Feb 21, 2015
Research at Rockefeller University described in Nature offers new insight into the mysterious process by which this system works to encode viral DNA in a microbe's genome for later use as guides for virus-cutting enzymes.
"Microbes, like vertebrates, have immune systems capable of adapting to new threats. Cas9, one enzyme employed by these systems, uses immunological memories to guide cuts to viral genetic code. However, very little is known about how these memories are acquired in the first place," says Assistant Professor Luciano Marraffini, head of the Laboratory of Bacteriology. "Our work shows that Cas9 also directs the formation of these memories among certain bacteria."
These memories are embedded in the bacterial equivalent of an adaptive immune system capable of discerning helpful from harmful viruses called a CRISPR (clustered regularly interspaced short palindromic repeats) system. It works by altering the bacterium's genome, adding short viral sequences called spacers in between the repeating DNA sequences. These spacers form the memories of past invaders. They serve as guides for enzymes encoded by CRISPR-associated genes (Cas), which seek out and destroy those same viruses should they attempt to infect the bacterium again.
Cas9's ability to make precision cuts within a genome -- viral or otherwise -- has caught the attention of researchers who now use it to alter cells' genetics for experimental or therapeutic purposes. But it is still not well understood just how this CRISPR system works in its native bacteria.
Some evidence suggested that other Cas enzymes managed the memory-making process on their own, without Cas9. But because of the way Cas9 goes about identifying the site at which to make a cut, the researchers, including co-first authors Robert Heler, a graduate student, and Poulami Samai, a postdoc in the lab, suspected a role for Cas9 in memory making.
In addition to matching its CRISPR guide sequence up with the DNA of the virus, Cas9 needs to find a second cue nearby: a PAM (protospacer adjacent motif) sequence in the viral DNA. This is a crucial step, since it is the absence of a PAM sequence that prevents Cas9 from attacking the bacterium's own memory-containing DNA.
"Because Cas9 must recognize a PAM sequence before cutting the viral DNA, it made sense to us that Cas9 would also recognize the PAM sequence when the system is forming a memory of its first encounter with a virus," Heler says. "This is a new and unexpected role for Cas9."
To test their hypothesis, Heler swapped the Cas9 enzymes between the immune systems of Streptococcus pyogenes and Streptococcus thermophilus, each of which recognizes a different PAM sequence. As a result, the PAM sequences followed, swapping between the two bugs -- evidence that Cas9 is responsible for identifying the PAM during memory formation. In another experiment, he altered the part of Cas9 that binds to the PAM sequence, and found the microbes then began acquiring the target viral sequences randomly, making them unusable.
Samai, meanwhile, looked at the relationship between Cas9 and three other Cas enzymes: Cas1, Cas2 and Csn2. Components of the same CRISPR system, these enzymes were already suspected to play a role in memory making without help from Cas9.
Read more at Science Daily
Previous research has shown that as modern cities grow in population, so do their efficiencies and productivity. A city’s population outpaces its development of urban infrastructure, for example, and its production of goods and services outpaces its population. What's more, these patterns exhibit a surprising degree of mathematical regularity and predictability, a phenomenon called "urban scaling."
But has this always been the case?
SFI Professor Luis Bettencourt researches urban dynamics as a lead investigator of SFI's Cities, Scaling, and Sustainability research program. When he gave a talk in 2013 on urban scaling theory, Scott Ortman, now an assistant professor in the Department of Anthropology at CU Boulder and a former Institute Omidyar Fellow, noted that the trends Bettencourt described were not particular to modern times. Their discussion prompted a research project on the effects of city size through history.
To test their ideas, the team examined archaeological data from the Basin of Mexico (what is now Mexico City and nearby regions). In the 1960s — before Mexico City’s population exploded — surveyors examined all its ancient settlements, spanning 2000 years and four cultural eras in pre-contact Mesoamerica.
Using this data, the research team analyzed the dimensions of hundreds of ancient temples and thousands of ancient houses to estimate populations and densities, size and construction rates of monuments and buildings, and intensity of site use.
Their results indicate that the bigger the ancient settlement, the more productive it was.
“It was shocking and unbelievable,” says Ortman. “We were raised on a steady diet telling us that, thanks to capitalism, industrialization, and democracy, the modern world is radically different from worlds of the past. What we found here is that the fundamental drivers of robust socioeconomic patterns in modern cities precede all that.”
Read more at Science Daily
Feb 20, 2015
Local rulers at the time likely used the shrines for divination, a practice aimed at predicting the future, the archaeologists involved in the discovery say.
Each of the three shrines consists of a single room holding a clay basin filled with ash and ceramic vessels. A wide variety of artifacts were discovered including clay idols with horns, stamp seals, censers used to burn substances and a vast amount of animal bones with markings on them. During divination practices, the rulers and diviners may have burnt some form of substances and drank wine, allowing them to experience "altered" states of mind, the archaeologists say.
"The logic of divination presumes that variable pathways articulate the past, present and future, opening the possibility that the link between a current situation and an eventual outcome might be altered," write Adam Smith and Jeffrey Leon, in an article published recently in the American Journal of Archaeology. Smith is a professor at Cornell University, and Leon is a graduate student there.
The fortress at Gegharot is one of several strongholds built at around this time in Armenia. "Evidence to date suggests that this coordinated process of fortress construction was part of the emergence of a single polity that built and occupied multiple sites in the region," write Smith and Leon.
Smith believes that Gegharot would have been used as an occult center for the rulers. "I would think that this is probably a cult center largely specializing in servicing the emerging rulers from the ruling class," he told Live Science in an interview.
At the time, writing had not yet spread to this part of Armenia so the name of the polity, and its rulers, are unknown.
Predicting the future
Smith and Leon found evidence for three forms of divination at Gegharot. One form was osteomancy, trying to predict the future through rituals involving animal bones, in this case the knucklebones of cows, sheep and goat.
The knucklebones, which were covered in burns and other markings, would have been rolled like dice in rituals attempting to predict the future, Smith said. "You would roll them and depending upon whether the scorched side or the marked side came up you would a different interpretation," Smith said.
Lithomancy, trying to predict the future through the use of stone, also appears to have been practiced at Gegharot. Inside a basin at one shrine, archaeologists found 18 small pebbles. "These stones appear to have been selected for their smooth, rounded shape and their color palette, which ranged from black and dark gray to white, green and red," Smith and Leon write. How exactly these unmarked stones would have been used in rituals is unknown.
