Defense Day

Well today is my thesis defense day. For those who are unfamiliar with the process, this is how it works at least at my university.

When you start out in a lab you do the experiments your boss tells you to do, with the goal of picking up a project. This usually involves taking up where another graduate student or post-doc left off, or reading the literature in your field and figuring out an important question to answer. Depending on how many years its been since your boss handled a pipette, he/she will suggest experiments that range from next to impossible to impossible. You spend a year screwing around, messing up experiments and hopefully generating some preliminary data to justify the research that will go into your thesis. Simultaneously you are taking graduate classes and applying to be a degree candidate. The requirements for this vary by university and department. It may require writing a review paper summarizing a related (or unrelated) field of science and defending it to a committee, or may be an actual exam in which you prove you’ve actually learned something in class.

Eventually, in the lab you sit down with a post doc who helps you design experiments that will actually work, and all of a sudden data arrives. If your boss asks you about the experiments he/she recommended either say you’re still working on it, that you’re waiting for an antibody, or pretend you don’t understand English. Then, quickly distract them with the interesting data you’ve been generating and they should soon forget about what you haven’t been doing. At this time you should be developing your possible/impossible filter, and judging your mentor’s advice accordingly.

The next step is to compile all the data you’ve been generating into a defense of your proposal. Most labs these days have you write something that resembles a grant, because it gives you critical experience in how to get people to give you money. The importance of this skill can not be underestimated for your future success as an academic scientist. You will be justifying the financing of your science for the rest of your career, and knowing how to get funding is probably more important than knowing any specific experimental technique. You present your grant, which consists of your primary aims, methods, preliminary results, etc, again to a committee. They grill you. If your lucky your committee will be composed of a mixture of docs who will defend you from the worst iniquities of the other members and docs who won’t be afraid to tell you your project actually sucks. Either way, you’re in for a treat.

Once you’re done with that congratulations! You are between 2 and 10 years away from graduation.


During this time you show up in the lab for about 12 hours every day, read email and surf the internet. Between reading boingboing and arguing with trolls you run experiments and review papers. After about a year three things might occur. (1) Your idea was good, so your experiments will work and you will publish. (2) Your idea was good so you will get scooped about half way through. (3) Your idea was good, but the science gods hate you, the experiments don’t work and you find out your hypothesis was totally incorrect. If 2 or 3, what do you do? Neither is the end of the world, and are incredibly common. So you come up with a new project. If you’re smart, you’ll figure out how to do it without defending a new proposal. Either way, you regularly meet with your committee (the one that will eventually review your thesis) and tell them what worked and what didn’t. Eventually something works (or you get scooped/screwed again – start over) and you write a paper.

The fun isn’t over yet. Now you have to write a thesis. This is actually fairly easy, but by now you’re so sick of your project you’d rather write about anything else. So you have to suck it up. You write an introduction – basically a review of your field and why your project is relevant to it – the chapters – you cut-and-paste your papers – and a discussion. When all is said and done you basically have a book, between 80 and 500 pages long justifying why your boss has been paying your stipend for the last 2-10 years. You turn it in to your committee and sleep for about 2 days.

The last bit is a little nerve-wracking. The public defense. It’s when everyone in the department shows up, along with your thesis committee and you give a talk that will hopefully show enough data that people will agree you deserve to graduate. It’s not that hard, by now, no one alive should know more about the subject than you, so make sure you don’t talk about anything of interest to anyone else in the department. If you do, you will be out of your element, they will ask you questions, and your 45 minute talk will take 2 hours. After that’s done, everybody leaves but your committee who then spend the next couple hours grilling you about every detail of your project with the goal of inducing panic and making you think that despite all their previous enthusiasm and supportiveness, they’re going to ground you at the last second. They won’t, it’s just hazing, but you have to accept it as the price of their service on your committee. After all, without the prospect of torturing a graduate student for a few hours there is absolutely no tangible reward for serving on a thesis committee for the last 2-10 years. Eventually they relent. If they don’t, grab your belly and yell, “Ow! my baby”, or if you are male say you just found out your wife/girlfriend/last one-night-stand is pregnant. Nothing is more terrifying to a thesis committee and major adviser than the prospect of a graduate student starting a family since it means they won’t be in the lab as much and will constantly import colds from day care.

Congratulations! Now you’re a PhD, and all your problems have just begun. You have to find a post doctoral position and write a grant to justify your existence. You will be subject to periodic reviews, more meetings, and have to travel around the world presenting your science to people who are trying to scoop you or prove you wrong. Your wife/husband likely lives on a different coast and you still make about 1/5th of what any other career requiring 25 years of education would provide. Rinse-repeat, and you’ve got science!

