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  • richardmitnick 9:11 am on February 19, 2018 Permalink | Reply
    Tags: , , Electric Eels, Electrocytes, , The Atlantic   

    From The Atlantic: “A New Kind of Soft Battery, Inspired by the Electric Eel” 

    Atlantic Magazine

    The Atlantic Magazine

    Dec 13, 2017
    Ed Yong

    Thomas Schroeder / Anirvan Guha

    In 1799, the Italian scientist Alessandro Volta fashioned an arm-long stack of zinc and copper discs, separated by salt-soaked cardboard. This “voltaic pile” was the world’s first synthetic battery, but Volta based its design on something far older—the body of the electric eel.

    This infamous fish makes its own electricity using an electric organ that makes up 80 percent of its two-meter length. The organ contains thousands of specialized muscle cells called Electric Eel. Each only produces a small voltage, but together, they can generate up to 600 volts—enough to stun a human, or even a horse. They also provided Volta with ideas for his battery, turning him into a 19th-century celebrity.

    Two centuries on, and batteries are everyday objects. But even now, the electric eel isn’t done inspiring scientists. A team of researchers led by Michael Mayer at the University of Fribourg have now created a new kind of power source [Nature] that ingeniously mimics the eel’s electric organ. It consists of blobs of multicolored gels, arranged in long rows much like the eel’s electrocytes. To turn this battery on, all you need to do is to press the gels together.

    Unlike conventional batteries, the team’s design is soft and flexible, and might be useful for powering the next generation of soft-bodied robots. And since it can be made from materials that are compatible with our bodies, it could potentially drive the next generation of pacemakers, prosthetics, and medical implants. Imagine contact lenses that generate electric power, or pacemakers that run on the fluids and salts within our own bodies—all inspired by a shocking fish.

    To create their unorthodox battery, the team members Tom Schroeder and Anirvan Guha began by reading up on how the eel’s electrocytes work. These cells are stacked in long rows with fluid-filled spaces between them. Picture a very tall tower of syrup-smothered pancakes, turned on its side, and you’ll get the idea.

    When the eel’s at rest, each electrocyte pumps positively charged ions out of both its front-facing and back-facing sides. This creates two opposing voltages that cancel each other out. But at the eel’s command, the back side of each electrocyte flips, and starts pumping positive ions in the opposite direction, creating a small voltage across the entire cell. And crucially, every electrocyte performs this flip at the same time, so their tiny voltages add up to something far more powerful. It’s as if the eel has thousands of small batteries in its tail; half are pointing in the wrong direction but it can flip them at a whim, so that all of them align. “It’s insanely specialized,” says Schroeder.

    How an electric eel’s electrocytes work (Schroeder et al. / Nature).

    He and his colleagues first thought about re-creating the entire electric organ in a lab, but soon realized that it’s far too complicated. Next, they considered setting up a massive series of membranes to mimic the stacks of electrocytes—but these are delicate materials that are hard to engineer in the thousands. If one broke, the whole series would shut down. “You’d run into the string-of-Christmas-lights problem,” says Schroeder.

    In the end, he and Guha opted for a much simpler setup, involving lumps of gel that are arranged on two separate sheets. Look at the image below, and focus on the bottom sheet. The red gels contain saltwater, while blue ones contain freshwater. Ions would flow from the former to the latter, but they can’t because the gels are separated. That changes when the green and yellow gels on the other sheet bridge the gaps between the blue and red ones, providing channels through which ions can travel.

    Here’s the clever bit: The green gel lumps only allow positive ions to flow through them, while the yellow ones only let negative ions pass. This means (as the inset in the image shows) that positive ions flow into the blue gels from only one side, while negative ions flow in from the other. This creates a voltage across the blue gel, exactly as if it was an electrocyte. And just as in the electrocytes, each gel only produces a tiny voltage, but thousands of them, arranged in a row, can produce up to 110 volts

    Schroeder et al. / Nature.

    The eel’s electrocytes fire when they receive a signal from the animal’s neurons. But in Schroeder’s gels, the trigger is far simpler—all he needs to do is to press the gels together.

    It would be cumbersome to have incredibly large sheets of these gels. But Max Shtein, an engineer at the University of Michigan, suggested a clever solution—origami. Using a special folding pattern that’s also used to pack solar panels into satellites, he devised a way of folding a flat sheet of gels so the right colors come into contact in the right order. That allowed the team to generate the same amount of power in a much smaller space—in something like a contact lens, which might one day be realistically worn.

