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The size of an atomic nucleus but weighing as much as a small asteroid—that's a tiny black hole for you. Here, the asteroid Ida.

Why Can't We Prevent An Asteroid Strike?

<p>
 When a meteor streaked over Russia last month and exploded in the sky above Chelyabinsk, shattering windows and injuring nearly 1,500 people, it was a reminder that the Earth moves blithely through a curtain of speeding asteroids, some of which occasionally pay a visit. Star gazers, of course, see these reminders many times a night in the shape of shooting stars—the glowing trails created by small specks of rock burning up as they enter the atmosphere. But when an object is large enough to make it through most of the atmosphere intact and strike—or nearly strike—the surface, “oohs” and “aahs” are not the first things on people’s lips.
</p>
<p>
 It was an asteroid, after all, whose impact—with resulting mega-tsunamis, super-heated dust clouds, and years-long dusk—contributed to the doom of the dinosaurs. A far smaller one in 1908 leveled 80 million trees with a force a thousand times more powerful than the Hiroshima bomb in remote Tunguska, Siberia. And on the very same day that the Chelyabinsk meteor made its presence known, a roughly Tunguska-sized asteroid known as 2012 DA14 skimmed between the Earth and some of our own satellites, a one-two punch that has people asking just what, exactly, we are doing to protect ourselves.
</p>
<div class="related"></div>
<p>
 In fact, “mind the asteroids” has been on the to-do list of the world’s spacefaring nations for some time. Scientists have long had a general portrait of the solar system’s historical population of asteroids, from keeping a tally of the craters on Earth, the Moon, and neighboring planets. Watching fragments of the Shoemaker-Levy 9 comet slam into Jupiter in 1994, the largest piece hitting with a force of 600 times the world’s nuclear arsenal, added a bit of urgency to the task of discovering the locations of asteroids whizzing about our system, recalls planetary scientist Don Yeomans, manager of the Near Earth Objects Program at NASA’s Jet Propulsion Laboratory. In 1998, NASA committed to finding and tracking 90% of asteroids greater than 1 km in size in ten years, which they finished slightly behind schedule. Though none of those are on track to hit us in the next 100 years, they are far from the whole population of asteroids that could harm us—the Tunguska object is thought to have been around 30 meters wide, less than 1/30 th the size of the smallest asteroid tracked by the 1-km survey.
</p>
<p>
 Given the recent scare from the Chelyabinsk meteor, you’d think rallying further support to find, track, and defend against asteroids would be relatively easy. But as a Congressional hearing last week on the topic showed, it’s not. Over and over again, Congress tried to wrap their heads around how much was reasonable to spend on the issue. It’s not a simple calculation for humans to make. Asteroid strikes are rare yet stupendously destructive—something they have in common with terrorist attacks and nuclear power plant accidents—but, says David Ropeik, a consultant and journalist who writes about risk perception, they are missing something that makes preparing for those disasters an easy sell—personal experience.
</p>
<div class="ad"></div>
<p>
 “When we think about risk, we’re not using our ‘rational,’ just-the-facts, analytical brain—we’re using our instinctual, feeling brain,” he says. And because none of these policymakers, or most of the public, have actually witnessed the destruction wrought by an incoming asteroid themselves, asteroid strikes don’t feel real.
</p>
<h2>
 Weighing the Odds
</h2>
<p>
 On the face of it, the numbers are pretty straightforward. An asteroid strike the size of the one linked to the dinosaur extinction is calculated to happen only once every 100 million years. But “civilization-destroying” impacts are estimated to happen every 500,000 years or so. Tunguska-sized asteroids, capable of destroying whole cities, are thought to hit every 300 years. They may not strike in populated areas—the interval for that, as estimated by a landmark 1992 NASA
 <a href="http://impact.arc.nasa.gov/downloads/spacesurvey.pdf">
  report
 </a>
 requested by Congress, is once every 3,000 years, and for specifically urban areas 100,000 years. But even if they hit in the oceans, they could cause enormous tsunamis on the coasts. At any rate, asteroids of various sizes will certainly strike us—perhaps not in the next few decades or even in the next hundred years, but within the foreseeable human future.
</p>
<div class="pullquote">
<p>
 At this point, we would need 10-20 years of advance notice to prepare.
</p>
</div>
<p>
 Here’s the thing about asteroid strikes that makes them different from many other natural disasters—they are preventable. If we know about an asteroid’s collision course ahead of time, we can nudge the object, changing its course so it whizzes by without hitting us. There are a variety of ideas on how best to do this, ranging from using a nuclear bomb to painting the incoming object white (or black) so photons will push it off track. But the technique that NASA officials say will likely make the most sense, depending on the situation, involves ramming it with a spaceship, similar to what NASA’s Deep Impact mission did to the comet 9P/Tempel in 2005. It’s a process that has to be carefully engineered: you have to know the asteroid’s size, shape, speed, projected orbit, and composition to calculate the effect of the impact.
</p>
<p>
 At this point, Yeomans estimates, we would need 10-20 years of advance notice to prepare—to build a ship, launch it, hit the asteroid, and allow time for the spacecraft’s small nudge to sufficiently skew the object’s trajectory so it misses Earth. “If you find one that’s going to hit tomorrow morning or within three weeks, or even within a few months, there’s not a whole lot you can do about it except evacuate the affected areas,” he says. “The search is the most important.”
</p>
<h2>
 Hunting for Asteroids
</h2>
<p>
 In 2005, as a follow-up to the survey begun in 1998, Congress asked NASA to find 90% of all asteroids 140 meters or larger by 2020. That phase is going slowly enough, however, that it won’t meet Congress’s goal in time. “We’ve done the best we could with the money that’s appropriated for us,” says Lindley Johnson, the NASA executive in charge of the Near-Earth Object Program. “The systems we have are for larger objects…We could do it with the assets we have available given enough time. But if you want to accomplish it on the order of a decade or two, you of course have to have more capable systems in order to do that.”
</p>
<div class="pullquote">
<p>
 The entire federal budget for asteroid detection is 1/20,000 th of what we spend on homeland security.
</p>
</div>
<p>
 The fact that such surveys exist is an improvement on earlier eras, but the pace of asteroid discovery and its dependence on public funding has some people worried. Not that an optimally supported search program would be that expensive: the National Academies of Science
 <a href="http://www.nationalacademies.org/printer/morenews/20090812.html">
  estimates
 </a>
 $100 million a year. By comparison, that’s the
 <a href="http://www.fhwa.dot.gov/programadmin/erelief.cfm">
  same amount
 </a>
 the Federal Highways Administration is authorized to give a state to rebuild roads after a single natural disaster. If building and testing a mitigation program are factored in, an asteroid defense system would cost something like $2 billion between now and 2025. That’s just under $200 million per year.
</p>
<p>
 But a program to prevent something that feels as distant as an asteroid strike, while relatively cheap compared to other government endeavors, may not always get the support it needs from elected officials, or the general public.
</p>
<p>
 Last week, construction and staff jobs at the Pan-STARRS telescope system in Hawaii, which is used for near-Earth-object observation, among other purposes, had to be rescued by an anonymous $3 million donation after federal funding was cut. Corey Powell, editor-at-large at
 <i>
  Discover Magazine
 </i>
 , recently estimated that the federal budget for asteroid detection is
 <a href="http://blogs.discovermagazine.com/outthere/2013/02/16/feds-finding-an-incoming-asteroid-is-120000th-as-important-as-homeland-security/">
  1/20,000 th
 </a>
 of what we spend on homeland security, and about
 <a href="http://blogs.discovermagazine.com/outthere/2013/02/20/the-case-for-building-a-death-star/">
  one-fifth
 </a>
 of Congress’s yearly budget for free postage. From the public’s point of view, maybe that’s enough: a recent headline at
 <a href="http://www.buzzfeed.com/nowthisnews/congress-holds-asteroid-hearing-because-there-are-749g">
  NowThisNews
 </a>
 quipped, “Congress Holds Asteroid Hearings, Because There Are No Other Problems.”
</p>
<p>
 Despite this apathy, the urgency in some quarters is such that the nonprofit B612 Foundation is planning to build and, in 2018, launch an asteroid-spotting infrared space telescope to pick up where NASA has slowed down.
</p>
<p>
 “There’s no sense in us trying to beat on the federal government to do it. Private initiatives in space are where things are heading these days,” says Rusty Schweickart, a former astronaut who co-founded B612. “When you really look at it, this is no bigger than a community putting in a performing arts center or a new wing on a hospital…you’re talking $400 million, so let’s just do it!” He estimates that in the six and a half years the telescope is expected to operate, it will find about 95% of the 140-meter asteroids NASA has been tasked with finding.
</p>
<h2>
 Political Hurdles
</h2>
<p>
 While B612’s telescope may speed detection along, ultimately it is governments that must decide what we should do when an incoming asteroid is sighted. Once an asteroid is found, space agencies will be able to determine approximately where on Earth it will strike, and it’s not hard to see how tensions might rise quickly, and how difficult it might be to hold a calm, reasoned discussion about which spacefaring nation should do what and who is responsible if things go wrong. Currently, a UN subcommittee is working to put together a protocol to address the issue before it becomes a crisis. But how much attention the problem gets will depend on how palpable policymakers feel it is.
</p>
<p>
 At a House hearing on March 19, with mentions of sequester bouncing around, one representative asked John Holdren, the president’s science advisor, to estimate the cost-effectiveness of an asteroid-strike-prevention program. Holdren answered with the facts—that when you consider the amount of human life that would be lost and amortize that over a reasonable number of years, you get something like 100 deaths per year due to asteroids. It’s relatively small compared to 1 million deaths annually from malaria and 5 million from tobacco, Holdren admitted.
</p>
<p>
 But that sort of accounting does not accurately reflect the possible devastation of a large strike. “What is the value of all civilization?” Holdren asked. “It is a very big number. We just can’t get at it that way.”
</p>
<p>
 That exchange illustrates the intractable nature of the problem, Ropeik says. “We haven’t evolved to have instincts for some risks that require a little more careful, rational thought, like this one.” Asteroid strikes occupy a tragic blind spot in the human mind. Like climate change, they are potentially avoidable but extremely difficult for us to confront. “It doesn’t feel real,” Ropeik says. “It feels just not-real enough to be able to ignore.”
</p>
<p>
 Perhaps to help things feel more real, it might help to revisit one of the only known accounts of the last time a major object struck the Earth: Tunguska, 1908. According to S.B. Semenov, who was sitting on the porch of a Siberian trading post that June evening, he first saw what looked like a fire above the trees before him. Then a shockwave blew him off the porch. His shirt was so hot, he said, that it felt like it was on fire. He was more than 40 miles away from the spot where the asteroid crashed into the Earth.
</p>
<div class="newsletter"></div>
<p>
 Image courtesy NASA
</p>