My education will delay post doc hell for a few more years as I now return to the medical wards, starting on surgery next month, and finish my training to be an MD. I then do a residency for 3-5 years. After that, if there is a Democrat in office and the country isn’t bankrupt, I may then choose to pursue a research career or a mixed clinical/research career. If there is a Republican (in other words no grants, a glut of post docs and general hostility to science) you primarily practice medicine and maybe do research on the side so you don’t perish from lack of publications. Last option, go to work for industry, make money, and live with that strange mixture of corporate politics, freedom from grants and moral ennui.

Anyone still want to pursue a career in science? Sounds like fun right? I’m teasing mostly, science is intellectually rewarding, you feel as if what your doing is valuable (when it’s working anyway), and you’re always around smart and interesting people. Further, you have a great deal of personal freedom and are occasionally rewarded by the discovery of something completely new. The problem is that many scientists feel only a small amount of their time is spent doing science, and too much of their time is administrative, writing grants, going to meetings, and otherwise trying to feed the two-headed beast of your fragile career and money-eating lab.

My advice for anyone about to start a PhD is very simple. Make sure to find a good mentor who is stable, financially and emotionally. Ideally have candidates when you are applying to grad school – but don’t fixate on one doc if after working in their lab for a bit you think they are crazy or cruel. Rotate through a few labs, get to know a few mentors in the university, and learn what you like and are good at before choosing a mentor.

As far as that choice goes the major division is between old and young. The advantage of a younger mentor is that you’ll get more direct interaction with your boss, learn more directly from them etc. But the risk is that they are less-established and may have to jump to another job while you’re there (this has been a huge problem in the last 7 years). The advantage of a more established scientist is that they know how to survive in science, will teach you grants, and will recruit lots of talent to the lab that will be the ones to teach you how to do the actual science. The risk is that their labs tend to be big, you have to be self-motivated, and if you’re not careful the boss won’t notice you’ve been floundering for a few years. Never work in the lab of a department-head unless they have good post docs. More than anything, the people have to be right, and willing to work with you, or you will be screwed.

When you start in a lab learn at least one or two useful assays that no one else in your lab knows, and make them rock solid. You now have a hammer, look for nails. Develop an understanding of everything that is done in your lab, but don’t try to master every technique. Instead barter the ones you have mastered for the ones other people have mastered. That way they are coauthors on your papers, and you get to be coauthors on theirs. Everyone is happy, the science is better, you learn to collaborate, and the division of labor ensures everyone is operating efficiently within their sphere of competence. Even if your stuff isn’t working, you’re still getting publications, and being a productive member of the lab.

That’s all I can say for now. I think I’m going to hit the NyQuil so I can actually get some sleep tonight and be coherent tomorrow. If all goes as planned I’ll be a PhD by 5PM tomorrow.


  1. Wow. . .and that’s what I want to spend the next ten-50 years of my life doing!?!? Yep, I think so.

    Good luck tomorrow!

  2. Best of luck!

    I haven’t got a date for my viva yet, but I hope it will be before Christmas. It’s a bit different in the UK as it’s a private occasion with only two examiners… but the grilling is the same if not worse. You can most definitely fail PhDs at this stage here.

  3. Ex-drone

    I don’t believe this is how Intelligent Design progressed. Perhaps, the DI braintrust are just more efficient.

  4. Good luck!

    Well do I remember my thesis defense day. Nerve-wracking, but the committee was pretty fair, by and large.

  5. Hope it goes well, and Im sure it will. As I tell our students, if your committee lets you defend and you aren’t ready, then your committee failed not you. Throughout my grad school, post-doc, PI life I know of no one who crashed at this point, so congratulations doctor.

  6. Good luck! I too remember when I went through this ritual as a candidate.

    Lorax’s point is dead-on — if one of my students were to fail the defense, the student’s committee (and I, as the advisor) would have failed the student.

  7. Good luck!!! I’m sure it will go well!

  8. Congratulations! As a sentimental alumnus, it warms the cockles of my heart to see a fine young man receive his degree from the greatest university in the country. Mr. Jefferson would be proud.

    You make a good point about choosing an advisor, which is that he or she is only a part of the equation. Your actual time as a student (and a great deal of your education) will involve the other members of the lab — postdocs and senior grad students. When you rotate in a lab, get a feel for whether you like these people and whether you believe they can pick up the slack as counselors and teachers when your mentor is unavailable.

    I’m less enamored of the “hammer and nails” recommendation. I don’t think it’s an invalid or improper strategy (although it’s clearly calibrated towards a large lab or highly collegial departments), but I think this approach leads you to miss out on a valuable opportunity, namely teaching others advanced techniques. Complicated assays and experiments often involve steps that are easy to overlook yet essential to success (independently calibrating flip-back and flip-down pulses on high-field cryoprobes is a good NMR example). It is better to practice your training approach as a student than later on when it’s YOUR precious NMR time or reagents that will go to waste because something wasn’t emphasized strongly enough. Training others is an important and difficult part of scientific practice. Better to get some practice with it while you still have someone else’s grant money to absorb the blow of failures.

