Cell and Molecular Biology graduate group, UPenn School of Medicine

CAMB students must carry out their thesis research under the mentorship of a faculty member of the Cell and Molecular Biology Graduate Group. The Thesis Mentor is the most important individual the student will interact with in the course of their graduate training. For this reason students should carefully evaluate their three rotation experiences in choosing the Mentor. If necessary the student can do additional rotations. At the end of all the rotations the Mentor is chosen and thesis research should commence as soon as possible. The Thesis Mentor is responsible for supporting PhD students beginning June 1st of the PhD. student's second year or the MD/PhD student’s fourth year. Below are documents from BGS with more detailed financial information.

FY 08 Mentor Cap Memo (pdf)

Within six months of passing the preliminary exam, the student must form a Thesis Committee, and have a committee meeting. Failure to formulate a Thesis Committee within this time frame will result in the student being placed on academic probation. The Thesis Committee must meet at least once a year for Ph.D. students and every six months for combined degree students to monitor the student's progress. The student's Program Chair will monitor the frequency of the meetings.

The Thesis Committee will be comprised of four (or more) faculty (not including the Thesis Mentor), at least three of whom must be members of the CAMB Graduate Group. One of the four faculty is designated as committee chair, and he or she must be a CAMB member. The committee should be constituted to include breadth as well as expertise in the particular research area of thesis work. No more than one faculty member per lab can serve on a student's committee. The Thesis Mentor is a non-voting, ex-officio member of the thesis committee.

The Thesis Committee is the student's advocate and advises the student on scientific direction. The thesis committee, in consultation with the mentor and the student, decides whether a student may defend his/her thesis. It may intervene if there is a serious disagreement between the student and the mentor. If a serious disagreement arises between committee members, the committee Chair should inform the relevant Program Chair. The Program Chair must approve the composition of each thesis committee in their Program, and, when necessary and at his/her discretion, may add additional members or reformulate a committee. If a dispute arises between a student and the thesis committee, and the student requests it, the decisions of a thesis committee will be reviewed by the CAMB Executive Committee.

The graduate student and his/her Program Chair shall jointly select the members of the Thesis Committee. The student should submit a list of potential committee members, indicating which faculty will serve as committee chair, to their Program Chair in writing. The Program Chair will respond in writing to approve the committee composition or make recommendations for other candidates. The Graduate Group Chair will adjudicate any disagreement on the composition of the Thesis Committee.

The Thesis Committee and the committee chair must be registered with the Graduate Group Office as soon as it is approved. Students must contact the Graduate Group Office before each thesis committee meeting is held. The Graduate Group Office will then send thesis committee evaluation forms (appendix) to the committee chair. The committee chair will write an overall summary of the committee's decisions. The summary will be returned to the Graduate Group Office to be placed in the student's academic file, and a copy will be forwarded to the student.

Per University policy, students who have not completed all requirements for the Ph.D., including the deposit of the dissertation, within 5 years of passing the preliminary examination cease to be candidates for the Ph.D. unless they satisfy the following re-evaluation process: At a special meeting of the Thesis Committee plus three members of the CAMB Executive Committee, the student will make a 50 minute presentation of work completed to date, plans for future experiments and a detailed timeline for completion. This must be approved by the Thesis Committee and the CAMB Executive Committee. This approval constitutes the "recertification"
required by the university.

BGS has mandated that all graduate groups ensure that the laboratory notebooks of their students are maintained properly. Students are requested to bring their most recent laboratory notebook to each thesis committee meeting. The chair of the thesis committee will appoint a member to review the notebook.

The objective is to ensure that students record their primary data in a way that will allow it to be analyzed appropriately and recovered when necessary. The objective is NOT to monitor the precise content of the notebooks, but to ensure that they are maintained in an acceptable format. There will be a great deal of variation between notebooks, but most notebooks will meet the following requirements:

Notebooks should have bound pages.
Entries should be dated and in ink.
Inserts should be stapled onto pages when practical.
Sufficient information should be recorded so that the reader can determine the objective, design, procedure, and results of an experiment.
The origins or properties of any special reagents used in experiments should be noted.
There should be an organizational scheme, e.g. a table of contents, that allows others to locate key experiments.
Primary data not entered into the notebook, like digital files, gels, photographs, microscope slides, animal records, etc. should be indexed in the lab notebook and their location and labeling clearly noted.

If these requirements are not applicable to specific students or projects, we ask that the thesis committee use its best judgment in advising the PI and the student of the best manner in which records should be kept. We ask that notebooks be checked at each thesis committee meeting until the thesis committee feels that the notebooks meet these requirements.

If weaknesses are detected in notebook organization, then the student and PI should receive guidance from the thesis committee on what improvements need to be made. It is the responsibility of the PI and the student to address issues as they arise.