<p>Asteroid strikes are rare yet stupendously destructive—something they have in common with terrorist attacks and nuclear power plant accidents—but, they are missing something that makes preparing for those disasters an easy sell—personal experience.</p>

Pursuing Dark Matter, Hundreds of Miles Above Earth

<section class="entry-content instapaper_body clearfix" itemprop="articleBody">
<div class="add-container clearfix" id="add-block-placer">
</div>
<p>
  “That’s a cosmic ray.” A few seconds later: “And that’s another cosmic ray.”
 </p>
<p>
  Samuel Ting, a Nobel Laureate and professor of physics at MIT, is standing before a monitor in his office above a high-ceilinged control room outside Geneva, Switzerland, calling out cosmic rays striking a detector orbiting hundreds of miles above the Earth. The monitor shows a schematic of the detector picking up the events. Lines draws themselves across the screen, turning green where they hit the instrument.
 </p>
<figure class="richtext-image full-width">
<img alt="" class="richtext-image full-width" src="https://staging.pbs.org/wgbh/nova/media/images/ams_on_iss_700k.width-990_0xrXzaJ.jpg"/>
<figcaption>The AMS detector aboard the International Space Station
        
    </figcaption>
</figure>
<p>
  The control room below is dominated by a map of the world that covers an entire wall. Unfurling across it in lazy S-curves are a series of trajectories—the future paths of the International Space Station, the orbital home of the Alpha Magnetic Spectrometer (AMS-02), a 7.5-ton, $2 billion device that’s tasked with looking for dark matter. Computers manned 24 hours a day by researchers monitoring AMS sit in a horseshoe shape before the massive map. Ting, lead researcher on AMS, has shepherded the project from the its conception nearly 20 years ago, and he looks at the detector schematic with a certain pride.
 </p>
<figure class="richtext-image full-width">
<img alt="AMS control room" class="richtext-image full-width" src="https://staging.pbs.org/wgbh/nova/media/images/ams-control-room.width-990_c9YiEQu.jpg"/>
<figcaption>Inside the AMS control room at CERN
        
    </figcaption>
</figure>
<p>
  Elsewhere in the sprawl of buildings that makes up CERN, physicists tend experiments that happen beneath their feet in the Large Hadron Collider. Here, the AMS team looks up instead, waiting for signs of dark matter via cosmic rays, the high-energy particles that whip through the solar system from regions beyond. Dark matter is one of the items on CERN researchers’ to-find list.
 </p>
<p>
  When the LHC comes back online in 2015 after maintenance is completed, physicists will continue searching for signs of dark matter in its more powerful collisions. But for the AMS team, the hunt for dark matter is happening now. As you read this, data from the detector is streaming down from the ISS to computers on Earth, each a tiny pixel in the very large picture that is the universe.
 </p>
<h2>
  Eighty Years
 </h2>
<p>
  The first suggestion of dark matter’s existence was in 1933, when Swiss astronomer Fritz Zwicky was studying the Coma galaxy cluster. He calculated the mass of those galaxies in two ways: first, by judging their speed, which is related to the pull of gravity they exert on each other, and then by judging from the light they released. Far from lining up, the two numbers were terrifically different. The gravitational mass was ten times more than the mass implied by the galaxies’ light. The best explanation, the one that drives the search for dark matter today, was that there was a whole lot of matter in those galaxies that telescopes couldn’t detect—matter that didn’t produce radiation or light of any kind.
 </p>
<aside class="pulledquote">
  What, exactly, it consists of is a puzzle.
 </aside>
<p>
  Cosmologists and astrophysicists have since built simulations of how dark matter might be distributed around the universe, producing beautiful three-dimensional mazes of clumps and strands. And research has established that there is much, much more dark matter—more than five times as much—than the kind of matter that makes up both us and the stars. But what, exactly, it consists of is a puzzle that experimental particle physicists and theorists alike have been spinning stories about for decades.
 </p>
<p>
  One leading idea is that dark matter is a particle that almost never interacts with anything else, called a weakly interacting massive particle, or WIMP. That would fit nicely into existing theories about the complement of particles that populate the universe. But first, researchers have to find them.
 </p>
<h2>
  Three Possibilities
 </h2>
<p>
  Sitting at a table in the CERN cafeteria, Heidi Sandaker, a professor at University of Bergen in Norway and a physicist on the ATLAS experiment in the Large Hadron Collider, sketches diagrams on a sheet of graph paper. She lays out the three types of experiments you can do that would show signs of dark matter.
 </p>
<p>
  For one of them, physicists place detectors at the bottom of a mine, where the earth filters out a lot of noise, to look for signs of an extremely rare interaction between a dark matter particle and a standard matter particle. The results of these types of interactions would be very subtle, perhaps just a few electrons out of place. The second option involves ramming particles together in an accelerator and checking afterward to see whether there’s less energy released than you’d expect, which could be a sign that a dark matter particle was created and went off on its merry way. And the third requires sending a detector up into space, far from the interference of the atmosphere, to see whether certain particles bouncing around out there are more or less numerous than you would expect, which could be the result of dark matter particles colliding with each other. The last, of course, is why AMS is up on the International Space Station.
 </p>
<figure class="richtext-image full-width">
<img alt="" class="richtext-image full-width" src="https://staging.pbs.org/wgbh/nova/media/images/bulletcluster_comp_f2048.width-990_AReSVNA.jpg"/>
<figcaption>The blue hues in this composite image of the "bullet cluster" show where dark matter is distributed. The image was created by gravitational lensing of galaxies in the background.
        
