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Dissertation, Oral Defense and Publication(s)

Dissertation

Students are required to submit a dissertation by the end of the fifth year unless the program director and respective thesis committees approve an extension.  Specific terms and conditions must be set prior to approval of an extension.  Students should submit a version of the dissertation document to their thesis committee 2-3 weeks before the defense date so that the committee has time to assess it.

In the 6-8 weeks leading up to thesis submission and defense, it is customary that students will be primarily focused on writing their thesis and preparing their defense, and that thesis advisors will provide the necessary flexibility and protected time to allow this. During the writing phase of the thesis, the advisor(s) will typically meet the student to give feedback on the overall structure of the thesis and may give general feedback on individual chapters. Since writing should be the key focus, the advisor should discourage additional experiments or analyses that are not critical to any results. Since the thesis is primarily for assessment by the thesis committee, it is not expected that the advisor would provide detailed comments or editorial direction as might be appropriate when, eg, preparing a manuscript for submission to a journal; rather, the writing should primarily be the student’s own.

Oral Defense

Dissertation projects are presented by each student in a formal seminar, which is often (although not necessarily) open to the public, followed by a closed question and answer session in which the student defends their thesis to the thesis committee. These two components together comprise the thesis defense. Although the seminar portion is typically open to the public, attendance can be more limited, if mutually agreed upon by the student and committee, eg, it could be limited to include only the committee or the committee plus select other attendees. The closed portion is typically for the committee and the student only, and the committee will use this time to ask in-depth questions about the thesis research and to ensure the student’s overall scientific proficiency in the field.  Although it is unlikely for students to fail at this point, thesis committees have the option to pass students conditionally if an unequivocal decision is not made.  In such cases, students will only receive their degrees after successful completion of additional requirements determined by the committees.

For completion of the PhD requirements, students are also required to have published at least one first author, peer-reviewed journal article or conference proceeding. This requirement is described in more detail below.

First author publication requirement

Each BCB student is required to publish at least one primary-author, peer-reviewed journal article or conference proceeding that is based on original research performed in the course of their PhD under their formal thesis advisor(s). The definition of primary author in this case includes co-first authorship, provided this designation is indicated in the published paper itself.

Rationale

The reason for this requirement is multifold, related to training, externally validation, and scientific communication.

  1. Appropriate Training. The first author requirement guarantees that the BCB student has both i) had the opportunity and ii) showed the ability to take a primary role in scientifically rigorous research. This also ensures that mentoring of BCB students is oriented towards developing the necessary skills and dissertation project(s) that would satisfy these conditions.
  2. External Validation of Scientific Rigor. The rigor of the research is implied by the acceptance of that work in a peer-reviewed journal. In the absence of the publication requirement, the claim of scientific rigor would rely solely on the judgement of internal committees, with no formal, external validation.
  3. Scientific Communication Skills. The first author requirement implies that graduating students have had a substantial role in the generation of a publishable manuscript. This process requires understanding or at least witnessing the primary method by which science is communicated in a given field.

Although it is conceivable that conditions (1)-(3) could be met through other means — for example, appropriateness of training judged by the thesis committee, external validation judged through formal feedback from suitable external seminars or other examination, scientific communication assessed via the thesis document itself – the first author publication requirement is by far the simplest,  most consistent (or least inconsistent), and most easily verifiable (by peer institutions, employers, funders, etc) way to achieve these goals.

Timing and exemptions

The standard rule is that the first author paper should be published or in press before the defense can be scheduled (ie, before the defense forms can be submitted). If this condition cannot be met before scheduling the defense then the defense can still be scheduled but only after the student must obtain a Defense Exemption from the BCB Executive Committee.

The request for an exemption should be signed by (or cc’d to include) both the mentor and the student’s committee members and should be sent to the BCB program director, who will then share it with the Executive Committee. The request must explain the status of the first author manuscript plus any relevant additional information. In particular:

  1. If the manuscript has been accepted, then include the acceptance email.
  2. If the paper not yet been accepted but has been positively reviewed, then include the reviews.
  3. In all other cases, provide enough information for the Executive Committee to judge the likelihood of the requirement being fulfilled by defense and/or graduation.

Exemptions will be considered by the committee on a case by case basis, although (a) is typically granted, (b) is often granted, and (c) will typically depend on circumstances.

If the first author requirement is not met by the time the student intends to schedule their graduation, then graduation can still be scheduled but only after the student obtains a Graduation Exemption. The process for requesting the Graduation Exemption is the same as that for the Defense Exemption (although the granting of one does not imply granting of the other).