MCDB Graduate Student Handbook
a. Purpose of the Independent Research Proposal. The purpose of the Independent Research Proposal is twofold: first, to test your ability to identify an important question or problem in contemporary biology; and second, to test your ability to formulate reasonable experimental approaches to advancing our understanding of that problem. This is the very essence of what you must do as an independent research scientist, and we want to be sure you are developing these skills. You will be evaluated on both counts. An important question in biology is not necessarily identical to what is currently "hot" in biology. An important question is one which, when answered, will advance in a fundamental way our knowledge not only of the immediate question under consideration, but of related biological questions as well. Keep this in mind when selecting your proposal topic --- be aware of what is going on in related areas of biological research, and how what you propose to do will relate to these other areas.
A typed copy of your 10-15 page oral proposal in its final form must be distributed to each Committee member one week before the scheduled examination date. Committee members may refuse to consider a proposal submitted after this time, necessitating cancellation and rescheduling of the Oral Examination.
b. Selecting a Topic. You should begin thinking about a proposal topic by the beginning of your second year in residence. In MCDB, the topic of the proposal must be outside the immediate research interests of the lab in which you are working. To the extent that you present a proposal based on what is going on in your lab, your thinking will unavoidably have been strongly influenced by your advisor and other members of the laboratory.
You may not discuss details of your proposal with members of your Doctoral committee, including your thesis advisor. However, it is appropriate for you to consult your advisor or members of your committee about the suitability of a particular topic for your proposal. Moreover, once you select a topic, you are perfectly free to seek as much information about that topic as you want, from as many people as you want (except your Committee). Part of developing your skills as a scientist is learning to seek out information, to talk with people about ideas, and to discuss science. You will almost certainly get different opinions and answers from different people, so in the end what you propose will have to be your own unique synthesis of all the various inputs you obtain.
c. Writing the Proposal. There are no specific rules about the format of the written proposal, or its length; however, doctoral committees generally prefer proposals of 10-15 pages. Some students use the general organizational scheme of a scientific paper as a guide; others use the suggested NIH R01 format for research grant proposals. Check with your advisor about the exact format you should use. Be aware that a well-written proposal makes a good impression on your committee. Have someone whose writing skills you trust go over it to check organization and clarity. State clearly, at the very beginning of your proposal (which must be typed and double spaced), the question you wish to address. In an Introduction Section, summarize the existing literature relevant to this problem. In a separate Experimental Section, describe the experiments you propose to carry out to investigate this problem. Remember that all experiments ultimately derive from an idea the investigator has about a likely explanation of an existing question. This is called the WORKING HYPOTHESIS. STATE VERY CLEARLY, YOUR WORKING HYPOTHESIS AT THE BEGINNING OF THE EXPERIMENTAL SECTION, so that your Committee will be able to follow the logic of your experimental plan. In most instances, it is sufficient to propose no more than three or four well thought out, well-designed experiments. However, you should communicate clearly in your proposal exactly what each experiment is intended to show, and you should be able to explain what any imagined outcome of each experiment would mean. Be sure to discuss any controls needed to clarify experimental outcomes.
It is also a good idea to practice presenting your proposal, as you approach the final stages of preparation, to a group of senior graduate students or post-docs. Encourage them to be as critical as possible; try to identify the weak points in your proposal before you distribute it to your Committee.
While it is impossible not to be nervous going into your oral exam, most students find they loosen up and start to relax 20-30 minutes or so into the session. Perhaps as much as anything else, this portion of the oral exam is a test of your ability to communicate effectively as a scientist, both verbally and in writing. In the best cases, the "exam" becomes an interesting and stimulating discussion among scientific colleagues, with plenty of give and take, and lots of exploration of tangential issues.