    </figcaption>
</figure>
<p>
  These different approaches complement each other because the search for dark matter has a lot in common with looking for your missing keys. It’s all about ruling out places they might be—or in this case, what traits dark matter might have. But unlike looking for your keys, coming up empty-handed at the end of one trawl for information can actually be cause for celebration.
 </p>
<p>
  Last year, the LUX experiment turned up no sign of dark matter at all, and scientists reported it with a certain sense of glee, according to Dennis Overbye, who
  <a href="http://www.nytimes.com/2013/10/31/science/space/dark-matter-experiment-has-found-nothing-scientists-say-proudly.html?_r=0" target="_blank">
   wrote about the “failure” wryly in the
   <i>
    New York Times
   </i>
</a>
  . That’s because the LUX experiment, one of the underground variety, would only detect signs of dark matter if the WIMPs were especially light and numerous. That it found nothing means that they must be on the heavier and rarer side, if they exist. (It’s not in the couch, everyone—onward, to the shelf in the bathroom!) Given the wide variety of error margins and detector types, lining up the results from all the different experiments isn’t a simple task. But that’s the idea.
 </p>
<p>
  In the years before the maintenance shutdown, experiments at the LHC already ruled out a swath of lighter solutions. But when the collider starts up again in 2015, it will be accelerating particles at higher energy levels than ever before. That means the collisions will be more intense, and in the traces that remain, researchers will be able to look for signs of dark matter candidates in the heavier, yet-to-be-ruled-out range. Physicists also intend to ramp up the number of collisions to many times more than when the LHC was working at lower energy levels, so that means there will be plenty of chances to see something, Sandaker says.
 </p>
<h2>
  Shower of Particles
 </h2>
<p>
  AMS, for its part, has been gathering data continuously since its launch in 2011. And the team has already seen some suggestive tentative results. As cosmic rays pass through the detector up on the space station, researchers on the ground can tell certain things about the particles. The detector has a cylindrical magnet at its heart, explains physicist Mike Capell, a senior research scientist on AMS, and when cosmic rays pass through the magnet, their paths curve ever so slightly. This curve, along with myriad other measurements taken by a suite of devices, tells researchers the particles’ momentum, charge, and classification—for instance, if it’s an electron versus a proton. Anywhere from a few hundred to a couple thousand particles whiz through every second, depending on where the space station is in its commute. (The display in Ting’s office, with one ray every few seconds, is a kind of “greatest hits” from that shower.)
 </p>
<p>
  AMS is taking a census of those particles, making a note of whether they’re, say, a stray nucleus from helium atom, one from a carbon atom, an electron, a positron (a particle with the same mass as an electron but opposite charge), or any number of other things. The idea is to see whether that census corresponds to what current theories about cosmic rays imply should be there. If there’s a discrepancy, that could be a signature of dark matter. For instance, when two dark matter particles collide, they are thought to produce an electron and a positron. If there are more positrons at high energies than expected, then that could be a clue that dark matter is out there, colliding with itself.
 </p>
<figure class="richtext-image full-width">
<img alt="CERN AMS control building" class="richtext-image full-width" src="https://staging.pbs.org/wgbh/nova/media/images/cern-ams-control-building.width-990_Iquj0EW.jpg"/>
<figcaption>The AMS control center at CERN
        
    </figcaption>
</figure>
<p>
  In 2013, the AMS team announced that they had, in fact, seen just such an excess. “You expect a fraction of positrons from garden-variety physics, but it’s not nearly as many positrons as we found,” Capell says. “So why would you have an excess of positrons? You would have them if you didn’t have garden-variety physics happening, if you had dark matter colliding.” Earlier experiments with the Fermi Large Area Telescope and the satellite-borne PAMELA had reported similar results, but not with AMS’s precision.
 </p>
<p>
  Still, it’s not proof that dark matter is producing these positrons. Unlike in LHC experiments, where researchers can control every input and predict outcomes in detail, AMS is just recording what nature produces. There could be other sources that explain the positron bump. One possibility among many is that the positrons are being emitted by a pulsar, a dense left-over from the death of a gigantic star that sprays out a plume of radiation. But if a pulsar were the source, the positrons would all be coming from one particular direction, and the AMS team has reported that was not the case.
 </p>
<p>
  Work to clarify those results goes on because there are still plenty of other things that could be yielding these results. “If this was dark matter, depending on the properties of the dark matter, we would expect to see deviations in other spectra and ratios,” Capell says. “For example, anti-proton to proton ratios would have something goofy. And we’re also working on that.”
 </p>
<h2>
  Twelve Million to Go
 </h2>
<p>
  Clearer answers will emerge as AMS continues to collect data. Yes, these extra positrons are predicted by theory, but so is a dearth of positrons at even higher energies, where the picture provided by AMS is still fuzzy. It’s a measurement that’s only possible with more time and more events recorded. “It agrees with the dark matter model, but it doesn’t prove it,” Ting says of the current data. “It’s necessary but not sufficient.”
 </p>
<p>
  Ting estimates it will take a few years to gather enough data to fill in the picture of the positrons, about 12 million more collisions between cosmic rays and the detector. For now, Ting says, “Something unusual is happening. We still do not know what it is.”
 </p>
<p>
  One the way out, I stop in the lobby outside the AMS control room, where the view from a camera looking out from AMS is projected on a screen. An array of solar cells looms and then drifts into shadow, leaving just the bright line of the edge of the Earth. Invisible to my eye, thousands of particles strike the detector and send their messages, via a string of satellites, down to this building. Here, they’ll be added to the great puzzle of experimental and observational results that is our sense dark matter and, in a way, of the universe.
 </p>
</section>
<p>
 Photo credits: NASA,
 <a href="http://www.flickr.com/photos/simsullen/sets/72157630882599456/with/7678048358/">
  Simon Bierwald/Flickr (CC BY-NC-SA)
 </a>
</p>

We're about 12 million cosmic ray collisions from better understanding dark matter, say physicists at CERN.

Saving the Sun

<p>The same technologies that will rid the electric grid of fossil fuels could also save it from potential disaster.</p>

Hope from the Deeps for Coral Reefs

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<div class="add-container clearfix" id="add-block-placer">
</div>
<p>
  Eight miles south of the island of St. Thomas, under a blazing Caribbean sun, Tyler Smith and Marilyn Brandt watch the ocean floor scroll by. Below the rolling fiberglass hull of their research vessel is a reef, and with a camera lowered on a cable, they can see what’s living down there and what shape it’s in. Platters of what looks like stone covered with muted yellow moss drift past—mountainous star coral and boulder star coral, mostly—with purple sponges waving gently. At 125 feet down, it’s deep for this kind of reef. Every now and then a white patch on the coral appears, looking shockingly bright in the twilight of the reef.
 </p>
<p>
  Each plate is coated with hundreds of organisms a few millimeters in size. These coral polyps, as the individuals are known, look like tiny flowers. Within their cells, they host algae that garner energy from the sunlight through photosynthesis and share it with the coral. The polyps create calcium carbonate armor for themselves over the course of their lifetimes, and when they die, their empty armor is what the next generation of polyps anchors themselves to, creating, over time, an enormous mass of calcium carbonate with a thin rime of vibrant life—a coral reef. “You get into it for the aesthetics,” reflects Smith, a professor of marine biology at the University of the Virgin Islands on St. Thomas.
 </p>
<figure class="richtext-image full-width">
<img alt="" class="richtext-image full-width" src="https://staging.pbs.org/wgbh/nova/media/images/coral-branch.width-990_aGdYsJr.jpg"/>
<figcaption>Coral reefs are built by individual polyps secreting calcium carbonate, which builds up over time to create elaborate structures.
        
