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jmfinizio

The oldest living Marine, a North Carolina woman, has died at age 107 - CNN - 0 views

  • Dorothy "Dot" Cole was the oldest living US Marine veteran when she died on January 7. She was 107 years old.
  • Cole decided she would take a stance to support her country after Japanese forces launched a surprise attack on the Pearl Harbor naval base in Hawaii on December 7, 1941.
  • "There were women volunteering with the Red Cross and knitting while sitting in church, so I thought I had to do something,
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  • She was 28 years old in 1943 when she became among the first wave of women to join the Marine Corps Women's Reserve
  • She attained the rank of sergeant before leaving the Marines.
  • The Marine Corps eventually saw its first female pilot in 1995, according to Military Times. All jobs in the military, including combat roles, were opened to women in 2016.
  • "She would want to salute all of the veterans for all the service that they've done and also the police and firemen,"
anniina03

Marine Labs on the Water's Edge Are Threatened by Climate Change - The New York Times - 0 views

  • A marine laboratory 85 miles southwest of New Orleans was designed to be a fortress against extreme weather. But it might be defeated by climate change.
  • It stands 18 feet above the ground on pillars with pilings that extend more than 100 feet underground. Its walls can withstand winds of up to 250 miles per hour.But the water is coming.
  • The assault from climate change is slower but more relentless than any storm, and will ultimately do more damage. It threatens researchers’ ability to study marine environments up close at a time when it’s more vital than ever to understand them.
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  • Fox Island Environmental Education Center, a Virginia institution that has opened up the wonders of the natural world to young people for more than 40 years, shut down in November. Between erosion and sea level rise, so much of the island’s salt marsh had disappeared that “it made it unsafe to run the program,” said Tom Ackerman, vice president for education at the Chesapeake Bay Foundation, which owns the island center.
  • because south Louisiana’s land is subsiding while the oceans are rising, the region has what may be the highest relative sea level rise in the country. “We’re just 10 to 30 years in front of the curve of everybody else,” he said.
  • Officials predict that, without action, the lab might need to shut down several dozen days each year within the next 10 to 15 years. The corrosive saltwater attacks the structure and has risen up through the soil into buried electrical cables, at one point causing a blackout. Some floods are accompanied by droves of fiddler crabs that sometimes find their way into the elevators.
  • Many marine labs are preparing to meet similar challenges, though they are in locations that are not yet facing the level of threat that Louisiana is.
  • At the Louisiana center, Ms. Conover sees educational value in their problems. Along with its mission as a scientific research facility, it is also a center for environmental education with visits from some 5,000 students each year. “If our parking lot is flooding when a group is here, we definitely talk about why we’re flooding on that given day, when five years ago we wouldn’t, given the same conditions.” That example, she said, “gives the perspective of what our coastal communities are dealing with.”
  • “Global sea-level rise is one of the greatest challenges facing society in the 21st century, and understanding how this phenomenon impacts coastal systems, infrastructure and the people who use them requires a regular coastal presence.”
carolinewren

Study: Global warming risks changes to ocean life unprecedented in the last 3 million y... - 0 views

  • Continued warming of the Earth’s oceans over the next century could trigger disruptions to marine life on a scale not seen in the last 3 million years, scientists warn in a study released Monday.
  • most dramatic disruptions would likely be averted if the world’s nations can bring greenhouse gas emissions under control in the coming decades, the authors write in the scientific journal Nature Climate Change.
  • Extrapolating from those records, the researchers predicted that even moderate climate change will cause significant disruptions, with local extinctions and species migrations occurring three times more frequently than today.
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  • “The intensity of this reorganization will depend, unsurprisingly, on the magnitude of warming.”
  • researchers seek to predict future impacts of global warming on marine life by examining how the oceans were affected during times of substantial temperature change in the distant past.
  • “Climate change may rapidly reorganize marine diversity over large oceanic regions,” s
  • More severe warming will have a major impact on marine life, with significant disruptions occurring across 50 to 70 percent of the world’s oceans, the authors concluded.
  • The impacts cannot fail to affect life on land, given the ocean’s role in supporting human populations
  • “When the temperature of the environment changes, animals and plants change in abundance locally or may move to new locations if the habitat is suitable,”
  • “These movements ultimately affect the food web and ecology, and if they are rapid, the food web may become uncoupled.”
  • humans “rely upon the ecosystem services that the interconnected web of life creates.”
annabaldwin_

