How did we arrive at global jihad? A student researching the madrassas of Northern Pakistan stumbled across some answers. Mandy Garner reports

When Sana Haroon began research on the history of religious mobilisation in the Federally Administered Tribal Areas (FATA) of Northern Pakistan in 2001, little did she know that it would become the focus of world attention. "I went to the tribal areas on September 9, 2001," she says. "Nothing much was happening there at that time. The focus was all on the assassination of an Afghan tribal leader."

Two days later, everything changed, although it was not until a month after the attack on the World Trade Centre that the Afghan connection was made. Haroon returned to the North West Frontier Province later that year, but with the start of US actions against Afghanistan, access to the tribal areas was impossible. Also, research on the history of the region seemed irrelevant in the face of war, refugee movement and increasing pressure to distinguish between religious practice and organisation there.

But five years on, the importance of understanding the roots of the links between religion and politics in the region are obvious, and a book on Haroon's research will be published by Hurst next year. Haroon, who is doing a postdoctoral thesis at the Institute of Historical Research, says there are very few historic academic studies of madrassas in the region. Her study covers 1878 to the present. Her PhD thesis, which she produced while at the School of Oriental and African Studies, covered the late-19th and early 20th century, and it was only by accident that she came across Afghan jihad material. "I became interested in the transference of ideology and how it mutated in different circumstances," she says.

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Haroon's approach is fairly radical within Islamic scholarship, which traditionally focuses on textual analysis, rather than on how ideas have changed according to their political, social and historical context. "Islamic scholarship always harkens back to the text, and it is easy to be swayed by that," she says.

In addition, the context itself is complicated. Pakistan has played a murky role in the rise of the Taleban - and there are impassioned views on the history of the region, not least of all those held by Afghan exiles.

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Haroon looked at the reasons for the rise of the Taleban and traced this to the particular history of the FATA, where millions of Afghans fled after the Soviet invasion in 1978. This region has traditionally operated according to its own tribal laws and is controlled only nominally by Pakistan. Pakistan inherited it from Britain as an unadministered region inhabited by nomadic groups with a separate culture to the rest of the country.

The role of religion has also been different. In the settled urban areas of Pakistan, the ulema , trained Islamic theologians who interpret the Koran, have a lot of authority and are active in political discussions. But in the FATA, the mullahs hold sway. They tend to be involved in more everyday rituals such as birth and death rites. Their main function is to lead prayer, oversee the mosque and give Friday sermons.

Haroon says that in the tribal areas the mullahs "have filled the state vacuum". Despite attempts to solidify the central Pakistani state, the FATA have kept their own law. Part of the reason is the 1,290km permeable border between Afghanistan and Pakistan and shared cultural practices. "There is a history of mullahs straddling the border. There's a lot of shared religious and cultural practices and intermarriage," Haroon says.

"When the Soviets invaded Afghanistan, the ulema on the Pakistani side of the border began to support the Afghan resistance. They did not directly mobilise armed forces but acted as facilitators of the resistance and propagandists," says Haroon, whose research was mainly based on British colonial records, Pakistani media and published statements and journals from the ulema . "The Pakistani ulema , who historically disdained cultural variants of Islamic practice, began to support the mullah-style leadership that dominated in the border regions."

Haroon has looked in particular at the role of Abdul Haq, the leader of an ulema -led madrassa. Haroon says he was originally approached through links with Afghans in the refugee camps and built up contacts with Afghan groups. He became convinced that the Afghan jihad was of relevance to the entire Muslim world, not just to the 4 million Afghan refugees in Pakistan. He encouraged old students to use his madrassa as an organisational and networking base and published news of the jihad in the monthly madrassa journal.

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One of his ex-students was Afghan resistance leader Maulvi Yunis Khalis. Haq strongly supported Khalis's group and facilitated its relationship with the Pakistani military and political authorities. The Pakistani authorities, says Haroon, were keen to keep the resistance on side, and none of their dealings with the jihad were officially recorded.

"It was all shady. The army sought out trustworthy individuals to give the cash and weapons to. Their primary concern was domestic - they didn't want the guns to be turned on them," she says.

Other governments, including Saudi Arabia's, also channelled money to the jihad through madrassas.

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By 1988, when the Soviets withdrew from Afghanistan, the resistance had moved across the border. But while the ulema -run madrassas in Pakistan had fomented involvement of Pakistanis in the war, when President Zia Al-Huq died the same year they turned their attention to more national issues. Many of the Mujahidin they had encouraged coalesced as the Taleban in the 1990s and maintained links with Haq's madrassa, despite his death, also in 1988.

"Very strong connections had been formed," Haroon says. Haq's successors claimed that 75 per cent of the Taleban had been trained at madrassas. But Haroon cautions against accepting this claim as proof that Haq's madrassa created the Taleban. "There is an ambiguity there. They certainly could not have done the full course." And once in power, she says, they reverted to a mullah-style religious leadership.

In Pakistan, many ulema upheld the Taleban as the model of how religious leaders should function as heads of state. After 2001, however, they became less vocal in their support, although Haroon says they are still sympathetic.

Haroon's work on how people are mobilised to fight in a foreign conflict has obvious interest for those looking to understand the situation in Afghanistan and the War on Terror.

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"If you look at the point at which the ulema began to support the resistance, it is hard to understand," she says. "But if you look at the long-standing ethnic and institutional ties to the community that organised the army of resistance, it is easier to comprehend."