The story of humanity is written in our genes, and thanks to modern science and technology, we are finally able to read it. In our latest cover story, J.M. Ledgard reports from where it—and we—all began ...

From INTELLIGENT LIFE Magazine, Summer 2009

An hour’s drive and a 600-metre drop in altitude from Nairobi is Olorgesailie, a Lower Palaeolithic archaeological site on the floor of the Rift Valley in Kenya. It is blisteringly hot. Nothing moves in the heat of the day except dust, gathering into twisters. There are puff adders in the grass, scorpions under the rocks. The lions are thin, the giraffes few, the elephants killed. It might be the closest we have to the Garden of Eden.

From the campsite it is possible to make out the outline of the prehistoric lake which once flooded the plain in soapy water. According to potassium-argon dating, hominids lived here for 900,000 years. They made handaxes which they used to butcher the hippos, zebras and baboons they hunted and scavenged. Olorgesailie stands for the gaping history of our species, a blurry, half-formed and dreamlike time from which archaeology can pull out only pieces. The Kenyan anthropologist Louis Leakey uncovered a Homo erectus skull here in the 1940s; the brain cavity was disappointingly small. There must have been grunts, gestures with stones, blood, the sky blotted with vultures, ape children kept back in the darkness. The sense of space here is immense. So too is the sense of known time, hominid time, known at first in the way a beast knows time, in light and darkness, but conscious all the same. The night sky is black lacquered. Satellites pass across it like trams. There are shooting stars. Sometimes there is the sound of hyenas.

“To the extent we are hardwired, it is probably as small bands of hunter-gatherers,” says Spencer Wells, the American geneticist who heads the Genographic Project. Its aim is to take 100,000 DNA samples from indigenous peoples around the world and write the songline of mankind’s journey out of Africa from a place like Olorgesailie, obliterating any literal interpretation of the Garden of Eden and replacing it with a new evidence-based creed.

The creed holds that every single non-African on the planet is descended from one or possibly two small bands of humans who made it on rafts and skins across the Red Sea at the narrows of the Bab el-Mandeb, or Gate of Tears, about 50,000 years ago. We are a more maritime species than we ever supposed, even if we keep close to the shore. These early humans, this Mayflower on foot, scavenged shellfish along the tideline and in the rock pools, increasing their range by a few kilometres a year. Within 5,000-10,000 years, without much need for adaptation, they had worked their way around India and across the land bridges that then linked Asia with a short sea crossing to Australia.

Some 99% of the human genome is shuffled from one birth to the next. The Genographic Project traces the 1% of the genome which is not shuffled—mitochondrial DNA (mtDNA) through the maternal line and the Y-chromosome through the paternal. These jokers in the pack allow geneticists to work back to our common ancestors. Our mtDNA appears to coalesce in a single woman, who lived on the African savannah 150,000 years ago. Our Y-chromosome survives from a single man, who lived in the Rift Valley of Kenya or Tanzania 59,000 years ago. So Adam and Eve did exist—90,000 years apart. The discrepancy is because, unlike the biblical Adam and Eve, this couple only represent the last common Ancestors we can trace genetically.

About 60,000 years ago, our species had crashed to 2,000 individuals, then recovered with the help of language and conceptual thinking. The speed of our spreading is alarming set against evolutionary time, as if we’re bacteria. The journey of each individual is arranged by haplogroup, a branch of migration marked by a genetic mutation. Since the 1848 revolutions, the spread of mechanised transport and the rise of “isms” culminating in globalism, couples have been shuffling their distinct genetic families, or haplogroups, some representing tiny indigenous peoples, others much of western Europe. In many respects the Genographic Project is a race against time. Indigenous peoples amount to just 350m of the 6.8 billion people on the planet. The number of languages has gone from 15,000 in 1492 to 5,900 today. The ancient bloodlines are almost gone. Soon only the vampires will be left.

