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patent secrecy orders
Interesting. The Federal government can essentially make a patent a classified document. At the end of fiscal year 2013, 5,445 such orders were in effect. The majority seem to have some link with the government (perhaps sponsored by a grant?), but 21 "John Doe" orders are included, issued with regard to a private patentee whose name is kept secret. Here's more on the Invention Secrecy Act.
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Apparently, there are certain inventions we don't want other countries to have. Seems possible to me.
Trade secrets are inventions you don't want to disclose for whatever reason... Secret patents are like secret courts in my opinion, i.e. not legitimate.
Whether or not we want others to have certain inventions is not something the government was granted power to determine. The Constitution is explicit with absolutely no implied or inherent powers. Anyone who can read the granted powers notices immediately that every power in there is a tiny narrow grant and that related powers were granted separately. For example, Congress was allowed to coin money. Now implied or inherent powers would say that the power to coin money carries with it all other related powers, which is what some folks would have you believe the N&P clause grants. But this belief is easily proven to be an illogical and false belief. The power to coin money could carry with it the power to determine the value of that money BUT the Framers did not see it that way and understood that the power to set the value of money was separate from and independent of all the other powers granted in the Constitution. And so the Framers explicitly included the power to set the value of the money. Additionally using the current paradigm about the N&P clause bringing in implied powers, the power to coin money would also carry with it an important police power, that of punishing counterfeiting. Yet once again the Framers understood that no connected powers were granted in any fashion, even through the N&P clause, and found it an absolute requirement to explicitly grant Congress the power to punish counterfeiting. Thus Congress is empowered to secure patents and copyright BUT Congress is not empowered to pass a law keeping things secret. Any reader of the Constitution will note that, for good or bad, only one thing in the entire federal government may be kept secret and that is such parts of the Congressional journals as Congress determines should be kept secret. AND because the Framers recognized the need to explicitly grant secrecy power to Congress, the Framers would also have recognized the requirement to grant secrecy power to the executive and judicial branches, which the Framers did not do.
Doesn't a secret patent violate the entire reason for the existence of a patent system?
The whole point is to get good ideas documented and in the public domain so that technology can move forward with new ideas building on old ones.