Daily Archives: February 4, 2021

Encrypted Gun Registry: How to Preserve the Second Amendment? – The National Interest

Posted: February 4, 2021 at 6:54 pm

Whenever the issue of firearms ownership is brought up, those on both sides dig in and there is little way to truly find compromise. Supporters of the Second Amendment often already complain that their rights have been eroded. While theSecond Amendmentmay read, Congress shall make no law the truth is that there has been legislation that limits firearms ownership including the National Firearms Act of 1934, the Gun Control Act of 1968 and the Firearm Owners Protection Act of 1986.

Meanwhile on the other side of the issue, gun control advocates have called for greater efforts to conduct background checks. Earlier this year Rep. Sheila Jackson Lee (D-Texas) introducedHouse Resolution 127Sabika Sheikh Firearms Licensing and Registration Act, which called for at least twenty-four hours of training with every firearm an individual owns, require a psychological evaluation to obtain a license and even require owners of antique firearms to have such a license.

While it is unlikely Lees bill will be met with much support, there have been calls for a national gun registry. However, Second Amendment supporters, who naturally would oppose such a registry, may have an unlikely ally in privacy advocates.

A new study conducted by researchers at Brown University has found that an encrypted gun registry would bridge the divide on this issue. It suggests that it would make it more difficult for those legally barred from owning firearms from acquiring one, and also make it easier for law enforcement to trace firearms much in the way that automobiles can be tracked.

The study was led by Browns Seny Kamara, who began the work after staffers from U.S. Senator Ron Wyden (D-Oregon) reached out in 2018.

How successful such a national database would be all depends on whether every county in the country signs on, something Kamaraadmitted to Wired magazine couldbe a tall order.

People in different parts of the country are going to feel differently about it, so the idea was to design something like a national gun registry that could potentially be voluntary, Kamara explained.

Rather than being a true national registry, this would work as a series of non-centralized data bases, all of which would be encrypted to maintain privacyyet could be accessible to law enforcement via a physical authentication token. Such a key would ensure that officials could gain access while the general public could notand because it is encrypted, in theory it would be inaccessible to hackers.

The study did not look into a plethora of issues, such as how it would handle private sales, what information would be contained in the registry or even how data could be shared across a decentralized network. For one thing what happens if a firearm is sold or transferred to another user in a different database? How would that be tracked?

While ablockchainthat is used inbitcoin and other cryptocurrenciescould potentially play a role, it is meant to allow the transfer of digital money without disclosing the user. In this case the user and associated physical firearm is what is registered. If that firearm is sold, stolen or otherwise changes hands without updating the database the information is completely useless!

All of those facts make it obvious to see that the National Rifle Association and other groups that support the Second Amendment would remain opposed to the database. It would only servelaw abidingindividuals and put a burden on gun shops and dealers to report the transactions of the sales.

However, at this point the Brown study wasnt so much to develop an encrypted network but rather to even determine if was possible. About the best possible takeaway on this is that at least Sen. Wyden was exploring the feasibility of the technology and not writing actual legislation.

Far too often, lawmakers write bills without having a good grasp of technology, especially when it comes to encryption, Wyden toldWiredin a statement. My view has always been that making good public policy depends on knowing what is possible on the technical side. So when I had the idea to create a new kind of secure gun registry, I was hoping Professor Kamara could give me a gut check on whether this was a harebrained idea or not.

Peter Suciu is a Michigan-based writer who has contributed to more than four dozen magazines, newspapers and websites. He regularly writes about military small arms, and is the author of several books on military headgear includingA Gallery of Military Headdress, which is available on Amazon.com.

Image: Reuters.

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Encrypted Gun Registry: How to Preserve the Second Amendment? - The National Interest

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The noisy ocean: Humans have made the world’s seas a very loud place to live – USA TODAY

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Scientists say there is a big increase in the humpback whale population around New York City thanks to cleaner water that has led to an abundance of small fish the whales love to eat. (Oct. 7) AP Domestic

The ocean has become a very noisy place.

The world's seas are much louder than they were in pre-industrial times, "becoming more and more a raucous cacophony as the noise from human activity has grown louder and more prevalent," according to astudy published Thursday.

The noise has had an impact on marine animals worldwide, affecting their behavior, physiology and, in some cases, their overall survivability. Higher ocean noise levels can reduce the ability of animals to communicate with potential mates, other group members, their offspring or their feeding partners,the National Oceanic and Atmospheric Administrationsaid.

Sounds travel very far underwater. For fish, sound is probably a better way to sense their environment than light, said Francis Juanes, an ecologist at the University of Victoria in Canada and a co-author of the paper.

Noise can also reduce an ocean animal's ability to hear environmental cues that are vital for survival, including those key to avoiding predators, finding food and navigating to preferred habitats, NOAA said.

The researchers sifted through thousands of data sets and research articles documenting changes in noise volume and frequency to assemble a comprehensive picture of how the ocean soundscape is changing and how marine life is affected.

From the songs of whales to grinding arctic sea ice, the world's oceans' natural chorus is performed by a vast ensemble of geological and biological sounds, according to the study, which was led byCarlos Duarte, a marine ecologist at the Red Sea Research Center in Saudi Arabia.

For example, snapping shrimp make a sound resembling popping corn that stuns their prey. Humpback whale songs can resemble a violinists melodies.

But for more than a century, sounds from human activities on the high seas, such as fishing, shipping, recreational boatingand development, have increasingly added to the mix, making modern oceans far noisier than ever before.

For many marine species, their attempts to communicate are being masked by sounds that humans have introduced,Duarte said.

That noise can travel long distances underwater, leading to increases and changes in ocean noise levels in many coastal and offshore habitats.

"This onslaught of noise, which far exceeds the Navys own safety limits for humans, can have a devastating effect on marine species especially whales, who use their keen sense of hearing for almost everything they do," the Center for Biological Diversity said.

A humpback whale and her calf.(Photo: L. Candisani/Courtesy Instituto Aqualie)

Thestudy maps out how underwater noise affects countless groups of marine life, including zooplankton and jellyfish, according to The New York Times.The extent of the problem of noise pollution has only recently dawned on us, study co-author Christine Erbe,director of the Center for Marine Science and Technology at Curtin University in Perth, Australia, told The Times.

Surprisingly, its not just noises added human activities have also made some areas of the ocean quieter, the study found. For example, the deterioration of habitats such ascoral reefs and the hunting of large marine mammals, including highly vocal whales, has led to drastic declines in the abundance of sound-producing animals.

In addition, the loss of sea ice because ofthe planet's rapidly warming climate has drastically altered the natural acoustics of arctic marine environments.

When people think of threats facing the ocean, we often think of climate change, plastics and overfishing. But noise pollution is another essential thing we need to be monitoring, said Neil Hammerschlag, a University of Miami marine ecologist, who was not involved with the paper.

There is hope, however: The study authors argue that the harmful effects of noise pollution could rapidly decline through the mitigation and regulation of sources of marine noise.

Changing ocean soundscapes have become the neglected elephant in the room of global ocean change, the study authors write. In an era when societies increasingly look to the blue economy as a source of resources and wealth, it is essential that ocean soundscapes be responsibly managed to ensure the sustainable use of the ocean.

The study was published Thursday in the peer-reviewed journal Science, a publication of the American Association for the Advancement of Science.

Contributing: The Associated Press

Read or Share this story: https://www.usatoday.com/story/news/nation/2021/02/04/ocean-noise-humans-have-made-seas-very-loud-place-live/4390434001/

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The noisy ocean: Humans have made the world's seas a very loud place to live - USA TODAY

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Could Climate Change Be More Extreme Than We Think? – The Atlantic

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Photo Illustrations by Brendan Pattengale | Maps by La Tigre

Images above: Glaciers from the Vatnajkull ice cap, in Iceland

Brendan Pattengale is a photographer who explores how color can convey emotions in an image. In his photo illustrations throughout this article, the colors of the original photos have been adjusted, but the images are otherwise unaltered.

This article was published online on February 3, 2021.

We live on a wild planet, a wobbly, erupting, ocean-sloshed orb that careens around a giant thermonuclear explosion in the void. Big rocks whiz by overhead, and here on the Earths surface, whole continents crash together, rip apart, and occasionally turn inside out, killing nearly everything. Our planet is fickle. When the unseen tug of celestial bodies points Earth toward a new North Star, for instance, the shift in sunlight can dry up the Sahara, or fill it with hippopotamuses. Of more immediate interest today, a variation in the composition of the Earths atmosphere of as little as 0.1 percent has meant the difference between sweltering Arctic rainforests and a half mile of ice atop Boston. That negligible wisp of the air is carbon dioxide.

Since about the time of the American Civil War, CO2s crucial role in warming the planet has been well understood. And not just based on mathematical models: The planet has run many experiments with different levels of atmospheric CO2. At some points in the Earths history, lots of CO2 has vented from the crust and leaped from the seas, and the planet has gotten warm. At others, lots of CO2 has been hidden away in the rocks and in the oceans depths, and the planet has gotten cold. The sea level, meanwhile, has tried to keep uprising and falling over the ages, with coastlines racing out across the continental shelf, only to be drawn back in again. During the entire half-billion-year Phanerozoic eon of animal life, CO2 has been the primary driver of the Earths climate. And sometimes, when the planet has issued a truly titanic slug of CO2 into the atmosphere, things have gone horribly wrong.

Today, humans are injecting CO2 into the atmosphere at one of the fastest rates ever over this entire, near-eternal span. When hucksters tell you that the climate is always changing, theyre right, but thats not the good news they think it is. The climate system is an angry beast, the late Columbia climate scientist Wally Broecker was fond of saying, and we are poking it with sticks.

The beast has only just begun to snarl. All of recorded human historyat only a few thousand years, a mere eyeblink in geologic timehas played out in perhaps the most stable climate window of the past 650,000 years. We have been shielded from the climates violence by our short civilizational memory, and our remarkably good fortune. But humanitys ongoing chemistry experiment on our planet could push the climate well beyond those slim historical parameters, into a state it hasnt seen in tens of millions of years, a world for which Homo sapiens did not evolve.

When theres been as much carbon dioxide in the air as there already is todaynot to mention how much theres likely to be in 50 or 100 yearsthe world has been much, much warmer, with seas 70 feet higher than they are today. Why? The planet today is not yet in equilibrium with the warped atmosphere that industrial civilization has so recently created. If CO2 stays at its current levels, much less steadily increases, it will take centurieseven millenniafor the planet to fully find its new footing. The transition will be punishing in the near term and the long term, and when its over, Earth will look far different from the one that nursed humanity. This is the grim lesson of paleoclimatology: The planet seems to respond far more aggressively to small provocations than its been projected to by many of our models.

