Elsewhere, he notes the Prophet’s references to “the seven earths”; El-Naggar claims that geologists say that Earth’s crust consists of seven zones. In another passage, the Prophet said that there were 360 joints in the body, and other Islamic researchers claim that medical science backs up the figure. Such knowledge, the thinking goes, could only have been given by God.

Nobody can just write what he thinks without proof. But we have real proof that the story of Adam as the first man is true.

Critics are quick to point out that Islamic scientists tend to use each other as sources, creating an illusion that the work has been validated by research. The existence of 360 joints, in fact, is not accepted in medical communities; rather, the number varies from person to person, with an average of 307. These days most geologists divide Earth’s crust into 15 major zones, or tectonic plates.

El-Naggar even sees moral meaning in the earthquake that triggered the 2005 tsunami and washed away nearly a quarter of a million lives. Plate tectonics and global warming be damned: God had expressed his wrath over the sins of the West. Why, then, had God punished Southeast Asia rather than Los Angeles or the coast of Florida? His answer: Because the lands that were hit had tolerated the immoral behavior of tourists.

The influence and popularity of El-Naggar—as a frequent guest on Arab satellite television, he reaches an audience of millions—does not sit well with Gamal Soltan, a political scientist at Al-Ahram Center for Political and Strategic Studies, a Cairo-based think tank.

“This tendency to use their knowledge of science to ‘prove’ that the religious interpretations of life are correct is really corrupting,” he tells me. Soltan, who got his doctorate at the University of Northern Illinois, works in a small office that’s pungent with tobacco smoke; journals and newspapers lie stacked on his desk and floor. “Their methodology is bad,” he says. Soltan explains that Islamic scientists start with a conclusion (the Koran says the body has 360 joints) and then work toward proving that conclusion. To reach the necessary answer they will, in this instance, count things that some orthopedists might not call a joint. “They’re sure about everything, about how the universe was created, who created it, and they just need to control nature rather than interpret it,” Soltan adds. “But the driving force behind any scientific pursuit is that the truth is still out there.”

Researchers who don’t agree with Islamic thinking “avoid questions or research agendas” that could put them in opposition to authorities—thus steering clear of intellectual debate. In other words, if you are a scientist who is not an Islamic extremist, you simply direct your work toward what is useful. Scientists who contradict the Koran “would have to keep a low profile.” When pressed for examples, Soltan does not elaborate.

The emphasis on utility wasn’t always present here. The Napoleonic occupation from 1798 to 1801 brought French scientists to Egypt. The arrival of the Europeans alerted Egyptians to how far behind they’d fallen; that shock set in motion a long intellectual awakening. During the 150 years that followed, institutions for higher learning in Cairo gave the city an international reputation for prestigious institutions, and the exchange of scholars went in both directions, with Egyptians going west and Americans and Europeans coming here.

Then came the 1952 coup led by Gamal Abdel Nasser that toppled King Farouk I. Nasser was the first modern leader to position himself as a spokesman for the whole Arab world. His brand of nationalism was meant to unify all Arab people, not just Egyptians, and it set them in opposition to America and Europe. “After Nasser, Arab nationalism raised suspicions about the West,” Soltan says.

In Soltan’s view, the twin forces of Islamization and government policy have inadvertently worked together to blunt scientific curiosity. “We are in a period of transition,” he says. “I think we are going to be in transition for a long time.”

People and the authorities are still grappling with religion’s place in Egyptian society, resulting in a situation similar to one in Europe during the time of Copernicus and Galileo, when scientific knowledge was considered threatening to the prevailing religious power structure. For now, the door on freedom of thought has nearly been shut. As Soltan points out, “Cairo University has not received Western professors since the 1950s, and because of the turmoil in the country, many professors who didn’t like the regime were excluded from the university.”

I walk the campus of Cairo University prior to meeting Waheed Badawy, a chemistry professor who has taught there since 1967. His students, male and female, wander in and out during our talk; the women all wear head covers, highlighting the degree to which religion is particularly strong among the young. He wears a white lab coat, and there are religious verses posted on his laboratory walls and corkboard. Yet Badawy, who specialized in solar energy conversion while working for Siemens in Germany in the 1980s, does not consider himself an “Islamic scientist” like El-Naggar. He is a scientist who happens to be devout, one who sees science and religion as discrete pursuits.

