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Everybody in Bushra “Halima” Cheema’s local area in Lahore, Pakistan, knew two things about her: she was unhappily married and she was pious. She was a religious teacher but beyond that, she didn’t make much effort to make friends. For five years, Cheema ran the girls’ section at a local madrasa which catered to both genders. Outside this role, she was a lay preacher, going to the homes of housewives to teach them about the Qur’an.

It was a shock to everyone when along with two other women – housewives who had been her students in these private sessions – she left for Syria in December 2015, taking her four children with her but leaving her husband behind. Suddenly the attention of the national media was focused on her local area of Johar Town, an unremarkable middle-class suburb where the streets are lined with small, boxy houses; several steps up from the makeshift shacks in the city’s expansive slums, but nothing compared with the mansions of Pakistan’s super-rich in the former colonial districts. Media commentators agonised. If extremism could grow here, an area by no means wracked with the poverty often seen as a driving force for militancy, then perhaps it could grow anywhere.

The madrasa where Cheema had taught felt an immediate effect. Pakistan’s authorities, which have a patchy history with militant groups (often tacitly supporting them where they are seen to further the country’s foreign policy aims), are profoundly anxious about ISIS establishing a foothold in the country and are cracking down hard. Soon after the news of Cheema’s departure broke, the intelligence services searched the madrasa and closed down the girls’ section.

One hot Lahore afternoon in spring, around six months after Cheema’s departure, I visited the madrasa. A line of sandals sat along the blue and white tiling outside the main room, where boys wearing traditional white salwar kameez were preparing for prayer time. Conspicuously, there were no girls anywhere to be seen; the upper two floors of the building, where the girls’ school had operated, remained sealed off by Pakistan’s security agencies.

Mohammed Ishfaq and Naeb Amir, two of the teachers, stepped outside to talk to me. “Things were good before this, but now there are problems teaching and praying here,” said Amir. “The number of students – even boys – has decreased. People are afraid to visit. Many don’t want to send their kids here.”

Ishfaq jumped in. “We are teaching an approved syllabus to the boys, but we don’t know what Halima was teaching the girls. There’s no evidence that she changed the syllabus, and we didn’t know about it if she did. We never heard her mention Syria or ISIS or sectarianism. Everyone was surprised.”

I asked what they thought of Cheema’s actions: had she done the wrong thing in going to Syria? “She did wrong,” Ishfaq said, immediately. “Women cannot travel without the permission of their husband. She went against Islam.”

Pakistan’s madrasas have attracted international attention ever since the US invasion of Afghanistan in 2001. After Pakistan joined the war on terror as an ally of America, this enormous, unregulated network of religious schools – which had provided fighters to the Taliban – came under scrutiny as a driving force for violence.

Numerous academic studies have since contested the direct linkage between madrasas and membership of a terrorist organisation: Pakistan has tens of thousands of madrasas with well over a million students. Clearly, it is a small minority that go on to become fully-fledged jihadis. However, as Ishfaq’s comments show, even when a madrasa does not have a direct link to a terrorist group, most teach a restricted and conservative version of religion. There is little oversight of what is being taught.

Madrasas are a firmly embedded part of Pakistani society and a means by which the conservative religious lobby retains its power. What is the relationship between these religious schools and extremism? Are they fostering intolerance and holding the country back? And why have attempts at reform faltered?

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Religious seminaries long predate the Partition of India in 1947, when Pakistan was formed. The first madrasas were born at the end of the 10th century, long before institutionalised education began in Europe (around the 13th century). These schools were distinct from madrasas today; in addition to teaching the Qur’an and hadith, they also taught mathematics, science and literature.

In the 1800s, a new type of madrasa was born in south Asia with the emergence of the Deoband school of Islam, focusing almost exclusively on religious teachings and abandoning the study of rational sciences. Several academics have argued that this trend was a reaction to British colonialism: firstly, Britain imposed the policy of separating religion and education, leading to an exclusive focus on religion in madrasas, and secondly, Deobandis and others developed a distinctive Muslim identity in the face of colonial subjugation.

