College of Science & Engineering

The Thesis

Purpose of the Thesis

A thesis is the culmination of your graduate work at WWU. The purpose of the thesis is to provide you with the experience of designing and conducting original and independent research, carrying out a research project, and reporting on the investigation in accordance with the accepted norms of the scientific discipline. Indeed, the purpose of the M.S. degree is to educate, guide, and train you to be independent scientific investigator.

Choosing a Thesis Research Project

As a graduate student, you should pursue a project that is of interest to you, under the guidance of your thesis advisor and Thesis Committee. Their insight regarding the originality, importance, and feasibility of different research projects will help you define the scope of your thesis project. The help of the Committee during the selection and planning of a thesis research project can make a huge difference in developing a successful thesis project that can be completed in a timely manner.

The sooner you start planning your thesis project, the better. An early start will give you every opportunity to define a rewarding project of reasonable scope. Also, by beginning the planning process right away, you will have a better chance to meet deadlines for internal or external funding for your research (see Section 9), and may even be able to start collecting data sooner. Note that two of the core courses in the graduate curriculum (501 and 525) will provide opportunities to hone your research ideas.

Your general research topic should be presented to the Thesis Committee at the time of the first meeting of that committee (second quarter of your first year). Do not initiate research involving human subjects or live vertebrates until permission has been received from the relevant oversight committee (Human Subjects Review Committee, for more information see their website; Animal Care and Use Committee, for more information see their website). Prompts for these approvals are on the Thesis Topic Approval card (see Section 5.3). You should not seek signatures on this card until any and all relevant approval processes have been cleared. In addition, MESP students planning to conduct research at Shannon Point Marine Center will need to fill out an application for use of facilities before beginning the thesis research. You can obtain this application from SPMC’s webpage. Research requiring SPMC staff time, boat use, and SCUBA support should be planned and coordinated with SPMC personnel in advance of final thesis topic approval.

During your second quarter, you will prepare a detailed thesis proposal following departmental guidelines (see Section 5.4.1). You must get the approval of this proposal from your Thesis Committee after meeting with them during the third quarter of your first year.

Biology 690–Thesis Research

You may register (online) for thesis credits, Biology 690, during the M.S. program, under the following restrictions:

  • You cannot register for Biology 690 until you have Advanced to Candidacy (see Section 5.2) and have had your thesis topic approval card signed and accepted by the Graduate School (see Section 5.3).

  • You must have a minimum of 12 hours of Biology 690 credit in the M.S. program, to complete a M.S. degree, but you may count up to 21 credits of Biology 690 toward the 45 credit total for the degree.

  • All grades for Biology 690 are K (incomplete), until the thesis is defended. When the “Recommendation for Master’s Degree card” is signed after the thesis defense, the thesis advisor indicates on the card the 12+ hours of thesis credit and the grade (S or U). It is not necessary to complete a “K removal card.”

Many graduate students use Biology 690 credits to “fill out” the credits in their programs, and to maintain sufficient credits to qualify for financial assistance. If you receive Financial Aid, you should be mindful of the credit criteria used by the Financial Aid Office to evaluate eligibility; check with that office regarding these criteria and register for the credits necessary for maintaining financial aid status. See Sections 8.2.1, 9.1.2, and 9.1.3 regarding the minimum number of credits for which you must be enrolled to remain eligible for TAships, RAships, and Graduate Work-Study. If you use Biology 690 credits for maintaining eligibility for funding, be mindful of the fact that you can only register for a maximum of 36 credits of Biology 690 during your time at WWU.

Writing the Thesis

Perhaps the most valuable advice the faculty can give a graduate student on writing a thesis is that it is more challenging and takes more time and effort than one would think. As a rule of thumb, the first complete draft of the thesis should be finished at least one quarter prior to the quarter planned for defense and graduation. Keep in mind that the final copy of the thesis must be submitted to the Graduate School about a month prior to the end of the quarter in which you expect to graduate.

Writing the thesis actually begins with the development of the thesis proposal, as the proposal may form the core of the Introduction and Methods sections of the thesis. You should begin writing the rest of the thesis as soon as you have obtained results. At that time, you can also revise the description of the Methods, if necessary. Also, if the thesis research takes on new directions from what was originally planned, you may need to substantially rewrite the Introduction5. You should plan on having multiple rounds of revisions as you work with your thesis advisor to hone a well-written thesis. Before beginning to write up the results, you should seek input from your Thesis Committee members on data analysis and how best to interpret your results.

