Research is expensive. But it can do anything from cure diseases to create a digital revolution.

So it’s an issue when universities say they don’t get the funding they deserve. In a recent report, the Council on Governmental Relations, an association of universities and research institutions, argues that the nation’s research will decline if the federal government doesn’t provide more support.

While universities have a point, a murky federal grant-making system is part of the problem. There is a lot of money at stake. Some universities charge the federal government (which pays for more than half of all university research) nearly 70 percent in “indirect costs” on top of the basic grant amount. That means a $1 million grant really costs $1.7 million. The indirect costs include expenses such as administrative support staff, library use and building maintenance.

Private foundations, if they pay at all, pay much lower indirect rates than the government. At Knight Foundation, direct costs – costs that can be detailed – are allowed, but the policy is not to pay general percentages for indirect costs, according to Eric Newton, senior adviser to the president. Foundations that want to see exactly what they are paying can be skeptical of indirect costs. “We do think overhead is a real cost,” said Wendy Garen, CEO of the Ralph M. Parsons Foundation, but something about indirect costs “does not seem appropriate.”

It doesn’t help that the indirect cost system is confusing. In my recent opinion piece in the Stanford Social Innovation Review, I note two universities in Nashville, less than two miles apart, with rates almost 12 percent apart for similar research. You might say some colleges specialize in research that is simply more costly. But you also might say that some are simply better at negotiating higher rates.

Rates for facilities and administrative costs are worked out between a university and the federal government, but the public can’t peer behind the curtain. Transparency laws don’t extend to indirect costs. There is no central database of what the government pays in indirect costs.

Research universities frequently post the final indirect rates online. But details of the actual negotiations are not public. How much did a university ask for initially? What did the government counter? What are the big cost categories? We don’t know.

Federal negotiators say their process is effective and that privacy protects “proprietary” information contained in rate proposals. Universities say research details, if made public, would encourage theft of intellectual property.

But it’s difficult to see how greater funding won’t come without greater openness. Databases of government payments, general terms of negotiations, more uniform rules – all of these things would seem to make the arguments for payments stronger. If additional library costs are essential to helping cure cancer, can’t we find a way to discuss that and still not reveal research secrets?

Anthony Cave was a reporting intern this summer at Knight Foundation, researching indirect costs. For more information, read Cave’s op-ed on indirect costs in the Stanford Social Innovation Review.