So, the deal is that by making the RFID reader while at work, he violated the patent. There is a common law exemption for experimental use, but it has been whittled down to almost nothing by the federal court system. The actual manufacturor can control or prevent any scientific inquiry into any patented device that occurs in any context from which the person engaged in the inquiry might benefit, such as when a University benefits from research by improving their reputation. So, basically, you can do research, but if you publish, you're fucked. This requires a legislative solution.

Under the common law "experimental use" defense, individuals who used a patented invention were free from infringement liability if the use was experimental.1 The experimental use defense originated in an 1813 Appeals Court opinion, Whittemore v. Cutter, 29 Fed. Cas. 1120 (C.C.D. Mass. 1813) (No. 17,600), in which Justice Storey stated that "It could never have been the intention of the legislature to punish a man who constructed such a machine merely for philosophical experiments, or for the purpose of ascertaining the sufficiency of the machine to produce its described effects." As used in the nineteenth century, "philosophical" use referred to scientific experimentation. In subsequent cases, courts distinguished between commercial versus non-commercial research for purposes of determining the type of experimental use entitled to exemption.

However, the recent decision of the Court of Appeals for the Federal Circuit in Madey v. Duke University significantly narrowed the experimental use doctrine, and is likely to influence significantly the way in which academic scientific research is conducted. The court held that the "very narrow and strictly limited experimental use defense" can be exercised only if the use of the patented invention is "solely for amusement, to satisfy idle curiosity, or for strictly philosophical inquiry." Further, the defense does not apply if the use is "in furtherance of the alleged infringer’s legitimate business," regardless of the "profit or non-profit" status of the user.

Another important right that has been interpreted away.