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JCGS Home > Academic
Programs > Ph.D. Programs > Biochemistry
and Molecular Biology > Program Rules
Rules Governing Graduate Students in the Biochemistry and Molecular Biology Program
(updated September, 2008)
General
Financial Support
Course Selection
Laboratory Rotations
Seminar Course
Research
Qualifying Examinations
Research Committees
Comprehensive Examination
Appendix I: Guidelines for Ph.D. thesis Proposals
Appendix II: Additional guidelines important for progression toward a thesis 1. GENERAL
The Jefferson College of Graduate Studies (JCGS) catalog explains the structure and rules that apply to students in all Ph.D. Programs. This document explains specific rules and requirements for Ph.D. students in the Biochemistry and Molecular Biology Program. It is the responsibility of each student to be aware of these requirements and to follow them. Failure to abide by these rules can lead to a student's dismissal from the Program. If questions arise about interpretation of the Program requirements below, the student should meet with the Ph.D. Program Director for resolution.
In addition to the regulations outlined by the Jefferson College of Graduate Studies, students in the Biochemistry and Molecular Biology Ph.D. program are expected to obtain a B or better in each of the required Biochemistry courses. These include GC550 (Foundations in Biomedical Sciences), BI525, BI535, PR613 and BI614. Failure to receive a B or better in GC550 will result in repeating all or part of the course. Failure to receive a B or better in other required biochemistry courses will be remediated in consultation with the Program Director and the Program Committee.
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2. FINANCIAL SUPPORT
All students accepted into the Ph.D. program are provided with financial support, except under special circumstances. All forms of financial support, i.e., fellowships, are for a twelve-month period. The choice of laboratory must be approved by the Program Director.
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3. COURSE SELECTION
Courses should be selected in consultation with the student's advisor and the Program Director. Prior to selection of a research laboratory, the Program Director will also serve as advisor. See the tables on the preceding page on Program Structure for a recommended course schedule.
M.D./Ph.D. students must consult with the Program Director regarding course requirements.
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4. LABORATORY ROTATIONS
Completion of three laboratory rotations is required for all first year Ph.D. students in the Biochemistry and Molecular Biology Program. In addition to providing students the opportunity to choose a thesis advisor, laboratory rotations serve as an introduction to different experimental systems and approaches and are an integral part of graduate training. The three laboratories selected should include the laboratories in which the student might consider doing thesis research. A fourth rotation may be elected during the first summer if desired.
Each rotation is approximately 10 weeks long. The student can request a change in laboratory rotation during the first three weeks of the rotation schedule, provided an alternative can be arranged. However, the student should discuss the reasons for such a change with the rotation advisor. At the end of each rotation, the student must complete a short paper describing what was accomplished. It should be completed and discussed with the faculty member by the end of the rotation period. The written document and the discussion will influence the faculty member's formal evaluation of student performance. The abstract and any written comments the faculty member chooses to add will be forwarded to the Program Director and retained in the student's file.
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5. SEMINAR COURSE
All students must register for the graduate student seminar course (BI 710, 720 and 730) each trimester until 9 credits of seminar have been completed. Students are encouraged to identify and participate in an informal journal club after completion of the seminar requirement.
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6. RESEARCH
At the end of the first academic year the student selects, in consultation with the Program Director, a laboratory in which to perform the thesis research. The choice must be from one of the laboratories through which the student has rotated.
Students are free to change research laboratories at any time, bearing in mind that another laboratory must agree to accept the student. There is no stigma associated with this. However, the matter should be carefully considered with all individuals involved before a final decision is made. The transition should be made in a manner that will be agreeable to the principal investigators of both laboratories.
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7. QUALIFYING EXAMINATIONS
Purpose of the Qualifying Examination
The qualifying examination represents the first of two steps towards advancement to candidacy for the Ph.D. degree in Biochemistry and Molecular Biology. The second step in this process involves the preparation and examination of the thesis research proposal (see Comprehensive Examination, below). The purposes of the qualifying examination are 1- To determine whether the student has the necessary conceptual background and knowledge base to advance to candidacy for the Ph.D. degree in the field of Biochemistry and Molecular Biology. 2- To determine whether the student has assimilated the information presented in the coursework and in laboratory rotations and can apply this information to an experimental setting.