To truly appreciate the coming changes to our planet, we need to plumb the history of climate change. So let us take a trip back into deep time, a journey that will begin with the familiar climate of recorded history and end in the feverish, high-CO2 greenhouse of the early age of mammals, 50 million years ago. It is a sobering journey, one that warns of catastrophic surprises that may be in store.

Read: Scientists have uncovered a disturbing climate change precedent

The first couple of steps back in time wont take us to a warmer worldbut they will illuminate just what sort of ill-tempered planet were dealing with. As we pull back even slightly from the span of recorded historyour tiny sliver of geologic timewell notice almost at once that the entire record of human civilization is perched at the edge of a climate cliff. Below is a punishing ice age. As it turns out, we live on an ice-age planet, one marked by the swelling and disintegration of massive polar ice sheets in response to tiny changes in sunlight and CO2 levels. Our current warmer period is merely one peak in a mountain range, with each summit an interglacial springtime like today, and each valley floor a deep freeze. It takes some doing to escape this cycle, but with CO2 as it is now, we wont be returning to an ice age for the foreseeable future. And to reach analogues for the kind of warming well likely see in the coming decades and centuries, we will need to move beyond the past 3 million years of ice ages entirely, and make drastic jumps back into the alien Earths of tens of millions of years ago. Our future may come to resemble these strange lost worlds.

Before we move more dramatically backwards in time, let us briefly pause over the history of civilization, and then some. Ten thousand years ago, the big mammals had just vanished, at human hands, in Eurasia and the Americas. Steppes once filled with mammoths and camels and wetlands stocked with giant beavers were suddenly, stunningly vacant.

The coastlines that civilization presumes to be eternal were still far beyond todays horizon. But the seas were rising. The doomed vestiges of mile-thick ice sheets that had cloaked a third of North American land were retreating to the far corners of Canada, chased there by tundra and taiga. The roughly 13 quintillion gallons of meltwater these ice sheets would hemorrhage, in a matter of millennia, raised the sea level hundreds of feet, leaving coral reefs that had been bathed in sunlight under shallow waves now drowned in the deep.

By 9,000 years ago, humans in the Fertile Crescent, China, Mexico, and the Andes had independently developed agriculture andafter 200,000 years of wanderinghad begun to stay put. Sedentary settlements blossomed. Humans, with a surfeit of calories, began to divide their labor, and artisans plied new arts. The Earths oldest cities, such as Jericho, were bustling.

Its easy to forget that the Earthcozy, pastoral, familiaris nevertheless a celestial body, and astronomy still has a vote in earthly affairs. Every 20,000 years or so the planet swivels about its axis, and 10,000 years ago, at civilizations first light, the Earths top half was aimed toward the sun during the closest part of its orbitan arrangement today enjoyed by the Southern Hemisphere. The resulting Northern-summer warmth turned the Sahara green. Lakes, hosting hippos, crocodiles, turtles, and buffalo, speckled North Africa, Arabia, and everywhere in between. Lake Chad, which today finds itself overtaxed and shrinking toward oblivion, was Mega-Chad, a 115,000-square-mile freshwater sea that sprawled across the continent. Beneath the Mediterranean today, hundreds of dark mud layers alternate with whiter muck, a barcode that marks the Saharas rhythmic switching from lush green to continent-spanning desert.

Imprinted on top of this cycle were the last gasps of an ice age that had gripped the planet for the previous 100,000 years. The Earth was still thawing, and amid the final approach of the rising tides, enormous plains and forests like Doggerlanda lowland that had joined mainland Europe to the British Isleswere abandoned by nomadic humans and offered to the surging seas. Vast islands like Georges Bank, 75 miles off Massachusettswhich once held mastodons and giant ground slothssaw their menagerie overtaken. Scallop draggers still pull up their tusks and teeth today, far offshore.

By 5,000 years ago, as humanity was emerging from its unlettered millennia, the ice had stopped melting and oceans that had been surging for 15,000 years finally settled on modern shorelines. Sunlight had waned in the Northern summer, and rains drifted south toward the equator again. The green Sahara began to die, as it had many times before. Hunter-fisher-gatherers who for thousands of years had littered the verdant interior of North Africa with fishhooks and harpoon points abandoned the now-arid wastelands, and gathered along the Nile. The age of pharaohs began.

By geologic standards, the climate has been remarkably stable ever since, until the sudden warming of the past few decades. Thats unsettling, because history tells us that even local, trivial climate misadventures during this otherwise peaceful span can help bring societies to ruin. In fact, 3,200 years ago, an entire network of civilizationsa veritable globalized economyfell apart when minor climate chaos struck.

There is famine in [our] house; we will all die of hunger. If you do not quickly arrive here, we ourselves will die of hunger. You will not see a living soul from your land. This letter was sent between associates at a commercial firm in Syria with outposts spread across the region, as cities from the Levant to the Euphrates fell. Across the Mediterranean and Mesopotamia, dynasties that had ruled for centuries were all collapsing. The mortuary-temple walls of Ramses IIIthe last great pharaoh of Egypts New Kingdom periodspeak of waves of mass migration, over land and sea, and warfare with mysterious invaders from afar. Within decades the entire Bronze Age world had collapsed.

Historians have advanced many culprits for the breakdown, including earthquakes and rebellions. But like our own teetering worldone strained by souring trade relations, with fractious populaces led by unsteady, unscrupulous leaders and now stricken by plaguethe eastern Mediterranean and the Aegean were ill-prepared to accommodate the deteriorating climate. While one must resist environmental determinism, it is nevertheless telling that when the region mildly cooled and a centuries-long drought struck around 1200 B.C., this network of ancient civilizations fell to pieces. Even Megiddo, the biblical site of Armageddon, was destroyed.

This same story is told elsewhere, over and over, throughout the extremely mild stretch of time that is written history. The Roman empires imperial power was vouchsafed by centuries of warm weather, but its end saw a return to an arid coldperhaps conjured by distant pressure systems over Iceland and the Azores. In A.D. 536, known as the worst year to be alive, one of Icelands volcanoes exploded, and darkness descended over the Northern Hemisphere, bringing summer snow to China and starvation to Ireland. In Central America several centuries later, when the reliable band of tropical rainfall that rings the Earth left the Mayan lowlands and headed south, the megalithic civilization above it withered. In North America, a megadrought about 800 years ago made ancestral Puebloans abandon cliffside villages like Mesa Verde, as Nebraska was swept by giant sand dunes and California burned. In the 15th century, a 30-year drought bookended by equally unhelpful deluges brought the Khmer at Angkor low. The hydraulic empire had been fed and maintained by an elaborate irrigation system of canals and reservoirs. But when these canals ran dry for decades, then clogged with rains, invaders easily toppled the empire in 1431, and the Khmer forfeited their temples to the jungle.

Hopscotching through these human disasters to the present day, we pass perhaps the most familiar historical climate event of all: the Little Ice Age. Lasting roughly from 1500 to 1850, the chill made ice rinks of Dutch canals, and swelled up Swiss mountain glaciers. Tent cities sprung up on a frozen Thames, and George Washington endured his winter of cold and privation at Valley Forge in 1777 (which wasnt even particularly harsh for the times). The Little Ice Age might have been a regional event, perhaps the product of an exceptional run of sunlight-dimming volcanism. In 1816, its annus horribilis, the so-called year without a summerwhich brought snows to New England in Augustglobal temperatures dropped perhaps a mere half a degree Celsius. While it is perennially plumbed by historians for insights into future climate change, it is not even remotely on the same scale of disruption as that which might lie in our future.

As Europe emerged from its chill, coal from 300-million-year-old jungles was being fed into English furnaces. Although the Earth was now in the same configuration that, in the previous few million years, had invited a return to deep, unthinkable ice ages, for some reason the next ice age never took. Instead the planet embarked on an almost unprecedented global chemistry experiment. Halfway through the 20th century, the climate began behaving very strangely.

Read: The strange future Hurricane Harvey portends

So this is the climate of written history, a seemingly eventful stretch that has really been the random noise and variability of a climate essentially at peace. Indeed, if you were to find yourself in an industrial civilization somewhere else in the universe, you would almost certainly notice such similarly strange and improbably pleasant millennia behind you. This kind of climate stability seems to be a prerequisite for organized society. It is, in other words, as good as it gets.

As we jump back 20,000 yearsto yesterday, geologicallythe world ceases being recognizable. Whereas all of recorded history played out in a climate hovering well within a band of 1 degree Celsius, we now see what a difference 5 to 6 degrees can makea scale of change similar to the one that humans may engineer in only the next century or so, though in this case, the world is 5 to 6 degrees colder, not warmer.

An Antarcticas worth of ice now rests atop North America. Similar sheets smother northern Europe, and as a result, the sea level is now 400 feet lower. The midwestern United States is carpeted in stands of stunted spruce of the sort that would today look at home in northern Quebec. The Rockies are carved up, not by wildflower-dappled mountain valleys, but by overflowing rivers of ice and rock. California is a land of dire wolves. Where the Pacific Northwest edges up against the American Antarctica, it is a harsh and treeless place. Nevada and Utah fill up with cold rains.

During World War II, at Topaz, the desolate Japanese American internment camp in Utah, prisoners combed the flats of the Sevier Desert for unlikely seashells, fashioning miraculous little brooches from tiny mussel and snail shells to while away their exile. The desert seashells were roughly 20,000 years old, from the vanished depths of the giant Pleistocene-era Lake Bonnevillethe product of a jet stream diverted south by the ice sheet. This was once a Utahan Lake Superior, more than 1,000 feet deep in places. It was joined by endless other verdant lakes scattered across todays bleak Basin and Range region.

Elsewhere, the retreat of the seas made most of Indonesia a peninsula of mainland Asia. Vast savannas and swamps linked Australia and New Guinea, and of course Russia shared a tundra handshake with Alaska. There were reindeer in Spain, and glaciers in Morocco. And everywhere loess, loess, and more loess. This was the age of dust.

Ice is a rock that flows. Send it in massive sterilizing slabs across the continents, and it will quarry mountainsides, pulverize bedrock, and obliterate everything in its path. At the height of the last ice age, along the crumbling margins of the continental ice sheets, the rocky, dusty spoils of all this destruction spilled out onto the tundra. Dry winds carried this silt around the world in enormous dust storms, piling it up in seas of loess that buried the central U.S., China, and Eastern Europe under featureless drifts. In Austria, not far from the site of the voluptuous Venus of Willendorf figurine, carved some 30,000 years ago, are the remains of a campground of the same agetents, hearths, burnt garbage pits, hoards of ivory jewelryall abandoned in the face of these violent, smothering haboobs. Ice cores from both Antarctica and Greenland record a local environment that was 10 times dustier than today. All of this dust seeded the seas with iron, a vital nutrient for carbon-hogging plankton, which bloomed around Antarctica and pulled gigatons of CO2 out of the air and deep into the ocean, freezing the planet further.