Flour for the future?
At one shrine, on the fortress' east citadel, the archaeologists found an installation used to grind flour. Smith and Leon think that this flour could have been used to predict the future in a practice called aleuromancy.
"What is conspicuous about the grinding installation in the east citadel shrine is the lack of a formal oven for bread baking," Smith and Leon write. The shrine's basin "was clearly used for burning materials and certainly could have been used to bake small balls of dough, but it is unlikely that it would have been used to cook loaves of bread."
Stamp seals found at the shrine would have allowed people to punch a variety of shapes into dough. "One possibility (admittedly among many others) is that the stamps marked the dough that was then used for aleuromancy."
The shrines were in use for a century or so until the surrounding fortress, along with all the other fortresses in the area, were destroyed. The site was largely abandoned after this, Smith said.
At the time, there was a great deal of conflict in the south Caucasus with a number of regional polities fighting against each other, Smith said. The polity that controlled Gegharot seems to have been wiped out in one of those conflicts.
Although the rulers who controlled Gegharot put great effort into trying to predict and change the future, it was to no avail — their great fortresses being torched in a cataclysm they could not avoid.
Read more at Discovery News
Parts of the United States are expected to have historic lows this week, as temperatures in the Southeast, Mid-Atlantic and central Appalachians may drop to the coldest they've been since the mid-1990s, according to the National Weather Service (NWS).
"Get ready for an even more impressive surge of Arctic air later this week as another cold front drops south from Canada," the NWS said in a statement.
That Arctic air in the form of a polar vortex eddy is dropping temperatures with a burst of bitterly cold air, the NWS said.
The freezing weather is part of a weather pattern that began last year, when the polar vortex, a system of cold air swirling around the Arctic, began pushing cold air into the United States. This pattern continued on and off throughout the summer, explaining the cooler temperatures in the eastern United States, said Bob Oravec, a forecaster at the National Weather Service.
This cold weather can take hold, thanks to flows in the middle and upper levels of the atmosphere that travel from northwest to southeast.
"They form at different times of the year, and they tend to go farther south during the winter," Oravec said. "Right now, we have that favorable weather pattern — a northwest flow from Alaska across a big part of Canada into the United States."
He called it one of the more persistently cold winters in the United States. "Especially this month, the temperature anomalies are way below average across a big part of the central to eastern United States," Oravec said.
Highs in the Southeast, Mid-Atlantic and central Appalachians will likely stay below 20 degrees Fahrenheit (minus 6 degrees Celsius) for much of today (Feb. 19) and Friday, and overnight lows may dip below 0 degrees F (minus 17 degrees C) in some places. A wind chill advisory is also in effect for these places, the NWS said.
Why Boston has record snow
A separate repeating weather system is to blame for the record snow levels in Boston and other parts of New England.
"Boston is now in the top two or three snowiest winters," said David Roth, a meteorologist at the National Weather Service's Weather Prediction Center in College Park, Maryland. "I'm pretty sure parts of Maine are getting there, too."
Similar weather conditions that support the polar vortex are pushing cold air toward New England. This winter, "they've been sweeping across or south of the Great Lakes, been coming off the East Coast and then strengthening as ocean storms," Roth said.
Southern New England falls right in its path, "so you end up having this big comma head of snow that ends up falling over the region," Roth said. "That's usually good for a foot [0.3 meters] or so of snow."
In warmer seasons, the same weather pattern would likely cause rain and thunderstorms.
The storm system will continue to repeat until another storm or weather system changes it, he added. For instance, coastal storms can drag weather systems north or northeast, he said.
Many New Englanders are looking forward to a break from the snow. They've had four significant snowstorms since Thanksgiving, amounting to 96.3 inches (245 centimeters) of snow accumulation at Logan Airport, according to the NWS. The average snowfall for this time of year is 30.2 in (77 cm). The average for large snowfalls in 2015, some of which last two days, is almost 20 inches, the NWS found.
The rest of February will be cold in the eastern United States, the NWS predicts. From Feb. 24 to Feb. 28 the NWS has predicted that the eastern half of the country will have below-normal temperatures, and the West Coast will have above-normal temperatures.
But the days are getting longer as winter nears its end.
"No matter where you are in the eastern United States, the averages are coming up," Roth said. "The local sun angle is coming up each day. You're getting longer days."
Read more at Discovery News
This is yet another cosmic first for the veteran space telescope; astronomers have been able to compare Hubble observations of Beta Pictoris 1997 and 2012 and would therefore be able to track any morphological changes in its protoplanetary disk.
As the exoplanet’s orbit is predicted to have an orbital period of between 18-20 years, over the 15 years between observations, the exoplanet would have shifted considerably, but Hubble has noticed little change in the distribution of dust in the protoplanetary disk, confirming some models about how protoplanetary disks mingling with exoplanets work.
“Some computer simulations predicted a complicated structure for the inner disk due to the gravitational pull by the short-period giant planet,” said Daniel Apai of the University of Arizona. “The new images reveal the inner disk and confirm the predicted structures. This finding validates models, which will help us to deduce the presence of other exoplanets in other disks.”
From these observations, astronomers can see that the circumstellar dust is orbiting in unison with the exoplanet “like a carousel,” according to a Hubble news release. This suggests that the inner dusty disk is “smooth and continuous” as it orbits the star.
Beta Pictoris, however, isn’t believed to be a ‘typical’ young star with a protoplanetary disk.
“The Beta Pictoris disk is the prototype for circumstellar debris systems, but it may not be a good archetype,” said co-author Glenn Schneider of the University of Arizona.
Beta Pictoris was the first star to be discovered to have a bright circumstellar disk. It’s believed that asteroids and comets in the system are continuously colliding, populating the disk with copious quantities of dust. Also, a lobe-like feature in the disk is thought to be the dusty remains of a pulverized Mars-sized body.
Read more at Discovery News
|This fish shouldn’t be alive. Though I dunno, maybe it isn’t. Hard to tell with fish sometimes. Gotta get them some eyelids.|
Yet even there, life flourishes. And one group of fishes, the notothenioids, swims in those frigid waters nearly carefree, thanks to very special blood loaded with antifreeze. Some of these fish have even done away with oxygen-carrying red blood cells altogether, adopting thin, crystal-clear blood that doesn’t get as viscous as the temperatures drop. These fishes are tougher than you. So much tougher than you.
