Getting Involved in Research for Academic Credit

Students may enroll in Bio 490 (senior level) or Bio 390 (junior level), Independent Study, for one or two courses of elective credit towards the Biology major (see the College Catalog). Independent Study is performed with a Biology professor as an adviser, and involves an independent research project performed in that professor's laboratory. The exact nature of the project is outlined in consultation with that professor but typically involves the continuation of on-going research in the professor’s area of expertise. Some independent study projects result in a published journal article, some of which are on display outside the Biology office on the first floor of LSP. Many of the posters in LSP hallways also describe work done by students during 390/490 projects.  Different professors require different amounts of written work from the independent study student, but the Department requires a thesis at the end of the project, and a progress report at the end of the first semester in the case of two-semester projects.  See Written Reports link on this page. 

In a typical year, up to a third of the senior biology majors will enroll in Bio 490. Students who complete a two-semester project and who meet other requirements may be candidates for Departmental Honors; a successful oral defense of the project is required for Honors in Biology.  Requirements for Honors work are found here.

Any student with an interest in Bio 390 or 490 should talk to faculty about the possibility of doing research.  You will not be committing yourself! You may decide that research is not for you; that's fine. But don't hesitate to discuss the possibilities. You should think about one semester (fall or spring) or two semester projects. Talk to several faculty members about their work if you do not have a fixed idea of the area you wish to study. The specific project you do is not as important as the interactions you have with the faculty member who is sponsoring your research, the thought process involved in developing and testing your own hypotheses, and the opportunity to actively participate in your own education. You should think about your preferences for level of biological organization (population, organism, cell, molecule), the kinds of tools used in particular areas, and the styles of student/professor interaction that different faculty have. We also encourage you to talk to students who are currently enrolled in Bio 390 or 490 or who have done summer research projects. Most faculty members will advise two or at most three independent study students at a time. Students in Bio 390 or 490 must ordinarily have achieved a 3.0 average in major courses, but we have waived this requirement for students who have a strong commitment to research or who have shown improvement in their course work. If this policy affects you, don't hesitate to discuss your situation with potential research advisers.

  • Enrollment

    Enrollment in BIO390 or 490 requires that a professor agree to sponsor you, and the Department must agree that your record supports the probability of a successful independent study experience.  Discuss the possibility of Independent Study with faculty members well in advance of the semester you would like to begin. Be sure to finalize plans for your independent study during preregistration for your target semester. To help you with your planning, you can:

    • Speak to the Associate Chair of the Department about the possibility of doing independent study.
    • Speak to students who are doing independent study.
    • Examine
    • To get ideas about potential research directions, examine research opportunities described in the Biology Faculty web pages, on posters in the hallways of LSP, and in the page listing examples of previous undergraduate research projects.
    • Speak to several professors about doing independent study in their laboratories.
    • Finally, choose a professor with whom you wish to do independent study and ask him/her to sponsor you.  You must have express permission from your research advisor by the pre-registration period the semester you intend to begin.

    At the start of the semester, obtain a special registration form in the Biology Office or from the Registrar's Office.  You will need to include with this form a brief description of your research project (~1 page) as well as a bibliography of literature pertinent to the topic.  Your research mentor can help you prepare these items.  The form must be completed and turned in to the Associate Chair of Biology within the first week of the semester you begin your study.

