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BSCI 1510L Literature and Stats Guide: 3.1 Specific details regarding scientific writing

Introduction to Biological Sciences lab, first semester

3.1.1 Scientific names

In scientific writing (and in science in general), common names are rarely used.  The Latin binomial (i.e. "scientific name") is used instead.  There are several important rules regarding the use of scientific names.  Failure to follow these rules in your writing flags you immediately as an amateur scientist, so make it a practice to follow them.

1. Scientific names are always italicized.  When hand-writing text, you can underline them instead, but there is no excuse not to italicize when using a word processor.  Example: use Bos taurus, not Bos taurus.

2. The genus is always capitalized.

3. The species is never capitalized, even when it refers to the name of a place or person.  Be careful because word processors will often "auto-correct" a species name and incorrectly capitalize it or change the spelling.  Example: Juniperus virginiana, not Juniperus Virginia.

4. In its first use within a particular document, the genus is always written in full.  In subsequent uses, the genus can be abbreviated using the first initial and a period.  In the case where two species from different genera have the same abbreviation for their genus, prevent confusion by writing out the full genus.  Example: on first use, write Escherichia coli and reserve E. coli for subsequent references. 

5. A species name is never used without a genus or genus abbreviation.  Example: write Tribolium confusum or T. confusum but never just confusum.  It is OK to use the genus by itself if you mean to refer to multiple species within the genus.  Example: "There are many species of Drosophila that are affected by exposure to alcohol."

6. If you must use a common name, first define it in terms of the scientific name.  For example, "Pan troglodytes (chimpanzee)".

In this course, incorrect formatting of scientific names may result in a point deduction.

3.1.2 Data

The word "data" is plural.  Say "the data were …" not "the data was …".

3.1.3 Citing References in the Text

Each time a scientific paper makes reference to the work of others, it is expected that the paper's authors cite that work.  The exact method of citation varies depending on the journal.  In most biomedical journals and in very high-impact journals such as Science and Nature, citations are made through endnote reference numbers that are placed in the text as superscripts, or within parentheses or square brackets.  Although this format is more compact within the text, it is somewhat less convenient because it requires renumbering during the editing phase and requires the reader to go to the endnote to know anything about the citation.  We will use the more traditional method which is to cite the author or author's names, followed by the publication year.

3.1.3.1 General citation/reference patterns

Here is an example of a citation from the methods section of a paper:

            The following culture media were used for this method (Tsuzuki 1991): …

Sometimes a page, figure, or table number is also given if a specific part of the paper is being referenced rather than the paper in general, or if the work is a book rather than an article.  If there are two authors, their names are both listed.  If there are three or more authors, the name of the first author is listed, followed by "et al."

If the author's name is already being used in the text, the citation simply lists the date in parentheses, e.g.

            Dan and Hontela (2011) reported that triclosan was detected in breast milk, urine and plasma …

Each citation in the text of the article must be accompanied by a corresponding reference in the references section at the end of the paper (Section 2.1).  They are listed in alphabetical order by last name of the first author, then by publication year if more than one paper by that author is cited.  Here are the listings that would be added to the reference section for the example citations above:

Dan, A. B. and A. Hontela. 2011. Triclosan: environmental exposure, toxicity and mechanisms of action. Journal of Applied Toxicology 31:285-311. http://dx.doi.org/10.1002/jat.1660

Tsuzuki, M. 1991. Manual on Sterilization and Disinfection, Ishiyaku Publishers, Tokyo, 177–181.

3.1.3.2 Additional citation examples from Steingraber et al. (1985)

1. Both the name and date can go inside parentheses if the name is not actually part of your sentence. Not all journals include the comma between author and year. For example:

Enzymes are inhibited by cyanide (Grubb 1977).

Because enzymes are inhibited by cyanide (Grubb 1977), I expect to find....

Notice that the parenthesis is placed at the end of the sentence of clause containing the reference and that punctuation FOLLOWS the citation.

