THE OBAMA/GATES PENTAGON…. From a progressive perspective, there are a few concerns about Robert Gates staying on as Defense Secretary in an Obama administration. One of the main issues has to do with Gates’ deputies — Gates may be a sensible pragmatist, but deputies will have considerable influence on Pentagon decision-making, and they’re not as inclined towards pragmatism as their boss.

As Chris Bowers recently argued, “If Gates were kept on as Secretary of Defense, it apparently would also mean that all of his top advisors would also stay on.”

Fortunately, it appears this concern is working out even better than expected, and Gates’ team is going to see some significant changes

Although President-elect Barack Obama’s decision to keep Robert M. Gates at the helm of the Pentagon will provide a measure of continuity for a military fighting two wars, many of Gates’s top deputies are expected to depart their jobs, according to senior defense and transition officials.

Deputy Defense Secretary Gordon England, Gates’s right-hand man in running the Pentagon day to day, is widely expected to leave his post, said the officials, one of whom noted that England’s speechwriter is reportedly taking another job.

Leading candidates to replace England include Obama campaign adviser Richard J. Danzig, who could eventually replace Gates; Pentagon transition review team co-leader Michele A. Flournoy; and possibly former Pentagon comptroller William J. Lynn, said Obama transition officials and sources close to the transition.

The anticipated turnover of many key positions suggests that although Gates will help provide some continuity, the status quo will not necessarily endure at the Pentagon.

The four undersecretaries of defense, including former Cheney aide Eric Edelman, will be replaced, as will the undersecretary for intelligence, and the undersecretary for personnel. As one source close to the transition told the Post, “At the undersecretary level, you are pretty much hitting the reset button.”

It’s unclear if the shift in deputies was part an arrangement worked out between Gates and Obama’s team, or if these officials were planning to depart anyway. Either way, though, it addresses one of the bigger, if not the biggest, problem associated with Gates’ extended tenure.

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Follow Steve on Twitter @stevebenen. Steve Benen is a producer at MSNBC's The Rachel Maddow Show. He was the principal contributor to the Washington Monthly's Political Animal blog from August 2008 until January 2012.