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  1. #1 Keeping Science and Politics Seperate 
    I came across this great blog post last night. It talks about how science should be independent from any sources of "influence" not only for the good of science but for society as a whole. Worth reading in my opinion.
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  2. #2  
    That separation has the ideal for the past couple of hundreds of years but it's never been a reality in any systematic way. Governments have always funded science to achieve or promote political objectives. Universities have always been gatekeepers on basic research money. Private interests have always invested in scientific inquires that would ultimately lead to marketable ends.

    The only really "free" research has been in the hands of gifted and sometimes wealthy amateurs who pursued their own interests (and their own agendas) outside of the scientific community. It was never easy for these people to become recognized by scientific authorities and it's still incredibly difficult.

    In my own career I've seen papers squelched and projects shelved because the preliminary data either contradicted the "political" conclusion or uncovered an unintended negative consequence of past regulation. I don't know what the answer would be to solve this problem.
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