Carnegie Mellon University

Summary of Departmental Requirements

  • Satisfactory completion of six lecture courses of which four must be graduate courses from the Graduate Advisory Committee (GAC) proposed Core Elective list during the first year and maintenance of 3.0 QPA (cumulative after the first year, rounded to the nearest tenth)
  • Satisfactory completion of laboratory rotations, including oral presentations (first year)
  • Satisfactory completion of Thesis Proposal Defense (second year)
  • Annual Research Advisory Committee Evaluations (third through last year)
  • Annual Journal Club presentations (second through last year)
  • Teaching assistantship: 10 points (first through last year)
  • Total number of units required for completion of Ph.D. degree is 384 units (fifth year)
  • Students finishing their degree early may formally request any of the above mentioned requirements from the department head.
  • Satisfactory completion and defense of Ph.D. dissertation (fifth or sixth year) 

Orientation

Matriculating students arrive at the Carnegie Mellon campus in August to attend the University-wide orientation. The following week, the Department of Biological Sciences holds its orientation, which includes meeting the faculty and staff, course selection, tours of the Mellon Institute, safety training, TA training and ethics discussions. Of particular importance is the Introduction to Research, a series of faculty talks that provide students with an opportunity to select laboratories in which to rotate. Also during orientation, each first-year student consults individually with the departmental Graduate Advisory Committee (GAC) to construct a customized program of study that meets the student's specific interests and professional goals.

Course Requirements

Coursework

To receive the doctoral degree, all students must successfully complete at least six lecture courses, including four graduate level courses and up to two of six can be undergraduate courses.

  • All first-year students are required to take at least three courses for credit in each of the first two semesters. Courses taken pass/fail or as an audit do not count toward this requirement. Total units earned for each semester (including credit for doctoral research 03-900) must equal at least 48.
  • To remain in good academic standing, students are required to achieve at least a 3.0 QPA (rounded to the nearest thenth) at the end of the first year.
  • First-year students must also obtain a B or better grade in each of four courses selected from a list of Core Electives. The GAC will approve this list each year.

After the first year, each student’s Research Advisor and the Research Advisory Committee may recommend additional courses to enhance the student’s expertise in a subdiscipline.

Students continue to do research throughout the summer and, thus, are registered for 03-900; they do not, however, take summer courses unless the tuition obligations are met by either their advisor or another source.

Departmental Seminar

Each semester, all students are required to register for and attend the weekly departmental Research Seminar (03-750; 1 unit). Graduate students are strongly urged to meet the speakers to broaden their knowledge of cutting-edge biological science, to discuss career paths and strategies and to make useful contacts; the faculty host can arrange group meetings for interested students. Students also attend various informal seminars whose topics range from scientific integrity and ethics to professional development.

Graduate Research Seminar (Journal Club)

Each semester, all students are required to register for and attend the weekly departmental Journal Club (Graduate Research Seminar 03-755; 3 units) during which faculty members and students give 25-minute presentations. Second-year students present a research paper or topic from the literature, and more senior students present their research results; typically, graduate students give four Journal Club presentations. Each succeeding year, those students who speak at the Departmental Retreat, or who are graduating by May 15 of their fifth year, are not required to present a Journal Club that year. In lieu of a Journal Club presentation during their first year, students give a brief oral presentation describing each rotation project (scheduled after each rotation).

Doctoral Research

During each semester, including the first year, students register for Doctoral Research (03-900; variable units), which encompasses both the laboratory rotations during the first year and the thesis research during all of the succeeding years.

Grades

A student is expected to achieve at least a 3.0 QPA at the end of the first year. First year students must successfully complete the Core Courses in Biochemistry, Cell Biology, and Molecular Biology by earning a B or higher in each course; students who do not earn a B in either part of the course are given the opportunity to pass an additional exam to demonstrate mastery of the subject, which is a requirement for remaining in the Ph.D. program. Successful completion of the additional exam serves as evidence of sufficient mastery of the subject material; the final official grade does not change. The timing of the additional exam will be determined by the instructors.

