For a clear-headed discussion of academic freedom in the context of the John Yoo case, see here. I have a few of additional things to say on the matter.

When people typically argue that Yoo should be fired, they tend to resort to two main arguments.

The magic job title: Suppose you and I strike up a conversation, and you happen to ask me what I think about the power of the executive, and I reply that since the president is the commander-in-chief of the US armed forces, there is no legal limitation whatsoever on the orders he can give to the troops. Interesting, you say, can you write this down for me along with the references? Sure, I say.

That's just talk.

On the other hand, suppose I have a JD and have "white house legal counsel" as my job title. Further...

...Suppose you and I strike up a conversation, and you happen to ask me what I think about the power of the executive, and I reply that since the president is the commander-in-chief of the US armed forces, there is no legal limitation whatsoever on the orders he can give to the troops. Interesting, you say, can you write this down for me along with the references? Sure, I say.

Well now thats a war crime.

According to this view, writing down my opinions is clearly not a crime. Its my JD and my job title that magically transform writing my opinions into crimes.

And that, of course, is just silly - a lawyer is just someone who writes down his opinions in exchange for money. Nothing more, nothing less.

The consequence argument: A consequence of Yoo's writing down his opinions was that people were tortured, and therefore Yoo is guilty of a war crime. For example, Marty Lederman (an actual law professor - I am not just pulling random yahoos of the internets) writes,

...no one thinks a professor should be fired for having views deemed morally reprehensible or for producing a shoddy piece of work. The claim here is that the morally reprehensible views, and the shoddy work, in this case were put to use in official state conduct that facilitated and immunized horrific crimes. And that makes the question at least a bit more complicated...

Of course, nothing in this argument references the fact that Yoo was a white house legal counsel. In fact, if he just expressed his views to Bush over lunch, the argument would still hold. As long as his act results in torture or, in Lederman's words, is "put to use in official state conduct that facilitated and immunized horrific crimes," there is no difference whether he wrote it down in a memo or expressed it verbally.

Nor does he have to express it to Bush; it could be any kind of lower ranking official in the white house. Nor, come to think of it, would Yoo even need to do that; if he just published the arguments of his memo in a magazine, the effects would be the same.

You can see how this argument leads to a blanket restriction on speech. Once you start saying that some speech is a war crime based on the acts it inspires in other people (irrespective of its content - for this argument to work, it doesn't matter if Yoo is right or wrong!), free speech is pretty much in the toilet.

In our time, political speech and writing are largely the defense of the indefensible. Things like the continuance of British rule in India, the Russian purges and deportations, the dropping of the atom bombs on Japan, can indeed be defended, but only by arguments which are too brutal for most people to face, and which do not square with the professed aims of the political parties. Thus political language has to consist largely of euphemism., question-begging and sheer cloudy vagueness.

So wrote George Orwell almost sixty years ago. I'm reminded of this today by the emerging controversy over John Yoo - a number of people want this man fired because they don't like the legal opinions he wrote while working for the Department of Justice. Of course, if you have any commitment at all to "academic freedom," its impossible to support this. Cases like Yoo's, in fact, are exactly the reason why we have the tenure system -professors need job security precisely so that they can conduct independent and potentially unpopular scholarship. Unless you are perfectly content to live in a world without academic freedom - where the opinions of academics are up for review by their superiors - you have an obligation to support Yoo's right to hold his legal views and still keep his job. All in all, this case is a no-brainer.

Watch, however, how language is twisted in an effort to make Yoo's role seem larger than life. This piece at the Huffington posts quotes the following:

"Addington, Bybee, Gonzales, Haynes, and Yoo became, in effect, a torture team of lawyers, freeing the administration from the constraints of all international rules prohibiting abuse."

while Henry Farrell at Crooked Timber writes

...this is not, in the end, an issue of academic freedom. That is, it doesn’t concern Yoo’s ideas about the laws or communication of same; it concerns credible allegations that Yoo acted directly and deliberately, in his capacity as an employee of the US government to facilitate war crimes.

Of course, when all is said and done, all Yoo did was give his legal opinion. To bring Orwell's point home, you could argue directly that lawyers ought to be jailed if their opinions about the constitution are too wacky, but that would be far too honest.

This whole thing sort of reminds me of another disturbing trend: the way labels like "human rights" have been co-opted in the service of speech suppression. Read more about that here.

Update: This formulation is particularly amusing,

None of Yoo’s critics, to my knowledge, are arguing that he should lose his job for his ideas; rather that he should lose his job for actions that he took as a servant of the US government…

Of course, the actions in question consist of nothing more than writing down his ideas.

The Times has an article about Palestinian children's tv:

Another children’s program, “Tomorrow’s Pioneers,” has become infamous for its puppet characters — a kind of Mickey Mouse, a bee and a rabbit — who speak, like Assud the rabbit, of conquering the Jews to the young hostess, Saraa Barhoum, 11. “We will liberate Al Aksa mosque from the Zionists’ filth,” Assud said recently. “We will liberate Jaffa and Acre,” cities now in Israel proper. “We will liberate the whole homeland.”

The mouse, Farfour, was murdered by an Israeli interrogator and replaced by Nahoul, the bee, who died “a martyr’s death” from lack of health care because of Gaza’s closed borders. He has been supplanted by Assud, the rabbit, who vows “to get rid of the Jews, God willing, and I will eat them up, God willing.”

When Assud first made his appearance, he said to Saraa: “We are all martyrdom-seekers, are we not, Saraa?” She responded: “Of course we are. We are all ready to sacrifice ourselves for the sake of our homeland. We will sacrifice our souls and everything we own for the homeland.”