The $225,000 figure heading professor John Wysolmerski’s grant application to the National Institutes of Health is one of four grants he will need to keep up his study of the interface between bone metabolism and breast cancer. Out of the $225,000 would come 95 percent of Wysolmerski’s salary and 100 percent of his postdocs’ salaries and benefits. It would pay for $6,000 per month to keep his mice alive long enough to have their bones and hormones analyzed. And for untold amounts of paper in the printers, Internet hookups and chemical reagents. This year, Wysolmerski predicts, it will take five tries to get one grant funded, thanks to the most recent round of budget reallocations.

The punchline to the Bush administration’s budget proposal, which will consume Congress in debate for months to come, and to the House Deficit Reduction Act, which the president signed in to law just two weeks ago, goes something like this: Budget allocations will trim $2.2 billion in domestic programs while adding $1 trillion in economic stimuli and beefing up the defense budget. But erase personal feelings about the war, erase partisan allegiances and ideology and the welfare state, and what’s left, for Yale and its researchers, is both more and less dramatic than the percentages and dollar values would indicate.

So when Bush proposes a Research and Development budget increase to $137 billion in 2007, it will also mean a 3.4 percent decline in basic and applied research. It will mean a doubling of the National Science Foundation budget during the next half-decade and hefty infusions of cash to various physical science research entities, from the Department of Energy — up 11 percent — to the National Institute of Standards and Technology — up 55 percent. The lack of change to NIH’s budget will actually mean a 3.5 percent decrease in how much NIH can buy, due to inflation. A net 2 percent increase in R&D still means a decrease in the number of days Wysolmerski can come in to work and churn out another round of preliminary data to respond to a critique of his grant proposals.

At Yale, it’s a different set of numbers that matter: Number of dollars handed to Yale faculty to create an interdisciplinary Materials Research Science & Engineering Center in a record-breakingly high grant. Number of postdocs who do not make it onto the faculty because they cannot get funding for their research. Number of physical sciences faculty members grateful that their field is finally getting the resources it deserves. Number of mice killed when a grant is not renewed. The numbers don’t lie. But sometimes they equivocate, and, other times, they do not matter at all.

Nancy Brereton, Yale School of Medicine’s grants manager, said Wysolmerski’s grant application will go to an NIH committee, which will debate the scientific merits of his proposal and assign it a score. The top tier of all proposals the NIH receives are funded. In past years, a scientist who was in the 20th percentile had a decent shot at getting funding, but this year, she said, the cutoff has dropped down to the 14th percentile.

If their proposal is rejected, scientists can revise their grant up to three times based on NIH’s critiques. If that fails, they turn to non-federal sources, and if they still do not get funding, Brereton said, “You’re out on the street.”

“I don’t mean to laugh,” she said. “The funding is getting serious. It’s just not available unless you’re the top of the research crop. Yale gives you a startup package, but that doesn’t go too far.”

But Mitch Waldrop, director of government relations at NSF, which funds over 200 Yale researchers in economics and climate research, biology and physics, is cautiously optimistic.

“Congress is very, very supportive of basic research,” Waldrop said. “In both parties, everyone likes it and wants high-tech spinoffs in their state.”

Ultimately, Brereton said, School of Medicine researchers rely on NIH for $267 million of their $432 million of research. Suzanne Polmar, the director of grants and contracts for Yale College and the Graduate School of Arts and Sciences, said federal money from the DOE, NIH and the NSF accounts for upwards of 80 percent of researchers’ total funding.

John Tully ’64, a chemistry professor, was recently the beneficiary of this supportive atmosphere. He headed up a team which managed to nab a $7.5 million monster of a grant to start a Materials Science Research and Engineering Center, in conjunction with Southern Connecticut State University, which analyzes the basics of optical, electronic and magnetic properties of various materials. While the $7.5 million grant was a rarity — most NSF grants range from $60,000 to $150,000 in size — Tully said it is not the massive institutional grants but the smaller, individual grants that will be most affected by the new emphasis on physical science in the Bush administration.

Tully researches the dynamics of atomic interactions during chemical reactions. His specialty is not the end result but rather what happens while the reactions are taking place: the bonds that are breaking, forming and reconfiguring. But that means it is tough to find anyone other than the NSF — which he characterized as “very forward-looking” — to support something which only has practical applications in the longest of long-range scenarios.

But during the past half-decade or so, the NSF has had to be more frugal with its grants than counterparts in the biomedical sciences, such as NIH. These alternate organizations have seen a surge in popularity among Congressmen and can argue for more direct benefits to the research they fund, which is why the physical sciences departments at Yale are so optimistic about the Bush budget, several professors and deans in the engineering and physical sciences departments said. Thanks to the American Competitiveness Act, which increases funding for the physical sciences, Polmar said more money for the DOE and the NSF could benefit Yale.

