Biology, Molecular and Cellular

The First Two Years

Graduate students in Molecular and Cellular Biology are members of an interdepartmental and interdisciplinary training program called Molecules, Cells, and Organisms (MCO). MCO is comprised of faculty members from MCB as well as the departments of Chemistry and Chemical Biology (CCB); Organismic and Evolutionary Biology (OEB); Stem Cell and Regenerative Biology (SCRB); Department of Physics; and the School of Engineering and Applied Sciences (SEAS) The program consists of broad areas of research and teaching organized along the following key areas: Biochemistry, Chemical, and Structural Biology (BCSB); Cellular, Neuro and Developmental Biology (CNDB); Genetics, Genomics and Evolutionary Biology (GGEB); Systems and Computational Biology (SCB); and Engineering and Physical Biology (EPB).

Coursework

MCO first year graduate students take core courses in each of the fall and spring semesters. In both semesters, all students enroll in MCB300 (Laboratory Rotation). In the fall term, students enroll in MCB111 (Quantitative Methods) and MCB292 (Cellular Biology, Neurobiology and Developmental Biology) plus one additional elective course. The elective course selected in consultation with the Executive Committee. This faculty committee represents all key areas and advises students about elective course selections and lab choices within specific areas of research. The committee plays an important role during a student's first year.

In the spring term, in addition to MCB300, each student enrolls in MCB291 (Genetics, Genomics and Evolutionary Biology) and MCB293 (Biochemistry, Chemical, and Structural Biology) plus one additional elective course. The Executive Committee may advise students with advanced training in any of the core courses to substitute a more advanced course(s).

Electives are selected primarily from course offerings in the participating training program departments, as well as other offerings in related departments. Students select courses in consultation with the MCO Executive Committee. With approval of the Director(s) of Graduate Studies, students may cross-register in courses offered by the Massachusetts Institute of Technology (MIT).

In addition to academic coursework, all graduate students in the program must complete an 8-hour workshop in the Responsible Conduct of Research (RCR), to be completed by the end of the first year of study. Additionally, students are required to take an RCR refresher course after the fourth year of study.

In accordance with the Graduate School of Arts and Sciences, all degree candidates must maintain an average equivalent to B or better to continue in the program. Satisfactory progress is reviewed annually and students who fall below the grade minimum will ordinarily be given one term to improve their grades.

Laboratory Rotations

With nearly 60 participating faculty labs, the MCO program provides an invaluable opportunity for graduate students to observe and participate in a variety of laboratory environments. During the first year, students spend about 25% of their time conducting experimental research in faculty laboratories. Student will complete at least three 5-week rotations in MCO training faculty labs before selecting a thesis lab. Additional rotations are possible. The rotations will expose students to a wide range of research concepts, techniques, and model systems. Additionally, these rotations offer networking opportunities and serve to introduce new MCO graduate students into our extended scientific community. Ultimately, these immersive experiences will inform each student’s selection of a lab best suited for their doctoral research.

In addition to regular coursework, students register for MCB 300 once in each of the first two terms to designate research undertaken in lab rotations. MCB 300 does not correspond to the fall and spring term start and stop dates. Student can declare a home lab and a faculty advisor after three laboratory rotations. Ordinarily, students should be able to start in their thesis labs in the middle of the spring semester of the first year.

Nanocourses

Nanocourses are offered in a broad range topics during the course of an academic year. Participation in relevant nanocourses is required for all students in the MCO Training Program.

Foreign Languages

There is no foreign language requirement for the PhD degree.

Dissertation Research

Each student arranges for a permanent faculty dissertation advisor by the middle of the second semester and begins dissertation research thereafter.

Master of Arts (AM)

The AM is conferred as a non-terminal degree only, following successful completion of all G2 requirements including the Candidacy Examination, coursework, and teaching one required course.

Teaching

Each student is required to serve as a Teaching Fellow for one term. Ideally, this requirement will be completed by the end of the G2 year or by the end of the fall semester of the G3 year. Students are expected to teach either one of the large, introductory undergraduate laboratory-based courses such as Life Sciences 1a or 1b, Life and Physical Sciences A, MCB 80, or MCB 60, or a small, discussion-based advanced course. Teaching beyond the requirement is encouraged, but requires prior approval from the student’s advisor(s), dissertation committee members, and the MCO program leadership.

Advising

At the beginning of the first year of study, each student is assigned a “Neutral Advisor.” The Neutral Advisor is usually chosen from a research area different from that of the student, so that the advisor may serve as a sounding board and general guide. Although many students indicate an area of interest during the application process, interests can change during the first year of graduate study. The Neutral Advisor serves as a resource during the important decision-making process of the first year, as well as during the entire training period until the dissertation defense.

Candidacy Examinations and Evaluation

Students must complete their candidacy qualifying exam before September 30 of the second year. The Candidacy Examination Committee is composed of at least three faculty members. The student, in consultation with their advisor, selects a senior MCO faculty member to act as committee chair, and the MCO program leadership will select two additional committee members from the MCO faculty. The purpose of the candidacy examination is to assess the student’s qualification for independent research leading to the PhD degree. This encompasses various scholarly abilities: a solid background knowledge; familiarity with established ideas and open challenges in the chosen discipline; the ability to design experiments; and the ability to critically interpret their outcomes.

With advice and assistance from the advisor, the student prepares a Dissertation Research Proposal that outlines the plan for PhD research. The advisor must approve the proposal by signing the title page. The cover page should also include the date, time, and location of the exam. The student distributes this document to all committee members and the Graduate Office at least one week prior to the exam.

