Against the backdrop of human tragedy that continues to unfold in Pakistan, it may seem perverse to draw attention to the plight of the country's higher-education system. The massive floods this summer — the latest in a string of crises in the region — have crippled the nation's economy and forever altered the lives of millions. Humanitarian relief efforts are at full stretch and the situation remains dire.

But, amid the chaos, decisions must now be made about what kind of future Pakistan can expect. The country's universities are in a desperate state and need money from the international community. At this difficult time, higher education might seem like the lowest priority for international aid, but there is evidence that providing only immediate relief to a disaster-stricken nation can, in the long run, leave it poorer than it was before (see Nature 466, 1042; 2010).

There have been unprecedented investments in Pakistan's higher-education sector over the past decade, owing mainly to the patronage of former military dictator Pervez Musharraf. Budgets and research output have soared. But support — and funding — faltered when a civilian government replaced Musharraf in 2008, and the latest floods have diverted more money still. Hundreds of new laboratories and projects now stand on the brink of collapse.

Faced with flooding, recession and insurgency, Pakistan's government cannot be expected to support its universities on its own.

For some Pakistani scientists, the end of the higher-education system as they know it would be welcome news. As described on page 378, the rapid investment since 2002 has led to alleged waste and corruption at many of the country's universities. The body in charge of regulating the system, the Higher Education Commission (HEC) in Islamabad, has, by all accounts, avoided impropriety. But it has struggled to police the institutions it oversees. Critics argue, perhaps rightly, that the surge of funding under Musharraf did as much harm as good.

Benefits in the balance

It is undeniable that some mistakes were made in Pakistan's rush to develop its universities. Sharp salary increases under a new tenure system left some faculty members behind and created deep divisions on campuses. Goals for recruiting faculty members from abroad were probably unrealistic, given the nation's turbulent politics. And some Pakistani scientists say that the flood of cash led to colleagues ordering equipment they did not need and taking on students purely for the financial incentives — although just how widespread the problems are is difficult to gauge.

But much was achieved. Research institutes were set up, and students were sent abroad for study. Perhaps the greatest accomplishment was the establishment of the HEC itself: a well-run, well-staffed institution with the authority and budget it needs. An emphasis on publishing results directed academics towards research, often for the first time in their careers. Scientists who were capable of doing good work were given the chance to do so, perhaps for the first time in a generation.

Much of that progress now hangs in the balance. Just last week, finance minister Abdul Hafeez Shaikh told university officials that he would not release funds for a promised salary increase, leading 71 vice-chancellors to threaten en masse to resign. The money for hundreds of research projects is also being withheld, in part because of the flooding. The situation is reaching a crisis point, and is only exacerbated by the HEC's investigation of a scandal in which some politicians have been revealed to be in possession of fake degrees.

Push for progress

The financial and political situation is making it difficult for the HEC to do its job, but progress may still be possible. Even without new money, the commission can begin to correct some of the problems generated by Musharraf's well-intentioned largesse. It needs to raise standards and reduce waste; it could start by spreading its own admirably professional working practices throughout the wider sector, and rigorously enforcing ethics rules. In some cases this may require the HEC to step in, but where possible the commission should work with vice-chancellors and university leaders. Meanwhile, the best projects should be protected from the worst cuts: the government must not allow what progress has been made to reverse.

In a country where only half the population can read, higher education does not have strong support from voters, but politicians must recognize its value. They should look to neighbours such as India and China, which have made large investments in higher education as part of their broader development.

Politicians should protect the HEC and strive, where possible, to protect its funding. But, faced with flooding, recession and insurgency, Pakistan's government cannot be expected to support its universities on its own. Among other donors, the World Bank is now considering a US$300-million, three-year loan to aid the higher-education system; assuming that Pakistan's government will continue its commitment to the sector, that money should be released.

There are many problems facing Pakistan's higher-education system. But there is also cause for optimism. With proper management and sufficient funds, the progress made over the past decade can be preserved.