Ariella Rosengard of the University of Pennsylvania didn’t set out to scare anyone. She just wanted to investigate a little-understood part of the immune system by studying how viral proteins interact with it. At first, Rosengard worked with a common virus called vaccinia. But vaccinia rarely makes people sick, and she began to worry that it wouldn’t tell her much about the human immune system. So she turned to a closely related, far more fearsome virus: smallpox.   Smallpox virus isn’t easy to come by. Officially, it resides in only two places — secure labs in the United States and Russia. But Rosengard didn’t need the virus itself. Scientists have made its genetic code freely available on the Internet, giving her the data she needed to synthesize a key smallpox protein in the lab. Test-tube studies showed that it works far better than the corresponding vaccinia protein at blocking a key step in the human immune response. The discovery may help explain why smallpox kills, and it could lead to new treatments.   But when Rosengard published her report last month in the Proceedings of the National Academy of Sciences, a slightly defensive commentary appeared with it. The article said it would be unlikely to use the work as a blueprint for making vaccinia more like smallpox. It acknowledged, however, that “ the idea that bioterrorists might be tempted to attempt such an experiment has been suggested as a reason for considering it unwise to publish observations of this nature. “   Rosengard rejects the idea that basic science like hers should be put under wraps. “Think how many brilliant minds would not be able to participate in finding a cure,” she says. “ You can’t predict the mind of a madman. The best defense against any virus is understanding how it functions. “   Most biologists would agree. But these days, they find themselves grappling with a dilemma, as their tradition of openness clashes with the fear that well-intentioned research could be misused to develop bioweapons. As much as scientists fear aiding their enemies, they get unnerved when government officials talk about restricting their freedom to publish. One thing’s for sure — the problem won’t just go away. The Government has proposed a dramatic increase in funding for basic research on potential biowarfare agents. This means that many more scientists will study deadly germs, and they’ll inevitably want to publish what they find.