The Genographic Project, which is underwritten by National Geographic, IBM and the Waitt Foundation, revolves around the dazzling countenance of Spencer Wells (pictured below). With his blond hair, blue eyes and Nebraska roots, he is the ideal high priest to explain to white Americans that they are blacks gone curdy. His biography carefully notes that he was a “child prodigy with a love for both history and science” who entered the University of Texas at 16. He took his PhD at Harvard under the noted evolutionary geneticist Richard Lewontin, then worked for the founding father of population genetics, Luca Cavalli-Sforza, at Stanford. After a stint running a lab in Oxford and a couple of television shows, he became an explorer-in-residence at National Geographic, which he regards as “the world’s coolest job”.

For publicity’s sake, the project will help solve popular history questions. Did the Vikings leave a genetic imprint on America? How far did the Incas spread? But at its core is the hard science of population genetics.

Cavalli-Sforza’s “The History and Geography of Human Genes”, written with Paolo Menozzi and Alberto Piazza (Princeton University Press, 1994), is still considered the best overview of genetic diversity in humans. Cavalli-Sforza demolished the idea of there being different species of human being. No more Homo afer, asiaticus, europaeus, americanus and monstrous. Race, says Cavalli-Sforza, has hardly any useful biological meaning at all. It is about adaptation. Grain-eaters between the Baltic and Black Sea got pale skin, pale eyes and pale hair because they were under selective pressure to process more Vitamin D from limited sunlight. Lewontin, Wells’s other mentor, posited that if a nuclear war struck and only the Kenyan Kikuyu survived, they would still have 85% of the genetic variation of mankind; with a similar history and conditions, they too would turn blond and blue-eyed under the northern sun.

Cavalli-Sforza was the first to propose a global sample of genetic diversity, but his Human Genome Diversity Project foundered on insensitivity to indigenous peoples and a murky position on whether the DNA samples could be sold. The Genographic Project has learned from those mistakes. Instead of covering its costs with industrial sponsorship, it sells kits to interested members of the public, which in turn support a small legacy fund for indigenous peoples that sweetens their participation. The project has so far gathered 50,000 DNA samples from indigenous peoples. It has sold 300,000 kits at $100 a pop to the public in 130 countries. The major findings will be made public in 2011. “The biggest challenges have been bureaucratic and financial,” says Wells. The few remaining ethnolinguistic hotspots are in remote bits of rainforest, marsh, desert and steppe: National Geographic country.

The sequencing of nucleotides—the Lego bricks which build our DNA and RNA—within each gene segment is only possible with the power of computing, particularly the algorithms that allow for swifter and more detailed analysis of the data. The work on the Genographic Project is being done by the computational biology team at IBM’s vast research division in the Watson labs outside New York. The genome has a digital structure played out over long strands. It may be significant that we live in an age where the digital is more understandable to us.

The head of the IBM team is an Indian, Ajay Royyuru. IBM has used the Genographic Project as a way of sharpening its understanding of genetics. The goal was to build a statistical model for human variation and migration, he says, but the first lessons were ethical. IBM extended its non-discrimination policy to include genetic markers and helped make it law in the United States; it is now illegal to get rid of an employee because their genes indicate, say, a likelihood of multiple sclerosis.

The biggest advance Royyuru’s team has made is on new algorithms that could allow population geneticists to work with the 99% of the genome that is shuffled. Since the number of our ancestors grows by “two to the power for each generation removed”, the Genographic Project is only looking at a small part of any given person’s genetic inheritance, a few branches on a tree. So far, says Royyuru, the problem remains “NP-hard” (nondeterministic polynomial-time hard), meaning that it cannot be proven with the present computing power. But by applying parsimony, the logic of the simplest evident solution, the IBM algorithm could allow geneticists to say something about complex traits within given populations. Royyuru expects it could be applied to the growing field of personalised testing for genetic markers within the next decade, constituting a significant medical advance.

If you are not an indigenous person, you can buy a DNA kit. You “vigorously” scrape off cells from the inside of your cheek, insert the sample in a clear plastic vial and send it off to Washington, DC. For Europeans, the results are generally bland. About 80% of Europeans are descended from paleolithic hunter-gatherers, with the rest coming up the Danube with the first farming culture, or in smaller groups, such as Ottomans and attendant gypsies.