Administration of the Qualifying Examination
The qualifying examination will be scheduled late spring of the second year. The qualifying examination will be administered by an Examination Committee consisting of 4-5 faculty appointed by the Biochemistry & Molecular Biology Ph.D. Program. The examining committee will not include the student's research advisor. On the day of the examination, the student will be given 5 journal article abstracts selected by the Examination Committee. The student will be given a 2 hour “reading period” during which time the student will select 2 of these abstracts to form the basis of his/her examination. During the 2 hour “reading period” the student may consult textbooks and class notes but may not use a computer or read the manuscripts that correspond to the 5 examination-abstracts. Students are not permitted to discuss the contents of the abstracts with anyone prior to the examination. The purpose of the reading period is to give the student time to read the abstracts and to look up key background material relevant to the abstracts' contents.
The examination will immediately follow the “reading period”. The time allotted for the examination is 1.5 hours. During the examination the student will be asked to discuss the abstracts' contents. Questions will be posed concerning background material. It is expected that the student will be able to demonstrate depth of knowledge appropriate to a Ph.D. candidate in Biochemistry and Molecular Biology. In addition it is expected that the student will be able to demonstrate the ability to think critically and apply his/her knowledge of biochemistry and molecular biology to explain how results in the abstract may have been generated, what follow-up studies are made possible by the abstract, and the significance of the abstract to the field of biochemistry and molecular biology.
The Examination Committee will try to reach a unanimous decision of Pass or Fail. If the committee cannot reach a unanimous decision, the student may be given a Conditional Pass and be required to meet certain conditions before receiving a Pass. The student will receive a written statement of these conditions. If the student receives a grade of "Fail" for the examination, the student will be given one chance to repeat the examination. A second examination must be completed within 3 months of the initial examination date.
A student who fails two qualifying examinations will be dismissed from the Biochemistry and Molecular Biology Ph.D. Program.
Successful completion of the qualifying examination allows the student to proceed to the Comprehensive Examination (see below).
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8. RESEARCH COMMITTEES
Purpose of the Research Committee
The purposes of the Research Committee are 1- To ensure that the student is progressing at a reasonable rate and decide when the research goals have been met. 2- To administer an examination of the student's Ph.D. thesis proposal (comprehensive examination). 3- To administer the final examination of the thesis. In addition, the research committee serves as a resource for guidance, mentorship, and trouble-shooting of difficulties that may arise throughout the duration of the thesis work.
Makeup of the Research Committee
Upon selection of a research advisor, the advisor in consultation with the student shall choose the Research Committee. The Research Committee shall have at least 4 members and consist of the thesis advisor, and at least two other members of the Program. It is recommended that at least one member have a primary appointment outside of the Department and be an expert in the specific area of proposed research. Adding individuals to the committee that bring specific expertise to the committee as the research evolves is encouraged. A committee member other than the research advisor shall serve as the research committee chairperson. It is expected that members of the Research Committee will be available to help and counsel the student concerning the thesis research throughout its duration.
Required meetings of the Research Committee
The Research Committee should meet at least twice a year during the student’s period of research activity. Records of the outcome of these Research Committee meetings are to be documented using the Ph.D. Student Research Committee Report forms available for downloading from the JCGS web site – both the “INDIVIDUAL RESEARCH COMMITTEE MEMBER’S EVALUATION” and the “RESEARCH COMMITTEE CHAIR’S SUMMARY EVALUATION.” Student Research Committee Report forms should be returned to the Training Programs Office.