Read: When a killer climate catastrophe struck the worlds oceans

This parched Pleistocene world would have appeared duller from space, hosting as it did a quarter less plant life. CO2 in the atmosphere registered only a paltry 180 ppm, less than half of what it is today. In fact, CO2 was so low, it might have been unable to drop any further. Photosynthesis starts to shut down at such trifling levels, a negative-feedback effect that might have left more CO2unused by plantsin the air above, acting as a brake on the deep freeze.

This was the strange world of the Ice Age, one that, geologically speaking, is still remarkably recent. Its so recent, in fact, that today, most of Canada and Scandinavia is still bouncing back up from the now-vanished ice sheets that had weighed those lands down.

In 2021, we find ourselves in an unusual situation: We live on a world with massive ice sheets, one of which covers one of the seven continents and is more than a mile deep. For most of the planets past, it has had virtually no ice whatsoever. The periods of extreme coldlike the ultra-ancient, phantasmagoric nightmares of Snowball Earth, when the oceans might have been smothered by ice sheets all the way to the tropicsare outliers. There were a few other surprising pulses of frost here and there, but they merely punctuate the balmy stretches of the fossil record. For almost all of the Earths history, the planet was a much warmer place than it is today, with much higher CO2 levels. This is not a climate-denying talking point; its a physical fact, and acknowledging it does nothing to take away from the potential catastrophe of future warming. After all, we humans, along with everything else alive today, evolved to live in our familiar low-CO2 worlda process that took a long time.

How long, exactly? Fifty million years ago, as our tiny mammalian ancestors were still sweating through the jungly, high-CO2 greenhouse climate they had inherited from the dinosaurs, India was nearing the end of an extended journey. Long estranged from Africa and the august, bygone supercontinent of Gondwana, the subcontinent raced northeast across the protoIndian Ocean and smashed into Asia in slow motion. The collision not only quieted CO2-spewing volcanoes along Asian subduction zones; it also thrust the Himalayas and the Tibetan Plateau toward the stars, to be continually weathered and eroded away.

As it turns out, weathering rocksthat is, breaking them down with CO2-rich rainwateris one of the planets most effective long-term mechanisms for removing carbon dioxide from the atmosphere, one that modern geoengineers are frantically trying to reproduce in a lab, for obvious reasons.

Adding to this colossal Himalayan CO2 sink, the more recent buckling, tectonic mess that lifted Indonesia and its neighbors from the sea over the past 20 million years or so also exhumed vast tracts of highly weatherable ocean crust, exposing it all to the withering assault of tropical rainstorms. Today this corroding rock accounts for roughly 10 percent of the planets carbon sink. Over tens of millions of years, then, the stately march of plate tectonicsthe balance of volcanic CO2 and rock weatheringseems to have driven long-term climate change, in our case toward a colder, lower-CO2 world. As well see, humans now threaten to undo this entire epic, geologic-scale climate evolution of the Cenozoic eraand in only a few decades.

When Earths blanket of CO2 was finally thin enough, the planets regular wobbles were at long last sufficient to trigger deep glaciations. The ice ages began. But the climate was not stable during this period. The ice advanced and retreated, and while the descent into the wild episodes of the Pleistocene epoch could be leisurelythe depths of planetary winter taking tens of thousands of years to arrivethe leap out of the cold tended to be sudden and violent. This is where positive feedback loops come in: When the last ice age ended, it ended fast.

Coral reefs marking the ancient sea levelbut today lying deep off the coasts of Tahiti and Indonesiareveal that about 14,500 years ago, the seas suddenly jumped 50 feet or so in only a few centuries, as meltwater from the late, great North American ice sheet raged down the Mississippi. When a 300-foot-deep lake of glacial meltwater spanning at least 80,000 square miles of central Canada catastrophically drained into the ocean, it shut down the churn of the North Atlantic and arrested the seaborne flow of heat northward. As a result, tundra advanced to retake much of Europe for 1,000 years. But when ocean circulation kicked back into gear, and the dense, salty seawater began to sink again, the system rebooted, and currents carried the equators heat toward the Arctic once more. Temperatures in Greenland suddenly leaped 10 degrees Celsius in perhaps a decade, fires spread, and revanchist forests reclaimed Europe for good.

In Idaho, ice dams that had held back giant lakes of glacial meltwater about six times the volume of Lake Erie collapsed as the world warmed, and each released 10 times the flow of all the rivers on Earth into eastern Washington. The floods carried 30-foot boulders on biblical waves, through what were suddenly the worlds wildest rapids. They left behind a labyrinth of bedrock-scoured canyons that still covers the entire southeastern corner of the state like a scar. When the Earths climate changes, this is what it can look like on the ground.

As the ice sheets of the Northern Hemisphere finally lost their grip, darker land around the melting margins became exposed to the sun for the first time in 100,000 years, accelerating the ices retreat. Permafrost melted, and methane bubbled up from thawing bogs. Colder, more CO2-soluble oceans warmed, and gave up the carbon theyd stolen in the Ice Age, warming the Earth even more. Relieved of their glacial burden, volcanoes in Iceland, Europe, and California awoke, adding even more CO2 to the atmosphere.

Soon the Sahara would green again, Jericho would be born, and humans would start writing things down. They would do so with the assumption that the world they saw was the way it had always been. We were born only yesterday and know nothing, one of them would write. And our days on earth are but a shadow.

As we leap back in time again, we emerge before the final Pleistocene glaciation. Weve gone tremendously far back, 129,000 years, though in some ways weve only returned to our own world. This was the most recent interglacial period, the last of many breaks between the ice ages, and the last time the planet was roughly as warm as it is today. Once more, the seas have risen hundreds of feet, but something is awry.

As the Earths wobble and orbit conspired to melt more ice than the poles have shed so far today, the planet absorbed more sunlight. As a result, global temperatures were little more than 1 degree warmer than todays Anthropocene chart-toppersor maybe even the same. But sea level was 20 to 30 feet higher than it is now. (A full third of Florida was sunk beneath the waves.) This is sobering, as one paper put it.

Modelers have tried and mostly failed to square how a world about as warm as todays could produce seas so strangely high. Provisional, if nightmarish, explanations like the runaway, catastrophic collapse of monstrous ice cliffs more than 300 feet tall in Antarctica, which may or may not be set into motion in our own time, are fiercely debated in conference halls and geoscience departments.

Very soon, we may well have warmed the planet enough to trigger similarly dramatic sea-level rise, even if it takes centuries to play out. This is what the Exxon scientist James Black meant in 1977 when he warned higher-ups of the coming super-interglacial that would be brought aboutas a matter of simple atmospheric physicsfrom burning fossil fuels. But our trajectory as a civilization is headed well beyond the warmth of the last interglacial, or any other interglacial period of the Pleistocene, for that matter. So its time to keep moving. We must take our first truly heroic leap into geologic time, millions of years into the past.

Were more than 3 million years in the past now, and carbon dioxide in the atmosphere is at 400 parts per million, a level the planet will not again see until September 2016. This world is 3 to 4 degrees Celsius warmer than ours, and the sea level is up to 80 feet higher. Stunted beech trees and bogs line the foothills of the Transantarctic Mountains not far from the South Polethe last members of a venerable line of once-majestic forests that had existed since long before the age of the dinosaurs.

What weve glossed over in our journey back to this ancient present: the entire evolutionary history of Homo sapiens, three Yellowstone super-eruptions, thousands of megafloods, the last of the giant terror birds, a mass extinction of whales, and the glacial creation and destruction of innumerable islands and moraines. As we make our way backwards in time to the Pliocene, the glaciations get briefer, and the ice sheets themselves become thinner and more temperamental. About 2.6 million years ago they all but disappear in North America, as CO2 levels continue their slow climb.

When we arrive in the middle of the Pliocene, just over 3 million years ago, CO2 levels are high enough that weve escaped the cycle of ice ages and warm interglacials altogether. Lucy the Australopithecus roams a heavily forested East Africa. We are now outside the evolutionary envelope of our modern world, sculpted as it was by the temperamental northern ice sheets and deep freezes of the Pleistocene. But as to atmospheric carbon dioxide, 3 million years is how far back we have to go to arrive at an analogue for 2021.

Despite the similarities between our world and that of the Pliocene, the differences are notable. In the Canadian High Arcticwhere today tundra spreads to the horizonevergreen forests come right to the edge of an ice-free Arctic Ocean. Though the world as a whole is only a few degrees warmer, the Arctic, as always, gets the brunt of the extra heat. This is called polar amplification, and its why maps of modern warming are crowned by a disturbing fog of maroon. Models struggle to reproduce the extreme level of warming in the Pliocene Arctic. Its a full 10 to 15 degrees Celsius warmer in the long twilight of northern Canada, and the pine and birch woodlands of these Arctic shores are filled with gigantic forest-dwelling camels. Occasionally this boreal world erupts in wildfire, a phenomenon echoed by the blazes that today sweep ever farther north. Elsewhere, West Antarcticas ice sheet may have disappeared entirely, and Greenlands, if it exists at all, is shriveled and pathetic.

A common projection for our own warming world is that, while the wet places will get wetter, the dry places will get drier. But the Pliocene seems to defy this saw for reasons not yet fully understood. Its a strangely wet world, especially the subtropics, wherein the Sahara, the Outback, the Atacama, the American Southwest, and Namibialakes, savannas, and woodlands replace deserts. This ancient wetness might come down to inadequacies in how we model clouds, which are under no obligation to behave in physical reality as they do in simplified lines of computer code. Hurricanes were almost certainly more consistently punishing 3 million years ago, just as our storms of the future will be. And a more sluggish circulation of the atmosphere might have lulled the trade winds, turning El Nio into El Padre. Perhaps this is what brought rainsand lakesto the Mojave at this time.