Studying these critters is evolutionary biologist Paul Cziko of the University of Oregon, who happily drills through Antarctic sea ice and jumps into the water. Cziko is tougher than you. So much tougher than you. “It’s not that brave,” he says, “in part because the water is amazingly clear.” So at least there’s that.
|Cziko cutting a hole in 12-foot-thick sea ice. You know, like ya do.|
Here’s the problem, though. That irreversibility means that over time the crystals build up inside the fish, and having lots of foreign objects in your blood is usually something best avoided. But these fishes live for up to 30 years without obvious ill effects, so somehow they’re dealing with the accumulation of crystals. Scientists who study notoes once thought slightly warmer water temperatures in the summer allowed the crystals to melt, but Cziko and his colleagues measured temperatures around Antarctica for more than a decade and found the summers don’t get warm enough to help any. It could be that the spleen is somehow filtering the imprisoned crystals somehow, but no one really knows. “There’s no free lunch in evolution,” Cziko says. “The evolution of antifreeze proteins comes with a tradeoff, where you now have to figure out what to do with the ice crystals once they get into the body.” Conversely, it could be that the crystals aren’t that dangerous after all. “It’s really hard to prove that internal ice crystals are actually bad for the fishes. Having ice crystals in your body that could clog blood vessels certainly seems like it would cause problems. But if they didn’t have the antifreeze proteins they’d be frozen solid, and they wouldn’t survive at all.”
I know I mentioned earlier that these fish are tougher than you, and that’s true in the sense that they can survive when temperatures dip below 30 degrees F. But the icefish are also in their way quite vulnerable. “You catch them on a hook and line, maybe catch them in a trawl, and bring them up to the surface and they are essentially catatonic for half an hour,” Cziko says. “They’re pretty beat up. Without hemoglobin, they don’t easily recover from acute stresses like that.”
|That syringe is indeed filled with blood—the clear variety.|
Life is rough, and it don’t get much rougher than life in the Antarctic. But why would a creature even bother? Why not head north and find some kind of tropical paradise? Well, first of all the notoes wouldn’t be able to take the heat. As with the scaly-foot snail and its hellish environment, by adapting to the hardships they’ve been able to make a good living because so few creatures dare join them. The living may be rough, but it’s a profitable one.
Read more at Wired Science
Feb 19, 2015
Cope’s Rule holds that there is active selection for increasing body size in nature. The new study, published in the journal Science, finds this to be true. It appears that evolution follows certain rules and can, at least to some extent, be predicted.
“We’ve known for some time now that the largest organisms alive today are larger than the largest organisms that were alive when life originated or even when animals first evolved,” co-author Jonathan Payne, a paleobiologist at Stanford’s School of Earth, Energy & Environmental Sciences, said in a press release.
This is not to say that huge animals didn’t existed in the past. The gigantic dinosaur Dreadnoughtus, for example, measured 85 feet long and weighed about 65 tons. The point is that, as many animal lineages evolve, there is a tendency toward larger sizes, particularly if food resources, the environment and other factors remain relatively stable.
The effect has been dramatic for animals like horses. As seen in the accompanying image, the earliest horses were much smaller than those alive today. Humans, in general, are also growing larger. In Britain, for example, the average height of a 21-year-old man increased from 5’5” in the 1870s to 5’10” as of the 1970s, according to researchers from the University of Essex and the National University in Canberra.
For the latest study, Payne and his team tested out Cope’s Rule on marine animals. The scientists compiled a dataset that included adult body size measurements for individual species within more than 17,000 groups, or genera, of marine animals spanning five major phyla: Arthropods, Brachiopods, Chordates, Echinoderms and Mollusks.
“Our study is the most comprehensive test of Cope’s Rule ever conducted,” said lead author Noel Heim of Stanford University. “Nearly 75 percent of all of marine genera in the fossil record and nearly 60 percent of all the animal genera that ever lived are included in our dataset.”
Analysis of the massive dataset revealed that, over the past 542 million years, the mean size of marine animals has increased 150-fold.
“That’s the size difference between a sea urchin that is about 2 inches long versus one that is nearly a foot long,” Heim explained. “This may not seem like a lot, but it represents a big jump.”
The researchers additionally found that the increase in body size, which has occurred since animals first appeared in the fossil record around 550 million years ago, is not due to every animal lineage steadily growing bigger. It’s instead due to the diversification of groups of organisms that were already larger than other groups early in the history of animal evolution.
“That’s also something we didn’t know before,” Payne said. “For reasons that we don’t completely understand, the classes with large body size appear to be the ones that over time have become differentially more diverse.”
They suspect this is because of advantages associated with a larger size, such as the ability to move faster, to burrow more deeply and efficiently in sediment or to capture larger prey.
“It’s really a story of the survival and diversification of big things relative to small things,” Heim said.
Small things aren’t all staying small either. Yet another recent study found that certain spiders are growing bigger in urban areas.
There’s no need to fear monster-sized ants, termites or other such things in our lifetimes, though. Growth within a species — if it happens at all — occurs slowly and over many generations.
Read more at Discovery News
The treasure, probably exposed during recent storms, wasn’t immediately recognized by the divers.
“At first they thought they had spotted a toy coin from a game and it was only after they understood the coin was the real thing that they collected several coins and quickly returned to the shore in order to inform the director of the dive club about their find,” Israel Antiquities Authority (IAA) said in a statement.
Using metal detectors, marine archeologists uncovered nearly 2,000 coins that sat on the bottom of the Roman-era port for about 1,000 years. The coins came in different denominations, dimensions and weight: a dinar, half dinar and quarter dinar.
“The earliest is a quarter dinar minted in Palermo, Sicily, in the second half of the ninth century AD,” the IAA said.
Most of the pieces circulated by the Fatimid Caliphate, the Muslim dynasty that ruled an empire in large parts of North Africa and the Middle East from 909 to 1171. The coins also remained in circulation after the Crusader conquest, particularly in port cities.
According to Kobi Sharvit, director of the Marine Archaeology Unit of the Israel Antiquities Authority, there is probably a shipwreck of an official treasury boat on the seabed.
“The boat was on its way to the central government in Egypt with taxes that had been collected. Perhaps the treasure of coins was meant to pay the salaries of the Fatimid military garrison which was stationed in Caesarea and protected the city,” Sharvit said.
