Thanks to superb reporting by Science magazine's Jon Cohen, we now know the sorry story of how ill-informed legislators, too well-connected lobbyists and a huge pot of money combined to set a precedent that subverts scientific due process and is bad for sick people. It may not be, as National Institutes of Health director Dr. Bernadine Healy calls it, "as large a moral dilemma as we have ever faced in medical science," but it's an unfortunate episode with wider implications that deserve attention.

The story concerns a small, biotech firm, MicroGeneSys, with its eye on the vast market for an AIDS vaccine. The company believes its product, Gp160, is the best of many candidates for a so-called therapeutic vaccine (a vaccine that can be given as a treatment to people already infected with the virus, in contrast to the usual preventive role for a vaccine).

Preliminary tests suggest that Gp160 may be beneficial, but there is no solid evidence that it is better than the other possibilities. NIH believes the logical next step is a head-to-head trial of the most promising candidates. None of them may work: The concept of a therapeutic vaccine is still just an exciting new idea, nothing more.

There is an obvious commercial advantage, to say the least, to whatever AIDS treatment gets to market first. So MicroGeneSys did what it could to push its product. The company hired former Senate power Russell Long of Louisiana, whose 38 years in Congress could still be counted on to open most doors on Capitol Hill, and John O'Shaughnessy, a former assistant secretary whose firm lobbies executive branch agencies; in this case, the Department of Defense. They earned their pay.

At the request of Sens. Sam Nunn (D-Ga.) and John Warner (R-Va.), the Senate authorized $20 million for, in Sen. Nunn's words "the third phase of testing for a new vaccine which has shown great promise" and which Army medical experts say "should go to phase 3 as soon as possible." Both men took pains to point out that former senator Long was the man behind the amendment, Warner going so far as to note that Long's presence on the Senate floor that day (his right as a former member), was "not in the capacity of lobbying" (horrors, no) but "connoted the importance of this amendment."

Sen. Dan Inouye's (D-Hawaii) appropriations committee had already approved more specific language earmarking the funds for a large-scale Gp160 trial, but by the time that measure reached the House-Senate conference, some members were getting cold feet. Rep. John Dingell (D-Mich.) wrote urging that the choice of which vaccine to test, when and how "should be left to scientific peer review and not made by Congress." So the conferees added a back door, which required that the trial go ahead unless the secretary of the Army and the heads of NIH and the FDA all agreed in writing that it should not.

As this effort to legislate clinical decisions and end run scientific review provoked cries of outrage, led by NIH's Healy, the sound of flip flops could be heard all over town. The Department of Defense, which had earlier told Chairman Nunn that it approved the amendment, now says a Gp160 phase 3 trial would be premature. Sen. Nunn says his amendment was not "a narrow legislative earmark" but only money for the Army's doctors to use as they see fit. Russell Long isn't taking calls. The only happy camper is MicroGeneSys president Franklin Volvowitz, who is "delighted."

There's more to this story than what the right help in Washington can buy. It illustrates the terrible temptation of the soft DOD budget. The Defense budget is shrinking, but it can not decline as fast as has the military threat the country faces without causing economic havoc. So there is money in the budget that no one particularly needs for military purposes, and because it is a $300 billion budget, tiny percentages translate into huge sums. (One-tenth of one percent is $300 million.)

As if to make the point, the Senate, in this same bill, added $210 million for breast cancer research by the Army. That sum is larger than the NIH budget for breast cancer, which has itself more than doubled since 1990. The NIH is spending about as much as it feels can be well spent on this disease. Moreover, the Army, which didn't ask for the money, as in the AIDS case, is not the place to use it productively. Nonetheless, in the Year of the Woman, and in the U.S. Senate, home of Clarence Thomas/Anita Hill, few could be found with the courage to say "whoa."

No one pointed out, for instance, that prostate cancer -- arguably of greater relevance to the Army -- kills nearly three times as many men as breast cancer does women and that its incidence has been growing twice as fast. The NIH budget for prostate cancer research is $35 million.

The combination of politically correct diseases and loose money invites waste and, certainly in the AIDS case, abuse and possibly bad medicine. The roots of the Gp160 fiasco reach deeper, to the recent legislative practice of doling out "academic pork." These allocations of money dealt first with broad programs or facilities for particular institutions, and then, inevitably, with specific research projects. From there it was too short a leap to choosing a particular drug.

Congress, with the agencies' help, now needs to find a way to restore the integrity of the AIDS vaccine tests. Then, it could usefully take a look at how to keep academic pork-barreling from undermining the value of publicly funded research.

The writer, vice president of World Resources Institute, writes this column independently for The Post.