One of the more striking discoveries of recent years has been the revelation that most modern non-sub-Saharan African human beings typically have inherited a small but not insignificant part of their genome from otherwise extinct Neanderthals.

At the end of the 20th Century, scientific orthodoxy was that modern humans were 100% descended from the anatomically modern species that arose in Africa and spread all over the world, with Neanderthals going extinct. This not unreasonable “Out-of-Africa” orthodoxy soon metastasized, probably starting with 2000 speeches in the White House Rose Garden by Bill Clinton, Craig Venter, and Francis Collins celebrating the Human Genome Project into the current anti-science “Race Does Not Exist” dogma.

The new understanding of the role of Neanderthals, however, was largely forecast back in the late 20th Century by Gregory Cochran, who argued that, having spent several hundred thousand years evolving at higher latitudes in Europe, Neanderthals would have evolved certain more sophisticated adaptations to local conditions (such as cold winters) that the invading out-of-Africa peoples would have acquired through a limited amount of interbreeding.

If I recall correctly, Cochran, however, didn’t forecast that modern sub-Saharan Africans would turn out to be almost completely lacking in Neanderthal genes. That’s one of the striking racial differences between the two main races on earth: sub-Saharans and everybody else.

The current scientific understanding is that the two fundamental racial groups are the Out-of-Africa people and the Not-Out-of-Africa people (i.e., Sub-Saharans). (Interestingly, the old Multiregionalist Carleton Coon failed to anticipate that. He figured from looking at bones that African blacks and European whites were more closely related to each other than whites were to East Asians. Coon figured the mountains of Central Asia were humanity’s fundamental division, but it turned out to be the Sahara.)

Now, you might think that it’s pretty interesting that Greg Cochran underestimated the amount of genetic racial difference between blacks and everybody else when otherwise correctly forecasting results about a decade before they became technologically feasible to discover.

But here are bits of a very long article in the New York Times Magazine that skips over the disturbing parts about racial differences among modern humans to put the Neanderthal story in a more comfortable setting in which the bad guys are old-fashioned white racist scientists and their deplorable descendants who voted for Brexit.

It’s a pretty good example of how to reframe and spin a bunch of unsettling facts to make NYT subscribers feel even smugger about themselves.

Neanderthals Were People, Too

New research shows they shared many behaviors that we long believed to be uniquely human. Why did science get them so wrong?

By JON MOOALLEM JAN. 11, 2017

Joachim Neander was a 17th-century Calvinist theologian who often hiked through a valley outside Düsseldorf, Germany, writing hymns. Neander understood everything around him as a manifestation of the Lord’s will and work. There was no room in his worldview for randomness, only purpose and praise. “See how God this rolling globe/swathes with beauty as a robe,” one of his verses goes. “Forests, fields, and living things/each its Master’s glory sings.” He wrote dozens of hymns like this — awe-struck and simple-minded. Then he caught tuberculosis and died at 30.

Almost two centuries later, in the summer of 1856, workers quarrying limestone in that valley dug up an unusual skull. …

One British geologist, William King, suspected something more radical. Instead of being the remains of an atypical human, they might have belonged to a typical member of an alternate humanity. In 1864, he published a paper introducing it as such — an extinct human species, the first ever discovered. King named this species after the valley where it was found, which itself had been named for the ecstatic poet who once wandered it. He called it Homo neanderthalensis: Neanderthal Man.

Who was Neanderthal Man? King felt obligated to describe him. But with no established techniques for interpreting archaeological material like the skull, he fell back on racism and phrenology. He focused on the peculiarities of the Neanderthal’s skull, including the “enormously projecting brow.” No living humans had skeletal features remotely like these, but King was under the impression that the skulls of contemporary African and Australian aboriginals resembled the Neanderthals’ more than “ordinary” white-people skulls. So extrapolating from his low opinion of what he called these “savage” races, he explained that the Neanderthal’s skull alone was proof of its moral “darkness” and stupidity. “The thoughts and desires which once dwelt within it never soared beyond those of a brute,” he wrote. Other scientists piled on. So did the popular press. We knew almost nothing about Neanderthals, but already we assumed they were ogres and losers.

