Who said you have to release your method? If what you found through 'R&D' can be quickly reproduced through reverse engineering it's highly unlikely it was complex to figure out. On the other hand if your development is complex, and requires a great deal of time and effort to reverse engineer then your R&D has paid for itself by giving you a dramatic lead in time to market. If a company can't win the market with such a lead they don't really deserve protection. Lets also not forget copyright still exists to protect exact copies of the ultimate product.
Drugs are very easy to reverse engineer and it would kind of defeat the point if you created them and then didn't release them.
You have drugs at one end of the spectrum and software and business processes at the other. There is a huge cost associated with medical research due to the inherit complexity of the human body and the requirements governments put on proper testing. Any patent solution has to address that problem as well.
(And, yes, drug companies are doing a horrible job at doing real research, but that doesn't alter the substance of the argument.)
What's wrong with copyrighting work so someone can't just steal your entire source-code and call it their own? Just like you can copyright a book so nobody can steal that exact instance of your thought process but people can still write very similar books.
JRR did not patent 'the application of height-challenged individuals manually transported to a heated device for the purpose of destroying small amounts of jewelery', but the work is copyrighted so you cannot just find/replace the story so it reads Shrodo and Hamwise going to Mt Foomp with their trusty sidekick Bandalf.
To take a quote from your source: "Every writer owes a similar debt to those who have come before." - this is something I believe speaks more to the core of software development than the patent system we use today.
Terry Brooks' supposed imitation of The Lord of The Rings didn't stop it from generating hundreds of millions of dollars in revenue.
I actually support the idea that Terry Brooks should be able to reskin The Lord of the Rings if he feels like it. I bridle a bit at the label "supposed imitation", though. Read them both -- they're exact copies. Even those parts of LotR that are utterly irrelevant to anything are faithfully duplicated in Sword of Shannara.
If you spent billions comming up with a linked list where old records are automatically removed on traversal, then you got so big troubles that not even a goverment can save you.
And yeah, that is the level on innovation in software patents.
Curiosity, love, boredom, responsibility, etc... There are a lot of incentives other than profit and billions already gets spent in R&D for reasons other than profit.
But if profit is your motive, and patents don't exist, you have several options. One of the interesting ones is that of monetising expertise. People will copy you, but you are also known globally as the expert, for the simple reason that you can prove you developed it. So you not only have a market made of the people who will buy the stuff, but also of those who want to learn off the expert how to build the stuff. To make the most of this requires good marketing, and an acceptance that you should be developing your next thing for when the money slows down from the current one as the market saturates, but that is the same as today anyway.
Well that's good and well for an individual or a small group, but the classic case for patents is in things like pharmaceuticals. A patent protects someone from reverse-engineering something that a company may have spent years perfecting for hundred of millions of dollars.
> but the classic case for patents is in things like pharmaceuticals
That is also the classic case for patent abuse. Take a drug that works, tack on some non-active atoms somewhere, change the name, patent it, jack up the prices on the old drug when the patent is about to expire to push buyers to your new monopoly.
Please explain how customers are locked into the "new monopoly." If Screwitall-A can now be made generically and works just as well as the newly made and patented Screwitall-B, customers are totally free to switch to -A if they care about the cost.
(Customers usually don't care about cost, which is certainly a problem for holding down prices, but this doesn't seem anything like "patent abuse.")
All the money is in prescription drugs which isn't a 'free market' (speaking about the US here). I can't just order my generic prescription from whomever I want nor do I have unilateral control over what my doctor prescribes. The doctor may well have his/her own agenda.
Pharmaceuticals are also the classic case for an existing massive public and charity funded research and development network for absolutely vital medicine, that the industry is not willing to do because the existing model is completely and utterly broken from a public health perspective.