Exams – The Graduate Field of Biophysics at Cornell University

2019 Graduates from Biophysics with the DGS

Two exams are required by the Graduate School as benchmarks toward the Ph.D. Information about the Graduate School requirements and guidelines for these exams, please see the Exams section of the Graduate School site.

A-Exam: Admission To Candidacy Examination

To qualify as a Ph.D. candidate, each graduate student must pass the Admission to Candidacy, or “A exam.” This exam has both written and oral components.

Procedures

The A exam should be taken by the end of the second year if possible, but no later than the beginning of your seventh semester of registration. Not having obtained sufficient data is not an acceptable reason for delaying the A exam. You should consult with your committee about an acceptable date/time and reserve a room. The completed Schedule of Exam form for the A-exam must be filed with the Graduate School at least seven (7) days prior to the date of the exam. This on-line form is available on the Graduate School web site at https://gradschool.cornell.edu/forms/. It must be signed by all of the members of the Special Committee, the Director of Graduate Studies, and one of the GFAs. You should give a copy of the written proposal for your exam to each member of the examination committee at least a week before the oral exam.

Course requirements for the major (including BioMG 7510 “Ethical Issues”), and all or most for the minor, should be finished by the time of the A exam. Occasionally, the student and the Special Committee may feel an additional course is useful or important after the A exam and this may be recommended or required by the Special Committee.

Your examiners for the A exam are your Special Committee and one other member of the Cornell University faculty that you choose. (This person is usually, but not necessarily, from the Field of Biophysics). This fourth member should add breadth to the committee and have expertise closely aligned with the topic of your proposal. They will read your proposal and participate in your A-exam, however, they should not sign the Schedule or Results of Exam forms as they are not a permanent member of your committee.

You should have your entire official committee sign the Results form before they leave the exam room. After obtaining your committee and the DGS’s signature, take the form to the GFAs for their signature and transmission of the form to the Graduate School. This form must be filed within three (3) business days of the date of the exam.

Note: In accordance with the Code of Legislation of the Graduate Faculty, your A-exam is announced to – Field faculty. Please do not be concerned; Field faculty outside your Special Committee, although free to attend by Graduate School rules, rarely, if ever do.

The Written Proposal

In preparation of the A Exam, prepare a Thesis Proposal describing the background and motivation for the proposed thesis research, work accomplished so far, and an outline of the proposed research plan. The scope of the proposal should be arranged with the thesis adviser 10-15 double-spaced pages is suggested, and much longer proposal is generally not in the best interests of the student. The proposal should be given to each member of the Committee and the Field appointed member at least one week prior to the exam.

Your proposal will describe the research you intend to accomplish as a graduate student. The proposal should be well-formulated and in sufficient detail that it can be evaluated for its scientific merit. Include sufficient information to permit an effective review without readers having to refer to the literature. Brevity and clarity in the presentation will be considered indicative of an applicant’s approach and ability to conduct a superior project. The proposal must be written following the format specified below:

Abstract. This is a summary of the proposed work, with enough of an introduction to allow someone not expert in the field to understand what is planned and to appreciate its importance. This should be on a separate page and not exceed three vertical inches (single spaced).

** Sections (2) through (4) are not to exceed 10 pages (single spaced), including all tables and figures.

Specific Aims. State the specific purposes of the research proposal and the hypotheses to be tested.(Typically no more than half a page)

Background and Significance. Sketch briefly the background to the proposal. State concisely the importance of the research described in this application by relating the specific aims to field as a whole. Use this section to provide an account of any preliminary studies that might demonstrate the utility of the proposed project. (Typically about 3 pages)

Research Design and Methods. (Typically about 7 pages) Provide an outline of:
- (a) research design and the procedures to be used to accomplish the specific aims;
- (b) tentative sequence for the investigation;
- (c) statistical procedures by which the data will be analyzed;
- (d) potential experimental difficulties and alternative approaches that could achieve the desired aims.

Literature Cited. List all literature references. Each reference must include the title, names of allauthors, book or journal, volume number, page numbers, and year of publication. The referenceshould be limited to relevant and current literature. While there is not a page limitation, it isimportant to be concise and to select only those literature references pertinent to the proposedresearch.

Formatting. The proposal must conform to the following NIH requirements:

The height of the letters must not be smaller than 10 point; Helvetica or Arial 12 point is the suggested font (Arial 11 point will barely satisfy this requirement).
Type density, including characters and spaces, must be no more than 15 characters per inch (cpi).

