Monday, November 29, 2010

Crazy idea for revamping the PhD program...

We still run Biology PhD programs basically the same way people did 20-30 years ago. Professors offer graduate classes in their areas of specialty, often formatted not terribly different from advanced undergraduate classes. Students very often struggle to find graduate classes in which they're interested either to fulfill a requirement or to learn SOMETHING besides what they're doing in lab. The efficacy of these classes, especially those "concept-centered", is often low... the students "learn" a lot the same way they did in undergrad, where a ton is covered of which very little is directly relevant to them, and the portion that was relevant would have been picked up anyway through independent reading. Meanwhile, we largely fail to train PhD students at skills or concepts they will actually need: 1) grant-writing (there's an exception with one class here at Duke), 2) what it really takes to run a lab, 3) developing and giving lectures in a class, 4) outreach and speaking to the public, 5) career options besides becoming a clone of their PhD advisor.

Why? Because we (faculty) are lazy is why- if it worked for us, it's "good enough." I'm currently floating a proposal with various folks in Duke Biology for a three year "PhD roadmap" that I'd love to get feedback on. Here's the outline. The objectives were to come up with a roadmap that would do all this while not being overly onerous or annoying to the students or faculty. In this vision, all pieces could be "optional", but this overall plan would be laid out as a suggested roadmap- with the exception of the year 1 spring class (for which we'd need the full cohort to participate for it to work).

Year 1-

Fall: A) Take "tools" coursework (e.g., statistics, programming, Matlab)

B) Take “tutorial” course(s) based on interests rather than the usual concept-courses. We'd ask in-residence faculty to set aside time to do a course or two wherein they just meet with 2-5 students every week (or every 2 weeks) for an hour or two to talk about papers in an area of mutual agreement. Basically, PhD students take the initiative to tell faculty what they want to learn/ cover, identify faculty with that expertise, and then
meet with them in small groups to cover that material informally through directed readings and discussions (NOT PowerPoint lectures!). Ideally, it would be mutually beneficial, as the faculty member could use it as impetus to read some of the papers in a stack on their desk (or virtual stack in their RSS feed reader)

C) Take Bio307 Grad School 101 course (half-semester, 1 hr/ week).

Spring: A) Student-driven journal club/ presentations (presentation dates organized in fall). This course would meet twice a week: Tuesdays are class-like presentation by student on a contentious topic of their choosing (graded by peers on clarity, comprehensiveness, etc., of their presentation
), and Thursdays, students read and discuss a recent paper relevant to Tuesday's class. The student's temporary advisor would attend to give feedback, answer questions which the student doesn't know, etc., but the student is giving the presentations.
The purposes of this class are: have students intensely research something IN WHICH THEY'RE INTERESTED and then present it (no better way to know a subject); real lecture-style presentation experience; NSF pre-doctoral fellowship preparation before year 2; increasing self-sufficiency.
It'd be required, but very low effort except that which hopefully they're very interested. There'd be no tests- if it's not your presentation week, you just show up, listen, and provide feedback/ discuss.

B) Can also take more tutorial courses based on interest.

Year 2-

Fall: A) outreach activity on topic of interest: must reach people outside college/ university setting (K-12 activity/ presentation, or public presentation, or something else). Use creativity, and present something in a way people not in the field (e.g., your grandmother) will understand.

B) Can also take more tutorial courses based on interest.

Spring: grant-preparation class, like that currently offered in UPGG? Good timing for DDIG or NRSA prep, since due in fall of year 3.

Year 3- Fall and Spring: A) Each semester, student identifies a "mentor" besides their advisor and meets with them for an hour every other week to talk about the job and maybe "witness" parts. This type of mentorship currently happens in J Reynolds' class on college teaching. Preferably, one of two semesters, student identifies someone NOT in the department to take on this role (med school, teaching position, industry, government, etc).

B) Take Bio308 course on career options (good place to find people who could be mentors, half-semester, 1 hr/ week)


  1. Year 2 Fall: "present something in a way people not in the field will understand" might also be phrased "present something in a way people in the field will NOT understand..." That's actually the way I read it the first time!

    I didn't see "take your science writer to lunch," but this is an excellent start!

  2. Awesome- thanks, Karl! I added a quick parenthetical clarification. And definitely on taking the science writer to lunch, especially if his initials are KLB... :-)

  3. Year 3 spring - student identifies a mentor besides their advisor and meets to talk about job, and also how project is going.

