The current scandal in the academy concerning the American Psychological Association's knowledge of members assisting CIA torture raises fundamental questions.

http://chronicle.com/article/Damning-Revelations-Prompt/231591/?cid=at&utm_source=at&utm_medium=en

Among those questions:

1.  Should academics ever assist the military?

To me the answer to this question is "yes."  In time of war, this is patriotic.  Anthropologists assisting the Army in dealing with Afghan villagers has never seemed to me to be wrong.

Of course, I have no problem with scientists on our campuses doing research for corporations either... so long as they don't present their work ad disinterested and objective in scholarly journals.

2.  Should social scientists, such as psychologists, assist the CIA with torture?

A much tougher question of course.  I expressed some views on torture a half dozen years ago in another forum, where I received many, many responses:
http://societyforcriticalexchange.org/blog/blog3.php/2009/04/24/torture

Sub-questions include:

a.  What is torture?  This was hotly debated during the Bush Administration.  Is water boarding "torture"?  
http://www.npr.org/2007/11/03/15886834/waterboarding-a-tortured-history

b.  Is torture ever justified, if it can save lives?

Or are some practices so evil that they must be avoided no matter what the cost?

This last question resonates with the debate over whether it is ever justified to suspend our civil liberties in the face of a national emergency.  Certainly, Lincoln thought so when he suspended habeas corpus at the start of the Civil War.  

On the other hand, however, there is ALWAYS some crisis or threat that leads some people to suggest that our civil rights and liberties must give way to the meeting of an immediate perceived threat.

I think we tend to forgive Lincoln, but condemn California Governor Earl Warren and the others who interred Japanese-American citizens during WWII.   How do we reach such a conclusion... and are we right?

That may be the toughest question of all.  And it is certainly one that academics and all citizens will be called on to answer again and again in the future.