But Dean of Engineering Paul Fleury is skeptical.

“My first reaction is that I’ll believe it when I see it,” he said. “This kind of thing has been promised before and hasn’t materialized.”

At Yale, areas in which the University has not historically dominated, such as materials science and nanotechnology, are getting a boost from renewed interest from federal agencies, as evidenced by the $7.5 materials research grant.

“We are very competitive, but the hit rate for these agencies is below 10 percent, which means submitting 10 proposals to get one funded,” Fleury said. “People have to spend a tremendous amount of time preparing and submitting proposals, rather than conducting research.”

Each proposal means roughly six weeks of “all day, every day work” for Wysolmerski, or six months of twice-a-week revisions for Tully.

An average NSF grant for a physical scientist, roughly $100,000, with virtually no possibility of overlapping grants in the way medical researchers routinely do, has to pay for at least the $50,000 it takes to support one graduate student. Add to that the cost of chemical reagents, expensive equipment and, ideally, travel costs to and from conferences — Tully said that short of working with an entire research team, a rarity in the physical sciences, where funding has historically been limited, the next best experience for a scientist in training is to attend professional conferences — and there’s not much money left.

And that’s all after Yale taxes every purchase he makes at 63.5 cents on top of the dollar, meaning that for every dollar he spends, Tully, like all other Yale researchers, pays $1.64. Wysolmerski said he doubts Yale’s infrastructural costs are exactly proportional to the chunk the University takes out of researchers’ money.

“It’s a big revenue stream,” Wysolmerski said. “You have to figure that no matter how many grants there are, the lights will stay on, presumably. So, while the more research there is, the more research will cost the University indirectly, that’s only true up to a point. After that, it is pretty much gravy.”

The Kline Biology Tower at lunch hour is still a hive of activity, a kind of biology-industrial complex over which the White House’s Excel spreadsheets and inflationary calculations exert a heavy influence. In one lab, Cecilia Gurrier-Takada, a senior research associate, snaps her gloves on to show a graduate student how to use fluorescence labeling to analyze the ways in which the RNase enzyme cleaves DNA. In another, two technicians stare at a text file, a thousand computer screens of gene names and CTAG sequences for yeast. Gels are poured, pipette tips clicked into hazardous waste containers and rainbows of laminated posters with carefully shaded diagrams of protein conformations tacked up in linoleum hallways under fluorescent lights.

And in the back room of his office, Nick Ornston, a biology professor, is pulling red chairs into a circle around a cake. The celebration, he is quick to clarify, has nothing to do with his work — it is his wife’s birthday. Even so, he is waiting with bated breath to hear back from the NIH to see if they will fund his project, an analysis of how microorganisms adapt to their environment. The “take-home point,” he said, is that a stop-start funding mechanism results in massive lapses in continuity should a grant be a “non-hitter.”

He gestures out his office door, toward the hive of activity.

“All this will have to stop, and it’s very expensive to restart,” he said. “We live in perilous times.”

Federal grants support not only research projects but also training programs, educational scholarships and best-practices studies. More than that, Wysolmerski said, getting grants affects other Yale employees as well.

“Once you become head of your own lab, you’re an employer,” he said. “So I have technicians for a long period of time, and I know them and know their families, and if I can’t raise the money to pay their salaries, they will probably find another job, but I will have to lay them off.”

NIH spokesman John Burklow said in an e-mail that NIH will be able to minimize the effect of the 2007 budget on researchers.

“The budget request reflects the tough choices that had to be made to best preserve our investment in biomedical research and to support research for medical advancements that will improve the length and quality of human life,” Burklow said.

But Wysolmerski said those tough choices have dramatic repercussions for Yale research overall.

“The bottom line here, knock on wood, is that people have to work harder to get the money, but they still remain successful,” Wysolmerski said. “But it has a psychological effect. Everyone’s more anxious. It’s frustrating to get back a critique that just barely missed the cutoff and know that a few years ago you would have made it.”

Polmar said most researchers she works with are not worrying yet. A bill sponsored by senators Pete Domenici (R-NM) and Jeff Bingaman (D-NM) will increase funding throughout the sciences, and President Bush’s 2007 budget most likely lowballs NIH funding because the White House knows Congress will only add money to NIH.

“[Yale researchers are] not living in a shoebox,” she said. “They know that we’re supporting two wars and that there’s not a whole lot of money to be spent on the discretionary budget. But they have historically been successful at securing money and will hopefully continue to be.”