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Javier E

Neanderthal Genes Hint at Much Earlier Human Migration From Africa - The New York Times - 0 views

www.nytimes.com/...neanderthal-dna-africa.html

dna africa neanderthal migration genome

shared by Javier E on 01 Feb 20 - No Cached
  • From DNA recovered from the bones, researchers deduced that modern humans interbred with Neanderthals some 60,000 years ago, after leaving Africa.
  • People of African ancestry, it was thought, have little to no Neanderthal DNA.
  • Using a new method to analyze DNA, however, a team of scientists has found evidence that significantly reshapes that narrative.
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  • Their study, published on Thursday in the journal Cell, concludes that a wave of modern humans departed Africa far earlier than had been known: some 200,000 years ago.
  • The ancestors of humans and Neanderthals lived about 600,000 years ago in Africa
  • The scientists also found evidence that people living somewhere in western Eurasia moved back to Africa and interbred with people whose ancestors never left. The new study suggests that all Africans have a substantially greater amount of Neanderthal DNA than earlier estimates.
  • The research offers a view of human history “almost as a spider web of interactions, rather than a tree with distinct branches.”
  • These people interbred with Neanderthals, the new study suggests. As a result, Neanderthals were already carrying genes from modern humans when the next big migration from Africa occurred, about 140,000 years later.
  • The Neanderthal lineage left the continent; the fossils of what we describe as Neanderthals range from 200,000 years to 40,000 years in age, and are found in Europe, the Near East and Siberia.
  • The human genome is detailed in units called base pairs, about 3 billion such pairs in total. The scientis
  • ts found that Europeans on average had 51 million base pairs that matched Neanderthal DNA, and East Asians had 55 million.Dr. Akey’s previous research had indicated that East Asians carried far more Neanderthal ancestry than did Europeans.Africans on average had 17 million base pairs that matched Neanderthal DNA — far higher than predicted by the original models describing how humans and Neanderthals interbred.
  • They concluded that a group of modern humans expanded out of Africa perhaps 200,000 years ago and interbred with Neanderthals. Those modern humans then disappeared. But Neanderthals who lived after that disappearance inherited some modern human DNA.
  • sitation over the analysis of African DNA, Dr. Reich said the new findings do make a strong case that modern humans departed Africa much earlier than thought
  • It’s possible that humans and Neanderthals interbred at other times, and not just 200,000 years ago and again 60,000 years ago. But Dr. Akey said that these two migrations accounted for the vast majority of mixed DNA in the genomes of living humans and Neanderthal fossils.
  • In recent years, Dr. Reich and other researchers have found evidence that ancient people from the Near East moved back into Africa in the past few thousand years and spread their DNA to many African populations.
Javier E

Scientists find evidence of 'ghost population' of ancient humans | Science | The Guardian - 0 views

www.theguardian.com/...t-population-of-ancient-humans

human origins africa

shared by Javier E on 13 Feb 20 - No Cached
  • Arun Durvasula and Sankararaman obtained 405 genomes from four west African populations and used statistical techniques to work out whether an influx of genes from interbreeding was likely to have happened in the distant past. The analysis suggested that it had in every case.
  • The scientists went on to scour the African genomes for chunks of DNA that looked different to modern human genes. This allowed them to pull out sequences that most probably came from an ancient relative. By comparing these with genes from Neanderthals and Denisovans, they concluded that the DNA had to come from an unknown group of archaic humans.
  • “They seem to have made a pretty substantial impact on the genomes of the present day individuals we studied,” Sankararaman said. “They account for 2% to 19% of their genetic ancestry.” The four populations studied came from three countries: two from Nigeria, and one each from Sierra Leone and the Gambia.
Javier E

Lung Samples From 1918 Show a Pandemic Virus Mutating - The Atlantic - 0 views

www.theatlantic.com/...618972

pandemic virus samples 1918 flu history

shared by Javier E on 24 May 21 - No Cached
  • Why was the second wave, in late 1918, so much deadlier than the first wave, in the spring? These rediscovered lung samples hint at the possibility that the virus itself changed to better infect humans.
  • This new study brings the number of complete 1918 flu genomes to a grand total of three, plus some partial genomes.
  • Several changes showed up in the flu’s genome-replication machinery, a potential evolutionary hot spot because better replication means a more successful virus. The team then copied just the replication machinery of the 17-year-old’s virus—not the entire virus—into cells and found it was only half as active as that of the flu virus found in Alaska.
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  • Bloom and others have identified specific mutations that make the nucleoprotein better at resisting the human immune system. The first-wave flu viruses did not have them, but the second-wave ones did, possibly because they had had the time to adapt to infecting humans.
  • This mutation-by-mutation analysis of the 1918 flu virus would have been impossible to imagine at the time of the pandemic. Doctors then hadn’t even figured out that influenza was caused by a virus. “There’s no way the individual who saved these samples in 1918 had any idea of what could be done to them,” Mehle said. “To my mind, this is a beautiful example of fundamental research.”
  • Without the pathologist who painstakingly preserved these samples and the museums that kept them for decades before science caught up, our understanding of the 1918 flu would be all the poorer.
  • When the 1918 pandemic swept through the world, it apparently completely replaced whatever flu existed before. Its modern-day descendants continue to infect us today as seasonal flu.
Javier E

Ancient human migration into Europe revealed via genome analysis | Anthropology | The G... - 0 views

www.theguardian.com/...eanderthals-genetic-sequencing

human migration europe genome analysis anthropology ancient

shared by Javier E on 08 Apr 21 - No Cached
  • Genetic sequencing found the remains came from individuals who were more closely linked to present-day populations in east Asia and the Americas than populations in Europe.
  • All the “Bacho Kiro cave individuals have Neanderthal ancestors five-seven generations before they lived, suggesting that the admixture [mixing] between these first humans in Europe and Neanderthals was common,” said Hajdinjak.
  • Previous evidence for early human-Neanderthal mixing in Europe came from a single individual called the Oase 1, dating back 40,000 years and found in Romania.
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  • “We do not know who the first Europeans were that ventured into an unknown land,” he said.“By analysing their genomes, we are figuring out a part of our own history that has been lost in time.”
Javier E