Our modern coastlines would have been so far underwater that youd have to take great pains to avoid getting the bends if you tried scuba diving down to them. Today, traveling east through Virginia, or North or South Carolina, or Georgia, midway through your drive youll pass over a gentle 100-foot drop. This is the Orangeburg Scarp, a bluffhundreds of miles longthat divides the broad, flat coastal plain of the American Southeast. It comprises the eroded and smoothed-out rumors of once-magnificent sea cliffs. Here, waves of the Pliocene high seas chewed away at the middle of the Carolinasan East Coast Big Sur. This ancient shoreline is visible from space by the change in soil color that divides the states, and is visible on much closer inspection as well: To the east of this strange drop-off, giant megalodon-shark teeth and whale bones litter the Carolina Low Country. Though warped over the ages by the secret workings of the mantle far below, these subtle banks 90 miles inland nevertheless mark the highest shoreline of the Pliocene, when the seas were dozens of feet higher than they are today. But even within this warm Pliocene period, the sea level leaped and fell by as much as 60 feet every 20,000 years, to the rhythm of the Earths sway in space. This is because, under this higher-CO2 regime, the unstable ice sheet in Antarctica took on the volatile temperament that, 1 million years later, would come to characterize North Americas ice sheet, toying with the ancient coastline as if it were a marionette.

So this is the Pliocene, the world of the distant present. While todays projections of future warming tend to end in 2100, the Pliocene illuminates just what sort of long-term changes might inevitably be set in motion by the atmosphere weve already engineered. As the great ice sheets melt, the permafrost awakens, and darker forested land encroaches on the worlds tundra, positive feedbacks may eventually launch our planet into a different state altogether, one that might resemble this bygone world. Nevertheless, human civilization is unlikely to keep atmospheric CO2 at a Pliocene levelso more ancient and extreme analogues must be retrieved.

Were now deeper in the past, and the planet appears truly exotic. The Amazon is running backwards, and gathers in great pools at the foot of the Andes. A seaway stretches from Western Europe to Kazakhstan and spills into the Indian Ocean. Californias Central Valley is open ocean.

What today is the northwestern U.S. is especially unrecognizable. Today the airy, columnated canyons of the Columbia River in Oregon swarm with tiny kiteboarders zipping through gorges of basalt. But 16 million years ago, this was a black, unbreathable place, flowing with rivers of incandescent rock. The Columbia River basaltsold lava flows that spread across Washington, Oregon, and Idaho, in some places more than two miles thickwere the creation of a class of extremely rare and world-changing volcanic eruptions known as large igneous provinces, or LIPs.

Some LIPs in Earths history span millions of square miles, erupt for millions of years, inject tens of thousands of gigatons of CO2 into the air, and are responsible for most of the worst mass extinctions in the history of the planet. They live up to their namethey are large. But these mid-Miocene eruptions were still rather small as far as LIPs go, and so the planet was spared mass death. Nevertheless, the billowing volcanoes raised atmospheric CO2 up to about 500 ppm, a level that today represents something close to the most ambitious and optimistic scenario possible for limiting our future carbon emissions.

In the Miocene, this volcanic CO2 warmed up the world to at least 4 degrees Celsius and perhaps as much as 8 degrees above modern temperatures. As a result, there were turtles and parrots in Siberia. Canadas Devon Island, in the high Arctic, is today a desolate wasteland, the largest uninhabited island in the worldand one used by NASA to simulate life on Mars. In the Miocene, its flora resembled Lower Michigans.

The sweeping grasslands distinctive to our cooler, drier, low-CO2 world had yet to take over the planet, and so forests were everywherein the middle of Australia and Central Asia and Patagonia. All of this vegetation was one of the reasons it was so warm. Forests and shrubs made this planet darker than our own worldone still painted pallid hues in many places by bare land and iceand allowed it to absorb more heat. This change in the planets color is just one of the many long-term feedback loops awaiting us after the ice melts. Long after our initial pulse of CO2, they will make our future world warmer and more alien still.

As for fauna, were now so distantly marooned in time from our own world that most of the creatures that inhabited this leafy planet range from the flatly unfamiliar to the uncannily so. There were big cats that werent cats, and rhino-size hell pigs that werent pigs. There were sloths that lived in the ocean and walruses that werent related to todays walruses. Earths largest-ever meat-eating land mammals, African juggernauts like Megistotherium and Simbakubwa, not closely related to any living mammals today, tore early elephants apart with bladed mouths.

And with CO2 at 500 ppm, the sea level was about 150 feet higher than today. Approaching Antarctica in the middle Miocene by sea, the waters would be warmer than today, and virtually unvisited by ice. To get to the ice sheet, youd have to hike far past lakes and forests of conifers that lined the coast. Trudging past the trees and finally over endless tundra, you would come at last to the edge of a much smaller ice sheet whose best days were still ahead of it. An axiom about this land-based Antarctic ice sheet in paleoclimatology is that its incredibly stubborn. That is, once you have an ice sheet atop the heart of Antarctica, feedback loops kick in to make it exceedingly hard to get rid of. Barring true climatic madness, a land-based Antarctic ice sheet is essentially there to stay.

But in the middle Miocene this young Antarctic ice sheet seemed to have a temper. It might have been surprisingly dynamic, as one paper cheerfully puts it. As CO2 increased from just below todays levels up to about 500 ppm, Miocene Antarctica shed what today would amount to 30 to 80 percent of the modern ice sheet. In the Miocene, Antarctica seemed exquisitely tuned to small changes in atmospheric CO2, in ways that we dont fully understand and that were not incorporating into our models of the future. There will undoubtedly be surprises awaiting us in our high-CO2 future, just as there were for life that existed in the Miocene. In fact, the Antarctic ice sheet may be more vulnerable today to rapid retreat and disintegration than at any time in its entire 34-million-year history.

In the 16 million years since this mid-Miocene heat, the volcanic hot spot responsible for the Columbia River basalts has wandered under Yellowstone. Today it powers a much tamer kind of volcano. It could cover a few states in a few inches of ash and disrupt global agriculture for years, but it couldnt launch the planet into a new climate for hundreds of thousands of years, or kill most life on the surface. Unfortunately, there is such a supervolcano active on Earth today: industrial civilization. With CO2 likely to soar past 500 ppm from future emissions, even the sweat-soaked, Siberian-parrot-populated world of the middle Miocene might not tell us everything we need to know about our future climate. Its time to go back to a global greenhouse climate that ranks among the warmest climate regimes complex life has ever endured. In our final leap backwards, CO2 at last reaches levels that humans might reproduce in the next 100 years or so. What follows is something like a worst-case scenario for future carbon emissions. But these worst-case projections have continued to prove stubbornly accurate in the 21st century so far, and they remain a possible path for our future.

Were now about to take our largest leap, by far, into the geologic past. We hurdle over 40 million years of history, past volcanic eruptions thousands of times bigger than that of Mount St. Helens, past an asteroid impact that punched out a gigantic crater where the Chesapeake Bay sits today. The Himalayas slump; India unhitches from Asia; and the further back we go, the higher the CO2 level rises and the warmer the Earth gets. The Antarctic ice sheet, in its death throes, vanishes altogether, and the polar continent instead gives way to monkey puzzle trees and marsupials. We have arrived, finally at the end of our journey, in the greenhouse world of the early age of mammals.

Today the last dry land one steps on in Canada before setting out across the ice-choked seas for the North Pole is Ellesmere Island, at the top of the world. But once upon a time there was a rainforest here. We know this because tree stumps still erode out of the barren hillsides, and theyre more than 50 million years old. Theyre all thats left of an ancient polar jungle now whipped by indifferent Arctic winds. But once upon a time, this island was a swampy cathedral of redwoods, whose canopy naves were filled with flying lemurs, giant salamanders, and hippolike beasts that pierced the waters. At this polar latitude, on some late-fall evening of the early Eocene, the sun tried and failed to lift itself from the horizon. A pink twilight reached deep into the jungle, but soon the sun would set entirely here for more than four months. In this unending Arctic dark, the stillness would be broken by the orphaned calls of tiny early primates, who hopped fearlessly over stilled alligators that would start moving again when the sun returned from beyond the horizon. In this unending night, tapirs hunted for mushrooms and munched on leaf litter that was left over from sunny days past and that in the far future would become coal.

We have no modern analogue for a swampy rainforest teeming with reptiles that nevertheless endures months of Arctic twilight and polar night. But for each degree Celsius the planet warms, the atmosphere holds about 6 percent more water vapor, and given that global temperatures at the beginning of the age of mammals were roughly 13 degrees warmer than today, its difficult to imagine how uncomfortable this planet would be for Ice Age creatures like ourselves. In fact, much of the planet would be rendered off-limits to us, far too hot and humid for human physiology.

Not only was this a sweltering age, but it was also one cruelly punctuated by some of the most profound and sudden CO2-driven global-warming events in geologic historyon top of this already feverish baseline. Deep under the North Atlantic, the Eocene epoch kicked off in style 56 million years ago with massive sheets of magma that spread sideways through the crust, igniting vast, diffuse deposits of fossil fuels at the bottom of the ocean. This ignition of the underworld injected something like the carbon equivalent of all currently known fossil-fuel reserves into the seas and atmosphere in less than 20,000 years, warming the planet by another 5 to 9 degrees Celsius. Evidence abounds of violent storms and megafloods during this ancient spasm of climate changeepisodic waves of torrential rains unlike any on Earth today. In some places, such storms would have been routine, separated by merciless droughts and long, brutal, cloudless heat waves. Seas near the equator may have been almost as hot as a Jacuzzitoo hot for most complex life. As for the rest of the planet, all of this excess CO2 acidified the oceans, and the worlds coral reefs collapsed. Ocean chemistry took 200,000 years to recover.

The most jarring thing about the early age of mammals, though, isnt merely the extreme heat. Its the testimony of the plants. In higher-CO2 conditions, plants reduce the number of pores on their leaves, and fossil leaves from the jungles of the early Eocene have tellingly fewer pores than todays. By some estimates, CO2 50 million years ago was about 600 ppm. Other proxies point to higher CO2, just over 1,000 ppm, but even that amount has long bedeviled our computer models of climate change. For years, in fact, models have told us that to reproduce this feverish world, wed need to ramp up CO2 to more than 4,000 ppm.

This ancient planet is far more extreme than anything being predicted for the end of the century by the United Nations or anyone else. After all, the world that hosted the rainforests of Ellesmere Island was 13 degrees Celsius warmer than our own, while the current global ambition, enshrined in the Paris Agreement, is to limit warming to less than 2, or even 1.5, degrees. Part of what explains this glaring disparity is that most climate projections end at the end of the century. Feedbacks that might get you to Eocene- or Miocene-level warmth play out over much longer timescales than a century. But the other, much scarier insight that Earths history is very starkly telling us is that we have been missing something crucial in the models we use to predict the future.