    </figcaption>
</figure>
<p>
  But when the water temperature rises past a certain point and stays that way for weeks, as it has a marked tendency to do these days, the relationship between the coral and the algae breaks down. The algae are ejected from the coral, rendering it a ghostly white, and as time passes, the polyps starve to death. Along with a panoply of other threats, most of them traceable to humans—including ocean acidification, which interferes with corals’ ability to build their armor, overfishing, and sediment that smothers coral—this coral bleaching is part of the decline of reefs worldwide.
 </p>
<p>
  Some researchers think that deeper reefs, like the one off of St. Thomas, might be insulated from the worst of the damage by their distance from the warm surface. Last year, Smith and colleagues released a study  supporting the idea that deeper waters could be safe havens—the so-called deep reef refugia hypothesis. If the hypothesis turns out to hold, it might help make the difference between life and death for the builders of some of the planet’s most awe-inspiring ecosystems.
 </p>
<h2>
  Refugia’s Origins
 </h2>
<p>
  In 1969, ornithologist Jurgen Haffer put forth the idea that, over eons, scraps of humid forest could have served as long-term hideouts, or refugia, for bird species when their woodland habitat turned to dry savannah. When the coast was clear—or rather, moist—the birds, now perhaps evolved to be more different from each other than before, radiated outward again. Though the refugia theory started out as a way to explain the birth of new species, it has grown in importance in conservation biology. Researchers are actively seeking places whose preservation stands a good chance of aiding the survival of a large number of species.
 </p>
<p>
  For corals in particular, the idea can be traced back to 1996. While considering the causes of coral bleaching, Peter Glynn of the University of Miami wondered whether there weren’t places where death might not come so fast. Perhaps if cold water from the deeps welled up regularly to wash over shallow coral, or if species from the shallows could persist in deeper places, more secluded from the heat that starves corals on the heights, they might survive over the long term. And then they might send their seed to the decimated areas when the heat passed. In the years since, that simple statement has sparked a great deal of research. Glynn’s paper  has been cited nearly 500 times.
 </p>
<p>
  Some of the enthusiasm may stem from the fact that to be a coral scientist is to buy front-row tickets to a tragedy. Brandt, also a professor of marine biology at UVI, traces her vocation to falling in love with the reefs around Little Cayman Island on a summer research trip. Logan Williams, a UVI graduate student in marine biology who grew up on St. Thomas, recalls snorkeling among vivid, living corals as a child.
 </p>
<aside class="pulledquote">
  Glynn wondered whether there weren’t places where death might not come so fast.
 </aside>
<p>
  But starting in 1999, Brandt’s reefs began to disintegrate, succumbing to disease and probably stress from the periodic El Niño heating events that are becoming more frequent. “It was horrifying to watch,” she says. In Williams’ case, by the time she was in high school, the underwater landscape she remembered had fallen apart. “That was what made me become interested in studying coral,” she says. “I’ve heard other people say this, too. It’s like this for a lot of us.” Since 1960, more than 50% of the coral cover in the Caribbean has been lost, due in large part to bleaching, disease, and related problems.
 </p>
<p>
  Since Glynn’s regufia musings in 1996, reports of how a deep reef or a particular population of coral handled the heat and its aftermath have streamed in from around the world. Each one is a pixel in the picture of how deeper reefs respond to warming waters. But the picture is rather confusing. “People want to know, are they refugia? Yes or no?,” says Pim Bongaerts, a post-doctoral fellow at University of Queensland who studies the concept. “It’s not a black-and-white thing.”
 </p>
<h2>
  When Coral Turned White
 </h2>
<p>
  One problem is that many reports discuss a single bleaching event, leaving it unclear whether deep reefs are a useful refuge over the long term. Smith, who did his doctorate with Glynn, recently turned to a data set the latter had been constructing since 1973 to try to address this question.
 </p>
<p>
  About once a year, Glynn’s group had surveyed the corals in the Gulf of Chiriqui in Panama. In that time, two bleaching events had devastated the area, in 1983 and 1998. Glynn suggested that the analysis focus on the fortunes of one coral:
  <em>
   Millepora intricata
  </em>
  , a delicate species that’s especially sensitive to heat but lives in both deeper areas and the shallows.
 </p>
<p>
  They found that
  <em>
   M. intricata
  </em>
  had been completely wiped from the shallows in both events. However, small colonies had survived below 40 feet. Three to four years later,
  <em>
   M. intricata
  </em>
  reappeared in the shallows. Related species that did not have deep colonies never returned.
 </p>
<figure class="richtext-image full-width">
<img alt="" class="richtext-image full-width" src="https://staging.pbs.org/wgbh/nova/media/images/reef-fish.width-990_HjqaLFf.jpg"/>
<figcaption>Coral reefs are among the most diverse and fragile ecosystems on the planet.
        
    </figcaption>
</figure>
<p>
  So far, so interesting, but what about the very long term? To see whether
  <em>
   M. intricata
  </em>
  had survived the heating events of the past 5,000 years, one of the team members cored two shallow reefs. In the resulting columns of calcium carbonate, the majority of what they saw was
  <em>
   M. intricata
  </em>
  . The related species that did not have deeper populations could not establish strong footholds.
 </p>
<p>
  Taken together, these results suggested that the deeper water was serving as a refugia for the species—that its ability to survive at depth is what separated
  <em>
   M. intricata
  </em>
  from its unlucky cousins. The study doesn’t confirm, using genetic analyses or by tracking larvae, that the deeper colonies seeded the shallow ones. But the evidence is suggestive, and there are no other sources of
  <em>
   M. intricata
  </em>
  larvae around. “The
  <em>
   Millepora
  </em>
  was a clear case,” Smith summarizes. “It’s a species that’s really just hanging on, and this depth refuge was the key to keeping them around.”
 </p>
<p>
  And just last month, researchers
  <a href="http://www.nature.com/articles/nature14140.epdf">
   reported in
   <em>
    Nature
   </em>
</a>
  that depth was a major predictor of whether reefs around the Seychelles had recovered from the 1998 bleaching. Having measured everything from the fish population to the nutrient levels in the water at 21 reefs, they found that depth, along with the complexity of the reef’s branching structure, predicted whether it would recover 98% of the time. It set the community of refugia researchers humming.
 </p>
<h2>
  Uncertainties
 </h2>
<p>
  Lately, closer to home, Smith and his colleagues have been considering the existence of depth refugia in the Virgin Islands. In the Caribbean, reef mortality from bleaching has been tremendous. In 2005, many places in the region lost 90% of their coral to bleaching and to the diseases that followed. By 2100, NOAA predicts that severe bleaching will be an annual event in the Caribbean. If deep reefs can act as refugia there, they could be a godsend.
 </p>
<p>
  Yet in records from 2005 to 2013, three different bleaching episodes had counter-intuitive effects on deep reefs. One year, shallow coral bleached and deep coral didn’t, which seemed to chime with the Panama study. But other years, the reverse was true. One year, in a somewhat unnerving turn of events, the thermocline—a layer of water separating the warmer, higher waters from the cooler depths—shifted. The deep reefs were no longer in a cooler zone, and they suffered. In the other year, the issue seems to have been that deeper reefs, accustomed to relative temperature stability, were damaged by temperatures that would not have bothered shallower coral.
 </p>
<p>
  “Especially after the Eastern Pacific stuff, I was very much up on this idea of a depth refugium. I thought we were heading down this path,” Smith recalls. But looking at the data from the Caribbean once again makes it clear how very complex the picture is.
 </p>
<h2>
  Reefs of Tomorrow
 </h2>
<p>
  The future of reefs is unknown, and in a certain sense unknowable—there are so many factors in play. But there will certainly be a great deal of mortality among corals in the coming years. “The future will be interesting. Probably sad,” Smith says that day on the boat, tying up at the dock. He hopes that deep refuges, when and if they exist, can help preserve some of the species and their relationships that make up today’s coral reefs.
 </p>
<p>
  Already, scientists in Australia are
  <a href="http://www.nature.com/nclimate/journal/v3/n6/full/nclimate1879.html">
   calling for greater preservation of deep
  </a>
<a href="http://www.nature.com/nclimate/journal/v3/n6/full/nclimate1879.html">
   reefs
  </a>
  . Though they may be protected from the worst of the heat—at least some of the time—they are vulnerable to fishing and pollution. On their own merits, they appear to be home to a variety of new species and unusual ecosystems. And if they are refugia, so much the better.
 </p>
<p>
  Fortunately, depth refugia may not be the only way corals can grapple with the coming change. For instance, Steve Palumbi, a professor at Stanford, studies corals’ ability to evolve better heat resistance. There is some evidence that corals that can move to cooler waters are doing so. And on the island of St. John, just east of St. Thomas, Caroline Rogers of the USGS has discovered corals living in mangroves that appear to have survived catastrophic bleaching, despite living in warm, shallow water. Much of what allows corals to ride out hard times is still mysterious.
 </p>
<p>
  But the fact remains, even with these coping possibilities, that the world will be a very different place. The reefs of tomorrow will not look like those we know today, as coral scientists have already experienced. Brandt remembers showing an older diver photographs of beautiful stands of staghorn and elkhorn coral off the coast of Antigua, survivors of dying events that nearly wiped those species from the Caribbean.
 </p>
<p>
  “He got all misty-eyed,” she recalls. “He said, ‘I didn’t know that anything like that still existed.’ ”
 </p>
</section>
<p>
 Photo credits:
 <a href="https://www.flickr.com/photos/pacificklaus/7595946186">
  Klaus Stiefel/Flickr (CC BY-NC)
 </a>
 ,
 <a href="https://www.flickr.com/photos/theworldfishcenter/6325204318">
  WorldFish/Flickr (CC BY-NC-ND)
 </a>
</p>

