Whoa. I do agree with you that PhD's are becoming devalued, but getting a PhD is 100x harder than getting an MD, in my opinion. MS1, MS2 is a glorified college curriculum where you take some tests at the end of every block. MS3 and MS4, you literally just need to show up. It's cookie cutter and all planned out for you, you just have to get out of bed and follow your schedule. I know I'm describing an average medical student here, not an excellent one. However, navigating a PhD is so much more complicated than that, and takes a mature individual who can think critically and intellectually about the pieces he/she has to find a story, especially if you don't have a micro-managing PI behind you to do the sleuthing for you. It's hard, and I love it. I certainly have more respect for graduate students now than I did before entering this program.
Getting a PhD is not 100X harder than an MD. As someone who is nearly at the end of the MD and already did my PhD (admittedly, I don't very highly of it), I can say the PhD was probably equally hard as the MD. It's frontloaded-hard, while you're mucking about waiting for a break that will let you run with the experiments. The MD is more evenly difficult. And if you want to do well - which everyone should - it is arguably harder than most of the PhD. Then again, I didn't exactly do the 80+ hr workweeks that gbwillner did, so he may think differently.
Again, it's a matter of personality. I much prefer being on my own in the lab, doing my thing. I hate clinical medicine (but will have to do it, of course), which causes me anxiety to no end.
Aren't residents in various specialities now doing multiple fellowships as well to become super sub-specialized in their area of interest because this is what the job market requires? Does this mean that an MD is also worthless because you have to work a bit harder to be excellent at what you do?
They're doing that for better income/opportunities. Even without fellowships they can still be very well paid doing a different sort of career (generalist vs specialist or specialist vs. subspecialist, etc). Once you're done with residency, you should be guaranteed a 100K+ job. You should be competently trained for that job.
There's no such thing with the PhD-scientist track. You could muck through 3 postdocs and still not have a faculty job. You could be a perpetual postdoc. You could end up flying off to industry and working as a cog in the machine. People are doing these multiple postdocs not because they are not specialized and competent enough from just one postdoc. I expect they are doing it because they're basically waiting to accumulate enough papers, develop enough connections, and wait out until enough faculty at the university tier of their choice are retired in order to try to slide into that spot. Most never make it.
This is an interesting thought. However, you can't tell me that every brilliant scientific idea came out of the top labs in the country, so training a limited number of people at a handful of institutions will severely limit the creative flow of ideas in the scientific community. I also completely disagree in only training graduate students in "big wig" labs. These are the labs where the PI is never available, and therefore not mentoring, or the lab is full of Post-docs so the student never gets the opportunity to think for themselves. You reference this exact scenario in your post:
I definitely agree that the scientific process is hindered by these sorts of pressures, but we are a long way away from breaking free of this structure completely. We can't just close the door to those 80% of students who genuinely want to do research.
I agree that every brilliant scientific didn't come out of the top labs in the country, but a great majority do. I don't think we should have so many PhD students in the first place, nor do I think the PhD should be so easy to attain. Perhaps we should go to a more tiered system like they had in Russia. PhD = Kandidat Nauk (Candidate in Science). Getting a Doktor Nauk (Doctorate) requires many years or even decades of excellence in a field of study. Quite simply, we are awarding these honors too easily and too frequently. I will be the first to note that the criteria for my PhD were crap. We had a bunch of journal club BS seminars and a handful of biology courses. We didn't have a rigorous pre-research curriculum taking the biological sciences graduate student through the scope of neurobiology, cell biology, biochemistry, immunobiology, animal/human anatomy and physiology, microbiology and virology, genetics, etc. as well as methods courses in proteomics, genomics, molecular biology, biochemical methods, imaging and microscopy, etc.
Why don't we go back to rigorous graduate school entrance exams, where questions test extensive knowledge in biology (or chemistry, or physics, or whatever the field of choice)? Why don't we go back to open ended exam questions that test hypothesis design and asking students to come up with good scientific questions based on given scenarios, and knowledge of techniques to answer these questions? Instead, we have crappy standards where exams are regurgitative, the graduate student's independence is incredibly variable (between operating at post-doc level early on to plodding along under the PIs/postdoc army micromanagement, etc.).
The "structure" as you put it, was nonexistent as such for centuries. We had gentleman scientists, people who got to university positions as lecturers and researchers through their brilliance (rather than training program this and research program that), people who worked in industry, made some money and opened labs of their own, people who were funded by the benefactors/patronage of the aristocracy and industry.
All these modern academic funding mechanisms have perverted the structure of science. Instead of the university hiring someone and funding him for a time to do the research that he wants to do, we hire them (after multiple postdocs) into some limbo called tenure track, where their excellence is determined by their peers, who will determine what papers they have the right to publish and indeed what research they have the right to conduct; if the research is not interesting to the grant review committees, they get no grant. No grant, no tenure. No tenure, and they're out to work in teaching or as a cog in industry.
This is ideas by democracy. The good ideas are the ones committees and politicians think are good. Those are the ones that will get the money and the support. Who ever said democracy was a good thing for ideas? What scientific theory has come to fruition through a democratic process? If I remember correctly, most theories were invented by one person, by a handful of people, or were cobbled together by different scientists working on different parts of the patchwork (QM being the quintessential example). Theories were fiercely debated amongst competitors. I don't know of any theory that was proposed by a committee. I don't know any that arose out of a consensus of people gathered at a conference. Why would a committee be any better at determining what ideas should be tested? Why would one's competitors (who have a horrific bias) have the right to determine what and where we publish?