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This information applies to both thesis options

While every effort is made to insure that information on these web pages is accurate for the 2008-2009 academic year, the official policies are those stated in the Thesis Guidelines 2008-2009 .

Some General Advice

Your audience. Before writing any document you need a clear idea about your audience. For a senior thesis, write for an audience of senior biology majors, i.e. readers who have a broad background in biology in general, who are familiar with basic scientific ideas, but who are not experts in the specific area you have chosen for study. Keeping this audience in mind should make it easier to decide how much information to include and what to leave out.

Give yourself time. No writer (except Isaac Assimov, perhaps) can produce a clear, well-organized document in one sitting. An essential part of the writing process is getting the creative juices flowing, a process that goes on more or less subconsciously once you have generated a few fundamental ideas. Sit down early and sketch out a few ideas or an outline, then push this paper aside for a week or so. The ideas will perk in your brain, the things you want to say will start to take shape — a few opening sentences may even occur to you in the shower. Take advantage of this subconscious process; it will save you much painful time later and will allow you to avoid those all-nighters where you sit in front of a blank computer screen trying to force words that won’t come. Giving yourself plenty of time will also make it possible for you to get feedback on your drafts from others; all good writers gather advice from their colleagues about their writing.

Look at some models. If you are unclear about what your finished document should look like, look at some successful models: theses written by students who have already graduated. These are on file in the Biology Department office and can be checked out for short period of time (a few days) from the Biology secretary. But don’t read random theses; you need to look at the best ones if you are going to use them as models. So ask your faculty advisors for names of students who wrote particularly good theses. Choose theses to read that are the same type (proposal or experimental) as yours, and it is best to find some to read that address the same type of biology you are examining.

Text citations in scientific writing

It is absolutely necessary to indicate with text citations the sources of all material that you discuss that is not original (your own), including both facts and ideas (see Honesty in Writing, below). There are two parts to proper citations: the text citations themselves, and the Literature Cited section at the end of the thesis. Note that scientific style in this respect is very different from the style used in the humanities. For example, avoid the use of ibid. or loc. cit., and superscripts⁵ and numbers (2) completely. Do not use direct quotes from the literature; instead of quoting directly, rephrase in your own words and credit the source appropriately.

1. Text citations. There must be a text citation for each non-original item in your thesis, including facts and ideas as well as apt phraseology. When you state a fact or idea beyond common knowledge, you must give a reference to that statement in the form of a text citation. Citations in the text should be in the form of: “Faha (1998) stated that black is black.” or “Black was demonstrated to be white (Loving and Sundberg, 2003).” Always cite all authors of multiple-authored papers, as “Chang and Lee (1995) observed....”If there are three or more authors, cite their paper as in the following: “Marsh snails were found in blah blah blahty-blah (Sbertole et al., (2004).” et al. is an abbreviation of the Latin et alii, which means “and others.”] If an entire paragraph discusses information from one source, you can probably write the passage so that it is clear that the entire paragraph has non-original material from that single source. If a paragraph includes material from several sources (the more usual case), then you will have to use a text citation for each of the sources. Parenthetical text citations go inside terminal punctuation, as (Minehart, 2006).
2. Literature Cited. Please note that this section is called Literature Cited, and not Bibliography or References. List papers alphabetically by first author, and then by date if you cite more than one paper with the same first author. The format of these citations is standard and can be found in articles published in any of the major research journals, though usually each journal will have a few idiosyncrasies. The best practice is to follow the citation format found in one of the major journals in the field of biology in which you are working. Beware, however, that some journals, such as Science and Nature, use a shortened format that is not very informative: avoid these styles. In all your citations, be sure to include the title of the journal article and inclusive pagination. The usual sequence is: author(s), year, article title, journal name, volume, inclusive pages. Pay close attention to proper use of punctuation and abbreviations in reference lists. Here is an example of one correct style for a typical journal article:

   Cohen, I., J.A. Knopf, V. Irihimovitch, and M. Shapira. 2006. A proposed mechanism for inhibitory effects of oxidative stress on rubisco assembly and its subunit expression. Plant Physiol. 137: 738-746.

3. It is always awkward to deal with secondary sources, that is, the situation where you are referring to work published by Person A, but getting your information about that work not from a paper authored by A, but from a paper published by Person B. It is improper to cite Paper A, as you did not read it yourself. But you may want to acknowledge the work of Person A, even though you read only Paper B. Further complicating matters, Person B might have misinterpreted or misquoted Paper A. If you choose to cite the work of Person A under these circumstances, your Literature Cited section must list only Paper B. In the text you might write, “According to Franszicek (1980), Darwin in 1859 concluded . . . .” An alternative approach is: “Fact fact fact (Darwin, 1859, as cited by Franszicek, 1980).” Of course, the very best approach is to actually read the paper by Person A.
4. Citing sources on the Web: in word, DON’T. Possible exceptions might be a photograph you wish to use to illustrate something or a maybe a figure or drawing that represents someone else’s model that is not found anywhere in a primary reference. If you wish to use a web citation, be sure to clear it with your advisor(s) well in advance of turning in a draft.

Helpful hints for good scientific writing

Good writing in scientific disciplines is not significantly different from good writing in other disciplines. The rules of good grammar, punctuation, and style all apply. Precision and clarity of expression and good organization are essential. To be sure, one must master a vocabulary, quite large in some fields. This vocabulary can be intimidating, perhaps because scientific terminology is usually very precise in meaning, and because it is often based in Latin and Greek roots. However, excessive use of jargon can make a scientific paper nearly unintelligible. In addition, there are some conventions unique to scientific writing. Some of these conventions are listed below, but others are not easy to describe. A paper written outside these conventions may be technically correct but just does not “feel” right. The best advice is to take note of good writing as you read scientific papers. But note also that not all published papers are well written!

