget leaves funding for WFIRST an open question.

The budget crunch hit European science

Austerity measures across many European countries stricken by the financial crisis took a toll on scientists. The five member states contributing to CERN, Europe’s particle-physics laboratory near Geneva, Switzerland, approved a plan in September to reduce contributions by about $140 million over the next five years and to slow down the pace of smaller research projects to protect the lab’s flagship Large Hadron Collider, the world’s largest particle accelerator. And Italy and Britain said they will temporarily reduce their contributions to the European Synchrotron Radiation Facility in Grenoble, France. Other countries, looking to slash their budgets, announced freezes or reductions in scientific investments; for example, the Spanish government’s expenditure in research and development will drop by 8.37% next year. In October, UK scientists fought back against the funding cuts, rallying to protest in London. Eventually, the British government decided not to reduce science spending and agreed to protect the £4.6 billion (US$7.3 billion) core science budget over the next four years (see page 1010).

Arsenic-based life was discovered. Or not.

A cryptic announcement from NASA in November said that the agency had important astrobiology news, leading many to speculate that it was set to unveil extraterrestrial life. Instead, during a media conference on 2 December, researchers announced the discovery of ordinary earthly bacteria from Mono Lake in California that seemed to do something extraordinary — use arsenic as a building block for DNA and proteins, in place of the phosphorus relied on by other organisms. But as soon as the unprecedented finding was made public, it drew sharp criticism from the scientific community. Biochemists took to the blogosphere, attacking the methodology and assumptions of the original research and provoking a flurry of articles in the media. Further work will be needed to settle whether the bacteria actually do use arsenic in their biochemistry as opposed to just cleverly thwarting its toxic effects.

A morality expert was accused of mischief

In August, Harvard University found that Marc Hauser, a leader in the field of animal and human cognition, had committed eight counts of scientific misconduct. Hauser studies the evolutionary origin of characteristics such as morality, language and mathematical ability, and his work has been profiled in many news outlets, such as The New York Times and the Wall Street Journal. Many scientists in the field called on Harvard to release the details of its investigation, saying that they could affect any research that uses Hauser’s as a basis. As yet, Harvard has not done this. Hauser has retracted or amended at least three papers, which appeared in Cognition, Proceedings of the Royal Society and Science, respectively.

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Dec 25

Early Reports From the ‘Dark Matter’ of the Genome.

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Reported by Brandon Keim, December 22, 201, in Wired Science.

A visualization of physical chromosome arrangement (left) and histone modification readings (right) at a given DNA base location (the green dot). Peter Park/Harvard University.

A collection of new studies on the genomes of two model organisms has moved the frontiers of biology forward, and hints at methods that may someday make real the long-promised, as-yet-unfulfilled genomic revolution.

Published in Nature and Science, the studies go far beyond the level of genes that code for proteins, which represent just a small fraction of all genes and an even smaller fraction of all DNA in the genome.

Once thought to contain the blueprint of life, protein-coding genes were just the most visible ink in a parts list. The new studies both expand that list and begin to show how the parts are arranged — and how they interact.

“It’s become very clear that DNA sequences are just a building block. They don’t explain higher-order complexity,” said Peter Park, a Harvard University bioinformaticist and co-author of one of the Nature studies. “People are sequencing all these genomes, but it doesn’t actually tell us about the activities of the cell.”

Park is a contributor to modENCODE, short for the model organism ENCyclopedia of DNA Elements, a massive international collaboration of dozens of institutions and hundreds of researchers. They study an alphabet soup of transcription factors, messengers, regulators and other types of DNA that interact with protein-coding genes to sustain the processes of life.

It’s an effort that few people thought necessary a decade ago, when the Human Genome Project’s near-completion was marked by a White House ceremony where President Clinton announced that “it will revolutionize the diagnosis, prevention and treatment of most, if not all, human diseases,” and that “humankind is on the verge of gaining immense, new power to heal.”