  • Guidelines

    • Students must first secure the consent of a potential research adviser to pursue a 390 or 490.  That student’s record will then be reviewed and must be approved by the entire Department.
    • Credit will be given only for research conducted under the direct supervision of a member of the Department of Biology.
    • A student may not enroll for two credits of BIO 390 or 490 in a single semester.
    • A Biology, BFB, Environmental Science or Environment Studies major may satisfy only two of the required biology electives with BIO 390 or 490.  
    • Biochemistry and Molecular Biology majors may satisfy only one of the required electives with a BIO or CHM 390 or 490.  Note that with approval of the BMB adviser, BMB majors may also receive 390 or 490 credit for research done in the Chemistry department.
    • All BIO 390 and 490 projects will culminate with a written report that is to be reviewed by at least one additional Biology faculty member (called the second reader), prior to submission of the grade for the course. The adviser and the second reader consult on the grade for the work in all cases. The second reader may also be involved in a consultative role during the design and implementation of the project, but this is not required for all projects. This paper must be completed by the first day of final exams.
    • In the case of a two-semester project, a progress report is required at the end of the first semester, and the full written report is prepared in the second semester.
    • In certain circumstances, an independent study report will include work from more than two semesters or from a summer and two semesters (semesters must be clearly designated).
    • Regular grades will be given for all semesters of BIO 390 and 490. The P/NP option may not be exercised. The grade for work in independent study is decided by the independent study adviser in consultation with the second reader. The second reader brings to the discussion an opinion of the quality of the written work (progress report or final paper), while the adviser brings knowledge of the quality and amount of work accomplished and the degree of independence shown by the student. The grade on the written paper is one half the grade for the course and the second reader contributes half the grade on the written paper.  

  • Expectations

    Following is a copy of a memorandum that Emeritus Professor Richard Fluck gave to each of his independent study students. Although it is a  personal document specific to  Prof. Fluck's research and laboratory culture, the department feels that it accurately conveys our general philopsophy regarding the responsibilities of our independent study students.

     To: Biology 490 Students
    From: Richard A. Fluck
    Re: Independent Study in my Laboratory


    Students pursue independent study for various reasons. Some of you have done research before, have liked it, and want another chance to work on a research problem. Others of you have never done research and want to find out what it's like, whether you like it, and whether you can do it. Some of you look forward to the challenge of working independently and to the possibility of discovering something. Some of you find our standard courses too confining and would like the freedom you think Bio 490 will give you. Probably all of you know that Bio 490 will look good on your record.

    I need to know why you want to pursue independent study, because to some extent I will tailor my advising to meet your wishes. What are your goals in pursuing Bio 490? What do you hope to find out about yourself? What do you hope to accomplish?

    My philosophy and expectations:

    If you work in my laboratory, I will treat you as an apprentice--not as a technician to do my own research. However, except in very unusual circumstances, you will work on a research problem closely related to the ongoing project in my laboratory. Biological research--probably any kind of research--is complex, and it is usually foolish to jump into a new problem without the necessary background. My students and I have been working on various aspects of medaka development since 1974, and in that time we have learned a lot about the medaka embryo and have developed a number of standard procedures that you can use to get started on your own project; these procedures will give you a good base onto which you can add your own protocols.

    At any one time, we are usually pursuing several lines of investigation in the laboratory--some of them are old lines, while we have just opened others. I will do my best to describe for you the overall objectives of the study and to describe the alternative projects that you may choose to pursue yourself. I will have pursued each line enough to know that 1) it really is a problem worth pursuing, and 2) there are no major technical problems that will hinder you from pursuing the problem. You and I will then agree that one project is the best one for you to pursue, taking into account your background, interests, and time commitment (one or two semesters); and the likelihood of "success."

    Once we have settled on a project, it becomes your project. I will advise you, but you must take responsibility for the project--the literature search, the research, and the writing. And just as I will not come into the laboratory to do your experiments for you, I will not write your thesis or progress reports for you. These are primarily your responsibility; I am here to advise you. I will do my best to give you feedback about your performance and progress along the way. If you are doing well, I'll tell you. If you seem to be slacking off, I'll tell you that. But I will not ride you to get you to work. Frankly, I have better things to do.

    The Biology Department's "Department Guidelines for Independent Study" and "Criteria used in Evaluation of Independent Study Projects" contain useful information about independent study. You should read both documents carefully. I would like to state some additional expectations I have:

    I expect you to work on your project at least fifteen hours per week. This includes weekly meetings with me and also time spent reading, working in the laboratory, and writing. In fact, most students have found they must work more than fifteen hours if they hope to make reasonable progress. Many of the experiments you will perform will require large blocks of time--up to 10 hours at a stretch; you should plan your schedule accordingly.

