Despite the problems, science has been flourishing in Karachi and other Pakistani cities, thanks to an unprecedented investment in the country's higher-education system between 2002 and 2008 (see 'Rollercoaster budget'). As funding increased more than fivefold in that time, new institutes focusing on proteomics and agricultural research sprouted, and the University of Karachi's natural sciences department rose from nowhere to 223 in the 2009 QS World University Rankings.

But the money has stopped abruptly, after political scandal, economic recession and devastating flooding throughout the country. With funding set to be slashed for the second year running, the entire system is teetering on the brink of collapse, says Javaid Laghari, chairman of Pakistan's Higher Education Commission. "If we cut any further, it will be suicidal," he says. Last week, 71 university vice-chancellors threatened to resign after Abdul Hafeez Shaikh, the nation's finance minister, refused to commit funding for the cash-strapped system and told universities that they would have to find other sources of support — a tall order in a country in which even a small increase in tuition fees, for example, can lead to debilitating student strikes.

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The surge in higher-education investment occurred after the rise to power of General Pervez Musharraf in 1999, who as leader of the army had led a low-key coup d'état and installed himself as de facto president. Musharraf was a liberal progressive who hoped to modernize Pakistan. "It was a moment in Pakistani history that now seems so distant," says Adil Najam, an expert in international development at Boston University in Massachusetts.

With the economy booming in the early 2000s, Pakistani academics sensed an opportunity. Higher education had never had much popular support in the country, where literacy hovers at about 50%, but in Musharraf they saw a champion. In a series of reports, Najam and others made the case that if the nation could mobilize its universities, it could transform from a poor agricultural state into a knowledge economy (see Nature 461, 38–39; 2009). The group called for a new Higher Education Commission (HEC) to manage the investment, as well as better wages for professors, more grants for PhD students and a boost in research funding.

"One of the things about being a military dictator is that if you like an idea, you can do whatever you like with it," says Najam. Musharraf created the HEC and named Atta-ur-Rahman, a close adviser, as its first chairman.

Rahman, a chemist at the University of Karachi and, at the time, the minister for science and technology, enthusiastically set out to overhaul the nation's universities. With Musharraf's support, annual research funding shot up 474% to 270 million rupees (US$4.5 million in 2002) in the first year alone. The HEC set aside money for PhD students and created a tenure-track system that would give qualified professors a monthly salary of around US$1,000–4,000 — excellent pay by Pakistani standards.