    For now, such batteries would have to be actively recharged. Once activated, they produce power for up to a few hours, until the levels of ions equalize across the various gels, and the battery goes flat. You then need to apply a current to reset the gels back to alternating rows of high-salt and low-salt. But Schroeder notes that our bodies constantly replenish reservoirs of fluid with varying levels of ions. He imagines that it might one day be possible to harness these reservoirs to create batteries.

    Essentially, that would turn humans into something closer to an electric eel. It’s unlikely that we’d ever be able to stun people, but we could conceivably use the ion gradients in our own bodies to power small implants. Of course, Schroeder says, that’s still more a flight of fancy than a goal he has an actual road map for. “Plenty of things don’t work for all sorts of reasons, so I don’t want to get too far ahead of myself,” he says.

    It’s not unreasonable to speculate, though, says Ken Catania from Vanderbilt University, who has spent years studying the biology of the eels. “Volta’s battery was not exactly something you could fit in a cellphone, but over time we have all come to depend on it,” he says. “Maybe history will repeat itself.”

    “I’m amazed at how much electric eels have contributed to science,” he adds. “It’s a good lesson in the value of basic science.” Schroeder, meanwhile, has only ever seen electric eels in zoos, and he’d like to encounter one in person. “I’ve never been shocked by one, but I feel like I should at some point,” he says.

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  • richardmitnick 5:28 pm on March 3, 2017 Permalink | Reply
    Tags: , , The Atlantic,   

    From The Atlantic: “The Scary State of Volcano Monitoring in the United States” 

    Atlantic Magazine

    The Atlantic Magazine

    Feb 28, 2017
    Adrienne LaFrance

    One of the most volcanically active countries in the world is not ready for a devastating eruption.

    The lava flow from the Kilauea volcano moves over a fence on private property near the village of Pahoa, Hawaii, in 2014.

    One of the most volcanically active countries in the world is not ready for a devastating eruption.

    Thirteen days before Christmas, somewhere in the frigid waters of the Bering Sea, a massive volcano unexpectedly rumbled back to life.

    Just like that, Bogoslof volcano began its first continuous eruption since 1992, belching great plumes of ash tens of thousands of feet into the cold sky over the Aleutian islands, generating volcanic lightning, and disrupting air travel—though not much else.

    Bogoslof volcano. Posted: Dec 24 2016, 7:11am CST | by Sumayah Aamir, in News | Latest Science News

    The volcano is on a tiny island about 60 miles west of Unalaska, which is the largest city in the Aleutians. It has a population of about 5,000 people.

    Bogoslof hasn’t quieted yet. One explosion, in early January, sent ash 33,000 feet into the air. Weeks later, another eruption lasted for hours, eventually sprinkling enough ash on the nearby city to collect on car windshields and dust the snow-white ground with a sulfurous layer of gray. Over the course of two months, Bogoslof’s intermittent eruptions have caused the island to triple in size so far, as fragments of rock and ash continue to pile atop one another.

    Geologists don’t know how long the eruption will last. In 1992, the activity at Bogoslof began and ended within weeks. But more than a century ago, it erupted continuously for years. In the 1880s, volcano observers in the Aleutians had little but their own senses to track what was happening. Today, scientists use satellite data and thermal imagery to watch Bogoslof—signs of elevated temperatures in satellite data indicate that lava has bubbled to the surface, for example. But monitoring efforts are nowhere near what they could be. For the relatively remote Bogoslof, the absence of ground-level sensors is inconvenient, perhaps, but not necessarily alarming. Elsewhere, the dearth of volcano sensors poses a deadly problem.

    There are at least 169 active volcanoes in the United States, 55 of which are believed to pose a high or very high threat to people, according to a 2005 U.S. Geological Survey report.

    About one-third of the active volcanoes in the U.S. have erupted—some of them repeatedly—within the past two centuries. Volcanoes aren’t just dangerous because of their fiery lava. In 1986, volcanic gas killed more than 1,700 people in Cameroon. And one of the latest theories about the epic eruption at Pompeii, in 79 A.D., is that many people died from head injuries they sustained when boulders rained down on them.

    Hawaii’s Kilauea, Washington’s Mt. St. Helens, and Wyoming’s Yellowstone all have extensive monitoring. But many volcanoes in the Cascades have only a couple of far-field sensors, several geologists told me. The Pacific Northwest, which includes high-population areas in close proximity to active volcanoes, is of particular concern for public safety.

    “Most people in the U.S. perceive volcanic eruptions as rare, and [believe] that we’d be able to get advance notice because of the advance in science and instrumentation,” said Estelle Chaussard, an assistant professor of geophysics and volcanology at the State University of New York at Buffalo. “However, the massive eruption of Mount St. Helens, in Washington, was only 37 years ago, and it took until the volcano became active again in 2004 to start a truly comprehensive monitoring. … This kind of assumption is therefore very dangerous, because most of our volcanoes are not as intensively monitored as we think they are or as they should be.”