Each thesis advisor has a particular style of writing, largely influenced by the conventions of his or her sub-discipline and the journals to which any manuscript(s) describing the thesis research are likely to be submitted. Although your thesis advisor will not try to force a particular style upon you, they will undoubtedly make many editorial changes and suggestions on drafts. You should view these suggestions in the spirit in which they are made, as part of the learning process that is intended to help you become an independent scientific investigator. Do not, however, expect your thesis advisor to write or rewrite your thesis, in whole or in part.

Each thesis must be formatted in accordance with the Graduate School’s guidelines (see their website for a complete description of these specific guidelines). Past graduate students have compiled a list of helpful tips, which you can find at Biology’s website. Any of the standard type (font) styles are acceptable; Times Roman 12 pt is preferable. You and your thesis advisor are responsible for checking the final thesis before it is submitted to the Graduate School for the Graduate Dean’s approval.

Reference citation, footnoting, and other technical aspects of all Biology Graduate Program theses must be according to CBE Style Manual 3rd or later edition (A.I.B.S., Washington, D.C.). In developing a writing style, you may want to consult some of the references listed below.

  • Day, R. A. 1998. How to Write and Publish a Scientific Paper. 5th Greenwood Publishing Group, Inc., CT. 275 pp.

  • Knisely, K., 2005. Student Handbook for Writing in Biology. 2nd ed., Sinauer Associates, Sunderland, MA.

  • McMillan, V. E. 2001. Writing Papers in the Biological Sciences. 3rd ed. Bedford Books/St. Martin’s Press, NY. 207 pp.

  • Pechenik, J.A. 2004. A Short Guide to Writing about Biology. 5th edition. Pearson Ed. Inc., 302 pp.

  • Penrose, A.M. and S.B. Katz. 2004. Writing in the Sciences. 2nd ed. Pearson Ed., Inc., 448 pp.

  • Strunk, W., Jr. and E. B. White. 1979. The Elements of Style. 3rd ed. Macmillan Publishing Co., NY. 92 pp.

  • Wilkinson, A. M. 1991. The Scientist’s Handbook for Writing Papers and Dissertations. Prentice-Hall Advanced Reference Series, NJ. 522 pp.

Thesis Completion Procedure

As you near the completion of your M.S. degree, you must take a prescribed series of steps. The official deadlines for some of these steps vary from quarter to quarter, and are posted on the Graduate School website. Below is a list of the steps and their approximate deadlines. Unless noted otherwise, online forms for each of these steps are available at the Graduate School’s website.

Quarter before you intend to graduate

  • Apply for Degree (submit online form here) by the last day of the quarter proceeding the quarter in which you intend to graduate. A diploma fee is assessed by the University at this time.

  • Work with your advisor to revise thesis draft to acceptable form for committee review. You should complete a draft that is ready for your committee before the end of this quarter–at the very latest the first week of the following quarter.

Quarter in which you intend to graduate

  • Following advisor approval, the draft goes to committee members for review 2 weeks before a pre-defense meeting6.

  • Pre-defense meeting7. The goal of this meeting is for the committee to discuss the draft thesis, suggest revisions, and help you bring the thesis into final form. It is not intended as a defense, but rather to answer the following questions:

    • Are there major issues with the thesis that need fixing?

    • If and when to schedule a defense, or to meet again. If only minor revisions are needed, you and your committee can move forward with scheduling a seminar and defense. If there are major issues, the committee can arrange to review any revisions at a second pre-defense meeting prior to scheduling the seminar and defense.

  • You must incorporate revisions suggested by the committee under guidance of your thesis advisor. The amount of time taken for this depends on the extent of the revisions needed.

  • Schedule your oral defense. At least 2 weeks before your defense submit the oral defense form to the Graduate School (submit online form here). The deadline for the oral defense form is typically four weeks into a quarter, but see the Graduate School’s web site for specific dates. The oral defense should be held after and within one week of the seminar. In addition to submitting the oral defense form, reserve a room for your defense at the Biology office.