America's Enduring Caste System - The New York Times - 0 views

www.nytimes.com/...isabel-wilkerson-caste.html

caste us class inequality white privilege racial hierarchy system

shared by Javier E on 09 Jul 20 - No Cached
  • We in this country are like homeowners who inherited a house on a piece of land that is beautiful on the outside but whose soil is unstable loam and rock, heaving and contracting over generations, cracks patched but the deeper ruptures waved away for decades, centuries even.
  • Not one of us was here when this house was built. Our immediate ancestors may have had nothing to do with it, but here we are, the current occupants of a property with stress cracks and bowed walls and fissures in the foundation. We are the heirs to whatever is right or wrong with it. We did not erect the uneven pillars or joists, but they are ours to deal with now.
  • And any further deterioration is, in fact, on our hands.
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  • Many people may rightly say: “I had nothing to do with how this all started. I have nothing to do with the sins of the past. My ancestors never attacked Indigenous people, never owned slaves.” And yes
  • Live with it long enough, and the unthinkable becomes normal. Exposed over the generations, we learn to believe that the incomprehensible is the way that life is supposed to be.
  • Like other old houses, America has an unseen skeleton: its caste system, which is as central to its operation as are the studs and joists that we cannot see in the physical buildings we call home.
  • Caste is the infrastructure of our divisions. It is the architecture of human hierarchy, the subconscious code of instructions for maintaining, in our case, a 400-year-old social order.
  • Throughout human history, three caste systems have stood out. The lingering, millenniums-long caste system of India. The tragically accelerated, chilling and officially vanquished caste system of Nazi Germany. And the shape-shifting, unspoken, race-based caste pyramid in the United States. Each version relied on stigmatizing those deemed inferior to justify the dehumanization necessary to keep the lowest-ranked people at the bottom and to rationalize the protocols of enforcement.
  • Race does the heavy lifting for a caste system that demands a means of human division. If we have been trained to see humans in the language of race, then caste is the underlying grammar that we encode as children
  • We may mention “race,” referring to people as Black or white or Latino or Asian or Indigenous, when what lies beneath each label is centuries of history and assigning of assumptions and values to physical features in a structure of human hierarchy.
  • What people look like, or rather, the race they have been assigned or are perceived to belong to, is the visible cue to their caste. It is the historic flashcard to the public of how they are to be treated, where they are expected to live
  • in recent decades, we have learned from the human genome that all human beings are 99.9 percent the same. “Race is a social concept, not a scientific one,” said J. Craig Venter, the genomics expert who ran Celera Genomics when the initial sequencing was completed in 2000. “We all evolved in the last 100,000 years from the small number of tribes that migrated out of Africa and colonized the world.
  • Which means that an entire racial caste system, the catalyst of hatreds and civil war, was built on what the anthropologist Ashley Montagu called “an arbitrary and superficial selection of traits,” derived from a tiny fraction of the tens of thousands of genes that make up a human being
  • “The idea of race,” Montagu wrote, “was, in fact, the deliberate creation of an exploiting class seeking to maintain and defend its privileges against what was profitably regarded as an inferior social caste.”
  • Caste is the bones, race the skin. Race is what we can see, the physical traits that have been given arbitrary meaning and become shorthand for who a person is. Caste is the powerful infrastructure that holds each group in its place.
  • Caste is rigid and deep; race is fluid and superficial, subject to periodic redefinition to meet the needs of the dominant caste in what is now the United States
  • While the requirements to qualify as white have changed over the centuries, the fact of a dominant caste has remained constant from its inception — whoever fit the definition of white, at whatever point in history, was granted the legal rights and privileges of the dominant caste.
  • Thus we are all born into a silent war game, centuries old, enlisted in teams not of our own choosing. The side to which we are assigned in the American system of categorizing people is proclaimed by the team uniform that each caste wears, signaling our presumed worth and potential.
  • he said to himself, “Yes, I am an untouchable, and every Negro in the United States of America is an untouchable.” In that moment, he realized that the Land of the Free had imposed a caste system not unlike the caste system of India and that he had lived under that system all his life.
  • One afternoon, King and his wife journeyed to the southern tip of the country, to the city then known as Trivandrum in the state of Kerala, and visited with high school students whose families had been untouchables. The principal made the introduction.“Young people,” he said, “I would like to present to you a fellow untouchable from the United States of America.”
  • Social scientists often define racism as the combination of racial bias and systemic power, seeing racism, like sexism, as primarily the action of people or systems with personal or group power over another person or group with less power
  • over time, racism has often been reduced to a feeling, a character flaw, conflated with prejudice, connected to whether one is a good person or not. It has come to mean overt and declared hatred of a person or group because of the race ascribed to them, a perspective few would ever own up to
  • Who is racist in a society where someone can refuse to rent to people of color, arrest brown immigrants en masse or display a Confederate flag but not be “certified” as a racist unless he or she confesses to it or is caught using derogatory signage or slurs?
  • With no universally agreed-upon definition, we might see racism as a continuum rather than an absolute. We might release ourselves of the purity test of whether someone is or is not racist and exchange that mind-set for one that sees people as existing on a scale based on the toxins they have absorbed from the polluted and inescapable air of social instruction we receive from childhood.
  • Caste is the granting or withholding of respect, status, honor, attention, privileges, resources, benefit of the doubt and human kindness to someone on the basis of their perceived rank or standing in the hierarchy.
  • Caste is insidious and therefore powerful because it is not hatred; it is not necessarily personal. It is the worn grooves of comforting routines and unthinking expectations, patterns of a social order that have been in place for so long that it looks like the natural order of things.
  • Any action or institution that mocks, harms, assumes or attaches inferiority or stereotype on the basis of the social construct of race can be considered racism
  • Because caste and race are interwoven in America, it can be hard to separate the two
  • Any action or structure that seeks to limit, hold back or put someone in a defined ranking, seeks to keep someone in their place by elevating or denigrating that person on the basis of their perceived category, can be seen as casteism.
  • Casteism is the investment in keeping the hierarchy as it is in order to maintain your own ranking, advantage or privilege or to elevate yourself above others or keep others beneath you
  • What race and its precursor, racism, do extraordinarily well is to confuse and distract from the underlying structural and more powerful Sith lord of caste. Like the cast on a broken arm, like the cast in a play, a caste system holds everyone in a fixed place.
  • For this reason, many people — including those we might see as good and kind people — could be casteist, meaning invested in keeping the hierarchy as it is or content to do nothing to change it, but not racist in the classical sense
  • Actual racists, actual haters, would by definition be casteist, as their hatred demands that those they perceive as beneath them know and keep their place in the hierarchy.
  • Caste, along with its faithful servant race, is an X-factor in most any American equation, and any answer one might ever come up with to address our current challenges is flawed without it.
  • Race and caste are not the cause of and do not account for every poor outcome or unpleasant encounter. But caste becomes a factor, to whatever infinitesimal degree, in interactions and decisions across gender, ethnicity, race, immigrant status, sexual orientation, age or religion that have consequences in our everyday lives
  • The younger country, the United States, would become the most powerful democracy on Earth. The older country, India, would become the largest.
  • as if operating from the same instruction manual translated to fit their distinctive cultures, both countries adopted similar methods of maintaining rigid lines of demarcation and protocols.
  • The American system was founded as a primarily two-tiered hierarchy with its contours defined by the uppermost group, those identified as white, and by the subordinated group, those identified as Black, with immigrants from outside Europe forming blurred middle castes that sought to adjust themselves within a bipolar structure, and Native Americans largely exiled outside it.
  • The Indian caste system, by contrast, is an elaborate fretwork of thousands of subcastes, or jatis, correlated to region and village, which fall under the four main varnas — the Brahmin, the Kshatriya, the Vaishya, the Shudra and the excluded fifth, the Dalits. It is further complicated by non-Hindus — including Muslims, Buddhists, Sikhs and Christians — who are outside the original caste system but have incorporated themselves into the workings of the country, at times in the face of resistance and attack, and may or may not have informal rankings among themselves and in relation to the varnas.
  • African-Americans, throughout most of their time in this land, were relegated to the dirtiest, most demeaning and least desirable jobs by definition. After enslavement and well into the 20th century, they were primarily restricted to the role of sharecroppers and servants — domestics, lawn boys, chauffeurs and janitors. The most that those who managed to get an education could hope for was to teach, minister to, attend to the health needs of or bury other subordinate-caste people.
  • the caste lines in America may have at one time appeared even starker than those in India. In 1890, “85 percent of Black men and 96 percent of Black women were employed in just two occupational categories,” wrote the sociologist Stephen Steinberg, “agriculture and domestic or personal service.”
  • So, too, with groups trained to believe in their inherent sovereignty. “The essence of this overestimation of one’s own position and the hate for all who differ from it is narcissism,” wrote Erich Fromm, a leading psychoanalyst and social theorist of the 20th century. “He is nothing,” Fromm wrote, “but if he can identify with his nation, or can transfer his personal narcissism to the nation, then he is everything.”
  • “Narcissus could not conceive that he was in love with his own reflection,” wrote the Harvard clinical psychologist Elsa Ronningstam in her 2005 book, “Identifying and Understanding the Narcissistic Personality.” “He was caught in an illusion.”
  • The political theorist Takamichi Sakurai, in his 2018 examination of Western and Eastern perspectives on the topic, and channeling Fromm, wrote bluntly: “Group narcissism leads people to fascism.” He went on, “An extreme form of group narcissism means malignant narcissism, which gives to rise to a fanatical fascist politics, an extreme racialism and so on.”
  • “The survival of a group,” Fromm wrote, “depends to some extent on the fact that its members consider its importance as great as or greater than that of their own lives.”Thus, when under threat, they are willing to sacrifice themselves and their ideals for the survival of the group from which they draw their self-esteem.
Javier E