Qualifying Examinations

The Graduate Student Qualifying Examinations are intended to evaluate the ability of students to (1) identify important unanswered questions in various disciplines, (2) formulate scientific hypotheses or develop methods to solve these problems, (3) design and interpret scientific experiments, and (4) write clearly and persuasively. These exams serve as an educational vehicle to enhance the training of students, and allow the faculty to assess the suitability of students to progress to the next phase of the graduate program.

The exams consist of two sections: The Comprehensive Core Exams and the Thesis Proposal Defense. The Comprehensive Core Exams are administered during the first year at the end of each module of the Core course; the Thesis Proposal Defense is carried out by February 1 of the second year (approximately nine months after the beginning of a student's thesis research).

Thesis Proposal Defense

For this part of the qualifying exams, students 1) prepare a written thesis proposal outlining the research they will conduct during their graduate work, and 2) defend this thesis proposal in an oral examination. The proposal should demonstrate understanding of the background material, project rationale, experimental design, methods underlying the proposed project and possible outcomes.

Timing

The Thesis Proposal Defense takes place during the second year after students have spent 6-9 months working in the laboratory where they intend to carry out their thesis research. The deadline for completion of the written proposal is February 1; however, students are encouraged to schedule the defense as early as possible. The report should be submitted to the student’s committee at least one week before the oral defense.

Format of Written Proposal

The Thesis Proposal follows the style of an NIH grant proposal with a maximum length of 15 single-spaced pages (11-12 pt. font; page limit includes figures, but excludes Literature Cited).

  1. Specific Aims (approximately 1 page)
    State concisely and realistically what your research is intended to accomplish and what hypotheses are to be tested. Write 1-2 general paragraphs introducing the subject and its relevance to biology, and then simply list three or four specific questions to be addressed. This section is critical because it provides a framework for the reader to appreciate the connections between sections of the proposal.
  2. Significance (approximately 4-6 pages)
    Briefly sketch the background to the proposal, critically evaluate existing knowledge and specifically identify the gaps that the project is intended to fill, i.e., summarize the general knowledge of the field, and identify where your questions fit in. This important section displays your knowledge and understanding of the field and its current shortcomings. What are the major unanswered questions? Which ones can be answered with available tools? For which questions must new methods be developed?
  3. Experimental Design and Methods (approximately 8-10 pages)
    Discuss in detail the experimental design and the procedures to be used to accomplish the specific aims of the project. Include potential difficulties and limitations of the proposed procedures, and alternative approaches to achieving the aims.
  4. Literature Cited
    References should be cited within the text by first author and year (Smith et al., 1888; Wilson and Jones, 1919) and listed at the end of the proposal in alphabetical order by first author’s last name. The page limit does not include references.

Dissertation

As the final step in receiving the Ph.D. degree, the student must write and publicly defend a Doctoral Dissertation. The dissertation should make a significant contribution to science and contain material worthy of publication.

Timing

At the end of the fifth year the Graduate Programs Manager notifies the student, the Research Advisor and the Department Head that there is one year remaining in which the student is to complete all requirements for the Ph.D. degree. A student who is on track to complete the Ph.D. degree on time should make an appointment with the Graduate Programs Manager as early as possible to discuss processes and procedures.

Dissertation

Students consult with their advisors about writing the doctoral dissertation. Each student receives ample feedback from their advisor and their laboratory group about format, style, and content. Typically, the writing process takes a couple of months. For comparison, copies of previous dissertations may be found at the Mellon Institute Library.

The student should distribute their completed dissertation to their thesis committee at least 2 weeks in advance of their dissertation defense.

Public Presentation

The final examination consists of a public presentation of the work by the doctoral candidate followed by private questioning by the Thesis Committee to determine the student’s depth of knowledge and competency.