  • Schedule your thesis seminar. Submit Thesis Seminar form to the Biology Department (due two weeks before the thesis seminar). This form is available in the Biology Department office. The Thesis seminar should be held before and within one week of the defense. See Section 6.6 for further guidelines regarding thesis seminars.

  • Once your committee and advisor are satisfied that appropriate revisions have been incorporated and you have scheduled your thesis seminar and defense, the thesis is tabled in the Biology Office for review by faculty at least 1 week prior to the seminar.

  • Give your thesis seminar (based on near-final tabled thesis). Seminars will be scheduled for 1.5 hours, with an anticipated 45-50 minute talk and the remaining time for questions.

  • Defend your thesis. Given the pre-defense meeting in which issues with the thesis were dealt with, during the defense committee members might focus on questions that assess your general knowledge of the discipline. If you pass the defense, the committee signs the electronic Degree Recommendation Form. If questions arise at the seminar, defense or in faculty comments on the tabled draft, then you, with guidance from your advisor, incorporate appropriate revisions before the committee and advisor sign the e-form.

  • Submit final thesis to Graduate School. See the Graduate School’s web site for the deadline for this step. Congratulations!

The Graduate School policy for credit enrollment and quarter of graduation is a bit convoluted. According to the official policy, one must take at least 2 credits the quarter of, or immediately prior to, the quarter of graduation (not counting summer quarter). For example, if you officially graduate in fall you do not need to register for any credit in fall. As long as you registered for at least two credits in the previous spring. So what happens if you plan to graduate in fall but do not meet the official deadlines? As long as you finish all your thesis related work (e.g., seminar, defense, revisions, submission of thesis for printing) BEFORE the end of fall quarter (the last day of finals week) you will technically graduate winter quarter, but still do not have to take any additional credits. However, if you are further delayed, and not finish until after finals week of fall quarter, this would no longer be true, and you would have to take at least 2 credits winter quarter.

Thesis Seminar

You must present a seminar on the results of your thesis research, following the guidelines below:

  • Thesis seminars must be held on campus under the auspices of the Biology Department.

  • Thesis seminars are announced as Biology Department seminars. Because time conflicts are common for lecture spaces, schedule early to ensure getting a room with the technology that you need for your seminar. The office staff can help with room scheduling.

  • Prior to presenting a thesis seminar, you should give at least one practice talk with at least one Thesis Committee member present, usually your thesis advisor. We strongly recommend getting abundant feedback from your thesis advisor about the content and presentation of the thesis seminar.

Thesis Defense

What the Thesis Defense Covers

You should discuss with your thesis advisor and committee the nature of the defense and prepare accordingly. The defense questions aim to assess the breadth of your understanding of the major biological subdiscipline that is the foundation of your thesis, and to determine whether you can place your project in a proper context and understand its significance. The Thesis Committee members typically confine their questioning to knowledge they believe is related to your thesis. This might include details about the thesis itself as well as questions about the broader context in which your work fits.

Graduate Council Representative

Depending on availability, the Graduate Dean tries to appoint a member of the Graduate Council or another suitable representative to attend the thesis defense. The Graduate Council Representative’s role in the examination process is to act as a protector of your interests. The Representative is the judge of whether the exam was fairly conducted. If the Graduate Council Representative decides that the thesis defense was not fair, the defense is adjourned without decision, to be rescheduled at a later date. If the Representative decides that the thesis defense was fairly conducted, then the Thesis Committee members vote on whether or not the candidate passes. The Graduate Council representative may have a few questions to ask you about the thesis.

In recent years, time pressures, the limited availability of Graduate Council members, and schedule conflicts, have meant that most Biology Department thesis defenses have not been attended by a Graduate Council Representative. In these cases, the thesis advisor asks the graduate student if he/she thinks the thesis defense was fairly conducted. However, if you prefer to have a representative attend the thesis defense, a request to either the Graduate Program Advisor or directly to the Graduate School will increase the likelihood of the presence of a Graduate Council representative at your thesis defense.

