What a PhD is Not
It's not about knowledge. The jejune view of education is that education is about imparting facts upon students, like math or writing skills. This is partially true: the facts we learn in elementary school, like 2+3=5, are critical. But most of the facts and theories we are taught in high school and beyond are quickly forgotten. While I learned about the treaty of Westphalia and the black plague in history class, I can only recall the vaguest details about them.
In terms of graduate school, this is also true. The first couple years of a PhD program include classes that lay a foundation for research. But the details of those classes are quickly forgotten; I can tell you that Wnt is a trophic factor, and that trophic factors lead axon guidance, but I haven't a clue what Wnt signals to.
In the three to four years after classes, you do accumulate some specific knowledge in your research area, about techniques and recent findings. But this knowledge is so specific that as soon as you venture outside your area it's only tangentially informative.* In summary, the knowledge you get in your PhD is either quickly forgotten, or too focused to be widely useful; which says nothing of how little emphasis is put on reading papers and actually acquiring knowledge.
* These tangents can certainly be important, since finding connections between disparate fields can lead to innovation, but I don't think anyone would argue that the knowledge acquired in a PhD is best used in tangents.
A PhD is also not about learning how to think critically. A couple points here: 1. While the scientific method theoretically underpins how science is conducted and verified on a grand scale, it is less wontedly employed in practice. The typical scientific practice is to try new things, see what happens, and try to explain why after the fact. 2. A lot of the critical thinking you go through in science is troubleshooting, which is certainly challenging. But any creative endeavour entails troubleshooting, be it debugging programs or ameliorating marketing campaigns. The value added from a PhD over them is negligible. 3. The people who try to get a PhD are sharp to begin with, and already know how to critically think.
What it could be about:
Having considered what the PhD system is not about, I'm going to informally hypothesize (i.e. pontificate about) what it's actually about: socialization to science, signaling, credentialism, and data.
One of my favourite bloggers, Robin Hanson at Overcoming Bias, wrote about the value of high school:
The best evidence I’ve seen that school adds great value is the stories I’ve heard about how difficult are employees who grew up in “primitive” cultures without familiar schools. Apparently, it is not [that they] don’t know enough to be useful, but that they refuse to accept being told what to do, and object to being publicly ranked relative to co-workers.In other posts, Hanson expanded on this idea: school is not about expressing creativity or problem solving, it is about getting your homework in on time, and giving your boss (the teacher) what they want. While grades and intelligence are correlated, grades probably best correlate with diligence and obedience.
Similarly for a PhD, while your results are important, other factors like how you talk to your committee, or are involved in lab life are important. You need to be learn how to talk to others about science productively, including wrestling with your boss, or battling rivals. You have to learn how to deal with experiments that refuse to work, troubleshooting them, and coming to work the next day when they still don't work. You have to learn how to network in science, and get others' perspective and aid.
While none of these factors will show up directly in a thesis, they are all part of the maturation process. When you meet a science PhD, you can hope that they've already met these challenges with some success.
Credentialism / Signaling
As more people try to do science, the need to differentiate between people has become important. In the past, a bachelor's in biology or chemistry was enough to start a science-y job (beyond technician), but no longer. Now all a biology degree is good for is discussing pop science with your fellow waiters. If you have any desire to do science in a meaningful professional capacity, your recruiter needs to be able to show his boss he or she hired someone "qualified."
This holds outside science as well. A PhD tells institutions like school systems, investment banks, consulting firms, and the government know that you are minimally smart and socialized.
(Of note here is that having a PhD now is a minimum credential in academia. For faculty positions, or even post-docs, you will be evaluated on your publication history. It is outside of academia that the degree-credential, counter-intuitively matters most. People outside of academia are less able to evaluate your scientific accomplishments beyond the surface level.)
Signaling is closely related to credentialism, but socially: if you want to signal that you're a smart person (who has good genes to pass on), an easy(?) way to do that is to tack a few letters after your name, especially if one of them is D.
If you produce enough of it, you get three letters after your name. And there ain't no cheaper way to produce data than a 3rd-6th year grad student.
So that is my basic thinking about the PhD system: for the student, it's about getting a credential so you have move on to something else where you do your real work, whether it be a post-doc or in industry. For the system, it provides cheap, smart labor. And the socialization a PhD learns greases the relationship between institution and individual, so the PhD holder can keep working in science contentedly.
What the PhD system should be doing is another matter.