“Islam has no problems with science,” he says. “As long as what you do does not harm people, it is permitted. You can study what you want, you can say what you want.”

What about, say, evolutionary biology or Darwinism? I ask. (Evolution is taught in Egyptian schools, although it is banned in Saudi Arabia and Sudan.) “If you are asking if Adam came from a monkey, no,” Badawy responds. “Man did not come from a monkey. If I am religious, if I agree with Islam, then I have to respect all of the ideas of Islam. And one of these ideas is the creation of the human from Adam and Eve. If I am a scientist, I have to believe that.”

But from the point of view of a scientist, is it not just a story? I ask. He tells me that if I were writing an article saying that Adam and Eve is a big lie, it will not be accepted until I can prove it.

“Nobody can just write what he thinks without proof. But we have real proof that the story of Adam as the first man is true.”

“What proof?”

He looks at me with disbelief: “It’s written in the Koran.”

Tunis, Tunisia: After the hazy congestion of Cairo, the briny sea breeze and open spaces of Tunis are liberating. Anchored on the Mediterranean coast, Tunisia’s capital is rimmed by mountainous suburbs with palm trees and gardens trellised with bougainvillea. The town where I am staying is Sidi Bou Said. It has a kind of high-rent antiquity that feels like Italy or the south of France. Indeed, just 80 miles from Sicily, Tunis is physically closer—and culturally closer, too, many people say—to Mediterranean Europe than it is to much of the rest of the Arab world. “They’re not really Arabs,” my Egyptian translator says en route to the airport. “They’re French.” He does not mean it as a compliment.

“We have succeeded in keeping extremism and that mentality out of our schools and institutions,” says a government official who asks not to be named. “We are an island of 10 million people in a sea of Islamists. The extremists want to remove the buffer between religion and everything else, including science. There has to be a buffer between religion and science.”

Tunisia, a former French protectorate that became independent in 1956, shares with its Arab neighbors a poor human rights record and a president whose family has been charged with corruption. Freedom House, a nonprofit monitoring group, ranks it 179 out of 195 countries for press freedom. In March, a dissident was sentenced to three and a half years in prison (after already serving two years while awaiting trial) for decrying the lack of freedom. Yet, unlike the Egyptians who complain openly about their lack of freedom, the Tunisians I encounter tend to put things in a more optimistic light. One reason for the allegiance to their government is a widely held belief that the alternative to their president, Ben Ali, would be Islamic extremists. Another reason many support the government: It has been more effective than those of most Arab countries at delivering basic services, including education and health care.

Although officially Muslim, Tunisia maintains the closest thing there is in the Arab world to separation of mosque and state. In public sector jobs, beards and veils are banned. On the street, you see young women with their hair covered, but it is not unusual to see the same women wearing tight jeans, making the veil as much fashion accessory as religious garment. School textbooks lack information on different religions and religious beliefs. “Islamic science” is not a university subject here, as it is in Egypt; “Islamology,” which looks critically at Islamic extremism, is.

In contrast to the situation in Egypt, where even the most Western-oriented scientist I talked to at some point or other declares himself to be “a good Muslim,” in Tunisia the personal religious views of scientists I meet hardly seem relevant. Even so, I am reminded how science, like politics, tends to be local, addressing immediate problems using materials at hand. Sami Sayadi, director of the bioprocesses lab at the Biotechnology Center of Sfax, Tunisia’s second-largest city, spent more than a decade figuring out how to turn the waste of olives pressed for oil into clean, renewable energy. Olives have been a major export here since the heyday of Carthage and remain an icon for Arabs everywhere, making Sayadi’s achievement sound almost like modern-day alchemy.

Sayadi’s thinking is the kind of pragmatism the Tunisian government wants, and in recent years it has come to see science and technology as important tools of national advancement. There were 139 laboratories across different disciplines in 2005, compared with 55 in 1999. The government is actively promoting this growth.

Ninety minutes south of Tunis is the Borj-Cedria Science and Technology Park, a campus that will eventually combine an educational facility, an industrial and R&D center, and a business incubator. The park’s completion is still years away, however, and although some buildings and labs are in place, geologists, physicists, and other scientists laboring here work with equipment that in the West wouldn’t pass muster in many high schools. They pursue projects for the love of science.

