Eric Lichtblau and James Risen continue to feed us tidbits from their book on the NSA spy controversy on the front page of the New York Times. Today, they reveal that James B. Comey, acting as Attorney General while than-AG John Ashcroft, who was hospitalized for gallbladder surgery, “indicated he was unwilling to give his approval to certifying central aspects of the program.”

The domestic eavesdropping program was publicly disclosed in mid-December by The New York Times. President Bush, in acknowledging the existence of the program in a televised appearance two weeks ago, said that tight controls had been imposed over the surveillance operation and that the program was reviewed every 45 days by top government officials, including at the Justice Department. “The review includes approval by our nation’s top legal officials, including the attorney general and the counsel to the president,” Mr. Bush said, adding that he had personally reauthorized the program’s use more than 30 times since it began. He gave no indication of any internal dissent over the reauthorization.

Since when do presidents–or leaders at any level in any walk of life–note that there was internal dissent in the decisionmaking process? Executives make decisions after gathering input from their subordinates and then take responsibility for those decisions. Indeed, had there been no dissent, we would be reading about groupthink and Bush surronding himself with Yes men.

Thirteen paragraphs into the story, after quite a bit of acknowledged speculation, we learn:

What is known is that in early 2004, about the time of the hospital visit, the White House suspended parts of the program for several months and moved ahead with more stringent requirements on the security agency on how the program was used, in part to guard against abuses. The concerns within the Justice Department appear to have led, at least in part, to the decision to suspend and revamp the program, officials said. The Justice Department then oversaw a secret audit of the surveillance program. The audit examined a selection of cases to see how the security agency was running the program. Among other things, it looked at how agency officials went about determining that they had probable cause to believe that people in the United States, including American citizens, had sufficient ties to Al Qaeda to justify eavesdropping on their phone calls and e-mail messages without a court warrant. That review is not known to have found any instances of abuses.

So, there were concerns expressed by key personnel, they were taken seriously, and appropriate steps were taken. And it turns out that there were no abuses?

At its outset in 2002, the surveillance operation was so highly classified that even Larry Thompson, the deputy attorney general to Mr. Ashcroft, who was active in most of the government’s most classified counterterrorism operations, was not given access to the program. That led to uncertainties about the chain of command in overseeing law enforcement activities connected to the program, officials said, and it appears to have spurred concerns within the Justice Department over its use. Mr. Thompson’s successor, Mr. Comey, was eventually authorized to take part in the program and to review intelligence material that grew out of it, and officials said he played a part in overseeing the reforms that were put in place in 2004.

That’s the trade-off that always surrounds highly classified operations. The Manhattan Project was so secret that Vice President Harry Truman didn’t know about it.

But even after the imposition of the new restrictions last year, the agency maintained the authority to choose its eavesdropping targets and did not have to get specific approval from the Justice Department or other Bush officials before it began surveillance on phone calls or e-mail messages. The decision on whether someone is believed to be linked to Al Qaeda and should be monitored is left to a shift supervisor at the agency, the White House has said.

The White House has vigorously defended the legality and value of the domestic surveillance program, saying it has saved many American lives by allowing the government to respond more quickly and flexibly to threats. The Justice Department, meanwhile, said Friday that it had opened a criminal investigation into the unauthorized disclosure of the existence of the program.

The precise nature of the program remains unclear to me. From what I have gathered, though, the whole point of bypassing the FISA warrant requirement was that the nature of the surveillance did not conform to the standard law enforcement model. It was some manner of data mining or roving surveillance not tied to a specific person or place. Once the decision was made to run the program, it stands to reason that day-to-day decisions would be made by intelligence professionals rather than executive policymakers.