    Mount St. Helens Is Recharging Its Magma Stores, Setting Off Earthquake Swarms. https://www.wired.com

    Mount St. Helens spews steam and gray ash from a small explosive eruption in its crater on October 1, 2004. (John Pallister / USGS / Reuters)

    Almost half of the active volcanoes in the country don’t have adequate seismometers—tools used to track the earthquakes that often occur during volcanic eruptions. And even at the sites that do have seismometers, many instruments—selected because they are cheaper and consume less power—are unable to take a complete record of the ground shaking around an eruption, meaning “the full amplitude of a seismogram may be ‘clipped’ during recording, rendering the data less useful for in-depth analyses,” according to a 2009 report by the U.S. Geological Survey.

    “Using satellite radar and other systems, it should be possible to systematically keep a close eye on most all hazardous volcanoes around the world,” said Roland Bürgmann, a professor of planetary science at the University of California at Berkeley. “Currently, some volcanoes in the U.S. and globally are well-monitored, but most are not.”

    GPS helps fill in some of the gaps. As magma accumulates at the Earth’s surface, the ground bulges upward—and that bulge can be measured from space, using radar bounced off the ground. “That’s a big advance, because you don’t need sensors on the ground and, in theory, you could monitor all the Earth’s volcanoes,” said Paul Segall, a professor of geophysics at Stanford University. “The trouble is, there’s nothing up there that is designed to do that, and the orbital repeat times aren’t frequent enough to do a really good job.”

    “In my view,” he added, “We haven’t even gotten up to bare bones, let alone more sophisticated monitoring.”

    A plume from the Bogoslof eruption can be seen from Unalaska Island, 53 miles away from the volcano, on February 19, 2017. (Janet Schaefer / AVO)

    That’s part of why a trio of U.S. senators is reintroducing legislation aimed at improving the country’s volcano monitoring efforts. “For the past 34 years, we have experienced first-hand the threat of volcanic activity to our daily lives with the ongoing eruption at Kilauea,” Senator Mazie Hirono, a Democrat from Hawaii, said in a statement about the bill. “As recently as 2014, we had evacuations and damage to critical infrastructure and residences.”

    Looking up the slope of Kilauea, a shield volcano on the island of Hawaii. In the foreground, the Puu Oo vent has erupted fluid lava to the left. The Halemaumau crater is at the peak of Kilauea, visible here as a rising vapor column in the background. The peak behind the vapor column is Mauna Loa, a volcano that is separate from Kilauea.

    Mauna Loa lava flows tend to be larger and move faster than at nearby Kilauea. HVO image from 1984, person for scale. https://www.soest.hawaii.edu/GG/HCV/maunaloa.html

    The Hawaiian Volcano Observatory, on Hawaii’s Big Island, has been monitoring volcanoes since 1912—nearly four decades before Hawaii became a state. Today it’s considered one of the world’s leading observatories. Yet there’s little coordination between even the best observatories in the United States. The Senate bill calls for the creation of a Volcano Watch Office that will provide continuous “situational awareness of all active volcanoes in the U.S. and its territories,” and act as a clearinghouse for the reams of volcanic data that new sensor systems would collect.“Long-records of activity are especially important in volcano monitoring to successfully identify behaviors that differ from the ordinary,” Chaussard told me in an email, “and not all of our volcanoes have such records.”

    “Essentially everything we do now is empirical,” Segall told me, “but most of the really dangerous volcanoes haven’t erupted in modern instrumental times.”

    More data means a better opportunity to identify eruption warning signs, which Segall hopes could eventually make it possible to forecast volcanic activity the way we can predict severe weather like hurricanes. “I don’t know if it’s possible, but it seems a worthy goal,” he said. “We obviously have less ability to peer into the Earth as we do to peer into the sky.”

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  • richardmitnick 11:51 am on February 22, 2017 Permalink | Reply
    Tags: s joined in its orbit by 27 known moons and 13 known rings altogether every bit as bizarre as the planet itself, The Atlantic, , Uranus is incredibly far away between 1.5 and 2 billion miles from Earth   

    From The Atlantic: “The Many Mysteries of Uranus” 

    Atlantic Magazine

    The Atlantic Magazine

    Feb 2, 2016 [Just found this in social media.]
    David Moscato

    NASA / JPL-Caltech

    An ode to the oddball of our solar system.

    The best planet in our solar system is not, as Adrienne LaFrance claimed several months ago, Jupiter. Nor is it Saturn, as Ross Andersen argued in a rebuttal last month. I teach science for a living, which means I have a hard time allowing misinformation to pass by uncorrected—and after reading those articles, I knew I had to step in before any more intellectual damage was done.