    I really like that idea because I could have (and still could now) benefit from more structured and more diverse mentoring.

  4. After looking over your proposal for a revamp of the Ph.D. program, I had a few comments. I'm an ecology student, rather than pure biology, but I think your proposal gets more at the nature of a Ph.D. program in general and is not specific to biology necessarily. In general, I think this sort of revamp would be extremely valuable and would set Duke apart as a forward-looking program with more value to potential applicants.

    As we saw from one of the presenters in the "options after grad school" class, the number of people pursuing purely academic careers is declining. As more and more people seek a Ph.D. as a stepping stone to other careers outside of academia, a "skills-based" program like the one you describe will be increasingly valuable. In your blog post, you raised the question of whether the traditional system is even an efficient way to prepare people for academia, let alone other careers.

    As someone who is not interested in staying in academia professionally, I would love to see a program that incorporates skills, such as grant writing and communication, that translate to other disciplines. I'd also like to see more opportunities to connect with people outside of academia, and I think your ideas for outreach activities and mentorships could be good here.

    The idea for having classes based on skills, such as statistics or programming, is great. This is why I take classes now. As far as subject matter goes, I figure that I can usually get the relevant papers, ask some colleagues, and figure things out. Being able to learn new subject matter independently is, in my limited experience, a big part of success in any field, academic or otherwise.

    To your list of "tools" classes, I might add some opportunity to learn science outreach skills. Its great to require science outreach activities, but I think some training beforehand could go a long way towards improving these outreach experiences for all parties involved. Give students solid outreach skills before sending them out into the world. As an example, I do monthly science workshops with home school students that are all about third-grade age. I've had other Ph.D. students in the program describe their research, to third graders, using terms so technical that I don't understand them. It is (surprisingly) not obvious to everyone that scientific jargon is not lingua franca.

    Lastly, I like the idea of having more student-directed coursework, but I wonder how many students have developed sufficiently specific interests by their first semester in graduate school. You could argue that pushing students to engage specific topics could help them clarify early on where their interests may lie.

    In short, your proposal is full of great ideas. I think academic training is facing a sea change. The waves are going to crash, and institutions can either try to swim against them or ride the wave of the future (or some other less goofy metaphor).

  5. I enjoyed reading the crazy idea! I always grow tired of the excuse "well that's the way we've always done things," and I really appreciate that efforts are made to be progressive and suggest changes, even if they are not ultimately accepted. For me, one of the best things about being a Duke BioGrad has been how willing most of the professors are at helping new graduate students adjust to the academic life, even if they're not my advisor.

    I think many graduate students, especially those who would prefer to stay in the academic sector, would absolutely take 1 week out of multiple semesters to learn the tricks of the trade as you presented them. Some of the topics, such as grant writing, when to publish, looking for jobs, were touched upon in my version of the Grad 101 class but focusing on them for a whole semester, from folks who have Been There, would be priceless!

    I really like the idea of having a general programming/statistics course available for BioGrads, taught by professors who know what kinds of tools we're actually going to need. While I grew a lot as a graduate student by teaching these things to myself, such a jumpstart early on would have been very valuable. In my Systematics course, two entire weeks were spent getting the students up to speed on basic UNIX commands and Bayesian statistics; if the students had this experience prior to taking the course, there could have been more focus on material.

    I agree that graduate level knowledge needs to be disseminated in a form that is very different from the monotonous lecture. I got good experience from discussing primary literature in a few of the courses I took. However, I still believe traditional coursework holds tremendous value, at least it did for me.

    For example, one of the best courses I took as a graduate student was the Systematics course. It combined all the best things about lecture, discussing papers, and hands-on experience. We got to see how to use/troubleshoot/critique the tools developed by others to implement the theory we were learning. "Statistical Programming in R and Python" was similarly outstanding, because of the combination of theory and implementation. If I would have one complaint about the graduate level classes, it's that nothing similar exists for Population Genetics (the theory behind and how to use IM, Migrate, Structure, etc). It would be a shame if these types of courses were de-emphasized.

    I know that we're a broad department and what I said won't apply to everyone. If I were starting grad school over with the changes you suggested I would have taken advantage of most, if not all of them!

  6. Agreed, classes are often an inefficient use of time, and agreed, tutorials can be the sweet spot between independent study and classroom courses. But the success of a tutorial is highly variable, in my experience, and I'd encourage us (faculty and students) to come up with guidelines for how to structure a tutorial most effectively, especially if tutorials are going to become a big part of the program.

