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Biology 194A,B: Experimental Thesis

Thesis Guidelines

While every effort is made to insure that information on these web pages is current, the official policies are those stated in the Thesis Guidelines [pdf] .

Senior Exercise Performance Contract

Please download, read, sign and return the Senior Excercise Performance Contract [pdf] .

The Laboratory/Field Experimental Research Thesis

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

You will earn a total of 1.5 course credits for an experimental thesis. During the fall semester you will register for one-half credit of Biology 194A, and during the spring semester you will register for one full credit of Biology 194B. Although the amount of credit awarded differs for each semester, we expect that you will devote equal time and effort each semester, equivalent to that of a 1.5 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.

You will spend most of your efforts in this option testing and modifying your experimental design, conducting your experiments, and analyzing your results. The written product of this work will be similar in format to formal lab reports you have written in biology classes, although all aspects of your thesis will be much more extensive than a lab paper for a class. In addition to the final thesis, several specific assignments must be completed in the course of your thesis research:

  • Outline of Research (included in the senior exercise contract):
    For an experimental thesis, you must arrange for a place to carry out your research. Typically, this would be in the lab of (one of) your reader(s). You must discuss with your reader(s) what your needs will be for such things as facilities, equipment, supplies, and field sites. In fact, you should give these matters considerable thought prior to approaching a potential experimental thesis reader. You will submit a list of your research needs along with the senior exercise contract so that the department can determine how we can best meet these needs. The department will provide modest funding for expenses incurred in research ($500/student), but it is unlikely that we will purchase specialized equipment just for senior projects. You may NOT use department vehicles for regular transportation to a field site. For several reasons it is essential that you discuss your research needs with your thesis advisor(s) first and use his/her suggestions in drafting your list of research requirements. You may be able to use equipment and/or supplies available through your reader(s), and all reimbursements must be approved prior to purchase by your thesis advisor(s). In addition to a list of your research needs, you must also write an abstract that describes the problem you plan to address, the experimental approach you plan to take and a proposed calendar (time-line) for your research.
  • Progress Report
    This is a graded (P/NC), written report that describes the early progress you have made in obtaining experimental results and is due part way through the fall semester (see Deadlines). The purpose of this report is to demonstrate to your reader(s) that you have made reasonable progress in tackling your proposed thesis problem, have clearly identified any unforeseen obstacles, and have a plan to resolve them over the course of the remaining weeks of the semester. We want to know in detail how successful your experimental design has been to date and any problems you have encountered. You must receive a passing grade on this progress report in order to proceed with your thesis for the rest of the semester.
  • 1st Semester Draft
    This is a graded, written report that is a permanent grade on your transcript for Bio 194A and is due on the last day of classes, Fall Semester. This paper must include a complete, critical literature review of your topic, your materials and methods section, results to date along with any conclusions that can be drawn from the data you report, and the literature cited section. Your readers will expect the Introduction, Materials and Methods and Literature Cited sections to essentially complete and polished. You will report results of experiments in progress, so the Results and Discussion sections will be considerably less complete than those in the final, second semester version. A passing grade in Bio 194A is a requirement for enrollment in Bio 194B.
  • Complete Draft/Final Revised Version
    These are both graded final reports of your research, written in the format of a scientific paper, which includes an abstract, introduction with literature review and analysis, materials and methods, results, discussion with conclusions, and a complete literature cited section. The grades received on the complete draft and the final revised version will be averaged to generate the grade recorded on your transcript for Bio 194B.
  • Public Presentation
    All experimental thesis students are required to deliver a public presentation to students and faculty in a forum at the end of the Spring Semester, usually held in the evening.

How to Write Your Experimental (field/laboratory) Thesis

You must write your thesis in the format of a scientific journal paper, the sections of which are described below.