    The best planet is Uranus—Uranus the bizarre. Uranus the unique. Saturn may be flashy and pretty, and Jupiter may be huge and dramatic, but they can’t hold a candle to Uranus’s intrigue. While all the other planets spin like tops around the sun, Uranus lies on its side. It isn’t the farthest planet from the sun, yet it manages to be the coldest. Its magnetic field is nowhere near where it’s supposed to be, and its ghoulish blue-green atmosphere seems to alternate between dull stagnation and fits of activity.

    Even its name is unusual. Uranus is the only planet with a name derived from a Greek deity, rather than a Roman one. Correctly pronounced “YOOR-uh-nus,” it’s an homage to the Greek god Ouranos, Father Sky—who, it bears noting, is the father of Cronus (Saturn), and the grandfather of Zeus (Jupiter).

    In fact, Uranus has been breaking the mold as long as we’ve known about it. Mercury, Venus, Mars, Jupiter, and Saturn are all easily visible to the naked eye; humans have been gazing at those planets for millennia, but Uranus was the first planet discovered by modern astronomy. It’s so far away, and its movement so slow, that it was originally thought to be a star until Sir William Herschel revealed its planetary nature in 1781. Less than a decade later, it received a namesake chemical element: uranium, discovered in 1789. (Meanwhile, Neptune and Pluto didn’t make it into the periodic table for another 150 years.)

    The more astronomers studied this new planet, the clearer it became that it was an odd one. Consider the seasons on a world turned sideways: Summer on Uranus is two decades of non-stop sunlight, and winter is an equal amount of time spent in total darkness, facing the cold void of distant space. Day and night only exist during spring and fall, where they cycle every 17 hours. Some have suggested that the planet was knocked askew by a gravitational tug-of-war with a large moon that has since been lost; others have proposed that it was the result of a collision with a massive object (much larger than Earth), or even multiple collisions.

    This strange posture is just one on Uranus’s list of mysteries, a list that also includes its temperature. While the other gas planets are still slowly radiating out the heat of their formation, Uranus generates hardly any internal heat at all. No one is sure why, but that lack of heat may be the underlying cause of the planet’s extreme atmospheric temperatures: Deeper cloud layers get as low as 360 degrees below zero, colder than any other planet in the solar system, and yet the outer-most layer can reach more than 500 degrees, far higher than any other gas giant.

    Like Jupiter and Saturn, Uranus’s atmosphere is full of hydrogen and helium, but unlike its larger cousins, Uranus also holds an abundance of methane, ammonia, water, and hydrogen sulfide. Methane gas absorbs light on the red end of the spectrum, giving Uranus its blue-green hue. If you were to fly down through the layers of the atmosphere, the surrounding clouds would grow denser and denser, colder and colder, bluer and bluer as the gases absorbed more of the visible spectrum. And deep below the atmosphere you may find the answer to yet another one of Uranus’s big puzzles: Its unruly magnetic field is tilted 60 degrees from its rotational axis, much stronger on one pole than the other, and shifted a few thousand miles off-center. Some astronomers believe the warped field may be the result of vast oceans of ionic liquids hidden beneath the greenish clouds, full of water, ammonia, or even liquefied diamond.

    Perhaps Uranus wouldn’t be quite so mysterious if more spacecraft stopped by—but while Mars, Jupiter, and Saturn seem to receive a constant stream of high-tech fan-mail from Earth, Uranus has only been visited once. In 1986, Voyager 2 swung by on its way into deep space.

    NASA Voyager 2
    NASA Voyager 2

    It was the first and so far the only mission to get an up-close view of Uranus, and what the probe saw was, at first glance, dull. Voyager 2 observed little atmospheric activity, and few cloud formations. For a moment, it seemed the icy clouds held little of interest. But it’s been 30 years since the Voyager fly-by, and we’re wiser now.

    When Voyager visited, Uranus was just about at its solstice—the South Pole was almost directly facing the sun, and its North Pole was turned away. But as Uranus continued along its slow orbit, the seasons changed, and the northern hemisphere slowly came back into the light. In 2007, Uranus reached its equinox, the time when the equator faces the sun and the hemispheres receive equal sunlight. According to Imke de Pater, a professor of astronomy at the University of California, Berkeley, the earlier observations of Uranus were “nothing like what we’ve seen during the Equinox.” Over the past several years, astronomers have witnessed winds that blow hundreds of miles an hour, massive storm systems persisting for hours to years, bright cloud patches that migrate across the planet, and “dark spot” storms similar to the famous Neptunian version.

