The article kicked off not just a diet, but a movement. Appearing in the New England Journal of Medicine in January 1985, “Paleolithic Nutrition: A Consideration of Its Nature and Current Implications” argued that the human body is “genetically programmed” to run, not on a modern diet, but on the foods consumed by our Stone Age ancestors.

“The human genetic constitution has changed relatively little since the appearance of truly modern human beings, Homo sapiens sapiens, about 40,000 years ago,” S. Boyd Eaton and Melvin Konner wrote.

The authors reasoned that human bodies have been shaped more by our prolonged time as hunter-gatherers than by the brief span since the advent of farming. Meat, probably lots of it, as well as fruits and vegetables were in. The staples of agriculture – breads, cereals, milks and cheeses – were not.

Three decades later, that academic ripple is now a popular tidal wave. We have not just Paleo diets – the subject of multiple best-sellers – but Paleo exercise, Paleo sleeping and Paleo toilets. They’re all based on the premise that our bodies are more suited for Paleo-era habits.

But even as the “caveman” diet rose to become the most Googled diet in 2013 and 2014, evolutionary biologists were with much less advertisement using advanced DNA techniques, sometimes on ancient bones, to suggest that the original Paleo premise may be off-the-mark: In fact, it seems, we have evolved.

Over the last year alone, prominent scientific journals have published evidence of genetic shifts in humans over the last 10,000 years – apparently in response humankind’s transition to agriculture.

Two relatively recent gene variants help humans survive with deficiencies characteristic of agricultural diets; another genetic shift appears to help fight the dental cavities that arose with farm-based staples; another changes the way humans digest fats; dozens of others help fight the diseases that came with living at higher densities.

Those new findings add to previous efforts showing that two other critical adaptations to new diets. After the domestication of milking animals, many humans evolved to digest milk. Separately, humans developed better ways to digest the starches characteristic of agricultural diets.

“It drives me crazy when Paleo diet people say that we’ve stopped evolving – we haven’t,” said Anne C. Stone, a professor of human evolution at Arizona State University who has shown that genes related to starch digestion appear to have changed in number apparently in response to farming. “Our diets have changed radically in the last 10,000 years and, in response, we have changed, too.”

While all this new evidence challenges the Paleo diet argument, it doesn’t necessarily disprove it, and Eaton and Konner, for their part, maintain that their central hypothesis – that there is a mismatch between our bodies and our diets – remains sound.

Yes, Konner acknowledged in an interview, there is more research that humans have evolved recently.

“There’s evidence that there’s been a lot more selection and genetic change in the last five to 10,000 years than previously thought,” he said. “This is a challenge to the Paleo diet claims – including mine and Boyd Eaton’s over the years.”

“But,” he said, “I don’t think it’s much of one.”

For one thing, he and Eaton say, the newly discovered genetic differences between Paleo hunter-gatherers and modern humans are not very numerous. While there may be some ways in which humans have adapted to agricultural diets, those are far outnumbered by the ways in which human bodies are suited for Paleo-era.

“There are – no question – genetic differences” between Paleo people and us, Eaton said. “But our metabolism is controlled by hundreds of genes and maybe more than that. So while there are differences, they do not affect our nutritional needs in a significant way.”

Moreover, Konner said, even if one concedes that there has been significant genetic change over the last 10,000 years, those changes would only catch us up to human diets from 10,000 years ago. But our diets have changed radically over the last 300 years alone – we consume less fiber, more refined grains, etc- and evolutionary forces can’t have altered our bodies so quickly over that time.

“The bulk of the chronic degenerative disease in our population is due to dietary changes in the last few centuries – they’re not necessarily related to the shift from hunter-gatherers to agriculture,” Konner said. “The biggest culprit with the current epidemic of diabetes, a looming problem world-wide, is refined carbohydrates. There’s no way humans could have adapted to that because they haven’t been around long enough.”

Moreover, the idea that we may be better suited for a Paleo diet has been validated in part by recent shifts in the government’s Dietary Guidelines for Americans. For example, the hunter-gatherer diets touted by Eaton and Konner included large amounts of cholesterol; with the 2015 Dietary Guidelines, the government dropped its sternest warning and numerical limit for cholesterol intake.

The outcome of the debate over their idea, however, rests for now on the ongoing research, which has accelerated markedly in recent years.

When Eaton and Konnner wrote in the ’80s, the human genome had not been fully sequenced, and it was far more difficult to detect evidence of recent human evolution.

