Second Year

During the second year of graduate school, each student must teach in one undergraduate-level Biology or Biophysics course (with a corresponding lab course) for each of two semesters. Students are expected to be serious and conscientious regarding their teaching responsibilities, as this is an excellent learning experience and is an important aspect of the university’s mission. Students who excel in their teaching responsibilities are eligible for departmental teaching awards. Students who do not successfully complete the teaching requirements will be placed on probation and may be subject to dismissal from the program.
Teaching assignments for second year students are made by Dr. Robert Horner ( (Cell Biology and Biochemistry laboratories), by Dr. Carolyn Norris (  (Genetics laboratory  and Developmental Biology laboratory).  Drs. Horner and
Norris are also responsible for teaching assistant evaluations in these laboratories.  Students are encouraged to communicate any course assignment preferences to the instructors listed above.  
Teaching assistantships in Biophysics for students beyond the second year will be assigned by Dr. Karen Fleming (  Evaluations will be made by individual course instructors.  Additional teaching opportunities are available for students beyond their 2nd year.
These teaching assistantships for Biology courses are assigned by Cindy Holstein.


GRADUATE BOARD ORAL EXAMINATIONS  (taken between September 1 and January 31 of the second year)
The Homewood Graduate Board requires all Ph.D. students to pass a comprehensive oral examination prior to award of the degree.  The objectives and purposes of the oral exam can be found at the Graduate Board website (  
The CMDB program requires students to take the Graduate Board Oral (GBO) examination before the end of the January during the second year of study (i.e. by January 31st of that year).  In order to be eligible to take the GBO examination a student must have a cumulative grade
point average of 3.0.  In addition, a grade of B- or better must be earned in all required courses.  (This means that while one or two B- grades will not necessarily doom you, you must in turn have some grades better than a B to satisfy the GPA requirement).  However, students who have a GPA of 3.0 or below can only take the GBO by permission of the CMDB Director(s).
In preparation for the oral examination, students must write a thesis research proposal in the form of an NIH postdoctoral fellowship application. This research proposal should be distributed to the examining committee two weeks before the exam. The purpose of the research proposal for the GBO exam is twofold: 1) it provides a framework for student and advisor to establish a working plan for the student’s thesis research and 2) it provides the members of the GBO committee with a sense of what the student plans to focus on for their thesis research and may be used as a “jumping off point” for questions during the exam. The oral examination, however, is designed to test the breadth and depth of a student’s knowledge and his or her reasoning abilities. While the research proposal is expected to be of high quality and the committee is welcome to provide feedback on this document, the student should be judged based on their
performance during the oral examination. 
The possible outcomes of a GBO are: unconditional pass, conditional pass, and fail.  
A conditional pass is given when a student’s exam performance indicates weakness in one or more specific areas in which a specific remedy can be identified to correct the weakness (typically writing a paper, taking a course, or giving a seminar).  The conditions required by the committee must be successfully completed by the deadline stipulated by the committee, which should be no later than six months after the original exam date (for conditions requiring a longer time frame, such as courses only offered the following spring, the committee can stipulate such a deadline). When a student is required to take a course to fulfill a GBO requirement, this course must be taken for a letter grade and the student must receive a B- or better. Note: only the GBO committee can decide when the conditions have been met and a student has fulfilled the conditions and successfully passed the GBO examination. The student’s advisor, CMDB Program Director and Department Chair can offer advice, but do not make this decision. Therefore, the student should contact the Chair of their GBO Examination Committee if they have any questions about whether they are appropriately meeting the conditions this committee has set for them. 

A fail is given when the overall performance on the GBO exam is unsatisfactory and/or no specific remedy for the weaknesses is readily identifiable. If recommended by the GBO Examination Committee, students may be allowed to retake the GBO examination one time only
within six months of the original exam date. Students will be re-examined by the same GBO committee unless written approval is obtained from the CMDB Program Director. 