A Marine Attacked an Iraqi Restaurant. But Was It a Hate Crime or PTSD? - The New York ... - 0 views

  • After a Marine attacked an Iraqi restaurant inPortland, Ore., his family said he was provoked bytrauma, not hate, and that he needed help, not jail time.
  • PORTLAND, Ore
  • The Iraqi family who ran it felt welcome in this eclectic city.
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  • After about a half-hour, he got up, walked over to the cash register, began cursing about Iraq, and threw a chair at a waiter’s head, sending him dazed to the floor.
  • Portland has been on edge over a sharp increase in hate crimes this year.
  • As the case unfolded over the summer, it raised questions about what constitutes a hate crime and how effectively the legal system treats combat veterans who suffer from PTSD.
  • There is no evidence that combat veterans are more prone to committing hate crimes, but studies suggest combat veterans with PTSD commit violent acts at a much higher rate than civilians.
Javier E

Elliot Ackerman Went From U.S. Marine to Bestselling Novelist - WSJ - 0 views

  • Years before he impressed critics with his first novel, “Green on Blue” (2015), written from the perspective of an Afghan boy, Ackerman was already, in his words, “telling stories and inhabiting the minds of others.” He explains that much of his work as a special-operations officer involved trying to grasp what his adversaries were thinking, to better anticipate how they might act
  • “Look, I really believe in stories, I believe in art, I believe that this is how we express our humanity,” he says. “You can’t understand a society without understanding the stories they tell about themselves, and how these stories are constantly changing.”
  • his, in essence, is the subject of “Halcyon,” in which a scientific breakthrough allows Robert Ableson, a World War II hero and renowned lawyer, to come back from the dead. Yet the 21st-century America he returns to feels like a different place, riven by debates over everything from Civil War monuments to workplace misconduct.
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  • The novel probes how nothing in life is fixed, including the legacies of the dead and the stories we tell about our pas
  • “The study of history shouldn’t be backward looking,” explains a historian in “Halcyon.” “To matter, it has to take us forward.”
  • Ackerman was in college on Sept. 11, 2001, but what he remembers more vividly is watching the premiere of the TV miniseries “Band of Brothers” the previous Sunday. “If you wanted to know the zeitgeist in the U.S. at the time, it was this very sentimental view of World War II,” he says. “There was this nostalgia for a time where we’re the good guys, they’re the bad guys, and we’re going to liberate oppressed people.”
  • Ackerman, who also covers wars and veteran affairs as a journalist, says that America’s backing of Ukraine is essential in the face of what he calls “an authoritarian axis rising up in the world, with China, Russia and Iran.” Were the country to offer similar help to Taiwan in the face of an invasion from China, he notes, having some air bases in nearby Afghanistan would help, but the U.S. gave those up in 2021.
  • With Islamic fundamentalists now in control of places where he lost friends, he says he is often asked if he regrets his service. “When you are a young man and your country goes to war, you’re presented with a choice: You either fight or you don’t,” he writes in his 2019 memoir “Places and Names.” “I don’t regret my choice, but maybe I regret being asked to choose.”
  • Serving in the military at a time when wars are no longer generation-defining events has proven alienating for Ackerman. “When you’ve got wars with an all-volunteer military funded through deficit spending, they can go on forever because there are no political costs
  • The catastrophic withdrawal from Afghanistan in 2021, which Ackerman covers in his recent memoir “The Fifth Act,” compounded this moral injury. “The fact that there has been so little government support for our Afghan allies has left it to vets to literally clean this up,” he says, noting that he still fields requests for help on WhatsApp. He adds that unless lawmakers act, the tens of thousands of Afghans currently living in the U.S. on humanitarian parole will be sent back to Taliban-held Afghanistan later this year: “It’s very painful to see how our allies are treated.”
  • Looking back on America’s misadventures in Iraq, Afghanistan and elsewhere, he notes that “the stories we tell about war are really important to the decisions we make around war. It’s one reason why storytelling fills me with a similar sense of purpose.”
  • “We don’t talk about the world and our place in it in a holistic way, or a strategic way,” Ackerman says. “We were telling a story about ending America’s longest war, when the one we should’ve been telling was about repositioning ourselves in a world that’s becoming much more dangerous,” he adds. “Our stories sometimes get us in trouble, and we’re still dealing with that trouble today.”
Lindsay Lyon