COVID-19 Changed Science Forever - The Atlantic - 0 views

www.theatlantic.com/...617262

science history crisis pandemic

shared by Javier E on 17 Dec 20 - No Cached
  • New diagnostic tests can detect the virus within minutes. Massive open data sets of viral genomes and COVID‑19 cases have produced the most detailed picture yet of a new disease’s evolution. Vaccines are being developed with record-breaking speed. SARS‑CoV‑2 will be one of the most thoroughly characterized of all pathogens, and the secrets it yields will deepen our understanding of other viruses, leaving the world better prepared to face the next pandemic.
  • But the COVID‑19 pivot has also revealed the all-too-human frailties of the scientific enterprise. Flawed research made the pandemic more confusing, influencing misguided policies. Clinicians wasted millions of dollars on trials that were so sloppy as to be pointless. Overconfident poseurs published misleading work on topics in which they had no expertise. Racial and gender inequalities in the scientific field widened.
  • At its best, science is a self-correcting march toward greater knowledge for the betterment of humanity. At its worst, it is a self-interested pursuit of greater prestige at the cost of truth and rigor
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  • Traditionally, a scientist submits her paper to a journal, which sends it to a (surprisingly small) group of peers for (several rounds of usually anonymous) comments; if the paper passes this (typically months-long) peer-review gantlet, it is published (often behind an expensive paywall). Languid and opaque, this system is ill-suited to a fast-moving outbreak. But biomedical scientists can now upload preliminary versions of their papers, or “preprints,” to freely accessible websites, allowing others to immediately dissect and build upon their results. This practice had been slowly gaining popularity before 2020, but proved so vital for sharing information about COVID‑19 that it will likely become a mainstay of modern biomedical research. Preprints accelerate science, and the pandemic accelerated the use of preprints. At the start of the year, one repository, medRxiv (pronounced “med archive”), held about 1,000 preprints. By the end of October, it had more than 12,000.
  • The U.S. is now catching up. In April, the NIH launched a partnership called ACTIV, in which academic and industry scientists prioritized the most promising drugs and coordinated trial plans across the country. Since August, several such trials have started.
  • Researchers have begun to uncover how SARS‑CoV‑2 compares with other coronaviruses in wild bats, the likely reservoir; how it infiltrates and co-opts our cells; how the immune system overreacts to it, creating the symptoms of COVID‑19. “We’re learning about this virus faster than we’ve ever learned about any virus in history,” Sabeti said.
  • Similar triumphs occurred last year—in other countries. In March, taking advantage of the United Kingdom’s nationalized health system, British researchers launched a nationwide study called Recovery, which has since enrolled more than 17,600 COVID‑19 patients across 176 institutions. Recovery offered conclusive answers about dexamethasone and hydroxychloroquine and is set to weigh in on several other treatments. No other study has done more to shape the treatment of COVID‑19.
  • SARS‑CoV‑2’s genome was decoded and shared by Chinese scientists just 10 days after the first cases were reported. By November, more than 197,000 SARS‑CoV‑2 genomes had been sequenced. About 90 years ago, no one had even seen an individual virus; today, scientists have reconstructed the shape of SARS‑CoV‑2 down to the position of individual atoms
  • Respiratory viruses, though extremely common, are often neglected. Respiratory syncytial virus, parainfluenza viruses, rhinoviruses, adenoviruses, bocaviruses, a quartet of other human coronaviruses—they mostly cause mild coldlike illnesses, but those can be severe. How often? Why? It’s hard to say, because, influenza aside, such viruses attract little funding or interest.
  • COVID‑19 has developed a terrifying mystique because it seems to behave in unusual ways. It causes mild symptoms in some but critical illness in others. It is a respiratory virus and yet seems to attack the heart, brain, kidneys, and other organs. It has reinfected a small number of people who had recently recovered. But many other viruses share similar abilities; they just don’t infect millions of people in a matter of months or grab the attention of the entire scientific community
  • Thanks to COVID‑19, more researchers are looking for these rarer sides of viral infections, and spotting them.
  • These factors pull researchers toward speed, short-termism, and hype at the expense of rigor—and the pandemic intensified that pull. With an anxious world crying out for information, any new paper could immediately draw international press coverage—and hundreds of citations.
  • “There’s a perception that they’re just colds and there’s nothing much to learn,” says Emily Martin of the University of Michigan, who has long struggled to get funding to study them. Such reasoning is shortsighted folly. Respiratory viruses are the pathogens most likely to cause pandemics, and those outbreaks could potentially be far worse than COVID‑19’s.
  • Their movements through the air have been poorly studied, too. “There’s this very entrenched idea,” says Linsey Marr at Virginia Tech, that viruses mostly spread through droplets (short-range globs of snot and spit) rather than aerosols (smaller, dustlike flecks that travel farther). That idea dates back to the 1930s, when scientists were upending outdated notions that disease was caused by “bad air,” or miasma. But the evidence that SARS‑CoV‑2 can spread through aerosols “is now overwhelming,”
  • Another pandemic is inevitable, but it will find a very different community of scientists than COVID‑19 did. They will immediately work to determine whether the pathogen—most likely another respiratory virus—moves through aerosols, and whether it spreads from infected people before causing symptoms. They might call for masks and better ventilation from the earliest moments, not after months of debate
  • They will anticipate the possibility of an imminent wave of long-haul symptoms, and hopefully discover ways of preventing them. They might set up research groups to prioritize the most promising drugs and coordinate large clinical trials. They might take vaccine platforms that worked best against COVID‑19, slot in the genetic material of the new pathogen, and have a vaccine ready within months
  • the single-minded focus on COVID‑19 will also leave a slew of negative legacies. Science is mostly a zero-sum game, and when one topic monopolizes attention and money, others lose out.
  • Long-term studies that monitored bird migrations or the changing climate will forever have holes in their data because field research had to be canceled.
  • negligence has left COVID‑19 long-haulers with few answers or options, and they initially endured the same dismissal as the larger ME community. But their sheer numbers have forced a degree of recognition. They started researching, cataloging their own symptoms. They gained audiences with the NIH and the World Health Organization. Patients who are themselves experts in infectious disease or public health published their stories in top journals. “Long COVID” is being taken seriously, and Brea hopes it might drag all post-infection illnesses into the spotlight. ME never experienced a pivot. COVID‑19 might inadvertently create one
  • Other epistemic trespassers spent their time reinventing the wheel. One new study, published in NEJM, used lasers to show that when people speak, they release aerosols. But as the authors themselves note, the same result—sans lasers—was published in 1946, Marr says. I asked her whether any papers from the 2020 batch had taught her something new. After an uncomfortably long pause, she mentioned just one.
  • The incentives to trespass are substantial. Academia is a pyramid scheme: Each biomedical professor trains an average of six doctoral students across her career, but only 16 percent of the students get tenure-track positions. Competition is ferocious, and success hinges on getting published
  • Conservationists who worked to protect monkeys and apes kept their distance for fear of passing COVID‑19 to already endangered species.
  • Among scientists, as in other fields, women do more child care, domestic work, and teaching than men, and are more often asked for emotional support by their students. These burdens increased as the pandemic took hold, leaving women scientists “less able to commit their time to learning about a new area of study, and less able to start a whole new research project,
  • published COVID‑19 papers had 19 percent fewer women as first authors compared with papers from the same journals in the previous year. Men led more than 80 percent of national COVID‑19 task forces in 87 countries. Male scientists were quoted four times as frequently as female scientists in American news stories about the pandemic.
  • American scientists of color also found it harder to pivot than their white peers, because of unique challenges that sapped their time and energy.
  • Science suffers from the so-called Matthew effect, whereby small successes snowball into ever greater advantages, irrespective of merit. Similarly, early hindrances linger. Young researchers who could not pivot because they were too busy caring or grieving for others might suffer lasting consequences from an unproductive year. COVID‑19 “has really put the clock back in terms of closing the gap for women and underrepresented minorities,”
  • In 1848, the Prussian government sent a young physician named Rudolf Virchow to investigate a typhus epidemic in Upper Silesia. Virchow didn’t know what caused the devastating disease, but he realized its spread was possible because of malnutrition, hazardous working conditions, crowded housing, poor sanitation, and the inattention of civil servants and aristocrats—problems that require social and political reforms. “Medicine is a social science,” Virchow said, “and politics is nothing but medicine in larger scale.”
  • entists discovered the microbes responsible for tuberculosis, plague, cholera, dysentery, and syphilis, most fixated on these newly identified nemeses. Societal factors were seen as overly political distractions for researchers who sought to “be as ‘objective’ as possible,” says Elaine Hernandez, a medical sociologist at Indiana University. In the U.S., medicine fractured.
  • New departments of sociology and cultural anthropology kept their eye on the societal side of health, while the nation’s first schools of public health focused instead on fights between germs and individuals. This rift widened as improvements in hygiene, living standards, nutrition, and sanitation lengthened life spans: The more social conditions improved, the more readily they could be ignored.
  • The ideological pivot away from social medicine began to reverse in the second half of the 20th century.
  • Politicians initially described COVID‑19 as a “great equalizer,” but when states began releasing demographic data, it was immediately clear that the disease was disproportionately infecting and killing people of color.
  • These disparities aren’t biological. They stem from decades of discrimination and segregation that left minority communities in poorer neighborhoods with low-paying jobs, more health problems, and less access to health care—the same kind of problems that Virchow identified more than 170 years ago.
  • In March, when the U.S. started shutting down, one of the biggest questions on the mind of Whitney Robinson of UNC at Chapel Hill was: Are our kids going to be out of school for two years? While biomedical scientists tend to focus on sickness and recovery, social epidemiologists like her “think about critical periods that can affect the trajectory of your life,” she told me. Disrupting a child’s schooling at the wrong time can affect their entire career, so scientists should have prioritized research to figure out whether and how schools could reopen safely. But most studies on the spread of COVID‑19 in schools were neither large in scope nor well-designed enough to be conclusive. No federal agency funded a large, nationwide study, even though the federal government had months to do so. The NIH received billions for COVID‑19 research, but the National Institute of Child Health and Human Development—one of its 27 constituent institutes and centers—got nothing.
  • The horrors that Rudolf Virchow saw in Upper Silesia radicalized him, pushing the future “father of modern pathology” to advocate for social reforms. The current pandemic has affected scientists in the same way
  • COVID‑19 could be the catalyst that fully reunifies the social and biological sides of medicine, bridging disciplines that have been separated for too long.
  • “To study COVID‑19 is not only to study the disease itself as a biological entity,” says Alondra Nelson, the president of the Social Science Research Council. “What looks like a single problem is actually all things, all at once. So what we’re actually studying is literally everything in society, at every scale, from supply chains to individual relationships.”
Javier E

