Conventional wisdom holds that if you could bring back someone from 40,000 years ago, he or she would blend perfectly well with today's population.

After all, the fossils show that our ancestors were "anatomically modern" by 100,000 years ago, and by 40,000 B.C., they were creating complex tools and art.

It was easy to assume our species hadn't evolved much since then.

Now molecular biology is overturning that assumption.

Evidence for more recent evolution is coming not from fossils but from patterns seen in the DNA of contemporary people. Genes show that blue eyes, for example, apparently didn't exist until 6,000 years ago, and the ability to digest milk goes back just 7,000 years.

Scientists have compared genes from different ethnic groups and found more recent genetic mutations are changing the way some people metabolize food, store fat, grow hair, and fight disease.

One new mutation that appears only in Asians may improve hearing and balance.

Some of the more recent changes have not spread through the world uniformly - affecting only those of European, African, or Asian ancestry. Would any future findings suggest that some group had traits that might be considered superior to others?

Already, for example, some scientists have theorized that recent genetic changes have endowed Ashkenazi Jews with higher average intelligence.

To deal with such potentially inflammatory ideas, the National Institutes of Health assembled a meeting in 2008 on the social and ethical implications of natural selection in humans. "There was a spirited debate about whether we should be engaged in this research at all," said Josh Akey, a geneticist from the University of Washington. Some argued that no good could come of it, he said.

Akey and other scientists who do this work say they hope to advance medicine by revealing why some people are more vulnerable than others to HIV, malaria, flu, autoimmune diseases, allergies, diabetes, alcoholism, and obesity.

The scientists argue that none of this work points to the superiority of one group or person over another. It's an old misconception that evolution is elevating humanity up some ladder of perfection, he said, or that one group could be more evolved than another.

"When we talk about natural selection, people think about survival-of-the fittest," Akey said, "but that's not really how it works."

Local environments bend the course of evolution. Traits that would make someone "fit" in one place could prove to be liabilities in another.

Several genetic mutations protect against malaria, for example, though they can also cause diseases including sickle cell anemia. A few researchers have speculated that conditions known as torsion dystonia and Gaucher's disease are associated with higher intelligence.

New genetic anomalies could be seen as diseases or advantages, depending on the context.

These new "footprints" of recent evolution would have been invisible even a few years ago, before an explosive growth in the ability to analyze DNA and map genes.

Much of that DNA was collected through a project called HapMap - which included samples from 90 Nigerians, 90 Americans of European ancestry, 45 people from Tokyo, and 45 from Beijing. The collection is not meant to be all-inclusive but to provide a sample of the world's diversity.

What has been revealed so far is that some altered versions of genes are spreading fast, as if they were incurring some advantage to their owners. The biologists can tell how fast a gene is spreading by how much extra DNA it's trailing along with it, said Sharon Grossman, a geneticist at Harvard.

At first, a new advantageous gene takes a whole stretch of genetic material with it as it passes from parents to children, she said. Over time, the chunks of DNA break apart, and the advantageous genes can pass through the generations less encumbered.

The size of the genetic entourage works as a kind of molecular clock. The more recently a change has appeared, the larger the entourage of other genes traveling along with it.

That method has shown that some changes are surprisingly recent, Grossman said. The mutation that gives some people blue eyes appears to have been around only in the last 6,000 years, for example.

To help calibrate their clock, she and her colleagues relied on earlier work that had analyzed ancient DNA scraped from bones.

The ancient DNA showed that until about 7,000 years ago, nearly everyone was lactose intolerant, and after that several new mutations started spreading through the population that allowed people to better digest the sugars in milk.

That enabled the researchers to compare their age estimates based on the amount of tagalong DNA with those derived from dating of the fossils.

In recent years, biologists have found more than 100 other stretches of human genetic code that appear to have changed in the last 30,000 years or so.

The bad news is the more recent the genetic change, the more other genes will be attached to it, and the harder it is to distinguish which genes are important for natural selection and which are coming along for the ride.

Harvard's Grossman said she and her colleagues found a statistical method to narrow the search. In a paper published last month in Science, they showed how their method could identify genes that had begun to spread during the last 30,000 years.