The situation may soon change. In its hunger for patents and profits, the Tunisian government is giving out four-year contracts to labs whose work has industrial applications. Senior researchers at Borj-Cedria currently make about $1,100 a month (a livable but modest wage here), but the new program would give anyone who earns a patent a 50 percent stake in royalties.

Still, Tunisia’s support of science has clear limits: Projects whose aim is solely to advance knowledge get no support. “Everyone would like to do [basic] research,” says Taieb Hadhri, Minister of Scientific Research, Technology, and Competency Development, who has held the cabinet-level post since the department was created in 2004. “I’m a mathematician by training, and I would also like to do [basic] research. But that will have to come later. We have more pressing needs now.”

And the push toward advancement here is not entirely free from the pull of tradition, as I learn when I visit Habiba Bouhamed Chaabouni, a medical geneticist who splits her time between research and teaching at the Medical Faculty of the University of Tunis and seeing patients at the Charles Nicolle Hospital, also in the capital. In 2006, she won a L’Oréal-UNESCO Women in Science Award, a $100,000 prize given to five women, each representing one of the continents, for her work analyzing and preventing hereditary disorders. When she greets me in her office, she is wearing a white lab coat. Test tubes clink as they spin in a centrifuge to separate strands of a patient’s DNA that Chaabouni will examine later.

Chaabouni recalls the early days of her career, in the mid-1970s, when she saw children afflicted with disfiguring diseases. “It was very sad,” she says. “I met families with two, three, four affected siblings. I wanted to do something about it, to know how to prevent it.” There was no facility for genetic research at that time, and for two decades, she lobbied government officials hard for it. “We wanted better conditions and facilities. They also saw we were publishing in international [peer-reviewed] journals. I think the policymakers finally understood the value of developing research.”

The Tunisian medical-genetics community, which includes about 100 doctors and technicians, now publishes more than any other Arab country. “We looked on PubMed, and we’re ahead of Egypt,” Chaabouni says, beaming. “Not by a lot, but remember, we’re one-tenth the size.”

Over the last 30 years, Chaabouni has also seen how people who once resisted her message have begun listening. Once, genetic counseling or even coming in for certain treatments almost amounted to a social taboo; now, it is becoming more accepted, and things that were once simply ignored or not spoken of—such as autism in children, which is being identified more commonly—are more often out in the open.

For all that, Chaabouni still sees how her advice sometimes clashes with her patients’ beliefs. Like many Arab and Muslim countries, Tunisia has a high incidence of congenital diseases, including adrenal and blood disorders, that Chaabouni has traced to consanguinity.

“It’s a custom here, and in the rest of the Arab world, to marry cousins, even first cousins,” she tells me, though the practice is becoming less common. “Of course, that means they share a lot of genes from common sets of grandparents.”

In other fields, pure research does not get support; in medical genetics, even practically applicable knowledge can spark conflicts with Islamic culture. “Taking a blood sample to study abnormalities is not a problem,” Chaabouni says. “That’s just investigation. The problem is when you take the results of research into the clinic and try to give genetic counseling to patients. Then you have people who won’t accept the idea that they have to stop having children or that they shouldn’t marry their cousin.”

Today prenatal screening and genetic testing is more widely accepted, and when it’s necessary to save the mother’s life, doctors terminate pregnancies. Islamic law permits abortion in cases of medical necessity (where the mother’s life is in jeopardy) until 120 days in utero, at which point it regards the fetus as “ensouled” and abortion becomes homicide. For Chaabouni, the challenge is mainly one of communication. “They look for arguments why you may be wrong,” she says. “They go to other doctors. In the end, they usually follow our advice, but it’s hard because you’re giving them bad news that may also go against what they believe.”

Mohammed Haddad, an Islamology specialist at the Université de la Manouba in Tunis, points out the many little assaults that can turn people’s minds against scientific advances. For example, a sheikh recently declared that he’d found a cure for AIDS—spelled out in the Koran. “He was from Yemen, but they reach us by satellite, and it’s all a big business,” Haddad says. “People listen, and it’s a problem. In this situation, many will die.”