Genetically speaking, my genes are the unsalted of the bland. I was born in the Shetland Islands, of Yorkshire Norman stock. Predictably, comfortingly, my Y-chromosome haplogroup is identified as I1a. “Because of its high frequency in western Scandinavia,” my results read, “it is likely many Vikings descended from this line. The Viking raids on the British Isles might explain the dispersal of this lineage as well.” The I1a Northmen migrated from Africa, through the Middle East to the Balkans and on to western Europe.

About 28,000-23,000 years ago they helped found the sensual “Gravettian” culture, weaving cloth from natural fibres and carving voluptuous figurines, fertile in their swollen breasts, belly and hips. They then took refuge from the last glacial maximum in Iberia. When the ice retreated, they made their way up the French coast to populate parts of Britain and Norway.

At least I am not a Neanderthal. One of the Holy Grail questions of anthropology, which persisted until recently, was whether Europeans had some Neanderthal blood. The groundbreaking research by Svante Paabo at the Max Planck Institute in Leipzig, examining DNA extracted from Neanderthal bones, shows that is not the case.

The lead researcher for the European part of the Genographic Project is Lluis Quintana-Murci of the Pasteur Institute in Paris. He spends some of his time in the Central African Republic studying the links between Bantu and pygmies. In Europe, he hopes to help solve the mystery of the Basques. Are they relic hunter-gatherers, as some Basque nationalists claim? An extensive study of the Basque lands in Spain and France together with control groups from non-Basque Asturias and Aragon may settle the question and shed light on the Basque language, which “doesn’t belong to any known linguistic family”.

My partner is Czech, and her  mtDNA is haplogroup K. At first glance this is a quirky group associated with Ashkenazi Jews, but it is in fact also a common Slav maternal line. Our youngest son, Hamish, has lived all his life in the Rift Valley. He speaks a little Swahili, but also inherits from his Mum the M17 marker which indicates Kurgan descent. These pre-Scythian nomads glittered on horseback, leaving burial mounds—kurgans—filled with gold across the Eurasian steppe. The Ashkenazi marker is interesting, no question, but the Kurgan brings me back to one of the definitive films of my childhood, “Highlander”, in which two (almost) immortals, a Scottish Highlander played by Christopher Lambert and a Kurgan played by Clancy Brown, engage in mortal swordplay.

WE ARE ALL AFRICAN NOW 2What does it mean to be a couple of thousand generations removed from Adam when, say, Donne and his sonnets are already a cosmos away after only eight generations? On the level of modern history the genographers are no big deal. A haplogroup is so vague as to be useless to genealogists. I could stand on a street in Edinburgh and find more people who shared my I1a haplogroup than my green politics, much less my star sign. But on the level of deep ancestry the Genographic Project is a very big deal. Matt Ridley, author of  “Genome” and a former science correspondent for The Economist, believes the genome revolution “is the biggest development in human history, bar none”. Within that, “out of Africa is a huge story”.

Most of genetics looks forward—to the elimination of disease, cloning, perhaps even the creation of a new species. But if we as a species are but nature’s brief experiment with self-awareness, the Genographic creed is a moment of Copernican consequence, when we truly awake to our origins and journey.

We are all Africans. We originated in Africa. That is proved by the continent’s rich genetic inheritance. Africans are more diverse than the rest of humanity put together, because they are drawn from the pool of humans who did not leave. As Wells points out, two Africans from the same village could be more divergent from each other than either is from a non-African. The question is whether this new understanding will reinforce prejudices against Africans, or help end them.

As Africa’s population rises and parts of the continent collapse under economic and environmental pressures, eugenics may reappear. This would be revised eugenics, conceding the physical superiority of Africans in everything from penis size to sprinting, but holding that they are not selected for problem solving, having never benefited from the training ground of the Eurasian steppe (with its need for microliths, clothing and portable shelters). “To give them equality is to sink to their level, to protect and cherish them is to be swamped in their fecundity,” wrote the novelist H.G. Wells, a proponent of eugenics.