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9. COMPREHENSIVE EXAMINATION
The student is required to prepare a written research proposal and defend the proposal orally before the Research Committee. The Comprehensive Examination must be completed by December 15 of the third year. The proposal will describe the student's thesis research in the format of an NIH R01 grant proposal. The proposal will consist of the following sections: a. Specific Aims, b. Background and Significance, c. Preliminary Studies, and d. Research Design and Methods. Guidelines for the preparation of a “New NIH Research Project Grant” are described on the National Institutes of Health's web site and can be downloaded from there. These guidelines (including font size, reference format, and content) should be adhered to except for the page limitation which is 20 pages (instead of the 25 page NIH page limitation). In most cases, a 15 page-long proposal will be sufficient and is recommended. Sections a-d should be assembled with a face page listing the title of the proposal, date/time/location of the defense meeting, the student's name, and the names of the thesis committee members. While the student is free to consult with the faculty concerning the appropriateness of methodology, techniques, etc., the written proposal should reflect the student's own thinking and preparation and, therefore, should have no substantial faculty input on its construction. Drafts of the written proposal should not be shown to any member of the committee before final copies of the proposal are given to the Research Committee. The exclusion of faculty input to the written document should not, however, prevent the student from discussing the specific aims of the proposal with the thesis advisor prior to preparing the proposal. The student should treat the proposal as he/she would treat a formal application for funding to a national funding agency; indeed, students are strongly encouraged to submit predoctoral grant applications.* The student should demonstrate an awareness of alternate experimental pathways that could be taken if key experiments do not yield the anticipated results. The proposal must be submitted to the Research Committee and the Program Director two weeks prior to the scheduled examination.
* Under some circumstances, a student will have submitted a predoctoral grant application prior to completion of the Comprehensive Examination. In such cases, students should discuss their plan for the Comprehensive Examination with the Program Director.
The Comprehensive Examination is an integral component of the training program. The purposes of this examination are 1- To ascertain that the questions being addressed and the scope of the research being proposed are appropriate. 2- To ascertain that the student has an adequate grasp of the background literature and understanding of the field of research. 3- To ascertain that the research being proposed is technically feasible and that adequate contingencies in response to a variety of experimental outcomes have been planned for.
The student should expect the Research Committee to look for a clear and logically organized written presentation, i.e., mastery of the written format as well as of the subject matter. The methods selected should be appropriate, clear and concise, including explanations of data collection and analysis and statistical evaluation. The thesis proposal examination should begin with a 15-20 min. presentation by the student that includes the goals of the research and the overall approach to fulfilling these goals. During this period, the presentation should not be interrupted by the Committee except to request necessary clarifications.
After completion of the presentation, Research Committee members will question the student. While questions will be based on the proposal, the student should understand that relevance is decided by each Committee member, and anticipate questions that can be drawn from several scientific disciplines. The student should be familiar with the methodologies that are proposed. In general, the more important the approach or technique is to the proposal, the more in-depth questioning the student can expect.
The Research Committee will give a grade of Pass, Conditional Pass or Fail. If the decision is Conditional Pass, the student will receive a written statement of the conditions he/she must meet before receiving a Pass. Alternatively, the student may be asked to defend the same proposal again. A student who receives a grade of Fail will have one chance to repeat the Comprehensive Examination.
A student who fails two Comprehensive Examinations will be dismissed from the Program.
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10. APPENDIX I
Guidelines for Writing the Ph.D. Thesis Proposal
First, prepare an outline of the experiments that might answer the question. Next, go back and expand the ideas you have generated into a full proposal.
When preparing your proposal, bear in mind that, since some of the members of your committee will not be expert in the area of the proposal, the background review of the literature is very important. The experimental design and techniques are the meat of the proposal. Each specific aim must be addressed by appropriate experiments. Give enough detail so that the reader can determine if an experiment is appropriate. There is no need to give details of common procedures. If you are not sure whether to include a procedure, ask the chairperson of your committee.
There are several problems in design of which you should be aware:
- Mutually dependent results. If a negative result is obtained does it eliminate all possible future experiments? Such a result can make the whole plan unfeasible. Always consider what you would do if things do not work out the way that you expect them to.
