Torture of Iran’s political prisoners is reportedly commonplace at Tehran’s notorious Evin Prison.

The jailing of three US-Iranian academics in Iran on accusations of fomenting a ‘velvet revolution’ signals that Iranian academics and academic freedom could be casualties of the tense stand-off between Iran and the United States.

The Iranian judiciary has said it will decide this week whether to indict the imprisoned scholars on charges of espionage and threatening national security. Last month, the country’s intelligence ministry warned Iranian academics and scientists that contact with foreign institutions, or attendance of international conferences, could result in their being considered spies.

Haleh Esfandiari, the 67-year-old director of the Middle East Program at the Woodrow Wilson International Center for Scholars in Washington DC, and Ali Shakeri, a founder of the University of California’s Center for Citizen Peacebuilding, were arrested on 8 May. Kian Tajbakhsh, a researcher working on humanitarian issues with the Open Society Institute, based in New York, was arrested three days later.

The three are being held in Tehran’s Evin Prison, long notorious for the torture of political prisoners. Their incarceration has triggered protests from academic and human-rights organizations worldwide, including the American Association for the Advancement of Science, Amnesty International, the American Association of University Professors, Human Rights Watch, and Scholars at Risk.

The broader implications of these developments have not been lost. The arrests “raise grave concerns about the ability of internationally recognized scholars and intellectuals to safely visit Iran,” notes Scholars at Risk, an international network of universities and colleges that seeks to defend the human rights of academics around the world. The organization thinks they signal a “wider attempt to intimidate intellectuals and to limit academic freedom in Iran.”

How can we effectuate covert or overt actions against a sovereign government, and expect them to take that sitting down?

The crackdown is already having a “chilling effect” on international collaboration, says Fatemeh Haghighatjoo, an Iranian psychologist and visiting fellow at Harvard’s John F. Kennedy School of Government. She likens it to the repression of foreign contacts in the Soviet Union at the height of the Cold War.

For the moment, researchers in the natural sciences seem to be less affected than their social-science colleagues. Haghighatjoo, a reformist former member of parliament and a renowned human- rights advocate, says academics who deal with Iran’s social, cultural or political situation are at the most risk.

Yousef Sobouti, an astrophysicist and director of the Institute for Advanced Studies in Basic Sciences (IASBS) in Zanjan, Iran, seems to confirm as much when he says he has never encountered difficulties with the regime. “Just today, I signed letters for eight of our students and faculty members to attend conferences in countries ranging from Japan, Russia to Europe and the United States.” Reza Mansouri, a physicist at Sharif University of Technology in Tehran, and a deputy science minister under reformist former president Mohammad Khatami, is similarly sanguine. He shrugs off the intelligence ministry’s threat as a warning – aimed mainly at naive younger researchers – to be vigilant in all dealings with the West.

Mansouri says Iranian academics have long been targeted by foreign intelligence services, and claims such efforts have increased recently. “Intelligence agents have tried hard to contact Iranian scientists visiting research institutions abroad, or attending conferences,” he says, “with the very obvious goal of having intelligence information about Iran”.

Some stories of such approaches are “unfortunately true,” agrees David Rahni, an Iranian-born chemist at Pace University in New York. But Rahni is less cool than physical scientists Nature spoke to in Iran about the impact of recent events. He says they will make colleagues in Iran “think twice about communicating; it will have a negative impact on the country’s science”.

For Haghighatjoo, the regime is rolling back years of slow progress on the opening up to the outside world undertaken by presidents Rafsanjani and Khatami. Of 20 Iranians she invited to a recent workshop on the future of democracy in Iran at the Massachusetts Institute of Technology in Cambridge, only two showed up, she says, with the others declining for fear of retribution or after the Iranian security services forbid them to attend.

But, like other academics, Haghighatjoo dismisses the idea that the crackdown represents a return to the anti-science, anti-academic years that followed the inception of the current Iranian theocracy in the 1979 revolution. She sees it more as a tactical response to current international and domestic politics.

President Mahmoud Ahmadinejad’s government is increasingly unpopular at home, risking defeat in next year’s parliamentary elections and in the presidential elections of 2009. The current repression, says Haghighatjoo, is not like the purge of university liberals that followed Ahmandinejad’s 2005 election. It is simply that of a regime clinging on to power through “zero tolerance of any dissent” and is targeting any opposition, including that from conservatives, that threatens its grip.

And the United States has made no secret of the fact that it is spending millions to encourage some of the forms of dissent under attack, under the rubric of “pro-democracy support”. Haghighatjoo, along with many academic and human-rights groups, sees this as both incomprehensible and counterproductive, playing into the hands of the regime by providing a pretext to attack independent pro-democracy groups and academic reformers.

“How can we as Americans spend millions of dollars to effectuate covert or overt actions against a sovereign government, and expect them to take that crap sitting down?” says Rahni. Esfandiari’s husband, Shaul Bakhash, himself an academic expert on Iran, has also attacked the policy: “Loose talk of regime change and allocation of money supposed to advance democracy in Iran has done a great deal of harm to Iranian academics, intellectuals and researchers,” he told the Financial Times. “It also feeds the paranoia of the Iranian regime of American intentions.”