An employee of Whole Foods in Ann Arbor, Michigan, was fired in 2007 for apprehending a shoplifter. More specifically, he was fired for touching a customer, even though that customer had a backpack filled with stolen groceries and was running away with them.

I regularly see security decisions that, like the Whole Foods incident, seem to make absolutely no sense. However, in every case, the decisions actually make perfect sense once you understand the underlying incentives driving the decision. All security decisions are trade-offs, but the motivations behind them are not always obvious: They’re often subjective, and driven by external incentives. And often security trade-offs are made for nonsecurity reasons.

Almost certainly, Whole Foods has a no-touching-the-customer policy because its attorneys recommended it. "No touching" is a security measure as well, but it's security against customer lawsuits. The cost of these lawsuits would be much, much greater than the $346 worth of groceries stolen in this instance. Even applied to suspected shoplifters, the policy makes sense: The cost of a lawsuit resulting from tackling an innocent shopper by mistake would be far greater than the cost of letting actual shoplifters get away. As perverse it may seem, the result is completely reasonable given the corporate incentives – Whole Foods wrote a corporate policy that benefited itself.

At least, it works as long as the police and other factors keep society’s shoplifter population down to a reasonable level.

Incentives explain much that is perplexing about security trade-offs. Why does King County, Washington, require one form of ID to get a concealed-carry permit, but two forms of ID to pay for the permit by check? Making a mistake on a gun permit is an abstract problem, but a bad check actually costs some department money.

In the decades before 9/11, why did the airlines fight every security measure except the photo-ID check? Increased security annoys their customers, but the photo-ID check solved a security problem of a different kind: the resale of nonrefundable tickets. So the airlines were on board for that one.

And why does the TSA confiscate liquids at airport security, on the off chance that a terrorist will try to make a liquid explosive instead of using the more common solid ones? Because the officials in charge of the decision used CYA security measures to prevent specific, known tactics rather than broad, general ones.

The same misplaced incentives explain the ongoing problem of innocent prisoners spending years in places like Guantanamo and Abu Ghraib. The solution might seem obvious: Release the innocent ones, keep the guilty ones, and figure out whether the ones we aren't sure about are innocent or guilty. But the incentives are more perverse than that. Who is going to sign the order releasing one of those prisoners? Which military officer is going to accept the risk, no matter how small, of being wrong?

I read almost five years ago that prisoners were being held by the United States far longer than they should, because ''no one wanted to be responsible for releasing the next Osama bin Laden.'' That incentive to do nothing hasn't changed. It might have even gotten stronger, as these innocents languish in prison.

In all these cases, the best way to change the trade-off is to change the incentives. Look at why the Whole Foods case works. Store employees don't have to apprehend shoplifters, because society created a special organization specifically authorized to lay hands on people the grocery store points to as shoplifters: the police. If we want more rationality out of the TSA, there needs to be someone with a broader perspective willing to deal with general threats rather than specific targets or tactics.

For prisoners, society has created a special organization specifically entrusted with the role of judging the evidence against them and releasing them if appropriate: the judiciary. It's only because the George W. Bush administration decided to remove the Guantanamo prisoners from the legal system that we are now stuck with these perverse incentives. Our country would be smart to move as many of these people through the court system as we can.

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Bruce Schneier is chief security technology officer of BT. His new book is Schneier on Security.