MADISON – In a criminal trial, as any fan of TV cop-and-court shows knows, the prosecution states its case first and the defense goes second. The accused can appear in deep trouble, at first blush, but the weight of evidence submitted by the defense often carries the day.

Not only does that make for appealing television drama, but it’s pretty much how the legal system works in real life. Those who file the charges speak first, the accused then get a chance to rebut.

So it goes with the challenge to three stem-cell patents held by the Wisconsin Alumni Research Foundation, the 80-year-old group that helps UW-Madison patent and license the best ideas from researchers at UW-Madison. A preliminary decision by the U.S. Patent and Trademark Office looks bad if you’re watching this drama play out at home – but Wisconsin has yet to have its day in “court.”

The Patent Office announced two weeks ago it has rejected three patents filed by Dr. James Thomson, the world-famous UW scientist who discovered how to keep human embryonic stem cells in an unchanged state. In language that is typical in such cases, the patent office said Thomson’s discoveries were “obvious to one of ordinary skill.”

For all the gleeful predictions by those who would like to see WARF’s patents overturned, the fight isn’t even half done. And, at the end, no one should be surprised if Wisconsin’s patents on stem-cell discoveries are upheld in whole or at least substantially so.

“It’s important to remember that the patent office has yet to see any of our information,” said Carl Gulbrandsen, the managing director of WARF and a lawyer with years of experience in defending challenges to intellectual property. “Our expectation is that we’ll end up with the patents intact.”

Gulbrandsen is not alone in that prediction. Private lawyers with no personal stake in the case say there’s nothing new in challengers’ arguments. In the end, about three-quarters or more of all patents retain their patent status after re-examination. The next phase begins in about 45 days when WARF must file its appeal of the preliminary decision. All in all, the process could take years. Meanwhile, the patents remain in force.

What’s behind this challenge to the patents? One of the prime movers is Madison native John Simpson, stem cell project director for the Foundation for Taxpayer and Consumer Rights, a non-partisan, non-profit consumer advocacy organization based in Santa Monica, Calif.  Even Simpson agrees that Thomson and his colleagues “are brilliant researchers who have made substantial contributions to our understanding of stem cells.”

Rather, Simpson asserts that WARF has chilled stem-cell research elsewhere.

“The problem has been the arrogant and aggressive – some have said bullying – way that WARF has chosen to assert its patents and the negative impact that has had in the United States,” Simpson wrote. “Start-up biotech firms eager to do potentially life-saving research couldn’t get funding for license fees, academic researchers chafed at unreasonable restrictions and some stem cell research was driven overseas, where WARF patents are not recognized.”

Let’s be clear: The only thing WARF declines to do is to donate its stem cells to for-profit companies or private labs.

WARF has all but given away its stem cells to 400 academic researchers in nearly two-dozen nations, and trains those researchers in how to properly use those cells in their own labs. Because it exists to protect and commercialize UW inventions, however, WARF declines to simply hand off its intellectual property to others who might profit by their use. Private groups can buy WARF stem cells at $125,000 per batch, a fair price given how much those companies and labs stand to gain if their research leads to a billion-dollar cure. They just can’t get stem cells for free.

Even though an academic researcher can buy WARF cells for $500 – yes, $500 – and come to Madison for inexpensive training, Simpson and friends still claim WARF is blocking the schoolhouse door.

If anything has driven stem-cell research offshore, it’s the 2001 order by President Bush that restricts federal funding here to research on a small number of embryonic stem cell lines. About $35 million in federal dollars will be devoted to embryonic stem-cell research in 2007. That’s less than what Stanford University – in Simpson’s state – will receive in California research dollars ($50 million) this year. And that’s just one of many California universities doing stem-cell work. Where’s the “negative impact”?

Wisconsin’s stem-cell patents are being challenged because California and select East Coast interests (read: Harvard University) can’t have everything their own way. Let’s see what happens when Wisconsin takes the stand in its own defense.

Still is president of the Wisconsin Technology Council. He is the former associate editor of the Wisconsin State Journal in Madison.