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I have worked in senior positions in facilities similar to prisons, and also worked for a while in a maximum security prison. Such organizations have a myriad of policies and procedures that staff are very familiar with that set standards for how inmates are to be treated and their rights protected.
Even if I had received a memo from the governor of my state saying that as of now all human rights of my charges and all abuse laws were suspended, my staff would still have been obliged to follow all policies and procedures unless they were specifically directed to ignore them.
I can see how that might be the case as far as the policies and procedures of an institution that had already been in place for some time. But facilities like Camp Delta, Camp X-Ray, and the American administration of the detainee camps in Iraq were new, and starting off under the pronounced impression that they were part of an unprecedented effort where the old norms no longer applied. There wasn't a legacy of "set procedures" for the Guantanamo Bay camps. They were built from the ground up, and partially staffed by newcomers coming from an entirely different operations specialty than the military police. And the camps in Iraq were seen as an extension of that newly inaugurated era- the "Great War On Terror", as the original acronym had it.
Also in reference to your experience- there's also a profound difference between the orders of a State governor, and the orders of the President. To refer to your hypothetical, one of the primary rationales for maintaining traditional standards of human rights despite an executive order from a State governor countermanding them is the fact that Federal law supercedes any change a State might make in that regard. The President of the USA isn't legally bound like that- not in that respect, anyway. And the record is clear as to what executive powers President George W. Bush has attempted to bestow upon himself by his own signature; and how he sent the message across the board, both as Chief Executive and Commander-In-Chief, that a new regime was in place, breaking with the definitions and standards of human rights formerly officially upheld as part of the American tradition.
Your comment raises the practical question of ways and means, specifically in regard to how that stance played out down the military chain of command in regard to specific orders and policy changes. It's a good question, and one that hasn't been investigated nearly enough, in my view. Sgt. Eric Saar has some things to say about that in his book about his experiences at Gitmo;
http://www.amazon.com/Inside-Wire-Intelligence-Eyewitness-Guantanamo/dp/1594200661
I have it around, maybe I can retrieve it later today and quote some excerpts.
In the meantime, a few links:
http://www.humanrightsfirst.org/blog/cardona/2006/05/general-miller-takes-stand.aspx
http://www.pbs.org/wgbh//pages/frontline/torture/paper/rules.html
http://www.historycommons.org/entity.jsp?entity=thomas_m._pappas
http://physics.uark.edu/hobson/NWAT/04.06.12.html
http://physics.uark.edu/hobson/NWAT/04.06.26.html
(I can hear Elephantman carping about the provenance of the links already...as if anyone at, say, Townhall.com or World Net Daily actually cared about any of this- to the extent of their not even attempting to challenge the factuality of any of the findings contained in the links above. )