Runaway religious radicalism has made its debut in the heart of the nation's capital. Nevertheless, many well-known Pakistani political commentators seem bent upon trivialising the Lal Masjid episode. Although the mosque's bloody siege has now ended in bloodshed, for them the comic sight of the bearded Maulana Abdul Aziz fleeing in a burqa is proof that this episode was mere puppet theatre. They say it was enacted by hidden hands within the government, expressly created to distract attention away from General Musharraf's mounting problems, as well as to prove to his supporters in Washington that he remains the last bulwark against Islamic extremism. Some writers conclude that this is a contrived problem. They are dead wrong.

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

Even after burqa-d 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 electricity, gas, phone, or web site -- or even to shut down their illegal FM radio station. Operating as a parallel government, the mullah duo, Maulana Abdul Rashid Ghazi and Maulana Abdul Aziz, ran their own Islamic court. They received the Saudi Arabian ambassador on the mosque premises, and negotiated with the Chinese ambassador for the release of his country's kidnapped nationals. But for the outrage expressed by China, Pakistan's all-weather ally, the status quo would have continued.

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, Chaudhry Shujaat Husain, described the burqa brigade militants as 'our daughters' with whom negotiations would continue and against whom 'no operation could be contemplated.'

But this still does not prove that the fanatics were deliberately set up, or that radicalism and extremism are a fringe phenomenon. The Lal Masjid mullahs, even as they directed kidnappings and vigilante squads, continued to lead thousands during Friday prayers. Uncounted thousands of other radically charged mullahs daily berate captive audiences about immoralities in society and dangle promises of heaven for the pious.

What explains the explosive growth of this phenomenon?

Imperial 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 had killed more than one million people. Nevertheless, the Vietnamese did not invest in explosive vests and belts. Today if one could wipe America off the map of the world with a wet cloth, mullah-led fanaticism will not disappear.

I have often asked those of our students at Quaid-e-Azam University who toe the Lal Masjid line why, if they are so concerned about the fate of Muslims, they did not join the many demonstrations organised by their professors in 2003/4 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, or the very notion that they could be considered the equal of men.

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, now under the grip of the Taliban, 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. It is a shame that less than 65 per cent of Pakistani children have schools to go to, and only 3 per cent of the eligible population goes to universities. 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 in spirit by thousands of similarly educated Muslims in Pakistan and the world at large. It is not clear to me whether persons with degrees are relatively more or less susceptible to extremist versions of Islam.

The above, as I have argued, are insufficient causes although they are significant as contributory reasons. There are more compelling explanations: 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 madrasas across Pakistan.

But most of all, it has been the cowardly deference of Pakistani leaders to mullah blackmail. Zulfikar Ali Bhutto had suddenly turned Islamic in his final days as he made a desperate, but ultimately unsuccessful, attempt to save his government and life. A fearful Benazir Bhutto 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 the Shariah to Pakistan.

Such slavish kowtowing had powerful consequences. The crimes of mullahs, because they are committed in the name of Islam, go unpunished today. The situation in Pakistan's tribal areas is dire and deteriorating. Inspired by the fiery rhetoric from mosques, fanatics murder doctors and health workers administering polio shots. They blow up video shops and girls schools, kill barbers who shave beards, stone alleged adulterers to death, and destroy billboards with women's faces. No one is caught or punished.

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 proselytising and 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 April 12, to terrify the last few hold-outs, the Lal Masjid mullahs declared in their FM radio broadcast that 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 refuse to cover their faces. There should have been instant outrage. Instead, fear and caution prevailed.

The university administration was silent, as was the university's chancellor, General Musharraf. A university-wide meeting of about 200 students and teachers, held in the physics department, eventually concluded with a condemnation of the mullahs' threat and a demand for their removal as head clerics of a government-funded mosque.

But student opinion on burqas was split: Many felt that although the mullahs had gone a tad too far, covering of the face was indeed properly Islamic and needed enforcement. Twenty years ago this would have been a minority opinion.

What explains the ambivalence of the Pakistani establishment towards extremism? In good part it comes from not knowing whether to cultivate the Taliban -- who can help keep Indian influence out of Afghanistan -- or whether to fight them. One grieves for the officers and jawans killed in the battle with fanatics. It must feel especially terrible to be killed by one's former friends and allies.

One hopes that the Lal Masjid episode will end the ambivalence of General Pervez Musharraf [Images] and his 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 citizen who hears such sermons should record them, and lodge an official charge that will be taken seriously. In the tribal areas, the dozens of currently operating illegal FM radio stations should be closed down using force if necessary. Run by mullahs bitterly hostile to each other on doctrinal or personal grounds, they incite bitter tribal and sectarian wars.

Second, the government must not minimise the danger posed by madrasas. 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.

Establishment of new madrasas must be strictly limited. Apologists say that only 5 to 10 percent of madrasas breed militancy, and thus dismiss this as a fringe phenomenon. But if the number of Pakistani madrasas is 20,000 (give or take a few thousand; nobody knows for sure) this amounts to 1,000 to 2,000. Although all are not equally lethal, this is surely a lot of dangerous fringe.

The madrasa reform programme has fallen flat on its face, and future efforts will do no better. Introducing computers or teaching English cannot transform the character of madrasa education away from brainwashing.

Did the adeptness with which the Lal Masjid managed its web site really bring it into the 21st century? It is time instead to radically improve the public education system and make it 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.

Note that the Lal Masjid ideologues -- and others of their ilk -- do 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 are 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.

Professor Pervez Hoodbhoy is chairman and professor at the Department of Physics, Quaid-e-Azam University in Islamabad.