Question: According to Objectivism , am I being rational by putting nothing above the judgment of my own mind? Or (according to Objectivism), am I being irrational by rejecting the authority of an MD?

Answer: Objectivism holds that one key element of the virtue of independence is thinking for yourself. Ultimately, no matter what anyone tells you, you have to decide what is true based on your own context of knowledge. Only you can judge for yourself the objectivity of your reasoning. Only when you think something through do you know fully that the conclusion is logically derived from the facts.
However, it is a fact that on any given topic there are usually others who know a heck of a lot more than most of us do. If we have very good reasons to think that they are not lying and have been objective in their reasoning, then we have good reason to incorporate their information into our knowledge (provided, of course, that we can integrate it with what we already know and with our own experience). You can get news of the world from a newspaper. You can learn science by testing the theories in a textbook. You can take medicines based on the advice of doctors, pharmacists, and medical researchers. And those are just a few examples of rational ways in which we use the information of reliable experts.
Ultimately, you must decide for yourself. But bear in mind that often one cannot refute claims that lack evidence. In such cases, the burden of proof lies with the person advancing the hypothesis. So a doctor might rightly ask if there is any evidence for some hypothesis, and if there were no evidence in its favor, he would be right to reject it without making further argument. That's how the burden of proof works.
It is the height of rationality to think for yourself and not accept arguments that merely come from an authority. But rationality also requires that one be objective, and base conclusions in the facts. Whatever you decide, you should do so based on the best evidence and arguments.

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