There is much to applaud in The Post's welcome entry into the debate over the wisdom of distributing funds for scientific facilities through direct congressional earmarking {"Merit and Money," editorial, June 1}. Unfortunately, it is also marred by some erroneous assumptions and by a misplaced and unwarranted cynicism about the motives of those engaged in the debate.

First, it should be understood that the earmarking issue is not about corruption. There is nothing in the Association of American Universities vote for a "moratorium" or in what we said about it that justifies The Post's use of that term. Neither the universities, in seeking such earmarks, nor Congress, in making them, has behaved illegally, immorally or unethically. The debate is about which policy will best serve the nation's interest in promoting high-quality science. Surely, that is important enough.

Second, the assumption that animates The Post's position is that the rich and successful AAU institutions voted for a "moratorium" on seeking earmarks in order to protect the advantage they have in merit-based competitions. That is both bad political analysis and a too-easy cynicism about motives.

Among the universities that have sought and won earmarks are several quite eminent AAU members. There is every reason to believe that most AAU universities would be formidable competitors should they choose to pursue that course. In fact, the truth about why 43 of them pledged not to do so is simpler: there is deep and genuine concern among the heads of many of America's major universities that a very successful system of supporting academic science is being undermined, and that what may replace it will serve the nation considerably less well.

Third, The Post accepts as proven the assertion that the current system is rigged against aspiring institutions. There is no dispute that it is hard to build academic quality. It takes strong state, local and private support, good judgment and good management. But it can be done. More than 125 universities now receive more than $10 million a year in federal research funds. There are 19 names among the top 100 recipients of federal research funds that were not there 20 years ago and four among the top 25. They moved up by building quality locally and then entering a national research support system that recognized what they had built.

Finally we, too, support programs for developing institutions and young scientists, but the same questions need to be answered: By what criteria should they be judged and who should do the judging? In a world increasingly dependent on the intellectual achievements that come from university laboratories, it would be unsound policy for the United States to turn away from scientific merit, fairly judged by qualified persons, as the basis for its science policies.

I hope The Post is wrong in dismissing so lightly the possibility that Congress will enact a competitive national program to help universities rebuild their scientific facilities. Rep. Robert Roe (D-N.J.) is not so pessimistic. His bill (H.R. 1905) would authorize a program in the National Science Foundation that would encourage quality science and recognize the aspirations of institutions on the way up. Those are purposes that The Post appears to applaud. The Post's support would be welcome.

ROBERT M. ROSENZWEIG President Association of American Universities Washington