Some of the models are starting to catch up. In 2019, one of the most computationally demanding climate models ever run, by researchers at the California Institute of Technology, simulated global temperatures suddenly leaping 12 degrees Celsius by the next century if atmospheric CO2 reached 1,200 ppma very bad, but not impossible, emissions pathway. And later that year, scientists from the University of Michigan and the University of Arizona were similarly able to reproduce the warmth of the Eocene by using a more sophisticated model of how water behaves at the smallest scales.

The paleoclimatologist Jessica Tierney thinks the key may be the clouds. Today, the San Francisco fog reliably rolls in, stranding bridge towers high above the marine layer like birthday candles. These clouds are a mainstay of west coasts around the world, reflecting sunlight back to space from coastal California and Peru and Namibia. But under higher-CO2 conditions and higher temperatures, water droplets in incipient clouds could get bigger and rain down faster. In the Eocene, this might have caused these clouds to fall apart and disappearinviting more solar energy to reach, and warm, the oceans. That might be why the Eocene was so outrageously hot.

This sauna of our early mammalian ancestors represents something close to the worst possible scenario for future warming (although some studies claim that humans, under truly nihilistic emissions scenarios, could make the planet even warmer). The good news is the inertia of the Earths climate system is such that we still have time to rapidly reverse course, heading off an encore of this world, or that of the Miocene, or even the Pliocene, in the coming decades. All it will require is instantaneously halting the super-eruption of CO2 disgorged into the atmosphere that began with the Industrial Revolution.

We know how to do this, and we cannot underplay the urgency. The fact is that none of these ancient periods is actually an apt analogue for the future if things go wrong. It took millions of years to produce the climates of the Miocene or the Eocene, and the rate of change right now is almost unprecedented in the history of animal life.

Humans are currently injecting CO2 into the air 10 times faster than even during the most extreme periods within the age of mammals. And you dont need the planet to get as hot as it was in the early Eocene to catastrophically acidify the oceans. Acidification is all about the rate of CO2 emissions, and we are off the charts. Ocean acidification could reach the same level it did 56 million years ago by later this century, and then keep going.

When he coined the term mass extinction in a 1963 paper, Crises in the History of Life, the American paleontologist Norman Newell posited that this was what happened when the environment changed faster than evolution could accommodate. Life has speed limits. And in fact, life today is still trying to catch up with the thaw-out of the last ice age, about 12,000 years ago. Meanwhile, our familiar seasons are growing ever more strange: Flycatchers arrive weeks after their caterpillar prey hatches; orchids bloom when there are no bees willing to pollinate them. The early melting of sea ice has driven polar bears ashore, shifting their diet from seals to goose eggs. And thats after just 1 degree of warming.

Subtropical life may have been happy in a warmer Eocene Arctic, but theres no reason to think such an intimately adapted ecosystem, evolved on a greenhouse planet over millions of years, could be reestablished in a few centuries or millennia. Drown the Florida Everglades, and its crocodilians wouldnt have an easy time moving north into their old Miocene stomping grounds in New Jersey, much less migrating all the way to the unspoiled Arctic bayous if humans re-create the world of the Eocene. They will run into the levees and fortifications of drowning Florida exurbs. We are imposing a rate of change on the planet that has almost never happened before in geologic history, while largely preventing life on Earth from adjusting to that change.

Taking in the whole sweep of Earths history, now we see how unnatural, nightmarish, and profound our current experiment on the planet really is. A small population of our particular species of primate has, in only a few decades, unlocked a massive reservoir of old carbon slumbering in the Earth, gathering since the dawn of life, and set off on a global immolation of Earths history to power the modern world. As a result, up to half of the tropical coral reefs on Earth have died, 10 trillion tons of ice have melted, the ocean has grown 30 percent more acidic, and global temperatures have spiked. If we keep going down this path for a geologic nanosecond longer, who knows what will happen? The next few fleeting moments are ours, but they will echo for hundreds of thousands, even millions, of years. This is one of the most important times to be alive in the history of life.

This article appears in the March 2021 print edition with the headline The Dark Secrets of the Earths Deep Past.

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Could Climate Change Be More Extreme Than We Think? - The Atlantic

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Genomics and genre – Science Magazine

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If the double helix is an icon of the modern age, then the genome is one of the last grand narratives of modernity, writes Lara Choksey in her new book, Narrative in the Age of the Genome. Hybridizing literary criticism with a genre-spanning consideration of a dozen distinct literary works, and imbued throughout with deep concern for the peripheral, the possible, and the political, the book seeks to challenge the whole imaginative apparatus for constructing the self into a coherent narrative, via the lexicon and syntax of the molecular.

To a reading of Richard Dawkins's The Selfish Gene (1976) as a repudiation of class struggle and E. O. Wilson's Sociobiology (1975) as a defense of warfare, Choksey juxtaposes another kind of ambiguous heterotopia in which genetic engineering is a tool of neoliberal self-fashioning. In Samuel R. Delany's Trouble on Triton (1976), Bron, a transgender ex-gigolo turned informatics expert, is caught between sociobiology and the selfish gene, between the liberal developmentalism of progressive evolution, and the neoliberal extraction and rearrangement of biological information. Even the undulating interruptions and parentheticals of Bron's thoughts [mimic] the description of the activation and silencing of genes, she suggests, tying together gene and genre in a way that encapsulates neoliberal alienation.

Choksey next explores the ways in which collectivist fantasies of biological reinvention under Soviet Lysenkoism fused code and cultivation through a close reading of Arkady and Boris Strugatsky's Roadside Picnic (1972) in which cultivated utopian dreamworlds become contaminated by alien forces, resulting in fundamental ecological transformations beyond the promised reach of human control. The novel brings to light not forgotten Soviet utopias but literal zombies and mutations. In a world where planned cultivation fails entirely in the face of the unfamiliar, even as new biological weapons are being developed, Earth itself viscerally reflects a fractured reality of lost promisesa world in crisis with all meaning gone, and survival itself a chancy proposition.

Framed as a family history, The Immortal Life of Henrietta Lacks is actually a horror story, argues Choksey.

As the promise of precision medicine emerged, so too did new forms of memoir. In Kazuo Ishiguro's Never Let Me Go (2005) and the film Gattaca (1997), for example, the traditional aspirational narrative of a pilgrim's progress is subverted: As the unitary subject disappears into data, algorithms, and commodities, a new grammar of existence emerges, albeit one in which the inherited problems of the pastracism, ableism, and the fiction of heteronormativityremain ever-present.

In Saidiya Hartman's Lose Your Mother (2006) and Yaa Gyasi's Homegoing (2016), Choksey sees a reorientation of genomics away from the reduction of self to code and toward new forms of kinship and belonging that offer a reckoning with the histories of brutalization and displacement upon which liberal humanism is founded. Even as genomics seeks to locate the trauma of enslavement at the level of the molecular, communities seeking reunion and reparation know that technology alone cannot do the cultural work of caring for history that narrative can offer.

Reading Rebecca Skloot's The Immortal Life of Henrietta Lacks (2010) as a biography of Black horror which tries, time and again, to resolve itself as family romance, Choksey identifies the perils of narratives unable to recognize their own genre. She argues that by blurring the lines not between fact and fiction but between horror and family history, the dehumanization of Black lives as experimental biomatter echoes inescapably with larger histories of the extraction of Black flesh for the expansion of colonial-capitalist production.

What emerges as most compelling out of this entire tapestry of readings is the author's interpretation of the limits and failures of the extraordinary cultural power of the genome. Concluding that genomics has privileged a particular conception of the human that is in the process of being reconfigured, Choksey ventures that the uncomplicated subject, the Vitruvian Man of the Human Genome Project, has reached its end. What is left is neither dust, stardust, nor a face erased in the sand (as Foucault would have it) but rather whatever might emerge next from the unwieldy kaleidoscope of possible meanings.

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Genomics and genre - Science Magazine

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Illumina CFO on using genome tech to beat pandemic – Financial Director

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From the start of the coronavirus outbreak, technology from Illumina has been at work helping defeat the pandemic. As a result of two Chinese university teams using the US biotechs sequencing equipment, the genome (or genetical material) of the coronavirus was published on January 10, 2020 and vaccines from Oxford University/AstraZeneca, Moderna and Pfizer-BioNtech vaccines were designed within days of this blueprint being revealed.

The latter two are the worlds first genome-based vaccines and have been developed without the companies ever needing to have the virus on site. Sequencing is instrumental to understanding not only the make-up of the virus, but its epidemiology, how it mutates, how it evolves, and also to develop a vaccine for it, says Illumina CFO Sam Samad.

One year on and sequencing the virus is as important as ever in the pandemic fight. Illuminas technology is powering genomic surveillance in countries around world, such as at the Sanger Centre in Cambridge where the COG-UK team identified the new B1.1.7 variant; and in the US where Illumina is working with the US CDC and the company, Helix, to plot the path of new variants across US States.

Our ability to use sequencing to do surveillance, is critical. We need to understand how the virus is mutating and how its also transmitting across communities. Surveillance will also tell us whether the virus is evolving to escape the vaccines that are now being delivered in most countries.

That really underscores the importance of our technology in this fight, says Samad, who joined the San Diego, California-based firm at the start of 2017. Other pandemics will happen in the future, so the question also becomes how do we prevent them? How do we, catch them before what happened with Covid repeats? asks the Canadian.

Illumina was founded in 1998 based on BeadArray technology discovered at Tufts University. Arrays require a prior knowledge of the genome of the sample being investigated. In 2007, Illumina acquired the UK-based company, Solexa, for its next generation sequencing (NGS) technology which Illumina has gone on to develop. NGS doesnt require any understanding of the sample to be analysed and can work out the full genome of any organism.

Illumina has gone on to develop a range of products servicing the sequencing, genotyping, gene expression and proteomics markets has resulted in the rapid growth of its share price- resulting in the firm having a market value of $54bn by the start of the year.

Major sites have been developed in Foster City, near San Francisco, Cambridge in the UK focusing on R&D, and an Asian hub in Singapore combining shared services and manufacturing functions, as well as a major plant in China.

Infectious diseases is just one area of focus for Illumina. Another is oncology, where the company is working with a number of pharma and biotech companies to develop cancer testing to determine which medicines are best for which cancer patients. NGS is also fundamental to identifying the cause of rare genetic diseases in families; and to understanding the chromosomal health of an unborn baby through non-invasive prenatal testing (NIPT).

Oncology is now our biggest area, but we also work in genetic diseases, and reproductive health and non-invasive prenatal testing, taking sequencing and evolving it into a standard of care in health systems around the globe. Just shy of 50 percent of our revenues are in the clinical setting, says Samad.

