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  Comprehensive Exams FAQ

Golden Rule : This is a compilation of guidelines and advice; it is not Departmental policy. Official policy is found in the Departmental Guide to Graduate Studies. When in doubt, ask a knowledgeable source: your Ph.D. mentor, the chair of your comprehensive exam committee, or even the Director of Graduate Studies. This is only a guide to frequently asked questions; every comprehensive exam committee operates somewhat differently, so don’t assume that the experiences of another graduate student apply to your situation.

A. Choosing a committee.

  1. Who should I choose? Keep in mind that your comprehensive exam committee most often forms the core of your thesis committee. So, choose individuals that you think will give you sound advise and direction during your graduate career. You may want to consider the breadth of what you will be doing and see if there is an area where your mentor has less experience and a committee member can offer expert advice regarding this aspect of a thesis.
  2. Who should I NOT choose? Now that’s a hard question. You may think twice if committee members offer the same strengths. You do not want to avoid a faculty member as a potential committee member just because you think s/he will be a “hard” committee member (asking you tough questions and such). Keep in mind that every faculty member in this Department wants our students to succeed, and to complete the highest quality thesis possible.
  3. How many committee members do I have? There are three members of your comprehensive exam committee; your mentor is not a member of this committee.
  4. Why isn’t my mentor on the comprehensive exam committee? In the MCDB program, no. Your mentor is not present in the room, and may not even examine the document. In the EE program, mentors often sit in on the exam, but do not participate in the questioning.
  5. Who is chair of the committee? The chair of your thesis committee is your mentor. But the chair of your comprehensive exam committee is chosen by the Director of Graduate Studies. This person is ultimately responsible for ensuring that the topic approved by the committee is “do-able” and will set the ground rules for what is expected in the three topics you present, and how the examination is conducted.
  6. Who is on my thesis committee? There are typically five members of a thesis committee. Three of these are most often members of your comprehensive exam committee, since they have gained a good understanding of how you think about scientific problems. Your mentor is the fourth member, but s/he does not serve on the comprehensive exam committee. A fifth member of your thesis committee must come from outside of the Department. This person may come from outside of the University. Moreover, there is nothing that prevents you from including more than five members on your committee; this may be important if your thesis project is broad, and you would like the input of more than five people.

B. Choosing a topic.

  1. When should I start? Start early. Read papers and find topics that interest you. If its trendy, but doesn’t excite you so that you can not think deeply about it, don’t put time into it.
  2. What kind of topic do I choose? Just like in real estate, there is one watchword here: focus, focus, focus. A topic should not be too broad. If you are thinking “my topic will be about the regulation of cell division in organism X,” you are too broad. Projects should address some particular burning question that remains open, given the current literature.
  3. How do I write about the topic? Start by having a hypothesis. The topic should be asking a specific question, like “What is the role of protein Y in regulating cell division in organism X?” That is a focused project, with testable hypotheses and predictions that can be made. A broad description about some interesting area of science does not constitute an exam topic.
  4. Can I talk with my mentor? This will vary, but as a general rule usually only so far as to get broad advice. Most mentors will be glad to hear what your topics may be, and offer criticism like, “What specific question are you asking?” or “Is it feasible to work on this problem?” Mentors will typically take a hands-off stance and not critique your approaches or offer advise on how to design experiments or write the manuscript. That is up to you. This is a learning experience.
  5. Can I talk with others in my lab, or my fellow graduate students? A good guideline would be that such discussion are fine if they are broad. Asking, “do you think this topic is too narrow?” is just fine. Asking, “I think doing this experiment is not good; what would you do?” is not fine. All of the ideas in the proposal should be yours. Asking someone to read your manuscript is fine when the reader knows that they will be pointing out where they can’t follow your logic, or can’t understand why you are doing an experiment. Don’t expect readers to offer new experimental designs. If they do, question why you would take their advice; after all, by the time you write the proposal you should be the expert in this field.
  6. But what if I have questions about this topic? Read. If you cannot find answers in the literature, consider sending an email to the author of the paper asking them about the points you find confusing. Faculty members often get questions from other scientist regarding aspects of their work.

