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Javier E

In Iceland's DNA, New Clues to Disease-Causing Genes - NYTimes.com - 0 views

  • Scientists in Iceland have produced an unprecedented snapshot of a nation’s genetic makeup, discovering a host of previously unknown gene mutations that may play roles in ailments as diverse as Alzheimer’s disease, heart disease and gallstones.
  • Decode, an Icelandic genetics firm owned by Amgen, described sequencing the genomes — the complete DNA — of 2,636 Icelanders, the largest collection ever analyzed in a single human population.
  • With this trove of genetic information, the scientists were able to accurately infer the genomes of more than 100,000 other Icelanders, or almost a third of the entire country
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  • While some diseases, like cystic fibrosis, are caused by a single genetic mutation, the most common ones are not. Instead, mutations to a number of different genes can each raise the risk of getting, say, heart disease or breast cancer. Discovering these mutations can shed light on these diseases and point to potential treatments. But many of them are rare, making it necessary to search large groups of people to find them.
  • The wealth of data created in Iceland may enable scientists to begin doing that
  • For example, they found eight people in Iceland who shared a mutation on a gene called MYL4. Medical records showed that they also have early onset atrial fibrillation, a type of irregular heartbeat.
  • they identified a gene called ABCA7 as a risk factor for Alzheimer’s disease.Previous studies had suggested a gene in the genetic neighborhood of ABCA7 was associated with the disease.But the Icelandic study pinpointed the gene itself — and even the specific mutation involved.
  • Since Dr. Stefansson and his colleagues submitted their initial results for publication, they have continued gathering DNA from Icelanders.The scientists now have full genomes from about 10,000 Icelanders and partial genetic information on 150,000 more.
  • Dr. Stefansson said that means that his firm could generate a report for genetic disease on every person in Iceland
  • Iceland is a particularly fertile country for doing genetics research. It was founded by a small number of settlers from Europe arriving about 1,100 years ago. Between 8,000 and 20,000 people came mainly from Scandinavia, Ireland and Scotland.
  • The country remained isolated for the next thousand years, and so living Icelanders have a relatively low level of genetic diversity. This makes it easier for scientists to detect genetic variants that raise the risk of disease, because there are fewer of them to examine.
  • celand also has impressive genealogical records. Through epic poems and historical documents, many Icelanders can trace their ancestry back to the nation’s earliest arrivals. Geneticists use national genealogy databases to look for diseases that are unusually common in relatives — a sign that they share a mutation.
  • the company is now investigating a gene, found by Decode, with a strong link to cardiovascular disease in Iceland. (He declined to name the gene.)
Javier E

Study Reveals Genetic Path of Modern Britons - NYTimes.com - 0 views

  • In A.D. 410, Roman authority in Britain collapsed and Romano-British society disappeared from history under the invading tides of Angles and Saxons from northern Europe. Historians have been debating ever since whether the Romano-British were wiped out or survived by adopting their conquerors’ language and culture
  • A fine-scale genetic analysis of the British population has now provided the answer. The invaders and the existing population lived side by side and eventually intermarried extensively. The people of south and central England are now genetically well mixed, with Saxon genes accounting for only about 20 percent of the mix
  • The British Isles were wiped clean of people by the glaciers that descended toward the end of the last ice age, and were repopulated some 10,000 years ago by people who trekked over the broad land bridge that then joined eastern England to Europe north of the Rhine. The researchers say they can identify the genetic signature of this early migration, which survives most strongly in people from the western extremity of Wales.
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  • But the geneticists see no trace of the Danelaw, the Danish rule over northern England from the ninth to the 11th century, nor of the Norman Conquest of England in 1066. The numbers of invaders may have been too small to leave a demographic imprint
  • in the case of the Normans, who had previously emigrated from southern Denmark to Normandy, it is hard to distinguish their genes from those of the earlier Danish invaders.
  • The researchers found that the modern British population falls into 17 clusters altogether, based on genetic relatedness. Though very similar, the groups are genetically distinguishable, and even the main population cluster, that of southern and central England, is distinguishable from the populations of France, Germany and other European countries.
  • The people of the southern and central parts of England form a homogeneous population, but all around the Celtic periphery, in Cornwall, Wales and Scotland, lie small clusters of genetically different populations that have maintained their identity over the generations. This is a surprise, given that the Celtic peoples who ruled most of England until Caesar’s invasion in B.C. 55 were assumed to be fairly homogeneous.
  • Dr. Donnelly and his colleagues managed to sidestep this recent churning of the population history by seeking out elderly people who lived in rural areas and whose grandparents had been born locally. Because individual genomes are composed of random samples of the four grandparents’ DNA, the researchers were in effect looking two generations into the past and testing the population of the late 19th century.
  • They analyzed the DNA of their 2,000 subjects at 500,000 sites along the genome, and then organized them into the 17 genetic clusters. They also analyzed the genomes of 6,000 Europeans in the same way, and could thus identify the source populations in Europe from which each of the 17 British clusters was derived.
  • The migrations revealed in that way match the known historical record but also point to events that have not been recorded, such as a major migration from northern France that accounts for about one-third of the ancestry of the average person in Britain.
  • “History is written by the winners, and archaeology studies the burials of wealthy people,” Dr. Donnelly said. “But genetic evidence is interesting because it complements that by showing what is happening to the masses rather than the elite.”
Javier E

