Good post Haggis, and I'm inclined to agree with most of what you wrote. There's a lot of nonsense in standard medical practice, largely I think because both doctors and patients have egos, agendas, beliefs, and other human characteristics. Nice cartoon too, made me laugh on a day that I needed it (but that's another long story), and like a lot of good jokes, it has an edge of bitter truth about it.
We seem to have hijacked this thread quite far afield from your original post, but since you kept on contributing to it I assumed you were still interested. And I should apologize: I did unjustifiably assume you support homeopathy, because of the way you used it as an example of an absolute statement I made. A misinterpretation of your tactics (didn't I say somewhere in this thread that I screw up sometimes?). That's what happens when all we have is text on a page, without the clues to meaning of body language, tone of voice, etc. I hope we're both rational enough we can work around stuff like that, 'cause I think I kinda like you...
Not only is there a placebo effect, there's also what's called a nocebo effect, which is the precise opposite: if you expect something to do you harm, it will, even if its harmless. I was recently reading about a test in which some people known to be allergic to a particular plant were blindfolded and their left arms were rubbed with the plant, their right arms with something innocuous, but they were told the opposite. Guess where the rash appeared? On their right arms. What possible explanation is there for that? I have no idea.
No doubt there are deep mysteries (about the mind-body connection in this case) we don't understand, and possibly never will. But it's important to keep trying, and that's what science is about. My point, really, has been all along that science is the only reliable means we know for determining the truth content of empirical claims. It does not, and cannot, claim to know everything, but claims that have passed its tests we can justifiably have considerable confidence in. Similarly, claims that haven't passed its tests we should view skeptically.
But science gets it wrong too sometimes, so that, as you observed, treatments once thought to be safe according to what we knew at the time turn out not to be. Thalidomide comes to mind, and DDT. There's an interesting book on this general subject I recommend to your attention: Why Things Bite Back
,by Edward Tenner (that's just an underline, not a URL). It's subtitled, "Technology and the Revenge of Unintended Consequences," which is a pretty good summary of what it's about.
I've now had time to take a careful look at the links to the NITRF you provided, and I note some papers on the dangers of vaccination and the link to Alzheimers. I don't doubt Dr. Fudenberg's legitimacy, his credentials are very impressive. In fact I'd have been very surprised at anyone claiming vaccines are completely safe, the real issue is relative risk considering the whole population. There's no such thing as zero-risk technology, and I'd assume a priori that some people are going to be hurt by vaccinations. The links to autism and Alzheimers are tenuous but suggestive, and obviously there's more work to do there. Stephen Barrett's attitude is "not proven," which is true enough in a strict sense, but doesn't justify ignoring the question now. Everybody's body chemistry is a little bit different (otherwise we'd all be genetically identical) so not everybody will react the same way to vaccinations, or any medical treatment. In my own case, for instance, the common antibiotic amoxil doesn't work very well on me or any of my children, which is really too bad, because it's cheap, about $10 for a standard prescription. Something in our body chemistry seems to metabolize the stuff too fast for it to do its job. When I need an antibiotic, which fortunately isn't very often, I have to get some $50 stuff and eat a lot of yoghurt at the same time, or it kills off all my normal intestinal fauna, with nasty side effects.
Another point I'd like to make, in response to some other posts in here about the nature of skepticism: I don't know that there's anything that could be called a skeptical movement or community, but I'm a skeptic personally, in the sense I described in the fourth paragraph above, about testing claims. Some of the people who seem to have set themselves up as skeptical spokesmen, like James Randi and Richard Dawkins, aren't doing skepticism as an idea any favours, regardless of whether they're right or not. They generally are, I think, in their respective areas of expertise, but they're also pretty difficult people to like. Condescending, judgemental, dismissive, contemptous, are all words I've seen used to describe them, and a lot of people who consider themselves skeptics take their cue from that. I think that's a fatal mistake, it just closes off discussion and puts people's backs up. When so much of the skeptical literature, especially on the Internet, is cast in those terms, it's an easy trap to fall into. I try really hard to avoid it.
But I don't always succeed.