Egyptian chemist Ahmed Zewail first proposed building a $2 billion science and technology institute in Cairo 12 years ago, just after he won a Nobel Prize. Then-President Hosni Mubarak promptly approved the plan and awarded Zewail the Order of the Nile, Egypt’s highest honor. Within months, the cornerstone was laid in a southern Cairo suburb for a “science city” due to open in five years.

But while Zewail, who has taught at Caltech in California since 1976, went on to collect more awards and honorary doctorates abroad, his pet project got mired in a jungle of bureaucracy and corruption.

His growing popularity in Egypt, where he was touted as a possible presidential candidate after mass protests brought down Mubarak this year, seemed to threaten the officials overseeing the institute, so they blocked it every way they could.

“We didn’t get anywhere,” Zewail told Reuters back in February.

But with revolution now sweeping the Middle East, Egypt’s ruling military council and interim civilian government gave the project the green light in June. Supporters hail the decision as a positive step toward a new, more modern Middle East.

“Some people in the old regime were not happy with the limelight focused on Dr Zewail,” said Mohammed Ahmed Ghoneim, a professor of urology at Egypt’s University of Mansoura and a member of the board of trustees. But now, he noted with satisfaction, “the decision makers have changed.”

The project is a “locomotive that will pull the train of scientific research in this country,” he said.

The poor state of science in the Middle East, especially in Arab countries, has been widely documented. Only about 0.2 percent of gross domestic product in the region is spent on scientific research, compared to 1.2 percent worldwide. Hardly any Arab universities make it into lists of the world’s 500 top universities.

But Arab scientists say the first steps toward change have been taken.

A recent Thomson Reuters Global Research Report showed countries in the Arab Middle East, Turkey and Iran more than doubled their output of scientific research papers between the years 2000 and 2009. The progress admittedly started from a low base, rising from less than 2% of world scientific research output to more than 4% at the end of the decade, but the curve is definitely pointing upwards.

“The region is taking a growing fraction of an expanding pool,” the report said.

“The Arab-Muslim world has improved greatly, even if the universities are still pretty mediocre by and large,” said Nidhal Guessoum, an Algerian astrophysicist who teaches at the American University of Sharjah in the United Arab Emirates.

“The educational system in primary and secondary schools is still lagging behind world standards, but relative to what it was 30-50 years ago, there is clearly a huge improvement.”

AN ISLAMIC GOLDEN AGE

In many ways the Arab world is seeking a return to a glorious past. In the so-called Islamic Golden Age between the eighth and thirteenth centuries, the region was on the cutting edge of science. Back then, the best scientific minds worked in Baghdad, Cairo or Cordoba in then-Muslim Spain.

Muslim mathematicians invented algebra and Muslim astronomers mapped the heavens. Hospitals were so advanced in the Islamic world that the most important medical textbook in European universities from the thirteenth to seventeenth centuries was a Latin translation of The Canon of Medicine, completed in 1025 by the Persian physician and philosopher Ibn Sina, better known in the West as Avicenna.

But starting in the 17th century, the scientific revolution catapulted Europe far ahead of the Middle East. The rulers of the Ottoman Empire, which included most of the Middle East, seemed unwilling or unable to keep up with the times.

Reasons put forward for the decline range from the shattering effect of the Mongol invasions in the 13th century to the colonial exploitation the region suffered in the 20th.

Economic historians say Europe’s growing sea power in the 15th and 16th centuries shifted its trade focus to the oceans, slowing commerce on the overland routes that crisscrossed the Middle East.

Another theory blames the nature of Islam itself.

THE ROLE OF ISLAM

While it may not be the main impediment, Islam certainly plays a role in limiting the scope of science in the Muslim world. Ideas that seem to contradict the Koran are often greeted with suspicion, and are sometimes outright rejected by religious authorities. Many Muslims cite the Koran to deny the theory of evolution, for instance, much like fundamentalist Christians who use the Bible to refute Charles Darwin.