| Harvard Magazine - 0 views

  • Who Killed the Men of England? The written record of history meets genomics, evolution, demography, and molecular archaeology.
  • more than a million men vanished without a trace. They left no descendants. Historians know that something dramatic happened in England just as the Roman empire was collapsing. When the Anglo-Saxons first arrived in that northern outpost in the fourth century a.d.--whether as immigrants or invaders is debated--they encountered an existing Romano-Celtic population estimated at between 2 million and 3.7 million people. Latin and Celtic were the dominant languages.
  • Yet the ensuing cultural transformation was so complete, says Goelet professor of medieval history Michael McCormick, that by the eighth century, English civilization considered itself completely Anglo-Saxon, spoke only Anglo-Saxon, and thought that everyone had “come over on the Mayflower, as it were.”
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  • Working along an east-west transect through central England and Wales, the scientists discovered that the mix of Y-chromosomes characteristic of men in the English towns was very different from that of men in the Welsh towns: Wales was the primary Celtic holdout in Western Britannia during the ascendance of the Anglo-Saxons. Using computer analysis, the researchers explored how such a pattern could have arisen and concluded that a massive replacement of the native fourth-century male Britons had taken place. Between 50 percent and 100 percent of indigenous English men today, the researchers estimate, are descended from Anglo-Saxons who arrived on England’s eastern coast 16 centuries ago.
  • So what happened? Mass killing, or “population replacement,” is one possible explanation. Mass migration of Anglo-Saxons, so that they swamped the native gene pool, is another.
  • Yet no archaeological or historical evidence from the fifth and sixth centuries hints at the immense scale of violence or migration that would be necessary to explain this genetic legacy. The science hinted at an untold story.
  • across entire fields of inquiry, the traditional boundaries between history and prehistory have been melting away as the study of the human past based on the written record increasingly incorporates the material record of the natural and physical sciences.
  • The study of the human past, in other words, has entered a new phase in which science has begun to tell stories that were once the sole domain of humanists.
  • Thomas had found that genetically, not one of the English towns he sampled was significantly different from the others. Welsh towns, on the other hand, were significantly different from each other and from the English towns.
  • Most importantly, he found that inhabitants of  the Dutch province of Friesland were indistinguishable genetically from the English town-dwellers. Friesland is one of the known embarkation points of the Angl0-Saxons--and the language spoken there is the closest living relative to English.
  • The implications are profound: “Suddenly, we have all these genuine historical observations that need to be taken on board by historians and archaeologists and they raise a whole series of new questions, focusing particularly on…what is going on at the intimate level of this new civilization that is being born in the ruins of the Roman empire. The history of Europe will never be the same.”
  • But most archaeologists and historians who understand the economic capacity of the era, he noted, “find such massive contributions to the English gene pool to be completely unacceptable.
  • “But still, the genetic data are quite robust,” Thomas pointed out. “This is where the idea of an apartheid-like social structure comes in.” He has advanced a theory that a sexually biased, ethnically driven reproductive pattern, in which Anglo-Saxon males fathered children with Anglo-Saxon females and possibly Celtic females, while the reproductive activities of Romano-Celtic males were more restricted, is the most plausible explanation for the demographic, archaeological, and genetic patterns seen today. 
  • In an attempt to explain the remarkable similarity between Frisian and English towns, Thomas and colleagues constructed a population simulation model on a computer. He tested many theories: common ancestry dating back to the Neolithic age; background migration over centuries and even millennia; and a mass-migration event that, he calculated, would have had to involve at least 50 percent replacement--the movement, in other words, of a million people.
  • Simulating such an advantage, and choosing an arbitrary figure of 10 percent migration, Thomas found that the Y chromosomes of native Britons could have been replaced in the general population in as few as five generations. 
  • by the 1970s, he continues, scholars began to realize there never was a homogenous “nation” of Germans in northern Europe, just small tribes that coalesced along the Roman frontier in what were political and cultural, rather than biological, federations, as their very names suggest: Alemanni, meaning “all men”; Goths, meaning “good guys.”
  • The Romans, scholars believed, provided a common enemy, and that unified the disparate Germanic tribes. This line of reasoning led historians to a further thought: maybe the Anglo-Saxon identity was similarly socially constructed, and not biological after all
  • More recent historical scholarship, therefore, has increasingly emphasized discovering the extent to which the barbarian migrations were really a process of ethnogenesis--the creation of new ethnic identities, as the merchant’s story illustrates.
  • “There is lots of evidence for it,” McCormick says. “But now you have Mark Thomas telling us that you could actually study mating patterns. That is utterly unanticipated.” The work raises a host of new questions: What was women’s role in the barbarian settlements? Were Anglo-Saxon men mating with Celtic women? Or were there women in those invading boats, and if so, how many? What happened to the Romano-Celtic men? Were they killed? 
  • There is some support for this in ancient English laws, which indicate that Britons and Anglo-Saxons were legally and economically different even in the seventh century, long after the initial migration. Thomas cited wergild (blood money) payments as one example: “Killing an Anglo-Saxon was a costly business, but killing a native Briton was quite cheap.” This points to differences in economic status. And differences in wealth “almost always result in differences in reproductive output,” he said. “Sometimes two- and three-fold differences.” To the extent Anglo-Saxons were able to have and support more children, this could lead to a gradual replacement of the indigenous Y-chromosome over many generations
  • The Y-chromosome can be a particularly revealing signature of the past when compared to other kinds of genetic data. Among African Americans in the United States, for example, Y-chromosomes are about 33 percent European, he says, though the proportion varies from city to city. But those same African Americans’ mitochondrial DNA, which comes from the female line, is only about 6 percent European. And that, says Reich, “tells you about the history of this country, in which men contributed about three-fourths of the European ancestry that is present in the African-American population data. The data speak to a history in which white male slaveowners exploited women of African descent--a fact that is well documented in the historical record. That there is evidence of this in genetic data should be no surprise.”
  • Most Americans associate Medellín with the drug cartels of that isolated region. But the remoteness has also preserved a genetic legacy that can be traced to the conquistadores. As described in a paper by Andrés Ruiz-Linares of University College London, the Y-chromosomes of men in Medellín are 95 percent European, while the mitochondrial DNA of the women is 95 percent Native American. Spanish men and Native American women created a new population--confirming the recorded history of the region.
  • The pattern of sexual exploitation by a dominant group seen in the preceding examples is not at all unusual in the human genetic record, says Reich’s frequent collaborator, Nick Patterson, a senior research scientist at the Broad Institute of MIT and Harvard. The Icelandic sagas record that the exiles who settled that island raided Scotland and Ireland, kidnapping Celtic women. And the genes corroborate this account. The mitochondrial DNA of the women is Celtic, the Y-chromosomes are Nordic
  • Fortunately, the science of the human past has progressed in these other areas no less than in the field of genetics. Innovations in archaeological analysis have had a profound impact
  • After the fall of the Roman empire, “you get this layer called ‘dark earth’” in the archaeological stratigraphy, he says. “People thought the empire fell and the cities turned into garden [plots]. That is how dark earth was understood up until about five years ago,
  • “In the Roman excavations,” says McCormick, “there were pots and stone buildings and columns.” But then suddenly you get a layer of nothing but dark, humus-looking soil. What actually happened, Galinié and others have found, is that people shifted to organic building materials. “They had thatched roofs and wooden houses, they didn’t have Roman garbage removal, and they just dumped the ashes and charcoal from their hearths out in the road and all of that compacted. It is extremely rich, extremely dense,
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    Who Killed the Men of England? The written record of history meets genomics, evolution, demography, and molecular archaeology.
Javier E

Genetic sequencing: U.S. lags behind in key tool against coronavirus mutations - The Wa... - 0 views