Write to illuminate, not to confuse. Use the simplest language consistent with that goal. Write clearly and concisely, using correct grammar and spelling. Organize and express your thoughts clearly and succinctly. Eliminate irrelevant information, no matter how interesting it is, and no matter how hard you worked to ferret it out.

Have someone (in addition to your faculty readers) read your drafts before you produce the final copy. Have them tell you whether the organization and style make sense; ask all of your reviewers to be frank and honest. Some people read their papers out loud rapidly; if you stumble while doing this, you probably need to make significant improvements. Poorly written reports will receive lower grades.

Your thesis must be double-spaced on 8½" x 11" paper, with a left-hand margin of at least one inch. Be sure that the printout is legible and that all required features of scientific writing, such as italicizing scientific names (Nereis succinea), formulae with subscripts (H₂CO₃), and units with superscripts (K⁺, cm^-2, m², etc.) are correct. If you use Greek letters, be sure they print correctly (μ and β, not m and b).

Some other important conventions in scientific writing are:

1. It is perfectly acceptable, even preferable, that you write in the first person. In fact, doing so often makes your writing much clearer and stronger, e.g. “I chose this experimental system because… ” or “I hypothesize that… ”
2. Spell out completely all words and phrases you intend to abbreviate the first time you use the term; use a minimum of abbreviations, or your thesis will resemble an alphabet soup. Excessive use of abbreviations and acronyms can destroy comprehensibility.
3. Use present tense for facts and other commonly accepted knowledge; e.g., “ATP is the energy currency of the cell.” Use past tense for historical events, and for what other people did; e.g., “Wong (1983) showed that Species Y is a protandrous hermaphrodite that breeds from May through August. Wong (1983) also noted that Species Y did not breed in 1980, because the environment never reached the critical temperature.”
4. Avoid jargon and freight train constructions. A freight train is a sequence of nouns masquerading as adjectives.
5. Avoid passive constructions; they are wordy, often ambiguous and weak. For example, write “Nitkin (1996) observed that species Q always… ”, or “Species Q always… (Nitkin, 1996).v but do not write, “It was observed that species Q always… (Nitkin, 1976).”
6. A sentence that begins with the word “This” is most likely ambiguous.
7. Use the correct singular and plural forms of all words. Be aware that datum, phenomenon, criterion, medium are pluralized as data, phenomena, criteria, and media, respectively. Always make your subject and verb agree in number.
8. Number your pages on ALL drafts.
9. Always italicize scientific names of organisms. Do not italicize the names of higher taxa, such as families, classes, or phyla, or of common names.
10. Scientific names are always taken as singular, no matter how many individuals are indicated: “Thiara granifera was collected from Whitefield Creek.” vs. “Snails were collected from Whitefield Creek.”

When you finish writing your thesis, proofread it very carefully. Ask yourself again if each sentence you wrote is the most meaningful, concise, and truthful statement that you can possibly make. After printing it out, proofread it again and ask a friend to do so as well.

Some appropriate references on writing

• Barnard, C., Gilbert, F., & P. MacGregor. 1993 Asking Questions in Biology: Design, Analysis and Presentation in Practical Work. Addison-Wesley Publ. Co.
• Day, R. A. 1998. How to Write and Publish a Scientific Paper, 5^th ed. Oryx Press.
• Huth, E.J. 1994. Scientific Style and Format: The CBE Style Manual for Authors, Editors, and Publishers, 6^th ed. Cambridge Univ. Press.
• Lobban, C.S., and M. Schefter. 1992 Successful Lab Reports. Cambridge Univ. Press.
• Pechenik, J.A. 1997. A Short Guide to Writing about Biology, 5^th ed. Addison-Wesley-Longman, New York.
• Penrose, A.M., and S.B. Katz. 1998. Writing in the Sciences. St. Martin’s Press, Inc.
• McMillan, V.E. 2001. Writing Papers in the Biological Sciences, 3^rd ed. Bedford/St. Martin’s Press, NY.
• Woodford, F.P., ed. 1986. Scientific Writing for Graduate Students. A Manual of the Teaching of Scientific Writing. Council of Biology Editors, Inc., Bethesda, MD.

Honesty in Writing

We expect the ideas in all your writing for your thesis to be the original products of your own reflections and analyses. Of course, you will not derive these ideas in a vacuum; they will arise from a combination of your study of the ideas of others and your own original contributions. It is therefore necessary for you to make a careful distinction between ideas that you adopt from other sources, and those you develop yourself.

You do this by citing in the text the sources of those ideas from others that you adopt or discuss in your thesis. We must assume that any ideas that you do not cite as coming from others are your own. If that is not the case, then you are being dishonest about the intellectual origins of your thesis. When in doubt, cite. Anything you say that is not general knowledge should be supported by a reference. Whether you learn something from reading, from a class lecture, or from discussions with others, you must acknowledge the source when you use that information in your thesis. This applies not only to factual information but also to ideas. Failure to acknowledge your sources will be treated as a violation of the rules for academic honesty.

It may appear to you that these rules are somewhat harsh, but in fact they are fundamental to the practice of science. Science is a collection of ideas about the way that nature “works”, ideas refined by experiment and observation. People who contribute these ideas are entitled to the credit for them. It is no more proper to borrow an idea without giving credit to the source than it is to borrow a car without asking the owner's permission. You will want to be recognized and acknowledged for your own original contributions; it is only fair that you accord the same treatment to others.