Genetics Reveal Europe Is One Big Family - NYTimes.com - 0 views

rendezvous.blogs.nytimes.com/...eveal-europe-is-one-big-family

genetic genome human European people ancestor race

shared by Javier E on 08 May 13 - No Cached
  • From Ireland to Turkey, Europeans are all related, sharing a link with ancestors who were alive just 1,000 years ago, according to a new genetic study.
  • Peter Ralph and Graham Coop of the University of California used genomic data for 2,257 Europeans to conduct the first such study of an entire continent.
  • A separate study, based on DNA recovered from ancient skeletons, revealed last month that the genetic makeup of modern Europe was established by a wave of newcomers to the continent 6,500 years ago, more recently than previously thought.
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  • other research suggests everyone alive in the world today shares a common ancestor from sometime in the past 3,500 years.
  • As recently as the 1950s, British schoolchildren were still studying pre-World War II textbooks that divided Europeans into Germanic, Alpine and Latin “types” according to the shape of their noses.
  • scientists had been arguing for 50 years that all humans were too closely related to be divided into races. “The few externally visible differences like skin color or nose shape are not enough to justify divisions,” he said.
  • Modern Italians and Spaniards have relatively few common ancestors compared with other European populations, which may be explained by their geography and history.
  • “There have been many studies that we’ve been involved in showing that groups which are fighting each other furiously all the time are actually extremely closely genetically related,” Mark A. Jobling, a geneticist at England’s Leicester University, told Associated Press. “So for example Jewish and non-Jewish populations in the Middle East are extremely similar genetically, but to tell them they are genetic close relatives isn’t going to change their ways.”
Javier E

Gains in DNA Are Speeding Research Into Human Origins - NYTimes.com - 0 views

www.nytimes.com/...search-into-human-origins.html

dna research human origins neanderthal denisovan interbreeding

shared by Javier E on 31 Jan 12 - No Cached
  • genetic analysis shows, modern humans encountered and bred with at least two groups of ancient humans in relatively recent times: the Neanderthals, who lived in Europe and Asia, dying out roughly 30,000 years ago, and a mysterious group known as the Denisovans, who lived in Asia and most likely vanished around the same time.
  • Their DNA lives on in us even though they are extinct. “In a sense, we are a hybrid species,
  • A third group of extinct humans, Homo floresiensis, nicknamed “the hobbits” because they were so small, also walked the earth until about 17,000 years ago. It is not known whether modern humans bred with them because the hot, humid climate of the Indonesian island of Flores, where their remains were found, impairs the preservation of DNA
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  • Comparing genomes, scientists concluded that today’s humans outside Africa carry an average of 2.5 percent Neanderthal DNA, and that people from parts of Oceania also carry about 5 percent Denisovan DNA. A study published in November found that Southeast Asians carry about 1 percent Denisovan DNA in addition to their Neanderthal genes.
  • as few as six couplings all those tens of thousands of years ago might have led to the current level of ancient immune alleles.
  • This means that our modern era, since H. floresiensis died out, is the only time in the four-million-year human history that just one type of human has been alive,
  • Were they romantic couplings? More likely they were aggressive acts between competing human groups, Dr. Stringer said. For a model, he pointed to modern hunter-gatherer groups that display aggressive behavior among tribes.
  • The value of the interbreeding shows up in the immune system, Dr. Parham’s analysis suggests. The Neanderthals and Denisovans had lived in Europe and Asia for many thousands of years before modern humans showed up and had developed ways to fight the diseases there
  • When modern humans mated with them, they got an injection of helpful genetic immune material, so useful that it remains in the genome today. This suggests that modern humans needed the archaic DNA to survive. The downside of archaic immune material is that it may be responsible for autoimmune diseases like diabetes, arthritis and multiple sclerosis, Dr. Parham said, stressing that these are preliminary results.
  • little is known about the Denisovans — the only remains so far are the pinky bone and the tooth, and there are no artifacts like tools. Dr. Reich and others suggest that they were once scattered widely across Asia, from the cold northern cave to the tropical south. The evidence is that modern populations in Oceania, including aboriginal Australians, carry Denisovan genes.
Javier E

A History of the Iberian Peninsula, as Told by Its Skeletons - The New York Times - 0 views