That may very well still happen, but not on the timetable that many scientists expected. With some exceptions, such as breast-cancer-susceptibility mutations and single-gene conditions like Huntington’s disease and Marfan syndrome, identifiable genetic variation has done relatively little to explain disease or development. Promising pathways and mechanisms have been flagged and are now being explored, but understanding is slow in coming.

Over the past two years, a series of high-profile genome-wide association tests (comparisons of variation at genomic “hotspots” in thousands of people) suggested new pathways. But they didn’t provide anticipated explanations for disease, and the limitations of standard genomics entered the scientific mainstream. Discussions of “missing heritability,” or the roughly 95 percent of disease risk that’s heritable to the naked eye but can’t be tagged in a sequencer, appeared in the New England Journal of Medicine and Nature.

All this represented not a failure, but a dawning realization of just how extraordinarily complicated each genome is. As the process of learning builds on the Human Genome Project’s early steps, researchers are taking fine-grained looks at each genome’s full DNA and chemical components, then trying to understand how all these work together at different scales, from molecules to cells to whole organisms.

“The goal of modENCODE is to identify all the functional elements in the genome, and to understand what the genome is doing, which is the next step beyond knowing the sequence,” said Brenton Graveley, a University of Connecticut development biologist.

An overview of datasets for the fruit fly section of modENCODE. Image: Science

In one of the Nature papers, Graveley and dozens of other researchers used new DNA-sequencing techniques to take a base-by-base look at the fruit fly genome, hoping to identify pieces missed in earlier studies. (He compared earlier examinations to “going into a grocery store and not thinking bananas were a fruit, because you the only fruit you know are apples.”)

They identified 2,000 previously unknown genes, which now account for one-eighth of the fruit fly’s genome. Beyond that, they identified more than 100,000 new elements, or molecules that aren’t genes but may still have function in the genome. In fruit flies, about 40 percent of the genome fits this description. In humans, it’s closer to two-thirds.

The second Nature study looked at non-DNA chemical “information” on the genome, which is made from chromatin: DNA wrapped around proteins called histones, and combined with still more proteins, all of which affect how the DNA works.

This approach is known from epigenetics (epi means outside) but the new examination was unprecedentedly thorough, looking at dozens of epigenetic factors, at every single DNA base. The resulting “chromatin landscape” revealed regions that once seemed dead, but now appear involved in gene regulation. It’s also just a beginning.

“At each location on the sequence, we can measure all these different attributes of chromatin. There are hundreds of attributes, and we only now know what a couple of dozen do,” said Park. “How these marks translate into gene regulation is important. Right now we just see correlations. We don’t necessarily understand the mechanisms behind this.”

A streamlined representation of the interplay between transcription factors and microRNAs in the roundworm. Image: Science

Such mechanisms, and how genetic elements and regulatory layers interact as cells function and organisms develop, is the province of the two Science papers. These provide network-level analyses, or “wiring diagrams,” of the fruit fly and roundworm, said Yale University bioinformaticist Mark Gerstein, co-author of the roundworm paper.

Gerstein’s specialty is network structure. In other research he’s compared the characteristics of gene networks between organisms, and even between bacteria and computer operating systems. That work has hinted at the importance of network structure to producing wildly different organisms from common genetic components. (Humans and mice famously share almost the same set of genes.)

“Previously, people had looked at transcription factor networks in E. coli and yeast, but nobody had ever looked at this scale of network in an animal,” said Gerstein. “You can start to see patterns: a microRNA that regulates a transcription factor, transcription factor that regulates microRNA, a feedback loop. We observe many of these.”

In a commentary accompanying the Science papers, University of Edinburgh geneticist Mark Blaxter likened modENCODE to the Large Hadron Collider, investigating the nature of the genome’s “dark matter.”

“It is not currently possible to compute an organism from its genome,” he wrote, but the modENCODE work will “bring this goal closer.”

Despite the volume of the studies, joined by 17 more studies released in tandem in the Journal of Genome Research, the modENCODE work is just beginning. “We’re looking at a vast amount of data. We’re just scratching the surface,” said Park. Future studies will look in greater detail at different tissue types and stages of development.