  9. When you start in a lab learn at least one or two useful assays that no one else in your lab knows, and make them rock solid.

    I was lucky enough to step into a lab and learn some techniques from an older student who is now graduating. So I’ll have that to position myself with. (Unfortunately, he was a lot better at it than I’ll ever be…)

    The advantage of a more established scientist is that they know how to survive in science, will teach you grants, and will recruit lots of talent to the lab that will be the ones to teach you how to do the actual science. The risk is that their labs tend to be big, you have to be self-motivated, and if you’re not careful the boss won’t notice you’ve been floundering for a few years.

    Wow, this looks familiar. Save the “few years” part, of course; I haven’t been here that long. But I am one of about 9 “siblings.”

    Since luck is only based on misunderstanding of statistics, I won’t wish you good luck. But I will say that my thoughts are with you, and I hope for the best.

  10. Caledonian

    Good luck!

  11. Congratulations!
    I think you have discovered some universal truths in the above post.
    I am sure there are more in your thesis 🙂
    Take care,

  12. Matthew D. Skinta

    I defended only this past summer, so I feel your pain…. congratulations!

  13. You don’t need luck – you have brains. If they, for whatever reason, take a break at any time during the defense, you have charm. If charm fails, you have shouting.

    Congrats – and remember, you are owed at least 3 parties for this. We can’t wait to throw one for you.

  14. Drugmonkey

    Best of Luck and remember, you do know the most about your topic of anyone in the room…

    let us know how it goes so we can virtual toast, eh?

  15. You will do well in your defense and be a known as Dr. Denialism in about 2 hour and 13 minutes from now!

    No luck involved in your case, since you are smart.

    As for the strategy you raised of doing an MD/PhD so you can use your MD degree to pay the bills during scientific dark ages of Republican rule is interesting. I never thought of it that way.

    Do let us know if you made it.

  16. Good Luck!

    I’ll be up in the spring…..

  17. Tegumai Bopsulai, FCD

    Dr. Hoofnagle, I presume?

  18. Hope it was relatively painless!

  19. Done, graduated, be at the bar at around 6pm.

  20. melatonin

    congrats, Dr Hoofnagle 🙂

  21. I read this post earlier today, and I came back explicitly to say…


    Hopefully I’ll be joining you in PhD-hood come May.

    (And yes, for those of you who know about obscure academic graduation traditions, I did actually intend the “hood” pun buried in there.)

  22. Congratulations! If the post-viva experience of my friends (and myself) is any guide, the main question is what time you will finally leave (or be carried) from the bar…enjoy!

  23. CaptainBooshi

    Well, I’m just finishing my first semester as a physics grad student, and I’m still enthusiastic (although really ready for the break), so I’ve gotten past the first hump! Now I just have everything you described to go.

  24. Wahoo, congrats, have a drink for me 🙂

    (Hopefully I’ll be in your shoes in a year or so :))

  25. W00t!!1! I’ve been trying to call! Should have know that the news would be on the blog!

  26. Congratulations, and welcome to the ranks. BTW, working for the Dept. Chair when he has a junior faculty member who can give a lot of attention isn’t so bad. I went from thesis defense to post-doc (industry) in five days. Whew. Haven’t had a PB&J sandwich since grad school. Most vivid memories of grad school? End of the month lentil soup. Feeds a family of two for two days for about $2. Waiting for the end of the faculty meeting to grab the leftover food. Oh yeah – the research.

  27. May all random or semi-random occurrences outside of your control work towards your favor with regards to your thesis defense.

    Er…good luck, that is.

  28. Congratulations!!!!

  29. minimalist

    Congratulations, man! Once you’ve slept off that hangover, head back to the bar. You earned it.

  30. Justin Moretti

    Congratulations, Dr H.

    Try not to rape your liver too badly in your celebrations, though verily the liver is indeed evil and must be punished.

    You should know, in your happy drunken haze, that you have just successfully divested me of any remaining thought I might have had of being an academic. :-p Good luck for the rest of Medicine.

    (BTW What specialty do you intend doing? Or aren’t you sure yet?)

  31. Good Job Mark! I just did mine, Nov 29…
    Feels great to be done!
    SO where the hell is Tommy Palmadei?

  32. Congrats on the PhD.
    If I start now, I can have a shot at mine by the time I’m 60.

  33. Congratulations!

  34. How did they let you graduate without a first author publication (other than reviews)?

  35. I have two first-author manuscripts completed but they let me go back before acceptance because of deadlines for medschool. We’ll get them published sometime this year.

    Very astute question. Don’t worry, I’ll let everyone know when they get out there.

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