Coral reefs face a bleak future, but survival may come from a very unlikely place—the dark, cold depths of the ocean.

Gene Sequencing Speeds Diagnosis of Deadly Newborn Diseases

<div class="related"></div>
<p>
 The genome is full of secrets. And some of them can kill you: Tiny alterations in key genes can send a newborn’s body into a downward spiral as poisons build up, seizures wrack the brain, and organs go into failure.
</p>
<p>
 When doctors see a patient whom they suspect of having such a disease, they call in clinical geneticists, who have a keen eye for symptoms that point to specific conditions. Even so, for newborns with a genetic disease, death may come before an answer.
</p>
<p>
 For older children whose symptoms were not evident immediately, their families must often go through what is called a “diagnostic odyssey” as clinicians conduct test after test trying to determine the cause. It’s a phrase that encompasses all the pain, fear, and uncertainty of not knowing what you can do to help your child, whether they will live to adulthood or die next year, and even whether you should have another child, knowing there’s a chance they will suffer in the same way.
</p>
<p>
 In the last few years, however, something remarkable has happened—so quickly that clinical geneticists’ voices are filled with awe when they talk about it. Nearly science-fictional advances in the speed and cost-effectiveness of genome sequencing now allow physicians to sequence large swaths of their patients’ genomes, or even, in a few select places, the entire genome. If traditional genetic tests, which usually check for a particular disease, are like pointing a telescope at a distant star, then this is like standing in a planetarium surrounded by the Milky Way, lost in a sea of brightness and information. Last fall, two papers in
 <i>
  JAMA Pediatrics
 </i>
 showed the effects of deploying these methods on a large scale, with exciting results. The rise of these techniques signals a shift in how genetic diseases are diagnosed and treated.
</p>
<h2>
 Race Against Time
</h2>
<p>
 To give a sense of the stakes here, perhaps one of the most immediate changes is for babies who, in the normal way of things, might never have lived long enough for their parents to get a diagnosis, not to mention a hope of saving them. One such newborn recently arrived at the Rady Children’s Hospital in San Diego. The baby shook with constant, uncontrollable seizures, even when treated with the strongest anti-epileptic drug available. Though the doctors upped the dose to the point where the infant had to go on a ventilator, the seizing went on. “The EEG readings are telling us that this baby, as we watch it, is frying its brain,” recalls Dr. Stephen Kingsmore, who is the president and CEO of the Rady Children’s Institute of Genomic Medicine, which works with the hospital. “And so we are counting the days until this baby will die. We are aware that progressive neurologic damage is happening as we watch.”
</p>
<p>
 Traditional genetic tests may take months or weeks to come back, by which time this child would have been long gone. At the Rady Institute, however, a whole genome sequence can be turned around in an average of four days. The Rady family gave $120 million to help establish the Institute of Genomic Medicine that Kingsmore leads, and it’s widely acknowledged as a leader in these techniques. Within 72 hours of the child’s arrival, geneticists were looking at a whole genome sequence, checking their suspicions against the data. And there the problem was: The infant had a mutation in a gene for an enzyme that controls the breakdown of the amino acid lysine.
</p>
<figure class="richtext-image full-width">
<img alt="" class="richtext-image full-width" src="https://staging.pbs.org/wgbh/nova/media/images/genome-sequencer.width-990_xwPE7AR.jpg"/>
<figcaption>Genome sequencing has come down in price considerably, enough so that it can be cost effective in clinical settings.
        
