GUIDELINES FOR THE Ph.D. QUALIFYING EXAMINATION
DEPARTMENT OF MICROBIOLOGY GRADUATE TRAINING PROGRAM
UNIVERSITY OF ALABAMA AT BIRMINGHAM
Each student will be expected to pass, before the beginning of the third year of full-time graduate study, an examination which leads to partial fulfillment of qualification for admission to candidacy for the Ph.D. degree. This exam consists of a written proposal of an experimental approach to test an original hypothesis in an area of biological research, followed by an oral defense of the proposal which will include an examination on general scientific background.
The main purposes of the qualifying examination are to help train students to function as successful scientists, to help in the evaluation of their academic progress, and, when needed, to provide a mechanism for strengthening skills and/or basic scientific background. During the examination the student will have an opportunity to put together ideas and hypotheses, to express these ideas in writing and to defend them orally. The student should expect and appreciate criticism of his/her research proposition and should accept the challenge of the exam as a valuable aspect of the learning experience and preparation as a research scientist.
The performance on this qualifying examination will be judged acceptable if the Microbiology Graduate Faculty is assured that the student can:
1) develop and originate a critical approach to a scientific problem by:
a) envisaging a significant, original hypothesis and formulating a practical experimental approach to its solution;
b) expressing this research problem concisely in writing;
c) presenting and defending these ideas orally in an effective manner before a selected examining group.
2) demonstrate a sufficiency of basic background information.
procedural guidelines and TIMETABLE
Please see the following web pages for specific guidelines for the current proposition examination:
http://www.microbio.uab.edu/QualifyingTopics/Proposition.htm
http://www.microbio.uab.edu/QualifyingTopics/timetable.htm
selection of topic and submission of the abstract
Topics may be formulated independently by the student after consultation with faculty, research mentors, senior students, or the proposition coordinators. The topic should not be based on an ongoing project (NIH, NSF, Cancer Center, etc.) developed by any faculty member on campus and furthermore cannot be a direct or obvious extension of past and present studies in the laboratory of the advisor. This is not to say that students will not be allowed to do a proposition in the general area of their own proposed research. For example, a student who has joined a laboratory that studies bacterial pathogenesis may certainly offer a proposal in this general area. If, during development of the hypothesis, the student has any questions regarding potential overlap of the proposal with his/her lab, the student should approach the faculty proposition coordinator, who will make the final decision regarding unacceptable overlap after discussions with the student's mentor and the Microbiology Graduate Committee.
The student’s advisor may play no role in developing the hypothesis or writing either the abstract or the proposition. Both advisor and student must consider themselves on a strict honor system in this regard. On the other hand, it is important that students understand from the outset that although they must originate and develop the hypothesis themselves as well as design the experiments to test it, they are encouraged and even advised to discuss their ideas with other students, postdocs, and faculty (with the exception of the mentor). In particular, it is strongly recommended that the students seek critical editorial help in the preparation of the written proposal- good sources of advice in this respect are advanced students who have already been through the procedure.
The Abstract should:
1) 1) state a significant1 and original2 problem;
2) state a testable hypothesis3;
3) be a logical. understandable, clear and concise statement of the problem, hypothesis and experimental design required to test the hypothesis. It should be in acceptable scientific prose and free from jargon and excessive abbreviations.
The entire abstract package will be 3 pages in length: one page abstract approval form (see below), one page with the title, student name and abstract (single spaced, 1 inch margins, 12 pt. Arial or Helvetica), and one page of essential complete references (title, all authors). The abstract should propose a project of approximately one-year’s duration. A hard copy of the abstract package should be delivered to Debbie Sirles on or before 5PM on the deadline date. The abstract and references (pages 2 and 3) should also be emailed.
1"Significant" implies that the problem chosen for investigation would appreciably advance knowledge in a specific area of research. In other words, the planned study should not be a small step forward, a trivial "mop up" of existing phenomenology, or a repetition of experiments done with one organism in another, etc.
2"Original" implies that the problem proposed for study has not been previously adequately studied or that the proposed hypothesis has not been previously formulated (in a grant or paper available to the student) and that the proposed experimental approach uses methodologies and/or systems that have not been used to study the problem.
3"Testable" implies that methods and procedures needed for the research can be worked out and the appropriate experiments conducted in a reasonable period of time; this does not mean that all methods and/or procedures be already worked out at the time the proposition is written. An "hypothesis" is a positive statement of assumption, whereas a "null hypothesis" is a negative statement of assumption. Therefore a "look-see", "either-or" or "whether if" investigation does not contain a hypothesis. Clearly, the testability of a hypothesis requires that the proposed experiments be able to differentiate between the correctness or incorrectness of the hypothesis and to reveal the correctness of alternative hypotheses that could have been proposed based on existing knowledge at the time the proposition is written.
