Hope from the Deeps for Coral Reefs

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<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://www.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://www.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.

Life Needs (Some) Radiation

<div class="related"></div>
<p>
 In 1987, a group of researchers in France discovered something peculiar. When they protected single-celled organisms from background radiation—the sort that comes from cosmic rays and radioactive rocks—the creatures’ growth was stunted. Colonies that receive a background dose of radiation actually grew more quickly than their shielded brethren. That’s radiation—not vitamins, not nutrition, not anything people generally suggest you should get more of.
</p>
<p>
 Was background radiation somehow required for life?
</p>
<p>
 The dangers of radiation
 <a href="http://www.methodquarterly.com/2014/11/the-cat-went-over-radioactive-mountain/">
  loom large in our cultural memory
 </a>
 . With good reason: From the melting, cancerous jaws of factory workers exposed to radium-infused paint in the 1920s, to the gruesome after-effects of the atomic bombs dropped on Japan, the results of exposure speak vividly against taking radiation lightly.
</p>
<figure class="richtext-image full-width">
<img alt="" class="richtext-image full-width" src="https://www.pbs.org/wgbh/nova/media/images/licorne_w5SB1up.width-990_fkiNuDG.jpg"/>
<figcaption>Aboveground nuclear bomb tests, like this French test over Fangataufa Atoll, have seared the image of dangerous radiation into our collective memories.
        
    </figcaption>
</figure>
<p>
 On the cellular level, radiation’s particles wreak havoc on DNA, ripping through the double helix like bullets and causing the creation of corrosive free radicals. Irradiated cells form strange structures in their nuclei as they attempt to replicate themselves, the genetic material twisting and clumping sickeningly. The general rule is the less radiation exposure, the better: In this view, “there is no safe amount of radiation,” says New Mexico State University researcher Hugo Castillo.
</p>
<p>
 Separately, however, since life’s beginnings—long, long before humans began toying with things like uranium—all organisms have been exposed to what is known as background radiation. This is naturally occurring, with some of it coming from the sky, in the form of cosmic rays, and some of it coming from the Earth, from isotopes like potassium-40 in the soil and rock. The amounts are not huge—something like having a
 <a href="https://www.radiologyinfo.org/en/info.cfm?pg=safety-xray">
  mammogram every couple of months
 </a>
 —but they exist.
</p>
<p>
 You’d think that when you protect cells from the natural background radiation, they’d do better—no radiation means no stress, no damage, faster growth. But as the French experiment suggested, some level of radiation may be beneficial.
</p>
<p>
 Since the 1987 paper, a small community of researchers have worked to understand what happens to cells in low-radiation environments. In the Gran Sasso Cosmic Silence experiments, under a mountain in Italy, scientists have found that cells grown under such conditions respond more poorly than controls to damaging radiation. And at France’s Laboratoire Souterrain de Modane, a team has been studying the evolutionary effects of very low radiation. “We wanted to quantify as precisely as we could what effect radiation is having on cells,” says Nathanael Lampe, a graduate student there. But there are limited places on the planet where it’s even possible to contemplate such experiments.
</p>
<p>
 Castillo, his supervisor Geoffrey Smith, and their colleagues at NMSU have such a set-up: In a salt mine deep beneath the New Mexico desert, they are investigating background radiation’s importance to life in a very unusual series of experiments. In
 <a href="http://journal.frontiersin.org/article/10.3389/fmicb.2017.00177/full">
  a paper published this February
 </a>
 in
 <i>
  Frontiers of Microbiology
 </i>
 , they report that, indeed, bacteria grown in an extremely sheltered environment there—at levels of background radiation nearly 80 times lower than at the surface—appear to be stressed. It’s the same kind of reaction you get if you starve cells or heat them, but in this case, it’s because of the lack of radiation. That implies that there is something cells have evolved to expect, over the eons, from the background.
</p>
<div class="ad"></div>
<h2>
 Down Deep
</h2>
<p>
 Castillo and Smith’s New Mexico group works out of a small lab in a shipping container more than 2,000 feet underground, in a man-made system of caverns created for storing nuclear waste. The facility, called the Waste Isolation Pilot Plant, has socked away thousands and thousands of containers bearing strongly worded labels since 1999, in chambers chiseled from a salt formation. Entering the WIPP facility is not for tourists, and even the scientists are few. The team only has access for a few months out of the year, and on the way down, they crowd in a small elevator. “After 20 seconds, all the light is gone,” Castillo says, recalling his first trip down. “I’ve never seen such darkness before in my life.”
</p>
<figure class="richtext-image full-width">
<img alt="WIPP Panel 7" class="richtext-image full-width" src="https://www.pbs.org/wgbh/nova/media/images/wipp-panel-7_x3NdAAb.width-990_rO5Dh2K.jpg"/>
<figcaption>A corridor in Panel 7 in the Waste Isolation Pilot Plant.
        