C. Writing the three proposals.

  1. What should be in the short proposals I have to write? First, keep them focused. The ideal proposal sketches the background of an issue, and leads the reader to a question that clearly must be answered to continue in this field. Your committee will want to ensure that you have chosen a topic where you can write a proposal that will work. No committee wants to send a student off to write a proposal that they know will fail.
  2. What do I include besides an outline of the topic? The steps taken to answer a question are usually encapsulated as “Specific Aims.” Some committees like to see Specific Aims in proposals; others are more flexible. But bear in mind that crafting your Specific Aims is half the battle in designing a good grant. So, in our example of like “What is the role of protein Y in regulating cell division in organism X?” the Specific Aims may be along the line of “1. To determine if Protein X controls transcription directly,” or “2. To determine if Protein X binds to Protein Y, thereby modulating its activity.” Notice that these are not experiments. Footprinting, two-hybrid screens, ChIP assays and such may be used to answer these questions, but these are the means by which Specific Aims are answered. An experiment is not an aim.
  3. So I don’t include any methods in my proposal? We didn’t say that. Committees may like to see some indication as to how the Specific Aims will be addressed. This will help the committee decided if the student is on a feasible track, and can complete the proposal. So, stating a Specific Aim of “To determine if Protein X binds to Protein Y, thereby modulating its activity,” may be expanded by stating, “this will be accomplished by a two-hybrid screen.”
  4. What about overlap with my project? You are supposed to choose a project that is not directly related to your thesis project. This ensures that the ideas contained in the proposal are your own, and also allows the student to expand their lines of thinking. Ideally, the process of writing your comprehensive exam will open you up to new and different ways of approaching scientific questions. Does that mean if you are working on yeast for your thesis you can’t ask any questions that involve yeast? No. But if your thesis is “The regulation of process X by post-translational means in yeast”, then a topic like “The regulation of process Y by post translational means in yeast” is likely to be deemed too close. And so would, “The regulation of process X in organism Y.” It is to your advantage to choose a topic that will help you think about science in a different way than you do for your thesis work. In this way the comprehensive exam serves to make the student a broad thinker.
  5. Which topic will be chosen of the three I submit? There is no way to predict this, but your committee will select a topic they believe you can complete successfully. You should be comfortable with all three topics you submit.
  6. Is it true that my committee may reject all three topics? This has been known to happen, usually if they are not well written or well developed (that is, if one cannot see how the question can be answered, or even what the proposed question is).

D. Writing the chosen proposal.

  1. Where do I start? Read, read, and read some more. Then read even more. Become an expert in your topic. You should have done a significant amount of reading to ask the initial question, but now you have to live and breathe it. This will give you perspective on what has been done, and how people have approached this field in the past. You should become familiar with the tools and techniques available to address your Specific Aims. To do this, make sure you read primary literature, not just review papers.
  2. What do I do with the Specific Aims? If you haven’t done so already, formulate the steps necessary to address your big question. Then divide and conquer. Devise experimental schemes to address each Specific Aim. When all is done, the results of the experiments should answer the big question you have chosen.
  3. Which experiments do I explain? I have more than one approach I could use. Good. Justify which tactic you think is best. Then devise alternative strategies. Make sure you have back-up plans, especially for risky experiments. Don’t assume everything will work. Think about what you would do if the results of an experiment tell you something that is in conflict with your hypothesis.
  4. Do I write about each Specific Aim separately? For my proposal, they are all inter-related. This is not good : don’t make the Specific Aims dependent on each other. This is a downfall of many grants. It should be rare that any of the experiments require specific outcomes from any of the other lines of experimentation. So, if Specific Aim 1 is to isolate the protein and determine if it binds DNA, don’t craft Specific Aims 2 and 3 so that they assume that it does indeed bind DNA, or even that the protein can be isolated. Each Specific Aim should provide an achievable route to answer a specific question or set of questions.
  5. Will my mentor read and comment on my proposal? Typically not. Don’t be surprised when your mentor takes the hands-off approach. S/he trusts your committee to guide you in this process. Most mentors will refuse to look at or to comment on your proposal.
  6. So who do I get to read it? Of course it is beneficial for someone to read your proposal and point out when things don’t make sense, or insufficient background is provided. Your peers in your second-year class are ideal candidates. Sometimes a more senior graduate student in your laboratory will be helpful. But in all cases, they will point out where you aren’t making sense. They shouldn’t (and most likely won’t) offer any suggestions as to what experiments to propose, or what back-up plans are best. They may say “well, what if the IP doesn’t work?” or “how many cells do you need to collect to extract RNA?” Comments like these point out areas of confusion. They won’t say “you’ll never get atomic force microscopy to work to assess binding; you should be doing a series of immunoprecipitations or maybe a yeast 2-hybrid screen.” It is your job to craft the Specific Aims and propose a feasible line of experimentation to answer the question.
  7. What if I find that fifteen pages is too short/too long? Well, if it seems too long, you aren’t doing your job. Typically, a single page is devoted to a quick outline of the problem and a short description of the specific aims, and maybe 4-5 pages are devoted to the background necessary both to educate the reader and to convince the reader that the question you propose to answer is a good one. The last 9-10 pages are dedicated to explaining how you will accomplish each specific aim. Since there are typically 3 Specific Aims, that leaves three pages each to describe the experiments, justify their approaches, explain how you will interpret any result you could get, and provide alternatives in case it doesn’t work anywhere along the line. If the document is short, you are not providing enough information. If the document is too long, trim it to make your prose more succinct and to-the-point.
  8. How much experimental detail should I include? Explain each experiment so that someone outside of the field can understand what hypothesis is being tested, what the results of the experiment may be, and why these results answer the question. Potential pitfalls, and comparisons of the strengths of your chosen method over others are good points to include. A detailed description of the buffers you will use is not useful. Include the information a reader needs to understand why the experiment is being done, and if it is likely to succeed.
  9. Can I read a real grant to get an idea as to how this is done? Absolutely. It’s a good idea to ask your mentor or one of your committee members if they could provide you with a copy of one of their funded grants. This will give you some insight as to how such a document is organized. But don’t expect a faculty member to provide you with a grant that is very close to your proposed topic. The purpose of examining a grant is to understand how to craft this complex document, not to gain ideas as to how to formulate your proposal.