The student must submit the abstract to three faculty members who will sign the Abstract Approval Form (available at http://www.microbio.uab.edu/QualifyingTopics/Approval%20form.doc). The abstracts will be approved based on originality as well as overall feasibility. At least one of these 3 faculty must have an appointment in the Department of Microbiology. If a student elects to have a member of the secondary faculty fulfill this requirement, he/she must obtain approval to do this from the proposition coordinator prior to submission of the signed abstract. The student's advisor must also sign the Abstract Approval Form to certify that there is no overlap of the proposal with an ongoing or previous project of the mentor's laboratory (or logical extension of such a project) and that the mentor did not communicate to the student in any way the hypothesis or the experiments to test it.
It is paramount that students do not wait until shortly before the submission deadline to seek abstract approval. This approach will in almost every case result in the student missing the abstract submission deadline, since many faculty will either ask the student to revise the abstract, will not approve the abstract, will be unavailable, or will be unable to read it immediately because of other commitments. The worst possible outcome would be for a sympathetic faculty member to hurriedly sign the abstract without being aware of obvious flaws in design until after the proposal is submitted. It is unacceptable for the student to pressure the faculty into signing the abstract because the deadline is at hand. Inadequacy in any one area will be sufficient grounds for faculty to decline to approve an abstract. The students are responsible for finding the appropriate faculty to sign their abstracts; i.e., the relevant faculty members who are sufficiently knowledgeable in the given area of the topic. Although approval of the abstract in no way guarantees that the final proposal will be satisfactory, careful appraisal of the abstract by the faculty and detailed discussions with the student should greatly improve the chances of a favorable outcome.
In the rare instance that the student cannot obtain approval for the abstract from 3 faculty by the deadline date, then the abstract approval form must be turned in on time bearing faculty signatures, with a "seen by only" notation from any faculty members who have withheld approval. The student can then have up to one additional week to obtain full abstract approval. However, this one week grace period in no way alters the deadline date for the submission of the full proposal.
Example proposals
The list below provides links to three example proposals that were prepared by Microbiology Students in fulfillment of the choce of topic, abstract, and written proposal requiremnts of their qualifying exams:
Sample 1. Characterization of Streptomyces coelicolor A3(2) σT regulation in response to oxidative stresses
Sample 2. Nod2 regulation of cryptidin expression in Paneth cells
written proposal
The full written proposition must be turned in by the designated deadline date http://www.microbio.uab.edu/QualifyingTopics/timetable.htm. Failure to do so constitutes failure, i.e., disapproval of the proposition.
Format
The final proposition should contain a copy of the original approved abstract and a title page with the student’s and mentor’s names. The remainder of the proposition should follow the topic headings outlined below (according to NRSA guidelines). It may also be helpful to review the NIH RO1 sample application. The sections encompassing the Research Plan (Specific Aims, Background and Significance, Research Design and Methods, and Literature Cited) may be especially helpful. (A section on Preliminary Results is NOT required for your written proposal.) The proposal should be written as an approximately 1-year project for 1 investigator and 1 technician.
Research Plan: Organize sections A-C of the Research Plan to answer these questions:
(A) What do you intend to do?
(B) Why is the work important?
(C) How are you going to do the work?
Do not exceed 10 single-spaced pages for Sections A-C.
A. Specific Aim(s). State the overall objective and describe concisely and realistically what the specific research described in this application is intended to accomplish and any hypotheses to be tested. (1/2 to one page)
B. Background and Significance. Briefly sketch the background to the present proposal, critically evaluate existing knowledge, and specifically identify the gaps which the project is intended to fill. State concisely the importance of the research described in this application by relating the specific aims to the broad, long-term objectives. Briefly indicate how the experiments proposed will allow you to realize the Specific Aims. (~ 3 pages)
C. Experimental Design and Methods. Outline the experimental design and the procedures to be used to accomplish the specific aims of the project. Make the distinction between description of the proposed experiments and statement of methods. Include the means by which the data will be collected, analyzed and interpreted. Indicate explicitly how the results obtained will fulfill the specific aims. Describe any new methodology and its advantage over existing methodologies. Discuss the potential difficulties and limitations of the proposed procedures and alternative approaches to achieve the aims. Point out any procedures, situations or materials that may be hazardous to personnel and the precautions to be exercised. (~ 6 pages)
The Anticipated Results section of the previous proposition format has been eliminated. However, for your benefit, it is important that you are aware of what was previously requested in this section, since you will be expected to provide this information during the oral examination. Briefly, examples were provided, in the form of figures, diagrams, and tables, of the types of results expected from each of the essential experiments; the purpose of each experiment, and the conclusions to be drawn, were described.
