Lobbyists and science policy wonks had enough to pore over when the Bush administration released its 2,000-plus-page final budget request last week for the 2009 fiscal year. Supporters of the physical sciences had reason to be hopeful, but looming ahead, as it did last year, was the prospect of another showdown with the White House over spending priorities that could again marginalize proposed increases for research and development programs within the American Competitiveness Initiative, which was authorized in the America COMPETES Act but not fully funded in the 2008 omnibus appropriations legislation passed in December.

Those programs, designed to emphasize long-term economic growth by boosting research in the sciences, typically come from a few sources, such as the National Science Foundation, the National Institute of Standards and Technology and the Department of Energy's Office of Science. So it came as a bit of a surprise to some when they began to scrutinize the portion of the budget dedicated to the Department of Defense's basic research initiatives, which the administration graced with an unusual increase in the neighborhood of $270.5 million, or 18.9 percent, over last year's request -- bringing the total to $1.7 billion.

"These investments are made to support national security but, due to the broad effects of basic research, also contribute to ACI innovation goals as well," John Marburger III, the director of the White House Office of Science and Technology Policy, said before the House of Representatives' Committee on Science and Technology on Thursday.

The origin of the requests is a series of memos and letters whose ultimate recipient had every reason to be sympathetic to increased defense spending for basic research: Robert M. Gates, the secretary of defense and former president of Texas A&M University, where, among other pursuits, he pushed for a major DoD grant for research in infectious diseases as well as numerous other basic research projects.

“In fact, it clearly came from Secretary Gates," said Tobin Smith, associate vice president for federal relations at the Association of American Universities. Smith said Gates responded in particular to an August 24 memo written by John J. Young Jr., the director of Defense Research & Engineering at the Pentagon, recommending a $300 million boost for "foundational" research.

That was followed up in October by CEOs of major corporations, including Boeing, Intel and Lockheed Martin, urging Gates to stick to a 3 percent target for basic research funding, a goal that the department has fallen short of even as its overall funding for Defense Research, Development, Testing and Evaluation has increased by a third in the past five years. Six members of the House from both parties seconded Young's letter, urging Gates to "take those views into account when considering your budget request" for fiscal 2009.

The Pentagon was evidently paying attention. In a February 4 news briefing on the day the budget was released, Tina W. Jonas, the department's chief financial officer, confirmed: "This is a specific initiative that the secretary and the chairman are putting emphasis on."

It's "a very significant boost and what many people regard as a long-overdue recognition of the key role that DoD plays in the physical sciences,” said Kei Koizumi, the director of the R&D Budget and Policy Program at the American Association for the Advancement of Science. The department's role in such peer-reviewed basic research has declined since the end of the Cold War. About 60 percent of its funding goes to academic institutions for research projects, Smith estimated, and the department remains the top funder of academic-based engineering research, covering about 37 percent of such projects.

“This is a starting point for hopefully what is supposed to be increases that are to continue for the next five years," Smith added. "This is not supposed to be a one-time deal; it’s supposed to increase over time, at least that’s our understanding from the DoD.”

The basic research component of the budget is part of an overall $11.48 billion request for DoD science and technology funding, including applied research and advanced technology development. As part of the administration's effort to reduce non-competitive Congressionally directed funding -- commonly known as earmarks -- it's important to note that the budget's $1.7 billion figure for basic research is $65 million over the 2008 appropriated level, including earmarks. Removing them first, as the budget does by default, the increase stands at $270.5 million above the president's 2008 request, indicating the shift in administration priorities amid pressure within the Pentagon. DoD basic research is 14.8 percent of the DoD science and technology budget in 2009, compared with 13.3 percent last year, Marburger said at Thursday's hearing.

According to an AAU analysis, the budget request includes $3.29 billion for the Defense Advanced Research Projects Agency, or DARPA, an increase of 11 percent above the 2008 funding level, or 6.5 percent above the 2008 request. Nearly $196 million of that money would go to the Defense Research Sciences program. Separately, the Defense Experimental Program to Stimulate Competitive Research would receive $2.8 million, a reduction of $14.1 million from the 2008 funding level. The Government-Industry Co-sponsorship of University Research program receives no request at all for 2009, compared to the 2008 funded level of $6.2 million.

William S. Rees Jr., the deputy under secretary of defense for laboratories and basic sciences, was traveling and did not respond to several requests for comment.