Largest Prime Discovered | Mathematics | LiveScience - 0 views

  • The largest prime number yet has been discovered — and it's 17,425,170 digits long. The new prime number crushes the last one discovered in 2008, which was a paltry 12,978,189 digits long.
  • The number — 2 raised to the 57,885,161 power minus 1 — was discovered by University of Central Missouri mathematician Curtis Cooper as part of a giant network of volunteer computers
  • "It's analogous to climbing Mt. Everest," said George Woltman, the retired, Orlando, Fla.-based computer scientist who created GIMPS. "People enjoy it for the challenge of the discovery of finding something that's never been known before."
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  • mathematicians have devised a much cleverer strategy, that dramatically reduces the time to find primes. That method uses a formula to check much fewer numbers.
  • the number is the 48th example of a rare class of primes called Mersenne Primes. Mersenne primes take the form of 2 raised to the power of a prime number minus 1. Since they were first described by French monk Marin Mersenne 350 years ago, only 48 of these elusive numbers have been found, including the most recent discovery. [The Most Massive Numbers in the Universe]
  • mber is the 48th example of a rare class of primes called Mersenne Primes. Mersenne primes take the form of 2 raised to the power of a prime number minus 1. Since they were first described by French monk Marin Mersenne 350 years ago, only 48 of these elusive numbers have been found
  • the 48th example of a rare class of primes called Mersenne Primes. Mersenne primes take the form of 2 raised to the power of a prime number minus 1
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    An interesting article that reminded me of the discussions we had last year on whether math was invented or discovered. With regard to prime numbers, could we ever stop finding "new" ones? Can we ever find a formula to pinpoint every single prime number without dividing it by other numbers?
catbclark

How We Learned to Kill - NYTimes.com - 0 views

  • “There are two people digging by the side of the road. Can we shoot them?”
  • Were the men in their sights irrigating their farmland or planting a roadside bomb?
  • My initial reaction was to ask the question to someone higher up the chain of command.
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  • I wanted confirmation from a higher authority to do the abhorrent, something I’d spent my entire life believing was evil.
  • I realized it was my role as an officer to provide that validation to the Marine on the other end who would pull the trigger.
  • I also received affirmation to a more sinister question: Yes, I could kill.
  • The primary factors that affect an individual’s ability to kill are the demands of authority, group absolution, the predisposition of the killer, the distance from the victim and the target attractiveness of the victim.
  • In war, of course, there are many ways to kill. I did so by giving orders. I never fired my weapon in combat, but I ordered countless others to
  • Before killing the first time there’s a reluctance that tempers the desire to know whether you are capable of doing it
  • . Despite the rhetoric I internalized from the newspapers back home about why we were in Afghanistan, I ended up fighting for different reasons once I got on the ground — a mix of loyalty to my Marines, habit and the urge to survive.
  • The more I thought about the enemy, the harder it was to view them as evil or subhuman. But killing requires a motivation
  • If someone is shooting at me, I have a right to fire back
  • Until that moment, our deployment in Afghanistan had been exhilarating because we felt invulnerable. This invulnerability in an environment of death was the most powerful sensation I’d ever experienced.
  • The fog of war doesn’t just limit what you can know; it creates doubt about everything you’re certain that you know.
  • The madness of war is that while this system is in place to kill people, it may actually be necessary for the greater good. We live in a dangerous world where killing and torture exist and where the persecution of the weak by the powerful is closer to the norm than the civil society where we get our Starbucks.
clairemann

Farming fish in fresh water is more affordable and sustainable than in the ocean - 0 views

