"Welcome to the Land of the Pure," a feminist professor proclaimed with a twinkle during my recent research trip to Pakistan. Yet in the aftermath of the assassination of Salman Taseer, the governor of the Punjab, I was to find that the polarisation of "impure" outspoken liberals and those known locally as "fundos" is greater than ever.

While I witnessed elite academic groups discussing politics and poetry with similar passion over copious amounts of illegal alcohol, it was sobering to watch as every vehicle entering university campuses was checked for bombs.

Of the two cities I visited, Karachi's long-term inter-ethnic violence is perhaps beginning to recede, whereas Lahore is still coming to terms with its new status as a prime target for terrorists. This status was made especially apparent in the gun attack on the Sri Lankan cricket team in 2009 and the devastating bomb attack on Data Darbar, a Sufi shrine, in 2010.

Pakistan currently endures a stark East-West divide, and both Lahore and Karachi are in the comparatively safe eastern region. The UK government advises against all travel to the west of the country, where the two provinces, Balochistan and Khyber Pakhtunkhwa, are in the grip of insurgency, the latter subject to regular unmanned drone attacks. The author Zahid Hussain described this as an unprecedented situation, with the US "using robots to target individuals for killing in another country with which it is not officially at war".

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The "blowback" from drone killings has contributed to many middle-class Pakistanis joining the resistance and the rise of the Pakistani Taliban. In the frontier city of Peshawar, where I lived for 10 months in 1993-94, female lecturers are currently striking to achieve some regularisation of their profession, and women's colleges and girls' schools are frequent targets for the ruthlessly patriarchal militants.

Given this background, I was pleasantly surprised by the cultural and intellectual energy I encountered. I visited the Lahore University of Management Sciences (LUMS), one of South Asia's leading institutions of higher education. Javed Hamid, the uncle of Mohsin Hamid (author of Booker-nominated novel The Reluctant Fundamentalist), was the first dean of LUMS, and Mohsin's father, Naved Hamid, was professor of economics there.

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These two University of Cambridge and Ivy League-educated men, together with other academics, dedicated themselves to establishing LUMS in the 1980s. Mohsin told me that LUMS students are highly intelligent but tend to be new to critical thinking, so working as a lecturer there can be very rewarding. However, it is widely recognised that the institution has witnessed a creeping Islamisation in recent years, with religiously conservative staff members being promoted to the senior management team and scholarships being granted to underprivileged students by Islamist groups.

Another of Lahore's outstanding universities, Forman Christian College (FCC), was founded in 1864 by an American Presbyterian missionary. Today, it not only schools a large proportion of Christians (Pakistan's largest religious minority at about 2 per cent of the population), but also Muslims of all religious and secular persuasions.

If the trip showed me anything, it is the absence of uniformity in the Pakistani academy. From the Ivy League model adopted at LUMS and the multicultural tolerance evident at FCC to the dire situation of women academics in Peshawar, the picture revealed is one of brave, dissenting academics grappling with a highly complex, privatised higher education system.