Teaching Requirements

Students are required to serve as graders and teaching assistants (TAs) during their tenure in the department. Each student must earn a minimum of 10 points in order to graduate. A flexible point system, subject to change, enables an equitable distribution of work; typically, points are awarded according to the following scale: 1 point = 4 to 5 hours/week or 60 to 75 hours/semester.

The assignments, made by the Department Head in early summer, may require the student to assist the faculty lecturer in preparing materials for class, grading student work, leading review sessions and bookkeeping. No student is required to serve as the instructor for a course or have final judgment on course grades. In addition, the department requires that all TAs complete a sexual harassment training session given by Human Resources.

Research Advisor

Selection of Research Advisor

Each student selects a Research Advisor by the last day of spring semester of the first year, submitting their first and second choices to the Co-Chairs of the Graduate Advisory Committee. If your Research Advisor is not in the Department of Biological Sciences, you will need to have the Ph.D. Student Support Agreement Form signed and returned to the Department Head. The final choice of Research Advisor requires approval by the Department Head and students should be prepared to begin thesis research in their laboratories by early to mid-May.

If after the third rotation they have not yet identified a Research Advisor, students may be permitted to carry out a fourth rotation in May, subject to faculty availability and approval by the Department Head. Those students who remain without a Research Advisor after the end of the last rotation must withdraw from the program.

Although usually a faculty member with a primary appointment in the Department of Biological Sciences, a Research Advisor may hold a faculty position in another Carnegie Mellon department or, rarely, at another institution, provided they have advising privileges in the Department of Biological Sciences and are associated with a departmentally-approved interdisciplinary program like the CNBC.

Change of Research Advisor

A student may change advisors with the mutual consent of the new advisor and the Department Head. An advisor may request that a student leave the laboratory after verbal and written notification of a lack of effort, lack of research aptitude, failure to obey laboratory policy and procedure, failure to comply with University regulations, behavior detrimental to the laboratory or another activity that warrants this action. Consideration of this action must be brought to the attention of the student, the Research Advisory Committee and the Department Head.

Research Advisory Committee

Each student, together with the Research Advisor, selects and invites a Research Advisory Committee, which consists of at least three faculty members: the student's Research Advisor and at least two faculty members with relevant expertise in an allied field. At least two members of the committee (including the Research Advisor) must be faculty who hold primary appointments in the Department of Biological Sciences. This committee administers the Thesis Proposal Defense and then meets with the student at least once a year to provide guidance and to monitor the overall progress of the research project. It is the responsibility of the Research Advisor and the student to schedule these meetings. One committee member from another department or institution must be added to the Research Advisory Committee for the Thesis Defense. Students are encouraged to include local “external” members as early as possible to provide broader advice during their graduate career. When the research work is completed, the student writes the formal dissertation and submits it to the Research Advisory Committee in preparation for the Dissertation Defense. Students should consult their advisors about writing the dissertation.

Evaluation

Students are required to meet at least once a year with their Research Advisory Committee. To facilitate deeper discussion of research plans, students are encouraged to schedule their RAC meetings within a week after their Journal Club presentations.

Written Report to the Committee

Students are required to complete Parts 1-4 of the RAC Report Form (found at www.cmu.edu/bio/resources/forms ) and return it along with their current CV to their respective RAC as well as to the Assistant Department Head for Graduate Affairs at least two days prior to the scheduled meeting. Students are encouraged to respond in brief, bulleted format, unless otherwise directed. Students are expected not to spend more than two hours preparing this document, with the exception of the research progress summary (Question 1 of Part 1).

Note that this document will NOT become part of a student's permanent record in the departmental office. However, the student, advisor, RAC, and the Assistant Department Head for Graduate Affairs may want to save a copy.

Documentation

A Research Advisory Committee Evaluation form should be filled out after each Research Advisory Committee meeting and submitted to the Biological Sciences Graduate Programs Office. Completed forms are kept on file. Copies of the form are also available in the Biological Sciences Graduate Programs Office.