Joan Strassman has a nice post at Sociobiology about how to choose a PhD program. I agree with most but not all of what she has to say.
I don’t agree that you just avoid M.Sc. programs if you think you might want a PhD. Unless you’re sure you want a PhD, doing an MSc is a good way to hedge your bets. It’s a much smaller commitment, both on your part and on the part of your advisor. If you’re unsure exactly what you want to work on, an M.Sc. can be a good way to find out, and gives you a natural way to change directions as your interests evolve. Lots of people do an M.Sc. in one lab and a Ph.D. on a somewhat different topic in another lab. But to do this you have to start, and finish, your M.Sc. first. If you start a Ph.D. and then for whatever reason decide you don’t want to finish it, you can often take an M.Sc. instead, but that’s colloquially known as a “terminal” M.Sc. If you do that, you’ll typically have a very hard time convincing anyone to take you on for a Ph.D. After all, you already tried and failed to finish one Ph.D.–why should anyone think you’ll succeed on your second try, or choose you over a competing applicant who hasn’t failed to finish? You may not think that’s fair, but that’s the reality.
There are other reasons to do an M.Sc. first. You’ll get a paper or two out of your M.Sc. thesis, which will make your CV stronger when you eventually finish grad school and enter the academic job market. Doing an M.Sc. and then a Ph.D. does extend your total time in grad school, but often not by much because you get all your coursework out of the way during your M.Sc. An M.Sc. also can qualify you for various jobs (e.g., certain environmental consulting positions, some technician/lab manager positions) for which a bachelor’s would not qualify you, so it’s not as if you’ve wasted your time if you end up deciding not to go for a Ph.D. And as for funding, while some universities don’t provide funding for their M.Sc. students, many do.
Note that I’m not saying you should do an M.Sc. to find out if you want to go to grad school at all. You should do your homework and figure that out before you start applying to graduate programs. You should be doing an independent study or honors research project, taking research assistant positions, and talking to your TAs to find out what doing research, and graduate school, is like.
UPDATE: Zen Faulkes has a nice post on why grad students fail. Many of these pitfalls can be avoided by doing your homework, and honestly assessing your own background and motivations, before you start applying.
Other advice I’d add:
Choosing the right advisor is more important than choosing the right program. I went to Rutgers because I wanted to work with Peter Morin, even though the Rutgers EEB program wasn’t on any lists of the top graduate programs in EEB. I’ve never regretted the choice. Don’t get me wrong, it’s fun and stimulating to be part of a top graduate program because you have the opportunity to interact with so many really good faculty and students. But your relationship with your supervisor is going to be much more important to your grad school experience. If you get on well with your supervisor and your labmates, you’ll have a good experience in grad school. If not, not. And once you leave, who your supervisor was counts for more than which program granted you your degree. When I was looking for jobs, I wasn’t viewed as a Rutgers graduate–I was viewed as a Morin lab graduate.
The exception to the above is that you definitely do not want to do your PhD at the same university where you got your bachelor’s (and your MSc, if you got one). If you don’t leave the nest, people will assume you can’t fly. Getting a bachelor’s in one place and both your graduate degrees somewhere else is fine. And getting a bachelor’s and master’s in one place and a Ph.D. someplace else is fine too. But getting your Ph.D. and all your pre-Ph.D. degrees in one place looks bad, even if you do different degrees under different advisors.
Here’s some advice I really can’t emphasize enough, because it concerns a really common mistake prospective grad students make. Before you contact any prospective advisor (at least in N. America), do your homework. Have a good look at their website, and read a couple of their papers. Then write each prospective advisor a personal email which is addressed specifically to that person and only to that person. Describe your background, interests, and long-term (i.e. post-grad school) goals, and say specifically why you want to join their lab (which doesn’t mean having a specific project in mind, of course). If you don’t do that, you’ve already gotten off on the wrong foot, and with many supervisors (including me) you’re already pretty much doomed. Most every decent advisor is very busy, and receives many, many inquiries from prospective students, many of them obviously bulk emails (many but not all of which come from students in developing countries). Every professor I know deletes such emails without reading them. If you can’t be bothered to take the time to do your homework before contacting me, why should I take the time to reply to you? Rather than signaling that you’re seriously interested in my lab, you’ve just signaled to me that you’re the kind of student who likes to cut corners and who doesn’t show initiative. Plus, if you don’t do your homework before contacting me, I’m just going to reply by asking you about your background, interests, long-term goals, and what specifically interests you about my lab. I mean, how else am I supposed to reply? So why not just save us both some time and send me a detailed, personal email to start with?
And then once you’ve corresponded with a few prospective advisors and narrowed the field to a few top choices, make sure to visit those labs before you make your final decision, and ideally before admission decisions are even made. Besides meeting your prospective advisor, you’ll get to meet their current grad students, see the facilities, and check out the city and the surrounding area. I actually insist on meeting prospective students face to face, with rare exceptions for students who are highly recommended by close colleagues whose judgment I trust. And no, skype or a phone call isn’t really a substitute. Most prospective advisors will at least encourage a visit even if they don’t insist on it, and will be happy to pay for it. Both you and your prospective advisor are considering making a big commitment to each other. It’s to the advantage of both of you to be as sure as possible that you’re a good match.