    Uranus’s trips around the sun take just over eight decades, but it doesn’t travel alone. It is joined in its orbit by 27 known moons and 13 known rings, altogether every bit as bizarre as the planet itself. The rings of Uranus aren’t made of bright ice like Saturn’s—they’re more reserved, mostly rock and dust, and so dark they can be hard to spot (even Voyager 2 overlooked Uranus’s two outermost rings). But when Saturn’s rings have dissipated, as astronomers suspect will happen millions of years from now, Uranus’s surprisingly stable rings—which come in all sorts of strange flavors—will remain long into the future. One appears to be made entirely of dust knocked off the moon Mab by asteroid impacts; another dusty ring seems to have disappeared sometime in the last few decades, while a different ring appeared elsewhere; and perhaps most incredibly, one of the rings “breathes,” expanding and contracting around five kilometers once every several hours. According to Mark Showalter of the SETI Institute, these rings are “totally unlike anything else we’ve seen.”

    And then there are the moons, which, like Uranus itself, bear unusual names—most moons in our solar system inherit their names from Greek mythology, but Uranus’s moons come from English literature. There’s Umbriel, strangely dark except for a mysterious bright band; Oberon, covered in craters and one very large mountain; Miranda, scarred by cracks and fissures so extreme they put the Grand Canyon to shame; and two dozen more.

    When describing the motion of Uranus’ moons, Showalter uses words like “random” and “unstable.” The moons are constantly pushing and pulling each other gravitationally, which makes their long-term orbits unpredictable, and over millions of years some are expected to crash into each other. In fact, at least one of Uranus’s rings is thought to be the result of such a collision.

    An image from the Hubble Space Telescope of the planet and its rings (NASA)

    Learn enough, and it’s impossible to not be entranced by the beautiful chaotic dance of Uranus’s ring and moon system. Hidden among those strange movements may be the keys to understanding the unusual gravitational interactions of bodies across the cosmos.

    So why not take a closer look?

    Astronomers have considered sending an orbiter to Uranus, but there are complications. For one, Uranus is incredibly far away, between 1.5 and 2 billion miles from Earth. Besides that, Uranus is hard to predict. We don’t know what to expect from the fluctuating temperatures of the planet’s upper atmosphere, and while the chaotic motion of the moons is too slow to threaten a spacecraft, there’s reason to suspect we haven’t yet spotted all of the moons and debris orbiting the planet.

    “What I’d really like to do,” says Glenn Orton of NASA’s Jet Propulsion Laboratory, “is get a probe into the atmosphere.” There, astronomers might be able to start unraveling some of Uranus’ most enduring puzzles: the deep structure of its atmosphere, the cause of its off-kilter magnetic field, and perhaps the reason for its frigid internal temperatures.

    Until then, we can only gaze at the planet across 2 billion miles of space, guessing at its secrets. The best questions in science are the unanswered ones, and the best planet in the solar system is seventh from the sun, shrouded in methane and in mystery.

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  • richardmitnick 2:56 pm on December 3, 2016 Permalink | Reply
    Tags: , , The Atlantic,   

    From The Atlantic: “Fancy Math Can’t Make Aliens Real” 

    Atlantic Magazine

    The Atlantic Magazine

    Jun 17, 2016 [Where has this been?]
    Ross Andersen


    Universe map Sloan Digital Sky Survey (SDSS) 2dF Galaxy Redshift Survey
    Universe map Sloan Digital Sky Survey (SDSS) 2dF Galaxy Redshift Survey

    Inflationary Universe. NASA/WMAP
    Inflationary Universe. NASA/WMAP

    Last week [at the time of this article], The New York Times published an op-ed titled, Yes, There Have Been Aliens. As its headline suggests, the piece makes an extraordinary claim. “While we do not know if any advanced extraterrestrial civilizations currently exist in our galaxy,” its author writes, “we now have enough information to conclude that they almost certainly existed at some point in cosmic history.”

    That we could know such a thing is not inconceivable. For decades now, a small group of “interstellar archaeologists” has pored over star surveys, looking for evidence of long-dead civilizations, in the form of enormous technological structures. Reading that headline in the Times, I wondered: had one of these astronomers seen something extraordinary?

    Alas, I was disappointed.

    Adam Frank, a professor of astrophysics at the University of Rochester, wrote the essay that appeared in the Times. Frank is a gifted scientist, and a thoughtful science writer. He begins the op-ed with an enthusiastic update on the ongoing exoplanet revolution. I must confess I share his enthusiasm. I suspect that future historians of science will wonder what it was like to live in this moment. A little more than two decades ago, we weren’t sure whether there were any planets outside our solar system. Now we have reason to believe that nearly all stars host planets, and that many of them are rocky and wet like our own. No generation of humans has ever gazed up at night skies so pregnant with possibility.

