Group items tagged

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,

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.”

the cost to collect molecular data from each blood sample was about $2,500 — which did not include the cost of analysis. But the price for tests similar to Dr. Snyder’s will also decline in the future

Dr. Church looks forward to the day when current research becomes a routine clinical procedure that combines inherited genomic information with analyses of RNA, proteins, metabolites and microbes in our bodies.

Dr. Snyder is a co-founder of a company, Personalis, in Palo Alto, Calif., that is developing software and other tools to interpret genomes after sequencing

The primary resource for detailing the path of human evolution will always be fossil specimens.

In devising such scenarios and filling in the human family bush, researchers must consult a large and diverse array of fossils, and they must also employ refined excavation methods and records, geochemical dating techniques, and data from other specialized fields such as genetics, ecology and paleoecology, and ethology (animal behaviour)—in short, all the tools of the multidisciplinary science of paleoanthropology.

It is generally agreed that the taproot of the human family shrub is to be found among apelike species of the Middle Miocene Epoch (roughly 16–11.6 mya) or Late Miocene Epoch (11.6–5.3 mya). Genetic data based on molecular clock estimates support a Late Miocene ancestry. Various Eurasian and African Miocene primates have been advocated as possible ancestors to the early hominins, which came on the scene during the Pliocene Epoch (5.3–2.6 mya)

the Clovis model was recently bolstered by new DNA analysis ancestrally connecting indigenous peoples in Central and South America to a boy from the Clovis culture whose 12,700-year-old remains were found in 1968 at a site in Montana.

she said she believed that humans had reached these plateaus even earlier, around 100,000 years ago, and might have come not overland from Asia but by boat from Africa.

Professor Boëda, who succeeded Dr. Guidon in leading the excavations, said that such early dates may have been possible but that more research was needed. His team is using thermoluminescence, a technique that measures the exposure of sediments to sunlight, to determine their age.

In what may be another blow to the Clovis model of humans’ coming from northeast Asia, molecular geneticists showed last year that the Botocudo indigenous people living in southeastern Brazil in the late 1800s shared gene sequences commonly found among Pacific Islanders from Polynesia.

How could Polynesians have made it to Brazil? Or aboriginal Australians? Or, if the archaeologists here are correct, how could a population arrive in this hinterland long before Clovis hunters began appearing in the Americas? The array of new discoveries has scholars on a quest for answers.

But he added that if the results obtained here in Serra da Capivara are accurate, they will raise even more questions about how the Americas were settled.“If so, then whoever lived there never passed on their genetic material to living populations,” said Dr. Waters, explaining how the genetic history of indigenous peoples links them to the Clovis child found in Montana. “We must think long and hard about these early sites and how they fit into the picture of the peopling of the Americas.”

“I’m old enough to know that when somebody says words like ‘never,’ or ‘forever,’ or ‘the rest of eternity’ in the Middle East, it usually means something like six months to 30 years. If anyone had said to me as a young man that one day I would travel to Egypt or Jordan with Egyptian and Jordanian visas stamped in my passport, I would have said, ‘Let’s not get carried away.' ”

“I have seen people change. They are not born again but they change, somewhat.

There is intriguing neuroscience research that suggests that it may be possible to boost the efficacy of psychotherapy with drugs that share some of ketamine’s effects, somewhat the way athletes can enhance their performance with steroids

How might this work? D-cycloserine is an antibiotic that, like ketamine, increases the activity of glutamate in key brain regions, which promotes connections between neurons. It seems to amp up the molecular machinery of learning. And psychotherapy is all about learning — to overcome fear and to better handle stress, among other lessons.

For decades, psychoanalysts were against medicating anxiety at all, because they believed it would interfere with the therapeutic process. Fortunately, those days are largely over. Many are now comfortable giving patients anti-anxiety benzodiazepines like Klonopin if they are having a hard time grappling with issues that arise in therapy.

While conspiracy theories might falsely claim the virus was concocted in a lab, the virus’s genome makes clear that it arose in bats.

Sophisticated computer programs can then figure out how all of those mutations arose as viruses descended from a common ancestor. If they get enough data, they can make rough estimates about how long ago those ancestors lived. That’s because mutations arise at a roughly regular pace, like a molecular clock.

Tracking viral mutations demands sequencing all the genetic material in a virus — its genome. Once researchers have gathered the genomes from a number of virus samples, they can compare their mutations.