Oikos Blog 
Talk to the grad students of the lab you’re interested in. Very important.
By: Jim Bouldin on February 12, 2012
at 9:46 pm
While grad advisor is perhaps more important than institution, I’d add that you want to make sure there’s at least one or two other professors at the same institution who you’d be willing to work with (and who’d be willing to work with you) if necessary. You never know what will happen: your advisor may take another job elsewhere and you may not be able to (or want to) follow. Your advisor may do something Very Bad and be forced to resign. (It happens.) Your advisor may die. You don’t want to be stuck at a bleh institution with no advisor and no reasonable back-up half-way through a PhD.
By: Margaret on February 13, 2012
at 4:00 pm
In principle I agree with this advice Margaret–even though in practice I violated it myself. Had Peter Morin left Rutgers or been hit by a bus or whatever, there wasn’t anyone else at Rutgers I’d have wanted to work with. Indeed, before I visited Rutgers, I’d heard a rumor that Peter might be leaving. So I asked him point blank if he was leaving. He said no, I took him at his word, and it worked out fine.
Yes, going somewhere where there’s only one person you could possibly see yourself working with is something of a risk. But it’s typically a small risk, albeit one with potentially-major consequences for you if it comes to pass. When deciding whether to take that risk, you have to weigh up your other options. For instance, if you choose to work with someone who’s not your first choice, you thereby *guarantee* you won’t be doing the science you most want to do, just to avoid the low risk that your first choice will die/leave/be fired. It’s kind of like saving money for retirement. If you invest too conservatively, thereby avoiding any significant risk of losing all your money, you earn a low rate of return, thereby pretty much guaranteeing you won’t have enough for retirement.
Of course, my remarks here only apply if you do have a clear-cut first choice advisor. If there are several people you could see yourself working with, and some of them are all at the same same university, then yes, it makes total sense to choose that university.
In my own case, my other leading option was also someone who was the only person at his university with whom I wanted to work, so there was no bet-hedging reason to choose that person over Peter. And I wasn’t admitted to my third option, which was a program that did have several people with whom I could’ve seen myself working. Ironically, *all* of those people retired or left that program during my time as a grad student! So had I been admitted to, and chosen to attend, that apparently less-risky program, that’s the one that would’ve ended up putting me in a difficult position!
As I’ve discussed elsewhere on this blog, there’s a limit to how much you can plan your life. You have to have some faith that things will work out (perhaps even better than you ever could’ve planned), and some resilience when they don’t.
By: oikosjeremy on February 13, 2012
at 4:25 pm
I agree in part with you, but think that it’s still important for prospectives to think about a back-up plan. I think it’s likely that most prospective graduate students don’t have such a focused idea of what they want to do and that there is only one place that they can do it that they have to take the sort of risk you did. You were smart (by asking Morin if he was moving) and you were lucky (that he didn’t get hit by a bus). But some people will be smart and unlucky. I think that prosepctives ought to have a Plan B when risking graduate school. For some, that Plan B may be willingness to moving with an advisor. But for others with family or other constraints, that Plan B should probably be how-to-finish-your-dissertation-at-the-same-institution-if-your-advisor-leaves-the-picture, and the easiest way to hedge that bet is to make sure there are others in the prospective department that can become your advisor. (And, as a side note, it’s great to have these back-up advisors as awesome committee memebers if nothing does happen to your advisor.)
I think of it as diversifying one’s retirement portfolio rather than investing one’s entire retirement in one stock.
By: Margaret on February 13, 2012
at 5:11 pm
All good and perceptive points.
By: oikosjeremy on February 13, 2012
at 5:16 pm
Yes! MSc is often an excellent choice, maybe especially for younger students. It is clearly useful to have done some kind of work (other than in college) before applying for a PhD program. An MSc is one kind of work that can be a good background for a PhD. It is often hard to convince people that it’s a good idea, but I’m not really sure why.
I admit I didn’t follow my own advice, but here’s the excuse: I was 32 when I applied to grad school and felt the clock ticking a bit. That feeling was influenced by advice but not based on any data. Maybe similar feelings make the decision one way or another for many people.
By: Andrew Latimer on February 13, 2012
at 11:21 pm
I didn’t do an MSc myself. But I had no reason to. I knew a PhD was what I wanted to do, I knew it was essential for achieving my long-term goal (becoming a prof), I knew what it would involve, I was eager to do it (as opposed to, e.g., being burned out after my bachelor’s), and I had every reason to believe that I was ready for it. And all that was true even though I was only 22. So three months after I finished my bachelor’s I started my PhD at Rutgers.
So I don’t know that I’d cite youth per se as a reason to do an MSc first. I’d rather cite the reasons outlined in the post. But I certainly agree with your larger point that one should have a reason for avoiding (or not avoiding) an MSc. Indeed, I think a fair summary of the post, and the comments, would be: “There are reasons to do an MSc first. If they apply to you, do it. If they don’t, don’t.”
By: oikosjeremy on February 13, 2012
at 11:38 pm
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