    </figcaption>
</figure>
<p>
 “It turned out that the seizures were treatable with injections of vitamin B6, arginine, and a modified diet” with low lysine, Kingsmore says. These treatments will be lifelong, but they protect the brain from further damage. Ten days after being admitted, the baby went home.
</p>
<p>
 It’s enough to make your head spin, especially since it wasn’t that long ago that single mutation tests were a pretty exciting technology, says Dr. Seema Lalani, a clinical geneticist at Texas Children’s Hospital and Baylor College of Medicine who led one of the new
 <i>
  JAMA Pediatrics
 </i>
 studies. When she started her training in 1999, such assays were already a big part of a geneticist’s toolkit. Then in the early 2000s, the chromosomal microarray (CMA), which allowed geneticists to look at multiple regions of the genome, came on the scene. If the genome is a book, she explains, then “CMA was able to help us with finding if there was a page or a paragraph missing.”
</p>
<div class="pullquote">
<p>
 “The entire field of inherited genetic disorders was going to be cracked open. Progress was going to massively accelerated.”
</p>
</div>
<p>
 Still, as progress on sequencing accelerated, a new world came into view for Lalani and other geneticists. 2009 was a key year. In August, a team led by Jay Shendure
 <a href="https://www.nature.com/articles/nature08250.epdf">
  published a proof-of-concept paper in
  <i>
   Nature
  </i>
</a>
 demonstrating that even if you just sequenced the portion of the genome that makes proteins—the exome—you could identify the gene behind a genetic disorder. In November, they published another study where they put it into practice: They discovered the gene behind Miller syndrome, a disorder whose precise cause was unknown, using exome sequencing.
</p>
<p>
 That changed everything. “That’s when we knew it had really hit,” remembers geneticist Dr. Leslie Biesecker of the NIH, who was present at the American Society of Human Genetics meeting in Honolulu that year, when the researchers first released their work to the community. “The entire field of inherited genetic disorders was going to be cracked open. Progress was going to massively accelerated.” This was like getting all the letters in all the words of a very significant part of the book.
</p>
<p>
 Indeed, research boomed. Between 2010 and 2015, about 250 new genes a year were connected to human disease. The number of genetic disorders with a known cause skyrocketed, and plans to take the technology from the lab to the clinic got into gear. “It happened faster than any of us thought and paid off more richly than any of us thought,” Biesecker says. Within a couple of years, there were labs set up where doctors could send patient samples for clinical sequencing.
</p>
<div class="ad"></div>
<h2>
 Limitations
</h2>
<p>
 Still, these kinds of sequencing can’t help with everything. Children with autism, for instance, don’t have nearly the luck with whole-exome sequencing as some others, Lalani says, noting that only about 4–5% of them get useful information. The sequences also don’t just come off the presses with an answer written in red ink. Instead, it’s just a jumble of letters that geneticists have to pore over carefully, going through a list of genes that their experience has taught them may go along with certain symptoms. Even then, mistakes can be made. “There are certain genes in the genome that are very hard to interpret,” Kingsmore says. In those cases, assuming a simple cause-and-effect relationship may be a mistake.
</p>
<p>
 All the same, in a surprising number of cases, clinicians can go to their patients and their families with a useful answer. In their
 <i>
  JAMA Pediatrics
 </i>
 study, Lalani and colleagues used whole-exome sequencing with nearly 300 infants suspected of genetic diseases that came through their hospital doors over the course of five years, starting in December 2011. These were children who, like the baby in San Diego, were critically ill. In 36% of cases, a genetic diagnosis came back.
</p>
<p>
 For some, the diagnosis meant a different course of action than might have been taken without the information. Sometimes doctors could tell families definitively that there was nothing that could be done for the baby, beginning the process of helping them think through what would come next. For others, the genetic information meant a better chance at life, pointing toward treatments like heart transplants or stem cell transplants and away from medications and other therapies that had no bearing on the disorder. As well, in a surprisingly high number of cases, Lalani says, the doctors could give the parents of children who had died information about whether future children would be likely to have similar problems.
</p>
<p>
 The number of cases in which sequencing gave useful information is similar to what Kingsmore and colleagues reported in a study two years ago, suggesting that this may be the yield doctors can expect when sequencing infants suspected of a genetic disease in an intensive care unit.
</p>
<p>
 In the other recent
 <i>
  JAMA Pediatrics
 </i>
 study, an Australian team focused on older children seen by geneticists at a clinic at the Royal Children’s Hospital in Melbourne, the kind of children for whom the diagnostic odyssey had gone on and on—in this case an average of six years. They were suspected of having a genetic disease, but had not had any sequencing. With sequencing of the whole exome, 52% of them received a diagnosis. For about a quarter of those, it changed their treatment plan. It also changed plans for future tests. For instance, says Dr. Tiong Tan, a clinical geneticist at Victorian Clinical Genetics Services who coauthored the study, one child had been lined up to have a spinal tap and a brain MRI. But they were canceled after the sequencing came back with a clear answer. “You can avoid a whole bunch of tests by making a specific diagnosis,” Tan says.
</p>
<div class="pullquote">
<p>
 It cost $6,838 less to just sequence the children right away than to go through a lengthier set of tests and visits with other specialists.
</p>
</div>
<p>
 That’s an important observation, because another focus of the study was cost. While sequencing prices have plummeted, these tests still cost thousands of dollars. Insurance companies may question whether such an expensive option is worth it. Part of the goal with this study, Tan says, was to see whether doing sequencing when patients first come into the clinic results in not only a less painful, frightening, and dangerous process—about 60% of the children had had to go under general anesthesia at some point for a diagnostic procedure—but also a cheaper one.
</p>
<p>
 As it turns out, it does. According to the study, it cost $6,838 less to just sequence the children right away than to go through a lengthier set of tests and visits with other specialists. The researchers hope that this study will encourage the Australian government to include whole-exome sequencing in the list of treatments that the national health service will pay for and help colleagues in other countries make similar cases to insurance companies.
</p>
<p>
 While sequencing is changing how patients and families get answers, it’s also provoked some interesting observations about these diseases. More often than expected, when the results come back, the geneticists realize the child has a disorder that they didn’t know could look like this. Years of training and clinical observation have trained their eyes to certain symptoms, textbook cases. But about 30% of the diagnoses the Melbourne team saw were surprising. Often, Tan says, “the exome sequencing shows us an unknown form of a known syndrome.”
</p>
<p>
 Lalani and her colleagues experienced this too. “We saw this recurrently, again and again,” she says. “About 38% had atypical presentation of their disorders” or a form that hadn’t been recognized before. As doctors continue to explore the use and usefulness of these tests, they may learn not only what to tell their patients and their families, but more about how these diseases work, potentially benefiting patients who have yet to be born.
</p>
<div class="newsletter"></div>
<p>
 Photo credits: garymilner/iStockphoto, Roy Kaltschmidt/Lawrence Berkeley National Lab
</p>

<p>Newborn genetic diseases are often swiftly fatal, but gene sequencing can help doctors make life-saving diagnoses.</p>

How CRISPR is Spreading Through the Animal Kingdom

<p>
</p>
<p>
 Fifteen years ago or so, when
 <a href="https://www.ed.ac.uk/roslin/about/contact-us/staff/helen-sang">
  Helen Sang
 </a>
 , a geneticist at the Roslin Institute in Edinburgh, and her colleagues wanted to get a gene into a chicken, the process was anything but fast.
</p>
<p>
 They would begin by making a virus that would insert genetic material into a chicken embryo. As the embryo developed, they would cross their fingers and hope that some of the cells that received the infusion of DNA became the chicken’s reproductive cells. Even if they did, it took waiting six months until the chicken reached maturity and could be bred to get a generation of chickens that had the gene in all their cells.
</p>
<div class="related"></div>
<p>
 Depending how on the process went, by that point, more than a year might have passed. And the researchers still would not have gotten to do the actual science they were interested in—studying how the new gene worked in chickens, for instance. Even in mice, the well-studied, well-understood workhorses of the biology lab, it could be a lengthy and delicate process to get an animal that carried a gene of your choice. And if you were thinking of trying out a gene in a less-studied animal, say, parakeets or honey badgers, it could take a significant chunk of your career just to figure out how to do it.
</p>
<p>
 This was the reality of doing science that involved gene engineering for many years, and researchers still managed to make enormous progress. One of Sang’s projects, to develop chickens that lay eggs containing melanoma and multiple sclerosis drugs,
 <a href="https://www.technologyreview.com/s/407193/drugs-sunny-side-up/">
  made headlines in 2007
 </a>
 , for instance. The idea was to harvest the drugs from eggs, part of a trend to grow pharmaceuticals in engineered organisms. (It’s not as far out as it might seem at first blush, as
 <a href="https://www.nytimes.com/2009/02/07/business/07goatdrug.html">
  the FDA has already approved
 </a>
 goats that make antithrombin, an anti-blood-clotting protein, in their milk, and insulin is now commonly grown by vats of engineered bacteria.)
</p>
<p>
 But in the last few years, a new technology has arrived on the scene. CRISPR-Cas9 gene editing has made its way into labs around the world. It’s a comparatively cheap, fast, and adaptable way of precisely snipping out pieces of the genome and swapping in new pieces, which can be used directly on the DNA in reproductive cells and
 <a href="http://www.genetics.org/content/199/1/1#sec-4">
  produces a finished mouse in three weeks
 </a>
 . In chickens, it nearly halves the amount of time needed, Sang says. The tools are so quick, she says with a laugh, that “I sometimes think I should have sat with my feet up for a long time and waited for them to come.”
</p>
<p>
 With something like this in hand, ideas that might have seemed overwhelmingly difficult are now potentially doable. In particular, scientists have swiftly adapted CRISPR tools for use in animals beyond mice, fruit flies, and other model organisms. That opens up a whole menagerie of creatures where quick, accurate gene editing is possible, with implications for agriculture and medicine.
</p>
<div class="pullquote">
<p>
 “I sometimes think I should have sat with my feet up for a long time and waited for them to come.”
</p>
</div>
<p>
 In Sang’s lab, using CRISPR, the researchers are able to get their genes into chicken eggs with much higher efficiency. Using viruses, they succeed only a portion of the time, but now, with CRISPR and some additional screening, the success rate approaches 100%.
</p>
<p>
 Other parts of the process have gotten more efficient as well. “CRISPR has come along when we’ve got a lot of genome sequence information,” Sang says. She and her colleagues can make informed choices about which genes might be most interesting or useful to put into a modified animal, without having to do as much testing ahead of time in dish-grown cells as they used to. She is now interested in using CRISPR to give chickens greater resistance to disease, especially to the avian flu. If there are some strains of hardy chickens that can stand up to an infection, perhaps researchers can figure out what quirks of the genome contribute and then use CRISPR to make alterations in meat and laying breeds.
</p>
<p>
 The hold-up now, Sang says, is not the time it takes to make chickens anymore, but having proper facilities to house them.
</p>
<div class="ad"></div>
<h2>
 CRISPR at Sea
</h2>
<p>
 CRISPR has also opened new doors for Anna Wargelius, a salmon geneticist at the Institute of Marine Research in Bergen, Norway. For many years, she and her colleagues had been working toward the goal of making a salmon for farming that was sterile, so that if any escaped into the open sea—a real risk in Norway, where salmon are farmed in the ocean—they would not be able to breed with wild ones.
</p>
<p>
 The group wanted to use genetic engineering to study which genes were involved in the development of salmon reproductive, or germ, cells. But they had little luck with zinc fingers, an earlier form of gene editor. “We had tried for several years to functionally study genes, but it did not work well in salmon,” she said. When they read a study demonstrating that CRISPR could work in zebrafish, the most common fish model organism, they were delighted. “We were just so happy to see this technology,” she recalls. “We were ready!” In 2014, the group published
 <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4177897/">
  a paper
 </a>
 demonstrating that CRISPR could be used to knock out genes in salmon. Since then, they have successfully made salmon without germ cells, and are moving on to using CRISPR to see whether the fish can be encouraged to generate more of their own omega-3 fatty acids.
</p>
<figure class="richtext-image full-width">
<img alt="" class="richtext-image full-width" src="https://staging.pbs.org/wgbh/nova/media/images/atlantic-salmon.width-990_mCDnygF.jpg"/>
<figcaption>Sterile farmed salmon wouldn't be able breed with wild populations if they escaped.
        