    </figcaption>
</figure>
<p>
 When the researchers disembark at the bottom of the shaft, they are cocooned in a bubble of salt, exceptionally poor in natural radioisotopes, and so far down that cosmic rays can’t penetrate. They make their way to the lab space, where their neighbors are physicists doing similarly sensitive experiments. Finally they come to their most important piece of equipment: A steel vault, built by the military before World War II, that does not have the trace radiation that steel made afterwards acquired as a result of the fallout when the atomic bombs went off. That means that it does not have the trace radiation that everything aboveground acquired as a result of the fallout.
</p>
<p>
 Within this vault, hidden in the salt bubble, more than 2,000 feet underground, the background radiation level is already ten times less than at the surface. The group has erected even more shielding around an incubator, bringing down the level to 79 times less than normal. And there they have grown two kinds of microbes:
 <i>
  Shewanella oneidensis
 </i>
 and
 <i>
  Deinococcus radiodurans
 </i>
 , both stalwarts of radiation biology experiments. In a control incubator with identical bacterial cultures nearby, they have added back in an amount of radiation comparable to the surface.
</p>
<p>
 It’s delicate work, designing an experiment where you know the effects are from the lack of background radiation, and not from, say, myriad other small differences that can creep in. You must account for differences in air pressure, if the cells are grown in different places; too, the cells aboveground and below may grow more genetically distinct over time, making it harder to tell what alterations are radiation-related. The best course of action, if possible, is making the level of radiation the sole difference between control and treatment, as the New Mexico team has done.
</p>
<div class="newsletter"></div>
<p>
 In the shielded incubator,
 <i>
  D. radiodurans
 </i>
 grows more slowly, its numbers lagging behind controls throughout the duration of the experiment, they report, in line with what’s been found by prior groups.
 <i>
  S. oneidensis
 </i>
 , however, after a short delay, matches the growth numbers of the controls.
</p>
<p>
 Delving into this, the group checked the organisms’ expressions of 10 genes involved in coping with stress. They found that
 <i>
  D. radiodurans
 </i>
 was laboring along with few of these genes expressed any differently from the norm, and apparently suffering for it.
 <i>
  S. oneidensis
 </i>
 , on the other hand, had at least doubled the expression levels of some of them. “This is a subtle effect,” Castillo says. “But it appears the cells can turn some genes on and off to compensate for this lack of radiation.” Moving the microbes to the control incubator with more radiation erased both the growth problems and the change in gene regulation, confirming the connection with radiation.
</p>
<p>
 The genes that
 <i>
  S. oneidensis
 </i>
 upregulated are associated with particular kinds of genetic repair. Specifically, they help mend damage caused by free radicals, which can be produced by radiation exposure, but also can be made by cells themselves as waste products. Since they certainly aren’t getting free radicals from radiation, this suggests that
 <i>
  S. oneidensis
 </i>
 may be responding to an over-abundance of free radicals produced internally, Castillo hypothesizes. Perhaps the usual steady dose produced by background radiation on the surface serves as a signal to the cell to keep free radicals low—like a finger pushing on a button. Maybe without those regular prompts from the environment, cells accumulate the molecules to an unhealthy level and then struggle as a result.
