In 2005, a few months after a sham election that saw Mubarak returned for his fifth term with more than 90 percent of the vote, Gad was appointed to lead the team that would gather Tutankhamun’s genetic code. There was just one problem: he had never actually worked on ancient DNA samples before — no one in Egypt had. So the Discovery producers brought in a forensic anthropologist and Egyptologist called Angelique Corthals, who was based at the KNH Centre for Biomedical Egyptology in Manchester, UK, to teach him.

The lab built for the project, located beneath the lofty, dusty exhibition halls of the Egyptian Museum, is a network of futuristic underground rooms with shiny floors, UV lights, and sterilized walls: Corthals calls it “the bat cave.” When she arrived in June 2006, she and Gad’s team equipped it with the necessary scientific equipment, including a sequencing machine worth half a million dollars, and the latest forensic kit for extracting and amplifying DNA. “The budget was amazing,” she told me, later. “We could order whatever we wanted.”

Then she showed them how to extract ancient DNA using the “window technique”: slicing a plug of bandages, skin and flesh from a mummy, before using a biopsy needle, a hand-cranked drill surrounded by a hollow tube, to retrieve a sample of powdered bone. Afterwards, the square plug is eased back into the hole: done correctly, the damage barely shows. The novice team learned the techniques on the run as they embarked on their first project for Discovery: the search for Hatshepsut, one of the few female pharaohs, whose mummy had never been found.

The idea was to test DNA from anonymous remains from the Valley of the Kings that might be Hatshepsut, and compare them with known members of the royal family. In just a couple of months, Corthals and Gad had established a very tentative link between two of the mummies. The breakneck speed of filming meant that there was no chance to firm up the results, however: the preliminary hints were enough for Discovery’s documentary, Secrets of Egypt’s Lost Queen, and a cover story in National Geographic.

With Hatshepsut out of the way, Discovery pushed the team along: it was time to move on to Tutankhamun himself. The plan was to put together a royal family tree by testing Tutankhamun, along with ten other potentially related mummies. These included the nameless pharaoh from tomb KV55, and the two foetuses from Tutankhamun’s tomb. Gad sampled most of these mummies in the biopsy room under the museum, with Corthals’ help.

Tutankhamun, though, was still in his tomb, 300 miles away in the Valley of the Kings. Extracting bone samples from his mummy would be a pivotal scene in Discovery’s next film. To head off criticism that he was selling the pharaohs’ secrets to foreigners, Hawass decided that for this key moment, the team entering Tutankhamun’s tomb would have to be entirely Egyptian. Corthals would stay in Cairo watching via a live video link, and for the first time in his lightning-fast training, Gad would be on his own.

ON THE MORNING OF FEBRUARY 24, 2008, it was time to enter the pharaoh’s tomb.

“You could feel the tension coming up, up, up from everybody,” Gad told me. If he applied too much pressure with the biopsy needle, one of Tutankhamun’s fragile bones could easily snap. “But I put my faith in God, and we did it.”

Two-and-a-half hours later, 15 tiny bone samples from sites scattered across each of the king’s legs had been safely deposited into little plastic tubes.

When Gad was finished, Corthals asked for a close-up shot on the video link. The fragments looked charred, and not as clean as the samples that they had taken from the other mummies. Tutankhamun was not going to be an easy mummy to deal with.

To determine how the royal mummies were related, the team now moved on to amplifying fragments of mitochondrial DNA, which is passed down the maternal line, as well as DNA from the male-determining Y-chromosome, which goes from father to son. The main goal, however, was genetic fingerprinting, Gad’s speciality, on the DNA inherited from both parents.

Unfortunately, over the millennia, black resins and other materials used in the embalming process had crept into the mummies’ bones. The effects were particularly bad for Tutankhamun, whose embalmers had poured so many bucketfuls of unguents over his mummy that it was found stuck fast to the bottom of his coffin. These impurities clung tight to the king’s DNA, blocking chemical reactions and turning the samples inky black. It took six months to figure out how to remove the contaminants, and prepare the samples for analysis.