E. The Oral Exam.

  1. What sort of presentation should I prepare? Every committee is different, and they will decide what sort of presentation they wish to hear, including its length, breadth and format. Most committees like to hear you speak about your proposal, so initially plan for about a 20-30 minute presentation. Some committees will ask you questions the whole time, and you will just get to your last slide when 2 hours have past by. Some committees sit and listen and then ask questions. DON’T prepare an 80-slide 60-minute talk. DON’T walk in and merely ask “So, any questions?”
  2. In terms of questions I could be asked, is everything really “fair game”? No, not really. The point of the oral examination is to determine if the student has thought about their proposal, why its important, and how it can go wrong. This is what you need to do as an independent investigator. They will also want to know how you think on your feet (rather than spouting pre-formed answers to obvious questions), and when you know that you don’t know the answer. There’s no shame in saying, “I don’t know that.” That is FAR better than making something up. It is unlikely that, out of the blue, some one will ask you “please draw all non Watson-Crick base-pairing interactions found in yeast tRNAs for me on the board; be sure to include all those involving modified bases as well.” But if you are proposing to examine tRNA folding, you should be aware of what kinds of interactions are common, what modified bases do, and be able to draw them if asked. In this case, such a question is fair.
  3. Is it true that everybody’s proposal is picked apart and I’m going to look stupid? Well those are two different things. Of course a committee of three well-trained scientists who have been writing grant proposals for years can find cracks in a grant written by a second year graduate student on a topic they have only been reading about for six months. If that weren’t true then either you should have a faculty position or your committee members shouldn’t have theirs. But keep in mind that there are holes is every grant; only about 10%-30% of grants sent to most study sections are ever funded, and most of those have been re-submitted after a committee has reviewed it and has found faults the first time around. But every proposal can serve as a platform for exploring how someone thinks about problems. That is what is important.
  4. I’m getting nervous even thinking out this; what if I panic? Don’t. You need to go into that room with a clear head. We only admit students we think will succeed. If you made it to the second year you can succeed. The only enemy you will even find in that room will be yourself. Your committee is there to make sure that you can think clearly and are prepared to go on with your dissertation research. They are not there to cull 25% of the second year class. Relax, know your topic, craft a proposal that addresses a topic and then think about the questions put to you. If you do that, you can’t fail. If you get so tied up that you can’t explain the difference between DNA and protein, then you have a problem. Just like a thesis defense, your committee doesn’t bother to gather and perform the examination if they don’t expect you to be able to pass. You just have to be prepared and show them that you know what you are talking about.

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