  • A tidal wave of interest is building in farming the seas. It’s part of a global rush to exploit oceanic resources that’s been dubbed the “blue acceleration.” Optimistic projections say that smart mariculture – fish farming at sea – could increase ocean fish and shellfish production
  • We see far fewer technical, economic and resource constraints for freshwater aquaculture than for ocean farming, and far greater potential for land-based fish farms to contribute to global food security.
  • The most important species groups – carp, tilapia and catfish – are herbivorous or omnivorous, so they don’t need to eat animal protein to thrive.
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  • Raising marine fish is a different proposition. The harsh ocean environment makes production risky, and the biology of these species makes many of them difficult and costly to breed and grow.
  • Improvements in technology have reduced, though not eliminated, the amount of fish used in feeds, especially for farmed salmon. It now takes half as much fresh fish to raise salmon as it did 20 years ago.
  • Marine fish farming is currently done in sheltered bays and sea lochs. But there is growing interest in a new high-tech method that raises fish in huge submersible cages anchored far from land in the open ocean. It’s risky business, with high operating costs. Expensive infrastructure is vulnerable to intense storms.
runlai_jiang

Elephant Seal Facts (Genus Mirounga) - 0 views

  • The elephant seal (genus Mirounga) is the world's largest seal. There are two species of elephant seals, named according to the hemisphere in which they are found. Northern elephant seals (M. angustirostris) are found in coastal waters around Canada and Mexico, while southern elephant seals (M. leonina) are found off the coast of New Zealand, South Africa, and Argentina.
  • At sea, elephant seals range solo. They return to established breeding colonies each winter. Females become mature around 3 to 6 years of age, while males mature at 5 to 6 years.However, males need to achieve alpha status to mate, which is normally between the ages of 9 and 12. Males battle each other using body weight and teeth. While deaths are rare, scarring is common. An alpha male's harem ranges from 30 to 100 females. Other males wait on the edges of the colony, sometimes mating with females before the alpha male chases them away. Males remain on land over the winter to defend territory, meaning they don't leave to hunt.
  • Elephant seals have been hunted for their meat, fur, and blubber. Both northern and southern elephant seals were hunted to the brink of extinction. By 1892, most people believed the northern seals to be extinct. But in 1910, a single breeding colony was found around Guadalupe Island off Mexico's Baja California coast. At the end of the 19th century, new marine conservation legislation was put in place to protect the
Emily Horwitz

Drought May Have Killed Sumerian Language | LiveScience - 1 views

  • A 200-year-long drought 4,200 years ago may have killed off the ancient Sumerian language, one geologist says.
  • no written accounts explicitly mention drought as the reason for the Sumerian demise, the conclusions rely on indirect clues.
  • his was not a single summer or winter, this was 200 to 300 years of drought," said Matt Konfirst, a geologist at the Byrd Polar Research Center.
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  • Sumerian culture disappeared around 4,000 years ago, and the Sumerian language went extinct soon after that.
  • geological records point to a long period of drier weather in the Middle East around 4,200 years ago, Konfirst said. The Red Sea and the Dead Sea had increased evaporation; water levels dropped at Lake Van in Turkey, and cores from marine sediments around that period indicate increased dust in the environment.
  • Around the same time, 74 percent of the ancient Mesopotamian settlements were abandoned, according to a 2006 study of an archaeological site called Tell Leilan in Syria. The populated area also shrank by 93 percent, he said.
  • great drought, two waves of marauding nomads descended upon the region, sacking the capital city of Ur. After around 2000 B.C., ancient Sumerian gradually died off as a spoken language in the region. For the next 2,000 years, the tongue lingered on as a dead written language, similar to Latin in the Middle Ages, but has been completely extinct since then, Konfirst said.
proudsa

Journal of the Marine Biological Association of the United Kingdom - The size and compl... - 0 views

  • During evolution, dolphins may have increased the computational performance of their cytoarchitectonically ‘simple’ neocortex by a multiplication of relevant structures (resulting in a hypertrophic surface area) instead of increasing its complexity.
    • proudsa
       
      Interesting addition to our discussion of whether other beings could have the ability to process as highly as humans
anonymous

Trump's Plan to Bar Muslims Is Widely Condemned Abroad - The New York Times - 1 views