</p>
<h2>
 “A Billion Detectors”
</h2>
<p>
 Still, this opens up an even greater mystery. Background radiation is sparse stuff, just a few particles bouncing through a very large volume of space. And cells are tiny—the vast, vast majority of the cells in a dish grown on the surface are never struck by a particle at all, says Lampe, from the French group, who has been modeling the number of mutations arising from the background. “This is why observations of different biological effects in underground labs are so fascinating,” he says. If in the normal course of life cells are never struck by a radiation particle, how in the world does the presence or absence of such particles register? Perhaps the answer lies in incredibly swift and complete communication between cells. “If you have a cell population, you effectively have an array of a billion detectors,” Lampe proposes. “They can aid each other in figuring out what’s going on with the radiation background.” And perhaps it takes only a very small, conditioning dose of free radicals—or something else, something still unknown—to keep closely communicating cells at the surface in working order.
</p>
<div class="pullquote">
<p>
 “If you have a cell population, you effectively have an array of a billion detectors.”
</p>
</div>
<p>
 Then, though, there are the effects observed by the Italian group, led for many years by Luigi Satta of the Italian National Institute for Nuclear Physics, which has been working on the problem since the late 90s. In those experiments, yeast, hamster, and human cells were grown in low-radiation environments underground and also in a lab on the surface. Then, the underground cells were brought up and both sets were given challenging doses of radiation. The team found that cells grown below had more DNA damage afterwards, measured by the appearance of twisted wads of DNA in the nucleus. “If the cells had been living for a few months in an environment in which the background radiation was normal,” says Massimo Pinto, a radiation scientist who worked on the experiments, “these cells were more ready to respond to an insult in the form of a challenge dose. The sister cells that had an artificially reduced background radiation level were not as capable.”
</p>
<p>
 It’s a peculiar finding—why would being without radiation make cells more vulnerable? One theory is that very low doses of radiation can cause cells to keep their repair machinery switched on, and those without it are unprepared, like a runner who skipped one too many workouts before a marathon. But the answers are not clear yet. Satta says that the next step would be to try similar experiments with fruit flies, to get a sense of whether the effect occurs in more complicated creatures. “All this suggests that these experiments should go on,” he says, “but due to budget limitations, this plan is unfortunately not sure.”
</p>
<p>
 Still, despite the difficulty of finding dependable funding for such esoteric experiments, “we’ve got a very fascinating phenomenon on our hands,” Lampe says. Life has evolved to take advantage of the light shining down on Earth, by developing photosynthesis. It’s evolved to take advantage of an oxygen-rich atmosphere, using it to help generate energy at the cellular level. It’s evolved to be comfortable at a specific range of temperatures commonly available on our planet. Is it any wonder that there may be another, less noticeable aspect of our environment that we’ve missed the significance of until now?
</p>
<p>
 Image credit:
 <a href="http://www.flickr.com/photos/7969902@N07/511287693">
  Pierre J./Flickr (CC BY-NC-SA 2.0)
 </a>
 , NASA, U.S. Department of Energy
</p>

