I think this is a very interesting topic that you have raised. However, I do not agree that whoever writes the protocol or pays for the study should own any potential IP coming out of the clinical trial. I think it is a very gray area who owns the IP, but it could be either the sponsor, the investigator, or a combination of both, ultimately whoever had a substantial contribution to the discovery. Determining patent ownership can actually be a very difficult thing, and it needs to be handled very carefully. Having good documentation definitely makes it an easier process. In order to avoid any potential arguments over invention ownership, I believe it is important that the sponsor consider this prior to starting the clinical trial, and have an agreement in place with the investigator as to how to handle inventions which may come out of the clinical trial. Perhaps this could also be housed within the clinical trial protocol.