A big change in Illuminas offering came five years ago when it pivoted from a mainly research approach, supplying instruments, reagents and consumables to academic labs and large genome centres, to focusing on clinical applications of genomics. It acquired Verinata Health, a leading provider of NIPT, and with it, NGS and Illumina started to become as familiar to clinicians as they had been to scientists.

The speed of development reflects the need to innovate in a fast-changing area of science. I think we have an obligation through our technology to move fast.

What you thought was possible 10 years ago, is completely different than what we think is possible today. Who would have thought that through sequencing, we could offer early screening to potentially predict, find it and cure cancer before it becomes deadly, he says.

The pace of development was challenged by the coronavirus pandemic where the majority of staff had to move to remote working but having lab staff designated essential workers meant operations could continue unabated. It meant R&D and manufacturing staff could come to the labs to continue work, says Samad.

A colour coding of sites, from green meaning nothings wrong to red, requiring all staff working remotely, except for essential functions was devised. At some point, most of our sites became really red and orange, resulting in 7,500 out of 8,000 staff working from home, but everybody handled it really well, he says.

Samad came into Illumina with a skill set in finance developed across the healthcare sector. After completing a finance degree and MBA at McMaster University in Ontario, he joined US pharma giant Eli Lilly where over the course of 12 years he rose from being a financial analyst to finance director of the groups Swiss operation before finishing as CFO of Eli Lilly Canada.

It was an opportunity to develop the rigour and discipline demanded by working in finance in a global player. I cant emphasise enough how important it is to get some experience in a large, well-run disciplined institution like Eli Lilly. It was really, really important for me just to get those building blocks and foundations in my career, he says.

But it was at Cardinal Healthcare, another major US player, that he went on to group leadership roles, as CFO of its pharma segment and then treasurer of the whole firm, positions demanding strong decision-making. If you get it wrong, you can send the company into a tailspin that might mean it goes bankrupt, because youre talking about debt issuances and capital availability, he says.

There was also the challenge of addressing the expectations of debt investors, where conservatism pays off in terms of how you manage your cash position, adds Samad.

The opportunity to become group CFO at Illumina offered the chance to join a fast growth company with an offer based on cutting edge science. I felt there was so much runway ahead as the space was so under-penetrated, he says.

What he could bring was the discipline needed for a business that had listed 20 years ago but he says was still operating in an accelerated growth, start-up mode, with some processes not having been fully built out.

What Samad sought to develop was a stronger engagement between the finance team and the rest of the business in an organisational structure for optimally supporting the business through single point accountability.

We needed, for example, a research and development (R&D) person in finance that supports the R&D organisation and another in finance supporting the commercial organisation, and another specifically supporting the product side of the business.

The first six months of Samads time finessing the finance function was a process of evolution. You dont get a structure right the first time, you do it incrementally, and you do it over time, he says.

A major innovation was devising exhaustive and comprehensive dashboards on data visualisation software Tableau covering everything from revenues to balance sheets and R&D. Its reviewed by the executive team twice a month, but I want people to have access 24/7.

That helps with speed of decision making, but it also helps in terms of managing bandwidth and understanding resource constraints on the organisation. because youre not having to ask people all the time to run reports for you, adds Samad.

Despite the challenges presented by the coronavirus pandemic, in September 2020, Illumina announced the proposed $8bn acquisition of cancer screening specialist Grail. The deal raised some eyebrows in the market given that Illumina had created and spun out Grail just four years previously, but the move reflects the willingness to consider any action that can bring together the right ingredients for value creation, even if it appears unwieldy.

Samad says the decision reflects a strategic assessment that Grails proposition today: using blood-based tests known as liquid biopsies to catch cancer early, would fit well in the group, after we had stepped out of the space, to allow it to thrive and evolve through $2bn of R&D funding.

Following fantastic, really promising results for the Grailtests, the decision was taken in late 2019 to acquire the business to grow Illuminas footprint in cancer. But what was crucial to explain to the market was that its a $60bn target market thats totally incremental to us, says Samad.

You need to set the stage in terms of how you explain it to your shareholders, to make sure they get why we can accelerate this market with our commercial capability, with global our operations, he adds.

Samad says he balances him time between priorities such as explaining Grail the story to investors, to focusing on areas for funding over the next five-year cycle.

These are often very difficult conversations, that are always emotional. So you need your people to help and you need to have a good rapport with your executive team, your peers and partners to do that as well, he says.

He says that without his key staff in accounting, treasury, FP&A, and leaders across global regions, I wouldnt be able to have the capacity and bandwidth that would allow me to focus on the key things, he explains.

Samad says closing the Grail deal created a unique set of challenges with the restrictions that we have in terms of travel. But a big focus of ours is that even in times of global crisis, we are really focused on making sure that we continue to find opportunities to move our strategy forward.

We believe these times present a unique opportunity for companies that really focus on executing on their strategy. If they are bold and make big steps, they will come out on the other side of this ahead, he adds.

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Beyond DNA: The rest of the story – Science Magazine

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ILLUSTRATION: MICHELLE KONDRICH

The availability of a fully sequenced human genome and genome-wide analyses of genetic variation have made DNA-based ancestry tests possible. These consumer DNA tests are now widely marketed as a way to discover or confirm family history. But what do they really tell us about our past, and what do they leave out? We asked young scientists to tell us about their family traditions, stories, and culture, and how they understood their DNA test results in the context of their lived experiences. Their stories are below. To read more reflections by young scientists, find past NextGen Voices pieces at https://science.sciencemag.org/collection/nextgen-voices. Follow NextGen Voices on Twitter with hashtag #NextGenSci. Jennifer Sills

My family comes from Jamaica and the Virgin Islands. There is no meal I would rather have than my mom's home-cooked traditional Jamaican food. Now living in Florida, my mom grows many fruits and vegetables native to Jamaica in a garden that occupies her entire yard. When I visit, we spend most of our time together outside picking fresh mangoes, ackee (a tropical fruit grown in Jamaica), or whatever else happens to be in season. On Christmas, she makes oxtail (a kind of beef stew, my personal favorite), fried dumplings, and ackee with saltfish (its traditional complement of salted cod). These foods are well-spicedalthough not always spicyand flavorful.

Where my family originated is mostly hearsay, and the full history beyond a few generations is hard to trace. My DNA test results confirmed that we have some background in Europe and likely moved to the Caribbean through the slave trade. The details echoed a story on my mom's side of the family that one of our ancestors was the child of an Irish slave master and a woman he enslaved.

I have mixed feelings about the business model of consumer DNA test companies, which make their profit based on the use of others' genetic informationin my mind, the most personal information one can share. However, my mom really wanted me or my dad to do the test to see how that side of our ancestry looked. I chose a company that gives users more control over who can access the results. Of course, these tests are not as accurate for those of us from non-European backgrounds, but the results were roughly what I expected, and it is humbling to think about where our family began compared with where it is now.

Gregg Duncan Fischell Department of Bioengineering, University of Maryland, College Park, MD 20742, USA. E-mail: gaduncan{at}umd.edu

My family is Han, the largest nationality of China. Like most families in China, we celebrate the Spring Festival (Chinese New Year) by gathering together to make and eat jiaozi (dumplings filled with vegetables and meat), which are shaped like ancient Chinese gold ingots to symbolize wealth. We hang festival couplets (two lines of poetry with the same number of words) that are painted along with intricate designs on red paper, and we put red lanterns and red candles on display throughout the house; the decorations symbolize happiness and protect us from the mythical monster named Nian, who is said to be afraid of the color red. While we wait for the New Year to arrive, we listen to Hebei Bangzi, the local opera, which sounds similar to the Beijing opera but is more difficult for people outside Hebei province to understand because the singers use pronunciations unique to the region. In my hometown (Shijiazhuang, Hebei), people of the same surname gather together to extend best wishes to their elders before the first sunrise of the new year.

Such traditions are a reminder that my surname (Ji) is not common in China. I hoped that finding out more about my family's origins would help to explain my unusual name. My DNA test results told me that 46.34% of my genome came from North China (Han), 20.13% from South China (Han), and 12.21% from Northeast Asia (Japan). I was disappointed that the results contained no detailed information that I found useful. I do not know how many Chinese people have a genetic pattern similar to mine, andunlike scientific researchthe company did not give me the raw data of my genome. Without more information about how the company analyzed my genomic data, I don't know what conclusions I can draw or even whether I should believe the test results.

Yongsheng Ji Division of Life Science and Medicine, University of Science and Technology of China, Hefei, Anhui, 230026, China. Email: jiys2020{at}ustc.edu.cn

Fifteen years ago, I probably would have said that my family didn't have a French cultural identity, despite being raised in France. Today, after having been expatriated 10 years in New Zealand, I can confirm that we have a strong French cultural identity, especially when it comes to food. Yet, after we returned to France 3 years ago, our attachment to our home country and its culture and traditions did not feel quite the same. I believe that we unintentionally took bits of New Zealand back to France with us.

Our ever-evolving celebration of Mardi Gras encapsulates our cultural journey. Before our move, we had always celebrated the French holiday in its traditional (if less religious) form. Around the end of February, we would make and eat loads of French crpes, and kids would dress up in festive costumes and attend the carnival. After our move, we discovered that New Zealanders do not observe Mardi Gras, so we adopted a different yet similar tradition, which was brought to the country from overseas and stuck: Halloween. Every year on the 31st of October, my eldest boy dressed up in a scary costume. But because good food is so deeply rooted in our culture, Halloween candy didn't feel sufficient. To supplement the prepackaged treats, we created our own tradition of the Halloween scary lunch. Each year, I would prepare a lunch box filled with funny and scary little monsters, skeletons, and ghosts made of pancakes, carved fruits, and (for the mummies) baked sausages in pastry strings.

Now back in France, we have resumed our celebration of Mardi Gras in February. The kids dress up for school and for carnivals, just like Halloween, but with an emphasis on festive instead of scary, and we make crpes, as we've done in the past. We've also kept our own multicultural family traditions. To adapt our New Zealand Halloween lunches, we now have a Halloween-themed French dinner in October. We've also updated the tradition of hiding a fve (trinket) in our galette des rois (king cake) by using a koru necklace (a traditional kiwi artifact) instead.

