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Randomized controlled trials raise a number of ethical issues. Physicians who participate in such trials must be in a state of "equipoise," or genuine uncertainty about the relative merits of the two arms of the trial. Otherwise, they would be ethically compelled to recommend the treatment they preferred. However, an agreement to participate in a masked trial is an agreement to deny oneself access to the knowledge that might allow one to judge which therapy is better. Physicians may dodge this dilemma in a number of ways. First, they may refuse to participate in randomized control trials. However, this does not allow assumptions about treatment to be tested. Second, they may judge participation ethically acceptable if other clinicians believe that an alternative treatment is better. By this formulation, individuals do not need to be in a state of equipoise, as long as the expert medical community is. Finally, they may use alternative methodologies, such as retrospective studies; crossover studies; or nonmasked, nonrandomized selection of alternative treatments with careful risk stratification and data collection. All of these solutions may be valid ways of dealing with the ethical dilemmas associated with randomized controlled trials.

Two misconceptions about informed consent concern the difference between the legal and moral justification for it, and the rationale for more rigorous consent for research than for "standard" therapy. Legally, informed consent for therapy is a risk-management tool that functions essentially as a release of liability. If the patient is informed of all expected or potential side-effects or toxicities of a treatment, he cannot sue because those side effects occur. The moral doctrine of informed consent is derived from a respect for the patient's autonomy as well as the patient's vulnerability. The physician's goal is not to minimize liability, but to help the patient make the best decision. These two goals are not necessarily incompatible, but they often lead to different attitudes toward informed consent and different decisions about what information needs to be shared with patients. If the goal is risk-management, then informed consent forms should be encyclopedic, providing the "whole truth" to patients. This would, however, not meet the moral goals of shared decision-making, because few patients could make sense of such data. Informed consent for research often leads to a different paradox. If a new therapy becomes available and a physician thinks it may benefit a patient, the physician may use it in an uncontrolled manner. This does not require the approval of an institutional review board and does not need the more rigorous approach to informed consent generally associated with research. In contrast, if the physician wants to evaluate the effectiveness of the same therapy carefully and intends to gather data to do so, he will need to describe his protocol, defend it before an institutional review board, and provide a more carefully written and closely scrutinized informed consent form. The paradox derives from the fact that the patient in the first, uncontrolled situation is inevitably at higher risk of harm than the patient in the second situation. The distinction between informed consent for treatment and informed consent for research is based on a distinction that is growing ever more cloudy and ever less relevant to the moral goals that informed consent seeks to achieve. Current standards for informed consent for research are, in many ways, counterintuitive and probably counter-productive.