The storming of Islamabad's Lal Masjid mosqueis over. Prof Pervez Hoodbhoy asks why this came to pass and whether the government and the larger society has learnt it lesson or will more such incidences follow.

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The stench of decomposed bodies fills the air in and around the mosque. Bullet-pocked and blood-stained walls speak of ferocious battles between the Islamic militants holed up inside and Pakistan army commandos. The official casualty count is 107, but many say that the real toll is much higher.

Religious radicalism has made its debut in the heart of the nation's capital. Nevertheless, many Pakistani political commentators have trivialised Lal Masjid. For them, the comic sight of the bearded Maulana Abdul Aziz, leader of the mosque, fleeing in a burqa proved that this episode was mere puppet theatre. They said it was enacted by hidden hands within the government, created to distract attention from General Musharraf's problems, as well as to prove to his supporters in the west that he remains the last bulwark against Islamic extremism. These commentators are dead wrong.

Yes, this bloody showdown need not have happened at all. The Lal Masjid militants had been given a free hand by the government - or at least parts of it - to kidnap and intimidate. For months, under the nose of Pakistan's intelligence agencies, large quantities of arms and fuel were smuggled inside to create a fortress in the heart of Pakistan's capital.

Even after the burqa-clad students of Jamia Hafsa (the women's Islamic University adjacent to Lal Masjid) went about their violent rampages to enforce Islamic morality in February, no attempt was made to cut off the mosque's electricity, gas, phone, or website. The government did not even shut down the mosque's illegal radio station. Operating as a parallel government, the mullah duo, Maulana Abdul Rashid Ghazi and Maulana Abdul Aziz, ran their own Islamic court.

For a state that has not shied from using even artillery and airpower on its citizens, the softness on the mullahs was astonishing. Even as the writ of the state was being openly defied, the chief negotiator appointed by Musharraf described the burqa brigade militants as "our daughters" against whom "no operation could be contemplated".

Yet this does not prove that the fanatics were engineered by the state, or that extremism is a fringe phenomenon. The Lal Masjid mullahs, even as they directed kidnappings and vigilante squads, continued to lead thousands during Friday prayers. Thousands of other radical Pakistani mullahs daily berate captive audiences about immoralities in society, and dangle promises of heaven for the pious.

What explains the explosive growth of extremism in Pakistan? America's policies in the Muslim world are usually held to blame. But its brutalities elsewhere have been far greater. In tiny Vietnam, the Americans killed more than 1m people. The Vietnamese did not invest in explosive vests and belts. Today, even if one could wipe America off the map of the world with a wet cloth, mullah-led fanaticism would not disappear. At my Quaid-e-Azam University, I often ask students who toe the Lal Masjid line why, if they are so concerned about the fate of Muslims, they did not join the demonstrations in 2003 against the immoral US invasion of Iraq. The question leaves them unfazed. For them, the greater sin is for women to walk around bare-faced.

Extremism is often claimed to be the consequence of poverty. But deprivation and suffering do not, by themselves, lead to radicalism.

People in Pakistan's tribal areas have never led more than a subsistence existence. Building more roads, supplying electricity and making schools - if the Taliban allow - is a great idea. But it will have little impact upon militancy.

Lack of educational opportunity is also not a sufficient cause. Over a third of Pakistani children do not attend school, and only 3 per cent of the eligible population goes to university. But these are improvements over 30 years ago, when terrorism was not an issue. More importantly, violent extremism has jumped the educational divide. The 9/11 hijackers and the Glasgow airport doctors were highly educated men, and were supported by thousands of similarly educated Muslims in Pakistan and around the world.

One can easily find more compelling explanations for the rise of extremism in Pakistan: the official sponsorship of jihad by the Pakistani establishment in earlier times; the poison injected into students through their textbooks; and the fantastic growth of madrassas.

But most of all, it has been the cowardly deference of Pakistani leaders to mullah blackmail. Zulfikar Ali Bhutto suddenly turned Islamic in his final days as he made a desperate, but unsuccessful, attempt to save his government and life. His daughter Benazir made no attempt to challenge the horrific hudood and blasphemy laws during her premierships. And Nawaz Sharif went a step further by attempting to bring Sharia law to Pakistan.

Such kowtowing had powerful consequences. The crimes of mullahs, because they are committed in the name of Islam, go unpunished. In Pakistan's tribal areas, fanatics inspired by the fiery rhetoric from mosques murder doctors and health workers administering polio vaccinations. They blow up girls' schools, kill barbers who shave beards, stone alleged adulterers to death and destroy billboards with women's faces with impunity.

Public silence has allowed tribal extremism to migrate effortlessly into the cities. Except for the posh areas of the largest metropolises, it is now increasingly difficult for a woman to walk bare-faced through most city bazaars. Reflections of Jamia Hafsa can be found in every public university of Pakistan. Here, as elsewhere, a sustained campaign of intimidation is showing results. In fact, it would do little harm to rename my university, now a city of walking tents, as Jamia Quaid-e-Azam.

On 12th April, the Lal Masjid mullahs declared on their radio station that Islamabad's Quaid-e-Azam University had turned into a brothel. They warned that Jamia Hafsa girls could throw acid on the faces of those female university students who refused to cover their faces. There should have been instant outrage. Instead, fear and caution prevailed. The university administration was silent, as was the chancellor, one General Musharraf. A university-wide meeting of about 200 students and teachers, held in the physics department, eventually concluded with a condemnation of the mullah's threat and a demand for their removal from a government-funded mosque. But student opinion on burqas was split:  many felt that although the mullahs had gone a tad far, covering of the face was indeed properly Islamic and needed enforcement. Twenty years ago this would have been a minority opinion.

One hopes that the Lal Masjid episode will end the ambivalence of Musharraf's regime towards Islamic militancy. But will it? And what needs to be done? First, hate-preaching mullahs must be stopped. The government should announce that any Pakistani citizen who hears hate sermons should record them and lodge an official complaint that will be taken seriously.

In the tribal areas, the dozens of illegal FM radio stations, which incite bloody tribal and sectarian wars, should be closed down using force if necessary.

Second, the government must not minimise the danger posed by madrassas. It is not just their gun-toting militants, but the climate of intolerance they create in society. Where and when necessary, and after sufficient warning, they must be shut down. The madrassa reform programme has fallen flat on its face. Introducing computers or teaching English cannot transform the character of madrassa education away from brainwashing. Did the adeptness with which Lal Masjid managed its website really bring it into the 21st century? The public education system must be improved and made a viable alternative.

The Lal Masjid battle is part of the wider civil war within the Islamic world waged by totalitarian forces that seek redemption through violence. Their cancerous radicalism pits Muslims against Muslims, and the world at large. It is only peripherally directed against the excesses of the corrupt ruling establishment, or inspired by issues of justice and equity.

The Lal Masjid ideologues did not rouse their followers to action on matters of poverty, unemployment, poor access to justice, lack of educational opportunities, corruption within the army and bureaucracy, or the sufferings of peasants and workers. Instead their actions were concentrated entirely on improving morality - meaning kidnapping prostitutes and destroying video stores. They did not consider as immoral such things as exploiting workers, cheating customers, bribing officials, beating their wives, not paying taxes, or breaking traffic rules. Their interpretation of religion leads to bizarre failures in logic, moral reasoning, and appreciation of human life.

-The author is chairman and professor at the department of physics at Quaid-e-Azam University,