The thesis proposal should be written in the format of an NIH postdoctoral fellowship grant application.  The proposal should include sufficient information to permit an effective review without reviewers having to refer to the literature. Brevity and clarity in the presentation are important. The proposal (including any tables or figures) should not exceed 10 pages single- spaced with one inch margins and a font size of 12.  The proposal must be distributed to committee members at least 2 weeks before the exam date.
Writing an effective grant/thesis proposal entails knowledge of the background literature, understanding the basis of, limitations to, and inherent risks in the available approaches, and an ability to design controlled experiments that will be needed to provide definitive information. Students should prepare the initial proposal with only minimal guidance and input from the thesis advisor, but after that, the level of involvement of the advisor is at the discretion of the advisor. Some advisors take this as an opportunity to teach their students grant writing skills. Additionally, students should learn from this grant writing experience the value of writing and re- writing multiple drafts, and are encouraged to read each others’ proposals to make constructive criticisms regarding clarity and logic. Multiple rounds of editing and polishing are absolutely necessary for the final document to be clear and easy-to read for a broad audience, as is typically the case for most grant applications. 
i. Specific Aims. State the specific purposes of the research proposal and the hypothesis to be tested.  (<1 page)
The "specific aims" section should begin with a short introductory paragraph which provides some context of the work in the overall field of study: why is this field of study important and what are the current outstanding questions.  There should then be an enumeration of specific aims (generally 2-5 aims).  Each aim should center on an experimental goal or biological question that can be summarized in one or two lines.  After each specific aim, a few sentences of explanation should give a summary of the approaches that will be taken toward the experimental goal.  At the very end of the specific aims section, it is useful to have a paragraph describing how the proposed research will fit into the larger realm of research in the long run.  This section often includes potential applications or experimental directions that may be beyond the scope of the proposed time period, but which demonstrate the long-term significance of the proposed work.
ii. Background and Significance. Describe the background research necessary to understand the proposed work and why it is significant  (3-4 pages). Assume that the reader is a scientist, but not necessarily one who works in your specific field.  Review only those previous studies that are directly relevant to your proposed work; this is not a general review of the field but specific information to help the reader understand your proposal. You should provide them with a working understanding of what is known and, importantly, what is not known. Explain the significance the proposed work will have in our understanding of biological processes and in practical applications. 

iii. Preliminary Studies. (Optional for GBO) Describe your initial studies that support or provide proof of principle for your proposed research. (1-2 pages). Include a description of any studies that support the plausibility of your proposed research direction and the hypotheses you put forward and/or the feasibility of the approaches that you will use. Include only those data that are directly relevant for the proposal, and do so succinctly (this is a grant proposal, not a research paper). Include figures of the most relevant data.
iv. Research Design and Methods. Provide an outline of research design and the procedures to be used to accomplish the specific aims and a tentative sequence for the investigation (4-5 pages).
This is the central core of your proposal.  The goal of this section is to describe the experimental approaches that will be used to address each specific aim, including a concise description of experimental design for "standard" approaches, as well as a full description of any novel
experimental designs that you propose. When using established procedures, provide a brief description and then cite relevant literature for details.  For each experimental direction, you should note the nature of conclusions that might be drawn, the types of control experiments that will be needed to support these conclusions, and the potential experimental problems or ambiguities that might be encountered, along with alternative strategies to circumvent these problems. Provide some framework for how you will prioritize experiments. 
v. Bibliography (not included in page limit).

The GBO examining committee consists of five members plus two alternates.  The Graduate Board, which is a JHU committee that oversees GBO exams and approves examiner committee composition, requires that two or three members be from outside the student’s home
department.  The Graduate Board has in the past invalidated GBO exams administered by a committee with an incomplete attendance or with the incorrect composition. Therefore, the exam should not begin until the ENTIRE committee is present. If a committee member is unable to attend, they must be replaced by the appropriate alternate committee member before beginning the exam. The advisor is not a member of the examining committee, but may be a silent observer in the exam.
For graduate board oral examination committee membership eligibility, please check the appropriate section below, based on the primary departmental affiliation of the research advisor.  These rules are subject to change.  Please check with Academic Affairs Administrator for a final version. At least one outside member of the committee must be an Associate Professor or higher so that he/she may serve as chairman of the examination committee.
Advisor Department
Inside Members Outside Members
Biology If 2 Biology
If 3 Biology
3 Other JHU Departments*/Carnegie maximum of 2
2 Other JHU Departments*/Carnegie maximum of 1
Biophysics If 2 Biophysics
If 3 Biophysics
1 Other JHU Department* and 2 Biology
 2 Biology
Carnegie If 2 Carnegie
If 3 Carnegie
1 Other JHU Department and 2 Biology
2 Biology
Chemistry If 2 Chemistry
If 3 Chemistry
1 other JHU Department* and 2 Biology
2 Biology
If 2 NIH
2 Other JHU Departments* and 2 Biology
1 Other JHU Departments* and 2 Biology
* Carnegie & NIH are not JHU Departments and cannot be used to meet this requirement