The genesis of this idea, the historian Paige Madison notes, largely comes down to flukes of “timing and luck.” While King was working, another British scientist, George Busk, had the same suspicions about the Neander skull. He had received a comparable one, too, from the tiny British territory of Gibraltar. The Gibraltar skull was dug up long before the Neander Valley specimen surfaced, but local hobbyists simply labeled it “human skull” and forgot about it for the next 16 years. Its brow ridge wasn’t as prominent as the Neander skull’s, and its features were less imposing; it was a woman’s skull, it turns out. Busk dashed off a quick report but stopped short of naming the new creature. He hoped to study additional fossils and learn more. Privately, he considered calling it Homo calpicus, or Gibraltar Man.

So, what if Busk — “a conscientious naturalist too cautious to make premature claims,” as Madison describes him — had beaten King to publication? Consider how different our first impressions of a Gibraltar Woman might have been from those of Neanderthal Man: what feelings of sympathy, or even kinship, this other skull might have stirred.

There is a worldview, the opposite of Joachim Neander’s, that sees our planet as a product of only tumult and indifference. In such a world, it’s possible for an entire species to be ground into extinction by forces beyond its control and then, 40,000 years later, be dug up and made to endure an additional century and a half of bad luck and abuse.

That’s what happened to the Neanderthals. And it’s what we did to them. But recently, after we’d snickered over their skulls for so long, it stopped being clear who the boneheads were.

I’ll start with a confession, an embarrassing but relevant one, because I would come to see our history with Neanderthals as continually distorted by an unfortunate human tendency to believe in ideas that are, in reality, incorrect — and then to leverage that conviction into a feeling of superiority over other people. And in retrospect, I realize I demonstrated that same tendency myself at the beginning of this project. Because I don’t want to come off as self-righteous, or as pointing fingers, here goes:

… I happened to arrive in Gibraltar the week of the Brexit vote. Up in England, people were thundering about the working class versus elites, sovereignty and immigration, warning that British identity was being fouled by the European project. But in Gibraltar — a far-flung, fully detached nib of Britain, flanked by water on two sides and Spain on the third — the question was less philosophical: If the United Kingdom left the European Union, Spain might seize the opportunity to isolate Gibraltar, leaving the territory to shrivel up, like a flap of dead skin. The Gibraltarian government had already called on the House of Commons for help. There was concern that Spain would jam up the border again and that it might happen right away.

Around town, “Remain” signs hung everywhere. The atmosphere was edgy, as though everyone was holding hands, waiting to see whether a meteor would hit. It was like the hairline cracks between so many self-designated Us-es and Thems seemed to be widening, and some corrosive, molten goop was seeping out: mutual dependence curdled with contempt. Clearly it was happening back home in America too.

All in all, it was a good week to spend in a cave.

… What is clearer is that roughly 40,000 years ago, just as our own lineage expanded from Africa and took over Eurasia, the Neanderthals disappeared. Scientists have always assumed that the timing wasn’t coincidental. Maybe we used our superior intellects to outcompete the Neanderthals for resources; maybe we clubbed them all to death. Whatever the mechanism of this so-called replacement, it seemed to imply that our kind was somehow better than their kind. We’re still here, after all, and their path ended as soon as we crossed paths.

But Neanderthals weren’t the slow-witted louts we’ve imagined them to be — not just a bunch of Neanderthals. As a review of findings published last year put it, they were actually “very similar” to their contemporary Homo sapiens in Africa, in terms of “standard markers of modern cognitive and behavioral capacities.” … The real surprise of these discoveries may not be the competence of Neanderthals but how obnoxiously low our expectations for them have been — the bias with which too many scientists approached that other Us. One archaeologist called these researchers “modern human supremacists.” …

One of the earliest authorities on Neanderthals was a Frenchman named Marcellin Boule. A lot of what he said was wrong.

In 1911, Boule began publishing his analysis of the first nearly complete Neanderthal skeleton ever discovered, which he named Old Man of La Chapelle, after the limestone cave where it was found. Laboring to reconstruct the Old Man’s anatomy, he deduced that its head must have been slouched forward, its spine hunched and its toes spread like an ape’s. Then, having reassembled the Neanderthal this way, Boule insulted it. This “brutish” and “clumsy” posture, he wrote, clearly indicated a lack of morals and a lifestyle dominated by “functions of a purely vegetative or bestial kind.” A colleague of Boule’s went further, claiming that Neanderthals usually walked on all fours and never laughed: “Man-ape had no smile.” Boule was part of a movement trying to reconcile natural selection with religion; by portraying Neanderthals as closer to animals than to us, he could protect the ideal of a separate, immaculate human lineage. When he consulted with an artist to make a rendering of the Neanderthal, it came out looking like a furry, mean gorilla. …

Still, Boule’s influence was long-lasting. Over the years, his ideologically tainted image of Neanderthals was often refracted through the lens of other ideologies, occasionally racist ones. In 1930, the prominent British anthropologist Sir Arthur Keith, writing in The New York Times, channeled Boule’s work to justify colonialism. For Keith, the replacement of an ancient, inferior species like Neanderthals by newer, heartier Homo sapiens proved that Britain’s actions in Australia — “The white man … replacing the most ancient type of brown man known to us” — was part of a natural order that had been operating for millenniums.