    It is precisely this profusion of planets that gives Frank confidence that ours is not the first intelligent civilization. “Given what we now know about the number and orbital positions of the galaxy’s planets,” he tells us, “the degree of pessimism required to doubt the existence, at some point in time, of an advanced extraterrestrial civilization borders on the irrational.” Most of us have heard a version of this argument, late at night, around a campfire: Look at all the stars in the night sky. Is it really possible that all of their planets are sterile, and all of their predecessors, too?

    These arguments have their appeal, but it is an appeal to intuition. The simple fact is that no matter how much we wish to live in a universe that teems with life—and many of us wish quite fervently—we haven’t the slightest clue how often it evolves. Indeed, we aren’t even sure how life arose on this planet. We have our just-so stories about lightning strikes and volcanic vents, but no one has come close to duplicating abiogenesis in a lab. Nor do we know whether basic organisms reliably evolve into beings like us.

    We can’t extrapolate from our experience on this planet, because it’s only one data point. We could be the only intelligent beings in the universe, or we could be one among trillions, and either way Earth’s natural history would look the exact same. Even if we could draw some crude inferences, the takeaways might not be so reassuring. It took two billion years for simple, single-celled life to spawn our primordial lineage, the eukaryotes. And so far as we can tell, it only happened once. It took another billion years for eukaryotes to bootstrap into complex animal life, and hundreds of millions of years more for the development of language and sophisticated tool-making. And unlike the eye, or bodies with legs—adaptations that have arisen independently on many branches of life’s tree—intelligence of the spaceship-making sort has only emerged once, in all of Earth’s history. It just doesn’t seem like one of evolution’s go-to solutions.

    Frank compresses each of these important, billions-of-years-in-the-making leaps in evolution into a single “biotechnical” probability, which is meant to capture the likelihood of the whole sequence. For all we know, each step could be a highly contingent cosmic lottery win. Perhaps eukaryotes “usually” take tens of billions of years to evolve, and we lucked into an early outlier on the distribution curve. Perhaps we have been fortunate at every step of the way. Frank’s argument skips over these probabilities. Or rather, it bundles them up into a single, tidy unknown, that he can hammer with a big italicized number:

    “What our calculation revealed is that even if this probability [that technological civilization evolves] is assumed to be extremely low, the odds that we are not the first technological civilization are actually high. Specifically, unless the probability for evolving a civilization on a habitable-zone planet is less than one in 10 billion trillion, then we are not the first.”

    Absent a clear account of how often we can expect planets to spawn technological civilizations, we don’t have any way to evaluate that “10 billion trillion” number. We certainly don’t have grounds to say that the “odds are high” that some civilization preceded ours, or enough evidence to suggest that skepticism about the possibility “borders on the irrational.”

    See the full article here .

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  • richardmitnick 10:16 am on March 25, 2016 Permalink | Reply
    Tags: , , Clouds Might Ruin Our Chance to Spot Extraterrestrial Life, The Atlantic   

    From The Atlantic: “Clouds Might Ruin Our Chance to Spot Extraterrestrial Life” 

    Atlantic Magazine

    The Atlantic Magazine

    Mar 22, 2016
    Joshua Sokol

    Between the fall of 2012 and the fall of 2013, astronomers took a deep, long look into the atmosphere of GJ 1214b, a distant Earth-sized planet in a tight orbit around a cool, red star. Fifteen times it crossed the face of its star as the Hubble Space Telescope watched.

    NASA/ESA Hubble Telescope
    NASA/ESA Hubble Telescope

    Each time, starlight would pass through the thin ring of atmosphere around the planet. Some of it would catch on airborne molecules—methane, carbon dioxide, or maybe even water vapor—leaving a spectral fingerprint.

    At least that’s what the astronomers hoped. It had worked for bigger, hotter planets, and now we’d be able to understand the atmosphere of one of the most earth-like exoplanets known. Going forward, we would use the same method to look at ever more familiar worlds, sniffing for chemicals that might have been exhaled by living organisms. With this trial run on GJ 1214 b, however, there was just one problem.

    We saw nothing.

    Or, to say it in a kinder way, we saw something else amazing: a world enshrouded in alien clouds. The spectrum, painstakingly measured from light filtered through the planet’s atmosphere, didn’t show the telltale spikes and wiggles of molecules. Instead, it was featureless and flat.

