*Click to return to the Biology Honors Program webpage*

*Note, thesis template file is at bottom of this page

Quick links to the sections below:


1. Submit thesis to the Department: (electronic format only; due date is typically 3rd week of April)

The electronic copy should be in pdf format, except for supplementary data, such as videos, that cannot be converted to pdf format. The name of your file should be your full name. Submit to the Dropbox folder shared via email.

Following submission of your thesis, the Biology Faculty will review your work. You should hear back from your readers once they have read it. If you receive comments back from your readers, you can begin to incorporate any necessary changes, and you should consult with your research Advisor for any major corrections. Once all corrections have been incorporated, you are ready to compile the final copy of your thesis.

2. Thesis Defense: Schedule for the oral thesis presentations (“Defenses”) will be announced and posted in advance.

3. FINAL SUBMISSION: Deadline for submitting final, corrected copies of your thesis will be announced

Registrar Instructions for thesis submission.  NOTE: on the Submittable website submission choose "Place an embargo" option and select the CC BY-NC-ND option for license.

Your thesis advisor will likely want a final copy as well. We recommend that you make a final printed copy of your thesis to keep for yourself (if you don't do it now, you'll never do it!).

By 5:00pm: To the Registrar:
Refer to Registrar’s Thesis Guidelines above (don’t wait until that day). Please note that YOU are responsible for getting your thesis to the Registrar before the deadline. The Biology faculty are not able to advocate for a late thesis.

4. Breathe a huge and proud sigh of relief!
Congratulations on seeing this complex process through to the end!


During the end of Fall and prior to the start of Spring semester, work out a schedule for submission of drafts to your Advisor to ensure that the thesis in final form is ready for submission on the due date. The final stages of preparation take more time than you expect! This includes making figures, tables and legends, plus preparing the Table of Contents and List of Illustrations.


The sections of the thesis are as follows: Title Page, Abstract, Acknowledgments, Table of Contents, List of Tables, List of Figures, (List of Abbreviations, if applicable), Introduction, Methods (or Materials and Methods, if you prefer), Results, Discussion, Conclusions, and References. Conclusions may be omitted as a separate section, and included instead in the Discussion. Number all pages consecutively, including figures and figure legends.

Formatting requirements:

  • Spacing: Double-spacing required except for references and figure legends (single-spaced).
  • Font Size: 12 point.
  • Paper size: 8 1/2 x 11 inch.
  • Margins: 1 inch at the top, bottom and right side, and 1.5 inches on the left.
  • All pages must be numbered

You may choose whether or not to “right-justify” the text. Don't “orphan” a title or caption by leaving it as the last line on a page; if this happens, add blank lines at the bottom of the page so that the title will appear at the top of the succeeding page.


Style and content:

Biology theses should be understandable by all faculty and other senior majors in Biology, so terms must be identified and explained adequately. Use nonstandard abbreviations only to avoid frequent repetition. If you use abbreviations, define them in parentheses or in a footnote at their first mention, and include them in a List of Abbreviations at the beginning of the thesis.

Citing references:

  1. Throughout the thesis text, cite references by author(s) and year. Numerical references (e.g. “Sequencing the gene for the sodium channel12 led to predictions of the channel Architecture...”) are not acceptable in Amherst College Biology theses.
  2. If a paper has either one or two authors, include the last name or names and the date in all citations to the paper: “Watson and Crick (1953) first showed...” or “The nucleotides in DNA are arranged in a double helix (Watson and Crick, 1953).”
  3. If the paper has three or more authors, list the first author followed by et al., which is always underlined or italicized. For variety, consider occasionally writing out the English meaning of et al., which is “and colleagues”: “Noda et al. (1986) reported the sequence for the gene for the sodium channel...” or “In 1986 Noda and colleagues reported...”
  4. Organize your references alphabetically by author, and, for a given author, chronologically. Two or more papers by the same author or set of authors in the same year should be listed as 1987a, 1987b, etc., both in the thesis text and in the References section. Each combination of two or more authors is treated as a different author. The format for listing references in theReferences section of the thesis is detailed below.
  5. If you wish to refer to a paper which you weren't actually able to obtain and read but which was discussed and cited in a paper you did read, list only the paper you did read in the References section. For example, “Carpenter (1962), as pointed out by Jones (1966), argued that...” You would cite Jones (1966) in the References section, not Carpenter (1962).

Abstract. The abstract should be an approximately one-page summary of the thesis. It should be as specific as possible, consistent with brevity. For example, avoid writing “The implications of these results are discussed” and, instead, actually summarize the discussion.

Introduction. Begin with a statement of the problem addressed in your research. Then provide a detailed literature review of previous work relevant to the problem. End the Introduction with a statement of the specific rationale for your approach to the problem.

At an early point in the thesis–either in the Introduction or in Methods–name any organisms with which you worked, giving both the common and scientific names. Species names are underlined (Drosophila melanogaster) or italicized (Drosophila melanogaster).

