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A Politico article on the FDA and its questionable legal independence (from the executive) mentions that:

in 2011, the diminished autonomy of the FDA was made visibly apparent by a clash within the executive branch. Amid the upcoming presidential election and polarized abortion debate that would reemerge during the year’s campaigns, the scientific recommendation of FDA Commissioner Margaret Hamburg to make Plan B One-Step an over-the-counter abortion medication was overridden by HHS Secretary Kathleen Sebelius. This ruling, while reversed by a federal judge two years later, extends the concerning history of partisan influence upon the FDA and decisions unfounded by science, but rather politics.

On what basis did the judge reverse that ruling of the HHS Secretary?

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Apparently it was based on the interpretation of a 1938 law that limits HHS/FDA leeway in such decision making to certain scientific criteria:

According to the 1938 Food, Drug and Cosmetic Act, the secretary of the US Department of Health and Human Services (HHS) or her delegate, the commissioner of food and drugs, is to base drug approval decisions on evidence of safety and effectiveness, quality of manufacturing and processing, and accuracy of labeling [3]. In this law, Congress specifically did not give the secretary broad latitude to base decisions on other policy considerations.

The article I found (from a medical author who argued as amicus against the FDA/HHS) only quotes a brief part of the judges' decision which described the FDA/HHS actions as “arbitrary, capricious, and unreasonable”. Strangely enough, the decision was partially reversed on appeal, but only with respect to a brand-name drug; the generic version was approved basically by the appeals' court decision, so the FDA/HHS then gave up on their opposition.

The case name is Tummino v Hamburg; there seems to be a lot more commentary/material about it, but I didn't have time to go through it.

Another article touching on this case quotes & paraphrases from the decision that

the court explained that the decision was arbitrary and capricious because “[t]he motivation for the Secretary’s action was obviously political” and not based on the efficacy and safety requirements established by Congress.

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