The modENCODE work is also considered a warm-up for a similar project in humans, called ENCODE. It should generate comparable findings in the next two years.

“There remains much to be discovered to be discovered even about organisms that are as exhaustively studied as the fruit fly,” said Graveley. “In organisms like humans, there are undoubtedly many, many more mysteries to be uncovered.”

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Dec 25

Quantum dots are not dots: physicists

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Reported in PhysOrg, 21 December 2010 and provided by University of Copenhagen.

Researchers from the Quantum Photonics Group at DTU Fotonik in collaboration with the Niels Bohr Institute, University of Copenhagen surprise the scientific world with the discovery that light emission from solid-state photon emitters, the so-called quantum dots, is fundamentally different than hitherto believed. The new insight may find important applications as a way to improve efficiency of quantum information devices. Their findings are published on December 19th 2010 in Nature Physics.

Quantum dots are solid-state "artificial atoms" that are made up of thousands of atoms (yellow spheres) embedded in a semiconductor (blue spheres). Despite this complexity, the photon emission properties of quantum dots were hitherto believed to be like traditional atoms, where a point-emitter description is sufficient. Due to their mesoscopic dimensions, however, the point-emitter description is revealed to break down by comparing photon emission from quantum dots with opposite orientations relative to a metallic mirror.

Today it is possible to fabricate and tailor highly efficient light sources that emit a single photon at a time, which constitutes the fundamental unit of light. Such emitters are referred to as quantum dots and consist of thousands of atoms. Despite the expectations reflected in this terminology, quantum dots cannot be described as point sources of light, which leads to the surprising conclusion: quantum dots are not dots!

This new insight was realized by experimentally recording photon emission from quantum dots positioned close to a metallic mirror. Point sources of light have the same properties whether or not they are flipped upside down, and this was expected to be the case for quantum dots as well. However, this fundamental symmetry was found to be violated in the experiments at DTU where a very pronounced dependence of the photon emission on the orientation of the quantum dots was observed.

The experimental findings are in excellent agreement with a new theory of light-matter interaction developed by DTU-researchers in collaboration with Anders S. Sørensen from the Niels Bohr Institute. The theory takes the spatial extent of quantum dots into account.

At the metal mirror surface, highly confined optical surface modes exist; the so-called plasmons. Plasmonics is a very active and promising research field, and the strong confinement of photons, available in plasmonics, may have applications for science or solar energy harvesting. The strong confinement of plasmons also implies that from quantum dots can be strongly altered, and that quantum dots can excite plasmons with very large probability. The present work demonstrates that the excitation of plasmons can be even more efficient than previously thought. Thus the fact that quantum dots are extended over areas much larger than atomic dimensions implies that they can interact more efficiently with plasmons.

The work may pave the way for new nanophotonic devices that exploit the spatial extent of as a novel resource. The new effect is expected to be important also in other research areas than plasmonics, including photonic crystals, cavity quantum electrodynamics, and light harvesting.

More information: Article in Nature Physics: … 38/NPHYS1870

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Dec 21

Quantum or not? Mathematical equations resolve nanostructures behavior.

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Reported by PhysOrg in December 17, 2010.

Understanding the transport of electrons in nanostructures and biological molecules is crucial to understanding properties such as electrical conductivity or the biochemical behavior of molecules. However, determining whether the electrons are behaving according to the classical laws of motion or the quantum mechanical regime at the nanoscale is challenging because many nanostructures fall in a grey area between both regimes. Japanese researchers from the RIKEN Advanced Science Institute in Wako, with colleagues from Germany and Taiwan, have now devised a set of mathematical equations that can distinguish classical from quantum mechanical behavior of electrons in nanostructures.