2. Another way to cite a study is to make the last name of the researcher the subject or object of the sentence or clause and follow it immediately with the date of the study in parentheses:

Grubb (1977) found that cyanide inhibits enzymes.

Because Grubb (1977) found that cyanide inhibits enzymes....

These data support the conclusions of Grubb (1977).

3. If you wish to emphasize the date of the cited study, you can omit the parentheses:

As early as 1977, Grubb observed the inhibitory effect of cyanide on enzyme action.

This strategy is often effective for presenting an historical perspective of the problem (i.e., useful in Introduction).

4. It is INCORRECT to separate the date of publication from the author’s name:

Incorrect: Grubb found that cyanide inhibits enzyme action (1977).

5. If you wish to cite more than one study per reference, i.e., if more than one author has reached the same conclusion or worked on the same problem independently, you may list them together in the same parentheses and separate their names by semicolons:

Cyanide has been found to inhibit enzyme action (Grubb 1977, Smith 1980, Taylor 1983).

By convention, these citations are listed in chronological order.

6. In the case of more than three authors, you may use et al. (from "et alii", Latin for "and others"; although et al. is a Latin term it is in such common use that it is not italicized) after the first author’s name:

Cyanide has been found to inhibit enzyme action (Jones et al., 1985).

3.1.4 Grammar for scientific reports

Lab manuals are often written as imperatives (also known as directives), a grammatical mood where the author gives directions to an implied audience. For example, your lab manual may say:

“Pipette 15 mL of sterile solution and vortex to mix.”

However, this form should not be used in a research paper’s methods section, which should avoid the use of first person or the directive.

In narrative writing, such as the kind used in fiction, active voice is often preferred because it is more illustrative. However, in scientific writing (particularly in a methods section) passive voice has traditionally been employed because it emphasizes the actions of the procedure over the person who completed the task. The “I” or “we” who is incubating the cultures should be irrelevant to the action performed.

In active voice, the subject of a sentence performs the action described by the verb.

Example: We incubated bacteria cultures at 30°C.

In passive voice, the subject is the recipient of the action of the verb.

Example: Bacterial cultures were incubated at 30°C.

While some scientific journals have begun to allow the use of active voice, it is challenging to do so while also maintaining a scientific style and minimizing the use of first person. Until you have reached a mastery of scientific writing sufficient to know when this is appropriate, the best rule of thumb is to avoid first person and active voice all together in methods.  If the journal that you are writing for has a policy on active vs. passive voice, you should follow it.  Usually such policies are described in an "Instructions for authors" page on the journal's website.

3.1.5 Notes on formatting specific to this class

The best way to get a feel for the general patterns in formatting of journal articles is to examine recent papers in well-established scientific journals.  The exact format of a paper depends on the guidelines established by the publishing journal.  All journals publish "Instructions to Authors" which are available on the journal's website.  In this class, we will use the format of Ecology, a publication of the Ecological Society of America.  The format of Ecology is fairly typical for non-biomedical journals.  The primary difference is in the method of citation as discussed in Section 3.1.3 .  In this class we will use the author (year) form of citation primarily because it makes revising the paper easier since footnotes do not need to be renumbered with each edit. 

The form of a submitted paper is often different than its appearance when published in the journal.  For example, the article may be required to be submitted double-spaced with all of the figures and tables at the end, whereas in the published article it will probably be single-spaced with two columns per page and figures interspersed throughout the article at appropriate places.  For the paper you will write in this class, please follow these guidelines:

1. Pages should be numbered.

2. It is not necessary to have a running head at the top of the page.

3. Text may be single-spaced unless your TA specifically requests double-spacing.

4. Although it is common practice in journals to place text in two columns per page, that is neither necessary nor recommended in this assignment.

3.1.6 Discussing statistics and results of statistical tests

Please refer to Section 5.6 of the Excel Reference and Statistics Guide for information on appropriately discussing statistics in your paper.