www.nytimes.com/...iberia-prehistory-dna.html

iberia spain portugal DNA history

shared by Javier E on 19 Mar 19 - No Cached
  • With a total of 419 ancient human genomes obtained by various laboratories, Iberia offers a rich trove. Scientists have recovered only 174 ancient genomes in Britain, and just eight in Japan.
  • researchers have also uncovered evidence of migrations that were previously unknown. Iberia, it now seems, was a crossroads long before recorded history, as far back as the last ice age.
  • Iberian hunter-gatherers had a remarkable mix of genes, showing that they descended from two profoundly distinct groups of early European hunter-gatherers.
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  • One of these groups can be traced as far back as 35,000 years, thanks to a skeleton discovered at a site in Belgium called Goyet. The Goyet-related people spread across Europe, only to be replaced on much of the continent near the end of the Ice Age by a genetically distinct population. The earliest sign of the second group appears 14,000 years ago, known to researchers by DNA in a skeleton at an Italian site called Villabruna.
  • the Goyet and Villabruna people coexisted. Hunter-gatherers across the peninsula had a mixture of ancestry from the two peoples.
  • But whatever solitude Iberia might have offered came to an end about 7,500 years ago, when new people arrived with crops and livestock. These first farmers, originally from Anatolia, brought with them a distinctive genetic signature.
  • Ninety percent of the DNA from the later skeletons derives from the Anatolian farmers; 10 percent comes from the hunter-gatherers.
  • Starting about 6,000 years ago, Dr. Olalde and his colleagues found, hunter-gatherer ancestry in Iberian farmers actually increased to 20 percent.
  • A skeleton from an elaborate grave in central Spain about 4,400 years old belonged to a man whose ancestry was 100 percent North African
  • findings suggest that people were moving into Iberia from Africa more than 3,000 years before the rise of the Roman Empire. “These are cosmopolitan places,”
  • About 4,500 years ago, still another wave of people arrived, profoundly altering the makeup of Iberia.A few centuries earlier, nomads from the steppes of what is now Russia turned up in Eastern Europe with horses and wagons. They spread across the continent, giving up nomadic life and intermarrying with European farmers.
  • When they finally reached Iberia, these people spread out far and wide. “They really have an impact on the whole peninsula,”
  • DNA from the men, however, all traced back to the steppes. The Y chromosomes from the male farmers disappeared from the gene pool.
  • To archaeologists, the shift is a puzzle.“I cannot say what it is,
  • he ruled out wars or massacres as the cause. “It’s not a particularly violent time,”
  • Iberian farmers originally lived in egalitarian societies, storing their wealth together and burying their dead in group graves.
  • over several centuries, palaces and fortresses began to rise, and power became concentrated in the hands of a few. Dr. Risch speculated that the cultural shift had something to do with the genetic shift
  • The Bronze Age in Iberia was followed by the Iron Age about 2,800
  • Iron Age Iberians could trace some of their ancestry to new waves of people arriving from northern and Central Europe, possibly marking the rise of so-called Celtiberian culture on the peninsula.
  • scientists found a growing amount of North African ancestry in skeletons from the Iron Age. That may reflect trade around the Mediterranean, which brought North Africans to Iberian towns, where they settled down.
  • North African ancestry increased in Iberia even more after Romans took control. Now the peninsula was part of an empire that thrived on widespread trade. At the same time, people from southern Europe and the Near East also began leaving an imprint
  • The Basque speak a language that is unrelated to other European tongues. Some researchers have speculated that they descended from a population that had been distinct since the Bronze Age or earlier.Genetically, at least, that doesn’t seem to be the case. Before the Roman era, the Basque had DNA that was indistinguishable from that of other Iron Age Iberians
  • After the fall of Rome, ancient DNA in Iberia reflects its medieval history. Skeletons from the Muslim era show growing ancestry from both North Africa and sub-Saharan Africa.
  • The researchers were also able to group Spaniards into five genetic clusters. On a map, these groups form five strips running north to south. Those strips line up neatly with history.
g-dragon

DNA discovery reveals relatives of ancient Egyptians - CNN - 0 views

www.cnn.com/...index.html

discovery dna ancient egypt breakthrough

shared by g-dragon on 12 Sep 17 - No Cached
  • Ancient Egyptians and their modern counterparts share less in common than you might think.
  • decoded the genome of ancient Egyptians for the first time, with unexpected results.
  • preserved remains found in Abusir-el Meleq, Middle Egypt, were closest genetic relatives of Neolithic and Bronze Age populations from the Near East, Anatolia and Eastern Mediterranean Europeans.
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  • Modern Egyptians, by comparison, share much more DNA with sub-Saharan populations.
  • The findings have turned years of theory on its head
  • Heat and high humidity in tombs, paired with some of the chemicals involved in mummification, all contribute to DNA degradation
  • They found that the sample set showed a strong connection with a cluster of ancient non-African populations based east of the Mediterranean Sea
  • This is not just the DNA of one person. It's the DNA of the parents, grandparents, grandparents' parents, grand-grand-grandparents' parents and so forth
  • Strict social structures and legal incentives to marry along ethnic lines within these communities may have played a part in the Egyptians' genetic stasis
  • A lot of people has assumed foreign invaders ... brought a lot of genetic ancestry into the region," Krause said. "People expected that through time, Egypt would become more European, but we see the exact opposite
  • Modern Egyptians were found to "inherit 8% more ancestry from African ancestors" than the mummies studied. The paper cites increased mobility along the Nile, increased long-distance commerce and the era of the trans-Saharan slave trade as potential reasons why
  • The team's findings do come with one obvious caveat: "All our genetic data (was) obtained from a single site in Middle Egypt and may not be representative for all of ancient Egypt
Javier E

Suddenly, It Looks Like We're in a Golden Age for Medicine - The New York Times - 0 views

www.nytimes.com/...ine-biomedical-innovation.html

medicine innovation boom

shared by Javier E on 27 Jun 23 - No Cached
  • “I’ve been running my research lab for almost 30 years,” says Jennifer Doudna, a biochemist at the University of California, Berkeley. “And I can say that throughout that period of time, I’ve just never experienced what we’re seeing over just the last five years.”
  • the vaccine innovations stretch beyond mRNA: A “world-changing” vaccine for malaria, which kills 600,000 globally each year, is being rolled out in Ghana and Nigeria, and early trials for next-generation dengue vaccines suggest they may reduce symptomatic infection by 80 percent or more.
  • surveying the recent landscape of scientific breakthroughs, she says the last half-decade has been more remarkable still: “I think we’re at an extraordinary time of accelerating discoveries.”
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  • Beyond Crispr and Covid vaccines, there are countless potential applications of mRNA tools for other diseases; a new frontier for immunotherapy and next-generation cancer treatment; a whole new world of weight-loss drugs; new insights and drug-development pathways to chase with the help of machine learning; and vaccines heralded as game-changing for some of the world’s most intractable infectious diseases.
  • “You cannot imagine what you’re going to see over the next 30 years. The pace of advancement is in an exponential phase right now.”
  • the mRNA sequence of the first shot was designed in a weekend, and the finished vaccines arrived within months, an accelerated timeline that saved perhaps several million American lives and tens of millions worldwide — numbers that are probably larger than the cumulative global death toll of the disease.
  • As the first of their kind to be approved by the Food and Drug Administration, they brought with them a very long list of potential future mRNA applications: H.I.V., tuberculosis, Zika, respiratory syncytial virus (R.S.V.), cancers of various and brutal kinds.
  • A Nobel laureate, Doudna is known primarily for Crispr, the gene-editing Swiss Army knife that has been called “a word processor” for the human genome and that she herself describes as “a technology that literally enables the rewriting of the code of life.”
  • A couple of decades later, it looks like a golden age for new treatments. New trials of breast-cancer drugs have led to survival rates hailed in The Times as “unheard-of,” and a new treatment for postoperative lung-cancer patients may cut mortality by more than half. Another new treatment, for rectal cancer, turned every single member of a small group of cases into cancer-free survivors.
  • many of their back stories do rhyme, often stretching back several decades through the time of the Human Genome Project, which was completed in 2003, and the near-concurrent near-doubling of the National Institutes of Health’s budget, which helped unleash what Donna Shalala, President Bill Clinton’s secretary for health and human services, last year called “a golden age of biomedical research.”
  • Ozempic and Wegovy have already changed the landscape for obesity in America
  • although the very first person to receive Crispr gene therapy in the United States received it just four years ago, for sickle-cell disease, it has since been rolled out for testing on congenital blindness, heart disease, diabetes, cancer and H.I.V
  • all told, some 400 million people worldwide are afflicted by one or more diseases arising from single-gene mutations that would be theoretically simple for Crispr to fix.
  • in theory, inserting a kind of genetic prophylaxis against Alzheimer’s or dementia.
  • In January, a much-talked-about paper in Nature suggested that the rate of what the authors called disruptive scientific breakthroughs was steadily declining over time — that, partly as a result of dysfunctional academic pressures, researchers are more narrowly specialized than in the past and often tinkering around the margins of well-understood science.
  • when it comes to the arrival of new vaccines and treatments, the opposite story seems more true: whole branches of research, cultivated across decades, finally bearing real fruit
  • Does this mean we are riding an exponential curve upward toward radical life extension and the total elimination of cancer? No. The advances are more piecemeal and scattered than tha
  • “The biology and the science that we need is already in place,” he says. “The question now to me is: Can we actually do it?”
  • Sometimes these things just take a little time.
rachelramirez

