We know that industry funding can affect the outcome of scientific research in many subtle ways ranging from interpretation of results to research design, and this has been borne out by various studies (can we accept that as a premise, or am I going to have to hunt down a cite?).

 

My question to you is, should funding from environmental or advocacy groups, or even governments, be similarly suspect? Could these organizations be subtly manipulating scientific output in the same manner industry does? How could we tell the difference?

Yes, anyone with an agenda will have at least a little bit of bias. Obviously, this does not mean that the study is worthless. In any case, if it is important, there will be confirming research.

I know for a fact that many NIH, NSF and DARPA funded projects are biased towards the researchers' own personal agendas. The same applies to industry funded research. They are all biased towards continued funding, the interests of the researcher(s), publication acceptance, and/or the interests of the funding agencies, which often overlap or are even identical in many cases.

yup, I agree. from my own experience, i thought of an approach that would give me the result that wouldn't hurt the agency's objective, because i was afraid that in using the other, it would come up with something negative. but then i don't really know what the results would be. (i'm still working on it and being as objective and impartial as I can)

Perhaps blind funding would help, like they do when testing drugs, although there would still be the biase of the researcher as outlined above?