Another theory is that the coins belonged to a large merchant ship that traded among Mediterranean coastal cities and sank in the port.
Further excavations might help “answer the many questions that still remain unanswered about the treasure,” the IAA said.
No restoration is needed for the coins, which are perfectly preserved despite laying on the seafloor for about a millennium.
“This is because gold is a noble metal and is not affected by air or water,” Robert Cole, an expert numismaticist with the Israel Antiquities Authority said.
He added that several coins were bent and show teeth and bite marks, evidence they were “physically” inspected by their owners or the merchants.
Read more at Discovery News
Like all objects in free fall, raindrops move according to the laws of physics. One of those laws puts a barrier on how fast a free-falling object can travel. This terminal velocity is reached when the downward tug of gravity equals the opposing force of air resistance.
In 2009, physicists reported that they had discovered small raindrops falling faster than this terminal velocity. In that study, detailed in the journal Geophysical Research Letters, Alexander Kostinski and Raymond Shaw of Michigan Technological University, along with Guillermo Montero-Martinez and Fernando Garcia-Garcia of the National University of Mexico, measured 64,000 raindrops, and found clusters of "superterminal" drops falling faster than they should based on their size and weight, especially as the rain became heavier.
In the new study, Kostinski and his colleagues verified that initial finding using completely different instruments. The researchers clocked the speeds of 1.5 million raindrops passing through a laser beam during six rainstorms at a site near Charleston, South Carolina. All of the raindrops measuring 0.8 millimeters (0.03 inches) and larger fell to the ground at predicted speeds, but 30 to 60 percent of the smaller drops (those measuring about 0.3 millimeters, or about 0.01 inches) traveled faster than their terminal velocity.
"Occasionally, smaller drops (less than a millimeter) fall more than 10 times faster than expected," Kostinski told Live Science in an email. "On average, small drops move about 30 percent faster than expected, but it depends on rain type and strength."
The superterminal drops may be the result of fragmenting, in which a "parent" droplet breaks up into smaller droplets. "Right after the breakup, fragments move approximately with the speed of mother drops," Kostinski wrote. "The mother drop is large, and its terminal speed is much higher than the one of smaller drops. This is one possible reason for smaller drops (fragments), breaking the speed limit."
So-called turbulent wakes that form behind the raindrops may also explain the odd behavior. In those wakes, air resistance that's opposing gravity's downward pull would decrease. "If they fall behind another drop, air drag decreases (like a group of bikers behind a leader)," Kostinski wrote.
By using 21 laser precipitation monitors and a video device, the researchers also ruled out the idea that the speedy raindrops were the result of droplets splashing off the instruments or some kind of measurement error.
"The fact that a substantial fraction of drizzle-sized drops are moving faster than their terminal velocities suggest that we are not just seeing an outlier effect here," lead author Michael Larsen, an assistant professor of physics and astronomy at the College of Charleston, said in a statement. "That was a bit surprising to me and helped me realize that there's more science to be done."
Read more at Discovery News
The New Horizons probe captured images of Nix and Hydra, two of Pluto's five known satellites, from Jan. 27 through Feb. 8, at distances ranging from 125 million miles to 115 million miles (201 million to 186 million kilometers), NASA officials said. The photos have been spliced together to create a short movie showing Nix and Hydra circling Pluto.
ANALYSIS: Pluto and Moon Charon May Share Same Atmosphere
NASA released the new footage Wednesday (Feb. 18), 85 years to the day after American astronomer Clyde Tombaugh discovered Pluto at the Lowell Observatory in Flagstaff, Arizona.
"It’s thrilling to watch the details of the Pluto system emerge as we close the distance to the spacecraft’s July 14 encounter," New Horizons science team member John Spencer, of the Southwest Research Institute in Boulder, Colorado, said in a statement. "This first good view of Nix and Hydra marks another major milestone, and a perfect way to celebrate the anniversary of Pluto’s discovery."
New Horizons team members discovered Nix and Hydra in 2005 using NASA's Hubble Space Telescope. Scientists think both moons are between 25 miles and 95 miles (40 to 153 km) wide; New Horizons should nail down their sizes when it zooms through the Pluto system this summer.
Hydra is Pluto’s outermost known moon and circles the dwarf planet every 38 days, at a distance of about 40,200 miles (64,700 km). Nix lies 30,260 miles (48,700 km) from Pluto and completes one orbit every 25 days.
Two other Pluto moons, Styx and Kerberos, are smaller than Nix and Hydra, and are too faint to show up in the latest New Horizons images, NASA officials said. The dwarf planet's other known moon, Charon, blends into Pluto in the photos, creating a fuzzy white blob. (Charon is about 750 miles, or 1,207 km, in diameter — about half as wide as Pluto itself.)
The new photos were captured by New Horizons' Long-Range Reconnaissance Imager (LORRI), to help improve team members' understanding of the orbits of Nix and Hydra. The right-hand images have been processed to remove the Pluto-Charon glare and that of background stars, making Nix and Hydra easier to see, NASA officials said.
The streak extending to the right of Pluto and Charon is a result of overexposure, they added. (LORRI took the photos in a special mode that sacrifices resolution to boost sensitivity.)
Read more at Discovery News
Feb 18, 2015
New work by Josh Hihath's group at the UC Davis Department of Electrical and Computer Engineering, published Feb. 16 in the journal Nature Materials, could help technologists make that jump. Hihath's laboratory has developed a method to measure the conformation of single molecule "wiring," resolving a clash between theoretical predictions and experiments.
"We're trying to make transistors and diodes out of single molecules, and unfortunately you can't currently control exactly how the molecule contacts the electrode or what the exact configuration is," Hihath said. "This new technique gives us a better measurement of the configuration, which will provide important information for theoretical modeling."
Until now, there has been a wide gap between the predicted electrical behavior of single molecules and experimental measurements, with results being off by as much as ten-fold, Hihath said.
Hihath's experiment uses a layer of alkanes (short chains of carbon atoms, such as hexane, octane or decane) with either sulfur or nitrogen atoms on each end that allow them to bind to a gold substrate that acts as one electrode. The researchers then bring the gold tip of a Scanning Tunneling Microscope towards the surface to form a connection with the molecules. As the tip is then pulled away, the connection will eventually consist of a single-molecule junction that contains six to ten carbon atoms (depending on the molecule studied at the time).
