The crucial distinction between discovery and invention lies in their object: facts of nature are what they are and exist waiting to be discovered, while inventions are objects which would not exist without a creator. So intellectual property rights are a recognition of a crucial precondition of the life-serving creation of wealth -- and they are not, contrary to this complaint, a general reward for mental effort that is arbitrarily denied for some classes of thought.
...It would be unjust and contrary to the requirements of man's life to protect discoveries as intellectual property...In contrast, there is no injustice when inventors or artists peacefully withhold the use of their recipes for manufacturing things...
I am not sure that this distinction solves the problem. Suppose that a drug company tests hundreds of compounds at great expense and finds one that cures a common disease. The fact that the compound cures the disease sounds to me like a scientific discovery, in which case Perkins would put it in the public domain.
On the other hand, a business process, such as "one-click ordering" for which Amazon.com infamously claimed a patent, sounds like an invention. In that case, Perkins would treat it as intellectual property.
My personal view is that intellectual property law has to be pragmatic. If you take an absolute view that is always in favor of intellectual property, then I think you end up defending too much--business process patents, for instance. If you take an absolute view that is always against intellectual property, then I think you have destroyed the incentive to undertake some valuable activities--pharmaceutical research, for instance.