I think you might have misunderstood me. My point is, the phd coursework in biosci is a joke. Of course, ultimately, the only training for a research career is research experience.
My point is, I don't know of any advantage of doing a PhD over doing an MD + post-doc (the so-called "late boomers" in an NIH study), except perhaps the finances. In fact, PhDs don't do any better (and according to some studies, worse)at getting tenured than MD + post-doc people (and in fact this later route is the faster route). The NIH study showed that late boomers tend to be MORE productive, get funding more often and get tenured more than a PhD graduate.
And in my opinion, a PhD degree is not a training degree. It doesn't "train" you to do anything. You work in a lab. Exactly what you would've done anyway had you done a post-doc. You just do it earlier and with more free time to explore things. Most PhD graduates can't find a job in academia after they graduate.
Obviously, an MD only is not going to train you to become a scientist. Someone who only has an MD degree will not get tenured for a basic science department. But, a PhD won't generally get tenured either. So either way you'd have to do a post-doc. And, i think you are mistaken in thinking that a degree program could transform the way people think.
And, to refute your argument, Kandel and Mackinnon are not exceptions. If you count the number of Nobel prizes in Physiology and medicine, you'll see it's pretty much dominated by MDs. Then there are the physical science invasions (i.e. Crick, MRI people etc). If anything, the contribution by biology phd programs is highly incommesurate with the actual number of graduates they have produced.