By vibrating the tip of the STM while measuring electrical current across the junction, Hihath and colleagues were able to extract information about the configuration of the molecules.
Read more at Science Daily
The tiny towers apparently were created by the combination of wind, water and low temperatures, which combined to carve the frozen layers of sand in much the same fashion that a river carves a canyon, Mihai Andrei writes at ZME Science.
The wind breaks down the cohesion of soil particles and detaches and moves some of them, creating the shapes. Because the towers were so small, they melted away quickly, and most were already gone by the time that Nowicki tried to take more pictures of them, according to Andrei.
But wind erosion also carves bigger, longer-lasting sculptures on frozen beaches. Last March, a blogger who calls herself Fossillady shot these amazing pictures of intricate formations and what look like Georgia red stone cliffs, carved by the wind into the frozen sand at Pier Cove Creek in southwest Michigan.
Wind, of course, also helps to create sand dunes. Michigan is home to the biggest dune system in the world that’s associated with a freshwater lake, as described in this article by Michigan State University geography professor Randall Schaetzl. The dunes provide an important habitat for plants and animals.
From Discovery News
Every galaxy is cocooned inside a massive halo of dark matter, the invisible stuff that is thought to account for nearly 85 percent of all matter in the universe. The bigger the galaxy, the bigger the dark matter halo. The stars that we observe in any given galaxy accounts for a tiny fraction of the total mass of that galaxy — the halo can extend for hundreds of thousands of light years from the visible galaxy’s ‘edge.’
The visible stars and gas in a galaxy can therefore be thought of as just the ‘hub’ of that galaxy; the rest of the ‘wheel’ extends far into intergalactic space, but as it is composed of dark matter, which does not interact with electromagnetic radiation (light), it cannot be seen.
Although astronomers have known about these halos for some time, their gravitational impact on the visible stuff (stars, planets, gas) inside their host galaxies is poorly understood. And now dark matter’s impact on black hole evolution is under scrutiny.
“There seems to be a mysterious link between the amount of dark matter a galaxy holds and the size of its central black hole, even though the two operate on vastly different scales,” said lead author Akos Bogdan of the Harvard-Smithsonian Center for Astrophysics (CfA), Cambridge, Mass. Bogdan’s work, co-authored with Andy Goulding (of Princeton University), has been accepted for publication in The Astrophysical Journal.
The majority of galaxies are thought to contain a supermassive black hole in their cores and, by studying over 3,000 elliptical galaxies, Bogdan and Goulding gauged the masses of their monster black holes by clocking the speeds of the stars whizzing around the central black holes.
Then, to measure the total mass of dark matter those galaxies possessed, the researchers observed the X-rays generated by the hot gas the galaxies contained. The more hot gas the galaxy has, the more massive its halo.
With this information in hand, the researchers were able to deduce that there is a strong relationship between the amount of halo dark matter and mass of the central black hole. This dark matter correlation is much stronger than the relationship between the number of stars and black hole mass.
Read more at Discovery News
Dark matter is so named because it does not emit or absorb light -- or any other electromagnetic radiation. Its presence is inferred by how its gravity impacts stars, galaxies, dust and other visible matter.
Scientists calculate that ordinary, visible matter accounts for about 5 percent of the universe. The rest is dark matter and a repulsive force called dark energy, which is accelerating the universe’s expansion.
“What we know about dark matter is that it exists, and then very little after that,” physicist Michael Williams, with the Massachusetts Institute of Technology, told Discovery News.
“It would be nice if we could start to understand what dark matter is and how it affects the galaxy and the evolution of the universe, but just opening the door in particle physics to whatever is on the other side ... would be stepping into the unknown, which is exciting,” he said.
A promising doorway into the new frontier is located at Europe’s CERN particle physics laboratory near Geneva, home to the Large Hadron Collider, or LHC.
In 2012, researchers using the world’s most powerful atom smasher discovered a new subatomic particle, the Higgs boson, which is believed to give matter its mass. The work led to the 2013 Nobel Prize in Physics for two scientists who theorized the particle’s existence.
After a two-year upgrade to more than double its power, the LHC may now provide proof of other versions of the Higgs boson, as well as hypothetical subatomic partners of quarks, leptons and other members of physic’s standard family.
It is the lightest of these ghost particles that could match the footprints of dark matter, scientists said at the American Association for the Advancement of Science meeting in San Jose over the weekend.
“It’s unclear what it is. It could be the supersymmetry partner of the photon -- the photino -- or of the graviton -- the gravitino,” said Beate Heinemann, physics professor at the University of California at Berkeley.
Read more at Discovery News
Feb 17, 2015
Closest known flyby of star to our solar system: Dim star passed through Oort Cloud 70,000 years ago
In a paper published in The Astrophysical Journal Letters, lead author Eric Mamajek from the University of Rochester and his collaborators analyzed the velocity and trajectory of a low-mass star system nicknamed "Scholz's star."
The star's trajectory suggests that 70,000 years ago it passed roughly 52,000 astronomical units away (or about 0.8 light years, which equals 8 trillion kilometers, or 5 trillion miles). This is astronomically close; our closest neighbor star Proxima Centauri is 4.2 light years distant. In fact, the astronomers explain in the paper that they are 98% certain that it went through what is known as the "outer Oort Cloud" -- a region at the edge of the solar system filled with trillions of comets a mile or more across that are thought to give rise to long-period comets orbiting the Sun after their orbits are perturbed.
The star originally caught Mamajek's attention during a discussion with co-author Valentin D. Ivanov, from the European Southern Observatory. Scholz's star had an unusual mix of characteristics: despite being fairly close ("only" 20 light years away), it showed very slow tangential motion, that is, motion across the sky. The radial velocity measurements taken by Ivanov and collaborators, however, showed the star moving almost directly away from the solar system at considerable speed.
"Most stars this nearby show much larger tangential motion," says Mamajek, associate professor of physics and astronomy at the University of Rochester. "The small tangential motion and proximity initially indicated that the star was most likely either moving towards a future close encounter with the solar system, or it had 'recently' come close to the solar system and was moving away. Sure enough, the radial velocity measurements were consistent with it running away from the Sun's vicinity -- and we realized it must have had a close flyby in the past."