<p>Deep in the Earth, experiments are revealing how life suffers when it’s deprived of background levels of radiation.</p>

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>

Saving the Sun

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

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://www.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://www.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://www.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://www.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.

An artist's impression of CRISPR in action.

For Gene Drives, Resistance May Be Inevitable

<div class="related"></div>
<p>
</p>
<p>
 In the last few years, biologists have realized something remarkable: We might finally be able to beat evolution at its own game.
</p>
<p>
 Using the gene editing tool CRISPR, which snips DNA and inserts a new gene of the designer’s choosing, biologists can arrange it so that a gene will spread exponentially through a population of organisms. While that occasionally happens in nature, with certain caveats, evolution has generally been against us: If a few mosquitoes are released with a gene that prevents them from carrying malaria, the gene will be swamped in the gene pool. The mosquitoes will only pass it on to half their offspring, who will in turn pass it on to only half of theirs, and before long it will drop out of the population. In the meantime, malaria kills more than 1 million people per year, mostly children five years old or younger. And other mosquitoes spread Zika—linked to severe birth defects—and yellow fever and dengue fever, whose numbers have escalated alarmingly in recent decades.
</p>
<p>
 So when, in 2014, researchers began to point out that there was a way to help such genes take over, it caught people’s attention. If a mosquito is given a bit of DNA that not only codes for that gene but for the CRISPR machinery itself, then the CRISPR proteins will go around inserting themselves and their cargo, ensuring that all the insect’s offspring will have them, as will all of their offspring. As the gene (and the CRISPR machinery) are passed down, it will spread exponentially. Soon, it might take over the population or perhaps even the whole species—and, in this example, no mosquitoes would be capable of carrying malaria. The same technology could just as well spread a gene that could cause a mosquito population crash, however, which has yielded many calls for caution and prudence in studying gene drive systems, as these constructs are known.
</p>
<p>
 But there is a chink in gene drives’ armor. Specifically, it is possible for organisms to escape though an age-old trick, one that we’re growing more familiar with by the day—by evolving resistance, just as bacteria evolve resistance to antibiotics. In a recent paper
 <a href="http://biorxiv.org/content/early/2016/06/11/058438">
  posted to the biorXiv
 </a>
 , evolutionary geneticist Rob Unckless of the University of Kansas and colleagues lay out mathematical models of what may happen when gene drives are released, and find that even under the best of conditions, resistance is certain to arise. Exactly what that insight means—whether it is a fatal flaw in the technology, merely an obstacle to be overcome, or perhaps even a tool to be used—is still an unanswered question.
</p>
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<h2>
 Botched Repairs
</h2>
<p>
 It’s been known from the earliest work on
 <a href="http://www.pbs.org/wgbh/nova/next/evolution/crispr-gene-drives/">
  CRISPR gene drives
 </a>
 that resistance was a strong possibility. That’s because CRISPR will cut DNA only at places with a specific sequence of DNA bases. The recipe for the CRISPR machinery and its cargo gene then have to be pasted into that cut. The cell will usually cooperate because this bit of genetic material is designed to blend in. But with each cut, there is a chance that the cell will instead try to repair the gap by putting in some new DNA base pairs. “It tries to do its best,” Unckless says, “but it makes a lot of errors.”
</p>
<p>
 Once the gap has been repaired, it might well have a different sequence of DNA bases than the CRISPR system can cut. And after that, there’s nothing the gene drive system can do to it. It’s immune. “We think that is going to be the biggest source of resistance,” Unckless says, echoing a general consensus among a number of scientists. “CRISPR breaks the sequence, but instead of having the CRISPR machinery inserted, the repair is done through this [other] process.”
</p>
<figure class="richtext-image full-width">
<img alt="" class="richtext-image full-width" src="https://www.pbs.org/wgbh/nova/media/images/gene-drive-schematic_QCVdY0Q.width-990_EjbbviG.png"/>
<figcaption>Here, a mosquito with a gene drive (blue) mates with a mosquito without one (grey). In the offspring, one chromosome will have the drive. The endonuclease then slices into the drive-free DNA. When the strand gets repaired, the cell's machinery uses the drive chromosome as a template, unwittingly copying the drive into the break.
        
