I agree with much of what you say in your Christian Science Monitor article *The patent system: End it, don't mend it*. I disagree with the implicit argument that the purpose of a patent for an innovation in an invention is given for the purpose of giving a reward for the innovation. The purpose is to reward the disclosure of innovations that otherwise would remain undisclosed.
One of the earliest if not the first software patent was for the "setuid bit." Was this patent necessary for disclosure? I do not think so since the function was necessary to disclose for proper use of the UNIX system. I also believe that most patents do not disclose innovation that would otherwise remain undisclosed for a long period of time. Disclosure of innovations that would not otherwise be disclosed does further innovation.
While your article focuses on patents you mention copyrights. Copyrights are are difficult problem. Why is the "Mickey Mouse" copyright so long? I believe that artists should have copyrights, but the length of time should be short, say on the order of ten years. I also believe that some copyrights, such as those for user interfaces, should not be granted. Imagine if someone received a copyright for drawing equally space straight lines on a sheet of paper.
Keep up the good work and writing about it,