Passing or Failing the Thesis Defense

Once the thesis defense has concluded, the Thesis Committee members vote on: (1) whether you have passed the defense, and (2) whether your thesis is acceptable. The policy of the Biology Department states that these votes must be unanimous for a student to pass. If you pass the defense and your thesis is acceptable with minor revisions, then the Thesis Committee members will sign the Recommendation for Master’s Degree form, found here, and the signature pages. Your thesis advisor signs the form and signature pages after revisions requested by other committee members have been made.

If you do not pass the thesis defense, the Thesis Committee and you will schedule a second defense. If your thesis is not acceptable, the Thesis Committee and you will agree on a reasonable timetable for revising the thesis. If you subsequently pass the second exam and/or submit an acceptable revised thesis, then the Thesis Committee members sign the Recommendation for Master’s Degree form and the signature pages. Again, your thesis advisor is the last member of the committee to sign the form and signature pages. You have two chances to pass the final examination.

Even if you pass the initial thesis defense, you will probably have to make final revisions to the thesis, based on issues raised by the Thesis Committee.

If you have pressing deadlines that require the thesis be completed and signed off by a specific time (e.g., foreign visas, Graduate School requirements for finishing within 5 years), it is your responsibility to be sure adequate time is allowed for revisions, including time for Committee Members to review the revised thesis before signing off. Revisions will be required until the thesis is acceptable. The Thesis Committee is under no obligation to approve the thesis before it satisfies departmental standards. If you feel that you may have difficulty reaching this goal because of advising difficulties, personal issues, or any other reason, you should initiate discussions immediately with your advisor, Committee, Graduate Program Advisor, or Department Chair (as appropriate) to resolve these issues before your deadline is imminent.

Signature Pages

When you pass the thesis defense, your Thesis Committee members will sign the Recommendation for Master’s Degree form (see Section 6.7.3), and several signature pages for the bound copies of the thesis. You should have your Thesis Committee members sign more than enough signature pages for the number of copies to be bound. Each bound copy should have a signature page, with original signatures. You should make sure that your thesis advisor has the recommendation card and the signature pages in his or her possession before the start of the defense.

Duplicating, Binding, and Depositing the Thesis

When the final approved copy of the thesis is ready, you must take it unbound to the Graduate School so that it can be checked for conformity to the requirements of the University. You should also take the appropriate number of original signed signature pages, equal to the number of copies to be bound, to the Graduate School. After Graduate School approval of the thesis, the signature pages will be signed by the Graduate Dean.

Once the Graduate Dean has signed the signature pages, you will be notified by the Graduate School. Then you should deliver the thesis and the signed signature pages to Haggard Hall Copy Services for copying and binding. Specific information on the requirements for this process is posted at the Graduate School’s Thesis Guidelines publication website. Be sure to read this information.


Binding shall be in dark blue. Lettering must include the thesis title and author’s name, in gold. This done at Western Washington’s copy services.

Number of Copies

A minimum of four bound (hard cover) copies must be made:

  • two copies, including one with original signatures, must be deposited with the Graduate Office (both copies are for the library, one for the archive collection and one for circulation)

  • one copy is for the thesis chair

  • one copy is for the student

  • one copy is for the Biology Department

  • for MESP students: one copy for Shannon Point Marine Center

Some students might want more than five copies, if they have arranged to provide a copy of the thesis to another party. For example, if you performed thesis research in a National Park or a National Forest for their research, it would be courteous to provide the agency with a bound copy of the thesis. Also, many graduate students have extra copies made for distribution to friends, parents, thesis committee members, and others who helped with the thesis. These additional copies can be inexpensively bound with a soft cover and plastic strip binding at the same time the five hardbound copies are requested. There are also local and online companies that can copy and bind additional copies of your thesis.

Depositing the Thesis in the Graduate Office

Deliver two bound copies of the thesis to the Graduate Office.

Cost of Binding

The copy of your thesis for the Biology Department is paid for by the department by pro rating all costs for copying and binding, and then by paying the expense of one copy. For example, if you have 5 copies and pay $45 for binding and $20 for copying, the department will provide $13 as reimbursement, and you will pay for the other copies. SPMC will also reimburse MESP students for the copy for Shannon Point Marine Center.

If the thesis is thick enough, the student’s name should be put on the spine of the department copy. The date would be useful as well. The department will pay for this extra expense on the department copy only.