Instructions and the due date for the research proposal will be emailed to you on the first day of class. The proposal should be developed with your mentor and emailed to the course coordinator by the indicated due date. Typically, the proposal will be no more than one page and will include the following:

• A statement of the problem and its significance
• A general description of the proposed experiments
• A statement about how the experiments may be expected to address the problem

The proposal is required, but will not normally affect the student's grade. However, late proposals and proposals that do not contain the required information in the required format will adversely affect the grade. 

In research, it is difficult (if not impossible) to predict the amount of time and effort required to complete a research project. Unlike didactic laboratory experiments in BSCI 1510 in which specific results are expected, experiments in basic research are often ambiguous and results are sometimes difficult to obtain. For this reason, the effort made by a student to understand the experimental concept and perform the experiments is perhaps more important than the actual results. Consequently, the final grade for the course will depend heavily on the effort made in the laboratory. As a guideline, it is expected that the student work at least 4 hours a week in the lab for every hour of academic credit. For example, 4 credit hours would translate into approximately 16 hours a week of laboratory work.

This is a 10 to 18 page report on the work accomplished during the semester. One copy should be submitted to the mentor and another to the course coordinator. The report is due at the end of the day on the last day of class for the semester. The report should be written as a scientific journal article detailing original research with a title page; an abstract, and a main body that includes: introduction, materials, methods, results, discussion, and references sections. more information on the format and the content of each section will be distributed at midsemester.

After a discussion with the mentor concerning an outline and the general content of the paper, the student should independently prepare a rough draft that the student feels is of sufficient quality for the mentor to read. At this point, the mentor and student will continue to refine the manuscript until the mentor is satisfied with the final version. There are two important points to pay attention to, bearing in mind that 30% of your final grade is based on the written report:

• It will not be possible for the mentor and the student to refine the report adequately if the first draft is prepared too close to the deadline.
• A quality first draft will not only speed the process along, but also provide the mentor with a good evaluation of the student's progress during the semester and result in a higher grade for the student on this section.

Title page: this should include the project title, student's name, "Honors Thesis" or "Research Report", the month and year, department and university names, and the name of the research advisor. The research advisor is a faculty member; if some other member of the laboratory, such as a research associate, was the effective advisor, he or she should be thanked in an 'Acknowledgements' section, but should not appear on the title page. Example:

    The Nuclear Magnetic Resonance Spectra of Polypeptides in the Helical Configuration

                                                                  Jane Smith

                                                                Honors Thesis

                                                 Department of Biological Sciences
                                                           Vanderbilt University
                                                                   April, 2021
 

                                                 Research Advisor: Dr. Mary Jones

Acknowledgements: these are not required but are often included; they are a nice idea. If included in a thesis, they should be on a page of their own after the abstract and before the table of contents. In research reports for 3861 and 3961, they should be at the end of the main text before the reference list. Keep them brief and to the point; this gives them more impact. Note that if Mary Jones has a doctorate, she may be referred to as Dr. Mary Jones or as Mary Jones, Ph.D. (or M.D. or D.Phil.), but not as Dr. Mary Jones, Ph.D. Informal acknowledgements (ex. "I would like to thank Mary for...") are also acceptable if you feel they are appropriate.

Abstract and Table of Contents: are required for theses (abstract must not exceed 100 words) but are not required for 3861 and 3961 research reports.

Introduction: an introduction should always include the following three elements.

1. A general overview of the system or topic under study in terms that are understandable to a well-read scientist in a field outside of the thesis
2. Background to the work described in the thesis or report, including its significance; the reader is assumed to be from outside the field
3. A very brief summary of the work described in the thesis or report

A summary of previous work on this project by the student (directed or independent research) and if relevant, work done by others in the same laboratory should also be included in the introduction. Details are not required.

Page numbering: The title page should not be numbered, and the next page (abstract) should be page 2. Ideally, numbers should be centered at the bottom of each page. These are recommendations not requirements, because I do not want students to waste valuable time trying to change the numbering convention in their word processing programs. The only numbering requirement is that all pages must be numbered.

Fonts and formats: Use a 12 point serif font such as Times New Roman, Times, New Century Schoolbook, or New York. Times New Roman gives an excellent density of characters on the page. Sans-serif fonts such as Ariel and Helvetica are effective as labels (not as captions) in figures, but these fonts are difficult to read in the body of the text. If you vary fonts and styles, do so extremely sparingly (but note that italics should be used under certain circumstances, see below). Do not divide ordinary text pages into columns. Use an inch margin on all sides.

Text, including 'materials' and 'methods' sections, should be double-spaced. Figure captions and reference lists may be single spaced.

Figures and Tables: should be numbered and inserted into the text with their captions. A figure should appear as soon as possible after the first reference to it. They should not be grouped at the end of chapters or at the end of the thesis or report. They may be incorporated in the text pages or on separate pages. If space allows, each caption should be on the same page as the corresponding figure or table.

If a figure or table is taken from another person's work, it should be acknowledged as the last sentence in the figure caption: "From Smith & Jones, 1998" or "Courtesy of Mary Wang".