For proportional spacing, the average for any representative section of text must not exceed 15 cpi;

No more than 6 lines of type within a vertical inch;
Margins, in all directions, must be at least 1/2 inch.

Applicants should check the type size using a standard device for measuring type size rather than relying on the font selected for a particular word processing/printer combination. Figures, charts, tables, figure legends, and footnotes may be smaller in size but must be readily legible. In preparing the application, use English and avoid jargon. If terms are not universally known, spell out the term the first time it is used, with the appropriate abbreviation in parentheses. The abbreviation may be used thereafter.

NOTE: Use the single spacing formatting above to make sure that your final proposal with figures

meets the requirements. Send an electronic copy in this format to all your committee members. Also print out hard copies in double space format to give to the committee, since this makes it easier for them to read and write comments.

The exam will consist of an oral presentation elaborating the thesis proposal, followed (or interrupted!) by oral examination covering, but not limited to, the student’s understanding of material related to the research topic, the student’s general background in the Areas of Required Competence (Table A), and the student’s research proposal. The Committee will review the student’s academic record and examine any potential weak areas to determine if additional course-work is required. The minor advisor may specify additional exam components as required for the minor. Students should feel free to chat with the DGS in advance about any aspect of the A-exam.

Satisfaction of requirements for the minor will be assessed by the minor field member at the A-exam.

The Oral Exam

The oral component is a defense of this proposal and you can expect that the majority of questions will be directly or indirectly related to your proposal and to areas that are considered off-shoots of it. The committee will likely ask you to explain, in more detail than the written format permits, background material and experimental protocols.

The committee will likely also ask broadly-based questions on basic concepts, to ensure you have strong command of foundational knowledge in Biophysics and your minor area(s). The committee member(s) representing the minor subject area(s) is particularly responsible to ascertain that you have achieved competency in that subject area.

In addition to the evaluation of your proposal, the A exam is the time when committee members will discuss and evaluate your course work as well as your performance in the laboratory. Please bring a summary of the courses you have taken and grades earned to be distributed to the committee at the time of the A-exam.

Note that the Field recommendation is that during the exam, the mentor (thesis advisor) should not ask questions or make comments except when asked by other committee members or when clarification is needed. The intended goal is to dissuade the mentor, who may have a vested interest in the outcome of the exam, from stepping in to justify the research or the particular experimental approach being used. The student is expected to fully defend the proposal by themself. However, the mentor should participate fully in the discussion of the student’s performance, after the student is asked to leave the room. In making this recommendation, the Field is aware that the Special Committee may run the exam in whatever way it deems appropriate.

The Field of Biophysics also uses the oral part of the exam for assessment. The student should be prepared to discuss which aspects of the Field they find constructive and useful for their education, and which aspects would benefit from change.

Possible Outcomes

The final outcome is determined by the Special Committee. Examples below are not exhaustive and are provided to assist the student in their exam preparation. Some factors that may be judged in evaluation of the A-exam are:

importance of the problem chosen
demonstration of a command of knowledge/research in the field.
evidence of creativity in formulating experimental approaches
feasibility of the proposed experiments
whether a range of different approaches are brought to bear on the problem
whether the scope of the proposed experiments is feasible for a 3-4 year project
adequacy of control experiments
clarity of the proposal
ability to deal with questions
communication / presentation skills/breadth of knowledge

1. Unqualified pass.
2. Conditional Pass. This option will be exercised when the committee decides that some aspect of the proposal / defense needs to be improved. In this case, the committee will specify the condition(s) required for the student to receive a pass and the timeline for fulfilling these conditions. This must be done in writing and the Graduate School must be informed of the details. This can be done in the form of an email from the Special Committee Chair to the Graduate School Student Services team (gradstudserv@cornell.edu).

Some examples of Conditional Pass:(a) The committee may specify that the proposal or that parts of it need to be revised within a certain time frame (i.e. improvement of writing; re-working of aspect of scientific research; addition of another section. (b) The committee may specify that the student carry out additional literature review, e.g. weekly written report of a paper, participation in existing journal clubs. This might be particularly helpful when the student appears to have weak command of the literature surrounding a particular area. (c) The committee may specify that the student complete a piece of research / a particular sub-aim within a certain time-frame. This is relevant when the committee has some concerns about the ability and/or motivation of the student to complete the PhD program.

Fail. inadequate. In that case, the committee will usually recommend one of two actions.

