Introduction to the Biology Senior Thesis

Why Must I do a Senior Exercise?

All Pomona concentrations require the completion of a senior exercise, a project that is intended to demonstrate that students can think independently and creatively about their chosen disciplines and can use the research tools of those disciplines. The Biology Department senior thesis represents the culmination of your biology education at Pomona.

What is the Senior Exercise in Biology?

The biology senior exercise consists of the identification of an interesting, unsolved question in biology and the formulation of an original, testable hypothesis.  It also includes designing a research protocol intended to test that hypothesis and evaluating the results.  Thorough analysis and clear communication are two immutable requirements for any senior thesis in biology.  There are two options:

A.  The research grant proposal

The grant proposal option is a one-half credit, one-semester exercise that requires you to write a research grant proposal like those that practicing biologists submit to granting agencies.  Such a proposal explains the exact nature of the problem and sets it within the context of work already accomplished in the field in order to explain why the problem is an interesting and important one to study.  The proposal then outlines, in considerable detail, the approach that you would use if you were actually to carry out the research.  Your aim here is to convince a granting agency that is familiar with the literature of your field, that the problem or question is an important one, and that your experimental approach is practical and likely to succeed.  We expect you to put in an effort throughout the semester equivalent to that of a regular, one-half credit course.

B.  The laboratory/field experimental research thesis 

The experimental thesis option is a two-semester exercise that requires you to design an original study, carry it out yourself, and write up your results in the form of a scientific paper.  As with the research grant proposal, the importance and significance of the research must be set in the context of what has been already been done in the field.

You will earn a total of 2.0 course credits for an experimental thesis.  During the fall semester you will register for one credit of Biology 194A, and during the spring semester you will register for one credit of Biology 194B.   We expect that you will devote equal time and effort each semester, equivalent to that of a 2.0 credit course extending over two semesters.

Students electing to undertake field research should discuss with a faculty member an appropriate project, one either closely related to the faculty member's own research or, with the approval of the faculty member, of the student's design.  Students electing to undertake laboratory research must realize that the project may necessarily be limited by the availability of necessary supplies and equipment in the laboratory of the faculty member in which they work and, accordingly, may need to be closely related to the research conducted in that laboratory.  If you would like to do laboratory research, your first step should be to contact the faculty member whose research is in the area most similar to your own interests so that the two of you can discuss an appropriate thesis project.

What Options Should I Choose?

Each option has its own rewards and frustrations, and each requires the demonstration of somewhat different abilities.  Both begin at the same point: the identification of an interesting problem to study that can be narrowed to a testable hypothesis.  The grant proposal allows you to tackle a rather sophisticated problem because typically a proposal describes 2-3 years of full time work.  A laboratory/field thesis demands that you identify a limited problem that you can reasonably address within two semesters.  This problem is narrower in scope than those in a grant proposal thesis simply because you will actually do the research that you propose.  It requires more long-term planning, but it also provides you with valuable practical experience and the satisfaction that comes from completing a piece of research yourself.  A laboratory/field thesis will sharpen your ability to cope with the unexpected, and the experience will teach you much about yourself and about the psychological demands of research.  This option is recommended for students who are interested in going to graduate school or for those who think they might be; the only way to discover whether you want to spend a career doing research is to try it.  An application to graduate school will be strengthened by having the experience of designing and carrying out your own research project.

How do I Choose a Problem?

For many students, this is the hardest part.  These suggestions might help:

  1. In your classes, keep a list of "unanswered questions" -those issues that your professor, text, or readings identify as unresolved.  Any upper-division biology course will introduce you to many such questions.
  2. Have you been involved in any undergraduate research projects (summer or academic year) that you found particularly interesting?  Think about expanding on your experience in this area.
  3. Think about laboratory or field exercises in your courses that you particularly enjoyed.  Think about ways to follow them up, and/or talk to the professor of that course about ways a course project could be expanded into a thesis.
  4. Look at current issues of Science, Nature, or Trends in ...(Genetics, Neuroscience, Ecology and Evolution, Plant Science, etc.)  All these journals have "News and Views" sections that report on new and interesting research directions in specific fields.
  5. Above all, begin planning well in advance!  A few days is not enough time to come up with a problem that will keep you interested for a whole semester or two.

Once you have found a topic, determine whether or not it meets all of the following criteria:

  1. Do you have sufficient background from your course work and/or research experience to address this topic?
  2. Is there a faculty member(s) in the Biology department who can serve as advisor(s) on this topic?
  3. If you are proposing to repeat a study but on a previously untested organism, is there a strongly compelling reason to do so?

How Soon do I Need to Decide on What I Will do?

You must submit a "contract" to the biology department with an outline of your problem before you can pre-register.  For a fall grant proposal or a year-long research thesis, this contract must be submitted before pre-registration in the spring of your junior year.  For a spring grant proposal, the deadline is pre-registration in the fall of your senior year

What do I Need to Arrange Before I Pre-Register?

