Friday’s eleventh-hour continuing resolution prevented a federal government shutdown, but while both sides have declared victory and pundits have already turned their attention to the looming debt-ceiling debate, Congress still has to prepare and pass the final budget for the last six months of FY 2011. Details about where the agreed upon $38 billion in cuts will come from are still emerging, but one of the hardest hit agencies will likely be the National Institutes of Health (NIH), the world’s largest investor in biomedical research.

The House FY2011 appropriations bill would cut the NIH budget by $1.6 billion. After accounting for biomedical inflation (each year the prices of research equipment and supplies increase by about 2 percent more than the general inflation rate), this would leave NIH funding at its 2001 level. An earlier Senate budget plan that aimed to cut $10 billion in spending would have maintained NIH funding at the FY 2010 level. But now that the target for cuts has nearly tripled, it’s likely that some of the cuts will come from NIH funds. Researchers and patient advocates are rightfully nervous—the cut would turn already competitive research grants into lotteries and slow scientific progress that translates into medical care.

The NIH’s total budget of $31 billion is responsible for one-third of Health and Human Services discretionary spending. But the suggestion that cutting its budget would make a meaningful dent in the deficit is ridiculous—it accounts for just 2.9 percent of total discretionary spending.

Private sources, like pharmaceutical companies, won’t make up the funding gap. Equivalent private funding simply isn’t available, and open-ended research doesn’t appeal to private funders even if it were. “Government funding is so important because it allows researchers to be creative,” notes Ben Corb of the American Society for Biochemists and Molecular Biology. “You don’t know where it’s going to take you. There’s a litany of accidental discoveries that would never have happened in an industrial setting.”

The current stop-and-start budget process, in which the chambers of Congress couldn’t agree on a full year’s appropriations bill and have opted instead for a series of short-term continuing resolutions, has already begun delaying projects. “NIH institutes and centers are rightly nervous to release new grant dollars when they have ongoing, multi-year grants they are already committed to fund, and they don’t know what their current fiscal year budget will be,” says Rebecca Riggins, a breast cancer researcher at Georgetown who recently had a project delayed for several months.

But the real damage will come after the proposed cuts take effect. The NIH is comprised of twenty-seven institutes and centers with particular focuses, including the National Cancer Institute (NCI) and National Heart Lung and Blood Institute; each will decide how to manage their individual cuts. The NCI will prioritize funding the same level of new grants (they currently fund 14 percent of new grant applications), but will have to cut funding from cancer centers. Others will have to choose between new and existing grants. When ongoing grants aren’t renewed, work may simply stop. “University departments will do their best to support promising research during a dry spell,” explains Riggins, “and there are a few foundations that provide bridge grants, but these resources aren’t abundant either.”

In the long term, funding scarcity will make it hard to attract top research scientists. Many have already left for more stable careers in industry. And US labs will continue to lose people not just to other fields but to other countries as well. Kelly Ruggles, a microbiologist at Columbia, says, “It used to be that people would come here to get trained in the sciences. Now, people are leaving for better opportunities in Singapore or China. There’s just more science than money right now.”

Of course, this is a difficult funding environment, but the proposed NIH cuts are based in part on ignorance. Legislators who understand the NIH tend to give it full-voiced support. When retired Representative John Edward Porter chaired the appropriations subcommittee that oversees the NIH, he held hearings with each of the twenty-seven institutes so members could hear directly from the researchers why they needed money and what they were doing with it. When, during the mid-’90s, the House Budget Committee proposed cuts to the NIH budget, Porter brought a troupe of Nobel laureates, esteemed scientists and business leaders in to meet with then-speaker Gingrich. The result? Instead of cutting the budget, Congress doubled the NIH budget over five years, because they saw that the funding was working. “I certainly learned that the money going to the NIH was money that was being tremendously well spent,” recalls Porter, “making a difference in the lives of human beings all over the planet.”

Lately Congress hasn’t bothered with such robust oversight. These days, the NIH is lucky to get one annual hearing in each chamber, in which the director has a few hours to give an overview of the entire entity. “If you don’t have hearings,” asks Porter, “how can you make the decisions that fund the government for the next year?”

Funding “basic science” doesn’t sound appealing in lean-budget times, but cutting research in times of economic woe is counterproductive. Nearly 90 percent of the NIH research budget gets distributed across the country, employing scientists and lab technicians. And miracle cures don’t spring fully formed from the R&D departments at Pfizer and Merck. Jon Retzlaff, director of government affairs at the American Association for Cancer Research, explains that basic science takes too long for pharmaceutical companies because “their investors don’t have that timeline. They take something very promising and then try to take that to the finish line. [The NIH] is really the foundation of everything that the pharmaceutical companies and biotech companies are able to do.”

The NIH budget is in peril because it’s such a substantial piece of the portion of the budget on the table to be cut. But the problem is the premise: that portion, nondefense discretionary spending, is a slim slice of the total. Each year 500,000 Americans die of cancer—the equivalent of losing 3,000 people in the Twin Towers every other day. Those who would cut the NIH budget to preserve traditional “defense” spending need to consider which enemies actually pose the greatest threats to American lives. If they did, they’d see that investing in biomedical research is our best defense.