(For students in GPP, a maximum of  2 NIH investigators may serve on the committee as inside members.)
The student's  research advisor should select the members of the committee and convey the list of possible examiners to the Academic Affairs Administrator.  The Academic Affairs Administrator will contact faculty, schedule the exam and complete the required paperwork with
the approval of the Program Director.  The paperwork is sent to the Graduate Board at least three weeks in advance.  The Graduate Board approves the committee and returns a copy of the examination form to the Department.  The Academic Affairs Administrator will confirm the appointment of the committee members and notify them of the date, time and place of the examination via email. 

The examination must be taken prior to the start of the fourth semester in residence (i.e., this deadline date usually would be January 31st). Any exemptions to this deadline must be obtained in writing from the CMDB Program Director.  If the student is required by his/her
committee to be retested, the requirement must be satisfied within six months of texamination.  
All examinations must take place on the Homewood Campus.

The written proposal is an exercise in grant writing and students should be given feedback by the committee on their ability to write and communicate scientific information.  However, students should keep in mind that the GBO is a test of general knowledge and scientific
reasoning, and is not based solely on the written proposal.  Although some questions will deal with issues directly related to the subject of the thesis proposal, many questions are only peripherally related to this topic.  Students should assume that any issues related to topics
covered by any of the core courses are possible subjects for questioning by the committee.
To successfully conduct research in biology and biophysics, a solid, general background in chemistry, biochemistry, molecular, cellular and developmental biology is essential.  As a starting point, you might review concepts in a text such as "Molecular Biology of the Cell" and a
rigorous biochemistry text.  Another very good suggestion is to choose a half dozen key papers in your field and read the methods sections of each in detail, making sure that you understand why each experimental approach was taken, how the experiments were designed, and how the authors were (hopefully) able to draw definitive conclusions.  One piece of advice for studying: concepts are more important than details.  Don't waste time memorizing facts: they won't be useful in the exam and you'll forget them in 2 months. 
An example:
      Should you memorize the name of every protein in a ribosome? No. 
      Should you try to understand what a ribosome is and what it does? Yes. 
Many students form study groups, as well as participate in ‘mock’ GBO exams administered by more senior students. These types of activities, as well as the day-to-day process of engaging in scientific discussions with your peers, lab mates, and seminar speakers, all contribute to preparation for doing well in the GBO exam.