In a game of billiards, the path of each ball is determined by the classical laws of motion. At the microscopic scale, equivalent objects may be governed by quantum mechanics, such that their exact path of movement could take several directions. Credit: 2010 iStockphoto/JamesBrey

On a , objects follow the classical laws of motion. Golf or billiard balls, for example, will follow exact, predictable paths. On a , objects such as electrons move according to the laws of quantum mechanics, where processes occur in a probabilistic manner. Measuring the properties of quantum mechanical systems, however, is challenging.

“In microscopic systems, it is very difficult to perform ideal measurements without disturbing the system,” explains Neill Lambert from the research team. As a consequence, measurements on quantum mechanical systems are difficult to distinguish from invasive measurements on classical systems, says Franco Nori from RIKEN and the University of Michigan, who led the research team. “It is important to be confident that experimental results are not originating from a classical effect, giving a false impression of quantum behavior.”

As a model system, the researchers chose the transport of electrons through vanishingly small pieces of matter known as . “Even measuring the current passing through a quantum dot represents an invasive measurement of the system,” Lambert notes. To identify quantum effects, he and his colleagues developed a set of criteria expressed as a mathematical inequality relationship for experimental data from these quantum dots. Any excess over a critical threshold in the formula by a parameter represents a clear sign of quantum behavior. In their simulations the researchers found several regimes at low temperatures where quantum effects in the dynamics of electrons in the quantum dots should occur.

The inequality relation derived by the researchers is based on fundamental principles and therefore applies not only to the transport of electrons through quantum dots, but also to many open, microscopic electron transport systems, says Nori. He believes that it will soon be easier to determine whether electrons in nanostructures follow the rules of or take the classical route of their billiard-ball counterparts.

More information: Lambert, N., et al. Distinguishing quantum and classical transport through nanostructures. Physical Review Letters 105, 176801 (2010) . See the article here: … /i17/e176801 .

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Dec 18

Science’s Breakthrough of the Year: The First Quantum Machine.

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Reported by ScienceDaily (Dec. 17, 2010).

Until this year, all human-made objects have moved according to the laws of classical mechanics. Back in March, however, a group of researchers designed a gadget that moves in ways that can only be described by quantum mechanics — the set of rules that governs the behavior of tiny things like molecules, atoms, and subatomic particles. In recognition of the conceptual ground their experiment breaks, the ingenuity behind it and its many potential applications, Science has called this discovery the most significant scientific advance of 2010.

Science's Breakthrough of the Year goes to the first mechanical, vibrating device, which is as long as a hair is wide. The device is the first to reach the quantum ground state, a feat achieved by physicists at the University of California, Santa Barbara. (Credit: Aaron D. O’Connell and Andrew N. Cleland/University of California, Santa Barbara)

Physicists Andrew Cleland and John Martinis from the University of California at Santa Barbara and their colleagues designed the machine — a tiny metal paddle of semiconductor, visible to the naked eye — and coaxed it into dancing with a quantum groove. First, they cooled the paddle until it reached its “ground state,” or the lowest energy state permitted by the laws of quantum mechanics (a goal long-sought by physicists). Then they raised the widget’s energy by a single quantum to produce a purely quantum-mechanical state of motion. They even managed to put the gadget in both states at once, so that it literally vibrated a little and a lot at the same time — a bizarre phenomenon allowed by the weird rules of quantum mechanics.

Science and its publisher, AAAS, the nonprofit science society, have recognized this first quantum machine as the 2010 Breakthrough of the Year. They have also compiled nine other important scientific accomplishments from this past year into a top ten list, appearing in a special news feature in the journal’s 17 December 2010 issue. Additionally, Science news writers and editors have chosen to spotlight 10 “Insights of the Decade” that have transformed the landscape of science in the 21st Century.

“This year’s Breakthrough of the Year represents the first time that scientists have demonstrated quantum effects in the motion of a human-made object,” said Adrian Cho, a news writer for Science. “On a conceptual level that’s cool because it extends quantum mechanics into a whole new realm. On a practical level, it opens up a variety of possibilities ranging from new experiments that meld quantum control over light, electrical currents and motion to, perhaps someday, tests of the bounds of quantum mechanics and our sense of reality.”