  • called for a ban on the entry of Muslims into the United States, much of the rest of the world on Tuesday looked at the American presidential election with a mix of befuddlement and despair.
  • ignited widespread condemnation that crossed ideological and social lines in many countries.
  • Mr. Trump, like others, fuels hatred,” and “Our only enemy is radical Islamism.”
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  • “A lot of people in the Middle East think of the United States as the last place we can go if things turn really bad, as it is the place of freedom and liberty,”
  • But Mr. Trump’s position also had its admirers. His stance on Muslim immigration drew several hundred favorable comments on China’s Twitter-like social media site, Weibo, where supporters linked his idea to their own fears of the Uighurs, a minority Muslim group in China’s northwestern region, some of whom have resorted to militancy and violence.
  • Mr. Trump has incited particularly intense debate, not least in predominantly Muslim countries and in Europe, where far-right parties like Marine Le Pen’s National Front have been gaining ground by invoking anti-immigrant messages similar to those of Mr. Trump and where memories of 20th-century fascism still run deep.
  • Donald Trump strikes me as a very different kind of populist right-winger than the kind we’ve grown used to in Europe in that he shows a complete ignorance about the world
  • Mr. Trump depressed her.
  • No, a country that voted twice for Obama cannot elect a man like that.”
Javier E

When Autocorrect Goes Wrong (and So, So Right) - NYTimes.com - 0 views

  • Tech companies like Google, Facebook and Apple employ dozens of linguists — or “natural language programmers,” as they are known — to analyze language patterns and to track slang, even pop culture.
  • they can do amazing things: correct when you hit the wrong keys (the “fat finger” phenomenon) and analyze whom you are texting, how you have spoken with that person in the past, even what you’ve talked about.
  • It adjusts for whom you are communicating with, knowing that your choice of words with a buddy is probably more laid-back than it would be with your boss.
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  • the more you use it, the more it remembers, paying attention to repeated words, the structure of your sentences and tone.
  • All of which is fine, except that it turns the notion of the guiltless autocorrect on its head. These days, autocorrections are likely to tell the person on the receiving end something about you.
  • a digital consultant, has a colleague named Aran with whom she texts regularly. Yet even though his name is saved in her contacts list, to the iPhone he is simply “Arab Aran.” Bridget Todd, a social media editor at MSNBC, has on more than one occasion referred to a friend (“Whitney”) as “Whitey.” (Ms. Todd is African-American.)
  • Kathrin Lausch, a film and television producer, described texting with a director after a difficult shoot that involved a woman in a bathtub. “Hey, why don’t you masturbatemarinate| over the boards and get back to me tomorrow,” she told him. She did not notice until the next day, when he told her that he loved “how Europeans are so sexually free.” (She is from Germany.)
Javier E

Was There a Civilization On Earth Before Humans? - The Atlantic - 0 views

  • When it comes to direct evidence of an industrial civilization—things like cities, factories, and roads—the geologic record doesn’t go back past what’s called the Quaternary period 2.6 million years ago
  • if we’re going back this far, we’re not talking about human civilizations anymore. Homo sapiens didn’t make their appearance on the planet until just 300,000 years or so ago. That means the question shifts to other species, which is why Gavin called the idea the Silurian hypothesis
  • could researchers find clear evidence that an ancient species built a relatively short-lived industrial civilization long before our own? Perhaps, for example, some early mammal rose briefly to civilization building during the Paleocene epoch about 60 million years ago. There are fossils, of course. But the fraction of life that gets fossilized is always minuscule and varies a lot depending on time and habitat. It would be easy, therefore, to miss an industrial civilization that only lasted 100,000 years—which would be 500 times longer than our industrial civilization has made it so far.
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  • Given that all direct evidence would be long gone after many millions of years, what kinds of evidence might then still exist? The best way to answer this question is to figure out what evidence we’d leave behind if human civilization collapsed at its current stage of development.
  • Now that our industrial civilization has truly gone global, humanity’s collective activity is laying down a variety of traces that will be detectable by scientists 100 million years in the future. The extensive use of fertilizer, for example
  • Likewise our relentless hunger for the rare-Earth elements used in electronic gizmos. Far more of these atoms are now wandering around the planet’s surface because of us than would otherwise be the case. They might also show up in future sediments, too.
  • And then there’s all that plastic. Studies have shown increasing amounts of plastic “marine litter” are being deposited on the seafloor everywhere from coastal areas to deep basins and even in the Arctic. Wind, sun, and waves grind down large-scale plastic artifacts, leaving the seas full of microscopic plastic particles that will eventually rain down on the ocean floor, creating a layer that could persist for geological timescales.
  • ronically, however, the most promising marker of humanity’s presence as an advanced civilization is a by-product of one activity that may threaten it most.
  • The more fossil fuels we burn, the more the balance of these carbon isotopes shifts. Atmospheric scientists call this shift the Suess effect, and the change in isotopic ratios of carbon due to fossil-fuel use is easy to see over the last century. Increases in temperature also leave isotopic signals. These shifts should be apparent to any future scientist who chemically analyzes exposed layers of rock from our era. Along with these spikes, this Anthropocene layer might also hold brief peaks in nitrogen, plastic nanoparticles, and even synthetic steroids
  • Fifty-six million years ago, Earth passed through the Paleocene-Eocene Thermal Maximum (PETM). During the PETM, the planet’s average temperature climbed as high as 15 degrees Fahrenheit above what we experience today. It was a world almost without ice, as typical summer temperatures at the poles reached close to a balmy 70 degrees Fahrenheit.
  • While there is evidence that the PETM may have been driven by a massive release of buried fossil carbon into the air, it’s the timescale of these changes that matter. The PETM’s isotope spikes rise and fall over a few hundred thousand years. But what makes the Anthropocene so remarkable in terms of Earth’s history is the speed at which we’re dumping fossil carbon into the atmosphere. There have been geological periods where Earth’s CO2 has been as high or higher than today, but never before in the planet’s multibillion-year history has so much buried carbon been dumped back into the atmosphere so quickly
  • So the isotopic spikes we do see in the geologic record may not be spiky enough to fit the Silurian hypothesis’s bill.
  • Once you realize, through climate change, the need to find lower-impact energy sources, the less impact you will leave. So the more sustainable your civilization becomes, the smaller the signal you’ll leave for future generations.
  • “How do you know we’re the only time there’s been a civilization on our own planet?”
maxwellokolo