    For example, do we have skill-oriented learning objectives for biology PhD students? We might want to structure the tutorials to help students develop those skills. For example, not everyone will come into a PhD program already able to skim the literature efficiently for breadth or to quickly answer a specific question. Maybe we think it's important to develop students' ability to synthesize literature at the graduate level, either as background for planning a research project or as the meat of a paper. And what about developing skills in writing for scientific and lay audiences, with emphasis on both the process and the content of writing? A little attention to these skills early in a PhD students' degree could go a long way.

    One structuring element in tutorials could be a course contract among the students and faculty in a tutorial -- a document unique to each tutorial that lays out students' learning objectives, the ways that students and faculty plan to contribute to the tutorial, a tentative syllabus of readings and activities, and a statement of how this syllabus might change during the semester to accommodate developing interests. Revisiting this contract periodically could help keep everyone on track to achieve the stated objectives.

    One nit-picky comment, re: Year 1 spring -- surely you don't mean for students to *grade* their peers (i.e., friends). Does that ever work? Peer feedback, absolutely! But in my experience, grading takes all the utility and honesty out of that feedback. Otherwise, I very much like the active journal clubs you envision.

    And, finally, the explicit requirement for an outreach activity is great, especially if we allow students flexibility in how and when they fulfill this requirement.

  7. I think this restructuring would work very well for most students, and I especially like the idea of focusing on "tools" classes in the first year of grad school, with only one caveat: students may need to acquire more tools than one semester could afford.

    Does this mean we could someday have a statistics course at Duke?!

  8. I agree with most of what's been commented above and like the suggested changes.

    However, I learned so much from regular classes like Speciation and anything I took from Mark Rausher (i.e. classes that introduce students to questions in their field). I wouldn't call those useless and it would be a shame if they were replaced.

  9. Hi, all,

    Thanks for the comments so far- these are great! Let me clarify a few things:

    1) Despite my somewhat mocking tone and sweeping generalization, I don't think "normal" grad classes need to be eliminated. Certainly, there are some that are both good in quality and for which there is demand, and those are obviously not something to be sacrificed. However, my thought was to make such formal classes less of the "default", where less formal but more individualized (smaller-group, directed discussions/ paper-readings, where groups of 2-5 students suggest the theme rather than faculty member dictate it in advance) may be made more obviously available and encouraged. I like Alison's idea about an advance contract for these tutorials.

    2) The exact timing for anything here need not be dictated- obviously, people will discover tools they wish to learn after semester 1, and should not be prevented from doing so. The idea was to emphasize tools in semester 1 so as to open the most doors for things like Matt discussed.

    3) The grant-writing class at this time is (to my knowledge) just a hypothesis... no one has stepped up saying they're willing to teach the class, but Sonke has been pursuing that. One possibility may be to have the first lecture portion partner with the current UPGG and MGM grant-writing class, and then split off (UPGG and MGM do this already), but I have no idea if the associated instructor(s) would agree to that. But it does seem like something for which there is both need and interest, so it deserves to be pursued!

    Thanks again, all, these are great and helpful comments!!!

    Best wishes, Mohamed

  10. Totally agree with you! One of my favorite quotes is: "Give a man a fish and he'll eat for a day. Teach him how to fish and he'll eat as long as there are fish in the pool. But design a training program that helps him learn how to stock and manage his pool, and there is no telling how far he might go"
    Give learners something real, give them the tools then shove them out there to solve real problems - that is how humans and individuals develop to better themselves, their communities and the world!

  11. I am a 5th year mol. biology PhD student at a large school in the south. I have two thoughts/observations:

    1) The alternate mentor idea is a great one. I think that having regular feedback from someone besides the PI is critical, and I haven't heard of it anywhere, really. But an important part of that should be simply based on graduation goal-setting. That is, this is what the department and your committee expects, this is where you are, this is when you want to be done . . . a sort of progress report and pacing advisor. It's so simple, but so rare.

    2) This scheme as laid out still seems too academic-job based to me. It is a step in the right direction for more well-rounded students, but I think it could go farther. We have already integrated optional job training, mandatory teaching training and mandatory presentation/grant writing/journal club aspects at my school. It doesn't deal with the fact that there's 13 of us for every "traditional" job, though. Really train people in other avenues, or we will continue to have frustrated, sulky post-docs-for-life.

