President-elect Obama today announced he will retain Secretary of Defense Robert Gates in the top Pentagon post, and also said Sen. Hillary Clinton (D-N.Y.), a member of the Senate Armed Services Committee (SASC), will be nominated as secretary of state.

In almost two years as secretary, Gates has overseen marked progress in many ballistic missile defense (BMD) programs conducted by the Missile Defense Agency and its director, Lt. Gen. Henry “Trey” Obering III.

Gates and Clinton appeared with Obama at a press conference, along with other members of his national security team including Gen. James Jones, former Marine Corps commandant and former supreme allied commander. Jones, who will be the Obama national security adviser, retired from the corps last year.

Under Gates, substantial progress has been made in many missile defense development systems, including the Aegis/Standard Missile sea-based system that knocked down an out-of- control U.S. intelligence satellite, the Ground-based Missile Defense system now in ground silos in Alaska and California, and the Airborne Laser, which in recent years has met its milestones and which just achieved the first firing of the laser though the aircraft-mounted beam control/fire control system. (Please see separate story in this issue.)

Obama has said the United States needs a missile defense shield. However, he also has said he wishes to see proof that each BMD system works before funding it.

Clinton, who voted to send troops into Iraq, has been a low-key member of the Senate Armed Services Committee, which under Democratic leadership has been far more supportive of missile defense than the House Armed Services Committee.

Each of the Obama nominees will have to be confirmed by the Senate, and few problems are expected on that score. For Gates, that will mean his nomination will be reviewed by the SASC.

The SASC chairman, Sen. Carl Levin (D-Mich.), today responded to Obama’s announcement by praising the retention of Gates as the top Pentagon leader.

“President-elect Obama has selected a rock solid national security team,” Levin said.

“Continuing … Gates in the position of secretary of defense is an excellent and unique choice. It reflects President-elect Obama’s perspective that quality is a non-partisan characteristic. Secretary Gates’ courageous actions in restoring a measure of accountability in the Pentagon is a critical component of the change that President-elect Obama was chosen to bring about. His retention [at the Department of Defense] also underlines Secretary Gates’ recognition of the limits of military power and that America’s greatest source of power is the values for which it is willing to fight.”

Obama also nominated Arizona Gov. Janet Napolitano as secretary of homeland defense. Arizona is a border state with problems with border security issues.

“Finally, I would note that Secretary Gates has correctly stated that the conflict in Afghanistan should mainly be “Afghanistan’s war” and has stressed the need to accelerate the doubling of the size of the Afghan National Army, which is crucial to the defense of Afghanistan’s democracy and to stopping cross-border incursions from Pakistan. Those safe havens threaten the democracy in Afghanistan and threaten America.”