One hard copy and an electronic version of the proposal should be submitted to Debbie Sirles. After submission, the proposition coordinators will send the proposal to three faculty members for review. Upon approval of the written proposition, the student will then move on to the Oral Defense.
oral defense
The oral exam constitutes the second component of the Qualifying Examination in the Department of Microbiology. The oral component is an extension of the written proposal. Through appropriate questioning by the faculty, the student is expected to be able to further demonstrate his/her:
a) defense of the written critique of the proposition
b) ability to analyze and solve experimental problems
c) breadth and depth of knowledge in molecular cell biology
A passing grade results from an approved proposal as well as a satisfactory oral defense. If the student fails the oral exam, a retake can be arranged after a short waiting period, if the examining committee feels that this is an appropriate course.
The proposition coordinators will assign the members of the oral exam and designate one member of the committee to serve as chairperson. The student will be responsible for working with their committee chairperson and committee members to schedule the date of their oral defense, which should occur sometime prior to the end of December. The student will receive the critiques of their written proposition one week prior to their oral defense. The oral examination committee will consist of a minimum of 3 faculty; in some cases the proposition coordinator may deem it necessary to include a 4th member so that all aspects of the proposal are adequately examined. The exam will allow the student to verbally defend the critiques as well as demonstrate sufficient intellectual background for passing the exam and will generally last for about 2 hours. Final evaluation of the oral exam consists of PASS or FAIL and shall be determined by the oral exam committee.
During the Oral Exam the student should:
1) Present a clear and concise thirty-minute summary, clarification or development of his/her proposition, and a response to all comments made by the reviewers of the written proposition. (The precise nature of this introduction will be left to the student although it should not be a verbal recitation or recapitulation of the written proposition. Use of the board is strongly encouraged.);
2) Defend the proposition with concise and effective answers to questions;
3) Demonstrate ability to utilize the board effectively to graphically describe experimental protocols, expected results, etc.;
4) Demonstrate sufficiency of basic background information.
The exact format for the oral exam will be left up to the chairperson of the examining committee, but generally proceeds as follows: after the student's presentation, there are 2 or 3 rounds of questions with each examiner limited to 10 or 15 minutes per round. The first round usually deals specifically with the hypothesis and the experimental methods and procedures proposed to test it. The second round of questions should deal with alternative interpretations of existing literature upon which the proposition was based and/or alternative (or more likely) hypotheses that the student could have proposed, alternative results to be expected from the proposed experiments, and potential problems in conducting the proposed research. The third round of questions should deal with general background information.
If at earlier stages in the examination procedure (i.e., abstract or written proposal) the student did not develop the best approach to test the hypothesis, he/she has the opportunity to present more refined and/or better ways of doing so during the oral exam, either in the opening presentation or in responses to questions. All written critiques of the reviewers should be addressed in the oral examination.
The committee will meet in closed session at the end of the oral examination to decide if the student has passed the qualifying exam and to make any recommendations for the student's future training. The following levels of passing and failing will be recognized and recommended by the examining committee to the Graduate committee:
1) Pass without qualifications
2) Incomplete: will be converted to a pass if/when specific requirement(s) recommended by the examining committee for meeting deficiencies are fulfilled OR will be converted to a fail if requirements are not fulfilled
3) Failure of the examination
The student will be told immediately of the committee's decision. The chairman of the oral examination committee will complete the evaluation form and submit it to the proposition coordinator.
A passing grade on the examination will entitle the student to initiate the selection of a dissertation committee and to formally apply for admission to candidacy for the Ph.D. degree.
Students receiving the incomplete grade will be given assignments for meeting deficiencies, as for example:
a) re-defense of the same proposition
b) additional coursework to supplement scientific background
consequences of failure of the examination
Action subsequent to failure of the examination will be determined in discussions with the student, the student's advisor, and the Microbiology Graduate Committee. In general, the policy of the Department of Microbiology has been to allow one failure. However, depending upon individual circumstances, the Graduate Committee reserves the right to request termination of students who fail the first examination.
Return to Qualifying Exam Home Page
Updated November 15, 2007