Amman, Jordan: “The Koran says, ‘Read,’ but it does not even say ‘Read the Koran.’ Just ‘Read,’” says Prince El Hassan bin Talal, who greets me at the Royal Scientific Society, Jordan’s largest research institution—one that he helped establish in 1970. Hassan was heir to the throne until his brother, King Hussein, bypassed him in favor of Abdullah, Hussein’s own son. The 60-year-old prince, who speaks classical Arabic and Oxford English and has studied biblical Hebrew, can tick off a whole list of things that are wrong with Jordan, from Western governments and nongovernmental organizations that come proposing solutions without having identified the causes of problems, to a culture that does not value reading. He is bookish himself; during our 40-minute-plus interview, he refers to Kierkegaard, Karen Armstrong’s A History of God, and What Price Tolerance, a 1939 book by his wife’s relative Syud Hossain.

He is also candid, calling suicide bombers “social rejects” and questioning the validity of those who would take the Muslim world back to the times of the Prophet Muhammad. “Are we talking Islam or Islamism?” he asks, pointing out the difference between the religion and those extremists who use the religion to advance their own agendas. “The danger [posed by Islamists] is not only to Christians but also to Islam itself. The real problem is not the Arab-Israel issue but the rise of Islamism.”

Science, rather than religion, is the way to ensure a country’s future, Prince Hassan believes, and he has made supporting scientific achievement a personal mission for almost 40 years. He envisions projects that would promote regional partnerships, including with Israel—an idea that, despite official peace between the countries, remains controversial.

He notes that some important science initiatives are under way. One of the Royal Scientific Society’s pursuits is the Trans-Mediterranean Renewable Energy Cooperation, or TREC, a multinational effort that would use wind, water, geothermal, and solar resources to provide renewable energy from Oman to Iceland. If successful, the endeavor would take decades to be realized. Like Moses standing on Mount Nebo (in fact, the site of the Exodus story lies just about 20 minutes outside Amman), the 60-year-old Hassan knows that he is not likely to see this technological promised land himself.

Islam was open, a strong belief with dialogue. It was tolerant. Then we shifted to being dogmatic.

“Vision,” he says, “is not an individual thing. It’s a collaboration.”

“The biggest disaster in the region, I am sorry to say, is the loss of brainpower,” admits Hassan. The emigration of trained academics plagues the entire Arab world, and half of those students who graduate from foreign universities never return to the Arab states. “A large percentage of [America’s] NASA staff are of Middle Eastern origin,” Hassan notes.

In some ways, the brain drain in Jordan is more obvious than in Egypt because resources here are stretched to the breaking point. Conservative estimates put the number of Iraqi refugees living in Jordan at 700,000—an enormous burden considering that Jordan has just 6 million citizens. To put that figure in perspective, imagine the United States adding 35 million people in a period of four years.

The population influx has triggered inflation, soaring rents and property prices, and urban sprawl. Like Egypt, Tunisia, and Syria (and like Israel, for that matter), Jordan lacks significant natural resources; the country has little oil or fresh water. In fact, since most of the water from the Jordan River’s tributaries has been diverted and no longer flows to the Dead Sea, even the Dead Sea is dying. There are plans for resuscitating it, but they will require a delicate process of regional cooperation, including the Israelis and the Palestinians, and most likely Western aid.

Jordan also lacks financial resources, unlike the oil-rich Gulf states that can afford to treat knowledge and expertise as an accessible commodity, able to be imported as needed. Furthermore, the perception of danger—terrorists bombed three hotels in Amman in 2005, and Al Qaeda has admitted to killing an American diplomat—has all but shut the valve on Jordanian tourism and the considerable revenue it used to bring.

Jordan, the quip goes, is caught between Iraq and a hard place. For now, it embodies many of the issues that the Arab Human Development Report blamed for the region’s intellectual malaise, among them lack of freedom and dysfunctional, authoritarian governments whose security services have too much say; the triumph of who-you-know advancement over merit-based promotion; and poor communication between researchers within the region. Educational opportunities are limited, especially for girls and women. All of this means that if you are a talented scientist, there is a good chance you’ll leave.

“Science needs stability, democracy, freedom of expression,” says Senator Adnan Badran, who has a Ph.D. in molecular biology from Michigan State University, as we drink Turkish coffee at his office. “You must have an environment that’s conducive to free thinking, to inquiry. If you don’t, you’ll never be able to release the mind’s potential. It’s a very bleak story, a very disappointing story, about the state of science and technology in the Arab region.”

