Ten years later, another secretary of state, Madeleine Albright, wrote her own study on world affairs: "The Mighty and the Almighty: Reflections on America, God and World Affairs." Almost half the book dealt with Muslims and Islam.
The attacks brought religion back into public affairs for many western countries where faith had largely faded into the private sphere.
"It is a critical element in many national systems and in radical and extremist movements, but also in movements oriented to human rights, peace-building and civil society," he said.
Since that day, governments and researchers in North America and Europe have turned to sociology, psychology, anthropology and other disciplines trying to understand religiously motivated violence and work out how to prevent it.
The results are mixed. Religion's exact role in radicalism is unclear. Psychology and group dynamics may drive extremists more than faith. The Arab Spring could become a democratic option that trumps the jihadist ideology of al Qaeda.
For decades before September 11, policymakers and analysts in western countries exhibited what Appleby called a "secular myopia" about religion in politics. Since faith was supposed to be private, they mostly left it out of their analyses.
This happened despite the fact that ultra-conservative religious movements had appeared in many world faiths in those years and were often reflected in political action.
Iran staged an Islamic revolution and Afghans waged jihad against the Soviet Union. Jews settled in Palestinian territories, the U.S. Christian right emerged and Indian Hindus and Buddhist Sri Lankans went into nationalist politics.
Harvard professor Samuel Huntington was one of the few to grasp this trend. His 1996 book "The Clash of Civilizations" saw religions and cultures at the root of post-Cold War conflict. The West and Islamic world were bound to clash, he argued.
When al Qaeda attacked on September 11, "the initial reaction was that these people must be truly religious fanatics who were brainwashed," said Scott Atran, an American anthropologist at the National Center for Scientific Research in Paris who studies religious conflicts.
Although President George Bush argued Islam was a peaceful religion that the September 11 attackers had hijacked, the wars against Afghanistan and Iraq and heightened security at home made his "war on terror" look to many Muslims like a "war on Islam."
"BORN AGAIN" ISLAMISTS
In the years after September 11, social scientists studying Muslim extremists began shifting the focus from "Islamic" to "radical." Faith could boost extremism, they found, but the young men involved had first to be ready for radicalization.
"We found most of the people who joined (the extremists) had no religious education to speak of," Atran said. "They were 'born again' into it, often in their late teens or early 20s and often through their friends, sometimes very rapidly."
The main factor leading to violence was not religious fervor but a group of friends ready to sacrifice their lives. "What bonds people to do jihad is their friends," Atran said, seeing parallels to soldiers in war. "They die for one another."
Studying the biographies of the attackers in September 11, the 2004 Madrid train bombings and 2005 London bombings, experts found alienated young Muslim men seeking the sense of purpose and self-esteem that radical Islamist groups offered them.
"The purpose is a huge one, it's a good-versus-evil struggle with you on the good side," said Russell Razzaque, a British psychiatrist of Bangladeshi origin who was unsuccessfully wooed by Islamist recruiters at his medical school in London in 1989.
"These are young men in that stage of life when they are seeking significance, meaning, friends, glory and adventure," said Atran. "The radical ideologies speak to those needs."
Razzaque said Muslim students with a religious background were the least open to the radical recruiters he met.
NEW HOPE FROM ARAB SPRING
Since September 11, governments and academic experts have come up with various and sometimes conflicting ideas for preventing the radicalization of young Muslims in western countries.
One approach often favored by Muslim communities aims to counter al Qaeda's radical Islam by promoting a moderate interpretation of the faith, which some call "real Islam."
Atran called this "totally misguided," saying there is no one correct interpretation of any religion. He suggested social workers needed to work with potentially radical youths to give them peaceful heroes to emulate rather than Osama bin Laden.
One British program helps young Muslims discuss problems and resolve conflicts without trying to change religious views.
"This is psychologically driven, but it's religion friendly," said Cambridge University social psychologist Sara Savage.
Razzaque said the Arab Spring movement for democracy and freedom offered an unexpected new type of preventative strategy by undercutting the Islamists' argument that the Muslim world needed to form a new Islamic caliphate.
"What's going on in the Muslim world at the moment is the complete denial of the tenets of al Qaeda and extremist Islam," he said.
(Editing by David Storey)