Finally, the team got its first result from the boy king: a snatch of Tutankhamun’s Y-chromosome. Today, Gad says he can’t remember the actual moment when they realized they had their results. The version laid down in his memory is the one that the team re-enacted later for the TV cameras: a close-up of colored peaks on a computer screen followed by smiles and cheers, and team members shaking white-gloved hands.

THE GRAND, COLUMNED HALLS of the Egyptian Museum in Cairo are usually dominated by stone giant statues and sarcophagi arranged to dramatic effect. But on February 17, 2010, all attention was focused on three neatly wrapped mummies. Behind them, four men sat in a row, their heads just visible over a forest of microphones carrying the logos of the world’s TV companies.

Gad and the team had exciting news for the waiting journalists. After amplifying DNA from every mummy they tested, they had constructed a five-generation family tree. The anonymous KV55 mummy, the team said, was actually Tutankhamun’s father, the revolutionary Akhenaten, while the foetuses were most likely his daughters. But the most jaw-dropping revelation was the secret that had felled the 18th Dynasty: Tutankhamun’s parents had been siblings.

Hawass ensured that the announcement was accompanied by a media blitz, including a research paper published in the esteemed Journal of the American Medical Association and a four-hour special on the Discovery Channel called King Tut Unwrapped. He later took to the pages of National Geographic to play up the ancient soap opera. The union between Akhenaten and his sister “planted the seed of their son’s early death,” he wrote. “Tutankhamun’s health was compromised from the moment he was conceived.”

The team didn’t publish any information on the mummies’ racial or ethnic origins, saying that the data on the issue was incomplete. But that didn’t stop others from speculating. A Swiss genealogy company named IGENEA issued a press release based on a blurry screen-grab from the Discovery documentary. It claimed that the colored peaks on the computer screen proved that Tutankhamun belonged to an ancestral line, or haplogroup, called R1b1a2, that is rare in modern Egypt but common in western Europeans.

This immediately led to assertions by neo-Nazi groups that King Tutankhamun had been “white,” including YouTube videos with titles such as King Tutankhamun’s Aryan DNA Results, while others angrily condemned the entire claim as a racist hoax. It played, once again, into the long-running battle over the king’s racial origins. While some worried about a Jewish connection, the argument over whether the king was black or white has inflamed fanatics worldwide. Far-right groups have used blood group data to claim that the ancient Egyptians were in fact Nordic, while others have been desperate to define the pharaohs as black African. A 1970s show of Tutankhamun’s treasures triggered demonstrations arguing that his African heritage was being denied, while the blockbusting 2005 tour was hit by protests in Los Angeles, when demonstrators argued that the reconstruction of the king’s face built from CT scan data was not sufficiently “black.”

For IGENEA, the whole affair was linked to a marketing exercise. It appears to have had no access to the data itself except a snapshot of a computer screen in a TV show, and yet the company now advertises a Tutankhamun DNA Project, which it describes as a search for the pharaoh’s “last living relatives.” The company offers a variety of online DNA tests costing up to $1,500. The sweetener? If your profile matches that of the boy king, you get your money back. Gad refuses to even say whether IGENEA’s analysis of the DNA shown in the documentary is correct. “This is not,” he says, “how science should be conveyed.”

Is there any culture in history that so many are so keen to lay claim to, whether for financial or political gain? “Owning” the pharaohs, it seems, means establishing a privileged place in history to being the founders of civilization. No matter that the ancient Egyptians were almost certainly an ethnically mixed group. They have become a mirror for whoever looks at them, focusing and reflecting the battles and prejudices of today.