Rubbish, says Spencer Wells. There are no nasty genetic secrets out there about Africans, “certainly no differences in general intelligence”. Whites’ superior attitudes towards blacks, he reckons, is based on a “general correlation between latitudes and economic development”. Even if National Geographic is suffocated by political correctness and an obsessive need for a tidy narrative, he is right. If Africa is stunted, it is through circumstance, not genetics. Just look at the Nile-Saharan Genetic markers on President Obama’s Y-chromosome.
Besides, evolutionary biologists point out that cold rewarded as much as it punished. With plentiful reindeer, fish in the rivers, nutritious roots and berries, more water, more wood and fewer diseases, the living may have been easier in the north.

In any case, the genetic questions for Africa come rolling in. Who are the most ancient Africans? Why did some Africans select for milk digestion and others remain intolerant? Did the slave trade weaken natural selection in west Africa or strengthen it? What is the genetic legacy of Arabs and Europeans in east Africa?

There is agreement that Y-chromosome Adam would have looked much like a San Bushman of the Kalahari, with an epicanthic fold over the eyes, a hairless cocoa body, and a loose graceful gait. East and southern Africa would have been scattered with hunter-gatherer groups. They probably spoke click languages similar to the San. In modern times they were replaced by farming Bantu from western Africa. Now only the San and a few other groups like the Hadza in Tanzania keep alive the ancient hunter-gatherer traditions.

All this is provocative. Success for the Genographic Project undermines traditional beliefs. When I asked Spencer Wells about it, he took the Genographic Fifth Amendment: genetics tells us where we come from, not why we are here, or where we are heading. “We try to present it as one aspect of their history. We tell them it does not replace their mythos. It just means they are connected to people all over the world.”

Ajay Royyuru of IBM admits that he is “not used to using the part of my brain that deals with religious questions”. But he had a revelation, a year in. “The bulb went off in my head. All the differences we see in each other, colour of skin and the rest, I realised they were all so minor.” Religions, he says, have appeared and disappeared since Y-chromosome Adam. Royyuru acknowledges that the research means the end of any literal understanding of large parts of Hinduism. “I came to see these like clothes you wear. The human population has existed through all this.”

AfricaTry telling a Hindu nationalist or a Mormon, whose Book is confounded by genetics. “American-Indians are not the lost tribe of Israel,” says Wells evenly. “They are from Central Asia.” As science advances, so too will creationism. The clash of cultures will deepen between those who recognise genetic markers and their implications, and those for whom the price of acceptance is too high: ditching their creed. Right now, creationism is winning. The only major religion in Africa to uphold Darwin is the Roman Catholic church. Hominid finds in Kenya are stored in a vault in the National Museum to stop them being destroyed by religious fundamentalists. The persistence of creationism “is something we as evolutionary biologists cry about,” says Wells. “Literally.”

Yet the Exodus story as told by geneticists may prove more vivid than any religious tradition. There is poetry in the way the Lord parted the Red Sea for Moses, congealing the waters, then “dasheth in pieces” the pharaoh and his chariots. But the physical arc of the story is puny. Writing this, I’ve been listening to “Exodus” by Bob Marley.

Exodus: movement of jah people! So we’re going to walk—alright!—through da ropes of creation: We the generation (tell me why!) trod through great tribulation.

It is not the Rastafarian return to the Rift Valley that comes to mind as I listen, genetically elegant though it now seems, but the first hunter-gatherers making it through the Gate of Tears and heading for every point in our world.



"The Human Career" by Richard Klein, 1989.  The authority on human evolution.

"The History and Geography of Human Genes" by Luca Cavalli-Sforza, 1994.  The authority on evolutionary genetics.

"The Journey of Man" by Spencer Wells, 2002. Zippy if self-promotional.

"Genome" by Matt Ridley, 2000. The best overview of the genome.

"Self-Made Man and His Undoing" by Jonathan Kingdon, 1993. Rare insights and African knowledge.


Picture Credit: Sand Paper, khym54, whiteafrican, nd.strupler (all via Flickr); Andrew McConnell/WPN 

(J.M. Ledgard is The Economist's Nairobi correspondent and author of "Giraffe". His next novel is about the ocean. His last piece for Intelligent Life was about the tallest building in the world.)