@Jonathan Edwards in your excellent letter you say
From my perspective, criticism of these trials by patients, physicians and scientists like myself has nothing to do with ‘activism’ or with issues about whether the condition is physical or psychological. It is simply that this is poor research that serves the patient community very badly.
I think this is not an accurate comment. It is sensible and sufficient to focus on the methodological problems but it's not honest to say that the research isn't being criticized because it's "psychological". It is being criticized because it's based on a particular model (let's call it psychological-causation model) that claims the illness is perpetuated in large part by the thinking of the patient. The question of whether this model is correct is central to the debate and is not something that needs to be denied or downplayed. It's perfectly fine to criticize studies for their methodological problems alone but it's also not wrong to point out that there is no evidence the underlying assumptions (ie. the model) are correct and that a lot of patients think these assumptions are misguided and stigmatizing.
The CBT/GET people have framed the debate so that the message became "a vocal minority of patients don't like psychiatry/psychology" instead of "there is widespread patient opposition to the psychological-causation model". This should change.
There is also another interesting angle to look at this:
If researcher's assumptions about an illness are wrong, they will find it difficult to obtain positive results with a treatment based on these assumptions.
Unless the researchers consistently deviate from good methodology and/or distort their own clinical trial results.
If researcher's assumptions about an illness are wrong, you would expect to see patients criticizing their assumptions and any clinical trials would either show null results or be very flawed.
Patients see the flawed assumptions and researchers see the methodological problems and both observations are valid and important. They add up to one coherent picture.
Since the researcher's assumptions involve behaviour and thinking, and patients are well positioned to observe these over long periods of time, patients can contribute in a useful manner to the debate. The researchers do not have any evidence that shows patients actually have these damaging and false illness beliefs. It is just their opinion.
PS: so, where I'm going with all this is that maybe the next time you can say that you as scientist are pointing out the methodological problems, but that there also concerns about underlying assumptions of psychological causation.