Hawass and Gad’s triumphant announcement about Tutankhamun’s family triggered excited media coverage around the world. But what journalists didn’t report was that behind the scenes, the field of ancient DNA was locked in a bitter dispute. A few months later, the Journal of the American Medical Association published a short letter from Eske Willerslev and Eline Lorenzen at the Center for GeoGenetics in Copenhagen, Denmark, one of the world’s most respected ancient DNA labs. It tore Gad’s results — and his reputation — to shreds.

“In most, if not all, ancient Egyptian remains, DNA does not survive to a level that is currently retrievable,” the pair wrote. “We question the reliability of the genetic data presented in this study and therefore the validity of the authors’ conclusions.” Roughly translated, it meant: “we don’t believe a word of it.”

After the heady beginnings of the ancient DNA field in the 1980s and early 1990s, it didn’t take long for the fall. PCR turned out to be extremely susceptible to contamination, far more so than anyone had initially realized. Any trace of modern DNA in the environment — a speck of dust, a skin cell, a drop of sweat — could dwarf any ancient DNA present and skew the results. In study after study, further analysis revealed that many of the genes that researchers had reported so proudly weren’t ancient at all. Woodward’s 80-million-year-old dinosaur DNA? It actually belonged to a modern human.

Researchers had to start again, with incredibly strict techniques and controls. Some experts refused to study human mummies at all, arguing that with the available techniques it would never be possible to know for certain that samples had not been contaminated by people who had previously handled the mummies, or by the researchers themselves. Instead, they looked at other species — killer whales, penguins, cave bears — whose DNA is less likely to be floating around a lab.

Others scientists felt that the backlash had gone too far, however. They carried on working with human mummies, and publishing the DNA they amplified. The field divided into two camps — the sceptics and the believers — who published in different journals, attended different conferences, and refused to talk to each other. Researchers from the biggest labs, including Willerslev and Lorenzen, were in the sceptics’ camp. Many linked to the Egyptian Museum were believers.

Studies of Egyptian mummies were the most controversial of all, because DNA degrades quickly at high temperatures. Although it is possible to retrieve DNA from much older frozen specimens, such as mammoths, the sceptics argued that genetic material from Tutankhamun and his relatives couldn’t possibly have survived 3,000 years in the baking-hot deserts of Egypt. Far from uncovering the secrets of the pharaohs, Gad and his team had been fooled by cross-contamination with modern DNA.

Although Gad and his team wore gloves and masks when working on Tutankhamun, no previous archaeologists had done the same — from those unwrapping him in 1925 to those putting him through his CT scan some 80 years later. “You see TV people handling mummies with their bare hands, their sweat dripping on to the mummy,” Tom Gilbert, who heads two research groups at the Center for GeoGenetics, told me.“That’s a classic route of contamination.”

Gad’s team had used other safeguards, including repeating some of their results in a second lab. But critics countered that the team didn’t publish its raw data, and didn’t sequence much of the DNA they amplified. Lorenzen, one of the authors of the letter that attacked Gad’s work, told me: “When working with samples that are so well-known, it is important to convince readers that you have the right data. I am not convinced.” She says she felt obliged to speak out after seeing the huge press coverage the results gained, lamenting that what she saw as flawed conclusions would now be taught in school.

Other prominent scientists shared her concerns. The study “could do a much better job,” complained Svante Pääbo of the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, one of the founders of the ancient DNA field. Ian Barnes, an expert in the survival of ancient DNA at the University of London, said he would be “extremely cautious” about using the data. Gilbert, of GeoGenetics, was more blunt. “I’ve given up on the field a long time ago,” he said. “It’s full of crap.”

Gad and his colleagues had been under intense pressure “from Discovery and the forceful Hawass” to get results from incredibly difficult samples. Had they stared into a mix of messy data and contamination and imagined the family relationships they so desperately wanted to see? The team insisted their results were real. They couldn’t prove it, but they were convinced that the elaborate embalming techniques used on Egyptian royalty must have helped to preserve the mummy DNA.