    In a paper published in Nature, astronomers inferred that an opaque layer of clouds had blocked Hubble’s view. Suddenly, small planets around other stars seemed lot harder to probe, even for the world’s most powerful observatory. “They got a tremendous amount of Hubble Space Telescope time just to study that one planet in exquisite detail,” says Jonathan Fortney, an astronomer at the University of California, Santa Cruz. “And that spectrum came back flat as a line.”

    UC Santa Cruz

    At that point, you could still hold out hope. “It was still just one planet. We weren’t yet at the point where we had a couple others, but it really shows the seriousness of the situation,” he says.

    Within the year, though, one planet became several. In 2014, three more small worlds with their own cumbersome names—HD 97658b, GJ 436b, and GJ 3470b—turned out featureless and inscrutable. To this day, only a handful of molecules have been tentatively detected in the atmospheres above alien worlds smaller than Neptune.

    Clouds, as it turns out, are everywhere.

    You can find them in every atmosphere in our own solar system, even Pluto, which perhaps should have given us a hint. In endless permutations, they condense out of atmospheric chemistry, or cook up under the glare of the Sun. But in the puffy atmospheres of so-called “super-Earths”—which are common around other stars but absent from our solar system—astronomers were hoping for clearer skies.

    “This is a double edged sword,” says MIT’s Zach Berta-Thompson, who is currently trying to use Hubble to study the newly discovered GJ 1132 b, a small, rocky world thought to resemble Venus. “It’s really exciting to know that we have clouds that we didn’t expect in some of these planetary atmospheres,” he says. “But on the other hand it’s really frustrating, because as astronomers, clouds are our natural born enemies—whether those clouds are around Earth or another planet.”

    Berta-Thompson’s MIT colleague Sara Seager puts it more bluntly. Right now, Seager is working on building up a library of atmospheric signatures that might herald the presence of life on faraway planets. She hopes to find not just one but a handful of possibly inhabited worlds in the next few decades—a hard task made even harder if we keep seeing cloudy planets like GJ 1214 b.

    “That would be a disaster for everything we’re working towards,” Seager says. “If every planet has clouds to the level that one does, it might kill all our dreams.”

    “We need to be a little bit more creative in the observations we do,” Morley says. For one, we can study planets at times outside of when they are passing in front of their stars. Although looking at starlight shining through the ring of atmosphere is a powerful tool, our line of sight takes us the long way through sheets of clouds.

    The idea is that in other phases of the planet’s orbit, as it moves beside its star and then behind it, we can pick out starlight that reflects off the planet’s atmosphere. Or perhaps we could even see a glow from the atmosphere itself.

    For example, hotter planets shouldn’t be able to form the hazes that blanket colder bodies like Saturn’s moon Titan. Instead, molecules in these same hot atmospheres should emit their own faint light that would pass through clouds, which might be measurable with next-generation telescopes. Or on planets much colder than our own, clouds made from frozen grains of water, methane, or ammonia should be highly reflective, which will help us pick up the signature of those molecules.

    And for a vast swath of lukewarm planets, even those are completely covered by clouds, we can at least figure out what kind of clouds we’re dealing with by looking at how the reflected light changes with angle. “We should be able to tell the difference between different types of clouds or hazes,” Morley says.

    See the full article here .

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  • richardmitnick 5:40 pm on September 10, 2015 Permalink | Reply
    Tags: , , The Atlantic   

    From The Atlantic: “How Data-Wranglers Are Building the Great Library of Genetic Variation” 

    Atlantic Magazine

    The Atlantic Magazine

    Sep 9, 2015
    Ed Yong


    A huge project unexpectedly led to a way of finding disease genes without needing to know about diseases.

    Let’s say you have a patient with a severe inherited muscle disorder, the kind that Daniel MacArthur from the Broad Institute of Harvard and MIT specializes in. They’re probably a child, with debilitating symptoms and perhaps no diagnosis. To discover the gene(s) that underlie the kid’s condition, you sequence their genome, or perhaps just their exome: the 1 percent of their DNA that codes for proteins. The results come back, and you see tens of thousands of variants—sites where, say, the usual A has been replaced by a T, or the typical C is instead a G.

    You’d then want to know if those variants have ever been associated with diseases, and how common they are in the general population. (The latter is especially important because most variants are so common that they can’t possibly be plausible culprits behind rare genetic diseases.) “To make sense of a single patient’s genome, you need to put it in the context of many people’s genomes,” says MacArthur. In an ideal world, you would compare all of a patient’s variants against “every individual who has ever been sequenced in the history of sequencing.”

