Last month molecular geneticist and crusader for intellectual property reform Richard Jefferson wrote a Forum column for Scientific American in which he explained the concept of “innovation cartography”—the idea that mapping the vast and inscrutable world of patents will enable more players to create more innovations, some of which might end up doing a lot of good. Since then, Jefferson and his colleagues have launched a new version of The Lens, an open resource for searching and analyzing patents issued worldwide; published a paper in Nature Biotechnology on using The Lens to explore global gene patents; and announced a new round of funding from the Bill & Melinda Gates Foundation. I suspected Jefferson had more to say than he could fit into that Forum piece, so I gave him a call. Among other things, I learned that patents run in the family: Richard Jefferson is a descendant of Thomas Jefferson (Scientific American is part of Nature Publishing Group)

[An edited transcript of the interview follows.]

You’ve had earlier versions of The Lens online for quite a while, right? What exactly just launched, and how is it different?

What launched was the direct Web portal as a production site. What that means is we’re no longer embarrassed and hiding the URL from everyone but our friends. This is the platform to move forward with our ambitions, and our ambition is to solve the problem of problem solving.

“Solve the problem of problem solving”—What do you mean by that?

I’ve observed over the past 30 years that we have extra-inefficient innovation system, and this is not unsolvable. If we reduce the friction, cost, and opacity of the innovation system, there will be fewer barriers to entry and success. That will lead to product development by more players.

What’s wrong with the patent system in the U.S.?

When my great uncle Thomas started the U.S. patent system, he was obsessed with this bargain issue: You wouldn’t get a sanction until you disclosed your invention. But today the idea of patents as teachings has become risible. Companies have become incredibly skilled in hiding the ball. So we’ve repurposed patents. People have come up with ex post facto justifications about securing investment, and so on.

The patent system is in dire straits. The game is set where opacity and mendacity are celebrated. Some people say only solution is to get rid of patent system. There is some validity to that. But the purpose of The Lens is to render so much clarity that we have the tools for looking at policy and figuring out how to change it.

You’ve said that today’s IP system creates huge inefficiencies and ultimately benefits the biggest players. How so?

Let’s say your business is polymer fibers. A polymer company will spend a phenomenal amount of money mapping the world they need to navigate—hundreds of millions of dollars spent mapping the world of fiber chemistry, polymer chemistry, regulations, market research, and so on. But every polymer company does the same thing, and most of them will admit under duress, or the influence of single malt, that 90 percent of what they spend is precompetitive—it’s just knowing the lay of the land. Every one of these companies spends the same kind of money to get the same knowledge. And the expense comes from the opacity of the intellectual property system.

Think about cartography in the 1600s. Until people started aggregating maps, they had an incredibly inefficient system of commerce. It was every nation on its own. The only attractive mode was something that returned incredibly high margins – basically, stealing from people. Today, the need for very high margins means we have half a dozen erectile dysfunction drugs. If we could make the world of innovation easier to navigate, we’d be able to get enterprise interested in building, say, non-drug-based health interventions.

Let’s talk about patent hoarding. Are patent trolls the main problem, or is it more complex than that?

Everyone in the tech space develops a very large portfolio of patents—tens or hundreds of thousands of patents. No one can really grasp the scope of what those rights would mean, so they handle them like they’re nuclear arms—you screw with me and I’ll screw with you. Mutually assured destruction. The big companies end up doing cross-licensing relationships with one another at a relatively low cost. It’s a cartel. If you haven’t got enough weapons, you aren’t worth our time. But these guys realize this is a Pyrrhic victory at best. It costs so much to operate this way.

Then there are trolls, or “patent assertion entities,” who buy up patents as if they’re commodities. Trolls are a huge problem. They don’t make anything except lawsuits. They buy them up and hide the ball in shell companies, or by not registering transactions.

The shameful reality of the U.S. patent system is it is not obliged to register change in ownership. That is a shocking lack of transparency. With The Lens, one of the things you can do is try to extract truth of ownership by looking at patent families. Other countries do register change of ownership. So if I see that a certain family of patents in the U.S. is registered to the University of Michigan, but in Finland and Germany they’re registered to [the controversial patent aggregator] Intellectual Ventures, then it’s possible that Intellectual Ventures also has that patent in the U.S. but has never registered the change of ownership.

Part of the goal of the Lens is to shine light on patterns of ownership and use. With machine learning and data you can find shell companies. “Wait a minute, these companies all have the same PO box in Nevada, and the owner is the wife of a lawyer for Intellectual Ventures.”

Who is supposed to use The Lens? Lone inventors? Small businesses?

Small and medium enterprise is the biggest target. We’re not talking about startups, whose ambition is to leave the game. Small and medium enterprise wants to stay in. Small and medium enterprise is larger than anything else in society but mostly unengaged in setting priorities or using technology. We don’t see a lot of innovations coming out of small and medium enterprise.

Then there’s the public sector. We tend to conflate science with solving problems, but problems are solved by people using science is a tool. Most science in the world is done in the public sector, but the public sector is terrible at creating things. The public sector—the academic or public sector research-and-development community—is not a community at all. It’s a loose affiliation of anarchists fighting over parking spaces, tenure and grants.

Science is marvelous at introspection and poor at social integration. It’s the clergy: they are the unique pathway to truth. They build an extraordinary wall around themselves, with norms and procedures for joining, and it has a very substantial gateway effect. Science is the most beautiful thing we’ve ever developed as a species, and we’ve abused it terribly by letting it fall into the hands by these self-appointed clergy. Innovation cartography is about trying to use open data and the cloud, machine learning, data transparency, social aggregate computing to map the world of ideas so people can make things.

What exactly can these people do with The Lens? How is it more than the USPTO (U.S. Patent and Trademark Office) Web site?

The site search for the USPTO is an embarrassment. The most important function of The Lens is to collect and annotate collections of patents around the world. I can make collections of all of Qualcomms and Intellectual Venture’s patents and then expose them to the world. That is the core of science: the ability to share primary data.

Imagine if I put together things on shell companies. It’s not all going to be absolute. Does the same PO box equal the same company? Well, with The Lens I can share data with the world and let the community figure it out. That is so disruptive. If I start with a collection of 10 patents, then you go to those and click and say, “You forget this, this and this” and then share it—and then your uncle adds seven more. Pretty soon people are starting to annotate it. Before long 20 or 30 or 50 people have contributed to it, like Wikipedia.

The Wikipedia model is important. The Lens is in its infancy, just like Wikipedia once was. The criticism of Jimmy Wales back then was ludicrous and, at the same time, quite reasonable. It was a work in progress. I’m going to be hearing the same thing from the patent clergy. “Anyone can do patent search.” “It takes real professionals to do blah blah blah.” But it’s not going to take too long for people to find out that taking the Wikipedia philosophy can really make social change happen.

So what’s the next for The Lens?

A big goal for the next year or so is to make patents readable. We want a device that works as a dictionary, thesaurus, etcetera and makes reading a patent into a knowledge journey rather than a root canal. Busy people need to be sucked into staying on their site. Professionals assume they have a trapped audience so they’ve never learned human scale.

We expect to be the dominant force in innovation system transparency in a few years. There will be naysayers who say The Lens is nothing but a search site. But then people said Sergei and Larry just a search bar. Every disruption generally has a group of naysayers. Every disruption starts out inadequate.