This is more of a philosophical question, and rhetorical to boot. (I encourage hearing your opinions, but from a rhetorical standpoint this is an ask a question so I can answer it post.) At what point is a student ready? Obviously, there isn't any specific set of criteria, however there are some common guidelines and some esoteric guidelines. I also want to point out that in my worldview conferring a PhD means that the University or College is stating that this person is a trained scientist who is able to go out and independently establish their own research program whether it is in academia, industry, government, etc.
Of the common guidelines, the most obvious is the publication of, at least one, peer reviewed publication. I am not considering review articles here, although they are nice. By publishing a paper the student has demonstrated that they could generate a significant body of data related to some biological question. However, as the primary guideline this aspect ultimately fails in my opinion. First, publishing a paper with your name in the first author position does not truly demonstrate your involvement in the work. Maybe you did 50% of the experiments and the other authors contributed less so you got first and your mentor wrote the paper. This is not the same as someone who did 100% of the experiments and actually wrote the paper. Maybe a technician did most of the work and you came in and finished it up and your mentor knows, at least subconsciously, that you need the authorship more to help your career. In fact, lots of people publish rigorous papers that do not have PhDs. So, this can not be a criteria in and of itself. For the record, I am not suggesting that mentors actually think publishing a paper is sufficient, but this is an easy criteria to quantify and seems to be the standard fall-back position. My point is that a publication is necessary but it is not sufficient.
The esoteric guidelines are the ones that are difficult to quantify and will vary from mentor to mentor. This is where I ask myself if the student is a mature scientist.
"Well, how in the hell do you assess that?"
Good question *puts away magic eight ball*. There are several ways in which this can be determined. First, you can see how a student matures over time. Nothing demonstrates progress better than looking back and seeing where you started. Here, are some of my personal criteria in assessing whether a student is about ready to earn the PhD.
Ownership: when the student takes ownership of their project is a good indication they are in the final throws of earning the PhD. The student is no longer dependent on the mentor for direct guidance. This is when the student truly starts to be more of a colleague and less of a trainee.
Expertise: when the student knows more about their research project than the mentor (not so much knowing more factual information but having a deeper understanding of the research that they can more effectively use their knowledge).
Breadth: this goes hand-in-hand with expertise, but when a student can step back and relate their work to someone else's who works in a different area, well, that's just impressive.
I find these, admittedly, more subjective criteria are actually much better indicators of a PhD scientist than many others. Mastering a plethora of different techniques, even difficult techniques, is not a good indicator. Knowing lots of facts is not sufficient nor is publishing research papers. Many people can conduct difficult experiments, know a lot of things, and publish papers without the PhD and we do not spontaneously confer PhDs upon them. In most labs we call people who fit the latter three categories technicians or something similar. The difference between a technician and a PhD scientist, in my opinion, rest on the more intangible points I raised above. Now it is difficult to see how a student who has taken ownership and developed expertise and breadth would not be publishing papers and mastering a variety of techniques. You really can not do the former if you can not do the latter. In fact, I would say it is the mentor's job to train the student to learn the techniques and generate the data so that and while the student develops the more esoteric abilities.
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