Rana Dajani, a molecular biologist at Jordan’s Hashemite University outside Amman who is a practicing Muslim and wears a headscarf, said her Jordanian students can accept evolution in animal species, but stop short when it comes to agreeing that humans and apes had a common ancestor.

Their main objection is that the Koran said man is the highest being and going against that would be blasphemy.

“In their opinion, God intervened and put Adam on earth. If you accept evolution, there must have been several Adams, so that doesn’t work,” Dajani said at a conference in Cambridge, England, on Islam and science with Guessoum and other Arab scientists in May. In response, she tells her students not to treat the Koran as a science textbook.

“If there is a conflict between science and our interpretation of the Koran, then we have to reassess the interpretation.”

Astronomers meet resistance when they offer their mathematical calculations of the moon’s phases as a more reliable way to determine when the holy month of Ramadan should start, Guessoum said.

Muslims traditionally begin the annual fast when they see the first sliver of that month’s new moon with the naked eye. But this can result in some Muslim countries beginning Ramadan later than others because clouds impeded the sighting.

“Science can offer all kinds of answers but religious authorities do not want to submit to science. They want to be the ones who define the terms of the debate,” explained Guessoum, who earned his Ph.D at the University of California at San Diego. “This is the tug of war that we find even today.”

Research in fields such as human evolution, genetics, paleontology and anthropology was discouraged by many religious authorities as possible challenges to faith, the astrophysicist said. “People try to poke holes in the scientific results just to discredit them and not let them come to the fore.”

Even Egypt’s new science and technology institute would probably not escape this pressure completely, said Ghoneim.

“There’s a very narrow area that could face these restrictions, mainly in the field of stem cell research,” he said.

SOCIAL AND POLITICAL STRUCTURE

But scientists as a whole are wary of blaming Islam.

Qanta Ahmed, a British-born Muslim physician, said religion posed no problem during her two-year stint practicing critical care medicine in a Saudi hospital. She had no limits on her research and no complaints that she treated men and didn’t wear a headscarf.

“Even the most conservative families, where the women were gloved and wearing black socks, never objected,” she said.

Guessoum pointed to the scientific achievements of the past.

“For centuries, Islam and science not only coexisted very well but produced a glorious scientific civilization. If Islam was so good then, why is it so bad now?” he asked.

Instead, many say, the Middle East’s present-day political and social structures are the chief culprit, in particular the authoritarian nature of politics in the region.

Ahmed saw this at work in Saudi hospitals where she has worked as a staffer or consultant.

“You can identify brilliant researchers who you know will only rise so far because they don’t have the favor of the royal court, or they’re not from the right family or group,” she said. “It’s not a meritocracy.”

Dajani saw free thought and speech stifled across the Arab world.

“This is a political situation that has prevailed for at least 50 years and its roots may go back even longer,” she said. “The effect is not only on politics, but on the whole society. When you don’t have freedom to think, children don’t grow up questioning things. They agree with the status quo. So you reduce any kind of development in any field.”

Bureaucracy and cronyism have also conspired to stifle scientific progress. Research grants and academic jobs often go not to the most qualified, but the best connected, and they can stall or stop work in fields they either don’t understand or don’t agree with.

“People in key positions are often put there for political reasons, and you couldn’t question that before because there was no freedom to do so,” Dajani said. “We don’t have any problem getting funding abroad or locally. It’s the bureaucracy and management that really kill things.”

In addition to the political changes the region has seen in recent months, there must be guarantees that scientists will not be jailed, censured or declared heretics for something they’ve said or written, Guessoum said. “Then there will be a transformation of society and science will flourish.”

He called himself “an optimist in the long term” because the Arab Spring has accelerated modernizing trends he said were already underway.

“There is no doubt in my mind that more freedom and democracy, and more ability to debate, are going to promote science and open new avenues to explore,” he said. “In the long run, we’ll see significant improvements.”

(Reporting by Tom Heneghan in Cambridge, England, and Sami Aboudi in Cairo, Editing by Sonya Hepinstall)