In January, a team of Chinese and Australian researchers published the first genome of the new virus. Since then, researchers around the world have sequenced over 3,000 more. Some are genetically identical to each other, while others carry distinctive mutations.

The most closely related coronavirus is in a Chinese horseshoe bat, the researchers found. But the new virus has gained some unique mutations since splitting off from that bat virus decades ago.

Dr. Boni said that ancestral virus probably gave rise to a number of strains that infected horseshoe bats, and perhaps sometimes other animals.

It’s entirely possible, Dr. Boni said, in the past 10 or 20 years, a hybrid virus arose in some horseshoe bat that was well-suited to infect humans, too. Later, that virus somehow managed to cross the species barrier.

already, the genomes of the virus are revealing previously hidden outlines of its history over the past few months.

While the coronavirus mutations are useful for telling lineages apart, they don’t have any apparent effect on how the virus works.

The deepest branches of the tree all belong to lineages from China. The Nextstrain team has also used the mutation rate to determine that the virus probably first moved into humans from an animal host in late 2019.

In January, as the scope of the catastrophe in China became clear, a few countries started an aggressive testing program. They were able to track the arrival of the virus on their territory and track its spread through their populations.

But the United States fumbled in making its first diagnostic kits and initially limited testing only to people who had come from China and displayed symptoms of Covid-19.“It was a disaster that we didn’t do testing,”

As new cases arose in other parts of the country, other researchers set up their own pipelines. The first positive test result in New York came on March 1, and after a couple of weeks, patients surged into the city’s hospitals.

Dr. Heguy and her colleagues found some New York viruses that shared unique mutations not found elsewhere. “That’s when you know you’ve had a silent transmission for a while,”

And researchers at Mount Sinai started sequencing the genomes of patients coming through their hospital. They found that the earliest cases identified in New York were not linked to later ones.“Two weeks later, we start seeing viruses related to each other,”

Dr. Gonzalez-Reiche and her colleagues found that these viruses were practically identical to viruses found around Europe.

hey write that the viruses reveal “a period of untracked global transmission between late January to mid-February.”

Dr. van Bakel and his colleagues found one New York virus that was identical to one of the Washington viruses found by Dr. Bedford and his colleagues. In a separate study, researchers at Yale found another Washington-related virus. Combined, the two studies hint that the coronavirus has been moving from coast to coast for several weeks.

Dr. Boni and his colleagues found that the genome of the new virus contains a number of mutations in common with strains of coronaviruses that infect bats.

Some viruses evolve so quickly that they require vaccines that can produce several different antibodies. That’s not the case for Covid-19. Like other coronaviruses, it has a relatively slow mutation rate compared to some viruses, like influenza.

these are central to our national well-being. Our lives are threatened less by the Taliban in Afghanistan than by unregulated contaminants at home.

Initially, this concept was highly controversial among obesity experts, but a growing number of peer-reviewed studies have confirmed his finding and identified some 20 substances as obesogens.

The most important time for exposure appears to be in utero and in childhood. It’s not clear whether most obesogens will do much to make an ordinary adult, even a pregnant woman, fatter (although one has been shown to do so), and the greatest impact seems to be on fetuses and on children before puberty.

In this case, a starting point would be to boost research of endocrine disruptors and pass the Safe Chemicals Act. That measure, long stalled in Congress, would require more stringent safety testing of potentially toxic chemicals around us.

Science-based decisions to improve public health — like the removal of lead from gasoline — have been among our government’s most beneficial public policy moves

Dr. Blumberg, the pioneer of the field, says he strongly recommends that people — especially children and women who are pregnant or may become pregnant — try to eat organic foods to reduce exposure to endocrine disruptors, and try to avoid using plastics to store food or water. “My daughter uses a stainless steel water bottle, and so do I,” he said.

Endocrine disruptors are a class of chemicals that mimic hormones and therefore confuse the body. Initially, they provoked concern because of their links to cancers and the malformation of sex organs. Those concerns continue, but the newest area of research is the impact that they have on fat storage.

The role of these chemicals has been acknowledged by the presidential task force on childhood obesity, and the National Institutes of Health has become a major funder of research on links between endocrine disruptors and both obesity and diabetes.