To work out its trajectory the astronomers needed both pieces of data, the tangential velocity and the radial velocity. Ivanov and collaborators had characterized the recently discovered star through measuring its spectrum and radial velocity via Doppler shift. These measurements were carried out using spectrographs on large telescopes in both South Africa and Chile: the Southern African Large Telescope (SALT) and the Magellan telescope at Las Campanas Observatory, respectively.
Once the researchers pieced together all the information they figured out that Scholz's star was moving away from our solar system and traced it back in time to its position 70,000 years ago, when their models indicated it came closest to our Sun. Until now, the top candidate for the closest flyby of a star to the solar system was the so-called "rogue star" HIP 85605, which was predicted to come close to our solar system in 240,000 to 470,000 years from now. However, Mamajek and his collaborators have also demonstrated that the original distance to HIP 85605 was likely underestimated by a factor of ten. At its more likely distance -- about 200 light years -- HIP 85605's newly calculated trajectory would not bring it within the Oort Cloud.
Mamajek worked with former University of Rochester undergraduate Scott Barenfeld (now a graduate student at Caltech) to simulate 10,000 orbits for the star, taking into account the star's position, distance, and velocity, the Milky Way galaxy's gravitational field, and the statistical uncertainties in all of these measurements. Of those 10,000 simulations, 98% of the simulations showed the star passing through the outer Oort cloud, but fortunately only one of the simulations brought the star within the inner Oort cloud, which could trigger so-called "comet showers."
While the close flyby of Scholz's star likely had little impact on the Oort Cloud, Mamajek points out that "other dynamically important Oort Cloud perturbers may be lurking among nearby stars." The recently launched European Space Agency Gaia satellite is expected to map out the distances and measure the velocities of a billion stars. With the Gaia data, astronomers will be able to tell which other stars may have had a close encounter with us in the past or will in the distant future.
Currently, Scholz's star is a small, dim red dwarf in the constellation of Monoceros, about 20 light years away. However, at the closest point in its flyby of the solar system, Scholz's star would have been a 10th magnitude star -- about 50 times fainter than can normally be seen with the naked eye at night. It is magnetically active, however, which can cause stars to "flare" and briefly become thousands of times brighter. So it is possible that Scholz's star may have been visible to the naked eye by our ancestors 70,000 years ago for minutes or hours at a time during rare flaring events.
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"Fundamentally, intrinsic strains on crumpled graphene could allow modulation of electrical and optical properties of graphene," explained SungWoo Nam, an assistant professor of mechanical science and engineering at Illinois. "We believe that the crumpled graphene surfaces can be used as higher surface area electrodes for battery and supercapacitor applications. As a coating layer, 3D textured/crumpled nano-topographies could allow omniphobic/anti-bacterial surfaces for advanced coating applications."
Graphene--a single atomic layer of sp2-bonded carbon atoms--has been a material of intensive research and interest over recent years. A combination of exceptional mechanical properties, high carrier mobility, thermal conductivity, and chemical inertness, make graphene a prime candidate material for next generation optoelectronic, electromechanical, and biomedical applications.
"In this study, we developed a novel method for controlled crumpling of graphene and graphite via heat-induced contractile deformation of the underlying substrate," explained Michael Cai Wang, a graduate student and first author of the paper, "Heterogeneous, Three-Dimensional Texturing of Graphene," which appeared in the journal Nano Letters. "While graphene intrinsically exhibits tiny ripples in ambient conditions, we created large and tunable crumpled textures in a tailored and scalable fashion."
"As a simpler, more scalable, and spatially selective method, this texturing of graphene and graphite exploits the thermally induced transformation of shape-memory thermoplastics, which has been previously applied to microfluidic device fabrication, metallic film patterning, nanowire assembly, and robotic self-assembly applications," added Nam, whose group has filed a patent for their novel strategy. "The thermoplastic nature of the polymeric substrate also allows for the crumpled graphene morphology to be arbitrarily re-flattened at the same elevated temperature for the crumpling process."
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The study details a major shift in bottom-dwelling species in Italy's Po Basin, a region south of Venice known for its ecologically and commercially important shellfish as well as its tourism industry.
"The fossil record suggests that human activities can alter even those ecosystems that have been immune to major changes naturally occurring on our planet," said the study's lead author, Michal Kowalewski, the Thompson Chair of Invertebrate Paleontology at the Florida Museum of Natural History on the UF campus.
"We may be witnessing a permanent shift," Kowalewski said. "This restructuring could have lasting consequences for regional biodiversity, including the overall health of the broader marine ecosystems of the Adriatic."
Mollusks preserve well in the fossil record and tend to be sensitive to human-caused environmental change, making them a good indicator of marine ecosystem health. The study, appearing online this week in the Proceedings of the Royal Society B, documents rapidly changing marine communities in the northern Adriatic, one of Europe's most highly developed industrial and agricultural areas. Researchers tracked changes in shellfish communities by examining a collection of more than 100,000 fossil specimens from geological cores drilled in the region. They then compared the fossil data with surveys of present-day marine ecosystems conducted in the last four decades of the 20th century. The fossil record shows 125,000 years ago the Adriatic region's climate and sea level were similar to today. However, the authors found significant ecosystem changes in the most recent centuries, including a decline in seven out of the 10 historically dominant mollusk species.
The findings echo those of previous studies on Caribbean reef communities.
"The changes found by the study researchers are alarming, but there's reason to believe that other areas have been even more profoundly affected by the effects of pollution, habitat disturbance, lack of oxygen and climate change," said Steven Holland, a University of Georgia paleontologist not involved in the study. "This is a clear fingerprint of the effects of humans."
From Science Daily
“As we slowly approach the stage, our eyes transfixed on Ceres and her planetary dance, we find she has beguiled us but left us none the wiser,” said principal investigator Chris Russell, of the University of California, Los Angeles (UCLA), in a NASA news release. “We expected to be surprised; we did not expect to be this puzzled.”
These most recent images were acquired on Feb. 12 from a distance of around 52,000 miles (83,000 kilometers) as the robotic spacecraft slowly spirals in on its target. In this highest-resolution ever view of Ceres, each pixel represents 4.9 miles (7.8 kilometers).