    </figcaption>
</figure>
<p>
 Wargelius says the efficiency—the fact that every organism they generate has the gene they want very quickly—has rapidly accelerated work not just in her lab, but in other groups whose study species take a long time to reach reproductive maturity. Having to wait out multiple salmon generations, which are about three years long, to begin the real work is a serious and expensive gamble. “For everybody working with long-generation animals or plants, they are really happy with this,” Wargelius says, “because you can functionally start with something already in the first generation. It saves a lot of time and money.”
</p>
<h2>
 Pigs and Beyond
</h2>
<p>
 The subtlety of the changes that CRISPR allows is also advancing projects in some creatures in remarkable ways, says Simon Lillico, a geneticist at the Roslin Institute who works with pigs. Funded in part by a breeding company, Lillico and colleagues have been studying how to keep pigs from catching a viral disease called porcine respiratory and reproductive syndrome, or PRRS. While it may not be a household name for most people, the PRRS virus, which causes pneumonia and stillbirths and abortions in pregnant pigs, is behind massive losses in farming—
 <a href="https://www.prrs.com/en/prrs/cost/">
  $664 million a year in the U.S. alone, by one estimate
 </a>
 . The virus gets into pig blood cells by clinging to a surface protein called CD163, specifically to a particular stretch of the protein called domain 5.
</p>
<figure class="richtext-image full-width">
<img alt="" class="richtext-image full-width" src="https://staging.pbs.org/wgbh/nova/media/images/pig.width-990_y6XsQS2.jpg"/>
<figcaption>CRISPR pigs have successfully evaded a typically deadly virus.
        
    </figcaption>
</figure>
<p>
 Taking advantage not only of CRISPR’s efficiency and speed but its delicacy, Lillico and colleagues were able to
 <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5322883/">
  generate pigs that were missing just that snippet of CD163
 </a>
 . “When you put the virus on the pigs, it cannot infect them,” he says. “It’s kind of like a lock and key mechanism—the virus has the key, but we’ve removed the lock.” The domain-5-less pigs are otherwise healthy.
</p>
<div class="newsletter"></div>
<p>
 It’s not just pigs that are benefiting, Lillico says. It’s now more plausible to use pigs and other large mammals as models for human disease. There are some diseases and situations where mice might not be as good as a model as other mammals, he suggests, and CRISPR makes it more feasible for these options to be explored. There may be a more direct benefit, too: A group at MIT has also been
 <a href="http://www.sciencemag.org/news/2017/08/crispr-slices-virus-genes-out-pigs-will-it-make-organ-transplants-humans-safer">
  using CRISPR to remove portions of the pig genome
 </a>
 that contain remnants of old viruses, which might be a liability if ever it becomes possible to transplant pig tissues or organs into humans, an idea that’s been given some new life lately. And in Australia, a group at the CSIRO has been
 <a href="http://www.abc.net.au/catalyst/stories/4529197.htm">
  investigating how egg proteins can be modified with CRISPR
 </a>
 so that they don’t trigger allergies in those who eat them. (No honey badger or parakeet CRISPR studies yet, though, according to a search in PubMed.)
</p>
<p>
 “It’s only just starting,” says Helen Sang, who notes that the technique has caused a shift in many scientists’ thinking about whether it is worth trying to engineer animals. “Somehow, the fact that we have a new technology that is so easy to use, and so precise, it’s beginning to get people to think, oh maybe we will be able to use it,” she adds. “Because there are so many advantages, and there really are a lot of opportunities.”
</p>
<p>
<a href="https://www.flickr.com/photos/20bd10/8626819071/">
  Lotta Honkanen/Flickr (CC BY-NC-ND)
 </a>
 ,
 <a href="https://www.flickr.com/photos/matt_hintsa/9991638743/">
  Matt Hintsa/Flickr (CC BY-NC-ND)
 </a>
 ,
 <a href="https://www.flickr.com/photos/babasteve/7341687640/">
  Steve Evans/Flickr (CC BY-NC)
 </a>
</p>

<p>Gene editing with CRISPR is so fast, cheap, and adaptable that scientists in a variety of fields are putting it to use.</p>

Experts are studying a wide variety of eggplant relatives for their hardiness and ability to produce appealing, edible fruits. | Photo credit: Alice Henneman / Flickr (CC BY 2.0)

