I better hope so that Merck changed their protocols! I haven't done much research into the FDA's practices, but considering the powerful pharmaceutical lobby, one can imagine their influence on politicians, and indirectly on the FDA. American politics is corrupt from the ground up, and I think the FDA is no exception. As to preventing good treatments from hitting the market, Big Pharma are the masters of that, I'll discuss it in part 4.
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I think their influence is overstated in some regards. You mentioned the damage that was done to the stocksof companies who made bad choices... Had they only featured a single product line they likely WOULD have gone out of business. Can you think of companies who have had significant repeat events and actually recovered?
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Also, any insight front your background on whether the FDA or US Gov provides subsidies or grants for specific research projects in the medical field?
AFAIK the FDA doesn't fund any research, that is mainly done by the governmental agency NIH (National Institutes of Health, https://www.nih.gov/). For example, an annual academic research grant can be $1 million and up. Grants are usually given for a period of 2-3 years before they can be applied for renewal. Here in Canada the budgets are way less than that. One time one of our department researchers got a $500,000 grant. We felt like peasants, because most grants were in the range of 80-100k.
One thing I admire about the USA is (I think 25 years ago) when the recession was hitting hard, the US gvmt faced the decision to cut funds for research. They wisely chose not to do so, and the american research has boomed since then.