  • The lack of widespread genetic sequencing means the window is closing to find and slow the spread of variants such as the one first spotted in Britain, which appears to be much more transmissible, and those initially detected in Brazil and South Africa. All have been discovered in small numbers in the United States.
  • Now is when genetic sequencing — a process that maps out the genetic code of the particular virus that infected someone so it can be compared with others — would do the most good, while such variants are less prevalent in the U.S. population and action can be taken against them.
  • “We are in a race against time because of these mutations. And in that race, we are falling behind,”
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  • The problem echoes the country’s catastrophic stumbles early in the pandemic, when a lack of testing allowed the virus to spread widely. Currently, only a tiny fraction of all positive coronavirus tests in the United States are forwarded for further sequencing.
  • t if scientists don’t know what strains are moving through the population, the mutations that matter may pop up undetected.
  • For months, scientists have been sounding alarms and trying to ramp up genetic sequencing of test samples, but the effort has been plagued by a lack of funding, political will and federal coordination
  • Centers for Disease Control and Prevention Director Rochelle Walensky said Friday that the government is increasing the level of sequencing nationwide.“We have scaled up surveillance dramatically just in the last 10 days, in fact. But our plans for scaling up surveillance are even more than what we’ve done so far,”
  • Ultimately, the country needs real-time data — similar to the dashboards now used to track daily cases, hospitalizations and deaths — to track variants and their prevalence across the country
  • “None of that exists right now. We’re incredibly behind compared to other countries,”
  • The U.S. effort is so underdeveloped that it’s impossible to say exactly how many virus cases are sequenced daily.
  • The CDC has warned that the variant found in the United Kingdom — which British scientists said could be up to 70 percent more transmissible — could become dominant in the United States by March.
  • It also recently contracted with four private companies — Quest, Labcorp, Illumina and Helix — to conduct more sequencing. By mid-February, those contracts should hit full capacity, analyzing 6,000 samples per week, CDC officials said.
  • Illumina estimates that the country needs to sequence 5 percent of its coronavirus cases to detect a new variant when the variant represents about 0.1 percent to 1.0 percent of the country’s case
  • However, the United States so far has only sequenced about 0.32 percent of its total cases
  • the country ranks 38th out of 130 countries reporting whole-genome sequencing data.
  • The United States has sequenced 84,177 samples out of 25.7 million cases as of Friday, according to a Washington Post analysis. By comparison, the United Kingdom, in ninth place, has sequenced 214,000 genomes — almost 6 percent — of the country’s 3.7 million cases.
  • Unlike the United States, the U.K. invested in genetic sequencing early on in the pandemic, launching its genomics consortium in March with a $27 million investment and a multimillion-dollar boost late last year.
  • Even before the emergence of mutations such as the variants first discovered in South Africa and the United Kingdom, U.S. experts had been warning for months about the need for a national standard for genetic surveillance.
  • In May, the CDC launched a surveillance program for the coronavirus called SPHERES (SARS-CoV-2 Sequencing for Public Health Emergency Response, Epidemiology, and Surveillance). But, in practice, the program relied on a haphazard patchwork of academic labs contributing genetic sequencing on a volunteer basis.
  • A July report by the National Academies of Science said that “poor funding, coordination, and capacity” had led to a “patchy, typically passive, and reactive” U.S. sequencing effort.
Javier E

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

  • 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.
  • 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.
  • 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.
  • 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

Major Grocer to Label Foods With Gene-Modified Content - NYTimes.com - 1 views

  • Genetically modified ingredients are deeply embedded in the global food supply, having proliferated since the 1990s. Most of the corn and soybeans grown in the United States, for example, have been genetically modified. The alterations make soybeans resistant to a herbicide used in weed control, and causes the corn to produce its own insecticide. Efforts are under way to produce a genetically altered apple that will spoil less quickly, as well as genetically altered salmon that will grow faster
  • The labeling requirements announced by Whole Foods will include its 339 stores in the United States and Canada. Since labeling is already required in the European Union, products in its seven stores in Britain are already marked if they contain genetically modified ingredients. The labels currently used show that a product has been verified as free of genetically engineered ingredients by the Non GMO Project, a nonprofit certification organization. The labels Whole Foods will use in 2018, which have yet to be created, will identify foods that contain such ingredients.
  • “We’ve had some pretty big developments in labeling this year,” Mr. Hirshberg said, adding that 22 states now have some sort of pending labeling legislation. “Now, one of the fastest-growing, most successful retailers in the country is throwing down the gantlet.” He compared the potential impact of the Whole Foods announcement to Wal-Mart’s decision several years ago to stop selling milk from cows treated with growth hormone. Today, only a small number of milk cows are injected with the hormone.
Javier E

Opinion | We Need a New Language for Talking About Race - The New York Times - 0 views

  • The other day, while teaching a lecture class, one of us mentioned in passing that the average African American, according to a 2014 paper, is about 24 percent European and less than 1 percent Native American. A student responded that these percentages were impossible to measure, since “race is a social construction.”
  • the fact that race is a social invention and not a biological reality cannot be repeated too much.
  • However, while race is socially constructed, genetic mutations — biological records of ancestry — are not, and the distinction is a crucial one.
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  • To varying degrees, we have all inherited a muddled understanding of race, ancestry and phenotype from the Enlightenment,
  • if we don’t disentangle these concepts, we may miss the great promise of using genetics to push back against a very long and sad history of the misuse of science for pernicious purposes.
  • One of the key moments in the evolution of modern concepts of race occurred in France in 1741, when the members of Bordeaux’s Royal Academy of Sciences held a continentwide essay contest on the “cause” of dark skin and textured hair among African populations. Why, they asked, were Black people Black?
  • this contest signaled a new era of “scientific racism.” In the decades that followed, naturalists increasingly subdivided the human species into several so-called races by things like skin color, hair texture, skull shape and, most perniciously, according to supposedly transcendent essences.
  • genetics — or, for that matter, any science — has the potential to be misused, co-opted by racist ideologies and employed to bolster harmful narratives about racial purity or biological superiority.
  • There is no category for white in genetic analysis; half of his ancestry traces back to regions in Europe. We should never forget that whiteness, like Blackness, is just another social fiction.
  • If, throughout the 18th, 19th and 20th centuries, science put an enormous amount of effort into dividing the human species into separate categories, 21st-century genetic analysis promises to reveal just how meaningless those categories are — and how connected we’ve been all along.
  • it feels urgent that we develop new language for discussing the relationship between identity, ancestry, history and science
  • DNA analysis could help create that language by offering more nuanced ways of looking at individual origins and a more unifying narrative about our shared heritage
  • While, biologically speaking, the idea of individual human races with different origins is as farcical as the medieval belief that elves cause hiccups, the social reality of race is undeniable.
  • The multitude of population clusters, regions and genetic groups reflected in DNA tests counters existing narratives that try to reduce the astonishing variety of the human community to the four or five socially constructed races of man
  • But if we can, at the very least, embrace the understanding that race (a toxic social construction) and ancestry (a shared genetic history) are not only distinct but also fundamentally opposed — and teach that in our classrooms — it could go a long way toward freeing us from some of the binds in which scientific racism have trapped us.
  • The stories embedded in our genes beg to be told. They tell of ancestral diversity that stretches back thousands of years and ultimately underscores all that we — despite superficial physical differences — have in common.
Javier E

