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Monday, November 23, 2009

What I've learned about PhD committees

[Update: thanks to some excellent feedback, I thought I'd revisit this article and clean it up. I've tried to be clear where the revisions are, and only made minor clarifications to the body of the text where warranted.]

This has been a really bad week for me. It started with a botched committee meeting, a death in the family, and then a series of technical errors that have annoyed me to no end. All that has made me walk away from my computer in frustration several times, only to return and find something else that upsets me. Unfortunately, the technical issues are mostly just that: technical. They're not something that other people will learn anything from, with the possible exception of this:

I understand dbsnp 130 has now begun to include cancer causing mutations and pretty much everything else in their annotated snps. And, of course, there doesn't seem to be any mention of this on the web. Knowing this, you obviously shouldn't use it for filtering out "neutral" changes. It won't work. (If you're working on genetic variations from RNA-seq like I am, this warning might save you a few hours or pain - or better, prevent severe embarrassment if you start talking about filtering in front of an audience, as a fellow grad student and friend of mine did recently.)

Anyhow, the greater part of the lessons I learned this week were about Grad School, and what I learned about committee meetings can be summed up in a few quick points: [Note, this is advice on meeting with the committee as a body, not meeting with individual members.]
  • Your relationship with your committee is not [necessarily] a friendly one.
They may be friendly with you, but they're not there to give you friendly advice and guide you through your PhD. Instead, the committee (as a body) is really engaged in an adversarial relationship in which they are the gate keepers that will decide when you can leave this pit of doom, and they are the ones that will open the door at the end when they believe you're ready to depart. Yes, they do have the roadmap to letting you out, but they would much rather you figure it out yourself instead of asking them to help plan it. [To be clear, it is the job of your committee members individually to give you advice and help you out - and the job of your advisor to help you find that road map. The committee exists to make sure that you've satisfied the requirements. Every project is different, so you'll have to chart your own path - and the committee as a body knows where you'll end up, but not how you'll get there.]
  • Your committee is not interested in your progress - they're interested in your results.
The difference may be subtle, but it changes how I view my committee meetings. No more will I go in there with a "progress report" style presentation. Instead, I'm going to go in to present results, the same way I would if I were in a journal club presenting a paper. They don't care if I've learned new coding languages, solved 12 cold cases and rescued a baby from a burning house. They only want to know what my results look like - because those will go into my thesis, and that's all that matters. (Don't bother asking what they think your thesis should include... you should decide that, and then they'll tell you afterwards if you're wrong - see "roadmap" in the first point.)
  • Your committee is not expecting great things from you - they want you to know what they know.
Actually, they expect you to memorize useless details, be able to regurgitate the names of people in your field blindly, and know which journal has the highest impact factor in your field. What they're really after is that you should be able to point to the people they know in the field and explain how they solved the problems you're working on. If you know who they know, you'll know who's papers they read. [This probably sounds much more harsh than I meant it to be. Getting a PhD means you're an expert in your field, and thus know all the details - when you know all of them, that's when you're ready to leave. The purpose of the committee as a body is to ensure you're an expert, not that you're destined for a Nobel prize. The only criteria they have to judge you on is what they know about your field. So knowing what they know about your field is the way to show that you're an expert - after all, those are the questions they'll ask you to determine if you're right about what you know. And yes, as undergrads, we all learned that the right answer to a question is what the professor gave in his notes, not what you think the right answer is.]
  • When your committee asks you an opinion question, they aren't asking your opinion - they're asking their opinion.
This should be obvious to any 1st year undergrad student, but as a grad student, we tend to forget it. Professors may ask a question that starts with "what do you think about/is...." The correct answer is not what you think it is - it's what THEY think it is. (Remember this subtle point - it will probably be needed in your defense as well.) [Again, somewhat harsh, but it's like I've said above - they're asking you questions to test if you know the answers - and the correct answers, in their mind, will be what they know and what they believe. One on one, you can discuss and debate these issues with your committee members as individuals, but my committee meetings rarely seem to be discussions.]
  • Your committee won't know why your results are important unless you explicitly explain it to them.
Again, this is something you learn as an undergrad, but may have faded with time. A committee member looked at my presentation and said at the end (paraphrased) "You're just turning a crank and out pops Venn diagrams". Obviously, I didn't do a good job of explaining the 26,000 lines of code I've written and the novel algorithms that went into it.
  • Your committee will change their minds - and not know it.
Don't expect that your committee will remember what they told you last time... they don't. [It's probably been a year or more since last time you met. We all forget.] My last committee meeting, I was told me (explicitly) I should not include my ChIP-Seq work in my thesis. This time, they told me I'd be crazy to leave it out. (They may have used a different word... I was somewhat in awe at this point in the conversation.) [Clarification: What details may seem important to you are probably insignificant in their lives. Don't expect them to remember for you, and a year is a long time - things may have changed.]
  • Don't expect sympathy from professors.
Once you've irritated all your committee members by doing nothing but turning cranks, remember that your job is just to keep producing results - that's all that matters. When your committee has just discussed that you're not turning the crank fast enough, your advisor isn't going to come for a friendly chat to find out why - they'll just send you notes that antagonize you. They assume that nothing is going on in your life and that your results are just not there because you have become lazy. They were in grad school once, so they know that your inability to conquer impossible problems is just because you're off playing ping pong or getting coffee. (Be prepared for this - it's the inevitable result of a bad committee meeting, if you haven't taken my advice above.) [Again, harsh, but yeah, I was upset. Still, this was just an example. I do play ping pong, but I don't drink coffee, and yes, I did get a sarcastic email from my supervisor - probably deserved after such a poor presentation to my committee. As they say, Your Millage May Vary - if you're lucky enough to have a supervisor that is holding your hand through the process, that's great - but don't expect it. PhDs are all about preparing the student for the real world - and the real world is harsh.]
  • Professors are very good at juggling tasks, and the only way to learn is trial by fire
Since I've discussed it several times with my advisor that I'm doing too many things, and that's how it's been all year, maybe it shouldn't be a surprise I can't focus on turning out papers. It seems to me that the people who make the grade to become profs are the ones that are able to write grants while juggling 4 projects, and are able to make progress in all of them. That clearly makes sense - lousy PhDs don't make good profs. However, those people who make it to professorship are (in my opinion) often the ones that are naturally good at managing their own tasks. For those of us trying to manage too many tasks, don't expect them to help manage your priorities - they do it instinctively for themselves, and they expect you to do it instinctively too - even when your priorities are 180 degrees opposite from what you thought they were. [One of the major lessons I've learned is that in grad school, priorities are what you make them. Your committee exists to make sure they don't slip too far from what they think you need to accomplish - as much as we may all want hand holding, professors are busy people, and your priorities are exactly that: Yours to set and to juggle.]

