The research was funded by the U.S. Department of Energy.
[1] http://en.wikipedia.org/wiki/Bayh%E2%80%93Dole_Act
[2] http://www.mofo.com/resources/news/2002/10/the-governments-p...
Is a monetary incentive for the grant recipient really a greater moving force for the market within a specific industry than capitalistic competition amongst the existing forces in that industry?
Dr. Brown researches some disease. He's not particularly trying to come up with a treatment for it, just trying to understand it better. He's in academia, so he needs to publish papers to get tenure and receive grant funding. The NIH funds his research because it's somewhat promising and because he will do a good job educating students. Suppose his group happens to discover a chemical compound that seems to be effective in treating this disease. What happens next depends on whether the university can patent this discovery.
Before the treatment can be prescribed by doctors it needs to receive FDA approval, which requires expensive clinical trials. Without patent protection, no one (neither the university or outside companies) is willing to fund the trials because they won't have exclusive rights to sell the treatment once it's approved. Dr. Brown could work on the trials himself, but that would mean neglecting his other responsibilities. No one has a sufficient financial incentive to make the next step, so the treatment never makes it to the market.
The rationale for patenting it is the same as the rationale for patenting anything.
The rationale for the funding agency allowing it to be patented and then licensed out by the funded researchers is probably the real question, but there's probably at least an argument that it serves the public good by decreasing the direct public cost of research by sharing the upside reward with those actually doing the research work (which is only proprietary for a limited time, and that's an actually limited time, rather than the limited-in-name-only time that applies to copyrights.)
As a side benefit, UW gets some money and (depending how they do things) shares some with the individuals who did the work. Some of my co-workers recently went out for a lunch paid for by one of their patents--it's not a ton of money, but it's a neat thing when your past work buys you lunch.
AFAIK, the US patent law says that you can receive a time-limited monopoly for your invention in exchange for describing it in enough detail that others can reproduce your invention. if the patent matter is only reproducible using further information excluded from the patent description then the patent is invalid, IIUC.
So rather than saying "we have a totes sweet fusion reactor design, if you pay us we'll show you the schematics", UW publishes it to the world and if somebody thinks it looks good, they pay UW some money to use the design outlined in the patent, which is theoretically sufficient to reproduce the reactor.
But yeah, people will still think negative when hearing about "nuclear". Maybe we should change that to "Atomic" to make the distinction and give it a less negative connotation :-).
Some of the peculiar niche uses for petrochems are much less price sensitive than bunker A boiler oil, so they would make more money overall in the long run if people used oil more wisely, which sounds weird but is an economic truth. You care a lot about the price of gas in your car, but you probably don't really care about the cost of plastic in your legos, so if it went up by 10x it would still be a rounding error at the checkout line although in the long run they'd make more money.
The coal companies, on the other hand, are likely concerned.