One Man Was Wrongly Blamed For Bringing AIDS to America - The Atlantic - 0 views

www.theatlantic.com/...505412

aids patient 0 US history

shared by rachelramirez on 27 Oct 16 - No Cached
  • How One Man Was Wrongly Blamed for Bringing AIDS to America
  • One of those 40 cases was a Canadian flight attendant named Gaëtan Dugas.
  • “When the study got written up and was circulated beyond the immediate team to other people within the CDC, that ambiguous oval got interpreted by some as a zero,”
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  • As the 57th AIDS patient to reach the CDC team’s attention, Dugas was originally billed as Case 057. But since he came from outside California, and wasn’t even a U.S. resident, the investigators started referring to him offhandedly as the “Out-of-California patient”—or “Patient O” for short.
  • The CDC team did their best to naysay this misconception, but it gained steam globally in 1987, after the journalist Randy Shilts published his bestselling book And The Band Played On.
  • The idea fit with the prejudices of the day: Here was a modern Typhoid Mary, whose homosexuality and irresponsible promiscuity had brought a plague to American shores.
  • He sequenced the complete genomes of HIV taken from U.S. samples collected in the late 1970s, and showed that Dugas could not possibly have been the first AIDS patient in the U.S. Indeed, the disease likely entered the country from Haiti in 1971, flying under the radar for a decade before anyone realized what was happening.
  • HIV first started infecting humans somewhere in West Africa, having jumped into us from chimpanzees.
  • He also concluded that the virus must have arrived in the U.S. around 12 years before AIDS was formally recognized in 1981.
  • They reveal that HIV had spread from Africa to the Caribbean by around 1967, and had jumped into the U.S. by around 1971. It landed in New York City and began diversifying rapidly
  • By the time anyone noticed the first sign of AIDS in 1981, the virus had already hopped from coast to coast, and become genetically diverse.
  • This means that not only did Dugas not bring AIDS to America, but he didn’t spread it west either. He was a totally mundane part of a very unusual epidemic.
  • In 2010, evolutionary biologists used gene trees to prove that a man named Anthony Eugene Whitfield had knowingly infected many women with HIV. More recently, biologists used a pocket-sized DNA sequencer to track the evolution of Ebola in real-time, providing details about routes of transmission that helped to curtail the recent west African outbreak.
Javier E

The Jig Is Up: Time to Get Past Facebook and Invent a New Future - Alexis Madrigal - Te... - 0 views

www.theatlantic.com/...256046

technology startups future innovation

shared by Javier E on 20 Apr 12 - No Cached
  • have we run out of things to say and write that actually are about technology and the companies behind them? Or do we feel compelled to fill the white space between what matters? Sort of like talk radio?
  • There have been three big innovation narratives in the last few years that complicate, but don't invalidate, my thesis. The first -- The Rise of the Cloud -- was essentially a rebranding of having data on the Internet, which is, well ... what the Internet has always been about. Though I think it has made the lives of some IT managers easier and I do like Rdio. The second, Big Data, has lots of potential applications. But, as Tim Berners-Lee noted today, the people benefiting from more sophisticated machine learning techniques are the people buying consumer data, not the consumers themselves. How many Big Data startups might help people see their lives in different ways? Perhaps the personal genomics companies, but so far, they've kept their efforts focused quite narrowly. And third, we have the daily deal phenomenon. Groupon and its 600 clones may or may not be good companies, but they are barely technology companies. Really, they look like retail sales operations with tons of sales people and marketing expenses.
  • we've reached a point in this technology cycle where the old thing has run its course. I think the hardware, cellular bandwidth, and the business model of this tottering tower of technology are pushing companies to play on one small corner of a huge field.
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  • We've maxed out our hardware. No one even tries to buy the fastest computer anymore because we don't give them any tasks (except video editing, I suppose) that require that level of horsepower
  • more than the bandwidth or the stagnant hardware, I think the blame should fall squarely on the shoulders of the business model. The dominant idea has been to gather users and get them to pour their friends, photos, writing, information, clicks, and locations into your app. Then you sell them stuff (Amazon.com, One King's Lane) or you take that data and sell it in one way or another to someone who will sell them stuff (everyone). I return to Jeff Hammerbacher's awesome line about developers these days: "The best minds of my generation are thinking about how to make people click ads." 
  • On the mobile side, we're working with almost the exact same toolset that we had on the 2007 iPhone, i.e. audio inputs, audio outputs, a camera, a GPS, an accelerometer, Bluetooth, and a touchscreen. That's the palette that everyone has been working with -- and I hate to say it, but we're at the end of the line.
  • despite the efforts of telecom carriers, cellular bandwidth remains limited, especially in the hotbeds of innovation that need it most
  • Some of it, sure, is that we're dumping the computation on the servers on the Internet. But the other part is that we mostly do a lot of the things that we used to do years ago -- stare at web pages, write documents, upload photos -- just at higher resolutions.
  • The thing about the advertising model is that it gets people thinking small, lean.
Javier E

Neanderthals Leave Their Mark on Us - NYTimes.com - 0 views

www.nytimes.com/...ls-leave-their-mark-on-us.html

neanderthal human origins

shared by Javier E on 31 Jan 14 - No Cached
  • two new studies have traced the history of Neanderthal DNA, and have pinpointed a number of genes that may have medical importance today.
  • Among the findings, the studies have found clues to the evolution of skin and fertility, as well as susceptibility to diseases like diabetes. More broadly, they show how the legacy of Neanderthals has endured 30,000 years after their extinction.
  • Both studies suggest that Neanderthal genes involved in skin and hair were favored by natural selection in humans. Today, they are very common in living non-Africans.
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  • It is possible, Dr. Akey speculated, that the genes developed to help Neanderthal skin adapt to the cold climate of Europe and Asia.
  • Both teams of scientists also found long stretches of the living human genomes where Neanderthal DNA was glaringly absent. This pattern could be produced if modern humans with certain Neanderthal genes could not have as many children on average as people without them. For example, living humans have very few genes from Neanderthals involved in making sperm. That suggests that male human-Neanderthal hybrids might have had lower fertility or were even sterile.
  • Overall, said Dr. Reich, “most of the Neanderthal genetic material was more bad than good.”
Javier E

Inuit Study Adds Twist to Omega-3 Fatty Acids' Health Story - The New York Times - 0 views

www.nytimes.com/...-fatty-acids-health-story.html

diet evolution human origins fat digestion

shared by Javier E on 18 Sep 15 - No Cached
  • Today, at least 10 percent of Americans regularly take fish oil supplements. But recent trials have failed to confirm that the pills prevent heart attacks or stroke. And now the story has an intriguing new twist.
  • he journal Science reported that the ancestors of the Inuit evolved unique genetic adaptations for metabolizing omega-3s and other fatty acids. Those gene variants had drastic effects on Inuit’s bodies, reducing their heights and weights.
  • the discovery raised questions about whether omega-3 fats really were protective for everyone, despite decades of health advice. “The same diet may have different effects on different people,” he said.
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  • The researchers found several genetic variants at different locations in the genome that were unusually common in the Inuit, compared with people in Europe or China. Several of these variations occurred within a cluster of genes that direct construction of enzymes called fatty acid desaturases. (The genes are called FADS, for short.)
  • This discovery was particularly tantalizing, because the scientists knew that these enzymes helped regulate the different fats in our bodies, including omega-3 fatty acids.
  • one of these gene variants was present in almost every Inuit in the study. It is much less common in other populations: About a quarter of Chinese people have it, compared with just 2 percent of Europeans.
  • Natural selection is the only known way this gene variant could have become so common in the Inuit. Dr. Nielsen said this adaptation might have arisen as long ago as 20,000 years, when the ancestors of the Inuit were living in the Beringia region, which straddles Alaska and Siberia
  • To uncover the effect of this variant gene, the scientists compared the Inuit in their study with others with more European ancestry. Some had inherited a European version of the variant. People with two copies of the Inuit gene had different blood levels of fatty acids than people without them, the researchers found.
  • The adaptation did more than just change blood levels of fatty acids, the scientists found. Inuit who carried two copies of the variant gene were on average an inch shorter and 10 pounds lighter than those without a copy.“That’s quite extreme,” said Dr. Nielsen.
  • Indeed, it’s rare to find a single gene that can influence height and weight so drastically. In recent years, scientists have run a number of large studies pinpointing hundreds of genes that affect height and weight, but each one played a minuscule role in the variation from person to person.
  • Those studies missed this influential gene variant because they focused mostly on people of European ancestry. So Dr. Nielsen and his colleagues also investigated how it affects Europeans. As it turns out, the gene variant is linked to a drastic drop in height and weight in that population, too.
  • natural selection might not have favored the FADS variant but a neighboring, as yet unknown piece of DNA that conferred evolutionary advantages.As that gene spread through the Inuit population, the FADS variant might simply have been passed down with it.
  • Dr. Nielsen and his colleagues are planning to investigate the long-term health effects of the gene variants they’ve found. They may help explain why some of us metabolize fats more effectively than others, and why omega-3s haven’t been the heart panacea once hoped.
Javier E

