I have done my share of griping about the deluge of overly broad intellectual-property claims pouring out of the U.S. Patent and Trademark Office. So I suppose I should cheer when the courts try to block this stream. But this spring, a Hoover Dam of a ruling-in a patent case involving broad ownership rights to the latest generation of painkillers-raises more painful questions about our patent system than it resolves.

The case pits the University of Rochester against the drugmakers Pfizer and Pharmacia. The University of Rochester claims a broad patent on the underlying research for the insanely lucrative painkiller medications called cox-2 inhibitors-including bestselling Celebrex, made by Pharmacia. Pfizer, which is in the process of buying out Pharmacia, claims that it developed the drug independently and therefore shouldn’t have to pay royalties to the university.

The stakes could hardly be higher. Celebrex, the leader of the cox-2 crowd, is what the drug companies like to call a blockbuster-earning Pharmacia more than $1.5 billion annually since it came on the market in 1999, and raking in more than $3 billion last year. Also hanging directly on the verdict is an additional, and almost as large, revenue stream from another cox-2 blockbuster called Vioxx, manufactured by Merck.

In his surprising decision, Judge David G. Larimer of the federal district court in western New York invalidated the University of Rochester’s patent on cox-2 inhibitors, ruling that the university patent is too broad and nonspecific to be considered a full-fledged invention. Larimer’s decision hinges largely on the fact that the University of Rochester scientists never took what he calls the “last, critical step” of actually isolating a drug compound themselves.

Larimer’s ruling gives me a massive headache. At first blush, it is exactly what I have repeatedly called for. Larimer’s decision reminds us that a patent “must be sufficiently concrete so that it can be described for the world to appreciate the specific nature of the work that sets it apart from what was before.” The notion sounds obvious. But it has been almost entirely absent in the Wild West of intellectual-property claims in recent years. The patent office has handed out scores of vague, broad claims to entire areas, from instant messaging to human gene therapy.

But on closer inspection, the judge has it wrong. If our system is designed to reward innovation, we need to fairly consider the seminal research that makes an invention possible. If Larimer’s decision holds up, not only would it threaten the validity of countless dubiously broad patents (a good thing), it would also lead to a patent system that is fundamentally incompatible with the kind of basic research that universities do.

Let’s take a moment to consider what the University of Rochester researchers accomplished. The story begins back in the 1960s, when Rochester biochemist Donald Young studied an enzyme called cyclooxygenase, or “cox,” whose activity is blocked by aspirin and other anti-inflammatory drugs. Young’s research led him to distinguish between two distinct parts of the enzyme that he came to dub cox-1 and cox-2.

Further study of cox-1 showed that it does not even play a role in inflammation itself but rather, among other things, regulates the secretion of gastric acid in the stomach. In the distinction between the functions of cox-1 and cox-2, the team recognized a potential gold mine: they might be able to directly target cox-2, thereby suppressing pain and inflammation without causing stomach irritation, the bane of all previous painkillers-from aspirin to ibuprofen-that act on the cox enzyme.

Simply discovering cox-2 was an important contribution to the field. But the researchers didn’t stop there. By the early 1990s, Young’s team identified the gene in humans that is responsible for producing cox-2 and discovered how it causes inflammation within individual cells. The group even developed a method for testing to see whether given compounds might selectively inhibit cox-2 in humans.

No matter how you look at it, in other words, there is little question that the pioneering University of Rochester work paved the way for a new generation of painkillers that would be easy on the stomach. And in 2000-after eight years-the U.S. Patent Office granted the Rochester team a broad patent covering a “method” for selectively inhibiting cox-2.

What’s really at issue in this case is whether our patent system can reasonably be made to account for seminal research contributions like the one made by Young and his team. It is not a simple question. Sure, the university researchers didn’t do the costly drug development or the clinical testing required to bring Celebrex and Vioxx to market. And narrow and specific patent claims tend rightly to reward those who assume precisely those kinds of laborious and costly roles.

But universities are not in the drug development business. In this case, there seems to be little doubt that Celebrex and Vioxx are on the market today only because of the pathbreaking contribution made by the Rochester researchers. The university has already announced that it will appeal the decision; this will be a critical intellectual-property case to watch. Judge Larimer opined that a broad and nonspecific patent claim is little more than “an attempt to preempt the future before it has arrived.” I’m so strongly in agreement with that sentiment that it is echoed in the very name of this column. But we need a patent system that distinguishes between those who would “preempt” the future and those who actually help create it.