"For example, the department had a huge amount of patient information stored in their regular computer system. But the IRB demands an archaic pen and paper system for storing patient records, rather than using the computer system that exists. You could argue that maybe the department computer system was bad, but in that case it should be fixed, rather than creating a parallel system."

The department's clinical activities and research activities are subject to different Federal regulations, and the IRB doesn't have any authority over standard clinical care.

"Similarly with the issue of consent. The doctors were already giving questionnaires to the patients and already using them to determine what the treatment should be (counselling, medication, etc.) Why do the consent requirements suddenly become completely different when it's part of a study?"

Because it's part of a study. An entirely different ethical framework applies when you are trying to treat someone vs. when you're trying to learn how to treat them. Sometimes those criteria are laxer (for example, you can use investigational protocols and things that aren't yet standard of care). Sometimes they're not.

"Should the doctors be asking patients to fill out a consent form each time they give a questionnaire? Should the forms be in pen, even though mental patients can use pends to hurt themselves?"

Again, different contexts. They happen to be in the same locations, but very different contexts. For example, your doctor can access your entire medical record vs. a hospital's EHR system for your care. That does not mean that the doctor should be able to access all your information, for all time, for any reason.

"I don't know, but I do know that having bizarrely different criteria for a study versus normal medical practice seems unwise."

Most IRB regulations exist for a reason, and no, study vs. normal medical practice are different, because while the risks may be the same, who bears the benefits are not. The entire purpose of the IRB is to ensure the risks to the study subjects are kept to a minimum because they are also unlikely to bear most of the benefits. Medical ethics works on the ethics of a single patient.

They are different by design, and through long experience.

"I agree that it would be good to have better-defined criteria for stopping the study. It sounds like Scott had an informal goal of 100 data points, but didn't manage to hit this goal."

I meant that it would be halted if the patients become "Violent". Violent is not a clear definition.

Though he also probably should have had power calculations in his protocol. IRBs really don't like studies that don't have a chance of producing information.

"I'm sure IRBs do some good. But it's really hard to take the IRB's side in this particular case. They weren't even following their own rules (the person asking him to take ethics training hadn't taken the training herself-- which would have probably torpedoed his study even if he had done everything else right.)"

The person asking the questions are not necessarily the people who make the decisions. For example, most of the questions at an IRB I worked with were asked by admins, because they've got dedicated time to do it, and can go through a checklist for things like "Is violence well defined?" or "You seem to have deviated from the normal way this goes..."

After that, it goes to a formal committee who take a lot of training, who either approve, disapprove, or ask other questions.