France election: Le Pen attacks Macron as 'candidate of continuity' - BBC News - 0 views

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    France presidential election 2017 Far-right French presidential candidate Marine Le Pen has accused her pro-EU centrist rival Emmanuel Macron of being the "candidate of continuity". She linked Mr Macron to the unpopular current President, Francois Hollande, in whose cabinet he once served.
clairemann

Bottom Trawling for Fish Boosts Carbon Emissions, Study Says | Time - 0 views

  • It’s been well established by now that the agricultural systems producing our food contribute at least one fifth of global anthropogenic carbon emissions—and up to a third if waste and transportation are factored in.
  • According to calculations conducted by the report’s 26 authors, bottom trawling is responsible for one gigaton of carbon emissions a year—a higher annual total than (pre-pandemic) aviation emissions.
  • measures how much each so-called “pixel” contributes to global marine biodiversity, fish stocks and climate protection, based on a complex analysis of location, water temperature, salinity and species distribution, among other factors. It also tracks how much CO2 each pixel is capable of absorbing as a carbon sink.
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  • Worse still, the practice also impacts the ocean’s ability to absorb atmospheric carbon: if the water is already saturated from sources down below, it will be unable to absorb human-caused emissions from above, hamstringing one of our best assets in the fight against climate change.
  • Technological innovations such as green power generation and battery storage are vital for reducing global greenhouse gas emissions. But we still need to reduce atmospheric carbon, and so far technology has not been able to do that affordably and at scale.
Javier E