Remind the members of your committee of the place and time of the exam.
As a courtesy to committee members not on campus, the academic program coordinator will send parking passes to them. 
The academic program coordinator will make arrangements in advance and have your academic folder brought to the examination.
Part 1: Pre-exam closed committee meeting (generally 5-15 minutes)
Student leaves the room (but advisor stays).  There will be a general discussion of the student's progress in the first two years, strengths or weaknesses, and organization of the exam.
Part 2: Main part of the exam (generally ~90 minutes total)
Student presents the proposed project and answers questions.  The advisor is welcome in the room for this part of the exam but must remain silent. 
There are at least two formats for this part of the exam:
Formal: Approximately 10 minutes (keep it short – your examiners will have read your proposal and will be familiar with your project) are allotted for the presentation, with questions waiting until after the presentation.
Informal: The student starts the presentation and committee members interrupt with questions as they see fit. 
The choice of format is up to the committee and will be agreed upon at the beginning of the exam.  In most cases the committee will allow the student to choose the format.  With format (a), some type of timer should be used to signal the presentation time limit.
The exam is designed to assess whether the student is ready to pursue full time research toward a Ph.D. thesis.  This entails knowledge of background literature, understanding of limitations and risks to available approaches, and an ability to design control experiments that
will be needed to provide definitive information. 
The written proposal (and oral presentation) are concrete examples of the student's knowledge and intellectual skills and is thus certainly relevant to the exam.  In the past, some exams have been derailed by debates over the merits of experimental approaches taken in the advisor's lab or on interpretation of specific experiments that the student has already carried out.  While such discussions can be valuable, they should not be allowed to overshadow the focus of the exam on the student’s knowledge and critical abilities.  This is an exam of the student, not of the student’s advisor.
Rule 1: Don't panic during questions.  If you get asked a question that you can answer, answer it.  If you get asked a question that you can't answer, you might suggest how you would find out (experimentally or in the library).  If you get asked a question that you don't understand, ask the questioner to rephrase the question until you understand what is being asked.  If you know the answer, but can’t think of the specific name for something, admit it but describe what you do know – knowing something is better than knowing nothing.

Part 3: Post-exam closed committee meeting.
Student and advisor leave the room.  Members of the committee discuss the student's strengths and weaknesses, performance on the exam, and any other issues that might be relevant to the transition to full-time research status.  If there are significant deficits, the committee should decide on a course of action, either failing the student or giving a "conditional pass" (spelling out specific conditions).  If there are less significant deficits, the committee may decide on specific suggestions for the student or advisor.
Part 4: Post-exam meeting with student and advisor.
Student and advisor come back into the room.  Generally the chairperson gives a general summation of the results of the exam.
Although it is not a formal part of the GBO exam, it may be valuable to the student to:
(1) critique his or her own performance in the presentation and questions
(2) express any deficits that they feel they have in their graduate preparation and ask for suggestions regarding how to rectify the deficits (no one is perfect!).
Next, each member of the committee should give a few comments to the student that sum up strengths and weaknesses in the proposal and of the student's presentation.  These should be kept very short (a minute or so each) if the student did very well in the exam and passed, and may be longer if the student had significant deficits.
Finally, the chairperson of the committee should explain to the student any conditions for passage or re-examination, and the written exam record should be filled out by the chairperson and signed by the committee members. The student and mentor will be given a copy of any
specific conditions that need to be satisfied in the event of a ‘conditional pass’. Only the GBO committee can decide when the student has satisfied these conditions. The chair of the GBO committee is responsible for communicating with the chair of the Graduate Board
regarding the outcome of the exam, and also informs the Graduate Board in writing when the conditions have been satisfied. It is the responsibility of the student to communicate with the GBO committee chair to ensure that the conditions are understood and met.
Students who do not resolve the conditions their GBO exam by the deadline stipulated by the committee (usually within six months of the exam date) are subject to dismissal from the program.
Results of the oral examination should be recorded on the graduate board oral examination form that the chair of the committee receives. This form is subsequently recorded by the program office, Graduate Board, and finally by the Registrar.  (See Academic Program
Coordinator for these guidelines and forms.) 


In the second year of study and beyond, all students in the CMDB program are required to have an annual Thesis Committee meeting. A student’s review for a particular academic year must be completed by August 31st. No exceptions to this requirement will be made unless the student has a SCHEDULED thesis defense date. Students are responsible for setting up the meetings of the committees, which should be held on the Homewood Campus. If a student fails to meet this requirement, stipend and tuition support will not be provided for the upcoming semester and a student may be terminated from the program.  Before having the annual review, please obtain the appropriate form from the Academic Program Coordinator (see the Appendix for sample forms). 
Thesis Committee
After a student has chosen a laboratory for thesis research and has passed the GBO exam, he/she, in consultation with the research advisor, will select a minimum of two additional faculty members to serve on the Thesis Committee.  Often, these two faculty members were also on the student’s GBO committee, but this is not required.  There are no requirements for inside and outside members of the thesis committee, and the members can be from the same or different departments as the thesis advisor. Approval of the students’ advisor and the Graduate Program Director(s) is required for a student to change the members of their Thesis Review Committee.