  • TITLE.
    A good title is brief and informative. Try to encapsulate the research topic and objectives — i.e., what your thesis is about. Humor is not appropriate in a thesis title.
  • ABSTRACT.
    This short paragraph summarizes the entire thesis: the question you asked, the hypothesis you proposed, the approach you took, the results you predicted, the most important, specific (quantitative) results that you obtained, and the conclusions you drew. Refer to your experimental organism(s) by scientific name(s). The reader should be able to understand the purpose and conclusions of your study by reading this brief statement: it must be able to stand alone. Often a reader reads only your abstract. It is always best to write the abstract last, but it should not be merely a duplicate of your conclusions. Do not just cut and paste from other sections; write the abstract in its own, very concise style.
  • INTRODUCTION.
    In a typical research paper, this section briefly covers the general nature of the problem and the significance of the study; that is, why you undertook the study and what you hoped to learn. For a thesis, however, it is necessary to include an historical overview of your problem, its background, and its significance. This section will consist of a critical review of the work that has already been carried out in the field and define the question and hypothesis you propose to test. Critically discuss the background information relevant to the problem you have chosen to study; show why this problem is scientifically interesting and worth investigating experimentally. You should not merely state the conclusions of the work you are reviewing; instead, briefly describe the experiments, the actual results (in quantitative terms whenever possible), and THEN what the results mean. Do you agree with the interpretation of the results? Did the investigators use the most appropriate approach(es) to address their question? Taken together, the background information you present should lead the reader to the inevitable conclusion that it is important to know the answer to the question you have posed and that your hypothesis must be tested. The relevance of this background information to your research question and hypotheses should be made clear throughout the entire section.
  • MATERIALS AND METHODS.
    What did you do? Using the past tense, describe your methods concisely but in sufficient detail that your reader could duplicate your techniques. For field projects, you should describe your study area, how you selected the specific areas sampled or studied, and how you identified your organisms, etc. Be sure to include scientific names of species studied, your sample sizes, and the types of statistical tests used (if any). Scientific names should be given in full at the first mention, and thereafter the genus (but not the species) can be abbreviated to the initial, e.g., C. annuum.
  • RESULTS.
    What did you find out? Concisely present the results of your experiments and observations in words. Also include tables, graphs, diagrams, maps, etc., where appropriate. Be sure that all figures and tables are numbered, and referred to in the text by their numbers. Your text should describe the content of figures and tables and the significance levels resulting from statistical analyses, but it should not attempt to explain these results; leave this for your Discussion. Biology is a quantitative science, so be as quantitative as possible: it is much more informative to state that “species X has density of 34±5 m-2 at site A and 5±+2 m-2 at site B” than “species X is more abundant at site A than at site B”. Tables should include pertinent summarizing data such as mean values (± Standard error), and not merely exhaustive lists of primary data. All numerical data must abide by the significant digits allowed by the measurements themselves and subsequent calculations using measured values. Insert your Tables and Figures at the appropriate places in the text.
  • DISCUSSION.
    What does it all mean? In this section you evaluate and explain your data and other results, and discuss them in relation to other similar studies reported in the literature. As always, when you make a statement of fact beyond common knowledge, you must give a reference to that statement in the form of a text citation, using proper format (see Citing the Literature for details). In the text of your paper, the literature should be referred to as follows: “Lopez (2004) stated that . . ..”, or, “The animals were observed to blah blah blah (Kuwahara and Schmidt, 1999)”. Examine your data carefully, and then make the most informative and informed statements about them that you can. Distinguish between clear conclusions that derive from your study, and what is merely indicated or suggested. Discuss specific items of interest, such as (in the above example) why you think Species X is more abundant at site A than at site B. Discuss the significance of your study, both in relation to the specifics of your experimental system, and to more general principles of biology. You may find it appropriate to include brief comments on the accuracy, adequacy, and limitations of your own study, difficulties encountered, possible ways to circumvent these in the future, and ideas for future work, etc.
  • CONCLUSIONS.
    The Conclusions section is not the same as the Abstract. Rather, it should contain a brief summary of your results, stated as conclusions, and nothing more. Listing them as bulleted points is one convenient way to present them. Be certain that these conclusions are fully justified by your data.
  • ACKNOWLEDGMENTS.
    In this section you acknowledge help you received during any aspect of your project, including data and suggestions you received from others, as well as funding you or your advisor may have received from outside the department. It is always acceptable to discuss laboratory and field activities with others and to analyze data as a group, and you are free to discuss your ideas with others; scientists do this all the time. It is very important, however, that the final thesis document represent your own original thoughts, organization, and expression. It is always appropriate to recognize and thank those who have significantly assisted you with laboratory or fieldwork, calculations, or the formulations of ideas, e.g., “I thank my roommate Al Gnowing for many stimulating discussions and my advisor Dr. Nobel for teaching me how to use high explosives safely.”
  • LITERATURE CITED.
    This section is always the last of your thesis, and must include every paper you have cited in the text, and only those papers. See Citing the Literature for a description of how to present your literature citations.