The quantum machine proves that the principles of quantum mechanics can apply to the motion of macroscopic objects, as well as atomic and subatomic particles. It provides the key first step toward gaining complete control over an object’s vibrations at the quantum level. Such control over the motion of an engineered device should allow scientists to manipulate those minuscule movements, much as they now control electrical currents and particles of light. In turn, that capability may lead to new devices to control the quantum states of light, ultra-sensitive force detectors and, ultimately, investigations into the bounds of quantum mechanics and our sense of reality. (This last grand goal might be achieved by trying to put a macroscopic object in a state in which it’s literally in two slightly different places at the same time — an experiment that might reveal precisely why something as big as a human can’t be in two places at the same time.)

“Mind you, physicists still haven’t achieved a two-places-at-once state with a tiny object like this one,” said Cho. “But now that they have reached the simplest state of quantum motion, it seems a whole lot more obtainable — more like a matter of ‘when’ than ‘if.'”

Science’s list of the nine other groundbreaking achievements from 2010 follows.

Synthetic Biology: In a defining moment for biology and biotechnology, researchers built a synthetic genome and used it to transform the identity of a bacterium. The genome replaced the bacterium’s DNA so that it produced a new set of proteins — an achievement that prompted a Congressional hearing on synthetic biology. In the future, researchers envision synthetic genomes that are custom-built to generate biofuels, pharmaceuticals or other useful chemicals.

Neandertal Genome: Researchers sequenced the Neandertal genome from the bones of three female Neandertals who lived in Croatia sometime between 38,000 and 44,000 years ago. New methods of sequencing degraded fragments of DNA allowed scientists to make the first direct comparisons between the modern human genome and that of our Neandertal ancestors.

HIV Prophylaxis: Two HIV prevention trials of different, novel strategies reported unequivocal success: A vaginal gel that contains the anti-HIV drug tenofovir reduced HIV infections in women by 39 percent and an oral pre-exposure prophylaxis led to 43.8 fewer HIV infections in a group of men and transgender women who have sex with men.

Exome Sequencing/Rare Disease Genes: By sequencing just the exons of a genome, or the tiny portion that actually codes for proteins, researchers who study rare inherited diseases caused by a single, flawed gene were able to identify specific mutations underlying at least a dozen diseases.

Molecular Dynamics Simulations: Simulating the gyrations that proteins make as they fold has been a combinatorial nightmare. Now, researchers have harnessed the power of one of the world’s most powerful computers to track the motions of atoms in a small, folding protein for a length of time 100 times longer than any previous efforts.

Quantum Simulator: To describe what they see in the lab, physicists cook up theories based on equations. Those equations can be fiendishly hard to solve. This year, though, researchers found a short-cut by making quantum simulators — artificial crystals in which spots of laser light play the role of ions and atoms trapped in the light stand in for electrons. The devices provide quick answers to theoretical problems in condensed matter physics and they might eventually help solve mysteries such as superconductivity.

Next-Generation Genomics: Faster and cheaper sequencing technologies are enabling very large-scale studies of both ancient and modern DNA. The 1,000 Genomes Project, for example, has already identified much of the genome variation that makes us uniquely human — and other projects in the works are set to reveal much more of the genome’s function.

RNA Reprogramming: Reprogramming cells — turning back their developmental clocks to make them behave like unspecialized “stem cells” in an embryo — has become a standard lab technique for studying diseases and development. This year, researchers found a way to do it using synthetic RNA. Compared with previous methods, the new technique is twice as fast, 100 times as efficient and potentially safer for therapeutic use.

The Return of the Rat: Mice rule the world of laboratory animals, but for many purposes researchers would rather use rats. Rats are easier to work with and anatomically more similar to human beings; their big drawback is that methods used to make “knockout mice” — animals tailored for research by having specific genes precisely disabled — don’t work for rats. A flurry of research this year, however, promises to bring “knockout rats” to labs in a big way.