  12. I think that this is a fantastic idea, particularly with regard to year 3 and the identification of a mentor. From my own experience, and I am guessing that others can relate, there is not a lot of valuable interaction with faculty other than your PI (except for committees, which often does not lead to any real career advice anyway). When it comes time to gather referrals and recommendation letters, being familiar with more faculty members and, in turn, having them be more familiar with you, can only be productive.

    Thanks for posting and I hope that your implementation and execution are successful.

  13. Seems reasonable, although the enterprising student can initiate discussion groups and find most of these things on their own if they want. The graduate school, OIT, and various student groups already sponsor various workshops on public speaking, grant writing, teaching, and other job skills. Still, I'm always surprised by how few people take advantage of these opportunities, and if they were presented as a roadmap recommended by the department, more people might engage in them. I am strongly opposed to making any of these course requirements, however. Grad students should have the freedom to plot their own courses through grad school, and the support to seek help when desired.

  14. Great idea, Mohamed! I would be happy to talk with you about how we could tailor Bio390 to better suit the needs of our graduate students. Also, if another faculty member was willing to teach the grant writing course, I would be happy to help facilitate the writing workshops!

  15. For a long time, I have been keen on the idea of organizing PhD programs around training skills that we would like people to have when they graduate with a PhD. I like many of the ideas above. Currently, training in many skills varies from lab to lab: For example, I personally feel very well-prepared in terms of grant-writing, but I see the need for a broader-access training approach.

    One topic not discussed yet is research training. I personally would have benefited greatly from explicit training on being effective and efficient at carrying out a large research program. This is an area that many might expect to be the purview of the labs we are part of -- but, again, training varies from lab to lab, and having departmental support and guidance could be useful in helping students finish successfully and in a timely manner. Potential topics of discussion that would have been very useful to me:

    -How to come up with a *starting* question as a new grad student (which will, of course, be very different from the final core questions of your dissertation). What is a sufficient starting question to get going?

    -Collecting initial data. What does it mean to do a pilot study? (How are pilot studies different from "real" studies?)

    -Striking a balance between thinking/background research with doing (labwork/field observations/insert appropriate activity for your field)

    -Balancing interesting questions with reasonable methods. Where will the funding for your project come from? What does it take to create a new method? What are the trade-offs when you embark on a project with a method that no one around you uses? How can you figure out whether it is worth embarking on the project when you don't have a working method yet?

    Some students currently receive excellent training in these areas, I assume, but not everyone does. (It may be a particular challenge in the ecology end of the spectrum where I am, where rotations are difficult.) In this vein, I think it would be highly useful to have a first semester course or workshop geared at

    -writing fellowship proposals (in my mind, everyone should submit an NSF pre-doc or equivalent in the fall of their first year, unless they already have one, and writing them together as a cohort would be extremely valuable).
    -making a research plan for the first summer. What are realistic goals for the summer? Where will you be? What do you need to do ahead of time to get something out of it? How will it be paid for? How do you see this work fitting into your dissertation trajectory? (I had trouble planning for summers while I took classes during the school year, and I wasted several of them.)
    -writing small grant proposals for summer research (many are due in December and January, and it's good practice even if your lab is flush with funds).

    This course/workshop could easily integrate a number of the discussion topics I mentioned initially.

    In the "tools" end of the spectrum, I would encourage early statistical training specifically that is well-integrated with experimental design. It may be some time before students are analyzing their data, but they should start collecting it soon. So, how will you set up your experiments so that they can be analysed well?

    Also, I particularly agree with jtotheizzoe's point #1 re: checking in on graduation goals.

  16. A grant writing course : I am in strong favor of this. Many grad students in DukeBio are in strong favor of it as well. I know since I’ve explicitly asked them about it, and I’ve mentioned our inclinations to Sonke, who appears to be leaning towards it as well. However, having the course held in Spring 2nd semester would mean that no formal training is given for people applying to the GRFP in early first/second years.

    Suggestion : A 4 hour mini course on GRFP strategy, objectives, and assessment criteria, given in the first 2 weeks of the Fall semester.

    The presentation MUST be given by someone with explicit and thorough knowledge about GRFP evaluation criteria. This doesn’t have to be a program officer, but it must be someone who has fully understood what program officers and evaluators want. We’ve had too many students apply fully without understanding disqualifying criteria, or having some misconceptions about sections of the applications. Again this is information based on conversations I’ve had with grad students. This is several weeks of combined student time that could have been more focused and efficient.