He blames a tradition that began with the Ottomans in the 1500s: lowering educational standards and promoting dogma. “We were open. Islam was open, a strong belief with dialogue. It was tolerant, mixing with other civilizations. Then we shifted to being dogmatic. Once you’re dogmatic, you are boxed in,” he says. “If you step outside the box, you’re marginalized—and then you’re out. So you go west.”

That’s what Badran did, spending 20 years in France and the United States, where he earned four patents doing research for the United Fruit Company. His work, which focused on retarding ripeness in bananas, has had huge economic impact—billions of dollars, potentially, because it allows the company to ship its crops around the world without spoiling.

Even so, Badran returned home to Jordan, where he took up academic positions, including the presidency of Philadelphia University in Amman. In 1987, he was made the first secretary general of Jordan’s Higher Council for Science and Technology and was later appointed to the senate by the king of Jordan, Abdullah II. Then early in 2005, the king appointed Badran prime minister, the first scientist to hold that position. The king, who was educated at Royal Military Academy Sandhurst and at Oxford in the United Kingdom, and also attended Georgetown University in Washington, D.C., appreciated Badran’s position on the need for Arab glasnost.

“I wanted to destroy every vested interest, to get rid of cronyism, to build accountability and transparency by freeing the press,” Badran says. The circumstances of Badran’s term were difficult, however. “He was an excellent academic and scientist,” a journalist tells me, “but an ineffective politician.”

Any chance for Badran to advance his agenda went up with the smoke in November 2005 when suicide bombers targeted the three Amman hotels. As the government shifted its focus from internal reform to security, Badran was a casualty of change. The prime minister here serves at the discretion of the king—and also, many people say, by tacit approval of Jordan’s security services. In less than a year, Badran was ousted (his thinking was considered to be too idealistic for that time) and returned to his seat in the senate.

After leaving Badran, I get a primer on Jordan’s most dynamic and hopeful scientific collaboration. I speak with physicist Hamed Tarawneh at his cramped, dingy temporary office at UNESCO’s headquarters in Amman. Tarawneh, a tall, broad-shouldered chain-smoker with a disarming smile, left years ago to get his Ph.D. in Sweden and returned to Jordan just a few months prior to our meeting. He is in the process of assembling a staff of engineers and technicians for SESAME (Synchrotron-light for Experimental Science and Applications in the Middle East), an international laboratory organized around a machine that has wide applications in physics, biology, medicine, and archaeology. Only a handful of these versatile light generators exist, and this is the first in the Muslim world.

Jordan was selected as the site for SESAME after King Abdullah II donated land and ponied up $10 million for the facility that would house the synchrotron. The project is modeled on CERN, the Swiss high-energy physics lab formed after World War II to restore Europe’s tradition of scientific learning. When SESAME becomes fully operational in 2009—the facility at Al-Balqa Applied University near Amman should be complete this June—researchers will rotate through doing their work in weeks-long sessions. Like its European model, SESAME was conceived in part to motivate the region’s best and brightest to stay, or even to return from abroad; the laboratory should also create excitement and opportunity that will attract young students to science.

Tarawneh hopes SESAME will become a knowledge hub for the member states that pay annual dues, a group that now includes Bahrain, Egypt, Pakistan, Turkey, the Palestinian Authority—and Israel, the one country in the region that has a knowledge-based society but has been excluded from almost every other endeavor. “We are scientists,” Tarawneh says. “We don’t care about politics. So now we have a chance to discuss science here and work for the greater good of knowledge. It’s a very good start. It’s a cosmopolitan environment, which is what we’ve been lacking. Now we’ll all know each other as scientists, as people.”

I ask about the legions of scientists who have left Jordan, who regard it as a lost cause.

“Would I earn more if I went to Berkeley?” Tarawneh asks. “Yes, of course. But I am from here. I am an Arab. I am a Muslim. This is where I want to be. And why can’t we build something here that’s ours? In five years, others will see it’s useful, and it will become a world effort and create a culture of scientific inquiry here. Science is the way to break barriers. It’s about development and advancing people’s interests.”

Tarawneh’s enthusiasm makes SESAME’s success seem inevitable, but the king’s support and the international character of the project make it seem like much more than an individual triumph. It is precisely the kind of regional partnership that people like Prince Hassan say is the real road map to peace and prosperity in the Islamic world. As both machine and metaphor, a high-powered generator that shines light on scientific inquiry may be the answer to everyone’s prayers.