To Secure the Future of Food, Look to the Ancestors of Eggplant

<p>In a greenhouse in tropical southern Taiwan grows a small tree. From its hardy trunk sprout stems with wide, fuzzy leaves and sprays of white star-like flowers. Some of these flowers have already transformed into inedible green fruits about the size of marbles. Mohamed Rakha, a plant breeder here at the World Vegetable Center, splits open one of the fruits with his fingernail. “You can see a lot of seeds inside,” he says. Each one is packed with the plant’s DNA—and lots of potential.</p><p>Odd as it may seem, this fruit—a wild eggplant—is an ancient relative of the big purple eggplant sold in grocery stores worldwide.</p><p>At the World Vegetable Center, experts are studying a wide variety of eggplant relatives for their hardiness and ability to produce appealing, edible fruits—but it isn’t typical, business-as-usual breeding. Rather, plant breeders are on a mission to save the human diet from climate change.</p>
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<p>All of the fruits and vegetables available in markets and grocery stores today are products of domestication. Their ancestors were not-so-edible organisms like the little tree Rakha tends. But centuries ago, humans began to take the biggest and tastiest wild plants and breed them together. They repeated this over and over, weaving together the genes that made a juicier fruit or a fatter wheat kernel so that many generations down the line, modern plants are now quite different.</p><p></p>
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<figcaption><p>Eggplant seedlings at a street market near the World Vegetable Center | Photo credit: Veronique Greenwood</p>
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<p></p><p>These domesticated plants, despite their advantages, have some significant weaknesses. They’re not as sturdy as many of their wild relatives when it comes to resisting diseases, droughts, and other challenges. When a problem arises, they do not have the genetic diversity that allows wild populations to ride it out—all the individuals are so similar that what kills one, kills them all. And crops are already facing a serious challenge that’s bound to get worse: climate change.</p><p>As temperatures warm and pests shift their territories around the planet, large swaths of the human diet are at risk of crumbling under the onslaught of disease, insects, saltier water, and unbearable heat. Scientists estimate that U.S. corn, the country’s dominant crop, will see a decrease in yield of about 50 percent with a 4-degree Celsius temperature rise, which is predicted by the end of this century. In the later years of the 21st century, increased ozone in the atmosphere and lack of water due to climate change may reduce yields of vegetables by more than 30 percent, another study found.</p>
<p>These crops’ wild relatives—spunky, straggly plants—might be able to help. Breeders think that if they can collect seeds from these relatives, they may be able to breed resistance to drought, heat, and other threats back into the crops we depend on. But time is short. And so, in a daring move, scientists under the direction of the Global Crop Diversity Trust—based in Germany—have hatched a plan called the Crop Wild Relatives project. Starting in 2011, with 10 years of funding from the government of Norway, they set out on a mission.</p>
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<p>Large swaths of the human diet are at risk of crumbling under the onslaught of disease, insects, saltier water, and unbearable heat.</p>
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<p>In seed “safaris,” hundreds of scientists have fanned out in tall grasses, deserts, and remote mountains looking for wild relatives of staple food crops around the world. Since 2015, these missions have yielded 3,800 samples from 24 countries, including wild carrots from Bangladesh, wild eggplants from Tanzania, and wild sweet potatoes from Nigeria. The Kew Gardens Millennium Seed Bank in the United Kingdom has helped distribute the newfound seeds to breeders and researchers, who will grow them to find out exactly what their strengths are. In this global scheme, the World Vegetable Center in Taiwan is where the wild relatives of domesticated eggplant will get put through their paces.</p><h2><b>Standing Up to Pests</b></h2><p>The World Vegetable Center, founded in 1971 to develop crops for Asian countries, is headquartered in a cluster of low buildings ringed with fields just north of the city of Tainan. Palm trees dot the grounds between glass greenhouses where staff members conduct experiments and maintain the center’s enormous collection of seeds.</p><p></p>
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<figcaption><p>Seeds in storage | Photo credit: Veronique Greenwood</p>
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<p></p><p>On a cloudy day in October, Maarten van Zonneveld, the manager of the center’s seed collection, walks through the greenhouse where the wild eggplants will be grown, pointing out the beds built for new seedlings. The idea is that when the researchers find a plant that can stand up to a pest or keep producing despite a big jump in temperature, they will breed that wild variety with a standard, domesticated crop variety. If they manage to get a hybrid, they’ll keep refining it over the course of many generations.</p><p>This isn’t always a simple procedure because, just as with humans, offspring may not resemble their parents. If the offspring, which gets half its DNA from the wild relative parent, only inherits some of the genes necessary for a desired trait, it won’t benefit from it. And of course, the plant has to continue to produce lots of tasty vegetables as well. This process, called pre-breeding, can often take eight to 10 years or longer, just to get to the point where a seed company could take over.</p><p></p>
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<figcaption><p>Four different kinds of eggplant seeds (some wild) | Photo credit: Veronique Greenwood</p>
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<p></p><p>“For a seed company, a long-term project is two to three years,” says Philipp Simon, a USDA carrot breeder who leads the Global Crop Diversity Trust’s wild carrot project. “A seed company doesn’t want to work with a wild carrot relative—that would take forever from their frame of reference.” So pre-breeding, which creates the materials for mainstream breeders to use in their work, usually happens at universities and public institutes like the World Vegetable Center.</p><p>Eighty-nine new wild relatives of eggplant have been collected and will be grown at the center over the coming years. But in parallel, while those efforts get off the ground, the center’s collaborators at the University of Valencia in Spain have started to forge ahead using wild eggplant relatives that were already in gene banks. Geneticist Jaime Prohens and his group there have drawn on samples from Asia and Africa, as well as two distantly related American relatives, over the past several years. “This means crossing eggplant with a species that separated about 20 million years ago,” says Prohens—an exciting, if difficult, task because they have very different genes.</p>
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<p>Eighty-nine new wild relatives of eggplant have been collected and will be grown at the center over the coming years.</p>
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<p>To its surprise, Prohens’ team has already managed to get fertile hybrid plants from many crosses and, with some lab work, coaxed seeds from a few others. These will mix eggplant genes in new ways, and the most interesting specimens have arrived at the World Vegetable Center, where they will be evaluated for resistance to pests.</p><p>In the greenhouse, Rakha lifts the leaf of a potted cabbage plant to reveal hundreds of tiny whiteflies, which suck the sap out of eggplant leaves. The center keeps thriving populations of common crop pests like whiteflies in a special greenhouse for such experiments. Rakha and his colleagues hope that the new, hybrid plants will stand up to their scourge.</p><p>As researchers record what all these fresh infusions into the domesticated eggplant’s gene pool do in the field, the information will be entered into a database that anyone around the world can access, says Benjamin Kilian, the manager for the project at the World Crop Diversity Trust. “All pre-breeding data will be freely available,” he says.</p><h2><b>An Open Vault</b></h2><p>How swiftly might insights from the wild relatives project hit grocery store shelves? That depends on what researchers find and how seed companies decide to make use of the breeding material. Five seed companies are collaborating with the World Vegetable Center on the eggplant work, testing the new plants in their own fields. “These companies might select [the] most promising materials for their own breeding,” says Kilian, which would accelerate the eggplants’ arrival in stores. So far, no eggplant from the project has reached the consumer phase.</p><p>In just two years, the current funding for the Crop Wild Relatives project will end; partners and other stakeholders will have selected the most promising pre-bred materials and integrated them into their breeding pipelines by then. But the project’s legacy will remain in the seed banks of the world.</p><p>Van Zonneveld visits World Vegetable Center seed bank curators Yung-kuang Huang and Tien-hor Wu—“There are not many people who have seen more eggplant diversity than Mr. Wu,” Van Zonneveld says by way of introduction—and together the three scientists go down white corridors and up a flight of stairs to the door of a vault. Inside, it’s a frigid 41 degrees Fahrenheit. Heavy rolling shelving units can be pushed apart to reveal thousands of little silver envelopes, each one containing the legacy of a plant. “This represents a part of the history of man and plant,” says Van Zonneveld. “It’s one of the—if not <i>the</i> largest—public international gene bank of vegetable germplasm.” A thermostat senses the heat of our bodies and industrial fans slam on, sending a wave of cold air over the room and its precious contents, which anyone willing to do the import paperwork—seed company employee, scientist, interested gardener—can request.</p><p></p>
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<figcaption><p>Inside the World Vegetable Center seed bank with Yung-kuang Huang (left) and Maarten van Zonneveld (right) | Photo credit: Veronique Greenwood</p>
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<p></p><p>Wild relatives are not immune to troubles, as construction projects and other disturbances frequently threaten to encroach on their habitats. Still, they can be found in the most unlikely of places––it just takes a little practice to recognize them. Phillip Simon, the carrot breeder, has collected wild carrots by the roadside in Turkey, Tunisia, Uzbekistan, and Turkmenistan.</p>
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<p>“My first collecting trip was to what was at the time the USSR in 1989,” he says. In the United States Department of Agriculture’s gene bank are purple carrot seeds he collected near Homs, Syria, many years ago, which may not exist there anymore. The USDA has funding available for collecting missions focused on wild relatives, although not many scientists realize it, Simons says. And within the U.S., there are amateur groups that go out collecting as well, on the hunt for wild garlic and onion and carrots—the global seed safari, on a much smaller scale.</p><p>On the other side of the world in Taiwan, Van Zonneveld spotted a mung bean relative in the wild recently, and he brought it back to his office to press it. Now he carefully lifts a sheet of newspaper to reveal the delicate curl of the dried plant. Its unassuming yellow flowers not yet gone to seed, they resemble those of their much more famous cousin, a crop eaten by millions. For him, it represents the promise of a better future.</p>

<p>At the World Vegetable Center, experts are looking to the wild relatives of domesticated crops—like eggplant—to save the human diet from climate change.</p>

Veronique Greenwood

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