For example, they found that in Japanese and Chinese populations, a new version of a gene called protocadherin 15 is on the rise. It appears to alter the structure of hairs in the inner ear and thereby influences hearing and balance.

The Harvard team also found that changes in genes regulating the immune system were sweeping through the African populations. All the groups sampled for HapMap showed recent changes in genes that influence metabolism and fat storage.

All this new evidence from the molecular biology labs could put to test a radical hypothesis proposed by University of Utah anthropologist Henry Harpending. He and physicist Gregory Cochran argue that human evolution has actually accelerated since the widespread advent of farming.

They popularized this idea in their 2009 book, The 10,000 Year Explosion.

In an interview, Harpending said one factor driving this explosion is population. From 60,000 years ago to 3,000 years ago, the human population mushroomed from about a quarter of a million to 60 million. More people meant more variety and more new traits, some of which might prove advantageous in some places.

Harpending said that soon after our ancestors dispersed from Africa, about 40,000 years ago, they showed a burst of new genetic diversity. There's no agreed-upon explanation for this, he said, but he offers the radical possiblity that our ancestors picked up new genes by mixing with Neanderthals and other archaic people who had already settled in Asia and Europe.

The most beneficial genes then spread back into Africa.

If this really happened, he said, the evidence will be embedded in our DNA. One relatively new genetic variant our ancestors acquired about 40,000 years ago involves a gene called FOXP2, Harpending said. It's a gene thought to be connected to complex speech, since people with a defect in that gene have problems with language, and because chimpanzees and other apes carry a different version.

The surprising part of the story, Harpending said, is that DNA sampled from Neanderthal skeletons showed they carried the "modern" version of FOXP2 long before our ancestors acquired it. Could our ancestors have picked up such a beneficial gene from these apparent evolutionary losers?

Harpending said it's not as strange as it sounds.

Though the popular conception is that Neanderthal man was apelike and primitive, their brains were actually bigger than those of modern humans and there's still no agreement on why they died out.

In Harpending's view, the other factor that accelerated evolution was the invention of farming. Suddenly, people had to adapt to different diets, different ways of getting food, and different social structures.

Starvation and malnutrition got worse in farming groups, he said, because people could no longer move around and change food sources. Farming groups were dependent on just a few crops that could be wiped out by pests, disease, or drought.

Famines would have culled farming populations, favoring those who could survive better on a newly starchy diet, lower in protein and vitamins than the wild foods eaten by hunter-gatherers.

Natural selection also might have favored those who could handle wine and beer without becoming alcoholics, he said.

The implication for today, he said, is that people whose ancestors were hunter-gatherers or recent converts to farming are less adapted to modern life and more likely to suffer from diabetes and other diet-related problems as well as alcoholism.

The human immune system is changing too, he said, adapting to diseases that began to sweep through populations once farming enabled life in crowded cities.

Harpending makes the even more contentious case that farming also reshaped the human mind - favoring traits that allow people to deal with repetitive work and hierarchical society. In some ways, he said, farming people were tamed and domesticated along with their animals.

Individuals who were unruly, violent, or disruptive were killed off.

Evolution through domestication can happen in just a few centuries, said Washington's Akey, who also studies genetics of domestic dogs. He's comparing breeds to see where the DNA is separating the Great Danes from the dachshunds, the border collies from the poodles.

Oddly, he said, he has found a parallel - at the DNA level, dogs and humans are showing some of the same changes. It's possible, he said, that both dogs and humans needed to acquire new disease-resistance genes in response to crowding. Or it could be a reflection of the taming and domestication of both species.

Dog brains are smaller than those of their ancestors, the wolves, and likewise our brains are apparently smaller than those of our ancestors 20,000 years ago, Harpending said. The human brain hit its peak and then began shrinking.

It may mean our ancestors needed more brainpower to survive in the wild, or it could be that our brains have become better organized and more compact - just as computers have done, he said.

It's a mystery, but perhaps there's an answer somewhere in our DNA.

Contact staff writer Faye Flam at 215-854-4977 or fflam@phillynews.com.