It’s easy to get snooty about all this unenlightened paleoanthropology of the past. But all sciences operate by trying to fit new data into existing theories. And this particular science, for which the “data” has always consisted of scant and somewhat inscrutable bits of rock and fossil, often has to lean on those meta-narratives even more heavily. “Assumptions, theories, expectations,” the University of Barcelona archaeologist João Zilhão says, “all must come into play a lot, because you are interpreting data that do not speak for themselves.”

… The Washington University anthropologist Erik Trinkaus, who began his career in the early ’70s, told me, “When I started working on Neanderthals, nobody really cared about them.” The liveliest question about Neanderthals was still the first one: Were they our direct ancestors or the endpoint of a separate evolutionary track? Scientists called this question “the Neanderthal Problem.” Some of the theories worked up to answer it encouraged different visions of Neanderthal intelligence and behavior. The “Multiregional Model,” for example, which had us descending from Neanderthals, was more inclined to see them as capable, sympathetic and fundamentally human; the opposing “Out of Africa” hypothesis, which held that we moved in and replaced them, cast them as comparatively inferior.

The Multiregional Model of Carleton Coon and other mid-20th Century anthropologists was widely denounced as racist, while the “Out of Africa” model was celebrated as anti-racist for showing that we are all descended from Africans who overwhelmed and wiped out Europeans.

For decades, when evidence of a more advanced Neanderthal way of life turned up, it was often explained away, or mobbed by enough contrary or undermining interpretations that, over time, it never found real purchase. …

“To me,” says Zilhão, the University of Barcelona archaeologist, “there was a logical shock: If the paradigm forces you to say something like this, there must be something wrong with the paradigm.” Zilhão published a stinging critique challenging the field to shake off its “anti-Neanderthal prejudice.” Papers were fired back and forth, igniting what Zilhão calls “a 20-year war” and counting. Then, in the middle of that war, geneticists shook up the paradigm completely.

A group at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, led by Svante Paabo, had been assembling a draft sequence of a Neanderthal genome, using DNA recovered from bones. Their findings were published in 2010. It had already become clear by then that Homo sapiens and Neanderthals appeared in Eurasia separately — “Out of Africa was essentially right” — but Paabo’s work revealed that before the Neanderthals disappeared, the two groups mated. Even today, 40,000 years after our gene pools stopped mixing, most living humans still carry Neanderthal DNA, making up roughly 1 to 2 percent of our total genomes.

In this sentence “most living humans” doesn’t include sub-Saharan Africans.

The data shows that we also apparently bred with other hominids, like the Denisovans, about which very little is known.

It was staggering; even Paabo couldn’t bring himself to believe it at first. But the results were the results, and they carried a sort of empirical magnetism that archaeological evidence lacks. “Geneticists are much more powerful, numerous and incomparably better funded than anyone else dealing with this stuff,” Zilhão said. He joked: “Their aura is kind of miraculous. It’s a bit like receiving the Ten Commandments from God.” Paabo’s work, and a continuing wave of genomic research, has provided clarity but also complexity, recasting our oppositional, zero-sum relationship into something more communal and collaborative — and perhaps not just on the genetic level. The extent of the interbreeding supported previous speculation, by a minority of paleoanthropologists, that there might have been cases of Neanderthals and modern humans living alongside each other, intermeshed, for centuries, and that generations of their offspring had found places in those communities, too. Then again, it’s also possible that some of the interbreeding was forced.

I.e., rape.

One possibility is African immigrants raped European women. Or it might have been the hulking Europeans raping the more gracile Africans. Or maybe it was all romantic or arranged by elders. Nobody knows.

Paabo now recommends against imagining separate species of human evolution altogether: not an Us and a Them, but one enormous “metapopulation” composed of shifting clusters of essentially human-ish things that periodically coincided in time and space and, when they happened to bump into one another, occasionally had sex.