Finally, to celebrate the end of the current decade, Science news reporters and editors have taken a step back from their weekly reporting to take a broader look at 10 of the scientific insights that have changed the face of science since the dawn of the new millennium. A list of these 10 “Insights of the Decade” follows.

The Dark Genome: Genes used to get all the glory. Now, however, researchers recognize that these protein-coding regions of the genome account for just 1.5 percent of the whole. The rest of the genome, including small coding and non-coding RNAs — previously written off as “junk” — is proving to be just as important as the genes.

Precision Cosmology: Over the past decade, researchers have deduced a very precise recipe for the content of the universe, which consists of ordinary matter, dark matter and dark energy; as well as instructions for putting it all together. These advances have transformed cosmology into a precision science with a standard theory that now leaves very little wiggle room for other ideas.

Ancient Biomolecules: The realization that “biomolecules” like ancient DNA and collagen can survive for tens of thousands of years and provide important information about long-dead plants, animals and humans has provided a boon for paleontology. Analysis of these tiny time machines can now reveal anatomical adaptations that skeletal evidence simply can’t provide, such as the color of a dinosaur’s feathers or how woolly mammoths withstood the cold.

Water on Mars: Half a dozen missions to Mars over the past decade have provided clear evidence that the Red Planet once harbored enough water — either on it or just inside it — to alter rock formations and, possibly, sustain life. This Martian water was probably present around the time that life was beginning to appear on Earth, but there is still enough moisture on Mars today to encourage scientists seeking living, breathing microbes.

Reprogramming Cells: During the past decade, the notion that development is a one-way street has been turned on its head. Now, researchers have figured out how to “reprogram” fully developed cells into so-called pluripotent cells that regain their potential to become any type of cell in the body. This technique has already been used to make cell lines from patients with rare diseases, but ultimately, scientists hope to grow genetically matched replacement cells, tissues and organs.

The Microbiome: A major shift in the way we view the microbes and viruses that call the human body home has led researchers to the concept of the microbiome — or the collective genomes of the host and the other creatures that live on or inside it. Since 90 percent of the cells in our bodies are actually microbial, scientists are beginning to understand how significantly microbial genes can affect how much energy we absorb from our foods and how our immune systems respond to infections.

Exoplanets: In the year 2000, researchers were aware of just 26 planets outside our solar system. By 2010, that number had jumped to 502 — and still counting. With emerging technologies, astronomers expect to find abundant Earth-like planets in the universe. But for now, the sizes and orbits of larger planets already discovered are revolutionizing scientists’ understanding of how planetary systems form and evolve.

Inflammation: Not long ago, inflammation was known as the simple sidekick to our healing machinery, briefly setting in to help immune cells rebuild tissue damage caused by trauma or infection. Today, however, researchers believe that inflammation is also a driving force behind the chronic diseases that will eventually kill nearly all of us, including cancer, Alzheimer’s disease, atherosclerosis, diabetes and obesity.

Metamaterials: By synthesizing materials with unconventional and tunable optical properties, physicists and engineers have pioneered new ways to guide and manipulate light, creating lenses that defy the fundamental limits on resolution. They’ve even begun constructing “cloaks” that can make an object invisible.

Climate Change: Over the past decade, researchers have solidified some fundamental facts surrounding global climate change: The world is warming, humans are behind the warming and the natural processes of the Earth are not likely to slow that warming. But, the next 10 years will determine how scientists and policymakers proceed with this vital information.

Story Source:

The above story is reprinted (with editorial adaptations by ScienceDaily staff) from materials provided by American Association for the Advancement of Science.

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Dec 17

Physics Getting Freaky on Bed of Nails.

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Reported by Brandon Keim in Wired Science, December 15, 2010.

As-yet-unexplained laws of physics keep popping up in the darnedest places, like, for example, this bed of nails.

Perfectly arrayed in horizontal rows, one would expect their pattern to break down when shaken. But as this stop-motion video shows, they lose pattern in a very orderly way.

