The question of whether the doctor's obligations outweigh his/her morality or religious faith would seem to pit the freedom of conscience of the doctor against the freedom of conscience of the patient. Particularly in the case of end of life decisions, it raises the question of whose conscience should win out if the doctor and patient disagree about the morality of a particular course of action.
It seems to me there are a couple guiding principles that reduce the potential for conflict.
The first is that doctors should not be forced to perform procedures they feel are immoral. Thus doctors who believe that abortions or transplants are immoral should not be required to perform them.
Similarly, a patient should not be required to accept treatments that they consider immoral. Especially in the case of life altering or life ending decisions, it is easy to lose sight of the fact that a person is never required to follow the course of action recommended by their doctor, whether that be as simple as taking two tylenol or as complex as open heart surgery. It may be foolish not to follow your doctor's recommendations, but it is our right to be foolish.
If the patient is unable to make choices for him or herself, then the person with authority to make medical decisions -- a family member or someone who has been given a medical power of attorney -- has the right to accept treatment or not on the patient's behalf.
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