All Quiet on the Afghan FrontRobert Gates wants all advice to the president, not just advice from the military, to stay private.

Robert M. GatesDefense Secretary Robert M. Gates recently said that those advising the president on Afghanistan should keep quiet in public. This has been interpreted as a direct message to Gen. Stanley A. McChrystal, Obama's top commander in Afghanistan, who was asked last week whether a more limited counterterrorism effort would succeed in Afghanistan. He replied: "The short answer is: no. You have to navigate from where you are, not where you wish to be. A strategy that does not leave Afghanistan in a stable position is probably a short-sighted strategy." Gates said Monday: "It is imperative that all of us taking part in these deliberations provide our best advice to the president candidly, but privately."

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But Gates wasn't just talking about those under his direct command. "Those who are reading this as a rebuke to McChrystal are reading it too narrowly," says Pentagon spokesman Geoff Morrell. "This applies to everyone involved in the process."

That means White House aides. Administration aides have also been speaking, anonymously, about the general and his report on Afghanistan. In a Washington Post story two days after a secure three-hour meeting on the topic of Afghanistan, several administration sources expressed skepticism about McChrystal's thinking. "A lot of assumptions—and I don't want to say myths, but a lot of assumptions—were exposed to the light of day," one senior administration official told the Post. One of the key assumptions exposed, according to the Post, was the contention that the return to power of the Taliban would mean a new sanctuary for al-Qaida.

Any kind of thorough review tests even the most basic assumptions. The link between Taliban insurgents and al-Qaida is long-standing, so it is perhaps a sign of how rigorous the Obama process is that even this premise is now open to question. On Sunday, National Security Adviser Jim Jones was so wary of making the al-Qaida/Taliban connection that when asked on Face the Nation whether a return of the Taliban would mean a return of al-Qaida, he ducked the question.

But asking whether the connection exists is not the same as saying the connection is a myth that must be "exposed to the light of day." Plus, if McChrystal is laboring under a false assumption that the Taliban's success would bring a new sanctuary for al-Qaida, then his commander in chief has been harboring the same assumption. It's been at the center of Obama's worldview from March, when he announced the new strategy, to as recently as August. Two months ago, Obama said, "If left unchecked, the Taliban insurgency will mean an even larger safe haven from which al-Qaida would plot to kill more Americans."

Where does Obama stand on this issue today? Tuesday he spoke to the employees of the National Counterterrorism Center. "We know that al-Qaida and its extremist allies threaten us from different corners of the globe—from Pakistan, but also from East Africa and Southeast Asia; from Europe and the Gulf." What country is missing? Afghanistan, the country where, for months, Obama has talked about "al-Qaida and its extremist allies," which previously had meant the Taliban.

It was clear Monday at a George Washington University forum that Gates and Secretary of State Hillary Clinton believe that the connection still exists. "The thing to remember about Afghanistan is that that country, and particularly the Afghan-Pakistan border, is—is the modern epicenter of jihad," Gates said. "It is where the mujahedin defeated the other superpower. And their view is, in my opinion, that they now have the opportunity to defeat a second superpower, which, more than anything, would empower their message and the opportunity to recruit, to fundraise and to plan operations."

Gates also tipped his hand on another key question in Afghanistan: whether to send more troops. "The reality is that, because of our inability and the inability, frankly, of our allies, to put enough troops into Afghanistan, the Taliban do have the momentum right now." It's the kind of comment that lets you know what he thinks without him saying anything directly. Does Gates favor sending more troops? If so, it's something he's saying to the president only in private.

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John Dickerson is Slate's chief political correspondent and author of On Her Trail. He can be reached at . Follow him on Twitter.

Photograph of Robert M. Gates by Tim Sloan/AFP/Getty Images.

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