The advisor is not a member of the Candidacy Examination Committee and does not attend the exam itself. However, the advisor should inform the committee about the student’s proposal and work. This occurs in a pre-exam session without the student present.

The examination committee considers all the information available to inform the Candidacy Examination decision. This includes the student’s academic record in courses; the student’s rotation reports and the accompanying evaluation from rotation supervisors; the advisor’s report on the first year of research; and the written research proposal.

The examination is structured around the student’s presentation of the proposed research project. Though the project itself is not a target of the exam, it provides a good starting point for assessing the student’s preparation. To enhance the “real-time” character of the discussion, students are not allowed use of visual aids aside from drawing their own figures on a chalk or white board. Examiners are free to interrupt the presentation at any time to explore various threads in more detail. Each examiner is expected to lead at least one line of inquiry outside of the specific topic of the research proposal, into areas deemed essential basic knowledge in modern biology.

The exam has 3 possible outcomes:

  1. Pass: The student continues in the program towards the PhD.
  2. Pass with condition: The student faces a supplementary exam in the spring term of the G2 year. The committee may impose additional conditions to be met by that time (for example, teaching a specific course, or rewriting the research proposal). The supplementary exam has outcomes of Pass or Fail.
  3. Fail: The student leaves the program.

Dissertation Advisory Committees (DAC)

MCO PhD candidates report their progress to a dissertation advisory committee (DAC) at the beginning of each academic year to encourage forward thinking. The DAC may require more frequent meetings depending on the student’s progress, especially in the completion phase. The student invites 3-4 faculty members to join the DAC. Membership must include at least two faculty members from the MCO training program. The chair of the DAC must be a senior faculty member from the training program.

Students may request changes to the Examination Committee or DAC with the approval of the Director(s) of Graduate Studies.

The DAC has four main missions:

  1. To serve as an advisory committee that will provide professional advice on all aspects of the dissertation project, from experimental paradigms to project feasibility and timing, to the scientific impact of the work.
  2. To help monitor the student’s progress and ensure that major objectives and standards for completion of the dissertation are being met. In this capacity, the DAC determines whether the student’s research meets the requirements of the program and when the student may begin writing the dissertation.
  3. To help resolve any conflict between student and advisor or other lab members.
  4. To serve as liaison to the department and training program leaders as well as graduate administration.

Students submit a progress report to each committee member and to the Graduate Office one week in advance of their DAC meeting. The report’s cover page should be signed by both student and advisor and include the date, time, and location of the meeting. The format of the DAC progress report mimics a draft research manuscript whereby students are required to sketch the main figures of a paper(s) and add place holders for data that they plan to collect. A template is provided.

Power Point Slides are permitted at DAC meetings. The main part of a student’s DAC meeting entails a 20-40 minute student presentation consisting of results (if any) along with plans. Like the Candidacy Exam, committee members will typically interrupt the presentation with questions; and the presentation is followed by a discussion of progress and future plans and aims. Students should be concise in the report and consistent with format. Unlike the Candidacy Examination, advisors are encouraged to attend. The student’s advisor is not a member of the DAC and should endeavor to let the student present their own progress. It is critical that the advisor briefs the DAC on the student’s activities, preferably in a private session with the DAC prior to the student’s report, but this can be done via an email to the DAC members prior to the meeting. Whether the advisor stays or not, in order to provide an opportunity for both the student and advisor to communicate with DAC members on a confidential basis, the meeting will start with first the student leaving the room, and then the advisor leaving the room. When the student is not present, the advisor will have a chance to present their assessment of progress and whether the student is on course to graduate in a timely fashion. When the advisor is not present, the student may likewise communicate their assessment of progress and whether the advisor and the laboratory environment are providing the support needed. This is also an opportunity, if necessary, to share with the committee any other problems of a confidential nature with which the student may need help.

Dissertation Defense

To schedule a defense, students are required to have published or submitted at least one first author manuscript. Three to four years of full-time research are usually required for completion of the PhD degree. Students are expected to complete the program in their fifth year of study; and support is usually only provided until the end of the fifth year. Advisors must agree to support students beyond the 5th year of study.

Completed research is presented for approval as a written dissertation. Candidates should submit a copy of their dissertation to each member of their dissertation committee as well as the Graduate Office at least two weeks prior to their defense. The dissertation committee is often identical to the DAC.

Granting of the degree requires the approval of the candidate’s dissertation committee members, who review the dissertation and examine the student on the contents of the dissertation. Candidates will also be called upon to demonstrate the ability to formulate and defend original ideas on scientific topics not directly related to the subject of the dissertation.

Dissertation

The dissertation should include an abstract of not more than 350 words, stating the purpose, main results, and research conclusions. In addition, ordinarily, a dissertation must contain an introductory and concluding chapter, each no less than 5 double-spaced pages. The introductory chapter should set out the overall theme of the dissertation, describe the state of knowledge in the field before the student’s work began and any important advances made by others during the student's dissertation research, and describe the progression of the following chapters. The concluding chapter should attempt to draw overall conclusions from the dissertation research work, describe directions in which it could be usefully extended, and describe new questions that it has produced. Any exception to this structure must be approved, in advance, by the student’s Dissertation Advisory Committee.

Procedures and requirements for the final dissertation manuscript are described in Dissertations.

CONTACT INFO

Dr. Fanuel Muindi
Assistant Director, Graduate Programs