Period covered by the report: for theses, describe the whole honors project, not just the last semester. If you began the project before your senior year, you should very briefly note in your introduction how far the project had progressed when you began your formal honors work. Although you are not normally expected to describe the details of your earlier work, you should not assume that your readers are familiar with those details. If the reader needs to know about the previous work in order to understand the honors part of the project, a brief explanation is appropriate. In research reports for 3861 or 3961, in which the work is a continuation of earlier research, summarize the earlier work in the introduction.

References should be given in the text by author (use the form "et al." for references with more than two authors) and listed alphabetically at the end of the thesis in the style of Journal of Molecular Biology, Journal of Cell Biology, Evolution, or similar. The reference list should include all authors (unless there are more than 20, in which case you may use et al. after the first author, even in the reference list), titles, and beginning and ending page numbers.

The phrase "et al." as in "followed the procedure described by Smith et al.(1989)" is not normally followed by a comma, and has a period after al, but not after et. The comma is, however, used in the form "followed an established procedure (Smith et al., 1989)", when the whole reference is in parentheses. Like all non-English words inserted into an English sentence, the words should be in italics, or underlined. (Underlining is a recognized equivalent of italics.)

The phrase "Smith et al. (1989)" refers to the people, not the paper. The paper has its own title, not usually quoted in the body of the text. For this reason, it is correct to say "was described by Smith et al. (1989)", but not "was described in Smith et al. (1989)". Perhaps an exception might occur if Smith et al. were forced to eat their words.

Et al. is not normally used without a year. "Smith et al. (1989) showed ..." is correct. "Smith et al. showed ... (1989)" is not. "Smith et al. also found ..." is incorrect; it should be replaced either by "Smith et al. (1989) also found ..." or "Smith and his colleagues also found ...". Beware of this last construction; it is very easy to ascribe the leadership of a group to the wrong person this way!

Note the different meanings of "affect" and "effect".

The word "data" is plural. The singular (almost never required) is "datum". Refer, for example, to "these data", not "this data". The same applies to "media" and "criteria", but in these two cases, the singular forms ("medium" and "criterion") are often required.

Do not use apparently technical terms where plain English is clear and unambiguous. For example, "determined via SDS-PAGE" should not be used; "determined by SDS-PAGE" is clearer and therefore better. The reader should not have to pause unnecessarily, even for a fraction of a second, to wonder what you are talking about. The reader should never be expected to pause to admire your command of jargon, Latin, or other superfluous forms of language. Latin words and phrases are often very useful (see "et al.", above), but should not be used when they do not improve precision or clarity. If jargon is really necessary (which I doubt), its meaning should be defined at its first appearance.

Avoid ambiguities. For example, "was dialyzed against three changes of phosphate buffer; pH 7.0, etc., etc., for 1 day." What is a "change"? Was the solution dialyzed three times against a given volume of buffer, or was the buffer actually changed three times (for a total of four volumes)? Was it dialyzed for 1 day total or for three (or four!) days total?

Distinguish between primes (as in 5') and single quotes (apostrophes). Most word processing applications automatically change primes to quotes ("smart quotes", but not smart enough!), but this change can be undone.

The letter "u" is not an abbreviation for "micro" (as in "um" or "ul"). This is a leftover convention from the days before computers, when Greek letters were difficult to print. Use the Greek letter mu (µ) as in "µm" or "µl".

Results: these are often contained in figures; remember, figures are often highly technical. Results should be clearly stated in the text (if appropriate, including a reference to figures or tables) and easy for the cursory reader to find.

Laboratory

• Effort: includes but is not a strict measure of hours: we expect at least 4 hours a week on research for each hour of credit; keep in mind, effort is more than just hours.
• Engagement: this is where we distinguish between the student who really lives the research project and the one who simply does the work.
• Originality: at an appropriate level for the research (directed, independent or honors). Does the student have ideas? Are they any good?
• Initiative and follow-through: does the student pursue ideas and suggestions? Do they follow through with them? Do they persist when difficulties arise?
• Problem-solving: includes both solving problems that arise when things go wrong and interpreting positive and/or negative results.
• Technical competence: this includes everything from tidiness and physical lab organization to mastery of sophisticated equipment.

There will be a slight element of overlap which does not matter. For example, persistence is an element of both effort and follow-through, and originality will correlate with engagement.

Success in obtaining results may be reflected in grades for the various components of the laboratory grade, but is not in itself an element of the grade. Although unlikely, a grade of "A" is possible even with no results.

Paper and Presentation

Recall that the paper should be written as if it is a journal article presenting original research. 

• Clarity, organization. and presentation: includes conforming to length (time), style, layout guidelines, and general presentation quality. This is not intended to judge the degree of computer sophistication or resources.
• Adequate background and literature review: did the student give the readers/listeners a sound introduction to the area of research and demonstrate how past work has led to the problem which they are addresing?
• Scientific understanding: did the student understand the field and the work?
• Figures and Tables (visuals): were they appropriate and adequate, and including legends?

Exceeding the allowed length/time affects the first point. Insufficient length/time may affect any of the four areas, or in the case of an unusually lucid and concise student, may not affect any.

Grading for the paper and presentation does not directly consider volume of work completed or results obtained; these things are considered in the laboratory part of the grade. However, good papers and presentations are much more likely after a good semester of research.