Yes, it's true -- it's not the TSA's fault, all of this airport security craziness. The TSA is a government bureaucracy within a larger government bureaucracy, the Department of Homeland Security, and both organizations have as their mission the protection of American citizens from terrorism. They are going to do whatever they believe it will take, and is legal, to keep Americans safe. That is their bureaucratic imperative. But it is the mission of the President, and of the Congress, to supervise and monitor these bureaucracies, to hold them back when their mission comes into conflict with other missions, such as the protection of the privacy of American citizens.
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I believe Janet Napolitano knows this; from what I can tell, she's very good at her job. I also believe she is singularly focused on the department's mission. I'm told that the new TSA administrator, John Pistole, is a smart guy (not like the dopey fellow who ran the agency under President Bush). But he, too, has a mission, and a reputation, and his reputation will be ruined if a terrorist blows up a plane. (This is a separate issue, the pressure our juvenile, zero-defect culture places on government bureaucrats to never let anything bad happen ever.) So he will utilize whatever technology, and whatever techniques, he believes will prevent bad things from happening. Who can blame him? But who makes sure that, in pursuit of a worthy goal, he doesn't go too far?
And, oh yes, the privacy challenges posed by the TSA are most certainly not the fault of actual TSA workers, who certainly don't have the easiest jobs in the country.