As opposed to a rapid deceleration burn that would be carried out by spacecraft using conventional rockets for propulsion (in the case of NASA’s Cassini probe, for example), Dawn is taking the slow-yet-steady approach using ion engines. This form of propulsion allows continuous thrust for long periods of time, using tiny quantities of fuel. So rather than flying full-speed at Ceres, Dawn has slowly ‘danced’ into formation around Ceres, allowing us many weeks of a gradually sharpening view as the mission creeps up on the solar system’s innermost dwarf planet.
Of particular interest to planetary scientists remains the bright patches of landscape — including the one particularly bright feature shown in the image above (right frame). Other bright features are present, but the origin of this discrete spot is keeping astrogeologists guessing.
During Dawn’s journey through the asteroid belt — the region of space between the orbits of Mars and Jupiter — the Hubble Space Telescope detected plumes of water around Ceres. Could these plumes be associated with geysers leaking a sub-surface ocean of water into space, as observed at Saturn’s moon Enceladus and Jupiter’s moon Europa? If so, these bright features may highlight venting cracks in Ceres’ crust where water is being forced from the dwarf planet’s interior, venting to space as vapor and freezing on the surface as an icy residue, appearing as bright patches on the cratered surface.
Read more at Discovery News
Feb 16, 2015
The finding could alter the basic understanding of how two distinct life forms -- bacteria and eukaryotes -- begin the process of protein synthesis.
Jeffrey Kieft, PhD, professor of biochemistry and molecular genetics and corresponding author of the article in Nature, said scientists have long thought that the molecular signals that initiate protein synthesis in bacteria and eukaryotes are mutually exclusive. Scientists in Kieft's lab explored whether a structured RNA molecule from a virus that infects eukaryotic cells could function in bacteria. Surprisingly, they found that it could initiate protein syntheses, a process necessary for life.
"What we found bridges billions of years of evolutionary divergence," said Kieft, who is also a Howard Hughes Medical Institute Early Career Scientist. "We wanted to explore whether it was possible to bypass mechanisms that were specific to each domain of life and find a signal capable of operating in both."
Eukaryotes are organisms, such as plants, animals and fungi, whose cells contain a nucleus and are enclosed within membranes, while prokaryotes, such as bacteria, do not contain a nucleus.
In an article that accompanies the study by Kieft and his colleagues, Eric Jan, associate professor in the Department of Biochemistry and Molecular Biology at the University of British Columbia, calls the finding "surprising" and writes that the CU scientists and their colleagues "have shown for the first time that a bona fide signal in an RNA structure promotes protein synthesis in the two domains of life."
From Science Daily
The ability to use atmospheric nitrogen to support more widespread life was thought to have appeared roughly 2 billion years ago. Now research from the University of Washington looking at some of the planet's oldest rocks finds evidence that 3.2 billion years ago, life was already pulling nitrogen out of the air and converting it into a form that could support larger communities.
"People always had the idea that the really ancient biosphere was just tenuously clinging on to this inhospitable planet, and it wasn't until the emergence of nitrogen fixation that suddenly the biosphere become large and robust and diverse," said co-author Roger Buick, a UW professor of Earth and space sciences. "Our work shows that there was no nitrogen crisis on the early Earth, and therefore it could have supported a fairly large and diverse biosphere."
The results were published Feb. 16 in Nature.
The authors analyzed 52 samples ranging in age from 2.75 to 3.2 billion years old, collected in South Africa and northwestern Australia. These are some of the oldest and best-preserved rocks on the planet. The rocks were formed from sediment deposited on continental margins, so are free of chemical irregularities that would occur near a subsea volcano. They also formed before the atmosphere gained oxygen, roughly 2.3 to 2.4 billion years ago, and so preserve chemical clues that have disappeared in modern rocks.
Even the oldest samples, 3.2 billion years old -- three-quarters of the way back to the birth of the planet -- showed chemical evidence that life was pulling nitrogen out of the air. The ratio of heavier to lighter nitrogen atoms fits the pattern of nitrogen-fixing enzymes contained in single-celled organisms, and does not match any chemical reactions that occur in the absence of life.
"Imagining that this really complicated process is so old, and has operated in the same way for 3.2 billion years, I think is fascinating," said lead author Eva Stüeken, who did the work as part of her UW doctoral research. "It suggests that these really complicated enzymes apparently formed really early, so maybe it's not so difficult for these enzymes to evolve."
Genetic analysis of nitrogen-fixing enzymes have placed their origin at between 1.5 and 2.2 billion years ago.
"This is hard evidence that pushes it back a further billion years," Buick said. Fixing nitrogen means breaking a tenacious triple bond that holds nitrogen atoms in pairs in the atmosphere and joining a single nitrogen to a molecule that is easier for living things to use. The chemical signature of the rocks suggests that nitrogen was being broken by an enzyme based on molybdenum, the most common of the three types of nitrogen-fixing enzymes that exist now. Molybdenum is now abundant because oxygen reacts with rocks to wash it into the ocean, but its source on the ancient Earth -- before the atmosphere contained oxygen to weather rocks -- is more mysterious.
The authors hypothesize that this may be further evidence that some early life may have existed in single-celled layers on land, exhaling small amounts of oxygen that reacted with the rock to release molybdenum to the water.
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At least 18 sightings were reported during two 10-day periods in March and April 2012, when plumes appeared over an area known as Terra Cimmeria, located in Mars’ southern hemisphere.
The plumes extended over 500- to 1,000 kilometers (311- to 621 miles) in both north-south and east-west directions and changed in appearance daily. They were detected as the sun breached Mars’ horizon in the morning, but not when it set in the evening.
“Remarkably ... the features changed rapidly, their shapes going from double blob protrusions to pillars or finger-plume-like morphologies,” scientists investigating the sightings wrote in a paper published in this week’s Nature.
Spacecraft and ground-based telescopes previously had seen clouds made of carbon dioxide and water ice crystals on Mars, but the clouds were typically layered and never rose above 100 kilometers, or 62 miles, from the planet's surface, the researchers noted.
Clouds of dust can be kicked up into the atmosphere during storms, but these max out at about 37 miles in altitude, they added.
The plumes could be some sort of very unusual aurora, 1,000 times brighter than anything seen on Earth, triggered by a very strong magnetic pocket in the planet’s crust that drove solar wind particles out into the atmosphere.
Current understanding of Mars’ atmosphere, however, leaves all explanations wanting.
“Our explanation of this plume as an aurora would require an immense energetic flux, which our calculations show are highly unrealistic,” physicist Agustin Sanchez-Lavega, with the University of the Basque Country in Spain, wrote in an email to Discovery News.