“I don’t understand people’s harshness,” says Carsten Pusch, who joined the Egyptian Museum team soon after the samples were collected. He told me about detailing the months of painstaking experimentation it took to coax DNA from the mummies bones. “These people have never worked with royal mummies. This is pioneering work. I just wish everyone would give us more time.”

Time was the one thing they turned out not to have.

GAD SAT IN HIS CAIRO LAB as the demonstrations outside grew stronger by the day. It was January 2011. A month earlier, a young street trader from Tunisia had burned himself alive in protest at police corruption. The riots he triggered had become a wave of mass defiance against repressive regimes around the Arab world.

Few analysts had predicted that Egypt would become a hotbed of demonstrations, but after 30 years of Mubarak’s stifling rule, the frustrations of the citizens were fierce. Huge crowds were turning out to protest against the dictatorship.

Gad was itching to take part in the marches, but worried about jeopardizing his job. If there was going to be a revolution, he thought that he could better help build a new Egypt if he maintained his position of influence. But by the morning of Friday January 28, he could stand by no more. The day promised the biggest demonstration yet, since Friday prayers would provide a natural starting point for marches. Gad went to pray with his two sons-in-law in a mosque at the Cairo suburb of Nasr City, then walked the five miles to Tahrir Square.

Events that day exploded beyond everyone’s expectations. Hundreds of thousands of people from all walks of life demonstrated for a democratic Egypt, enduring violent attacks from pro-government groups as soldiers in tanks looked on. The police melted away. Normal order was suspended.

That night, the Egyptian Museum, which stands within sight of Tahrir Square, was broken into by thieves. The galleries containing items from Tutankhamun’s tomb and the surrounding period were worst hit, with glass cases smashed and their contents thrown, broken, onto the floor.

The authorities claimed that the rampage was carried out by opportunistic looters who entered through a glass skylight, but the fact that the ceiling is thirty feet high fuelled rumours that it was an inside job, staged by government supporters to make the demonstrators look bad. If so, the ruse backfired: once the break-in became apparent, young protesters formed a human chain around the museum to protect it from further attacks.

While Gad joined the protests, Zahi Hawass stuck with the regime. In the middle of the uprising he was rewarded with a promotion to the cabinet as minister of state for antiquities. The world’s most famous Egyptologist repeatedly denied reports that priceless artefacts around the country were being looted: nothing was missing from anywhere, including the Egyptian Museum, he said. “All of the Egyptian monuments are safe,” he wrote in a statement on his blog on February 2, adding later: “I want everyone to relax.” What was needed, he insisted, was a return to order. He appeared on foreign television expressing strong support for Mubarak.

A few days later, on February 11, Mubarak stepped down as president and the military stepped in. Hawass was forced to admit that antiquities were being looted after all, and his position began to unravel. His critics seized their opportunity, and he soon faced a string of accusations from stealing antiquities to corruption, all of which he denied.

In particular, he was attacked for his Tutankhamun projects, accused of illegally allowing National Geographic to exhibit Tutankhamun’s treasures abroad, and of threatening national security by allowing foreign researchers to study the royal mummies. The interim leadership was already under pressure from protesters wanting to purge remnants of Mubarak’s regime. In July 2011, Hawass was fired.

THAT AUTUMN, I met Gad in the leafy, sunlit garden of the Marriott hotel in Zamalek, an affluent district of Cairo, where we were served iced tea by scrupulously polite waiters. Gad, a small man in his fifties, fit in perfectly with his courteous manners and wry smile.

In a culture where prominent figures like Hawass are not slow to advertise their attributes and achievements, Gad is different. He is modest and thoughtful, and when he described his experiences to me, it felt as though his aim was not to impress but simply to share.

He brimmed with excitement about the revolution. He showed me videos of the clashes on his mobile phone, and pictures of his grandson, Ali, born into a new Egypt just two hours after Mubarak stepped down. With Egypt heading into the first democratic elections of its long history, Gad was elated about his country’s future. He called 2011 “the year of hope.”