    This is not that world, at least not yet. When Macarthur launched his lab in 2012, he started by sequencing the exomes of some 300 patients with rare muscle diseases. But he quickly realized that he had nothing decent to compare them against. It has never been easier, cheaper, or quicker to sequence a person’s genome, but interpreting those sequences is tricky, absent a comprehensive reference library of human genetic variation. No such library existed, or at least nothing big or diverse enough. So, MacArthur started making one.

    It was hard work, not because the data didn’t exist, but because it was scattered. To date, scientists have probably sequenced at least 5,000 full genomes and some 500,000 exomes, but most are completely inaccessible to other researchers. There might be intellectual-property restrictions, or issues around consent. There’s the logistical hassle of shipping huge volumes of data on hard drives. And some scientists are just plain competitive.

    Fortunately, MacArthur’s colleagues at the Broad Institute and beyond had deciphered so many exomes that he could gather thousands of sequences by personally popping into offices. Buoyed by that success, he started contacting people who were studying the genomes of people with cancer, heart disease, diabetes, schizophrenia, and more. “There’s a big swath of human genetics where people have learned that you either fail by yourself or succeed together, so they’re committed to sharing data,” MacArthur says.

    By 2014, he had amassed more than 90,000 exomes from around a dozen sources, collectively called the Exome Aggregation Consortium. Then, he had to munge them together.

    That was the worst bit. Researchers use very different technologies to sequence and annotate genomes, so combining disparate data sets is like mushing together the dishes from separate restaurants and hoping that the results will be palatable. Often, they won’t be.

    Monkol Lek, a postdoc in MacArthur’s lab who himself has a genetic muscle disease, solved this problem by essentially starting from scratch. He took the raw data from some 60,706 patients and analyzed their exomes, one position at a time. The raw sequences took up a petabyte of memory, and the final compressed file filled a three-terabyte hard disk.

    The prize from all this data-wrangling was one of the most thorough portraits of human genetic variation ever produced. MacArthur went through the main results in the opening talk of this week’s Genome Science 2015 conference, in Birmingham, U.K. His team had identified around 10 million genetic variants scattered throughout the exome, most of which had never been described before. And most turned up just once in the data, meaning that they lurk within just one in every 60,000 people. “Human variation is dominated by these extremely rare variants,” says MacArthur. That’s where the secrets of many rare genetic disorders reside.

    But unexpectedly, the most interesting variants turned out to be the ones that weren’t there.

    The graduate student Kaitlin Samocha developed a mathematical model to predict how many variants you’d expect to find in a given gene, in a population of 60,000 people. The model was remarkably accurate at estimating neutral variants, which don’t change the protein that’s encoded by the gene, and so have minimal impact. But the model often wildly overestimated the number of “loss-of-function variants,” which severely disrupt the gene in question. Repeatedly, the ExAc data revealed far fewer of these variants than Samocha’s model predicted.

    Why? Because many of these loss-of-function variants are so destructive that their carriers develop debilitating disorders, or die before they’re even born. So, the difference between prediction and reality reflects the brutal hand of natural selection. The variants are simply not around to be sequenced because they have long been expunged from the gene pool.

    For example, the team expected to find 161 loss-of-function variants in a gene called DYNC1H1. By contrast, the ExAc data revealed only four—and indeed, DYNC1H1 is associated with several severe inherited neurodevelopmental disorders.

    The model also predicted 125 loss-of-function variants in the UBR5 gene—and the data revealed just one. That’s far more interesting because UBR5 has never before been linked to a human disease.

    A full quarter of human genes are like this: They have a lower-than-expected number of loss-of-function variants. And while some of them are known “diseases genes,” the rest have never been pinpointed as such. So, if you find one of these variants in a patient with a severe genetic disorder, the chances are good that you’ve found a genuine culprit.

    That blew my mind. Here is a way of identifying potential disease-related genes, without needing to know anything about the diseases in question. Or, as MacArthur said in his talk, “We should soon be able to say, with high precision: If you have a mutation at this site, it will kill you. And we’ll be able to say that without ever seeing a person with that mutation.”

    These results speak to one of the greatest challenges of modern genomics: weaving together existing sets of data in useful ways. They also vindicate the big, expensive studies that have searched for variants behind common diseases like type 2 diabetes, heart disease, and schizophrenia. These endeavors have indeed found several variants, but with such small effects that they explain just a tiny fraction of the risk of each condition. But “all this data can be re-purposed for analyzing rare diseases,” says MacArthur. “Without those large-scale studies, we’d have no chance of doing something like ExAc.”

    “His talk really shows that you can’t anticipate what these data sets will show you until you put them together,” says Nick Loman from the University of Birmingham. “Our ability to interrogate biology if you can put hundreds of thousands, or millions, of genomes together is massive.”

    See the full article here .

    Please help promote STEM in your local schools.

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