Just this month, a new study in the journal Environmental Health Perspectives found that endocrine disruptors that are sometimes added to PVC plastic cause mice to grow obese and suffer liver problems — and the effect continues with descendants of those mice, generation after generation.

instead of allowing it to cement racialized ways of thinking, we can use these tests to highlight how meaningless genetic ancestry is compared with the many other factors that shape our experience of ourselves and our communities.

For most of human history, the concept of peoplehood — of belonging to a group larger than one’s extended family — has been largely determined by shared cultural practices (such as religion, customs and language) or political institutions.

This more capacious notion of belonging is how heritage is lived day to day for most people. I didn’t need a DNA test to identify as a Jew of European ancestry.

race science got a new lease on life when, in the 1950s, scientists discovered the molecular structure of DNA. By the 1980s DNA testing could reliably prove paternity

More than 26 million people are estimated to have taken genealogical DNA tests.

The answer goes back to the 18th and 19th centuries, when European colonialism and the slave trade birthed the modern concept of race.

As societies were built and genocides committed on the basis of racial hierarchy, it became imperative for racists to prove the biological existence of race. And so race “science” emerged, seeking to dislodge cultural heritage as the prime difference between groups of people.

“Aryan” became synonymous with “German,” excluding the many Jewish and Slavic speakers of the language.

et, no matter how strong it was, this sense of cultural heritage didn’t feel like enough for me. In a society that determines so much based on blood — money, connections, assumptions about character — culture by itself felt like an unreliable narrator of my identity.

Ironically, as academics were reaching the consensus that race is a social construct with no basis in biology — about 94 percent of human genetic variation occurs within so-called racial groups, with racial difference accounting for only 6 percent — the popularity of DNA testing was helping undermine that very idea.

almost 53 percent of Americans think biology at least somewhat determines their racial identity

Two-thirds of white Americans believe that their racial identity is determined by their DNA, compared with about half of black, Latino and Asian Americans

Only 35 percent of those surveyed believe that shared history or culture determines their racial identity.

DNA tests merely compare patterns in your genome with those of groups of people who have been identified as belonging to different ethnicities based on traditional genealogical research (vital records, family trees, etc.)

“If your 23andMe test says you’re 29 percent British, it’s because 29 percent of the pieces of your DNA were most likely to have come from a group that 23andMe’s reference library has labeled ‘British.’ ”

This means ethnicity estimates from companies like 23andMe and AncestryDNA tell a much narrower story than consumers — led along by marketing campaigns — read into them

such estimates are only as good as the companies’ pattern-matching algorithms and DNA reference libraries, which can be incomplete and haphazardly assembled

In fact, these companies’ ethnicity estimates for the same person can vary substantially.

In a society that continues to structure lives along the hierarchy of race, it is difficult to leave behind the reassuring neatness of blood ancestry — of, in an age of turbulence and uncertainty, knowing exactly and objectively who we are — for the reality of mixing, moving and contradiction that makes up our history on this planet.

As Chuck Hoskin Jr., then the Cherokee Nation’s secretary of state, wrote in response to Warren’s DNA testing controversy, “We are [tribal] citizens through historical documentation, adopted laws and a shared language and culture that make us unique.” DNA tests, he said, are “useless to determine tribal citizenship.”

Pfizer’s vaccine also contains nine other ingredients. Four of them are lipids with impossibly complex chemical names: (4-hydroxybutyl)azanediyl)bis(hexane-6,1-diyl)bis (ALC-3015); (2- hexyldecanoate),2-[(polyethylene glycol)-2000]-N,N-ditetradecylacetamide (ALC-0159); 1,2-distearoyl-snglycero-3-phosphocholine (DPSC); and cholesterol.

The vaccine also contains four salts: potassium chloride, monobasic potassium phosphate, basic sodium phosphate dihydrate and sodium chloride.

The key issue is not “human-competitive” intelligence (as the open letter puts it); it’s what happens after AI gets to smarter-than-human intelligence. Key thresholds there may not be obvious, we definitely can’t calculate in advance what happens when, and it currently seems imaginable that a research lab would cross critical lines without noticing.

Many researchers steeped in these issues, including myself, expect that the most likely result of building a superhumanly smart AI, under anything remotely like the current circumstances, is that literally everyone on Earth will die. Not as in “maybe possibly some remote chance,” but as in “that is the obvious thing that would happen.”