The Disease Detective - The New York Times - 1 views

  • What’s startling is how many mystery infections still exist today.
  • More than a third of acute respiratory illnesses are idiopathic; the same is true for up to 40 percent of gastrointestinal disorders and more than half the cases of encephalitis (swelling of the brain).
  • Up to 20 percent of cancers and a substantial portion of autoimmune diseases, including multiple sclerosis and rheumatoid arthritis, are thought to have viral triggers, but a vast majority of those have yet to be identified.
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  • Globally, the numbers can be even worse, and the stakes often higher. “Say a person comes into the hospital in Sierra Leone with a fever and flulike symptoms,” DeRisi says. “After a few days, or a week, they die. What caused that illness? Most of the time, we never find out. Because if the cause isn’t something that we can culture and test for” — like hepatitis, or strep throat — “it basically just stays a mystery.”
  • It would be better, DeRisi says, to watch for rare cases of mystery illnesses in people, which often exist well before a pathogen gains traction and is able to spread.
  • Based on a retrospective analysis of blood samples, scientists now know that H.I.V. emerged nearly a dozen times over a century, starting in the 1920s, before it went global.
  • Zika was a relatively harmless illness before a single mutation, in 2013, gave the virus the ability to enter and damage brain cells.
  • The beauty of this approach” — running blood samples from people hospitalized all over the world through his system, known as IDseq — “is that it works even for things that we’ve never seen before, or things that we might think we’ve seen but which are actually something new.”
  • In this scenario, an undiscovered or completely new virus won’t trigger a match but will instead be flagged. (Even in those cases, the mystery pathogen will usually belong to a known virus family: coronaviruses, for instance, or filoviruses that cause hemorrhagic fevers like Ebola and Marburg.)
  • And because different types of bacteria require specific conditions in order to grow, you also need some idea of what you’re looking for in order to find it.
  • The same is true of genomic sequencing, which relies on “primers” designed to match different combinations of nucleotides (the building blocks of DNA and RNA).
  • Even looking at a slide under a microscope requires staining, which makes organisms easier to see — but the stains used to identify bacteria and parasites, for instance, aren’t the same.
  • The practice that DeRisi helped pioneer to skirt this problem is known as metagenomic sequencing
  • Unlike ordinary genomic sequencing, which tries to spell out the purified DNA of a single, known organism, metagenomic sequencing can be applied to a messy sample of just about anything — blood, mud, seawater, snot — which will often contain dozens or hundreds of different organisms, all unknown, and each with its own DNA. In order to read all the fragmented genetic material, metagenomic sequencing uses sophisticated software to stitch the pieces together by matching overlapping segments.
  • The assembled genomes are then compared against a vast database of all known genomic sequences — maintained by the government-run National Center for Biotechnology Information — making it possible for researchers to identify everything in the mix
  • Traditionally, the way that scientists have identified organisms in a sample is to culture them: Isolate a particular bacterium (or virus or parasite or fungus); grow it in a petri dish; and then examine the result under a microscope, or use genomic sequencing, to understand just what it is. But because less than 2 percent of bacteria — and even fewer viruses — can be grown in a lab, the process often reveals only a tiny fraction of what’s actually there. It’s a bit like planting 100 different kinds of seeds that you found in an old jar. One or two of those will germinate and produce a plant, but there’s no way to know what the rest might have grown into.
  • Such studies have revealed just how vast the microbial world is, and how little we know about it
  • “The selling point for researchers is: ‘Look, this technology lets you investigate what’s happening in your clinic, whether it’s kids with meningitis or something else,’” DeRisi said. “We’re not telling you what to do with it. But it’s also true that if we have enough people using this, spread out all around the world, then it does become a global network for detecting emerging pandemics
  • One study found more than 1,000 different kinds of viruses in a tiny amount of human stool; another found a million in a couple of pounds of marine sediment. And most were organisms that nobody had seen before.
  • After the Biohub opened in 2016, one of DeRisi’s goals was to turn metagenomics from a rarefied technology used by a handful of elite universities into something that researchers around the world could benefit from
  • metagenomics requires enormous amounts of computing power, putting it out of reach of all but the most well-funded research labs. The tool DeRisi created, IDseq, made it possible for researchers anywhere in the world to process samples through the use of a small, off-the-shelf sequencer, much like the one DeRisi had shown me in his lab, and then upload the results to the cloud for analysis.
  • he’s the first to make the process so accessible, even in countries where lab supplies and training are scarce. DeRisi and his team tested the chemicals used to prepare DNA for sequencing and determined that using as little as half the recommended amount often worked fine. They also 3-D print some of the labs’ tools and replacement parts, and offer ongoing training and tech support