Ancient DNA Reveals History of Hunter-Gatherers in Europe - The New York Times - 0 views

  • in a pair of studies published on Wednesday 0c, researchers have produced the most robust analysis yet of the genetic record of prehistoric Europe.
  • Looking at DNA gleaned from the remains of 357 ancient Europeans, researchers discovered that several waves of hunter-gatherers migrated into Europe.
  • The studies identified at least eight populations, some more genetically distinct from each other than modern-day Europeans and Asians
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  • They coexisted in Europe for thousands of years, apparently trading tools and sharing cultures. Some groups survived the Ice Age, while others vanished,
  • when farmers arrived in Europe about 8,000 years ago, they encountered the descendants of this long history, with light-skinned, dark-eyed people to the east, and possibly dark-skinned and blue-eyed people to the west.
  • “We lack still an understanding of why these movements were triggered. What happened here, why it happened — it’s strange.”
  • Modern humans arose in Africa and expanded to other continents about 60,000 years ago
  • These early Europeans have almost no genetic link to younger remains of hunter-gatherers. It appears that the first modern humans in Europe may have disappeared along with the Neanderthals
  • he oldest DNA of modern humans in Europe, dating back 45,000 years, undermines such a simple story. It comes from people who belonged to a lost branch of the human family tree. Their ancestors were part of the expansion out of Africa, but they split off on their own before the ancestors of living Europeans and Asians split apart.
  • About 33,000 years ago, as the climate turned cold, a new culture called the Gravettian arose across Europe. Gravettian hunters made spears to kill woolly mammoths and other big game. They also made so-called Venus figurines that might have represented fertility.
  • When the glaciers retreated, some descendants of the Fournol continued living in Iberia. But others expanded north as a new population, which Dr. Posth and his colleagues called GoyetQ2. “It really seems like a peopling of Europe after the last glacial maximum,
  • Dr. Posth and his colleagues found DNA in Gravettian remains scattered across Europe. The scientists had expected all of the individuals to have come from the same genetic population, but instead found two distinct groups: one in France and Spain, and another in Italy, the Czech Republic and Germany.
  • “They were very distinct, and this was a very big surprise to us because they practiced the same archaeological culture,”
  • Dr. Posth and his colleagues named the western population the Fournol people, and found a genetic link between this group and 35,000-year-old Aurignacian remains in Belgium.
  • They called the eastern group Vestonice, and discovered that they share an ancestry with 34,000-year-old hunter-gatherers who lived in Russia.
  • That genetic gulf led Dr. Posth and his colleagues to argue that the Fournol and Vestonice belonged to two waves that migrated into Europe separately. After they arrived, they lived for several thousand years sharing the Gravettian culture but remaining genetically distinct.
  • It’s clear from the new study that they were not isolated entirely from each other. In Belgium, the scientists found 30,000-year-old remains with a mix of Fournol and Vestonice ancestry.
  • About 26,000 years ago, the two groups faced a new threat to their survival: an advancing wall of glaciers. During the Ice Age, from 26,000 to 19,000 years ago, European hunter-gatherers were shut out of much of the continent, surviving only in southern refuges.
  • the refuge of the Iberian Peninsula, the region now occupied by Spain and Portugal, by studying DNA in the teeth of a 23,000-year-old man found in a cave in southern Spain. His DNA revealed that he belonged to the Fournol people who lived in Iberia before the Ice Age. The researchers also found genetic markers linking him to a 45,000-year-old skeleton discovered in Bulgaria.
  • When these groups arrived in Europe, Neanderthals had already been living across the continent for more than 100,000 years. The Neanderthals disappeared about 40,000 years ago, perhaps because modern humans outcompeted them with superior tools.
  • The Vestonice, by contrast, did not survive the Ice Age. When the glaciers were at their most expansive, the Vestonice may have endured for a time in Italy. But Dr. Posth and his colleagues found no Vestonice ancestry in Europeans after the Ice Age. Instead, they discovered a population of hunter-gatherers that appeared to have expanded from the Balkans, known as the Villabruna. They moved into Italy and replaced the Vestonice.
  • For several thousand years, the Villabruna were limited to southern Europe. Then, 14,000 years ago, they crossed the Alps and encountered the GoyetQ2 people to the north. A new population emerged, its ancestry three parts Villabruna to one part GoyetQ2.
  • This new people, which Dr. Posth and his colleagues called Oberkassel, expanded across much of Europe, replacing the old GoyetQ2 population.
  • another climate shift could explain this new wave. About 14,000 years ago, a pulse of strong warming produced forests across much of Europe. The Oberkassel people may have been better at hunting in forests, whereas the GoyetQ2 retreated with the shrinking steppes.
  • To the east, the Oberkassel ran into a new group of hunter-gatherers, who probably arrived from Russia. The scientists named this group’s descendants, who lived in Ukraine and surrounding regions, the Sidelkino.
  • in Iberia, there were no great sweeps of newcomers replacing older peoples. The Iberians after the Ice Age still carried a great deal of ancestry from the Fournol people who had arrived there thousands of years before the glaciers advanced. The Villabruna people moved into northern Spain, but added their DNA to the mix rather than replacing those who were there before.
  • When the first farmers arrived in Europe from Turkey about 8,000 years ago, three large groups of hunter-gatherers thrived across Europe: the Iberians, the Oberkassel and the Sidelkino. Living Europeans carry some of their gene
  • The Sidelkino people in the east had genes associated with dark eyes and light skin. The Oberkassel in the west, in contrast, probably had blue eyes and may have had dark skin
  • These three groups of hunter-gatherers remained isolated from each other for about 6,000 years, until the farmers from Turkey arrived. After this advent of agriculture, the three groups began mixing, the scientists found. It’s possible that the spread of farmland forced them to move to the margins of Europe to survive. But over time, they were absorbed into the agricultural communities that surrounded them.
  • every continent will likely have its own history of hunter-gatherer migrations.
  • it is now possible to extract human DNA from cave sediments rather than searching for bones and teeth.
Javier E