… What would it have been like to look out over a grassy plain and watch parallel humanity pass by? Scientists often turn to historical first contacts as frames of reference, like the arrival of Europeans among Native Americans, or Captain Cook landing in Australia — largely histories of violence and subjugation. But as Zilhão points out, typically one of those two cultures set out to conquer the other. “Those people were conscious that they’d come from somewhere else,” he told me. “They were a product of a civilization that had books, that had studied their past.” Homo sapiens encountering Neanderthals would have been different: They met uncoupled from politics and history; neither identified as part of a network of millions of supposedly more advanced people. And so, as Finlayson put it to me: “Each valley could have told a different story. In one, they may have hit each other over the head. In another, they may have made love. In another, they ignored each other.”

It’s a kind of coexistence that our modern imaginations may no longer be sensitive enough to envision. So much of our identity as a species is tied up in our anomalousness, in our dominion over others. …

Some paleoanthropologists are starting to reimagine the extinction of Neanderthals as equally prosaic: not the culmination of some epic clash of civilizations but an aggregate result of a long, ecological muddle. Strictly speaking, extinction is what happens after a species fails to maintain a higher proportion of births to deaths — it’s a numbers game. And so the real competition between Neanderthals and early modern humans wasn’t localized quarrels for food or territory but a quiet, millenniums-long demographic marathon: each species repopulating itself, until one fell so far behind that it vanished. …

… (Across all of Eurasia, at any point in history, says John Hawks, an anthropologist at the University of Wisconsin-Madison, “there probably weren’t enough of them to fill an N.F.L. stadium.”) With the demographics so skewed, Stringer went on, even the slightest modern human advantage would be amplified tremendously: a single innovation, something like sewing needles, might protect just enough babies from the elements to lower the infant mortality rate and allow modern humans to conclusively overtake the Neanderthals. And yet Stringer is careful not to conflate innovation with superior intelligence. Innovation, too, can be a function of population size. “We live in an age where information, where good ideas, spread like wildfire, and we build on them,” Stringer told me. “But it wasn’t like that 50,000 years ago.” The more members your species has, the more likely one member will stumble on a useful new technology — and that, once stumbled upon, the innovation will spread; you need sufficient human tinder for those sparks of culture to catch.

And the larger your number, the more likely you are to benefit from a favorable genetic mutation.

“There was nothing inevitable about modern human success,” Stringer says. “It was luck.” We didn’t defeat the Neanderthals; we just swamped them.

Showing me around the Gibraltar Museum one morning, Finlayson described the petering out of Neanderthals on the Rock with unnerving pathos. Gibraltar, with its comparatively stable climate, would have been one of their last refuges, he explained, and he likened the population there to critically endangered species today, like snow leopards or imperiled butterflies: living relics carrying on in small, fragmented populations long after they’ve passed a genetic point of no return. “They became a ghost species,” Finlayson said.

It was the day of the Brexit vote. … I won’t describe the scenes I saw that morning — the blankness on people’s faces at the airport, phone calls I overheard — except to say that when I woke up on Nov. 9, after our own election, I felt equipped with at least a faint frame of reference. Reality seemed heightened and a little dangerous, because for so many people, including me, it had broken away from our expectations. We had misunderstood the present in the same way archaeologists can misunderstand the past. What was possible was suddenly exposed as grossly insufficient, because, to borrow Finlayson’s metaphor, we never imagined that the few jigsaw puzzle pieces we based it on constituted such a tiny part of the whole.

Even some on the winning sides seemed similarly stunned and adrift. Many, though, just felt vindicated. Later that summer, I came across an essay for a British weekly by the actress Elizabeth Hurley, a fervent Leave supporter, who was now doubling down. “Knock yourselves out calling us ill-educated Neanderthals,” she wrote, “and spit a bit more venom and vitriol our way. You are showing yourselves in all your meanspirited, round-headed elitist glory.”

When I read that, I took genuine umbrage — but on the Neanderthals’ behalf. And while I hate to admit it, I also felt a cheap but delicious tingle of smugness, because I now knew that “Neanderthal” wasn’t the insult Hurley thought it was — though this, I simultaneously realized, also closed a certain self-reinforcing loop and promoted, in me, the very round-headed elitist glory Hurley was incensed by, thus deepening the divide. It was dizzying and sad and maybe inevitably human, but still no help to us at all.

 Jon Mooallem is a writer at large for the magazine. He is also a contributor to “This American Life” and the author of the book “Wild Ones.”