When it came to research on the royal mummies, however, the revolution had brought catastrophic news. After Hawass’s departure, it became clear that the antiquities service had huge debts, owing hundreds of millions of dollars to various banks. The money that had poured in from the Tutankhamun exhibitions was gone.

The man who had defined archaeology in Egypt for more than a decade was out, and a succession of short-lived antiquities ministers arrived, each apparently unable to deal with the dire financial concerns, or stem the continued looting of archaeological sites across the country.

With so many other priorities and nobody clearly in charge, work on the mummies ground to a halt. Scientists on the team moved to positions elsewhere. Gad took up a desk job at the National Research Center, students scattered abroad and plans to search for the mummy of Nefertiti were shelved. Hawass had been the motivating force behind the mummy studies, and he had paid a high price. Now nobody at the antiquities service was interested in the work, or willing to risk approving it.

As we talked, I could see that Gad was upset by the criticisms of his work, and convinced that his results were correct. But with the ancient DNA lab standing empty, he had no way to prove it.

PERHAPS THE CROCODILE GOD, SOBEK, was smiling on Gad. In ancient times, the Egyptians embalmed reptiles as offerings to this ferocious deity. Thousands of years later, researchers in New York and Florida probed some of them with PCR. And to the astonishment of mummy DNA sceptics around the world, they obtained sequences that were undoubtedly crocodile.

The work, carried out in unimpeachable conditions, was published in October 2011, around the same time I met Gad. It was quickly followed by a convincing report of ancient DNA from mummified cats. Together, the two studies swept aside years of bitter argument. Even hardened critics like Gilbert were persuaded that, in some Egyptian mummies, at least, DNA does survive. In just a few months, the prospects for the field were dramatically reversed.

Researchers still argue over the role that contamination might have played in the Tutankhamun study. But the cat and crocodile results prove that Egyptian mummies should be amenable to a new wave of DNA technologies, dubbed next-generation sequencing, that don’t rely on PCR. Instead of amplifying specific target sequences, these methods read millions of small fragments in a sample at once, then use sophisticated computer algorithms to stitch the resulting sequences together. They give a broad picture of all DNA present in a sample, making it easier to spot contamination. Researchers can see if DNA from more than one individual is present, and to check for patterns of damage that you might expect in ancient DNA.

By targeting much shorter sequences, scientists can also probe even older samples, where the DNA is more fragmented, and gain much more detailed data than ever before, including entire genomes. Since 2010, leading ancient DNA labs, including Paabe’s in Leipzig and Willerslev’s in Copenhagen, have been using next-generation sequencing to decipher the genomes of a variety of ancient humans preserved in cold conditions: a 4,000-year-old Palaeo-Eskimo dubbed Saqqaq Man; Denisova Man, a novel human species unearthed in Siberia; and Ã–tzi the Iceman, a 5,300-year-old mummy found frozen in the Central Eastern Alps.

Now we know that DNA does survive in Egyptian animal mummies, using next-generation sequencing to stitch together the DNA of their human counterparts “isn’t rocket science,” says Gilbert. “What limits you is the size of a sample. For Denisova Man they had just a finger bone. Here they have the whole mummy.” In other words, obtaining entire genomes from ancient Egyptians could soon be routine.

The technique promises a far more intimate picture of the pharaohs. If used on Tutankhamun, it would retrieve DNA not just from the king himself but from all of the other organisms associated with his mummy; everything from the contents of his stomach, to the plant products used by his embalmers, to the infections he carried. Gad and his colleagues call it the “ancient Egyptian meta-genome.”

Next-generation sequencing may also transform the search for the genetic origins of the ancient Egyptians. Egyptologists could, in theory, use next-generation sequencing to look at the entire genomes of hundreds or even thousands of individuals: there are certainly enough mummies around. This could radically deepen their understanding of where these populations really came from, and how they moved around over time. For those who are interested in hearing the results, that just might solve the riddle over the pharaohs’ race and ancestry once and for all.