Well, even an "operating system" or process needs to be protected. I think the concerned is that any company could ultimately copy the design and run away with our revenues just because that company is already established in the industry. Your case in point, Microsoft. Keep in mind they are not the only or first maker of PC operating systems, but you don't see the government using MacOS or Linux however better they might be.
The company I worked for had two full-time patent lawyers working on site as permanent employees. The company owner was an inventor and when he died in 1989, had 130 patents in his name alone. The irony is that the company makes almost as much money challenging their patents then they do by making and selling products.
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