Neuroscience

NEUROSCIENCE THESIS INSTRUCTIONS


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DATES AND DEADLINES

(1) Due dates and presentation times are found here: Senior Honors Thesis

(2) When submitting your thesis to the Neuroscience faculty: prepare 3 printed copies of the thesis and mount them in black, spring-back binders (note: if one of the faculty members will accept a PDF instead of a printed copy, they will let you know). Turn in the theses to the current chair of Neuro department.

(3) Thesis presentations (also called oral defenses):  Students working in the labs of Profs. Turgeon and Baird will generally present separately from students working in the labs of Profs. Graf, Trapani, and other Biology Faculty, which typically present on the same day as the Biology Thesis presentations.

(4) The due date for submitting the final, corrected version of your thesis to the registrar is no later than noon on the next-to-last day of classes.  An additional hard copy of your thesis should be given to your advisor and a PDF of the final document emailed to Prof Baird. See the section below on Final Submission of the Thesis for details.

IMPORTANT: The Neuroscience faculty take the College's final deadline for submitting theses to the Registrar very seriously. We will not advocate on behalf of students who fail to submit their finalized copy on time.

ADVICE ABOUT TIMING

During the spring semester, work out a schedule for submitting drafts or sections of your thesis to your advisor for comments. This is to insure 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!

  • Remember to plan time for making figures, tables, and figure legends, plus preparing the Table of Contents and List of Figures—have someone show you how to use Microsoft Word do this automatically.
  • Allow plenty of time to print your thesis if you use a public printer because of the campus-wide rush of other thesis thesis students across majors.
  • After reviewing each section, it is very desirable for your advisor to be able to see and comment on a complete copy of your thesis containing your revisions ~7 days before the final printing.  Give yourself days rather than hours for duplicating and collating the thesis and submitting it to the faculty.
  • Things often don't go as expected, and without extra time built into your schedule you may not be able to meet the deadline with a document you are happy with.
  • Perhaps most important: frequently, frequently back up your data and text.
PRINTING COPIES OF YOUR THESIS

To print the thesis, use your own computer and printer or one at the computer center, not Biology or Psychology department computers and printers.  Also, you may not use other office supplies from the Biology or Psychology Department in preparing your thesis, and you may not make copies of your thesis on departmental copiers. Use facilities elsewhere on campus or in town, with due regard for scheduling during the busy thesis season.

THESIS FORMAT AND STYLE

See full copies of past honors theses

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SECTIONS

The sections of the thesis are as follows:  Title page, Acknowledgments, Table of Contents, List of Figures, (List of Abbreviations, if applicable), Abstract, Introduction, Materials and Methods, 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 Your Thesis:  Using Microsoft Word, you can use section headers to autopopulate and autopaginate your Table of Contents and List of Figure Legends.

FORMAT

  • Spacing: double-spaced required except for References section, which can be single-spaced
  • Type: 12 point
  • Paper size: 8.5 by 11 inch
  • Margins: at least 1 inch at the top, bottom, and right side, and 1.5 inches on the left

You may choose whether or not to 'justify' the text.  Don't "orphan" a heading or title by leaving it as the last line on a page. If this happens, enter a "page break" or add blank lines at the bottom of the page so that the heading or title will appear at the top of the next page with the text that comes under it.

THESIS CONTENT

General issues of style and content:

Science writing is different than other forms of writing. All thesis writers should read this excellent article on science writing: https://www.americanscientist.org/issues/pub/the-science-of-scientific-writing

Neuroscience theses should be understandable by all faculty and other senior majors in Neuroscience, 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 Table of Abbreviations at the beginning of the thesis.

Citing references:

Throughout the text of the thesis, cite references by author or authors and year.  Numerical references  ("Sequencing the gene for the sodium channel12 led to predictions of the channel architecture...") are not acceptable in Amherst College Neuroscience theses. 

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).”

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 others:"  "Noda et al. (1986) reported the sequence for the gene for the sodium channel..." or, "In 1986 Noda and others reported...."   The correct style for theses is to list all authors the first time a given paper is referred to in the thesis.  However, with the advent of 20-author papers this may simply be unwieldy in a particular case--use your judgment, but do try to follow this rule!

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 at the end.  Each combination of two or more authors is treated as a different author.   The format for listing references in the References section of the thesis is detailed below.

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).

SPECIFIC SECTIONS OF THE THESIS
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 thesisCeither in the Introduction or in the Methods sectionCname any organisms with which you worked, giving both the common and scientific names.  Species names are underlined (Rana pipiens) or italicized  (Rana pipiens).

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, and 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 published 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").

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 pointed out.  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. Include scale bars on microscopy images where appropriate.

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

IMPORTANT: All Figures should have a Figure Legend similar to every journal article you have read.

Discussion:

The Results section of a thesis should contain only a statement and presentation of the results, saving the discussion (i.e. interpretation, conclusions, suggestions for further work) for the Discussion.   A common mistake is to use the Results section to discuss results as well as to present them, and then - having nothing left to discuss - to use the Discussion section for vague speculation.

References:

We recommend using Zotero to format citations and references. The college offers many workshops in using Zotero for your thesis. The format for citing papers in the References section may be that of any major journal in area of Neuroscience in which you are working, but must include: 

  • all authors (no matter how many)
  • year of publication
  • title of the paper
  • name of the journal (titles may be abbreviated according to accepted PubMed formats)
  • volume number
  • inclusive pages (not just the first page)

Example:

Watson, J. D. and Crick, F. H. C. (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. 

FINAL SUBMISSION OF THE THESIS

After turning in the thesis draft and presenting the thesis defense, there is a tendency to feel that you are finished, but a final and very important step remains: making any corrections and turning in final copies of the thesis to the Registrar!

IMPORTANT: You must follow the Registrar's Guidelines for Thesis Submission: https://www.amherst.edu/academiclife/registrar/faqs/thesis_guide

  1. If the faculty found errors and corrections that you need to make, they will place their suggestions in the copy of the thesis that will be returned to you after your oral presentation. It is your responsibility to make the requested changes to your thesis before it is due to the Registrar. Consult with your advisor if you have questions about the changes.
  2. Make two final copies of the corrected thesis, starting with the versions you already printed and replacing the (presumably) few pages containing errors with corrected pages.
  3. No later than the-next-to-last-day of classes turn in 1) a final hard copy to the Registrar, 2) a final hard copy to your thesis advisor, and 3) email a final PDF version to Prof. Baird.

Congratulations on seeing this complex process through to the end!