Opinion | Want to See My Genes? Get a Warrant - The New York Times - 0 views

  • While there may be broad public support for a technique that solved serial murders, just because technology allows for a new type of investigation doesn’t mean the government should be allowed to use it in all cases.
  • 90 percent of Americans of European descent will be identifiable from their DNA within a year or two, even if they have not used a consumer DNA service
  • As for easy access, GEDmatch’s website provides exactly this opportunity. Consumers can take profiles generated from other commercial genetic testing services, upload them free and compare them to other profiles. So can the police.
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  • If the police felt free to use it in an assault case, why not shoplifting, trespassing or littering?
  • When you consent to genetic sleuthing, you are also exposing your siblings, parents, cousins, relatives you’ve never met and even future generations of your family
  • Legitimate consent to the government’s use of an entire family tree should involve more than just a single person clicking “yes” to a website’s terms and conditions.
  • the police usually confirm leads by collecting discarded DNA samples from a suspect. How comfortable should we be that a school resource officer hung around a high school cafeteria waiting to collect a teenager’s “abandoned” DNA?
  • All of these issues point to one problem: Police use of genetic genealogy is virtually unregulated
  • Our genetic and digital identities raise similar questions of autonomy, civil liberties, and intrusion by public and private entities.
  • Rather than wait for the courts to deal with difficult and novel issues about genetic surveillance and privacy, state legislatures and attorneys general should step in and articulate guidelines on how far their law enforcement agencies should go.
aidenborst

Tests Show Genetic Signature of Coronavirus That Likely Infected Trump - The New York T... - 0 views

  • President Trump’s illness from a coronavirus infection last month was the most significant health crisis for a sitting president in nearly 40 years. Yet little remains known about how the virus arrived at the White House and how it spread
  • The administration did not take basic steps to track the outbreak, limiting contact tracing, keeping cases a secret and cutting out the Centers for Disease Control and Prevention. The origin of the infections, a spokesman said, was “unknowable.”
  • The journalists, Michael D. Shear and Al Drago, both had significant, separate exposure to White House officials in late September, several days before they developed symptoms. They did not spend any time near each other in the weeks before their positive tests.
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  • The study reveals, for the first time, the genetic sequence of the virus that may have infected Mr. Trump and dozens of others, researchers said.
  • Viruses constantly mutate, picking up tiny, accidental alterations to their genetic material as they reproduce. Few mutations alter how a virus functions. But by comparing patterns of mutations across many genetic sequences, scientists can construct family trees of a virus, illuminating how it spreads.
  • The genomes believed by these researchers to be connected to the White House outbreak do not identify a recent geographic source, in part because they are unusual.
  • The results show that even weeks after it was identified, the White House outbreak would be better understood by sequencing samples of more people who were infected.
  • In a study released on Thursday, the C.D.C. cited genetic sequencing and intensive contact tracing that documented an super-spreading event at a high school retreat in Wisconsin.
  • But the Trump administration is not known to have conducted its own genetic analysis of people infected in the outbreak. The White House declined to respond to questions on genetic sequencing of Mr. Trump and the cluster of aides and officials who tested positive or became ill.
  • Scientists not involved in the research who reviewed the results agreed with the conclusion that the two samples sharing rare mutations strongly suggested they are part of the same outbreak.
  • “These genomes are probably going to be identical or nearly identical to the genome that infected the president,” said Michael Worobey, head of the department of ecology and evolutionary biology at the University of Arizona.
  • For months, the White House minimized the threat of the virus and eschewed basic safety precautions at official events, like wearing a mask or keeping people six feet apart.
  • At least 11 people who attended a Rose Garden celebration on Sept. 26 for Judge Barrett, which included an indoor event without masks, became infected with the coronavirus, including Mr. Trump.
  • The work is convincing, and it is the best way to piece together the progression of such an outbreak, said David Engelthaler, head of the infectious disease branch of the Translational Genomics Research Institute in Arizona, where he and colleagues have sequenced thousands of genomes to track the spread of the coronavirus, including devastating outbreaks at Native American reservations in the state.
Javier E

A man's discovery of bones under his pub could forever change what we know about the Ir... - 0 views

  • “Celtic” languages were not imports to the region but instead were developed somewhere in the British Isles or the Iberian Peninsula — and then spread eastward into continental Europe.
  • His doubts about the traditional view arose as he was studying inscriptions on artifacts from southern Portugal. The inscriptions on those artifacts strongly resembled the languages known as Celtic, yet they dated as far back as 700 B.C. This placed Celtic languages far from the Celt homelands in the middle of Europe at a very, very early date.
  • “What it shows is that the language that became Irish was already out there — before 700 B.C. and before the Iron Age,” Koch said. “It just didn’t fit with the traditional theory of Celtic spreading west to Britain and Iberia.”
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  • Numerous digs, most notably in Austria and Switzerland, have traced the outlines of the Celts. The artifacts offer evidence going back as far as about 800 B.C. The ancient Greeks and Romans also left written accounts of the Celts, and probably knew them well — the Celts sacked Rome around 390 B.C. and attacked Delphi in Greece in 279 B.C.
  • It seemed plausible that this group that had invaded Rome had invaded Ireland as well, and in the standard view, it was this people that eventually made it to Ireland.
  • For decades, however, archaeologists and other scholars have noted just how flimsy the evidence is for that standard account and how broad, nonetheless, is the application of the word.
  • n recent years, some archaeologists have proposed that the traditional story of the Celts' invasion was, in a sense, exactly wrong — the culture was not imported but exported — originating on the western edge of Europe much earlier than previously thought and spreading into the continent.
  • it flowed from the western edge of Europe, what he calls “the Atlantic zone” — into the rest of the continent. In many places of the Atlantic zone, he notes, people were buried in passages aligned with the solstices, a sign that they shared a unified belief system.
  • “From about 5,000 B.C. onwards, complicated ideas of status, art, cosmology were being disseminated along the Atlantic seaways,” Cunliffe said, and that culture then spread eastward.
  • “If we’re right, the roots of what is known as ‘Celtic’ culture go way way back in time,” Cunliffe said. “And the genetic evidence is going to be an absolute game-changer.”
  • If the new scholarship proves correct, exactly what to do with the word Celtic will probably be a matter of some dispute: Should it be applied to languages or cultures that, no matter how clearly defined, were largely uninfluenced by the historical Celts of continental Europe?
  • Complicating any answer are old ethnic antagonisms: The old notions of a distinct “Celtic race” or “Irish race” have been used not just for poetic tributes, but for scorn.
  • According to the genetic research, the Irish are at the extreme end of a genetic wave that washed across Europe, a wave of migrants that swept westward from above the Black Sea across Europe about 2,500 B.C.
  • The way to think about genetic variation in Europe is that it is more of a gradient than it is of sharp boundaries," said Bradley, the DNA researcher. "Sometimes, cultural features like language and natural borders can coincide with genetics, but most times not. Genetics is fuzzy, and it doesn't follow political and cultural borders."
  • "The public will always want a place on the map and for someone to point and say, 'This where the Irish are from,'
  • "But there’s going to be no way to do that. These groups were frequently traveling east-west across Europe, from one place to another. Everyone is a mix.”
Javier E