So, there you have it - it's been an educational week. I've learned:
  1. What a PhD committee is for.
  2. How to talk to and answer questions from committee members.
  3. What to expect from my committee and doing research.
  4. That I need to completely re-organize the way I manage my tasks.
While I'm helpless to do anything about the botched committee meeting, I have been able to work on that last point. I've changed how I manage my software, how I interact with my colleagues, what projects get my time, and I'm making a point of saying No to things that won't get me out of here. With luck, that will put me back on track - which is what my committee wanted in the first place, right?



Blogger Will said...

You may not believe it, but posts like this are unbelievably helpful to young naive grad students like me beginning to trudge their way into this messy, ill-conceived higher educational system. One wonders if people like Darwin would have made it 10 feet down the road in our day and age.

A quick word about the crank and Venn diagrams problem: please let me know when you solve this problem. What the bigwigs don't seem to understand is that just one point in the Venn diagram would have made a thesis 10 years ago. In RNA-seq this means you showed a mutation is unique to tumor tissue (or whatever). If there are 30-40 of those with less than a year's work shouldn't people be shocked and awed?

To paraphrase the late Notorious B.I.G.: More data more problems.

November 23, 2009 7:27:00 PM PST  
Blogger Anthony Fejes said...

Hey Will,

I'm glad you find this helpful - it's been a hard lesson to learn for me, and I'm very happy to spare someone else the pain.

As far as your second point, science is always progressing. What you do now would have got you a nobel prize 10 years ago, and in 10 years will only be a footnote in someone's undergrad thesis :P

Apparently shock and awe fades fast.


November 24, 2009 1:52:00 PM PST  
Anonymous Kate said...

ditto to what will said re: advice for us noobs. Except I had a sinking feeling while reading it--I suspect that when my time comes I'm going to end up making (some of) the same mistakes. Part of the learning process I guess, but it's going to be painful.

November 24, 2009 6:38:00 PM PST  
Blogger Keith Robison said...

Since I'm past the committee stage, I'm more interested in your observation about cancer mutations in dbSNP. These are somatic mutations, right? How did you figure this out and how are they annotated as far as evidence source?

November 25, 2009 5:36:00 AM PST  
Blogger Anthony Fejes said...

Hi Keith,

I didn't figure it out on my own - my colleague had it pointed out to her during a presentation (much to her embarrassment), and it has since been confirmed to me by other sources. I have also now verified it in two proteins of interest.

As for how they're annotated, I don't have an answer to that yet. I'm still in the process of working through the information I've been given, and I probably won't have a chance to seriously go through it till friday afternoon as I am required to give a talk on friday morning. If I find anything actionable, I'll post it on the blog.


November 25, 2009 8:47:00 AM PST  
Blogger Doug said...

Anthony, hang in there. It's always darkest before the dawn. In graduate school, doubly so.

My favorite quote from my graduate school experience.

Advisor: I don't understand why you've spent the last six months wasting your time on these experiments.
Me: (agape) Because, you told me I had to do them.
Advisor: Well, then you shouldn't have listened to me.

Hopefully some day this will all be a very good story to tell at cocktail parties.

November 30, 2009 6:00:00 AM PST  
Blogger Anthony Fejes said...

Hi Doug,

Thanks for the comment. I've heard the same advice from a few people now, and I think it's well worth taking. Fortunately, I'm not actually all that depressed or upset about it anymore.

Bad committee meetings happen, and as long as I can walk away from it and know that I've gained knowledge (wisdom, perhaps), then I'm still learning and making progress. That's really what being a student is about, so it's all good.

I love your story! It put a smile on my face, and it's good to know it happens to everyone - although I'm sorry for the wasted time you spend in the lab. Live and learn, right?

November 30, 2009 9:11:00 AM PST  
Anonymous Anonymous said...

Really good post Anthony. I found this exactly the same way, though in my case, my supervisor also realized we hadn't prepared a results oriented presentation and the next time around he worked with me a great deal in developing a really strong presentation. This was and is one of the key lessons of grad school, and it's a lot better if the supervisor helps with this.

November 30, 2009 11:23:00 AM PST  
Blogger Anthony Fejes said...

Thanks for leaving a comment, anonymous - it's also really good to know I'm not the only one who thinks this is how it should be done. In my case, I don't think my supervisor will be helping me put anything together, but I'm more than capable of building my own presentation structured around this format, now that I'm aware of it.

As a good example, I did a results based presentation on Friday, and it went pretty well. It's just too bad that none of my committee members came out to see it.

November 30, 2009 11:29:00 AM PST  

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