If the committee has confidence in the overall ability of the student to complete the Ph.D. program, then they may recommend that the student retake the A exam. In this case, they will specify whether an entirely new proposal on a different topic is to be written or whether they expect a major rewriting of the original proposal. Note that the rules of the Graduate School specify that a second A exam needs to be scheduled no later than 3 months after the first.
If the committee has serious concern about the motivation or ability of the student to complete the Ph.D. program, it could recommend that the student complete a piece of research, write a Masters-level thesis based on that work, and then defend that thesis.

Master’s Degree

The Field of Biophysics does not have a formal Master’s degree program. In cases in which a student decides that the Biophysics Ph.D. program does not meet his or her needs, or in which a student is judged to be unqualified for the Ph.D. program, the Special Committee typically recommends that the student write and defend the research work done and receive a Master’s degree. The requirements for a Master’s degree include the coursework normally taken by first-year students, at least two rotations, one semester of teaching, and a research-based thesis (including a thesis defense). At a minimum, the Special Committee of a Master’s degree candidate is composed of a chairperson and a faculty member representing a minor subject. The student may invite a third faculty member to be on the committee if he or she chooses. To take the Master’s degree path, the student must submit a Change of Program form to the Graduate School, requesting transfer from the PhD program to a Master’s program. This form will then be sent to the DGS for approval.

B Exam: Thesis Defense

The B-exam is the thesis defense. The completed dissertation should be submitted to the committee at least 1 week before the examination. The exam will begin with a public seminar describing the thesis research. This will be followed by a closed oral examination covering the dissertation.

As with the A-exam, a Schedule of Exam form needs to be filled out and signed by your committee and the DGS and then submitted to GFAs for transmission to the Graduate School at least 7 days before the examination date. You are also required to provide the title and abstract for your dissertation and the list of your publications to the GFAs for the announcement of your exam.

The completed Results of Exam form must be submitted within three (3) days of your exam.

Both of these forms are found on the Graduate School Forms page.

Thesis Format

A section of the Graduate School website (http://gradschool.cornell.edu/thesis-dissertation) is dedicated to information about the dissertation process, including the Thesis and Dissertation Guide. You are highly encouraged to follow the process it lays out in planning submission of your thesis and graduation.

The Graduate School Office of Academic & Student Affairs (http://gradschool.cornell.edu/academics/office-academic-and-student-affairs) also coordinates a number of workshops to assist you with thesis writing.

Your thesis may be organized either as a single work (traditional thesis) or as a series of relatively independent chapters (independent chapter thesis). In the latter case, there may be a unified introduction and bibliography or separate introductions and bibliographies. There may be a unified summary, or the two-page abstract (required of all theses) can serve as a summary statement for all chapters. Some examples of thesis formats are shown below.

Traditional Thesis

Independent Chapter Thesis

Literature Review

Materials & Methods

Results

Discussion

Conclusions

Literature Cited

Appendices

Chapter 1: General Introduction and Literature Review

Chapter 2:

Introduction

Materials and Methods

Results

Discussion

Literature Cited

Chapter 3: (as above)

Final Chapter including

General Discussion,

Speculations and

Conclusions

Appendices

The independent chapter option allows you to prepare your thesis as a series of papers in a format ready for publication, and chapters can be published before the thesis defense. The work in your thesis must be primarily, if not entirely, your own. If your published work includes co-author(s), you may cite the work of your co-author(s) in your thesis with appropriate acknowledgment, but you should not include the data of your co-author(s) in your thesis. An exception could be if data from a co-author are needed for clarity. In that case, the legend to the figure should explain this. You should acknowledge in the publication that the research is part of a thesis, and the Graduate School requires written permission from the publisher to include it in your thesis.

Full collections of dissertations are maintained in Mann Library. There is also a collection of theses of graduates in the Fields of Genetics, Genomics and Development and Biochemistry, Molecular and Cell Biology in the Keller Reading Room, Biotechnology Building, Room G09. You can view these by asking someone in the MBG Department Office (107 Biotech) to let you into this room. Please ask to be let into that room. NOTE: Materials are NEVER to be removed from this room.

Final Thesis Seminar

Thesis Defense | B Exam

To schedule the oral defense of the Ph.D. thesis (B exam): at least seven days before the exam you must distribute your thesis to the Special Committee; the thesis must be complete in all respects and editorially acceptable for final approval. The Schedule of B exam form must be filled out, approvals obtained and submission to the Graduate School must be completed at least seven (7) days prior to the exam. You should also provide the GFAs with the title and abstract for the thesis seminar, and a publication list including all manuscripts you have published, submitted or are in preparation.
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