The Graduate Group requires a dissertation to represent a definitive contribution to scientific knowledge and to show that a student possesses the ability to perform independent research. The Graduate Group feels that the dissertation should contain experimental information that answers a stated question and should display a logical progression of scientific thought. The main information contained in the dissertation should be of a caliber sufficient for publication in a reputable, refereed scientific journal.

Before beginning the process of writing and defending his/her thesis, the student must convince the thesis committee that thesis research is substantially finished and that the thesis is ready to be written. If the committee agrees that the experimental work is completed and is defensible, the "Permission to Write" form (appendix) must be signed by the committee chair and thesis advisor and returned to the Graduate Group Office. The committee should also agree on a time line that includes an approximate date for the defense. This is necessary to ensure that a time convenient for all committee members can be arranged and that an appropriate room can be scheduled. A draft of the thesis must be presented to each committee member and the CAMB office no later than two weeks prior to the scheduled defense. Failure to do this may result in cancellation of the scheduled thesis defense. Prior to distributing the dissertation to the thesis committee, it must be approved by the thesis advisor. It is typical for members of the thesis committee to ask for alterations prior to the dissertation’s final submission; such alterations can be requested at the thesis defense.

The dissertation is the document that summarizes the student’s experimental work, formally stating the hypothesis (or hypotheses), the background for forming the hypothesis, and the complete, logical set of experiments and methods used to prove or disprove the hypothesis. It describes primarily data obtained independently by the student, including those generated from incomplete and/or rotation projects (if desired), but may also describe collaborative work. For the latter, it is critical that the student be the primary author and provide the appropriate acknowledgments to other contributors. In addition to being a personal document, the dissertation is an invaluable lab resource and should be written as such.

The basic outline of the dissertation comprises five sections:

a) A General Introduction, which is intended to review in depth the literature that places all of the work in context and to state the initial hypothesis or hypotheses;

b) Materials and Methods, which should be complete and sufficiently detailed so that others can repeat the experiments without undue literature searches;

c) Results, which typically consists of more than one chapter, with each chapter corresponding to a completed or submitted manuscript or to work in progress. The chapters can contain their own Introductions (these cannot replace the General Introduction described above), Materials and Methods and Discussion sections. The text of these chapters may be more detailed than a completed or submitted manuscript; for example, the Methods should be completely described so that others can repeat the experiments or use the same technology.

d) Conclusions/Future Directions, which summarizes the student’s thoughts on what the overall body of work has accomplished and where it might be going. This section is required even if chapters in the Results section have their own Discussions.

e) References. Depending on the overall organization of the dissertation, these can be included at the end of each chapter or at the end of the document.

Following this general outline, the dissertation’s overall organization is up to the student in consultation with the thesis advisor and chair of the thesis committee. The written document must conform to the dissertation rules of the University (see the Dissertation Manual issued by the Office of Graduate Studies).

The thesis presentation will take the form of a public lecture. The lecture should be scheduled well in advance so that a time convenient to the entire committee can be found and notices can be sent to the faculty and student membership. The Graduate Group Office needs to know the defense date, title of the thesis and place and time of the defense at least three weeks in advance. The Graduate Group Office will then send a public notice to the University community advertising the thesis defense. The Graduate Group Office is responsible for the forms that are required after the thesis defense.

Every effort should be made to have the full four-member thesis committee present at the thesis defense. If a thesis committee member cannot be present at the defense, he/she may provide to the committee chair approval of and/or comments concerning the thesis prior to the defense. If that is not possible, the student is responsible for finding a substitute committee member, with the approval of their program chair. Following general questioning during the public phase of the presentation the thesis defense will commence. The defense is open only to the thesis committee and mentor. The decision on approval of the thesis will be made solely by a majority vote of the committee. The student should anticipate that the committee may require changes to the thesis that could include additional writing, editing and re-evaluation of data. Such changes must then be approved by the committee before the thesis is deposited. For this reason, it is imperative that thesis defenses be scheduled no later than two weeks before the deadline for depositing theses.

Before a student makes the appointment to deposit the thesis, the student must provide the Graduate Group Office with a copy of the abstract page, an original signed copy of the title page, and a mailing address where the postdoctoral training will be done. The Graduate Group Office will then provide the student with a signed 153 form, which must accompany the dissertation to the Graduate Division of Arts and Sciences (GAS).

The Graduate Division of Arts and Sciences sets three graduation dates each year in May, August, and December. A formal commencement ceremony is held in May. The Graduate Group Office will distribute a calendar for each degree period, giving the deadlines for signing up for graduation, and for defending and depositing the thesis. If a student is not able to graduate after they have signed up, they must re-apply for the next degree period. The graduate Group Office will guide students through the thesis submission and graduation scheduling.

A "Graduation Checklist" that includes all of these processes and procedures can be found in the Appendix.

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