Interoperability has become a much bandied around concept of late, but with good reason. As science becomes more expansive in scope, using large data sets from several sources and disciplines, to study long term problems that span many populations, geographies, jurisdictions and periods, interoperability becomes increasingly important.
Technical interoperability, of course, is the most common focus of conversation in this area. Recent rise in awareness has also focused on legal and semantic interoperability. One discussion that seems to be missing is financial interoperability.
Research funding is typically accompanied with conditions and obligations on the part of the researcher. The funding agency gives money to support the research, and the researcher, in turn, is required to adhere to certain conditions — the money may only be used for certain purposes (can't pay salaries, or can't buy hardware, or have to fly only certain airlines, etc.); periodic reports may be required; the money may have to be spent by a certain time, and so on.
In reality, however, a researcher typically has more than one research fund to draw upon. While one would expect the boundaries of the funds would be clearly defined, again, in reality that is not always the case. The research team's salary may be paid from multiple sources, and so may be the case also for expensive equipment, or other significant payments. This can create a problem if the expectations and conditions of the commingled funds are at odds. For example, federal monies usually require that research output from grants be made available to the general public in a free and open manner after a reasonable and expected embargo period has elapsed. Monies from a private funding source, on the other hand, may not impose such expectations, or even actively seek to make the results available only for the use of a limited audience.
Commingled funds can give researchers legitimate, and sometimes, even questionable, reasons to restrict access to their research output. For example, a researcher interested in pursuing a business venture based on the research outputs may deny public access to those outputs on the grounds that private monies were used for the research. In reality, private monies may have been only a part of the total funding, the rest coming from federal sources.
Pursuit of innovation, and creating value from it and benefitting from that value are laudable goals, but they should not be done on the back of public monies. Just like a firm hired to repair a public road has no authority to restrict or control access to that road, so should not researchers have control over access to research output resulting from public monies. Of course, to the extent that private investment is used for research, the researchers should have all the freedom to benefit from it, but they should do so without commingling funds from sources with conflicting public interests.
The bottom line: mix research monies only if they are financially interoperable.