DNA Deciphers Roots of Modern Europeans - NYTimes.com - 0 views

  • today’s Europeans descend from three groups who moved into Europe at different stages of history.
  • The first were hunter-gatherers who arrived some 45,000 years ago in Europe. Then came farmers who arrived from the Near East about 8,000 years ago.
  • Finally, a group of nomadic sheepherders from western Russia called the Yamnaya arrived about 4,500 years ago. The authors of the new studies also suggest that the Yamnaya language may have given rise to many of the languages spoken in Europe today.
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  • the new studies were “a major game-changer. To me, it marks a new phase in ancient DNA research.”
  • Until about 9,000 years ago, Europe was home to a genetically distinct population of hunter-gatherers, the researchers found. Then, between 9,000 and 7,000 years ago, the genetic profiles of the inhabitants in some parts of Europe abruptly changed, acquiring DNA from Near Eastern populations.
  • Archaeologists have long known that farming practices spread into Europe at the time from Turkey. But the new evidence shows that it wasn’t just the ideas that spread — the farmers did, too.
  • the Yamnaya, who left behind artifacts on the steppes of western Russia and Ukraine dating from 5,300 to 4,600 years ago. The Yamnaya used horses to manage huge herds of sheep, and followed their livestock across the steppes with wagons full of food and water.
  • “You have groups which are as genetically distinct as Europeans and East Asians. And they’re living side by side for thousands of years.”
  • Between 7,000 and 5,000 years ago, however, hunter-gatherer DNA began turning up in the genes of European farmers. “There’s a breakdown of these cultural barriers, and they mix,”
  • About 4,500 years ago, the final piece of Europe’s genetic puzzle fell into place. A new infusion of DNA arrived — one that is still very common in living Europeans, especially in central and northern Europe.
  • The closest match to this new DNA, both teams of scientists found, comes from skeletons found in Yamnaya graves in western Russia and Ukraine.
  • The hunter-gatherers didn’t disappear, however. They managed to survive in pockets across Europe between the farming communities.
  • it was likely that the expansion of Yamnaya into Europe was relatively peaceful. “It wasn’t Attila the Hun coming in and killing everybody,”
  • the most likely scenario was that the Yamnaya “entered into some kind of stable opposition” with the resident Europeans that lasted for a few centuries. But then gradually the barriers between the cultures eroded.
  • the Yamnaya didn’t just expand west into Europe, however. The scientists examined DNA from 4,700-year-old skeletons from a Siberian culture called the Afanasievo. It turns out that they inherited Yamnaya DNA, too.
  • was surprised by the possibility that Yamnaya pushed out over a range of about 4,000 miles. “
  • For decades, linguists have debated how Indo-European got to Europe. Some favor the idea that the original farmers brought Indo-European into Europe from Turkey. Others think the language came from the Russian steppes thousands of years later.
  • he did think the results were consistent with the idea that the Yamnaya brought Indo-European from the steppes to Europe.
  • The eastward expansion of Yamnaya, evident in the genetic findings, also supports the theory, Dr. Willerslev said. Linguists have long puzzled over an Indo-European language once spoken in western China called Tocharian. It is only known from 1,200-year-old manuscripts discovered in ancient desert towns. It is possible that Tocharian was a vestige of the eastern spread of the Yamnaya.
  • the new studies were important, but were still too limited to settle the debate over the origins of Indo-European. “I don’t think we’re there yet,” he said.
  • Dr. Heggarty speculated instead that early European farmers, the second wave of immigrants, may have brought Indo-European to Europe from the Near East. Then, thousands of years later, the Yamnaya brought the language again to Central Europe.
Javier E

Stop Making Us Guinea Pigs - NYTimes.com - 0 views

  • the International Agency for Research on Cancer declared that glyphosate, the active ingredient in the widely used herbicide Roundup, probably causes cancer in humans. Two insecticides, malathion and diazinon, were also classified as “probable” carcinogens by the agency
  • an announcement by the Food and Drug Administration that new breeds of genetically engineered potato and apple are safe to eat. Which they probably are, as are the genetically engineered papayas we’ve been eating for some time. In fact, to date there’s little credible evidence that any food grown with genetic engineering techniques is dangerous to human health
  • unlike Europeans, Canadians, Australians and others, we don’t subscribe to the precautionary principle, which maintains that it’s better to prevent damage than repair it.
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  • We ask not whether a given chemical might cause cancer but whether we’re certain that it does. Since it’s unethical to test the effects of new chemicals and food additives on humans, we rely on the indirect expedient of extensive and expensive animal testing
  • t the job of the F.D.A. should be to guarantee a reasonable expectation of protection from danger, not to wait until people become sick before taking products off the market
  • Even now, when it’s clear that more research must be done to determine to what degree glyphosate may be carcinogenic, it’s not clear whose responsibility it is to conduct that research.
  • Or — here’s an idea — how about Monsanto, which has made billions of dollars selling glyphosate and the associated seed technology.
  • While we’re at it, let’s finally start labeling products made with genetically engineered food
  • If G.M.O.s were largely beneficial to eaters, manufacturers would proudly boast of products containing them. The fact is that they have not.
  • We don’t need better, smarter chemicals along with crops that can tolerate them; we need fewer chemicals. And it’s been adequately demonstrated that crop rotation, the use of organic fertilizers, interplanting of varieties of crops, and other ecologically informed techniques commonly grouped together under the term “agroecology” can effectively reduce the use of chemicals.
katyshannon

'Anti-malarial mosquitoes' created using controversial genetic technology | Science | T... - 0 views

