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People care for a person injured in a blast on Monday, Dec. 3, 2012 in Peshawar, Pakistan. A bomb ripped through a police van as it was patrolling in northwestern Pakistan on Monday, killing several officers and wounding others, police said.Mohammad Sajjad/The Associated Press

There is an angry silent protest under way at the International Islamic University in the Pakistani capital these days, and it takes the form of hair: shiny, long, black hair, defiantly visible, as female students refuse to hide it under voluminous burkas.

The new president of the university recently ordered the nearly 9,000 students in its female college to cover up, and male students to grow out their beards and wear their trousers at ankle-bone level, a practice believed to be "more Islamic" by some conservative theologians.

The new president, Ahmad Yousif Al-Draiweesh, is from Saudi Arabia, and his interactions with students and faculty to date suggest he subscribes to the deeply conservative Saudi Wahabist school of Islam, says Ayesha Salim, a professor of Arabic in the women's college. His student body would appear not to share his politics – defiant girls in brightly coloured shalwar kameez fill the halls.

Mr. Al-Draiweesh might seem an odd appointment for the university: He was not one of the 10 candidates interviewed or short-listed by the search committee. Nor did he even apply. But the Saudis offered money, with the condition that this president be installed, according to Prof. Salim.

In this small transaction – conservative scholar in exchange for financial bailout – lies one important clue to much of what is happening in Pakistan today. Players in transnational conservative Islamist movements, such as the Saudis, see unstable Pakistan as an arena in which to advance their own agenda. At the same time, there is a long history in Pakistan of accommodation of Islamists by both government and the public, a sense of mutual interests nurtured over decades, and very little public will to oppose them, defiantly unveiled undergraduates notwithstanding.

The shooting by a Taliban gunmen in early October of 15-year-old Malala Yousufzai, a campaigner for girls' education, told the world – and Pakistanis – that Islamist militancy is alive and well. A lower-profile but savage campaign of violence targeting the country's Shiite minority – at least 350 Shias have been killed this year, including 50 people who died in five separate bomb attacks during the mourning festival of Muharram late last month – is another sign, as Wahabi fundamentalists consider them heretics.

Because there have been few attacks in Pakistan's main cities in the past 18 months, many people had developed a comforting but false belief that the level of violence had fallen. But, in fact, the Taliban and al Qaeda affiliates carry out attacks on civilians and the Pakistani military almost daily, in the tribal areas along the border with Afghanistan and in the northwestern province of Khyber-Pakhtunwa, and with increasing frequency in Shiite communities.

In the furious debate that followed the attempt to kill Malala, there has been intense focus on whether the army will or should carry out an operation aimed at eliminating militants in the territory of North Waziristan and how effective a campaign would be.

But the larger question is the perennial one: Is the military and intelligence establishment, a patron of Islamic militants, really interested in wiping them out? And who are the deep-pocketed players behind the scenes, encouraging the alliances?

The militant groups were created and financed by the intelligence agencies to serve first as a proxy against India; the Taliban were cultivated in Afghanistan as a "strategic asset," in the words of retired security officials. Even now, the military chief, Gen. Ashfaq Kayani, has said openly that the Taliban will be a significant power in Afghanistan, even if not the government, after the U.S. withdrawal, and that Pakistan must cultivate its relationship with them. He draws a distinction between the Afghan Taliban and his country's own militants, a distinction that most security analysts say is specious.

"The army is divided," said I. A. Rehman, who chairs the Pakistan Human Rights Commission and is a veteran analyst of national politics. "There is a very strong element which is sympathetic [to the Taliban.] This army is a religious one, religion is an instrument of indoctrination – there is no other national ideology."

General Mohammed Zia-ul-Haq, the former president who ruled for 11 years, made sure only devout and conservative Muslims like him were promoted in the army. The effects are still felt today, Mr. Rehman said in an interview in his office in Lahore. And even less religious officers find themselves conflicted. "Our constitution says this is an Islamic state and the Taliban also want that, so why should we fight them?" he characterized that argument.

The obvious answer to that might be – because they are killing you. The Taliban does not share the military's ambivalence, and has killed some 8,000 military personnel in the past six years, as well as 45,000 civilians.

"There ought to be a limit on stupidity," Mr. Rehman said. But to many ordinary Pakistanis, he added, the Taliban are considered "legitimate claimants to power.

Most mainstream political parties, with a few exceptions including the ruling Pakistan People's Party, do not seem to have much of a problem with the Taliban. Only two politicians actually identified them as Malala's shooters, despite the Taliban itself having claimed the act. The leading opposition figure Imran Khan talks about bringing them into government; his political movement, in turn, is widely believed to be bankrolled by the intelligence agencies.

The relationship remains, at a minimum, opaque. There have been no arrests in any of the Shiite murders, for example, even though the killers' identities are widely known in the community; the bombings at Muharram took place despite the government ostensibly taking elaborate security measures.

"We are basically a society held hostage," said Ghazalah Minallah, a prominent human rights activist in Islamabad. "The civilian government are puppets, the army is in partial control. It boils down to that invisible power lurking in the background that's been there since Zia's time if not before. The Taliban are not just bearded men running around in the mountains – they're in every institution in the country."

The Taliban have also been able to cultivate a romanticized image to a population with limited access to education and lacking a critical media. "The Taliban are associated with certain myths, of having stood against the British in the 18 th century," said General Talat Masood, a retired army commander. "It's romantic, and people find an identity with them."

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