The number of madrasas in Pakistan grew significantly during the 1980s, when both the United States and Saudi Arabia were pouring money into religious education in Pakistan, with the aim of supporting the rebels (or mujahideen) resisting the Soviet invasion of Afghanistan. In the 1990s, some madrasas served as feeder schools for militant groups fighting in Kashmir. The failure of successive governments to provide good quality, free schools for the population increased the appeal of these institutions, which promised not just free education and usually one meal a day for students, but the prospect of eternal salvation.

This social function was frequently paired with another agenda. Some madrasas have direct ties to banned extremist organisations; many more teach a sectarian and intolerant mindset. A 2002 report by the International Crisis Group acknowledged the importance of madrasas in Muslim societies, but said that at present, students’ “constrained worldview, lack of modern civic education and poverty make them a destabilising factor in Pakistani society”.

Today, 26,000 madrasas are registered in Pakistan. Officials estimate that there may be a further 9,000 unregistered madrasas. Analysts suggest there are many more. This rapid growth in the sector continued unabated until 9/11, when the government, then led by military chief General Pervez Musharraf, took stock and began half-hearted efforts at reform in the face of intense international scrutiny. The government pledged to reform curricula and register madrasas so they could be regulated and monitored, but it was a voluntary programme that faltered due to resistance from mullahs and a lack of political will to press the issue.

In 2015, a new push for regulation and reform began, following a horrific terrorist attack. In December 2014, Taliban gunmen stormed a school in Peshawar, the insurgency-wracked city in Pakistan’s northwest. They killed over 100 people, mostly children. The incident shocked an already blood-soaked nation, numbed by the frequency of terrible attacks. It prompted the government to draw up a broad-ranging National Action Plan that outlined measures to tackle militancy and extremism. Among other things, the government asked madrasas to submit information on their funding, spending and the identities of all students and teachers. The measures were, again, met with stiff resistance, with madrasa leaders saying that this process amounted to official harassment. Data collection was suspended in September 2015. Afraid of a backlash from the powerful religious lobby, the government – led by the right-wing Pakistani Muslim League-Nawaz (PML-N) – is once again reluctant to crack down.

The Punjab Provincial Assembly is an impressive colonial-era building in central Lahore. Set back from the road, its grounds are protected by a ring of security guards, barbed wire and metal detectors. In an air-conditioned backroom, with the news playing on a TV screen in the corner, I met government spokesman Zaeem Qadri, a bombastic man with a loud voice. He emphasised the strides forward that the Punjab government has made, “geo-tagging” 15,000 madrasas in the province by taking details of all students and teachers.

“Initially there were some reservations,” Qadri said. “But let me tell you madrasas are playing a very vital role in contribution [to] upgrading and bringing up the rate of education in Pakistan: 99 per cent of them have nothing to do with terrorism, it’s just a religious duty they are performing. It’s only 0.01 per cent of people who are into this. These people who are terrorists are not directly related to all those madrasas, they are doing it on somebody else’s behalf. It is seriously condemnable.”

His comments – boasting about how much has been done to bring this network under control while simultaneously commending the great service that madrasas do and implying a foreign influence in terrorist violence – neatly illustrates the ambivalence felt by many in government. This is a country, after all, where respect for religion is paramount, and where blasphemy carries a death sentence.

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In an unmarked safe house down a Karachi backstreet, Sadia Hasan, a madrasa teacher with extremist sympathies, told me how brainwashing works. “Most madrasa teachers don’t allow students to ask questions about religion or anything else,” she said, approvingly. “They only listen. Watch. They can’t ask anything. Listen to the teacher. Maybe you tell the student, ‘Go and stand there.’ They cannot ask me, ‘Why am I standing there?’ They simply go and stand there. After some time, the students might become activists – if you convey the order.”

Hasan teaches women rather than the young men who might go on to be fighters. “I educate women because ladies are the main person in the house. Educate the mother in right-thinking, and the whole house will change.”

It is true that students typically pass on what they have learnt in a madrasa to their families, giving teachers (including those, like Hasan, with sinister motivation) a reach beyond the classroom.

