So much is still unknown about the shooting at Fort Hood Army base and the motives of the alleged shooter, Nidal Malik Hasan, but still I have that same queasy feeling in my stomach that I've had before: this will not be good for Muslims.

First things first. Major Nidal Malik Hasan is in custody. We should judge him fairly and, if he is found guilty, punish him accordingly.

The same is true for Sergeant John M Russell. In May 2009 Russell shot and killed five of his comrades at a combat stress clinic in a US Army base in Iraq. Before that, Sergeant Joseph Bozicevich killed two American soldiers at his base just outside Baghdad in September 2008. What do these incidents point to?

We still have yet to understand how profound the depths are to the stresses of war, especially in cases of repeated exposure to war. And you don't have to be on the battlefield to be scarred. We are only now beginning to learn that the Predator drone pilots, sitting in offices in southern California and dropping bombs some 7,000 miles away from their targets, suffer the same if not higher stress disorders as soldiers on the battlefield.

Perhaps these shooting incidents also tell us something about the pressures not only of receiving but also of providing mental health services to people who have suffered traumatic events. Army suicides are at an all time high (nearly 150 servicemen and women in the US took their lives last year). Rates of domestic violence in the military are sky high and far too often turn deadly. What effect must that have on the mental health providers as well?

And what do we know about the stress of being on the receiving end of prejudice, as Hasan was reported to have been? This is nothing unique to Muslims. Racial prejudice can lead to all kinds of stress outcomes. Social science research in the US has studied this phenomenon, but not frequently enough when it comes to Muslims, a space slowly being filled by the relatively new publication, the Journal of Muslim Mental Health.

These are the kinds of questions we should be asking, not out of a desire to excuse, but to explain actions that seem beyond words. But I worry that the mood in the US is dimming and turning in a more sinister direction. The questions we will be hearing are: why are Muslims in the military? And, do Muslims even belong in the United States? The allegiances of America’s Muslims, all of them and not just those in the military, will be called into question. Once again, we will be judged for an act we didn’t commit or condone and have loudly denounced.

Am I being irrational? I don’t think so. Every year since 2001 the Washington Post-ABC News poll has asked Americans if they hold negative perceptions of Islam. When the latest poll was released in April 2009, the number was 48%, the highest yet recorded.

The coming days will be meaningful. Will this crime and tragedy spur action so that we can finally see that war has enormous costs and is not merely an occasion to celebrate heroism? Or will the American public take one man’s crime and churn it into the terrorism of religion?

Muslims, the newest minorities in the American imagination, will be bowing heads in mourning for the loss of life at Fort Hood but, with the dark clouds around them, they will be doing so with one eye open.