21 French Museums Will Add to Artsy's Online Collection - NYTimes.com - 0 views

artsbeat.blogs.nytimes.com/...dd-to-artsys-online-collection

art database museum collection

shared by Javier E on 17 Dec 14 - No Cached
  • the Art Genome Project, a digital classification system that draws connections between artists and artworks and makes suggestions much in the way that Pandora and other music services do. The site now features more than 230,000 images of art and architecture from more than 2,500 commercial galleries and 350 museums and other institutions.
Javier E

Ancient DNA is Rewriting Human (and Neanderthal) History - The Atlantic - 0 views

www.theatlantic.com/...554798

human origins dna migrations history archaology

shared by Javier E on 15 Mar 18 - No Cached
  • Sarah Zhang: You recently published two papers in which you analyzed over 600 genomes from ancient Europeans
  • Reich: In our hands, a successful sample costs less than $200. That’s only two or three times more than processing them on a present-day person
  • Reich: In Europe where we have the best data currently—although that will change over the coming years—we know a lot about how people have migrated. We know of multiple layers of population replacement over the last 50,000 years. Between 41,000 and 39,000 years ago in western Europe, the Neanderthals were replaced by modern human populations. The first modern human samples we have in Europe are about 40,000 years old and are genetically not at all related to present-day Europeans. They seem to be from extinct, dead-end groups.
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  • After that, you see for the first time people related to later European hunter-gatherers who have contributed a little bit to present-day Europeans. That happens beginning 35,000 to 37,000 years ago. Then the ice sheets descend across northern Europe and a lot of these populations are chased into these refuges in the southern peninsulas of Europe. After the Ice Age, there’s a repeopling of northern Europe from the southwest, probably from Spain, and then also from the southeast, probably from Greece and maybe even from Anatolia, Turkey
  • Again, after 9,000 years ago, there’s a mass movement of farmers into the region which almost completely replaces the hunter-gatherers with a small amount of mixture
  • And then again, after 5,000 years ago, there’s this mass movement at the beginning of the Bronze Age of people from the steppe, who also probably bring these languages that are spoken by the great majority of Europeans today.
  • Reich: Archaeology has always been political, especially in Europe. Archaeologists are very aware of the misuse of archaeology in the past, in the 20th century. There’s a very famous German archaeologist named Gustaf Kossinna, who was the first or one of the first to come up with the idea of “material culture.” Say, you see similar pots, and therefore you’re in a region where there was shared community and aspects of culture.
  • He went so far as to argue that when you see the spread of these pots, you’re actually seeing a spread of people and there’s a one-to-one mapping for those things. His ideas were used by the Nazis later, in propaganda, to argue that a particular group in Europe, the Aryans, expanded in all directions across Europe.
  • This was used to justify their expansionism in the propaganda that the Germans used in the run-up to the Second World War.
  • So after the Second World War, there was a very strong reaction in the European archaeological community—not just the Germans, but the broad continental European archaeological community—to the fact that their discipline had been used for these terrible political ends. And there was a retreat from the ideas of Kossinna.
  • one of the things the ancient DNA is showing is actually the Corded Ware culture does correspond coherently to a group of people. [Editor’s note: The Corded Ware made pottery with cord-like ornamentation and according to ancient DNA studies, they descended from steppe ancestry.] I think that was a very sensitive issue to some of our coauthors
  • Our results are actually almost diametrically opposite from what Kossina thought because these Corded Ware people come from the East, a place that Kossina would have despised as a source for them.
  • it is true that there’s big population movements, and so I think what the DNA is doing is it’s forcing the hand of this discussion in archaeology, showing that in fact, major movements of people do occur. They are sometimes sharp and dramatic, and they involve large-scale population replacements over a relatively short period of time. We now can see that for the first time.
  • Zhang: As you say, the genetics data is now often ahead of the archaeology, and you keep finding these big, dramatic population replacements throughout human history that can’t yet be fully explained. How should we be thinking about these population replacements? Is there a danger in people interpreting or misinterpreting them as the result of one group’s superiority over another?
  • When you see these replacements of Neanderthals by modern humans or Europeans and Africans substantially replacing Native Americans in the last 500 years or the people who built Stonehenge, who were obviously extraordinarily sophisticated, being replaced from these people from the continent, it doesn’t say something about the innate potential of these people. But it rather says something about the different immune systems or cultural mismatch.
  • Zhang: On the point of immune systems, one of the hypotheses for why people from the steppe were so successful in spreading through Europe is that they brought the bubonic plague with them. Since the plague is endemic to Central Asia, they may have built up immunity but the European farmers they encountered had not.
  • ut there have been profound and Earth-shattering events, again and again, every few thousand years in our history and that’s what ancient DNA is telling us.
  • if you actually take any serious look at this data, it just confounds every stereotype. It’s revealing that the differences among populations we see today are actually only a few thousand years old at most and that everybody is mixed.
  • I think that if you pay any attention to this world, and have any degree of seriousness, then you can’t come out feeling affirmed in the racist view of the world. You have to be more open to immigration. You have to be more open to the mixing of different peoples. That’s your own history.
Javier E

Obama to Leave the White House a Nerdier Place Than He Found It - The New York Times - 1 views

www.nytimes.com/...er-place-than-he-found-it.html

obama intellectual science culture

shared by Javier E on 01 Aug 16 - No Cached
  • Mr. Obama’s presidential science advisory committee has been the most active in history, starting 34 studies of subjects as varied as advanced manufacturing and cybersecurity. Scientists on the committee said they worked so hard because Mr. Obama was deeply engaged in their work.
  • In a recent interview with Bloomberg Businessweek, Mr. Obama listed science as one of the few subjects he intended to pursue after the presidency.
  • “The conversations I have with Silicon Valley and with venture capital pull together my interests in science and organization in a way I find really satisfying,” Mr. Obama said. Of the potential breakthroughs in genomic sequencing, “That’s just an example of something I can sit and listen and talk to folks for hours about,” he said.
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  • Mr. Obama’s reading lists are peppered with science and science fiction titles such as Elizabeth Kolbert’s “The Sixth Extinction,” Atul Gawande’s “Being Mortal” and Liu Cixin’s “The Three-Body Problem.”
  • But Mr. Obama’s grasp of real science before becoming president was sketchy. He once admitted to a room full of scientists to not doing “well enough in chemistry or physics to impress you much on those topics.” And some scientists who met Mr. Obama before the presidency said they were not wowed by his grasp of their fields.
  • “He’s an academic, he’s one of us,” Dr. Varmus said. “He’s a rational, levelheaded guy who makes decisions based on the evidence. Now, that might actually be a deficiency as a politician.”
Javier E