The video was taken by T. Lynn MacDonald, a student in the lab of University of Toronto physicist Stephen Morris. His specialty is experimental nonlinear physics, investigating how and why patterns emerge in interacting particles. Whether the particles are water molecules, grains of sand, inch-long nails or stars is just a matter of scale.

Morris’ lab received plenty of attention this year, first for research on theories of icicle formation and then for a “Supernova in a Jar.” Flying under the radar was MacDonald’s as-yet-unpublished work on nails, which shows them collectively transformed in a way typically seen when heat transforms crystal to liquid.

By shaking the bed of nails, “we ‘melt’ it,” wrote Morris in an email.

The observations represent an early research stage, with fuller investigations to come. “The emergence of collective behavior is exactly the point of the experiment,” wrote Morris. The experiment also hints at a non-scientific truth, articulated by mathematician Henri Poincaré and epigraphed on Morris’ website:

“The scientist does not study nature because it is useful; he studies it because he delights in it, and he delights in it because it is beautiful,” wrote Poincaré.

Video: Melting a liquid of nails: A perfectly ordered array of  nails “metls” like a crystal turns into a liquid. Credit: by T. Lynn MacDonald & Stephen Morris, University of Toronto.

Read more in “Pattern Formation in Vertically Vibrated Nails,” by T. Lynn MacDonald. Unpublished, available online (pdf).

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Dec 17

Using chaos to model geophysical phenomena.

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Provided by American Institute of Physics and read in PhysOrg.

Geophysical phenomena such as the dynamics of the atmosphere and ocean circulation are typically modeled mathematically by tracking the motion of air or water particles. These mathematical models define velocity fields that, given (i) a position in three-dimensional space and (ii) a time instant, provide a speed and direction for a particle at that position and time instant.

Geophysical phenomena are still not fully understood, especially in turbulent regimes,” explains Gary Froyland at the School of Mathematics and Statistics and the Australian Research Council Centre of Excellence for Mathematics and Statistics of Complex Systems (MASCOS) at the University of New South Wales in Australia.

“Nevertheless, it is very important that scientists can quantify the ‘transport’ properties of these geophysical systems: Put very simply, how does a packet of air or water get from A to B, and how large are these packets? An example of one of these packets is the Antarctic polar vortex, a rotating mass of air in the stratosphere above Antarctica that traps chemicals such as ozone and chlorofluorocarbons (CFCs), exacerbating the effect of the CFCs on the ,” Froyland says.

In the American Institute of Physics’ journal CHAOS, Froyland and his research team, including colleague Adam Monahan from the School of Earth and Ocean Sciences at the University of Victoria in Canada, describe how they developed the first direct approach for identifying these packets, called “coherent sets” due to their nondispersive properties.

These two images show that the most "coherent set," the most nondispersive transport time from Sept. 1 to Sept. 14, is in fact the vortex itself over this domain -- demonstrating that the new technique very accurately pinpoints the polar vortex at specific times. Credit: American Institute of Physics

This technique is based on so-called “transfer operators,” which represent a complete description of the ensemble evolution of the fluid. The transfer operator approach is very simple to implement, they say, requiring only singular vector computations of a matrix of transitions induced by the dynamics.

When tested using European Centre for Medium Range Weather Forecasting (ECMWF) data, they found that their new methodology was significantly better than existing technologies for identifying the location and transport properties of the vortex.

The transport operator methodology has myriad applications in atmospheric science and physical oceanography to discover the main transport pathways in the atmosphere and oceans, and to quantify the transport. “As atmosphere-ocean models continue to increase in resolution with improved computing power, the analysis and understanding of these models with techniques such as transfer operators must be undertaken beyond pure simulation,” says Froyland.

Their next application will be the Agulhas rings off the South African coast, because the rings are responsible for a significant amount of transport of warm water and salt between the Indian and Atlantic Oceans.

Read more: The article, “Transport in time-dependent dynamical systems: Finite-time coherent sets” by Gary Froyland, Naratip Santitissadeekorn, and Adam Monahan appears in the journal CHAOS. See: http://link.aip.or … 4/p043116/s1

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Dec 14

Designing a computer that can process and understand natural language.

