Sam Harris, a neuroscientist, challenged Bruce Schneier to a debate on whether Muslims should be singled out for additional screening at airports. Schneier patiently, and repeatedly, explains why (apart from the unconstitutionality and moral repugnance of this), it would be bad security practice. Harris changes the subject. A lot. But Schneier presents a model of how to use dispassionate reason to demolish intellectual laziness and xenophobia dressed up as "common sense."
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There are other security concerns when you look at the geopolitical context, though. Profiling Muslims fosters an “us vs. them” thinking that simply isn’t accurate when talking about terrorism. I have always thought that the “war on terror” metaphor was actively harmful to security because it raised the terrorists to the level of equal combatant. In a war, there are sides, and there is winning. I much prefer the crime metaphor. There are no opposing sides in crime; there are the few criminals and the rest of us. There criminals don’t “win.” Maybe they get away with it for a while, but eventually they’re caught.
“Us vs. them” thinking has two basic costs. One, it establishes that worldview in the minds of “us”: the non-profiled. We saw this after 9/11, in the assaults and discriminations against innocent Americans who happened to be Muslim. And two, it establishes the same worldview in the minds of “them”: Muslims. This increases anti-American sentiment among Muslims. This reduces our security, less because it creates terrorists—although I’m sure it is one of the things that pushes a marginal terrorist over the line—and more that a higher anti-American sentiment in the Muslim community is a more fertile ground for terrorist groups to recruit and operate.