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AIDS activists began to see the warning signs even before President Obama had fully settled into his new role in 2009. Just one day after the inauguration, the White House asked Ambassador Mark Dybul, head of the President's Emergency Plan for AIDS Relief (PEPFAR), to resign. The Obama administration had reportedly asked Dybul to spend several months overseeing the handoff for PEPFAR, one of President Bush's signature accomplishments. But that plan changed once President Obama actually took office.

Michael Gerson, a former Bush adviser and Washington Post columnist who championed PEPFAR, characterized the dispute as "Weasels vs. AIDS Relief." He worried for the 2 million people who had received lifesaving AIDS therapy thanks to the U.S. taxpayers' generosity. Christianity Today deputy managing editor Timothy C. Morgan, who has written extensively on the global AIDS crisis, saw trouble ahead.

"Even today, one evangelical leader expressed to me her fear that PEPFAR itself is going to be radically reshaped under the Obama administration," Morgan wrote on January 28, 2009. "That probably means so long to faith-based abstinence and fidelity educational programs in Africa and elsewhere. These efforts were at the heart of the Uganda success story in which HIV/AIDS rates and deaths were dramatically reduced. Countless families were held together as a result. This move sure feels like snatching defeat from the jaws of victory."

Every year, 2 million people die with AIDS. But the disease continues to spread because 3 million contract it annually. About 200,000 people in Uganda, a predominantly Christian nation, are being treated by drugs for AIDS. That number has increased from 10,000 only ten years ago thanks in large measure to PEPFAR. Yet even in Uganda, the crisis has not abated. Just last week, The New York Times cited Uganda in a story whose headline screamed for attention: "At Front Lines, AIDS War is Falling Apart." It's falling apart, among other reasons, because foreigners are shifting funds away from AIDS treatment toward easier-to-solve diseases. Indeed, a net that prevents the spread of malaria by mosquitoes costs less than AIDS drugs that cannot cure.

During the 2008 campaign, President Obama praised PEPFAR and promised he would boost funding by $1 billion annually. But when his administration released its first budget, PEPFAR received a $165 million increase. Of course, the global recession forced cuts in such "nonessential" spending. Still, it's hard to take this excuse seriously when the budget is bloated so many other places. In any event, The New York Times observed other factors at work with the AIDS budget. Dr. Ezekiel J. Emanuel, brother of Obama's chief of staff, Rahm Emanuel, had criticized President Bush's global health priorities. Writing in November 2008 for The Journal of the American Medical Association, Ezekiel Emanuel argued that the U.S. government could save more and younger lives by targeting lethal diseases such as tuberculosis and malaria, which cost much less than AIDS to treat.

Eric Goosby, the current head of PEPFAR, echoed this strategy shift when he defended the Obama administration's new treatment plans. He pledged himself to making decisions based on science. But science doesn't necessarily dictate funding priorities or solve the dilemma of which diseases to treat with limited funding.

"You treat the sickest first, no?" Goosby told The New York Times. "If you don't have unlimited resources, isn't that rational and ethical?"

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