SOMETIME IN the next few weeks, Harvard University will be making a decision that could signal the beginning of a new era in industrial-academic relations. University President Derek Bok will be deciding on a plan that would have Harvard help found a new company to develop commercial applications of discoveries made by its faculty members in the exploding new field of bioengineering.

Though the proposal is fundamentally different from anything that has been considered before, it has its roots in two trends that are not so new and have nothing to do with recombinant DNA. The first of these is the rapidly rising cost of education, particularly of research, and the disappearance of new sources of funding that can make up the difference between what federal sources provide and what is needed. Universities are therefore turning to the one heretofore unexploited source of money: the commercial development of a university's stock in trade -- new knowledge.

An entirely separate trend, but one that coincidentally reinforces that search for dollars, is a growing concern over the loss of this country's once unrivaled technological superiority. The major cause of the slippage is not a delcine in the quality of basic scientific establishment is still second to none -- but in the transfer of new discoveries to the marketplace. For the past few years, therefore, government, industry and academia have been talking about changes in their traditional relationship that would lower or remove the barriers that now divide the three into separate, often contending, worlds.

In the normal course of events, these trends might have led to some gradual changes. What has forced Harvard and others to abandon their normally cautious attitudes is the promise of seemingly unlimited profits to be made in biotechnology. When shares of Genentech, the first genetic engineering firm to go public, were recently offered on Wall Street, the stock exchange experienced one of the hottest buying days in its history. The relatively small number of scientists who have made the major discoveries in this field -- almost all of whom are university professors -- now either are instant multimillionaires or are besieged with offers from companies that want to begin their own operations.

The financial risks of the proposal Harvard is considering are significant, but they pale beside the ethical and educational questions it poses. For example, the university thinks its involvement might help protect professors from spending too much of their time on company business, but on the other hand it might simply end up pushing faculty members into making money for the school istead of teaching. Issues of secrecy -- essential to business but potentially lethal to the progress of research -- would immediately arise. Hiring and tenure decisions could be heavily influenced by commercial prospects instead of intellectual distinction. The research choices of whole departments could be subtly skewed toward the kind of research now commonly performed in industrial laboratories and away from the basic research that will form the basis of the next great leap forward.

In short, the potential conflicts of interest with a university's academic goals are legion. Nevertheless, many other universities are following the Harvard discussions closely. The schools' current financial needs and the magnitude of the possible payoffs make it likely -- and reasonable -- that some such experiements will be tried. Harvard and the others who follow need to take the time to find the right safeguards -- safeguards that will enable them to reap the profits while avoiding the many academic pitfalls.