“We favor the cloud scenario -- the condensation of water or carbon dioxide -- since the plume formed in the cold mornings, but we note for this to occur, a large drop in temperature is required at 200 km, something not foreseen by any atmospheric model. Therefore, very particular conditions occurred at that time in the area that currently we do not understand,” he added
The plume grew over the next several days and between March 20 and March 21 was captured by at least 18 observers using small telescopes.
The phenomenon appeared for a second time over the same area for 10 days between April 6 and April 16, 2012.
“Analysis shows the extreme altitude of the plume top to be above 200 km (124 miles), never before observed on Mars, and reaching the ionosphere and exosphere," the researchers wrote.
More clues may come from NASA’s MAVEN spacecraft, which arrived at Mars in September to study the planet’s atmosphere.
“MAVEN has the ability to see this type of feature very clearly, if it's observing at the right place and the right time,” lead scientist Bruce Jakosky, with the University of Colorado, told Discovery News.
Read more at Discovery News
For the flightless, waddling birds, foods come in just two flavors -- salty and sour -- according to the new study, which is published in the latest issue of the journal Current Biology.
“Penguins eat fish, so you would guess that they need the umami receptor genes, but for some reason they don’t have them,” co-author Jianzhi “George” Zhang of the University of Michigan said in a press release. “These findings are surprising and puzzling, and we do not have a good explanation for them. But we have a few ideas.”
Zhang and colleagues made the determination after sequencing the genomes for Adelie and emperor penguins. The researchers were surprised that they couldn’t find some basic taste genes, so they took a closer look at penguin DNA.
This led the scientists to conclude that all penguin species lack functional genes for the receptors of sweet, umami and bitter tastes.
You might think that’s obvious, because penguins aren’t exactly noshing on candy or umami-laden soy sauce. But the reason for the loss likely has more to do with temperature than what the penguins are eating. The clues for this are the missing taste receptors themselves.
Those for sweet, umami and bitter flavors are temperature sensitive. They don’t work well, if at all, if the individual is eating cold food in a cold environment. That’s one reason why people can’t taste the flavors in ice cream very well after a while. The cold dampens their taste buds, as well as ability to smell, a bit.
Penguins or their ancestors probably had all of the usual taste receptors at one point, but lost them when they moved to cold environments. Some penguins have since moved to warmer areas, but because all penguins trace their roots to Antarctica, penguins the world over are still hardwired, taste-wise, for eating in a colder habitat.
Read more at Discovery News
Feb 15, 2015
At the American Association for the Advancement of Science meeting, assistant professor of chemistry Joshua Goldberger reported progress in developing a form of germanium called germanane.
In 2013, Goldberger's lab at Ohio State became the first to succeed at creating one-atom-thick sheet of germanane -- a sheet so thin, it can be thought of as two-dimensional. Since then, he and his team have been tinkering with the atomic bonds across the top and bottom of the sheet, and creating hybrid versions of the material that incorporate other atoms such as tin.
The goal is to make a material that not only transmits electrons 10 times faster than silicon, but is also better at absorbing and emitting light -- a key feature for the advancement of efficient LEDs and lasers.
"We've found that by tuning the nature of these bonds, we can tune the electronic structure of the material. We can increase or decrease the energy it absorbs," Goldberger said. "So potentially we could make a material that traverses the entire electromagnetic spectrum, or absorbs different colors, depending on those bonds."
As they create the various forms of germanane, the researchers are trying to exploit traditional silicon manufacturing methods as much as possible, to make any advancements easily adoptable by industry.
Aside from these traditional semiconductor applications, there have been numerous predictions that a tin version of the material could conduct electricity with 100 percent efficiency at room temperature. The heavier tin atom allows the material to become a 2D "topological insulator," which conducts electricity only at its edges., Goldberger explained. Such a material is predicted to occur only with specific bonds across the top and bottom surface, such as a hydroxide bond.
Read more at Science Daily
Though the reporters acknowledged that “Health Canada and the U.S. FDA say the vaccine is safe. Hundreds of thousands of teenage girls in Canada have received the vaccine’s three doses, the vast majority without incident,” these caveats were largely overshadowed by dramatic and moving accounts of injured girls and ruined lives.
A few years ago such a story might have been ignored, but amid the current climate of vaccination concerns it provoked a firestorm of criticism from doctors and public health officials who claimed it was misleading and would fuel anti-vaccination fears.
The Star dug itself deeper when its columnist Heather Mallick defended the original reporting while acknowledging that “I’ve been trying to teach myself about statistics and science.”
“I’m reading doctor and science writer Ben Goldacre’s new book, ‘I Think You’ll Find It’s a Bit More Complicated Than That,’ about the widespread misunderstanding of research and results,” Mallick said.
Goldacre, a longtime, staunch proponent of vaccination, was alarmed that his name had been invoked in defense of anti-vaccination reporting and took to Twitter to admonish both Mallick and “The Star.”
After doubling down for nearly a week The Star acknowledged that they “failed” in their reporting and did not give proper weight to science. According to a story by Global News Canada:
“The Star’s publisher John Cruickshank said the paper failed the public in the way it presented its story…. Cruickshank took responsibility for the way the story was presented and said he understands why it could have given readers the false impression that Gardasil is dangerous.”
That same day the newspaper published an op-ed endorsed by 63 doctors and public health specialists that stated in part:
Although the article states in the fifth paragraph that “there is no conclusive evidence showing the vaccine caused a death or illness,” its litany of horror stories and its innuendo give the incorrect impression that the vaccine caused the harm. Very unfortunately, this article may well lead readers to doubt both the scientific evidence and the recommendations of the Public Health Agency of Canada, the Society of Obstetricians and Gynecologists of Canada, the National Advisory Committee on Immunization, and the Canadian Cancer Society about vaccination…. The Star presented the stories of women who have suffered greatly. The article was engaging, dramatic and might have created fear. But study after study has shown that there is no causal link between the events the Star reported and the vaccine. About 169 million doses of the HPV vaccine have been administered worldwide. In any given large population, there will be illness and death.
This sort of story is not unusual. Last year dozens of Colombian teens complained about strange symptoms including headaches, convulsions and fainting in the days and weeks after many of them got a HPV vaccination.
Read more at Discovery News