How U.S. can defeat coronavirus: Heed Asia?s lessons from epidemics past - The Washingt... - 0 views

www.washingtonpost.com/...a-b199-3a9799c54512_story.html

pandemic lessons asia policy crisis

shared by Javier E on 19 Mar 20 - No Cached
  • in wealthy places on China's periphery — Hong Kong, Taiwan and South Korea — a rapid response swung into action.One reason was that they had learned from the past.
  • “We were all burned very badly with SARS, but actually it turned out to be a blessing for us.”
  • Political will, dedicated resources, sophisticated tracking and a responsible population have kept coronavirus infections and deaths in Taiwan, Hong Kong and Singapore relatively low. South Korea, with more deaths, has led the way in widespread testing.
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  • In Taiwan, officials boarded planes arriving from Wuhan and assessed passengers for symptoms before allowing anyone to disembark. Within days, Singapore, South Korea and other Asian states had implemented similar steps.
  • A year after SARS, Taiwan established a National Health Command Center that brought together all levels and branches of government, preparing for the possibility of another disease outbreak. Its interventions over the past two months have been decisive in keeping Taiwan ahead of the curve
  • They didn’t hesitate, they didn’t want to die,” Wang said. “The mortality rate was so high [during SARS] and they didn’t know how bad this one was going to be. Nobody thought it was like the flu.”
  • As early as Jan. 5, Taiwan was tracing people who had been in Wuhan in the previous 14 days. Those with symptoms of respiratory infections were quarantined.
  • In subsequent weeks, authorities used data and technology to identify and track cases, communicated effectively to reassure the public, offered relief to businesses and allocated medical resources where they were needed most — rationing face masks and dramatically increasing their production.
  • On Jan. 27, Taiwan combined the databases of its National Health Insurance Administration and National Immigration Agency, allowing it to track everyone who had been in Wuhan in the recent past and alert doctors to patients’ travel histories
  • Now, Taiwan is hoping to keep its infection numbers down and has asked residents not to travel abroad after its biggest single-day jump of cases — 23 — on Wednesday. It is also barring most noncitizens from entering.
  • South Korea, meanwhile, has become the poster child for testing. Its success is rooted in a previous failure: The limited availability of test kits was seen as having aggravated the 2015 MERS outbreak, when the country suffered the second-highest caseload after Saudi Arabia.
  • More than 260,000 people in South Korea have been tested for the virus, the highest per capita anywhere, with testing and treatment fees covered by the government and drive-through centers capturing global attention
  • Whereas the United States and Japan keep testing tightly controlled by a central authority, South Korea opened the process to the private sector, introducing a path to grant “emergency usage approval” to tests for pathogens of pandemic potential.
  • Singapore, too, benefited from its own capabilities to test, as did Hong Kong and Japan. All developed their own diagnostic tests when the covid-19 genome sequence was published.
  • Outside mainland China, the territory had been the biggest casualty of the Communist Party’s coverup of the SARS outbreak, with some 300 deaths and little clarity on what was unfolding until it was too late.
  • This time, though, and without needing to be told much, Hong Kong residents took matters into their own hands. The city’s financial district was reduced to a ghost town in early February as companies closed offices. Bakeries known for hour-long weekend lines were abandoned.
  • Parties, weddings and family gatherings were canceled — without any government order. Almost everyone rushed to ­procure masks; a recent study ­estimated that 74 percent to 98 percent of residents wore them when leaving their homes. Voluntary social distancing was hailed as a key reason for the lower rate of infections.
  • From electronic wristbands to smartphone trackers, Asian jurisdictions have pulled out all the stops to ensure that suspected patients comply with quarantine and isolation orders, monitoring that is backed by laws that were tightened post-SARS.
  • Singapore used its FBI equivalent, the Criminal Investigation Department, to effectively interrogate every confirmed case with stunning granularity — even using patients’ digital wallets to trace their footsteps. Those caught lying face fines and jail time.
  • In South Korea, information on the movements of infected people before they were tested is collected and relayed over smartphones, creating a real-time ma
  • Taiwan tracks infected people’s whereabouts via smartphones
  • In Hong Kong, everyone subject to a compulsory quarantine must activate real-time location-sharing on their phone or wear an electronic wristband.
  • These measures have been backed by local populations that lived through previous epidemics and have largely shed concerns about privacy and tracking.
  • Americans should not focus “only on the kind of high-profile displays of state power that have made headlines from China” but also look at countries such as South Korea that are “balancing Democratic openness with rapid, concerted public-health action.”
  • Experts agree, though, that Western governments must be prepared to limit their citizens’ movements, mandate isolation for positive cases and track contacts regardless of privacy concerns.
Javier E

Opinion | Who Is Immune to the Coronavirus? - The New York Times - 0 views

www.nytimes.com/...coronavirus-immunity.html

research science Covid-19 immunity vaccine

shared by Javier E on 14 Apr 20 - No Cached
  • No such human-challenge experiments have been conducted to study immunity to SARS and MERS. But measurements of antibodies in the blood of people who have survived those infections suggest that these defenses persist for some time: two years for SARS, according to one study, and almost three years for MERS, according to another one. However, the neutralizing ability of these antibodies — a measure of how well they inhibit virus replication — was already declining during the study periods.
  • These studies form the basis for an educated guess at what might happen with Covid-19 patients. After being infected with SARS-CoV-2, most individuals will have an immune response, some better than others. That response, it may be assumed, will offer some protection over the medium term — at least a year — and then its effectiveness might decline.
  • One concern has to do with the possibility of reinfection. South Korea’s Centers for Disease Control and Prevention recently reported that 91 patients who had been infected with SARS-CoV-2 and then tested negative for the virus later tested positive again. If some of these cases were indeed reinfections, they would cast doubt on the strength of the immunity the patients had developed.
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  • Several of my colleagues and students and I have statistically analyzed thousands of seasonal coronavirus cases in the United States and used a mathematical model to infer that immunity over a year or so is likely for the two seasonal coronaviruses most closely related to SARS-CoV-2 — an indication perhaps of how immunity to SARS-CoV-2 itself might also behave.
  • Mild illness, in other words, might not always build up protection. Similarly, it will be important to study the immune responses of people with asymptomatic cases of SARS-CoV-2 infection to determine whether symptoms, and their severity, predict whether a person becomes immune.
  • the issue might be resolved by comparing the viral genome sequence from the first and the second periods of infection.
  • it is reasonable to assume that only a minority of the world’s population is immune to SARS-CoV-2, even in hard-hit areas. How could this tentative picture evolve as better data come in? Early hints suggest that it could change in either direction.
  • One recent study (not yet peer-reviewed) suggests that rather than, say, 10 times the number of detected cases, the United States may really have more like 100, or even 1,000, times the official number
  • if this one is correct, then herd immunity to SARS-CoV-2 could be building faster than the commonly reported figures suggest.
  • another recent study (also not yet peer-reviewed) suggests that not every case of infection may be contributing to herd immunity. Of 175 Chinese patients with mild symptoms of Covid-19, 70 percent developed strong antibody responses, but about 25 percent developed a low response and about 5 percent developed no detectable response at all
  • An alternative possibility, which many scientists think is more likely, is that these patients had a false negative test in the middle of an ongoing infection, or that the infection had temporarily subsided and then re-emerged
  • The balance between these uncertainties will become clearer when more serologic surveys, or blood tests for antibodies, are conducted on large numbers of people. Such studies are beginning and should show results soon. Of course, much will depend on how sensitive and specific the various tests are: how well they spot SARS-CoV-2 antibodies when those are present and if they can avoid spurious signals from antibodies to related viruses.
  • Based on the volunteer experiments with seasonal coronaviruses and the antibody-persistence studies for SARS and MERS, one might expect a strong immune response to SARS-CoV-2 to protect completely against reinfection and a weaker one to protect against severe infection and so still slow the virus’s spread.
  • But designing valid epidemiologic studies to figure all of this out is not easy — many scientists, including several teams of which I’m a part — are working on the issue right now.
  • getting a handle on this fast is extremely important: not only to estimate the extent of herd immunity, but also to figure out whether some people can re-enter society safely, without becoming infected again or serving as a vector, and spreading the virus to others. Central to this effort will be figuring out how long protection lasts.
  • Experimental and statistical evidence suggests that infection with one coronavirus can offer some degree of immunity against distinct but related coronaviruses.
  • then there is the question of immune enhancement: Through a variety of mechanisms, immunity to a coronavirus can in some instances exacerbate an infection rather than prevent or mitigate it.
  • administering a vaccine against dengue fever, a flavivirus infection, can sometimes make the disease worse.
  • concern that they might be at play is one of the obstacles that have slowed the development of experimental vaccines against SARS and MERS.
  • The good news is that research on SARS and MERS has begun to clarify how enhancement works, suggesting ways around it, and an extraordinary range of efforts is underway to find a vaccine for Covid-19, using multiple approaches.
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