Take, for example, the discovery that humans got the ability to digest milk – lactose tolerance – as they began to domesticate milking animals.

First, scientists had to discover that lactose tolerance is an inherited trait. This came about after scientists noticed similarities within families. Once that was established, scientists were forced to look for clues from geography and anthropology. What they found is that in populations where cattle had been long domesticated, most people could easily digest milk; in populations without domesticated milking animals, most could not.

“This trait seems to be common or extremely common only in populations which have established the custom of having milk regularly in their diet after weaning,” Stanford geneticist Luigi Luca Cavalli-Sforza wrote in 1972. “It is rare or absent in others.”

Eaton and Konner acknowledged this dietary adaptation in their 1985 paper, but said “very few other examples are known.”

Since then, however, the pace of evolution research accelerated rapidly, especially with the ability to sequence the entire human genome. It allowed researchers, for example, to compare the DNA of populations with different diets – new and old – and look for signs of adaptation.

Stone and her colleagues, for example, were interested in the varying abilities of people to digest diets loaded with starch. After the transition to agriculture, which brought steady supplies of wheat, corn, rice, barley, etc., the ability to digest starches likely became more useful. Did human bodies adapt?

To answer that question, the researchers compared the DNA from peoples with high-starch diets and contrasted it with remote peoples who ate low-starch diets.

The high-starch groups included European-Americans, Japanese and the Hadza, hunter-gatherers who rely on starch-rich roots. The low starch groups were African pygmies, some African cattle farmers and a Russian ethnic group known as the Yakut.

As the DNA analysis showed, individuals from the high-starch groups were roughly twice as likely to have inherited many extra copies of the AMY1 gene. People with more copies of the AMY1 gene tend to have more of an enzyme known as amylase in their saliva, and allows them to better digest starch.

This benefit, Stone said, may have been particularly critical for the survival of children.

“In populations where starch was a major component of the diet, being able to extract as many calories as possible as quickly as possible, likely was a lifesaver for kids who suffered from bouts of intestinal illness,” she said.

More recently, another advance gave scientists a direct way of comparing contemporary humans to our Paleolithic ancestors. They were able recover DNA from ancient bones.

In November 2013, for example, researchers announced that they had sequenced the DNA of a Siberian boy who lived 24,000 years ago. Then in October 2014, researchers announced that they had sequenced DNA from the bone of a human – a thigh discovered in Siberia – believed to be 45,000 years old. It is currently the oldest modern human genome .

“We now have some idea how people who lived 45,000 years before present were related to present-day people,” one of the researchers, Janet Kelso, said at the time.

One of the largest, most significant recent critical finds came from excavations done in advance of a railway project in Motala, Sweden.

In what were once wetlands and a shallow lake, workers led by archaeologist Fredrik Hallgren uncovered the remains of at least 11 humans. It was a strange find: skulls resting on wooden stakes. There were also, apparently as grave offerings, tools carved of bone and antler. One item was a knife made from a wild boar tusk.

While the cultural significance of the burial remains clear, the DNA extracted from the remains is unequivocal.

In a paper that appeared in December in the journal Nature, scientists looked at the DNA that has been recovered from the Motala remains and from those of more than 200 others ancient Eurasian humans. The ages ranged from 8,000 years old to about 2,000 years old – a span of time that covers ancient hunter-gatherers as well as early farmers.

In analyzing the DNA from those ancient remains, the scientists noted thousands of distinct places where there were DNA changes that didn’t seem just random – that is, the changes didn’t seem to be merely a case of genetic drift, but a sign that the human species was actually adapting to some aspect of its environment.

Out of those thousands of places, the scientists then highlighted 12 places in the DNA where the signs of selection were clustered. One of those clusters related to the digestion of milk – a confirmation of previous findings. Another related to how humans digest fatty acids. Two others may have a link to celiac disease. Others were related to skin color, which got lighter as human moved northward from Africa, and disease resistance.

“Europeans of 4,000 years ago were different in important respects from Europeans today, despite having overall similar ancestry,” the authors concluded.

Those findings, like the others, challenge the Paleo assumption that humans have not changed. What remains unanswered is how much. As good as the research techniques have become, and as far as the technology has advanced, the validity of the central premise of the Paleo movement remains uncertain. As Eaton and Konner advised said in 1985, any diet proposals, to be validated, must be tested with experiments.

“My overall opinion of this is that we don’t really know,” said Iain Mathieson, a Harvard med school researcher and a co-author of the Nature paper. “We do know there are some specific changes in humans. But they are a relatively small in number. To me it’s an open question. It’s a hypothesis.”

