Berkeley Law School Dean Chris Edley asks:
Berkeley Law School Dean Chris Edley: [T]he crucial questions... are these: Was there clear professional misconduct--that is, some breach of the professional ethics applicable to a government attorney--material to Professor Yoo's academic performance now?...
Dean Edley believes that this is a complicated question, to which we must never know the answer: the situation, he believes does "not warrant [Yoo's] dismissal or even a potentially chilling inquiry." The harm that would be done to academic freedom, Edley believes, is such that we must never take any steps to find out what the answer to Edley's question is.
I, by contrast, believe that we have already found out the answer to Edley's question.
I believe that this is a simple question.
A believe that this question has a very simple answer.
I believe that the answer is "yes."
In 2000, John Yoo published an article, "The Imperial Presidency Abroad" http://www.cato.org/events/000712con.html, in which he argued that President William Jefferson Clinton had unconstitutionally exceeded the bounds of his Commander-in-Chief powers:
accelerat[ing] disturbing trends in foreign policy that undermine democratic accountability and respect for the rule of law...
American troops... under... non-American... commanders, such as British General Michael Jackson.... [This] threatens that basic principle of government accountability. International or foreign officials have no obligation to pursue American policy, nor do they take an oath to uphold the Constitution...
Note that this is a very strange thing to write. In the customary laws of war, the decision whether or not to place soldiers under the tactical, operational, or strategic command of allies is within the appropriate commander's discretion whenever joint operations are underway. Thus the Duke of Wellington as theater commander placed British troops under Dutch command in the person of the Prince of Orange in the Waterloo Campaign. Thus did George Washington as commander-in-chief of the Continental Army place American troops under French command in the persons of the Marquis de Lafayette and the omte de Rochambeau during the Revolutionary War, thus did John Pershing as American field commander place American troops under French command in the person of Marshall Foch during World War I, and thus did Dwight Eisenhower as AEF commander place American troops under British command in the person of Field Marshall Montgomery during World War II. And nobody said "boo."
In striking contrast to what he had written thirty months before, on March 14, 2003 John Yoo wrote:
in the customary laws of war, the treatment of unlawful belligerents is left to the sovereign's discretion.... [T]he sovereign right of the United States on the treatment of enemy combatants is reserved to the President as Commander-in-Chief. In light of the long history of discretion given to each nation to determine its treatment of unlawful combatants, to construe these [congressional] statutes to regulate the conduct of the United States toward such combatants would interfere with a well established prerogative of the sovereign...
So we see, on the one hand, that when the President is William Jefferson Clinton, his Commander-in-Chief powers are so crabbed and restricted that Democratic President Clinton exceeded them by instructing American soldiers to obey the orders of the NATO theater commander.
And we see, on the other hand, when the President is George W. Bush, his Commander-in-Chief powers are so extensive and unconstrained that Congress's explicit authority to "make rules for the government and regulation of the land and naval forces" can place no restrictions at all on what lawful orders Republican President George W. Bush can give to mistreat, abuse, and torture persons held by the U.S. armed forces.
These two Commander-in-Chief powers are very different indeed.
To advance as your basic principle of Constitional construction "don't worry: it's OK if you are a Republican" is a breach of professional ethics serious enough to more than pass the bar set by Dean Edley--unless, of course, all legal reasoning is just a crock of manure to mask partisan maneuvering.
Now it is plain that John Yoo does not believe both of his 2000 and 2003 statements of the legal extent of the Commander-in-Chief power. Indeed, he believes neither: if he believed the 2000 statement, he would never in his life have written what he wrote in 2003; if he believed the 2003 statement, he would never in his life have put forward what he wrote in 2000.
This has a bearing on the duty of the university to ensure and promote academic freedom. As medieval history professor Ernst Kantorowicz said, upon his resignation from the university rather than bow to the Regents' demand that he swear that he would not advocate communism:
[I] wish to emphasize the true and fundamental issue at stake: professional and human dignity. There are three professions which are entitled to wear a gown: the judge, the priest, the scholar. This garment stands for its bearer's maturity of mind, his independence of judgment, and his direct responsibility to his conscience and to his God. It signifies the inner sovereignty of those three interrelated professions: they should be the very last to allow themselves to act under duress and yield to pressure. It is a shameful and undignified action, it is an affront and a violation of both human sovereignty and professional dignity that the Regents of this University have dared to bully the bearer of this gown into a situation in which--under the pressure of a bewildering economic coercion-‑he is compelled to give up either his tenure or, together with his freedom of judgment, his human dignity and his responsible sovereignty as a scholar.
Academic freedom--like all freedoms--is thus not free: liberty is always paired with responsibility. A professor is freed from coercion by others to shape or constrain or limit what he or she decides to say. In return, a professor takes on a twofold "responsibility to his conscience and to his god": an obligation (a) to think as hard as he or she can, and (b) to then tell the world what he or she thinks. A university in which professors are freed from external constraint and pressure and in turn obey the internal constraint that is their reponsibility to think hard and tell what they believe to be the truth is one in which there is academic freedom.
What does a university's obligation to nurture and guard academic freedom entail? Clearly it means that a university has to protect its members by coercion from outsiders. And clearly it means that a university has to protect its members from coercion by insiders--those other professors who do not like where professors' responsibilities to their consciences and gods lead them. But what are a university's obligations with respect to a professor who wants the freedom from coercion but does not accept the responsibility to think hard and to say what those thoughts are? What if a professor uses freedom from coercion and constraint not to tell the world what he thinks, but rather to say at one moment that there is one set of constitutional rules for Democratic Presidents and at another moment that there is a very different set of constitutional rules for Republican Presidents?
Is academic freedom vindicated by claiming that the university has no responsibility to censure, no responsibility to correct, no responsibility to discipline, no responsibility to dismiss someone who so violates his direct responsibility to his conscience and to his god?
I leave this issue as an exercise for the dean.
 Note the difference between "commander" on the one hand and "sovereign" on the other. The American President's powers are of the "Chief Executive" class, inherited from the powers of the British King as chief executive of the United Kingdom as its constitution stood in 1776. The British King in 1775 was not the "sovereign" but rather the commander of the army: ever since 1689, sovereignty in the United Kingdom was held by the King-in-Parliament, a very different entity than the King.