Illinois Rep. Bob Michel is one of those Republicans who finds virtue in faith to the party. Woe to the boatrockers. So it was a mite odd to see him lobbing mud pies at the altar.

"What happens when a distinguished scientist runs counter to the party line?" Michel asked. "What do you do, shut him into a cubicle? Demean the individual? I hear it is going on out there."

The high priest of biomedical research, Dr. Donald Fredrickson, who sees himself as "keeper of the flame," assured Michel that none of that happens to laboratory iconoclasts at the National Institutes of Health.

"We have no monopoly on ego at NIH," Fredrickson said. "But we have a lot of it per square foot."

This talk of party lines and egos was about the system through which NIH parcels out millions of dollars every year to biomedical researchers looking for keys to life and disease..

Congressional appropriators probably look at the NIH budget as closely as that for any other federal agency. But, beyond a certain point, they don't control it. In the end, it is the bureucrats and private citizens -- not the legislators -- who decide how the money is spent.

Michel, ranking Republican on the House Appropriations subcommittee for HEW, was worrying about an issue that perpetually shadows NIH: whether the parceling system is flexible enough to support and reward scientific innovators.

The issue is important as the House and Senate subcommittees review President Carter's fiscal 1981 budget proposals for NIH. Even with his recently announced cuts, Carter's budget puts emphasis on more support for research.

But members of Congress hear rumblings that NIH's "peer review" process for awarding federal research grants is bogged down by conservatism that honors the predictable and avoids daring proposals that might lead to biomedical breakthroughs.

There is in this feedback something that might be called "sour grapes syndrome." Inevitably, the researchers whose study proposals are rejected rumble loudest that the system is flawed and biased. There are charges that reviewers favor friends and acquaintances.

NIH, through various safeguards, has tried to insulate the system from this. But the rumbling still makes legislators nervous, and it ought to.How, for example, is a man like Bob Michel, who has spent most of his adult life in Congress, supposed to know the merit of studying the sterochemistry in valine ane leucine metabolism (an actual grant proposal title)?

No one expects him to. Rep. Henry A. Waxman (D-Calif), chairman of a public health subcommittee, said recently, "We as legislators aren't qualified to judge the research itself."

So Michel and others who sit on the Appropriations subcommittees that decide are flying somewhat blind when the country's most distinguished medical people come pleading for more research money.

If Frederickson and others tell them the research money is being spent wisely, which they do, the legislators must take it pretty much on faith. They may question whether the emphasis is on the right problem, but beyond that there is much uncertainty.

NIH responds to its duty by channeling all grant proposals through the peer-review process, a two-level screening system that Frederickson says is aimed at buying the best and most promising science.

Roughly, it works this way: An investigator at, say, Johns Hopkins University will draw up a proposal to study a facet of biomedicine. He sends it to NIH, telling what he intends and what he might find.

NIH sends the proposal to one of the 11 institutes in which the research most appropriately fits. The first level of peer review begins. A scientific study group, made up of nongovernmental researchers in that field, studies the proposal for merit and votes at one of its periodic meetings.

If approved, the proposal is given a score by each panel member. The proposal's average becomes its score for competing for funding. This makes fairness in scoring crutial, since only about 30 percent of approved proposals will get NIH money in fiscal 1981.

A second level of review occurs when a national advisory council or board (each of the 11 NIH divisions has these) looks over the approvals. These boards of scientists and laymen typically accept the study group's recommendations, although they are free to reject them or pick others.

Then, according to the amount of money available, NIH funds the proposals with the best scores. The 1981 budget envisions funding 5,000 grants. About 90 percent of NIH-funded research occurs this way -- off the NIH reservation in Bethesda at universities, hospitals and research centers, The rest, subject to in-house peer review, is done by scientists in NIH laboratories.

But there is no uniformity in allocating the "extramural" money, as NIH calls it, from one institute to another, and that rankles on Capitol Hill.

A proposal that might be good enough to win funding at the National Institute of Aging, for instance, might not be good enough for funding at the National Heart, Lung and Blood Institute.

This disparity has become a near-obsession with Rep. David R. Obey (D.-Wis.), a House subcommittee member who has given Frederickson a pain in the neck over the scoring and funding procedures used by NIH.

At hearings last year and again this year, Obey took the NIH director to task.

Heart, respiratory and blood diseases cause more than half of the deaths in the United States, for example, yet the Heart, Lung and Blood Institute will fund only about 20 percent of its grant approvals next year.

Obey was disturbed because he felt Frederickson ignored the subcommittee's instructions last year to put more grant money in the areas of most need. He ended a long colloquy by telling Frederickson he had "screwed it up really, to be perfectly frank about it."

Obey knows about these things because of his interest in health research and because he, like other subcommittee members, has cultivated an underground of informers and whistle-blowers in the research establishment who keep him informed.

These people surface in odd shapes and sizes in curious ways. Some chant the self-serving sour-grapes litany, but others complain that medical politics and peer-review conservatism keep the bright lights under wraps.

One of the most interesting of these adjuncts to the network of boatrockers was helped into being by Sen. Alan Cranston (D.-Calif.), who likes a lot of other 65-year-olds, wonders what biomedical science is doing in the field of aging.

Life never has been kind to boatrockers, so innocent charity led Cranston to let a little band of scientific renegades use his Senate majority whip's office on weekends the last year or so to try to figure out ways to light fires under the aging research establishment.

They came up with an organization, which, coincidentally, is holding its first national conference here this weekend. They call it the Fund for Intergrative Biomedical Research or FIBER. Their aim is to stimulate a cross-pollution of ideas that they feel the NIH structure is incapable of doing.

FIBER wants to attract private money to help finance research in aging and to push NIH toward more daring apporaches.

"You have to ask the dumb questions," said Dr. William Regelson, a Medical College of Virginia professor who heads FIBER. "What's going on here? Who's in charge? We want to force action because we feel there is a lack of leadership."

"Peer-review members try very hard but there is a protective mind-set at NIH," Regelson said. "We want to match ideas to problems, help promote good research that is rejected by the peers. We don't want to antagonize peer review or NIH. We're going to try to help them. We're like their Baker Street Irregulars."