A love story, Neanderthal-style

By Faye Flam, Bloomberg View

Scientists are showing Neanderthals some love. This is new, and required them to overcome some unscientific prejudices. It was only a few years ago that many anthropologists insisted that Neanderthals can’t possibly have contributed to human ancestry because they were too ugly to appeal sexually to their modern human contemporaries.

Wrong. DNA evidence showed six years ago that many ancestors of modern humans made love with Neanderthals. Scientists now know in some detail how sex with Homo neanderthalensis contributed to the gene pool of today’s Homo sapiens.

Yet our Pleistocene cousins still have an image problem and scientists deserve much of the blame, said John Hawks, a University of Wisconsin anthropologist who has been one of their leading defenders in blog posts dubbed the Neanderthal Anti Defamation Files. Not only were they complicit in the ugliness frameup, they also had deemed Neanderthals stupid. That doesn’t look smart now.

To be sure, the relationship between people and Neanderthals is complicated. About 350,000 years ago in Africa, two strains of prehistoric people diverged. One gradually evolved into bona fide modern Homo sapiens, probably around 200,000 years ago.

The Neanderthal branch left the cradle of humanity for Europe and Asia. Much later, some of the so-called modern humans also moved north, where the two branches encountered each other. The DNA evidence shows that they had evolved in somewhat different directions while they were apart, but not enough to prevent them from having sex and producing kids.

Science learned all this thanks to the ability to read Neanderthal DNA scraped from ancient bones. That advance allowed scientists to recognize telltale sequences in people today. Neanderthal DNA makes up between 1 percent and 5 percent of the DNA of people with European, Asian, Australian, or Native American ancestry.

How do these bits of Neanderthal DNA affect those who carry it? To find out, scientists looked at genetic and medical data for a group of 28,000 people. The results, published Thursday in the journal Science, showed that Neanderthal DNA was correlated with a host of different traits and susceptibility to health problems.

Some bits of Neanderthal DNA increased carriers’ risk of skin lesions known as actinic keratosis. Others cause blood to coagulate faster, thus slightly increasing the risk of stroke. Some increased the risk of depression; some decreased it. Some Neanderthal genes increased the risk of tobacco addiction in modern people.

That probably wasn’t a problem for Neanderthals. They knew how to control fire but there’s no evidence they smoked, even after having sex with modern humans.

One finding of possible relevance to today’s obsession with paleo dieting was a bit of DNA that influences the ability to digest carbohydrates. Neanderthals were apparently not as well- suited to eating carbs as the modern humans.

There seemed to be slightly more negative than positive associations with Neanderthal DNA, but not enough to worry anyone, said geneticist Josh Akey, a collaborator on this study.

But there’s still a question of whether these genes should be considered embarrassing – suggesting the breaking of some species-barrier taboo. Scientists are still arguing about whether Neanderthals constituted a separate species. Biologists no longer believe in the rule that animals of different species never mate. There are too many exceptions – grizzlies and polar bears, lions and tigers, dogs and wolves.

Hawks, the Neanderthal-defending anthropologist, said Neanderthals had many of the traits that seem central to being human. That’s a new discovery, too. Until recently, no one had found evidence that they created art or jewelry or complex bone tools. It was therefore incorrectly thought that they were incapable of symbolism. Some scientists assumed that Neanderthals couldn’t talk.

And then people started finding Neanderthal beads, paint pigments and bone tools finely crafted for leather work, said Hawks. Beyond that, humans and Neanderthals share distinct physiological traits in the structure of vocal tracts and inner ears, apparently critical in the ability to speak and detect the common frequencies of speech.

Scientists have also revised their view of Neanderthal extinction – long attributed to some deficit on their part. Maybe nothing dramatic happened at all, said Hawks. They would have made up a small fraction of the world’s population, and when larger groups of modern humans joined them in Europe they might have simply been absorbed.

Which comes back to the question of who would want to absorb them. Neanderthals look weird when encountered in museum dioramas, but anthropologists point out that the so-called modern humans of 50,000 years ago looked nothing like Wilma Flintstone or Betty Rubble, let alone Raquel Welch in that caveman bikini. For all we know, some of them were great cooks or singers. That we ridiculed Neanderthals so maliciously for so long says more about our shortcomings than theirs.

Faye Flam writes about science, mathematics and medicine. She has been a staff writer for Science magazine and a columnist for the Philadelphia Inquirer. She is author of “The Score: How the Quest for Sex has Shaped the Modern Man.”