- Achieving the goal requires finding something. Some kinds of proposals are often described as "fishing expeditions" (by analogy, with little chance of catching "the big one"). Don't plan on spending more than a fraction of your time seeking something that you may not find. Try to build into the proposal experiments that will yield results no matter how they turn out.
- Limitations on starting materials. Know how much starting material is available. Know what the cost (in money and labor) will be. Is the required size of the operation feasible?
Include a discussion of how you will interpret the data that you obtain. Just getting data (even quantitative data) is not enough. Consider including a brief section at the end on the possible pitfalls. Make it clear that you understand what the major limitations are. If you anticipate a major problem, then you should indicate how you would get around it.
It is most convenient for the reader to have the key figures and tables in the text. Choose them carefully.
Time Required to Prepare the Proposal. You should plan to spend about one month of full time work to prepare the proposal. Times may vary from three to six weeks. Two months is probably the limit!
Comments on Writing. In a well-written proposal the logic should be clear, and the writing should be free of distractions and should flow smoothly. This requires good use of transitions between sentences and paragraphs. Multiple rounds of editing/rewriting will be required in order to reach this goal.
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11. Appendix II
The PhD Thesis Manual –
http://www.jefferson.edu/jcgs/policies/documents/phd_thesis_manual_2010.pdf contains the JCGS requirements for the successful completion of the PhD degree from the time you matriculate until you complete your degree. These are minimal requirements that are supplemented and expanded by BMB Program- specific requirements and instructions.
Highlights from the PhD Thesis Manual which are important to your progress:
- page 6: Formation of the Research Committee
- JCGS minimum - research advisor and 2 graduate faculty; formed in consultation with advisor and Program Director. The composition of the Research Committee must be approved by the Program Director.
- chairman of committee – a member other than thesis advisor
- BMB – at least 4 members; including the thesis advisor, and at least two other members of the Program.
- page 6-7: Monitoring Progress
- 2 committee meetings per year, each year of research activity
- Use forms for reporting results: report from each committee member plus chairperson’s report – both available at http://www.jefferson.edu/jcgs/policies/documents/phd_res_comm_ind_fac_rept.pdf
- BMB – return all forms to Training Programs Office, 910 BLSB for required distribution
- Yearly meeting with Program Director
- Semi-Annual Report to JCGS from student
- BMB – requires Qualifying Examination prior to the Comprehensive Exam. The Qualifying Exam is usually scheduled in the late spring of the second year. For details see Item 7 at http://www.jefferson.edu/jcgs/phd/bmb/rules.cfm#select
- page 7: Thesis Proposal
- may be part of Comprehensive Exam
- page 8: Comprehensive Examination
- page 9: Readiness to Write
- Determined by Research Committee; JCGS notified by use of Chairperson’s report (see above)
- Designate format of thesis: Traditional or Manuscript
- page 10-12: Final Examination Committee and Defense of Thesis
- Candidate must present an open seminar of thesis work followed by a private defense before his/her Examining Committee
- “By the time of the thesis defense, the research work performed by the student should generally have reached a stage of completion such that at least one paper, representing work to which the student has been a primary contributor (though not necessarily sole first author), has been published or accepted for publication in a peer-reviewed journal.”
- Committee Membership: Research Committee; Program Director; JCGS Dean
- Arrange defense date with Dean’s Office at least one month prior to planned defense by contacting Lisa Lorenz at 3-8982 or Lisa.Lorenz@jefferson.edu
- BMB – notify Training Program Office of date and time in order to arrange room and A/V equipment for open seminar
- One month prior to defense request letter from Program Director to JCGS denoting readiness to defend
- page 13: Format of Thesis – Model 1, Traditional
- page 22: Format of Thesis – Model 2, Manuscript
Application for Degree/Certificate: Is available on Pulse to all registered students. Candidates for degree must complete this form and return to University Office of the Registrar. Deadline is usually December 31 of year prior to desired commencement.
PhD Degree Completion Checklist: http://www.jefferson.edu/jcgs/policies/documents/phd_degree_completion_checklist.pdf
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