Is Adlène Hicheur a dangerous terrorist? The French government certainly suspects so. When he was arrested in 2009, authorities said that Hicheur, then a postdoc in high-energy physics at the Swiss Federal Institute of Technology in Lausanne, was plotting terrorist attacks in France. Since then, they have held him in custody, without trial, at Fresnes Prison near Paris, while they gather further evidence.

Hicheur's family and close colleagues say the idea that Hicheur planned specific terrorist attacks is false and fantastical. They say that the French-Algerian physicist was involved in spirited online political debates about many topics, including terrorism. They argue that his arrest was a political message sent by the government to France's Muslim community, warning that everyone, no matter how educated, is under scrutiny.

Hicheur's work at CERN, Europe's premier high-energy physics laboratory near Geneva in Switzerland, certainly made for some good headlines — “Nuclear terror suspect is top physicist”, for example. And, at this stage, Nature is in no position to judge his innocence or guilt, which is a question for the French judicial system.

Hicheur's case seems a clear abuse of human rights.

Nonetheless, Hicheur's case deserves attention because to have held him in custody for so long, although legal under France's tough anti-terror laws, seems a clear abuse of human rights.

For the two years since his arrest, his online exchanges, which took place in web forums and chat rooms, have remained undisclosed by French authorities. Hicheur and his lawyers are eager to share what he said, but they are forbidden by law from doing so. He remains locked away and largely forgotten. This week a judge, who under the French system is independent of the police and prosecution, was scheduled to close a 'preliminary investigation' and hand the case to prosecutors, who will determine whether a trial should go ahead. Under French law, Hicheur could be held for a further 12 months without his case being heard, his defence team says.

Persecution of scientists, and physicists in particular, is nothing new. During the cold war, researchers on both sides of the iron curtain suffered for their political views. In the United States, Robert Oppenheimer's career was ruined by rumours of communist sympathies. And Soviet scientist and dissident Andrei Sakharov spent much of the 1980s in internal exile for his outspoken views on human rights and arms control.

Hicheur is part of a new generation. Even as his incarceration stretches into its third year, Omid Kokabee, a physicist trained in the United States and Spain, awaits trial in Iran on charges of “communicating with a hostile government”. Also in Iran, several physicists have been mysteriously assassinated in recent years by unknown agents presumably trying to slow the nation's nuclear programme.

These new cases are related to terrorism, not communism, but the similarities are abundant. As in the 1950s and 60s, there is the fear of an internal threat — a 'sleeper cell' that could activate at any time. The spread of technology to hostile governments is also a worry. Where once there was Klaus Fuchs, the German-born scientist turned Soviet spy, now there is Abdul Qadeer Khan, the Pakistani atomic-weapons researcher who ran a nuclear-trafficking ring.

However, there is one important difference. During the cold war, many scientists spoke out in defence of their imprisoned peers; today, the scientific community remains largely silent. Hicheur has had support from his closest colleagues, but CERN, where he once worked, has done its best to distance itself from him. Most scientific societies in France and Europe seem uninterested in the case. This indifference is part of a larger trend — in the United States, scientific organizations are eschewing human-rights campaigns for individual scientists in favour of broader (and blander) programmes of 'scientific cooperation' (see Nature 475, 431–432; 2011).

There are two reasons why this might be. The scientists persecuted during the cold-war era were senior researchers, whereas today's victims tend to be early-career postdocs and graduate students. Moreover, scientists on both sides of that earlier conflict were bound by national origins, ethnicity and religion — something that seems less true today. Western scientists should also ask themselves whether they are less willing to speak out on Hicheur's behalf because he is a practising Muslim.

There has never been a more important time to rally behind scientists such as Hicheur. This year has seen upheaval across the Arab world, as citizens throw off their oppressive regimes. As educated, free-thinking members of their societies, scientists can play a part in these political upheavals. These researchers can help to open their societies, and serve as a vital bridge between the Muslim world and the West.

Hicheur may have been just such a bridge. In his online debates, he says, he discouraged acts of terrorism against innocent civilians. Whether or not that is true, he should be released until his trial.