  • The metagenomic analysis itself — normally the most expensive part of the process — is provided free.
  • But DeRisi’s main innovation has been in streamlining and simplifying the extraordinarily complex computational side of metagenomics
  • IDseq is also fast, capable of doing analyses in hours that would take other systems weeks.
  • “What IDseq really did was to marry wet-lab work — accumulating samples, processing them, running them through a sequencer — with the bioinformatic analysis,”
  • “Without that, what happens in a lot of places is that the researcher will be like, ‘OK, I collected the samples!’ But because they can’t analyze them, the samples end up in the freezer. The information just gets stuck there.”
  • Meningitis itself isn’t a disease, just a description meaning that the tissues around the brain and spinal cord have become inflamed. In the United States, bacterial infections can cause meningitis, as can enteroviruses, mumps and herpes simplex. But a high proportion of cases have, as doctors say, no known etiology: No one knows why the patient’s brain and spinal tissues are swelling.
  • When Saha and her team ran the mystery meningitis samples through IDseq, though, the result was surprising. Rather than revealing a bacterial cause, as expected, a third of the samples showed signs of the chikungunya virus — specifically, a neuroinvasive strain that was thought to be extremely rare. “At first we thought, It cannot be true!” Saha recalls. “But the moment Joe and I realized it was chikungunya, I went back and looked at the other 200 samples that we had collected around the same time. And we found the virus in some of those samples as well.”
  • Until recently, chikungunya was a comparatively rare disease, present mostly in parts of Central and East Africa. “Then it just exploded through the Caribbean and Africa and across Southeast Asia into India and Bangladesh,” DeRisi told me. In 2011, there were zero cases of chikungunya reported in Latin America. By 2014, there were a million.
  • Chikungunya is a mosquito-borne virus, but when DeRisi and Saha looked at the results from IDseq, they also saw something else: a primate tetraparvovirus. Primate tetraparvoviruses are almost unknown in humans, and have been found only in certain regions. Even now, DeRisi is careful to note, it’s not clear what effect the virus has on people. “Maybe it’s dangerous, maybe it isn’t,” DeRisi says. “But I’ll tell you what: It’s now on my radar.
  • it reveals a landscape of potentially dangerous viruses that we would otherwise never find out about. “What we’ve been missing is that there’s an entire universe of pathogens out there that are causing disease in humans,” Imam notes, “ones that we often don’t even know exist.”
  • “The plan was, Let’s let researchers around the world propose studies, and we’ll choose 10 of them to start,” DeRisi recalls. “We thought we’d get, like, a couple dozen proposals, and instead we got 350.”
  • Metagenomic sequencing is especially good at what scientists call “environmental sampling”: identifying, say, every type of bacteria present in the gut microbiome, or in a teaspoon of seawater.
  • “When you draw blood from someone who has a fever in Ghana, you really don’t know very much about what would normally be in their blood without fever — let alone about other kinds of contaminants in the environment. So how do you interpret the relevance of all the things you’re seeing?”
  • Such criticisms have led some to say that metagenomics simply isn’t suited to the infrastructure of developing countries. Along with the problem of contamination, many labs struggle to get the chemical reagents needed for sequencing, either because of the cost or because of shipping and customs holdups
  • we’re less likely to be caught off-guard. “With Ebola, there’s always an issue: Where’s the virus hiding before it breaks out?” DeRisi explains. “But also, once we start sampling people who are hospitalized more widely — meaning not just people in Northern California or Boston, but in Uganda, and Sierra Leone, and Indonesia — the chance of disastrous surprises will go down. We’ll start seeing what’s hidden.”
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Sharks Nearly Went Extinct 19 Million Years Ago From Mystery Event - The New York Times - 0 views

  • Analysis of the fossil record shows a mysterious mass extinction that decimated the diversity of sharks in the world’s oceans, and they’ve never fully recovered.
  • these events give scientists an intimate look at how life recovers after a cataclysm
  • This extinction event transpired in the world’s oceans and decimated shark populations
  • ...10 more annotations...
  • but sharks slough off about 100 denticles for each tooth they lose, making them common in the fossil record.
  • The reddish clay, extracted from two sediment cores that had been drilled deep into the Pacific Ocean seafloor, contained fish teeth, shark denticles and other marine microfossils.
  • Nineteen million years ago, the ratio of shark denticles to fish teeth changed drastically:
  • sharks suddenly became much less common, relative to fish, during an era known as the early Miocene,
  • “We had a lot of them, and then we had almost none of them,”
  • “We wanted to know if the sharks went extinct, or if they just became less prominent.”
  • The reduction in shark diversity suggests that they experienced an extinction around that time,
  • “There were just a small fraction that survived into this post-extinction world,”
  • uggest that this was truly a “global event,”
  • Sharks never fully recovered from this incident, and they have been declining in abundance in recent decades because of overfishing and other human-caused pressures,
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