Try This on Fear Factor

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In the debate about what constitutes "torture" that swirled around the past few months, the term "waterboarding" was tossed around quite a bit. I'm leery of commenting on things I know nothing about, and equally leery of opinions coming from people I suspect know just as little. Here's a waterboarding you can watch if you care to. Most of the comments are useless --but these two get to the heart of the matter:
The reason waterboarding is different from other interrogation techniques is because other interrogation techniques are merely uncomfortable for a prisioner. Making them stand for the duration of the interrogation is uncomfortable. Open-palmed slaps are uncomfortable. Colder temperatures (not life threatening) are uncomfortable. But waterboarding isn’t merely uncomfortable, it’s a violation of their integrity as a HUMAN PERSON. I hate terrorists just as much as anyone else, but I happen to like humanity. And as evil as they are, waterboarding is considered torture by many because it puts the fear of death into a person entirely at the mercy of his interrogators. That’s the classic definition of torture.
I've always thought of torture as tormenting a person just because you can, but then this war has caused me to think about many issues for which glib answers were previously satisfying. Some time ago I asked my military expert, Little Bro, about it:
There are many ways of doing it but generally it involves a mask with a restrictive air-passage and high pressure water gushing into the mask. The trick is to leave enough air in the mask to make the "detainee" think that the mask isn't working right and that he can cheat out a desperate breath in the midst of flood of water. He is expecting relief but the moment he tries an alarming amount of water comes rushing in. The surprise at not being able to take that breath is what causes extreme hysteria. The average person holds out for about 30 seconds, KSM who trained to resist this tactic held out for 2 rumor has it.

He also provided the counter argument:
Is it moral? Well it is as moral as the side you are fighting for, and if it turns out that the guy is just some poor stooge that was just in the wrong place at the wrong time the fellow is not left with permanent injuries. The Geneva conventions were created for large armies of people in uniform. What do you do with thousands prisoners who were part of a battle that had already been fought. These types of prisoners on the whole have little intelligence value so it is pointless to torture them anyway, so why not be civil? But a terrorist is an unknown quantity. They have no rank or unit or immediate way of identifying their status. They may be a franchise unto themselves, they may be a key operative with information that could help us foil a thousand deadly plots. If you had Mohammed Atta in custody in August 2001, you would hate yourself forever if you didn't take the opportunity to pour the entire contents of the Nile down his cussed throat. It is certainly more humane than dropping bombs in general locations from 15,000 feet as I would say to Senator McCain.
Is that an "ends justifies the means" argument --doing evil that good may come? Or is it a Just War argument?