To gain feedback regarding scientific and career development, students will complete a self-assessment form prior to each committee meeting. Copies of the completed form should be distributed to committee members prior to the meeting. This self-assessment will be discussed at the committee meeting. Faculty will not sign off on a sucessfully completed meeting unless the self-assessment form has been completed and discussed.
2nd Year: Thesis Proposal Meeting

By August 31st of the second year
, students have their first committee meeting where they present their detailed thesis proposal and preliminary data to the committee.  At this time the student is expected to have a strong knowledge of the relevant background literature,
experimental procedures planned, and possible alternative approaches that may be required for their project. Students should revise their Thesis Proposal from the version submitted for their GBO exam and include any additional preliminary data in support of their proposal. The student should also prepare a ≈20 minute presentation that describes the background, preliminary data and the specific aims of their proposal. Thesis committee members should ascertain whether the students has sufficient command of the significance of their project and relevant background literature, along with knowledge of the approaches that they propose to use and alternatives that may be needed. The committee should also discuss the merits of the proposed work and the research plan.

A number of academic activities occur on a regular basis that constitute a large portion of the training experience in the CMDB Graduate Program.  Progress Reports, departmental seminars and Colloquia present opportunities for one’s horizons to be broadened and to be exposed to a wide array of subjects and experimental approaches.  As a significant adjunct to individual thesis training, student attendance at these activities is mandatory. In addition, individual
labs or groups of investigators with shared interests also have group meetings, journal clubs and other intellectual activities in which a student is expected to participate.
Progress Reports are held in Mudd 100 each Tuesday at noon and involve research talks from students in the CMDB program and postdoctoral fellows in the Biology Department. All CMDB students are required to present a Progress Report each year after their second year (see below).  Students are expected to regularly attend the Progress Report talks. 
Seminars. The Biology Department (Thursdays at 4PM), Biophysics Department (Mondays at 12PM), Chemistry Department (Wednesdays at 4PM) and Carnegie Institution (Mondays at 12:15PM) each sponsor seminar series which include talks by visitors from other universities.
Attendance at seminars is strongly encouraged, and attending at least one seminar per week is required. Notices concerning seminars in other departments are located on the bulletin board across from Mudd 100 and on each department’s web pages.  The schedule can be found on the Biology Department website at or a Hopkins-wide seminar listing can be found at
Biology Colloquia are held once a month during the academic year. This series involves members of the CMDB Training Faculty. These talks commence at 4:30PM on the first Wednesday of each month (with a few exceptions) and attendance by CMDB students is required. 
CMDB Program Retreat. During the Fall semester, there is a retreat for all CMDB students along with faculty, postdoctoral fellows, and research associates from the Biology Department, and training faculty from Carnegie, Chemistry, and Biophysics. During the retreat, members of the Training Faculty will present short talks about the research that is currently being conducted in their laboratories.  Graduate students and postdoctoral fellows also present their work at a poster session. In addition to the stimulating science, the retreat offers a chance for CMDB students to become acquainted with training faculty and other members of our scientific community in a relaxed and enjoyable atmosphere. CMDB students are expected to attend and participate in the retreat during each of their years in the program.


At the end of each academic year, the Program Director of the training program will convene the entire Training Faculty to discuss the progress of all graduate students. For first year students, performance in laboratory rotations and the students' coursework record will be evaluated after the first semester by the Program Director, and at the end of the first year by the Training Faculty. As discussed above, any student who receives two grades of C+ or worse during the first year, who has a combined GPA less than 3.0, or who fails to otherwise meet the conditions of a probation, may be subject to dismissal from the program. The performance of students in the second year and beyond will also be reviewed by the CMDB Program Director and the training faculty. Close attention will be paid to the outcome of the annual thesis reviews, as well as to the completion of other degree requirements (above).  Students failing to make adequate progress toward the Ph.D. degree will be placed on probation and may be subject to dismissal from the program.  Students entering the sixth year or greater of
graduate study must present a plan for completion of study, and obtain permission to continue in the program signed by the Program Director, in order to register.