Our unique and changing traditions showed me that we could be open to incorporating new values and ideas when we learned the results of our DNA tests. My husband and I are both researchers in ecology and environmental genetics, manipulating DNA data daily and studying insect population genetics. It seemed only natural that we would want to see our own DNA test results. We originally thought that the genetic admixture might be quite high within our family home given that we were born 12,000 km apartI grew up in northern France, and he was raised on the French island of La Runion in the Indian Ocean. We were quite surprised by the results. For instance, I learned that I had ancestors from Italy and Scandinavia but very little French or Western European lineage, whereas my husband, despite being born in the Southern Hemisphere, has more Western European lineage than I do. (His results could perhaps be explained by the fact that half of the first settlers in La Runion were from Brittany.) Although my husband has ancestors in many parts of the world where I do not (such as India, Africa, and Indonesia), we share an unexpectedly high rate of ancestry from the Iberian Peninsula (Spain and Portugal). The results have not changed our lives, but it is interesting to know that, genetically, we are more an Iberian family than a French one! We now want to travel to and discover more about the culture of these southwestern parts of Europe and pass on this heritage to our children. As ecologists, we are curious about the natural and geological histories of the Iberian region, but we would make food an important part of the trip as well. They may not have French crpes in Portugal, but I have heard that the delicious bolo lvedo (Portuguese muffins) are not to be missed.

Marie-Caroline Lefort Cellule de Valorisation Pdagogique, Universit de Tours, Tours, France. Email: marie-caroline.lefort{at}univ-tours.fr

As a Jewish woman born in Iran and living in Israel, I feel connected to the ancient history of my people. Because it is rare to find an Iranian woman in science who keeps Jewish traditions, I feel a responsibility to manifest all the good that is in each part of my background.

My family celebrates the traditional holiday of Rosh Hashanah (the Jewish New Year). Wearing white clothing to symbolize purity, we light candles and look into the flames as we give thanks and ask for blessings in the coming year. We celebrate this contemplative holiday with a festive meal steeped in symbolism and tradition. We eat apples dipped in honey and pomegranates to symbolize our hopes for a sweet, peaceful, happy new year that is full of good deeds. The honey represents sweetness, and the apple tree is the only tree that has more fruit than leaves, reminding us that we should maximize our purpose in this world. The numerous seeds in pomegranates, a native fruit of ancient Persia, symbolize the many good deeds we should carry out during the coming year. We also make a traditional Iranian-Jewish stew out of quince, a native fruit of west Asia (including Iran and Israel) that looks like an apple. The sweet smell fills the entire house with a magical floral and fresh perfume. During Rosh Hashanah, the shofar (an ancient musical instrument typically made of a ram's horn) is blown 100 times. The sound marks the time to make our wishes for the new year, which we read in Hebrew.

My DNA test results show that I am mostly Persian, with a very small percentage (0.8%) of Egyptian in my ancestry. The data echo the Biblical and rabbinical stories that I consider my roots. Our cultural history tells us that our ancestors were in ancient Egypt for hundreds of years before moving to Israel with Moses. In 722 BCE, the Jews were exiled from Israel to other regions, including Iran. My father was born in a city that was first settled by the exiled Jewish people from Israel, and my mom is from a city that is well known in Iran as the site of the story of Esther and Mordechai, traditionally told during the holiday of Purim. My family moved to Israel after the revolution in Iran in 1979. My DNA results mirror both these ancient tales and my own family's story.

Ruty Mehrian-Shai Pediatric Hemato-Oncology, Brain Cancer Molecular Medicine, Sheba Medical Center, Ramat Gan, 52621, Israel. Email: ruty.shai{at}sheba.health.gov.il

I've always struggled with being identified as simply Indian. My name reflects my Indian heritage better than I do, as a Montreal-born, New York City native living in Louisiana. No DNA test could reflect the mix of American and Indian cultural practices that my family has created. Take, for example, American Thanksgiving, which my family co-opted when I was young and combined with a traditional West Bengali feast. At our table, we served the turkey alongside traditional Indian luchi (oil-fried puffed dough) and fusion dishes such as vegetarian shepherd's pie with Indian spices. Because my birthday falls near Thanksgiving, the meal was often followed by a turkey-shaped ice cream cake, Indian sweets like jalebi (a bright orange pretzel of fried sweet dough), gulab jamun (fried syrupy-sweet milk balls), and a spiced tea. We did adhere to the American tradition of overstuffing ourselves with food.

During the holiday, we listened to Bollywood pop, with high-pitched Indian women singing in Hindi or Bengali. Later in the season, my father would mix in some Nat King Cole or Frank Sinatra, or we would play an album from jazz pianist Vince Guaraldi. Being in Queens, I would always play Christmas in Hollis by the Queens-native hip-hop group Run DMC. My parents enjoyed it about as much as I did their Bollywood music, which is to say, not much.

In December, the large extended family of cousins, uncles, and aunts (all with a different honorific based on their birth position relative to my parents) would come over, each removing their shoes at the door out of respect. The men, in sweaters and ties, played bridge cross-legged in a corner on the floor. The women, in saris and their finest gold necklaces and earrings (gaudier than any of the jewelry worn by the hip-hip artists I worshiped), congregated in the dining area, where they teased each other, told stories in Bengali, and prepared meals. Food was served constantly from the moment the first guests arrived until they left. The smell of food cooking, mostly oil and spices, radiated and permeated through every fabric of the house. Chatter, the sounds of food frying, and playful arguing filled every room with noise. Our home was festively decorated; Santa Claus had equal billing with Durga, Kali, and Ganesh.

The kids watched American football or challenged each other to an Indian game called carrom, which is similar to billiards but played on a flat smooth table on the floor. Players use their fingers to flick flat wooden discs into different corner pockets. We would play different tournament styles and use a mix of Bengali and English to taunt and tease each other over missed shots or lucky wins.

Before our current chapter as Americans, my family's Indian past stretches back to time immemorial, but India has a complicated history of invasions and rule. I hoped a DNA test would help clarify some ancestry questions. I wanted the results to say 25% Genghis Khan, 25% Gandhi, 25% Alexander the Great, and 25% unknown. What I got was 64% Central Asian, 30% South Asian, 3% Eastern European, 2% Southeast Asian, and 1% Siberian. So, I could claim Genghis, Gandhi, and Alexander! But of course, not really. I wondered when and where the mingling of my different geographic ancestors took place and if the results were more a reflection of the current genetic reference populations in those areas. The DNA results didn't make me feel differently about my identity, and they were not as interesting as the results I received from a genetic profile that revealed an inversion in one of my chromosomes. That genetic result made me realize how hardy our genomes are and how similar we are as humans; even the 1% or so that makes each of us unique is almost meaningless when considering the bigger picture.

Prosanta Chakrabarty Louisiana State University Museum of Natural Science, Baton Rouge, LA 708033216, USA. Email: prosanta{at}lsu.edu

ILLUSTRATION: MICHELLE KONDRICH

Born in South America, I identify as Latina and have always been aware of my mixed ethnicity. My family's celebration of Christmas and Novena (the previous 9 days, an important observance in Colombia) exemplifies our love of food, music, and dance. During the first 8 days, family and friends meet at different houses to share deep-fried cheesy dough and sweets. On Christmas day and the morning after, we eat homemade Colombian tamales wrapped in plantain leaves and boiled for hours, and we drink hot chocolatefirst adding salty cheese to the mugs and eating it with a spoon once it has melted (a delicacy unique to Bogot, Colombia's capital). Sometimes we also eat cheese arepas (flat corn bread) and almojabnas (cheese bread of Spanish-Arab origin). Meanwhile, my mum prepares about 20 liters of her famous ajiaco, a traditional soup from the Bogota plateau. She uses three kinds of potatoes (one of them endemic to the Northern Andes), guascas (Galinsoga parviflora), corn, chicken, capers, and cream. Toward the end of the day, the whole family gathers for a bowl of ajiaco. We admire our araucaria tree, decorated with lights and ornaments, and the creatively assembled nativity scene (often including llamas, lions, jaguars, and the occasional dinosaur) while waiting for midnight to come.

My family seems to carry music in our blood. There is always a moment when my uncle plays the guitar and everyone else joins in with percussion and voices, singing the melodies of cumbia, vallenato, and bambucomusical styles incorporating strings and accordions from Europe, wind instruments from Indigenous communities, and African drums. The upbeat tunes belie the bittersweet themes in the Spanish lyrics. Soon, everyone is dancing to the energetic, fast-moving rhythms of cumbia, salsa, and merengue. Salsa originated with the Latin and Afro-Latin son cubano and jazz musicians from the Bronx in the United States. The music later made its way to Colombia, where it developed into something new, incorporating cumbia and vallenato elements and a faster dancing style.

I took a DNA test because I work in the fields of population genomics and phylogenomics and thought it would be fun to see my own genome sequences. Half of the sites sequenced on my genome were assigned to populations in Spain, Morocco, and West Africa; the other half to Native American populations. The results were not a surprise, but they encouraged me to dig deeper into my family's history. I wish I could learn about and celebrate the Native American traditions of my ancestors, but most were never documented and are now lost. Important traditions are kept in the Amazon regions, such as chontaduro dancing, where communities share the chontaduro fruit (from the Bactris gasipaes palm) and drinks to celebrate abundance and usher in a good fishing season. Traditions around the cassava, plant growing seasons, and hunting also still take place, but because I grew up in the city, I don't feel personally connected to them. I do take pride in using the words from Quechua, Muisca, and even Arabic languages that have been assimilated into Colombian Spanish.

We knew my grandfather was Indigenous from the south (as the government labeled him back in the day), but the DNA test results suggest that our Indigenous ancestry could have been more recent and likely than we thought. I found the test interesting; I received a set of raw data that I can analyze myself, and the results brought my father and me together in a quest for the documents and stories surrounding my family.

Maria Fernanda Torres Jimenez Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden. Email: mftorres27{at}gmail.com

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Beyond DNA: The rest of the story - Science Magazine

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New York City Barely Tests for Virus Variants. Can That Change? – The New York Times

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Our machines could handle thousands or hundreds of thousands, said Dr. Neville Sanjana, a scientist with a lab at the New York Genome Center in Lower Manhattan. So the capacity is just not the issue.

The issue for research laboratories strangely enough, amid a pandemic that has probably infected more than a quarter of New Yorkers is access to samples. In New York, there is no high-volume pipeline of positive virus samples from hospitals or testing sites to research laboratories to conduct genetic surveillance.

Its really just organizing that sample collection that, I think, is whats missing, said Dr. Sanjana, whose research has involved searching for which medicines might block infection by inhibiting the human genes that the coronavirus hijacks.

What is needed, scientists said in interviews, is for the city or another entity to essentially bifurcate the current coronavirus testing process. Each day, tens of thousands of New Yorkers provide swabbed samples, which are generally sent to a few large laboratories for testing. If those labs could set aside a portion of the samples, those portions could later be used for genome sequencing if they turned out to be positive.