  • Hundreds of genetically modified mosquitoes that are incapable of spreading the malaria parasite to humans have been created in a laboratory as part of a radical approach to combating the disease.
  • The move marks a major step towards the development of a powerful and controversial technology called a “gene drive” that aims to tackle the disease by forcing anti-malarial genes into swarms of wild mosquitoes.
  • The procedure can rapidly transform the genetic makeup of natural insect populations, making it a dramatic new tool in the fight against an infection that still claims over 400,000 lives a year. The same technology is being considered for other human diseases and infections that devastate crops.
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  • They call on scientists to ensure that experimental organisms cannot escape from their labs, be released on purpose, or even find their way out accidentally in the event of a natural disaster. Researchers should also be open about the precautions they take to prevent an unintended release, they said.
  • But gene drive technology is so powerful that leading researchers have urged scientists in the field to be cautious. A warning published in August in the prestigious journal Science, by teams in the UK, US, Australia and Japan, said that while gene drives have the potential to save lives and bring other benefits, the accidental release of modified organisms “could have unpredictable ecological consequences.”
  • In the latest study, mosquitoes were engineered to carry genes for antibodies that target the human malaria parasite, Plasmodium falciparum. When released into the wild, researchers believe the modified insects will breed with normal mosquitoes and pass the anti-malarial genes on to their young, making an ever-increasing proportion of future generations resistant to the malaria parasite.
  • In lab tests, the modified mosquitoes passed on their anti-malarial genes to 99.5% of their offspring, suggesting that the procedure was incredibly effective and efficient. To track which insects inherited the antibody genes, the scientists added a tracer gene that gave carriers red fluorescent eyes.
Javier E

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

  • 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.
yehbru

Two New Laws Restrict Police Use of DNA Search Method - The New York Times - 0 views

  • Maryland and Montana have passed the nation’s first laws limiting forensic genealogy, the method that found the Golden State Killer.
  • New laws in Maryland and Montana are the first in the nation to restrict law enforcement’s use of genetic genealogy, the DNA matching technique that in 2018 identified the Golden State Killer, in an effort to ensure the genetic privacy of the accused and their relatives.
  • Beginning on Oct. 1, investigators working on Maryland cases will need a judge’s signoff before using the method, in which a “profile” of thousands of DNA markers from a crime scene is uploaded to genealogy websites to find relatives of the culprit
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  • The new law, sponsored by Democratic lawmakers, also dictates that the technique be used only for serious crimes, such as murder and sexual assault. And it states that investigators may only use websites with strict policies around user consent.
  • The laws “demonstrate that people across the political spectrum find law enforcement use of consumer genetic data chilling, concerning and privacy-invasive,” said Natalie Ram, a law professor at the University of Maryland who championed the Maryland law
  • “This bill strikes a balance between this very important technology to identify people that do the very worst things to our Marylanders, yet it balances that against the privacy concerns and the trust that we need from the public,” John Fitzgerald, the chief of the Chevy Chase Village Police Department
  • For one thing, the law states that by 2024, genealogists working on such cases must be professionally certified — a credential that does not yet exist.
  • Investigators may use only genealogy companies that have explicitly informed the public and their customers that law enforcement uses their databases, and that have asked for their customers’ consent to participate.
  • “We know well that most people do not read these kinds of forms closely,” Ms. Ram said. “This is likely to generate unwitting inclusion rather than actual consent.”
  • Unlike 23andMe and Ancestry, which have kept their immense genetic databases unavailable to law enforcement without a court order, GEDmatch and FamilyTreeDNA are eager to cooperate
  • Investigators cannot use any of the genetic information collected, whether from the suspect or third parties, to learn about a person’s psychological traits or disease predispositions
  • These searches are “the equivalent of the government going through all of your medical records and all of your family records just to identify you,” said Leah Larkin
criscimagnael

In a First, Man Receives a Heart From a Genetically Altered Pig - The New York Times - 0 views

  • A 57-year-old man with life-threatening heart disease has received a heart from a genetically modified pig, a groundbreaking procedure that offers hope to hundreds of thousands of patients with failing organs.
  • “This is a watershed event,” said Dr. David Klassen, the chief medical officer of the United Network for Organ Sharing and a transplant physician. “Doors are starting to open that will lead, I believe, to major changes in how we treat organ failure.”
  • It creates the pulse, it creates the pressure, it is his heart,
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  • It’s working and it looks normal. We are thrilled, but we don’t know what tomorrow will bring us. This has never been done before
  • Last year, some 41,354 Americans received a transplanted organ, more than half of them receiving kidneys,
  • But there is an acute shortage of organs, and about a dozen people on the lists die each day. Some 3,817 Americans received human donor hearts last year as replacements, more than ever before, but the potential demand is still higher.
  • Researchers hope procedures like this will usher in a new era in medicine in the future when replacement organs are no longer in short supply for the more than half a million Americans who are waiting for kidneys and other organs.
  • He is also being monitored for infections, including porcine retrovirus, a pig virus that may be transmitted to humans, although the risk is considered low.
  • But he added that there were many hurdles to overcome before such a procedure could be broadly applied, noting that rejection of organs occurs even when a well-matched human donor kidney is transplanted.
  • It takes a long time to mature a therapy like this.”
  • Mr. Bennett decided to gamble on the experimental treatment because he would have died without a new heart, had exhausted other treatments and was too sick to qualify for a human donor heart, family members and doctors said.
  • Mr. Bennett is still connected to a heart-lung bypass machine, which was keeping him alive before the operation, but that is not unusual for a new heart transplant recipient, experts said.
  • The new heart is functioning and already doing most of the work, and his doctors said he could be taken off the machine on Tuesday. Mr. Bennett is being closely monitored for signs that his body is rejecting the new organ, but the first 48 hours, which are critical, passed without incident.
  • It is the first successful transplant of a pig’s heart into a human being. The eight-hour operation took place in Baltimore on Friday, and the patient, David Bennett Sr. of Maryland, was doing well on Monday, according to surgeons at the University of Maryland Medical Center.
  • Xenotransplantation, the process of grafting or transplanting organs or tissues from animals to humans, has a long history. Efforts to use the blood and skin of animals go back hundreds of years.
  • In the 1960s, chimpanzee kidneys were transplanted into some human patients, but the longest a recipient lived was nine months.
  • In 1983, a baboon heart was transplanted into an infant known as Baby Fae, but she died 20 days later.
  • Two newer technologies — gene editing and cloning — have yielded genetically altered pig organs less likely to be rejected by humans.
  • the time to carry out better screening for infectious diseases, and the possibility of a new organ at the time that the patient needs it.
  • The heart transplanted into Mr. Bennett came from a genetically altered pig provided by Revivicor, a regenerative medicine company based in Blacksburg, Va.
  • The pig had 10 genetic modifications. Four genes were knocked out, or inactivated, including one that encodes a molecule that causes an aggressive human rejection response.
  • A growth gene was also inactivated to prevent the pig’s heart from continuing to grow after it was implanted,
  • In addition, six human genes were inserted into the genome of the donor pig — modifications designed to make the porcine organs more tolerable to the human immune system.
  • The team used a new experimental drug developed in part by Dr. Mohiuddin and made by Kiniksa Pharmaceuticals to suppress the immune system and prevent rejection.
  • “The anatomy was a little squirrelly, and we had a few moments of ‘uh-oh’ and had to do some clever plastic surgery to make everything fit,”
  • “the heart fired right up” and “the animal heart began to squeeze.”
  • He said his father had had a pig’s valve inserted about a decade ago, and he thought his father might be confused. But after a while, Mr. Bennett said, “I realized, ‘Man, he is telling the truth and not going crazy. And he could be the first ever.’”
Javier E