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The DeepQA project at IBMResearch is helping to make computers smarter in their interaction with people.

IBM is working to build a computing system that can understand and answer complex questions with enough precision and speed to compete against some of the best Jeopardy! contestants out there.

This challenge is much more than a game. Jeopardy! demands knowledge of a broad range of topics including history, literature, politics, film, pop culture and science. What’s more, Jeopardy! clues involve irony, riddles, analyzing subtle meaning and other complexities at which humans excel and computers traditionally do not. This, along with the speed at which contestants have to answer, makes Jeopardy! an enormous challenge for computing systems.

Code-named “Watson” after IBM founder Thomas J. Watson, the IBM computing system is designed to rival the human mind’s ability to understand the actual meaning behind words, distinguish between relevant and irrelevant content, and ultimately, demonstrate confidence to deliver precise final answers.

Known as a Question Answering (QA) system among computer scientists, Watson has been under development for more than three years. According to Dr. David Ferrucci, leader of the project team, “The confidence processing ability is key to winning at Jeopardy! and is critical to implementing useful business applications of Question Answering.”

Watson will also incorporate massively parallel analytical capabilities and, just like human competitors, Watson will not be connected to the Internet, or have any other outside assistance.

If we can teach a computer to play Jeopardy!, what could it mean for science, finance, healthcare and business? By drastically advancing the field of automatic question answering, the Watson project’s ultimate success will be measured not by daily doubles, but by what it means for society.

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Dec 14

Sleepless honey bees miscommunicate, too, research shows.

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Provided by University of Texas at Austin (news : web)

In the busy world of a honey bee hive, worker bees need their rest in order to best communicate the location of food to their hive mates, research from The University of Texas at Austin shows.

To deprive honey bees of sleep, Dr. Barrett Klein used a magnetic contraption called the "insominator" (on the left). Sleeping bees affixed with a small piece of metal were jostled awake when the insominator passed over them. Klein found that sleeplessness led to poor signaling by foraging bees about the location of food sources. Credit: Dr. Barrett Klein,

“When deprived of sleep, humans typically experience a diminished ability to perform a variety of tasks, including communicating as clearly or as precisely,” said Dr. Barrett Klein, a former ecology, evolution and behavior graduate student at the university. “We found that sleep-deprived honey bees also experienced communication problems. They advertised the direction to a food site less precisely to their fellow bees.”

For humans, imprecise communication can reduce efficiency, cost money, and in some cases, cost lives. For honey bees, Klein says it could affect their success in locating food, which could lead to a less competitive colony.

“While the importance of sleep has been studied in Drosophila flies for several years,” said Dr. Ulrich Mueller, professor of biology and study coauthor, “Barrett’s study is the first to address the function of sleep in a social insect in the context of its society, and the first to show that sleep deprivation impairs precision of communication in an insect.”

This movie spotlights one waggle dance by a forager that had been sleep-deprived the previous night. The average dance angle of this dance is superimposed over the dancer and variance around this angle indicates imprecision of signaling direction information.

The research was published in PNAS Early Edition this week.

There are various ways to poke and prod humans to force them to stay awake prior to measuring the effects of sleep deprivation. But how to make bees in a hive lose sleep?

Klein invented a magnetic machine aptly named the “insominator,” a contraption he passed over quietly resting bees during the night to deprive them of sleep. The bees, outfitted with small metallic backpacks, were jostled into activity by magnets in the insominator, and this was repeated over the course of normal time.

Barrett then recorded the behaviors of the sleepless bees and discovered they weren’t able to communicate as well the direction of nectar-filled flower patches to their sisters through their usual waggle dance.

“The dance was not necessarily wrong, but it was less precise than dances performed by bees that were not sleep-deprived,” says Klein. “We expect that a less precise dance would lead to fewer followers making it to the food source, and we hope to test this in the future.”

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Dec 14

Turing machine…

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A Turing Machine in the classic style:

Wow: A Turing Machine in the classical style

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