Its solvable, but it needs resources and it needs people to coordinate, Professor Heguy said, as she listed the necessary steps: A portion of the original sample would need to be set aside; RNA would need to be isolated from it; and someone would need to transport the RNA samples to a laboratory that does genome sequencing.

The citys goal of expanding sequencing at least tenfold will require enlisting a range of outside laboratories and research projects, big and small. The city anticipates that the largest share of the genomic sequencing will happen at a laboratory in Long Island City, Queens, that is run by a small robotics company.

The company, Opentrons, also runs a facility in Manhattan called the Pandemic Response Laboratory. That laboratory was built last year to help the city solve the testing crisis that emerged during the summer, when big commercial laboratories were struggling to handle the soaring caseload. People were having to wait several days, and sometimes a week or two, for coronavirus test results. The laboratory now tests 20,000 samples a day.

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New York City Barely Tests for Virus Variants. Can That Change? - The New York Times

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Epigenomic map reveals circuitry of 30000 human disease regions – MIT News

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Twenty years ago this month, the first draft of the human genome was publicly released. One of the major surprises that came from that project was the revelation that only 1.5 percent of the human genome consists of protein-coding genes.

Over the past two decades, it has become apparent that those noncoding stretches of DNA, originally thought to be junk DNA, play critical roles in development and gene regulation. In a new study published today, a team of researchers from MIT has published the most comprehensive map yet of this noncoding DNA.

This map provides in-depth annotation of epigenomic marks modifications indicating which genes are turned on or off in different types of cells across 833 tissues and cell types, a significant increase over what has been covered before. The researchers also identified groups of regulatory elements that control specific biological programs, and they uncovered candidate mechanisms of action for about 30,000 genetic variants linked to 540 specific traits.

What were delivering is really the circuitry of the human genome. Twenty years later, we not only have the genes, we not only have the noncoding annotations, but we have the modules, the upstream regulators, the downstream targets, the disease variants, and the interpretation of these disease variants, says Manolis Kellis, a professor of computer science, a member of MITs Computer Science and Artificial Intelligence Laboratory and of the Broad Institute of MIT and Harvard, and the senior author of the new study.

MIT graduate student Carles Boix is the lead author of the paper, which appears today in Nature. Other authors of the paper are MIT graduate students Benjamin James and former MIT postdocs Yongjin Park and Wouter Meuleman, who are now principal investigators at the University of British Columbia and the Altius Institute for Biomedical Sciences, respectively. The researchers have made all of their data publicly available for the broader scientific community to use.

Epigenomic control

Layered atop the human genome the sequence of nucleotides that makes up the genetic code is the epigenome. The epigenome consists of chemical marks that help determine which genes are expressed at different times, and in different cells. These marks include histone modifications, DNA methylation, and how accessible a given stretch of DNA is.

Epigenomics directly reads the marks used by our cells to remember what to turn on and what to turn off in every cell type, and in every tissue of our body. They act as post-it notes, highlighters, and underlining, Kellis says. Epigenomics allows us to peek at what each cell marked as important in every cell type, and thus understand how the genome actually functions.

Mapping these epigenomic annotations can reveal genetic control elements, and the cell types in which different elements are active. These control elements can be grouped into clusters or modules that function together to control specific biological functions. Some of these elements are enhancers, which are bound by proteins that activate gene expression, while others are repressors that turn genes off.

The new map, EpiMap (Epigenome Integration across Multiple Annotation Projects), builds on and combines data from several large-scale mapping consortia, including ENCODE, Roadmap Epigenomics, and Genomics of Gene Regulation.

The researchers assembled a total of 833 biosamples, representing diverse tissues and cell types, each of which was mapped with a slightly different subset of epigenomic marks, making it difficult to fully integrate data across the multiple consortia. They then filled in the missing datasets, by combining available data for similar marks and biosamples, and used the resulting compendium of 10,000 marks across 833 biosamples to study gene regulation and human disease.

The researchers annotated more than 2 million enhancer sites, covering only 0.8 percent of each biosample, and collectively 13 percent of the genome. They grouped them into 300 modules based on their activity patterns, and linked them to the biological processes they control, the regulators that control them, and the short sequence motifs that mediate this control. The researchers also predicted 3.3 million links between control elements and the genes that they target based on their coordinated activity patterns, representing the most complete circuitry of the human genome to date.

Disease links

Since the final draft of the human genome was completed in 2003, researchers have performed thousands of genome-wide association studies (GWAS), revealing common genetic variants that predispose their carriers to a particular trait or disease.

These studies have yielded about 120,000 variants, but only 7 percent of these are located within protein-coding genes, leaving 93 percent that lie in regions of noncoding DNA.

How noncoding variants act is extremely difficult to resolve, however, for many reasons. First, genetic variants are inherited in blocks, making it difficult to pinpoint causal variants among dozens of variants in each disease-associated region. Moreover, noncoding variants can act at large distances, sometimes millions of nucleotides away, making it difficult to find their target gene of action. They are also extremely dynamic, making it difficult to know which tissue they act in. Lastly, understanding their upstream regulators remains an unsolved problem.

In this study, the researchers were able to address these questions and provide candidate mechanistic insights for more than 30,000 of these noncoding GWAS variants. The researchers found that variants associated with the same trait tended to be enriched in specific tissues that are biologically relevant to the trait. For example, genetic variants linked to intelligence were found to be in noncoding regions active in the brain, while variants associated with cholesterol level are in regions active in the liver.

The researchers also showed that some traits or diseases are affected by enhancers active in many different tissue types. For example, they found that genetic variants associated with coronary heart disease (CAD) were active in adipose tissue, coronary arteries, and the liver, among many other tissues.

Kellis lab is now working with diverse collaborators to pursue their leads in specific diseases, guided by these genome-wide predictions. They are profiling heart tissue from patients with coronary artery disease, microglia from Alzheimers patients, and muscle, adipose, and blood from obesity patients, which are predicted mediators of these disease based on the current paper, and his labs previous work.

Many other labs are already using the EpiMap data to pursue studies of diverse diseases. We hope that our predictions will be used broadly in industry and in academia to help elucidate genetic variants and their mechanisms of action, help target therapies to the most promising targets, and help accelerate drug development for many disorders, Kellis says.

The research was funded by the National Institutes of Health.

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Epigenomic map reveals circuitry of 30000 human disease regions - MIT News

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Whole Genome Bisulfite Sequencing (WGBS) Market Expected to Witness High Growth over the Forecast to 2027 KSU | The Sentinel Newspaper – KSU | The…

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Table Of Contents: Whole Genome Bisulfite Sequencing (WGBS) Market

Part 01:Executive Summary

Part 02:Scope of the Report

Part 03:Research Methodology

Part 04:Market Landscape

Part 05:Pipeline Analysis

Part 06:Market Sizing

Part 07:Five Forces Analysis

Part 08:Market Segmentation

Part 09:Customer Landscape

Part 10:Regional Landscape

Part 11:Decision Framework

Part 12:Drivers and Challenges

Part 13:Market Trends

Part 14:Vendor Landscape

Part 15:Vendor Analysis

Part 16:Appendix

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Whole Genome Bisulfite Sequencing (WGBS) Market Expected to Witness High Growth over the Forecast to 2027 KSU | The Sentinel Newspaper - KSU | The...

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WEEKENDS AT THE SCIENCE CENTER: Genome in Me exhibit – WFSB

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'); $("#expandable-weather-block .modal-body #mrd-alert"+ alertCount).append(""+val.title+""); // if (window.location.hostname == "www.kmov.com" || window.location.hostname == "www.kctv5.com" || window.location.hostname == "www.azfamily.com" || window.location.hostname == "www.kptv.com" || window.location.hostname == "www.fox5vegas.com" || window.location.hostname == "www.wfsb.com") { if (val.poly != "" && val.polyimg != "") { $("#expandable-weather-block .modal-body #mrd-alert"+ alertCount).append('"+val.ihtml+""); $("#expandable-weather-block .weather-index-alerts").show(); $("#expandable-weather-block .modal-body h2").css({"font-family":"'Fira Sans', sans-serif", "font-weight":"500", "padding-bottom":"10px"}); $("#expandable-weather-block .modal-body p").css({"font-size":"14px", "line-height":"24px"}); $("#expandable-weather-block .modal-body span.wxalertnum").css({"float":"left", "width":"40px", "height":"40px", "color":"#ffffff", "line-height":"40px", "background-color":"#888888", "border-radius":"40px", "text-align":"center", "margin-right":"12px"}); $("#expandable-weather-block .modal-body b").css("font-size", "18px"); $("#expandable-weather-block .modal-body li").css({"font-size":"14px", "line-height":"18px", "margin-bottom":"10px"}); $("#expandable-weather-block .modal-body ul").css({"margin-bottom":"24px"}); $("#expandable-weather-block .modal-body pre").css({"margin-bottom":"24px"}); $("#expandable-weather-block .modal-body img").css({"width":"100%", "margin-bottom":"20px", "borderWidth":"1px", "border-style":"solid", "border-color":"#aaaaaa"}); $("#expandable-weather-block .modal-body #mrd-alert"+ alertCount).css({"borderWidth":"0", "border-bottom-width":"1px", "border-style":"dashed", "border-color":"#aaaaaa", "padding-bottom":"10px", "margin-bottom":"40px"}); }); } function parseAlertJSON(json) { console.log(json); alertCount = 0; if (Object.keys(json.alerts).length > 0) { $("#mrd-wx-alerts .modal-body ").empty(); } $.each(json.alerts, function(key, val) { alertCount++; $("#mrd-wx-alerts .alert_count").text(alertCount); $("#mrd-wx-alerts .modal-body ").append(''); $("#mrd-wx-alerts .modal-body #mrd-alert"+ alertCount).append(""+val.title+""); // if (window.location.hostname == "www.kmov.com" || window.location.hostname == "www.kctv5.com" || window.location.hostname == "www.azfamily.com" || window.location.hostname == "www.kptv.com" || window.location.hostname == "www.fox5vegas.com" || window.location.hostname == "www.wfsb.com") { if (val.poly != "" && val.polyimg != "") { $("#mrd-wx-alerts .modal-body #mrd-alert"+ alertCount).append(''); } else if (val.fips != "" && val.fipsimg != "") { // $("#mrd-wx-alerts .modal-body #mrd-alert"+ alertCount).append(''); } // } //val.instr = val.instr.replace(/[W_]+/g," "); $("#mrd-wx-alerts .modal-body #mrd-alert"+ alertCount).append(val.dhtml+"

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WEEKENDS AT THE SCIENCE CENTER: Genome in Me exhibit - WFSB

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