Researchers agree with Hasan that the authoritarian method of teaching at many madrasas – where the focus is on rote learning and discipline – can make people particularly susceptible to later brainwashing. Several NGOs in the insurgency-afflicted Khyber Pakhtunkhwa province in Pakistan’s northwest focus on teaching critical thinking, while Sabaoon, an army-run “deradicalisation” centre, teaches children to ask questions about religion and to interrogate the concepts being taught. (“It’s totally different to the teaching they might have had at a madrasa,” course convener Feriha Peracha told me.)

In many parts of Pakistan, madrasas are the only education available to impoverished families. “Most people would prefer not to send their children to madrasas,” journalist Najma Sadeque told me. “They do that because it’s a place where they can get free meals. It’s as basic as that. By not ensuring food security, not looking into economic and social problems, the authorities are breeding more and more militancy. I’ve been a journalist for more than 25 years and I still hear the same answers. Why do you send your children to the madrasa? Because they’ll get a meal and they’ll get some education. That’s all. That’s the only reason. Because they can’t afford to keep the children.”

* * *

In recent years madrasas have diversified. While the bulk of these religious seminaries still focus on young men from impoverished areas, there are now madrasas aimed at middle- and upper middle-class children; at girls; and at adults and older teenagers. This is seen by many as evidence of the steadily increasing dominance of religious conservatism in Pakistani society. A small but significant number of madrasas have direct ties to banned organisations (officials estimate that it is between 1 and 3 per cent). Jamat-ud-Dawa, classed by the UN as a terrorist group, runs 295 schools. While the majority do not, they still function as an important power base for conservative religious thought in the country. Many madrasas are run by Deobandist organisations or by conservative Islamist parties, such as the Jamat-e-Islami. There are very few – if any – liberal Muslims running madrasas, since they prefer instead to focus on mainstream, secular education.

“Madrasas are the ideological hub of extremism,” says Ayesha Siddiqa, an author and journalist who has studied the madrasa network. “Some are used much more proactively as a base for grouping or for consolidating power than others, but the institution on the whole is very central to the terrorism debate. If you start to look at madrasas from the perspective of control and say, ‘Shut these madrasas and things will be fine’, that’s just not doable, because there is a cultural demand for it, there’s a socioeconomic need for it and there are no alternatives. You can’t legally or even morally shut these places. Yet it would be pretending if you say [they] are innocent. I find this argument very pernicious – that there are good madrasas and bad madrasas. They are all marketing a certain ideology. That’s what makes them problematic.”

Some recent reform efforts have focused on modernising the teaching on offer at madrasas. This modernisation includes the addition of computer proficiency and the English language, which adds to the employability of students outside the religious sector. Some offer mainstream qualifications such as O Levels. “The problem is not that you don’t have computers, English or other subjects,” says Siddiqa. “In modern madrasas, they do all of that. This idea of these traditional seminaries where all you did was learn the Qur’an or fiqh [Islamic jurisprudence] or hadith, that’s not true. The more lethal ones are more modern. How do you regulate their ideological messaging? That’s the question which I’d like to ask." Siddiqa’s research on the issue suggests that people running madrasa networks are happy to incorporate these extras as long as the conservatism of the religious messaging is not affected. No government has made any serious attempt to intervene in religious syllabuses.

In a 2007 report on Pakistan’s madrasa network, the International Crisis Group criticised half-hearted reform efforts by the military government: “Plans are announced with much fanfare and then abandoned. As a result, madrasas remain either unregistered or registered under laws that have no effective implementation. The sectarian, jihadi content of the madrasa curriculum is untouched, and there is no meaningful control over money flows into and through madrasas and other religious institutions.”

There have since been three democratic elections and two different governments, yet the picture remains largely the same. Madrasas are a vital part of public life in Pakistan, as in other Muslim countries. Yet that does not mean they should be immune from reform and regulation. In the context of today’s Pakistan, they cannot realistically be eliminated – apart from the anger this would cause amongst the population, there is no alternative educational infrastructure to take their place. But it is clear that they should be reformed and monitored as a matter of urgency. As we have already seen, the longer successive governments fail to do this for fear of angering the conservative religious lobby, the stronger that lobby will become.