The Justice Department has been dogged by criticism that Gonzales, who had worked for Bush when he was governor of Texas and also served as White House counsel, operated it as though it was a branch of the White House instead of a politically independent division.
Asked by Specter if he would be prepared to resign if the president did not take his counsel on constitutional matters, Mukasey said, "If the president proposed to undertake a course of conduct that was in violation of the Constitution, that would present me with a difficult but not a complex problem. I would have two choices: I could either try to talk him out of it or leave."
Mukasey also noted that he would recuse himself from election matters pertaining to GOP presidential hopeful and former New York City mayor Rudy Giuliani, who is a close friend of his.
Another hot-button topic that could still come up at the hearing will be Mukasey's views on such such legal issues as the material witness law, which allows the government to hold witnesses temporarily to keep them from fleeing court proceedings.
So-called "dirty bomber" Jose Padilla, who was convicted on terrorism charges in August, was originally held on a material witness warrant instead of criminal charges. In an opinion piece in The Wall Street Journal published after the trial, Mukasey wrote that the Padilla case illustrated the fact that "current institutions and statutes are not well suited to even the limited task of supplementing what became, after Sept. 11, 2001, principally a military effort to combat Islamic terrorism."
Osama Awadallah, also detained on a material witness warrant because his phone number was found on a piece of paper in one of the Sept. 11 hijackers' cars, was later cleared of all charges, though his attorney said Awadallah was mistreated while in custody.
Both Padilla and Awadallah appeared before Mukasey during his time on the federal bench.
To his advantage, Mukasey has apparently gained the support of some of Gonzales' most outspoken critics.
Sen. Charles Schumer, D-N.Y., and Sen. Joe Lieberman, D-Conn., officially introduced Mukasey to the committee; Mukasey is from Schumer's home state, and he attended law school with Lieberman.
Schumer praised Mukasey for earning "a reputation for efficiency, fairness and integrity" throughout his career, but he didn't mince words in describing the current state of affairs at the Justice Department in calling it "an agency experiencing its greatest crisis since Watergate."
"From talking with him, it is clear that many of us are going to disagree with many of his views, and with some quite strongly. But at this time, the most important question is this: Will Judge Mukasey be independent enough and courageous enough to stand strong even against the man who nominated him, if that is what the law requires?" Schumer asked.
But Lieberman expressed faith in Mukasey, calling him a "man of the law, not a man of politics," and noting that he comes to the table with few ties to Bush.
Mukasey's palatability to both parties stems in part from his extensive experience in the federal court system.
President Reagan nominated Mukasey to the federal bench in 1987; he served as a judge in the Southern District of New York for more than 18 years until he joined the New York law firm Patterson Belknap Webb & Tyler in September 2006.