Use the past tense in describing specific findings of papers you cite. Thus: “Raymond (1979) found a supernormal period in sciatic nerve fibers...” not “Raymond (1979) finds a supernormal period...” Use present tense only for very well-known conclusions of cited papers or for accepted, basic facts that do not require citation: “There exists a concentration gradient of ions across all nerve membranes...”

Methods. Include details sufficient to allow a competent worker to repeat the experiment. Thus the methods will be more detailed than in most scientific papers. The Methods section of a thesis is not a laboratory protocol written in the imperative (“Adjust the pH to 7.4”), but rather a description of the methods that were used (“The pH was adjusted to 7.4”). Passive voice should be used throughout this section.

Results. Describe your results in words and also using tables and figures (i.e. graphs and illustrations). Figures should be located near their first mention in the text. Each figure must be accompanied by a legend, on the same page or on an adjoining page, even though the figure is also explained in the text. Legends should include a figure number and identifying material. Figures and tables must conform to the same margin requirements as other parts of the thesis.

Photos: The illustration should identify structures of note in your results. For example, don't say “Note union of aedaegus and uncus” without indicating what and where the aedaegus and uncus are on the photo. Indicate magnification wherever appropriate.

Graphs: The format and labelling of axes should be as prescribed by a major journal in the field and should be consistent throughout the thesis.

Discussion. The Results section of a thesis should contain only a statement and presentation of the results. Although a brief statement of interpretation or explanation is fine, avoid including extensive discussion here, as this is what the Discussion is for. A common mistake is to use the Results section to discuss as well as to present results, and then, having nothing left to discuss, to use the Discussion section for vague speculation.

References. The format for citing papers in the References section may be that of any major journal in the area of Biology in which you are working, but must include:

  • All authors (if more than 20, it is fine to say “et al.”)
  • Year of publication
  • Title of the paper
  • Name of the journal (underlined or italicized)
  • Volume number
  • Inclusive pages (not just the first page)
  • PMID # can be included as well, but is not required

Citations. We recommend writing out the complete name of the journal. However, it is acceptable to abbreviate if you feel you must, so long as the name remains intelligible. For example, Journal of Molecular Biology could be abbreviated as J. Mol. Biol., but not J. M. B. Examples:

Watson, J. D., Crick, F. H. C. Molecular structure of nucleic acids. A Structure for deoxyribose nucleic acid. Nature 171:737-738, 1953.

Watson, J. D. and F. H. C. Crick (1953). Molecular structure of nucleic acids. a structure for deoxyribose nucleic acid. Nature 171:737-738.

References to books should give the same information as for journal articles, and in addition, the title of the book, the editors (if appropriate), publisher, and the city of publication. Titles of books should be bolded in the References section. Example:

Rosenblatt, J. S. The sensorimotor and motivational bases of early behavioral development of selected altricial mammals. In: Spear, N. E. and Campbell, B. A. (Eds.) The Ontogeny of Learning and Memory, pp. 189-206. New York: John Wiley and Sons, 1979.


Reminder of Amherst College Honor Code and Biology Research Ethics Training

Your thesis is your original work. You stand by your data and your narrative. Where data, figures, or text is included from other sources, such as published literature, a former thesis, another student, or your advisor, it must be attributed to that source with appropriate citations. If you have any doubts or questions about how to handle included material that is not yours, check in with your advisor. Plagiarism is a serious offense.


Your grade and Honors recommendation for Biology 498/499 are based on your thesis work, and also on your thesis as a document, as submitted on April 17th. Some students work hard during the year but do not set aside enough time to do a good job in preparing the thesis document. What is available to the department is the thesis itself, but not necessarily all the late nights in the lab. If what you submit on the due date is not in final form, i.e. if it requires significant revision to bring it into line with these guidelines, your grade and Honors will be affected, no matter how much work you've done during the year. The expectation is that there will be only minor typographical corrections after the April 17th submission of the thesis.

If your thesis is accepted by the Department, you will graduate with honors (cum laude). If the Department decides that your thesis is of excellent quality, then you they will recommend that you graduate with high honors (magna cum laude). In rare cases, a thesis is deemed to be outstanding, and a recommendation of the highest honors (summa cum laude) is made. In making their recommendation for the level of Latin Honrs, the Biology faculty will not take into account (or even be aware of) your grade point average. However, the level of Latin Honors that is actually awarded by the College is determined by the recommended honors level from the Department in combination with your grade point average as determined by the Registrar after all grades have been submitted.


After handing in your thesis, you will give a Thesis Presentation (sometimes called the the “Defense”) to Biology faculty and students. They are scheduled toward the end of April each year. There is an understandable feeling of being finished when your thesis has been turned in, but be sure to plan time to consult with your Advisor about your thesis presentation.