Three clocks are ticking for the rattled rulers of Iran.

One clock, which they see in their favor, is a countdown to the day, perhaps a year or so away, when the country's scientists gain the capacity to produce a nuclear weapon.

A second counts the time until a September deadline, set by President Obama, for Tehran to respond to an offer of talks on the nuclear issue or face a stern response.

But it is the third clock, one that will influence the other two, that matters most to the regime of Supreme Leader Ayatollah Ali Khamenei and President Mahmoud Ahmadinejad.

It measures the moments until their legitimacy runs out. It is counted in the number of popular demonstrations since a flawed June 12 election, the instances of power struggles among the divided rulers, and the occurrences of stinging criticisms from respected Islamic clerics.

The Islamic Republic is in trouble as it struggles to ruthlessly stamp out dissent. And that was made clear again during the crackdown Thursday during a march by thousands of Iranians to the graveside of Neda Agha Soltan, the young woman killed in a June 20 protest.

Ms. Soltan's death serves as a powerful symbol of the victimization of Iranians by a regime that meddles in their daily lives and resorts to stealing elections to stay in power. But Iranians are also irked by reports of brutality used against hundreds of detained protesters in prison.

A regime that rules in the name of God and came to power in 1979 because of the shah's brutality can't survive for long by resorting to killing prisoners and brutalizing others.

One powerful Shiite cleric, Ayatollah Hossein Ali Montazeri, condemned this summer's crackdown by asking rhetorically in a statement this week: "Was the regime of the shah able to resist the wave of dissatisfaction by using terror, oppression, censorship, torture, forced confessions, and lying propaganda?"

More cracks at the top are starting to open. The supreme leader and President Ahmadinejad have engaged in an open quarrel over a key appointment. The intelligence chief was fired. Most of the grand ayatollahs refuse to recognize the election result, which was crudely rigged for Mr. Ahmadinejad. And two former presidents, Ali Akbar Hashemi Rafsanjani and Mohammad Khatami, are becoming more openly critical of the regime.

The supreme leader, who usually works behind the scenes, has had to become more public in an attempt to appear partially conciliatory. He closed a notorious prison and ordered many political prisoners released. But as his legitimacy slips, he has also had to rely more on the forces of the Revolutionary Guard, which often operate outside the law and the norms of justice. This militarization of the regime will only further spell its demise.

At root, Iran's problem is that its reigning theocrats do not respect the sense of justice as reflected in the hearts of their people. The supreme ruler cannot live in a contradiction in which he allows a modicum of democracy but then claims all secular powers in the name of Allah. He cannot trust young people to vote wisely but then send the religious police to arrest them for dating.

The world must condemn these brutal tactics but also wait as this regime slowly crumbles under its use of terror and fear.

The clocks on the nuclear issue keep ticking. But for now, it is the tick-tock counting the end of a regime that is drowning them out.