> ... there is no empirical evidence that [patents] serve to increase innovation and productivity ...
This seems to be a fundamental misunderstanding as to what purpose patents serve. The public benefit of a patent is that the information is public -- inventions which might previously have been kept secret are instead put into the light where others may use them. The cost to the public of patents are that such use must be deferred out of respect for the temporary monopoly granted to the patent holder.
That is, patents don't increase innovation or productivity -- that is by design. They are just a means of harnessing the innovation and productivity of individuals and encouraging them to make their work public instead of keeping it a secret. So it seems to me that the paper is arguing a strawman rather than making a useful point.