Be sure you also read the additional information that applies to both thesis options, including important reminders, general advice, and information on scientific writing, required format, and honesty in writing and science.

Deadlines for the Laboratory/Field Experimental Thesis

Your final grade in the course will be assessed a penalty of at least one grade point, and up to one grade point per day (weekends included) when deadlines for any of the following are missed: topic selection, outline, progress report, first draft, and final draft. All deadlines are at 5:00 PM on the specified day.

1) Contract submission:
After obtaining the signature of one reader and listing three additional faculty who agree to be potential second readers, submit contract, abstract, experimental design, research needs, reference list, and projected calendar to Dr. Hoopes.
Friday, Apr 18, 2008**
2) Progress report submission to both readers describing work completed to date. This report will receive a P/NC grade. Passing grade is required for registration for Bio 194B. Friday, Oct 17, 2008
If progress report receives a NC grade: this is the last day to withdraw from Bio 194A, without penalty. Thursday, Oct 24, 2008
3) 1st semester draft submission of entire paper to each reader. This paper will receive a permanent grade and will be what is recorded on your transcript for Bio 194A Wednesday, Dec. 10, 2008
last day of class
4) Complete draft submission of entire paper to Advisor and second reader if any. The grade received on this draft will contribute 50% to your final grade for Bio 194B. (*see note on previous page) Thursday, April 2, 2009
5) Public presentation.
(Readers will help you with instructions for how to prepare your presentation.)
Wednesday, April 29, 2009, 7 pm (and Thur, 4/30, if needed)
6) Final revised version*** will be submitted to each reader. The grade received on this version will be averaged with that received on the complete draft submitted earlier this semester to give a final grade for Bio 194B. Friday, May 1, 2009

**For students studying abroad in spring, 2008, the proposed type of thesis and advisor is due to Dr. Hoopes before departure. They will need to be in contact with their advisor while away, if beginning the thesis project in fall, 2008, because the contract submission deadline for students who are studying abroad in spring of their junior years is Friday, September 11, 2008 — i.e., Friday of the first full week of classes in the Fall Semester. In exceptional cases, contracts from other seniors wishing to conduct laboratory or field experimental theses may be submitted for consideration on the September 11 deadline if accompanied by a petition describing in detail the reasons for missing the April contract deadline.

*** Turn a hard copy of the final version to each reader. You must also turn in the complete drafts, with the reader’s comments, when you turn in the final draft. Also submit the final version on a CD in either pdf or Word format to Joni Loving in the Biology Dept. Office. Links to the abstracts will be put on the Department web page, and the full electronic version of your thesis will be available to future students for several years.

Please remember to put page numbers on ALL written material given to readers for feedback. When handing in your draft and final version to your readers, you should determine when you can pick up the graded and critiqued copy. Be sure to get your graded progress report back from faculty readers before the course drop deadline.