Did the First Americans Arrive via Land Bridge? This Geneticist Says No. - The New York... - 0 views

  • In her new book, “Origin: A Genetic History of the Americas,” Raff beautifully integrates new data from different sciences (archaeology, genetics, linguistics) and different ways of knowing, including Indigenous oral traditions, in a masterly retelling of the story of how, and when, people reached the Americas.
  • Raff skillfully reveals how well-dated archaeological sites, including recently announced 22,000-year-old human footprints from White Sands, N.M., are at odds with the Clovis first hypothesis.
  • the path to the Americas was coastal (the Kelp Highway hypothesis) rather than inland, and that Beringia was not a bridge but a homeland — twice the size of Texas — inhabited for millenniums by the ancestors of the First Peoples of the Americas.
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  • Raff effectively models how science is done, how hypotheses are tested, and how new data are used to refute old ideas and generate new ones.
  • Raff takes the reader from underground caverns in Belize to a clean lab at the University of Kansas where ancient DNA is tediously teased from old bones. She explains difficult to understand concepts — geoarchaeology, coalescence times, biodistance — with well-placed sidebars. The book is richly referenced, and informative footnotes and endnotes give readers an opportunity to take a deeper dive if they wish.
  • Given the fast and furious pace of discovery in this field, Raff is clear that not everyone will agree with her interpretations of the data. “All scientists must hold themselves open to the possibility that we could be wrong, and it may very well be that in five, 10 or 20 years, this book will be as out of date as any other,” she writes. “That possibility is what makes working in this field so rewarding.” That, she explains, is how science is done.
  • Jennifer Raff is a well-published scholar and accomplished scientific communicator who has contributed important insights into the genetic history and movement patterns of Indigenous Americans. She is at the forefront of a culture change in our science. And now she has written the book anyone interested in the peopling of the Americas must read.
Javier E

Common Ancestor of Mammals Plucked From Obscurity - NYTimes.com - 0 views

  • Humankind’s common ancestor with other mammals may have been a roughly rat-size animal that weighed no more than a half a pound, had a long furry tail and lived on insects.
  • In a comprehensive six-year study of the mammalian family tree, scientists have identified and reconstructed what they say is the most likely common ancestor of the many species on the most abundant and diverse branch of that tree — the branch of creatures that nourish their young in utero through a placenta. The work appears to support the view that in the global extinctions some 66 million years ago, all non-avian dinosaurs had to die for mammals to flourish.
  • a combination of genetic and anatomical data established that the ancestor emerged within 200,000 to 400,000 years after the great dying at the end of the Cretaceous period. At the time, the meek were rapidly inheriting the earth from hulking predators like T. rex.
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  • Within another two million to three million years, Dr. O’Leary said, the first members of modern placental orders appeared in such profusion that researchers have started to refer to the explosive model of mammalian evolution
  • Although some small primitive mammals had lived in the shadow of the great Cretaceous reptiles, the scientists could not find evidence supporting an earlier hypothesis that up to 39 placental mammalian lineages survived to enter the post-extinction world. Only the stem lineage to Placentalia, they said, appeared to hang on through the catastrophe, generally associated with climate change after an asteroid crashed into Earth.
  • the “power of 4,500 characters” enabled the scientists to look “at all aspects of mammalian anatomy, from the skull and skeleton, to the teeth, to internal organs, to muscles and even fur patterns” to determine what the common ancestor possibly looked like.
  • this formidable new systematic data-crunching capability might reshape mammal research but that it would probably not immediately resolve the years of dispute between fossil and genetic partisans over when placental mammals arose. Paleontologists looking for answers in skeletons and anatomy have favored a date just before or a little after the Cretaceous extinction. Those who work with genetic data to tell time by “molecular clocks” have arrived at much earlier origins.
  • the post-Cretaceous date for the placentals “will surely be controversial, as this is much younger than estimates based on molecular clocks, and implies the compression of very long molecular branches at the base of the tree.”
Javier E

Ice Age Europeans had some serious drama going on, according to their genomes - The Was... - 0 views

  • before researchers could start analyzing that genetic material, they had to get it. DNA degrades over time, so extracting it from ancient human remains is difficult and costly.
  • In the end, they had data from 51 individuals — a tenfold increase over the measly four that once gave researchers their only glimpses into this period.
  • "Trying to represent this vast period of European history with just four samples is like trying to summarize a movie with four still images," Reich said. "With 51 samples, everything changes; we can follow the narrative arc; we get a vivid sense of the dynamic changes over time.
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  • One of the oldest genomes studied came from a thigh bone discovered in Goyet Cave in Belgium and given the unwieldy name GoyetQ116-1. Radiocarbon dating pegs the Goyet individual at some 35,000 years old,
  • Around 1,000 years after the Goyet individual was found, a new culture swept through Europe: the Gravettians. Analysis of genetic material from the time shows that art and artifacts weren't the only things changing. The Gravettians' DNA was significantly different from their Aurignacian predecessors, suggesting that they were a completely separate lineage.
  • Goyet guy's descendants retreated to the Iberian Peninsula (modern day Spain and Portugal) and waited for their time to come again.
  • It did, some 15,000 years later. Probably spurred by climate changes as glaciers began to recede, this dormant lineage expanded back into the rest of Europe, bearing a new culture known as Magdalenian.
  • Not long after that, their genomes started to look like those of people from the Middle East and the Caucasus, suggesting that new arrivals from the southeast were mingling with — and in some cases supplanting — the existing population.
  • This was a surprise, because researchers used to think that transition happened much later, when Turkish farmers introduced agriculture to Europe some 8,500 years ago.
  • The genetic analysis allowed researchers to trace the inexorable decline of Neanderthal DNA, which was two to three times more prominent in early human genomes than it is in modern-day ones. This supports theories that early humans interbred with Neanderthals, but that their DNA was toxic to us and gradually weeded out by natural selection over the course of millennia.
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