This is a really underappreciated distinction: the huge difference in capital investment required to develop new inventions in different technical areas. It isn't taken into account in patent law - which sort of makes sense historically because it's a modern phenomenon in both extremes, for software to allow new inventions to be created with so little capital expenditure, and for new inventions in modern pharmaceutical research to require such vast capital expenditure. Such sensitive dependence on technical area for required investment to invent just didn't exist for most of the history of patents. It's a more interesting basis for critical analysis of software patents than simply saying that many software patents cover software that was obvious. That is only an argument that the Patent Office didn't do a good job at fulfilling its proper role under current patent law.

Except that it's still very hard to make distinctions about what is innovative in software design.

Node.js is pretty innovative. Is anything in there patentable? I think most people would agree it isn't.

You can't use the metric of capital investment either. It takes a lot of capital investment to mine BitCoins these days. Should I get a patent on the number that I find? If not, what's the difference between that and an algorithm I found through tuning a neural net, or through genetic algorithms?

I agree with you that RSA is the paradigmatic example of software that ought to be patentable. I still can't think of any objective way to show that, other than the judgment of other experts.

This really seems to boil down to arguing that the patent examiners in the software art unit need to do a better job evaluating whether patent application claims really are novel and non-obvious, like they're supposed to under current patent law.

For several years they were really overwhelmed as the volume of software patent applications exploded and they couldn't hire well-qualified software patent examiners at nearly the same rate. Traditional patent examining practice of looking primarily at existing patents and secondarily at academic publications to show the state of the art also tended to miss a tremendous amount of publicly known subject matter. The examiners have been getting steadily better and more creative in searching for references though.

Perhaps the rule that catches RSA, but not One-Click, is something like:

"An invention that applies old theory to solve an old problem in a new way."

The idea being that if the problem is long-known, and the theoretical underpinnings of the invention are long-known, yet the invention itself had not been previously described, then it must be novel and non-obvious.

In the One-Click case, the problem itself was new, so only the efflux of time could show if any solutions based on known theory were obvious or not.

I think a lot of the reason drug discovery and development takes so long, and requires patents to maintain commercial viability, is the government/FDA imposed regulatory requirement. While the basic research isn't included, it's not really the kind of stuff a drug company copies from another drug company, either -- the more product-specific discovery and development happens over a shorter time window, then you get ~10 years of clinical trials. The biggest risk if there weren't IP protection would be someone copying you during the clinical trial phase -- before you can sell it, but after most of the risk is eliminated (and money has been spent).

If we think the FDA is overall worthwhile (I think some kind of testing is key, but it could be more done by insurers for efficacy with the FDA focusing on safety, but the current system isn't horrible), I'd be willing to allow patents in that specific case, to compensate for the regulation.

There is not anywhere near as much societal benefit to third-party audited testing of one click or business process, so trade secret remains possible for a lot longer (at least until the product is fielded), at which point first mover advantage and constant innovation should be at least partially effective in compensating the inventor.

"The biggest risk if there weren't IP protection would be someone copying you during the clinical trial phase"

I think the biggest risk be other drug companies just waiting to see which drug was effective, and sold well, and then just copying the drugs that were effective/sold well.

The risk is definitely from the clinical trial stage through patent expiration -- I'm just saying it isn't at the early research stage.

Marketing could possibly mitigate some of the risk once it's on the market (branded viagra vs. other drugs), especially in a world without the FDA (where you would have anxiety about the safety and efficacy of arbitrary drugs). Pre-launch, but after disclosure, there wouldn't be much of a way to differentiate yourself.

Also, by the time the drug comes to market (after extended trials), the patent is well on its way to expiration. In 2010 they changed this so you get 12 years of exclusivity on the market. There are also lots of lame dirty tricks to refresh patents (slight changes in packaging, marketing, etc.)

Without the FDA/testing, you could possibly keep the drug's composition secret even once it's on the market; you could reveal info under NDA, or reveal trials info without revealing the compound. You could even imagine a situation where possession of the substance is under license, so no one could try to reverse engineer it.

I don't think that is necessarily better than what we have now, but this is a lot of why patents make sense in medicine more so than in software, even if they don't make sense in either or make sense in both.

Limiting software patents only to "non-obvious" ones sounds good in theory, but I suspect it breaks down in practice. Most software patents are written up in "mumbo jumbo" language, to use the term from the recent piece on This American Life. If you're a patent examiner, working under a backlog, and every day trying to wrap your head around obfuscated nonsense that doesn't even make sense to the original "inventors", are you really going to do complete diligence to determine obviousness? For that matter, is it even possible to determine?

I think it would be simpler just to eliminate software patents entirely. You can cherry-pick maybe one or two examples of possibly beneficial software patents (e.g. public key encryption as you mention), but for the most part software patents have been economically destructive. And further, even stuff like RSA would most likely get created without patents anyway, because that stuff tends to come out of academia where many researchers would be happy just to have some influential papers. I doubt profit motive is really even a significant factor.

> Limiting software patents only to "non-obvious" ones sounds good in theory, but I suspect it breaks down in practice.

You don't need to merely suspect. The law already ostensibly limits patents only to non-obvious ones. We can observe directly that it is breaking down in practice.

A lot of the money for drug research comes from federal grants (e.g., from the NIH).

This is a reasonable opinion - if you don't agree, please state your case rather than trying to suppress.

I have heard that drug companies actually lobby for the government to make drug discovery that expensive, as it keeps competitors at bay. Might just be a rumor, but still...