    A clear cut, concise information session, even something as short as 2 hours worth, will be invaluable to first years already focusing on content. Our Biograds are, based on my discussions with them, generally lacking in formal assistance for attacking the process. Given our successes with the GRFP, I think we could get a great ROI as it were, with a bit of time investment.

    Does it work? : A five year trend analysis can be done for success rates before and during the 5 year period, for the efficacy nuts out there.
    The time investment would be a small price to pay for even an average 1+ /year improvement in GRFP apps.

    The second year spring course should also be available to any second year who finishes their prelims early, but herein lies the catch : a second year who finishes their prelims early may not benefit from such a professional development course. If this “early bird” wants to apply for a DDIG, they will have one year of not having professional development support. So I propose moving an explicit grant writing course to the first semester of second year. There’s another reason for this : serious work on the grant writing course will mean students will have to focus their minds on what their long term projects are, and defend their thinking to a group of people, like they have to in UPGG. Such an experience is invaluable. It also helps any second years who are “early birds” and want to apply for a DDIG.

    I commend you for dedicating time and energy to improving how our department goes about things. If I have not explained myself well, please tell me, I will clarify.

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  18. From Carl:

    Thanks, Mohammed, for taking the initiative on this subject! I think it is generally under-appreciated by faculty. Most of my thoughts/concerns have already been addressed by previous comments, but I have a few additional twists to offer on some of them.
    First, I think you are right on in your list of five skills that aren't taught well. However, fixing this problem may be harder than it looks.
    1) grant-writing: this is a widely useful skill that is transferable to other fields.
    2) running a lab: many faculty aren't particularly good at this, so who should teach it?
    3) developing and giving lectures: same comment as #2. In addition, this assumes that people want to be professors, in direct contradiction to point #5.
    4) outreach: same comment as #2. Outreach is important, but innate ability varies widely. Training is great, but identifying skilled public communicators and encouraging them may be even more important.
    5) career options besides becoming a clone of their PhD advisor: Many professors are actively hostile to this possibility.

    As far as what to do in the first semester, GRFP writing would 1) begin to teach grant writing skills, 2) help with cohort bonding, and ideally, 3) lead to more students with cushy fellowships.
    Beyond this, I'd be very hesitant to require anything. One reason I came to Duke was the complete lack of course requirements. I took whatever I thought I needed.
    The tools course sounds useful, but runs the risk of becoming all things to all people. Of the three skills listed, one is not useful to me (Matlab), another I do frequently (programming), but choosing a common language would be tricky, and statistics is obviously useful to everyone. We do, in fact have nearly a dozen courses offered at by the stats department at Duke. But they are taught by Bayesian fundamentalists, and are too theoretical for most biograds' needs.
    The third year 'outside mentor' would be a good idea for most students. I've had no problem at all networking outside of academic science, and more than anything, students just need assurance on how easy this can be to do.
    Thanks again for taking on this task! If you act on what students really want, rather than what professors want to give them, then this effort will certainly be productive.

  19. Interesting link from Laurie:

  20. Comments from Michael Wade (Indiana):

    Provocative ideas! There are several types of 'tools of the trade' that students need to acquire. There are the tools of science, like statistics, experimental design and data analysis. I believe these are best learned by a combination of traditional in-class statistics/probability theory lectures (with exercises) and a project-based field course. For biostats, there is growing pressure to separate experimental design and data analysis away from informatics and gene/genomic sequence data analysis. There are also the tools of science practice, grant writing, lab management, ethics, paper writing, paper reviewing etc. Some mentors do this brilliantly for their own students while other students are left to absorb these on their own by watching others. Organized courses focused on applications for NSF preDocs/NSF DDIG tend to work very well, especially when all students participate. The tools of outreach, science-education, etc., are somewhat harder to actively 'teach', although some of my evolution students have discovered the option of doing their minor in science education (instead of, say ecology).

    A Careers in Biology lecture series can be great for exposure to a wider range of career paths than might be familiar to the faculty. it is important though that students participate beyond a single semester and speakers feel welcomed by students and by faculty. In practice, this means setting aside some decent funding for extra-seminar meals, reception, and discussions, comparable to that for research seminars with outside speakers.

    Basically, if the faculty see themselves as stewards of enormous raw talent, the program will be good. If the faculty see students as 'hands for my lab,' 'data producing machines,' or some other kind of 'academic fodder,' the program will not be very good--some might survive it and even go on to careers, but even the best will not feel that their talent is getting developed in a unique way.

    It is very challenging to have one program for a group of students, each of whom is unique in drive, ability, and interests.