    I expect all my students to share the routine work in the lab: feeding and otherwise caring for adult fish; collecting, cleaning, counting, and growing embryos; cleaning up after themselves, including washing and putting away their own glassware.

    I expect you to meet with me at least one hour each week. The agenda for these meetings is up to you and can include reviewing data, discussing the primary literature, going over experimental protocols, working on drafts of paper, etc.

    I usually ask my students to prepare a literature review(s) in the area of their project. Due fairly early in the first semester, these reviews get you into the literature, make you think carefully about your project, and get you started writing. These literature reviews have often formed the basis for the introduction of a thesis.

    I expect you to submit drafts of all your documents and to submit them early enough that I have time to study them carefully. We will agree on a series of due dates early in your project and then try to adhere to them. You will write all your documents on a Macintosh computer.


     Just a few words about honors. I believe that honors is something that is granted retrospectively. That is, a faculty committee looks at a thesis, the research it represents, and a thesis defense and then decides whether the work is worthy of Honors in Biology. I do not believe that honors should be a major goal of independent study. In fact, if an important reason for you pursuing independent study is that you may qualify for Honors in Biology, I'd rather not work with you. My experience is that this is not a good reason to do research. I love doing research, I have fun doing it. It's worthwhile in and of itself. If your work qualifies you for honors, fine. But honors should not be your major goal.

    If you want to have your project considered for Honors in Biology, it is your responsibility to make it worthy of consideration--to make both the research and the writing worthy of honors. I will not repeatedly edit your writing to get it into shape for a suitable thesis. It seems to me that your ability to do this is part of what the committee evaluates.

    In evaluating your project, the committee and I will look at two semesters of work--not one semester. Too often students slack off in the fall and then come on strong in the spring, hoping that a strong finish and good thesis will carry them into an honors defense. I will not permit you to do this; I expect you to put in two semesters of good work if you want me to support you application for honors.

  • Criteria for Evaluation

    These comments attempt to clarify the goals of BIO 390 and 490 as the Biology faculty perceive them, and to alert you to what we will be thinking about as we read your reports. We intend here to clarify the aspects of your research and written reports that we value most highly. We hope these criteria, and their explanations, are useful to you as you think about your research, and later as you prepare your progress report and final report.

    • Degree of difficulty of the project:  Some projects are "safer," more narrow in design, or tread more familiar ground than others. Where your project fits in this continuum is not something you should worry about – in large part it is your adviser's responsibility to help you find a project that is possible to do in the time available, and to ensure that it is challenging, asks interesting questions, and has clear focus. Evaluators recognize that some projects are higher risk ventures than others, and make allowance for this in their evaluation.
    • Actual importance or novelty of findings:  Although some projects may lead to publication and be blessed with beautiful, definitive results, this is a very minor criterion of a successful BIO 390 or 490 project. You may actually learn more from a project in which the findings are very modest and inconclusive, and your evaluators may be more impressed by the way you wrestle with such results than by less thoughtful treatment of "beautiful" results. BIO 390 and 490 are supposed to help you become a scientist in your approach, analysis and thought processes, and your project will be judged on the evidence that you have progressed in that direction. Importance or novelty of findings, in and of itself, is no real criterion of that progress.
    • Adequate analysis and understanding of your data and their significance (This and the following criteria are much more important in evaluation of your project than the first two).
    • Larger perspective on the questions being asked:  Do not forget this in your rush to amass data! Evaluators will be looking for evidence that you have thought about your findings, about how they bear on your original questions, and about the larger picture into which your project fits.
    • Adequacy of literature search: It is expected that you do a conscientious job here, and to the extent possible make connections between the work of others and your own. The relevant literature will be much more extensive in the case of some projects than others; do not worry about the number of entries in your "literature cited" list, so long as you have made a real effort to find literature and use it. Your evaluators will be rather discerning in this regard.
    • Clarity of presentation, grammatical writing, and careful organization.
    • Care in preparation of tables, figures, and formatting.
    • Careful adherence to prescribed guidelines:  These last three criteria are relatively easy to apply to any written report, and you will be evaluated negatively if you do not pay adequate attention to these aspects. It is easy for evaluators to recognize a sloppy job, and it is easy for you to avoid a sloppy job, simply by saving enough time at the end of your project to do a careful final preparation. Clear writing and organization will come more easily to some of you than others, but whether you consider yourself a good writer or a poor one, do not expect one draft to be all you will need!