    </figcaption>
</figure>
<p>
 If the repaired area prevents mosquitoes from being modified, depending on the modification, it might suddenly become a very handy thing to have. If all the mosquitoes that receive a gene drive die or become infertile or simply produce less offspring than those that are resistant, the resistant type will eventually take over. By putting our thumb on the scale of evolution on behalf of one gene, we create a situation where an opposing version can take over, if the benefits of having it are great enough.
</p>
<p>
 There are a lot of “ifs” in that paragraph, but what Unckless and his collaborators found in their models—which assign numbers to those unknowns—was that even at very low rates of erroneous self-repair, resistance is a clear specter. If 100 copies of the gene drive are released, and the rate of self-repair is as low as one in 100,000, resistant organisms will still make up half the population after 100 generations have passed. A larger population will have more problems with resistance than a small one—more cuts mean more chances for resistance to arise. And in fact, Unckless and his collaborators made a very conservative assumption for the rate for this kind of repair, to see whether resistance would happen even then. Experiments suggest the rate is much higher in real organisms, perhaps one in 100. “I think [resistance] will block the drive much sooner than their model predicts,” says Kevin Esvelt, an evolutionary engineer at MIT.
</p>
<p>
 By itself, this isn’t terribly surprising, says Omar Akbari, an entomologist and molecular biologist at UC Riverside. “It just highlights the fact that it’s going to be an issue,” he says.
</p>
<p>
 But the question of what effects this kind of resistance will have is something the community has been thinking hard about, says Valentino Gantz, a post-doc at UC San Diego who has made gene drives in fruit flies and mosquitoes. “This is exactly one of my worries from when we started going in to mosquitoes,” he says. “I was hoping that population geneticists would do a nice analysis such as [this] one.”
</p>
<div class="pullquote">
<p>
 “One of the realizations we’re coming to is that resistance is almost inevitable.”
</p>
</div>
<p>
 How big of a problem this will be depends on what exactly a gene drive’s goal is. “If you’re targeting dengue,” says Akbari, “if you’re able to block all disease transmission for a few weeks”—in order to create a situation in which after running its course in infected individuals, the virus cannot spread any further—“that could essentially eliminate the virus. So you don’t need it to last indefinitely.” On the other hand, if the goal is to create a lasting alteration—to permanently keep mosquitoes from transmitting Zika, for instance—it would be a non-starter if in a hundred mosquito generations, around four to eight years, half of all mosquitoes would again be able to spread disease.
</p>
<p>
 Which is why researchers have begun to design ways to thwart resistance. In one strategy, the CRISPR machinery cuts at a gene that is required for life, so that if the self-repair mechanism screws up, it’s lethal to the organism. In another, the CRISPR machinery can cut at five different sites, so that if one gets repaired so as to be immune, the others are still available. Another option would be to release a drive knowing resistance will arise, and, for however long is appropriate, releasing others that target the resistant genes, engaging in a kind of arms race with evolution.
</p>
<p>
 It’s possible, too, that resistance, in certain situations, could be useful. “One of the realizations we’re coming to…is that we think resistance, probably at least in a simple system, is almost inevitable, so maybe we should embrace that,” Unckless suggests. If a drive is gradually out-competed by a resistant version, well, maybe there are situations where that would be preferable. Perhaps resistance could be part of a containment plan, for example in situations where a population is already isolated from others, and the inevitable resistance could catch up with the drive before any pioneering individuals could leave and spread their genetic payload. This is still conjectural, however. And there are likely to be much more predictable tools to accomplish the same task.
</p>
<h2>
 Out of the Lab
</h2>
<p>
 Still, all these models and ideas and proposals being tossed around eventually have to acknowledge the fact that there have not been very many tests in real organisms or in realistic populations. No one thinks we have enough information yet about how gene drives work in practice to be able to reliably predict their effects.
</p>
<p>
 There are reasons aplenty why they might not function as planned. Anna Lindholm, an ecologist at University of Zurich, studies a naturally occurring gene drive system in mice, which is carried by males and spreads itself to more than 90% of the sire’s offspring. While researchers have never seen genetic resistance to the system evolve, she says, it hasn’t spread as quickly as you might think. That seems to be because of a simple fact of mouse mating behavior: These females mate with many males in quick succession, and the males with the drive often see their sperm out-competed by those of rivals. The drive is out of the game before it ever gets a chance to do its thing.
</p>
<p>
 A gene drive released in a mosquito population could nose-dive because of some unforeseen feature of the natural world—or even of the particular area where it is released. “When you’re doing it with one species of one mosquito in one location, it might work perfectly, exactly as on paper,” Gantz says. “And when you do the same exact experiment in a different location, it might just not work for some other reason.
</p>
<div class="newsletter"></div>
<p>
 “I think we’ve gotten to the point where I believe the technology should move toward generating mosquitoes that are field-ready and extensively testing them in the lab and making sure there are no unexpected behaviors of the system in populations in the lab before you go into the field,” he says.
</p>
<p>
 Gantz isn’t worried that a drive will spread too well, taking over populations so fast as to be uncontrollable. Rather, he is worried that a much-anticipated test will fall flat. Others in the community are more preoccupied with the first scenario. Esvelt and his colleagues have proposed a control mechanism that would split up the machinery required for the gene drive system and disperse it throughout the genome, arranging it so that without intervention, it will eventually go defunct. “We like that because it’s less of a blunt instrument,” says Charleston Noble, a graduate student at Harvard University who is working on the idea alongside Esvelt. But until more experiments happen, there is not enough information to tell which scenario is most likely.
</p>
<p>
 As such tests unfold and the data are released, scientists will be looking for signs of problematic resistance, and whether, with these new tools, we really can reliably steer evolution toward our own ends. Gene drives are potentially powerful, but also potentially very delicate—a technology full of contradictions.
</p>
<p>
 Image credits: Steve Dixon/Feng Zhang/MIT, Esvelt et al 2014 (CC BY)
</p>

<p>With the power to modify entire populations, gene drives promise to upend evolution—or not.</p>

Veronique Greenwood

Articles