It’s not that you can’t, in principle, survive creating something much smarter than you; it’s that it would require precision and preparation and new scientific insights, and probably not having AI systems composed of giant inscrutable arrays of fractional numbers.

Absent that caring, we get “the AI does not love you, nor does it hate you, and you are made of atoms it can use for something else.”

Without that precision and preparation, the most likely outcome is AI that does not do what we want, and does not care for us nor for sentient life in general. That kind of caring is something that could in principle be imbued into an AI but we are not ready and do not currently know how.

The likely result of humanity facing down an opposed superhuman intelligence is a total loss

To visualize a hostile superhuman AI, don’t imagine a lifeless book-smart thinker dwelling inside the internet and sending ill-intentioned emails. Visualize an entire alien civilization, thinking at millions of times human speeds, initially confined to computers—in a world of creatures that are, from its perspective, very stupid and very slow. A sufficiently intelligent AI won’t stay confined to computers for long. In today’s world you can email DNA strings to laboratories that will produce proteins on demand, allowing an AI initially confined to the internet to build artificial life forms or bootstrap straight to postbiological molecular manufacturing.

There’s no proposed plan for how we could do any such thing and survive. OpenAI’s openly declared intention is to make some future AI do our AI alignment homework. Just hearing that this is the plan ought to be enough to get any sensible person to panic. The other leading AI lab, DeepMind, has no plan at all.

An aside: None of this danger depends on whether or not AIs are or can be conscious; it’s intrinsic to the notion of powerful cognitive systems that optimize hard and calculate outputs that meet sufficiently complicated outcome criteria.

I didn’t also mention that we have no idea how to determine whether AI systems are aware of themselves—since we have no idea how to decode anything that goes on in the giant inscrutable arrays—and therefore we may at some point inadvertently create digital minds which are truly conscious and ought to have rights and shouldn’t be owned.

I refrained from signing because I think the letter is understating the seriousness of the situation and asking for too little to solve it.

the thing about trying this with superhuman intelligence is that if you get that wrong on the first try, you do not get to learn from your mistakes, because you are dead. Humanity does not learn from the mistake and dust itself off and try again, as in other challenges we’ve overcome in our history, because we are all gone.

If we held anything in the nascent field of Artificial General Intelligence to the lesser standards of engineering rigor that apply to a bridge meant to carry a couple of thousand cars, the entire field would be shut down tomorrow.

We are not on course to be prepared in any reasonable time window. There is no plan. Progress in AI capabilities is running vastly, vastly ahead of progress in AI alignment or even progress in understanding what the hell is going on inside those systems

Many researchers working on these systems think that we’re plunging toward a catastrophe, with more of them daring to say it in private than in public; but they think that they can’t unilaterally stop the forward plunge, that others will go on even if they personally quit their jobs.

This is a stupid state of affairs, and an undignified way for Earth to die, and the rest of humanity ought to step in at this point and help the industry solve its collective action problem.

When the insider conversation is about the grief of seeing your daughter lose her first tooth, and thinking she’s not going to get a chance to grow up, I believe we are past the point of playing political chess about a six-month moratorium.

The moratorium on new large training runs needs to be indefinite and worldwide. There can be no exceptions, including for governments or militaries. If the policy starts with the U.S., then China needs to see that the U.S. is not seeking an advantage but rather trying to prevent a horrifically dangerous technology which can have no true owner and which will kill everyone in the U.S. and in China and on Earth

Here’s what would actually need to be done:

Shut down all the large GPU clusters (the large computer farms where the most powerful AIs are refined). Shut down all the large training runs

Put a ceiling on how much computing power anyone is allowed to use in training an AI system, and move it downward over the coming years to compensate for more efficient training algorithm

Track all GPUs sold. If intelligence says that a country outside the agreement is building a GPU cluster, be less scared of a shooting conflict between nations than of the moratorium being violated; be willing to destroy a rogue datacenter by airstrike.

Frame nothing as a conflict between national interests, have it clear that anyone talking of arms races is a fool

Make it explicit in international diplomacy that preventing AI extinction scenarios is considered a priority above preventing a full nuclear exchange, and that allied nuclear countries are willing to run some risk of nuclear exchange if that’s what it takes to reduce the risk of large AI training runs.

when your policy ask is that large, the only way it goes through is if policymakers realize that if they conduct business as usual, and do what’s politically easy, that means their own kids are going to die too.