    Your final report – and your progress report – are too important to simply be thrown together. Care in writing, attention to details, adequate analysis of your results and careful thought about their meaning – these, together with evidence of careful planning and procedures, are the criteria that are really important in the ultimate evaluation of your project. Except for your adviser, those evaluating your work will be basing their judgment almost entirely on your thesis (together with your oral defense, if you are an honors candidate). If you think far in advance about what is expected in your paper, you will undoubtedly turn out a stronger product.

  • Written Reports

    This page includes instructions for both the progress report, which is written at the end of the first semester by students pursuing two semesters of independent study, and the final report, which is written by all independent study students.  Note that there is no difference in written reports for students who are or are not candidates for honors in biology.

    Standardized Title Page (use for both Progress Report and Final Report)

    The title page must include:

    • Informative title
    • Full name of student
    • Department to which the paper is being submitted
    • Name of adviser
    • Name of course
    • Indication whether the paper is to be considered for departmental honors
    • Date paper is submitted
    • Expected graduation date

    The Progress Report

    The Progress Report, submitted on the first day of exams of the first semester of a two-semester project, is a concise statement of the project at midstream. Although brief, it serves as a significant part of the first-semester grade, since staff members other than the adviser rely almost solely upon this statement as a basis for evaluating the student's performance.  How well the progress report is written is as important as the results it may contain.  It is strongly advised that preliminary drafts of the report be perused carefully by student and adviser before the final version is prepared.  The following specifications should be explicitly followed:


    The text of the report should be no more than six pages, double-spaced. The six pages do not include the title page.  In addition, extra space is allowed for a list of references cited in the text, and three pages for figures and tables.  Note that tables and figures are not inserted into the text.  If desired, a bibliography of literature read but not cited can be prepared as an appendix, but this normally is not expected. These length restrictions are meant to enforce conciseness, clarity, and careful choice of material to be included.


    • Introduction (purpose and brief background)
    • Methods and Results to Date
    • Discussion and Future Plans
    • Literature Cited

    As its name implies, the report should be both backward- and forward-looking.

    Margins should allow for written comments:

    • Left:  1-1/2 inches
    • Right:  1 inch
    • Top/Bottom:  1 inch

    Other aspects of text style, including the mode of reference citation in the text and the form of the bibliography, should follow the guidelines for biology papers in A Short Guide to Writing About Biology by Jan A. Pechenik.  In addition, grammar and sentence structure must be correct and ideas must be expressed clearly.

    Figures and tables.
    Figures should be carefully prepared, axes should be labeled, and a caption and explanatory legend provided.  The student should consider carefully how a given set of data should best be graphed, and consult with the adviser if uncertain whether points should be connected, curves smoothed, etc.  Tables should be provided with an explanatory legend.  All figures and tables should be referred to in the text, and should be specifically labeled.  Please see A Short Guide to Writing About Biology by Jan A. Pechenik.

    The Final Report

    The preparation and guidelines for the final report are identical for one- or two-semester projects.  There is no limit on length, but the contents should be subdivided under appropriate headings.  The final report should contain:

    • Abstract
    • Introduction
    • Materials and Methods
    • Results
    • Discussion
    • Literature Cited
    • Acknowledgments (optional)

    In addition, the guidelines described above under Progress Report should be followed with regard to the style of the text, and the figures and tables of the final report.  Preparation of the final report is as important as the research itself.  Adequate time should be reserved for the writing of the report, including drafts to be reviewed by the adviser.  In the case of one-semester projects, the expectations of the student in terms of the final report's quality remain the same.  Please see A Short Guide to Writing About Biology by Jan A. Pechenik for advice and formatting information.