Since the attacks on Sept. 11, 2001, genuine concerns about national security as well as politicking and fear have led to a shift in the balance between civil liberties and law enforcement. That much is indisputable, and widely discussed. Yet it’s rarely acknowledged that the attacks have also led to what’s essentially a separate justice system for Muslims.

In this system, the principle of due process is twisted and selectively applied, if it is applied at all.

Examples of the Muslims-only legal system abound, even though politicians and the press shy away from calling it that: Special detention centers for Muslims (Guantanamo Bay and the network of secret C.I.A. lockups, now said to be closed, where prisoners were almost routinely tortured); special trial procedures for Muslim prisoners (military tribunals); special allowances for agents dealing with Muslim suspects (extraordinary rendition, i.e. officially sanctioned kidnapping of foreigners).



The New York Police Department, we now know, conducted indiscriminate surveillance of Muslim workplaces, sites of worship and social gatherings. The sense of impunity in dealing with Muslims is so strong that New York officials won’t even tolerate any real discussion about the program, and certainly no oversight.

You could argue, I suppose, that these examples don’t amount to a separate system for Muslims, per se, but for people who commit acts of terrorism and just happen to be Muslim. But the N.Y.P.D. case seems to counter that position.

Here is an even more blatant example of how law enforcement has blurred the difference between a Muslim and a terrorist: Late last year, Wired magazine reported on F.B.I. training materials containing what Senator Richard Durbin of Illinois has called “crude stereotypes of American Muslims and Arab Americans.” That’s an understatement.

Agents learned that “Islam is a highly violent radical religion,” that “mainstream American Muslims are likely to be terrorist sympathizers,” and that Arabs have “Jekyll and Hyde” personalities. They also learned that “under certain circumstances, the F.B.I. has the ability to bend or suspend the law and impinge on the freedom of others.”

Mr. Durbin grilled Attorney General Eric Holder on this appalling lapse in standards last November, and Mr. Holder acknowledged that the training materials contained “misinformation.” But this is about much more that that. This is a sign of prejudice deeply ingrained in counter-terrorism and law-enforcement policies.

As the Times’s Charlie Savage reported on Thursday, the F.B.I. told the Senate Judiciary Committee that the offending material had been removed. But Mr. Durbin has expressed alarm that there were 876 pages “that included offensive materials” and that the F.B.I. had shared only “a handful” with Senate staff members, who were required to return the documents.

The F.B.I., Mr. Durbin said, plans no written report, nor will it make the training material available to Congress or the public. This is typical. When confronted with abuses and misbehavior in the so-called “war on terror,” government agencies start with denial, follow up with a grudging admission of missteps and then refuse to hold anyone accountable.

Those who buy into the line that we have to surrender some of our liberties to combat terrorism, and believe they are safe from the abuse of power because they are not Muslims, would do well to remember that the government has singled out other minority groups in the past, and may single out new groups in the future. Once, it was enough to be of Japanese descent to earn you transport to an internment camp.