You must complete and turn in a "senior exercise performance contract [pdf] ", which is at the end of this handout and includes:

Signature of one reader/advisor

The signature of one professor from the Biology Department who agrees to serve as the reader/advisor for your proposal or thesis.  The choice of potential advisors and a research problem go hand-in-hand, and an advisor won't agree to sign unless he/she is persuaded that your problem is well chosen and well thought out, and that he/she is an appropriate reader for your topic.  Give a professor some warning that you are going to ask him/her to serve as a reader (and be prepared to be turned down, especially if you approach her/him at the last minute), and discuss your ideas with him/her well ahead of time.

OPTIONAL - Names of three additional faculty

We ask for these suggestions because sometimes topics require an additional reader to be fairly evaluated. Not all theses will be assigned a second reader, however. List up to three additional biology faculty whom you suggest as potential readers for your thesis.  If you receive two readers, the biology faculty will make every effort to select the additional reader from this list of three in a way that will fairly distribute the overall senior thesis workload among the faculty, but we can not guarantee that we will select one from your list.

One-page description (abstract) of your thesis topic

You must outline the problem you have chosen to study and demonstrate by your description that you have the background knowledge to pursue this topic.

List of at least ten recent articles (reference list)

(typically papers published within the last 5 years, although there may be some exceptions)

Select these articles from the primary literature (original research articles).  They should both provide a thorough background and demonstrate the current understanding of the topic you wish to address.  Your reference list serves to convince the department that there is enough known about your topic to allow you to pursue it fruitfully and that you are sufficiently familiar with it.

List of research requirements

(experimental theses only)

For a laboratory/field thesis, you must discuss with your reader your particular research needs such as field sites, lab facilities, permits (if necessary), equipment, and supplies.   A contract for an experimental thesis must include a list of your research needs and a proposed budget.  Be advised that a thesis requiring more than $500 will be approved only if funds are available.

After submitting these materials, the department will meet and review all thesis contracts.  At that time, the faculty will decide whether each student has selected a topic that is reasonable and well researched.  If this is the case, you will be notified that your thesis contract has been approved (and who is your second reader if any).

Important Reminders For Both Options

Meet Regularly with Your Thesis Readers 

We hope that these guidelines will be helpful to you.  If you have any questions or are confused about any aspect of your thesis, it is always wise to consult with both readers (if you have two).  Although periodic meetings are not required, we recommend them very strongly, and it is optimal for your meetings to include both readers.  It is your responsibility to maintain close contact with your faculty readers throughout the course of your thesis, inform them of your progress and seek their advice as needed.  It is to your advantage to have your readers make suggestions in informal meetings during the semester rather than only on the final copy.

Your Thesis Must Be An Original Piece of Work 

We expect the ideas in your thesis to be an original product, of your own reflections and analyses.  Of course, they will arise from a combination of your study of the ideas of others and you own original contributions.  It is therefore necessary to make a careful distinction between ideas that you adopt from other sources and those you develop yourself.  You do this by citing in your text the sources of ideas from others that you adopt or discuss.  We consider the inclusion of any ideas of others that are not cited as a case of your being dishonest about the intellectual origins of your thesis.  When in doubt, whether you learned something from reading, from a class lecture, or from discussions with others, you must acknowledge the source when you use that information in your thesis.  This applies not only to factual information but also to ideas.  You know that in other types of writing, you must provide a reference for a direct quote in addition to putting that statement in quotation marks to indicate that the wording is not your own.  However, if you paraphrase another source, you must also acknowledge that source because the basic idea is someone else's, even if the particular words are yours.  Failure to acknowledge your sources will be treated as a violation of the rules for Academic Honesty, as described in the College catalog.  If you have a question about what constitutes plagiarism, consult your ID 1 handout, the description in your Bio 40, Bio 41C, and/or Bio 41E lab manuals, lecture notes on plagiarism from other courses, and/or your readers. 

You should obtain your information from the primary literature; do not use textbooks or review articles as your principle sources of information.

These ethical rules are fundamental to the practice of science.  Science is a collection of ideas about the way that nature "works", and these ideas are refined by experiment and observation.  People who contribute these ideas are entitled to the credit for them; ideas are intellectual property.  You will want to be recognized and acknowledged for your own original contributions, and it is only fair that you treat others accordingly.

The very fact that this section of the guidelines in large part repeats what we have stated earlier is an indication of how seriously we take the issue of academic honesty.  We expect that you will, too.

The entire Biology Department faculty hopes that when you have finished, you will consider your senior thesis as the best work you have done at Pomona College.  It is our fervent desire that you will look back on your thesis with pride as a rich learning experience.