Writing science papers

This advice is intended for students who need to write-up an experiment for a class. I’ve listed some brief thoughts on what should go into the various sections of a laboratory write-up and added tips that will hopefully please your Type A teacher, since I was one. But don’t just follow the advice here: you need to first find yourself an example article from the primary literature so that you have something to emulate. Don’t skip that step, because the idea behind a write-up is that you are producing a document that could be submitted to a journal for publication.  You probably won’t end up doing that (no offense), but understanding the process of science and the format of submission will help you.  So go to the library and browse your a journal, or download an article by searching Google Scholar. Search for something fun, like, “cats, fur balls, vomit” … something that you wouldn’t mind reading a science paper on. Pay special attention to how they pitch the question.

manuscript-layout

Title

  • Should convey the “issue,” the approach, and the system (organism).
  • Format with sentence-style capitalization (i.e., capitalize the first letter of the first word, and nothing else. Some Journals Still Put Titles in Title Case or EVEN ALL CAPS, but I think those two formats are archaic and dying.  Center on the title page.
  • Avoid crafting titles with colons. Other people like them, a lot, but I’ve always found them annoying.  Reason: they are overused.
  • Provide your name, institution, address, e-mail, and telephone and fax numbers below the title.

Abstract

  • The abstract is a miniature version of your paper, and might have a single sentence that summarizes each of the major sections (Introduction, Materials and methods, Results, Discussion) of your paper … but you can make it have one or two additional sentences if needed.
  • Begin the abstract at the top of page 1, just underneath the title. It’s usually OK to single space the Abstract (the rest of the manuscript can be double spaced).
  • The first sentence should attempt to interest the reader in the issue. It is useful to imagine a reader who is predisposed to be uninterested in your topic, and thus imagine it is your job to convince him/her otherwise.
  • Describe the general approach utilized to address your hypothesis on the issue.
  • Summarize the main results briefly but without using statistical support (e.g., don’t give p-values and such).
  • Conclude with a general statement about the importance of the study, answering the question, Why should anyone care?  (Don’t include that as question, by the way…it’s just your unwritten quest.)

Introduction

  • Aim for 3-5 paragraphs, and aim for a general audience that is educated in your general field but not necessarily familiar with your question or approach. It is best to imagine a reader who is both busy and easily bored. Most people are.
  • Get your reader excited about the issue or question while using the absolute minimum of background information and definitions. The introduction is not a place to “review” all the relevant literature. If you really want to do that, write a review paper. Similarly, don’t craft sentences that only define terms. Every sentence should be written to help persuade the reader that something is interesting and not fully understood: you are introducing the question.
  • Convince the reader that the experiment has not been published previously. There are invariably articles that come close, but you should persuade reader that they don’t fully address the issue.
  • Pitch a hypothesis. This is your opinion of what you think explains this or that.
  • Provide a description the general experimental approach that will give you the data to address your hypothesis.
  • When citing published literature, use the “Name-Year” system. For example (Darwin 1859). You do not need a comma after “Darwin” and you do not need a page number. When you are citing several sources at once, arrange them chronologically and separate them by a comma (Darwin 1860, Jones 1861).

Materials and methods

  • Describe experimental equipment and methods so that another laboratory could (1) find or make the reagents/equipment, (2) repeat your techniques, and (3) follow the same statistical approach.
  • Describe the source (e.g., collection locality with latitude and longitude; company; colleague) and relevant characteristics (e.g., size, age, sex, genotype) of the biological material used.
  • Include a description of experimental as well as control treatments, with number of replicates.
  • Indicate, in parentheses, the manufacturer of specific reagents and equipment (e.g., item C0750, Sigma Chemicals, St. Louis).
  • Capitalize copyrighted names (e.g., Petri dish, Parafilm, Tween, Eppendorf, Clorox).
  • Include information about location, day length, and (laboratory) temperature when relevant.
  • Include photograph or drawing of experimental set-up if needed.
  • Fully describe all statistical analyses that were used and how they allowed you to address the hypothesis. Be specific about what the tests do. E.g., “Means were compared with a Student’s t-test.”
  • Indicate software package used (but only in parentheses); add the software’s author(s) to literature cited section.
  • You do not need to specify which program you used for graphing. You also do not need to specify the program you used collect data (Excel, e.g.) or the word processing program.
  • Use the past tense throughout (e.g., “the data were collected”).
  • Avoid using words that reveal that the manuscript is the result of a “class assignment.”
  • Use the metric system (cm, g, 56 °C).  Yes, even if you live in the backwards United States.

Results

  • First mention whether experimental protocol actually worked (e.g., “90 percent of the birds survived the experimental treatments”), then describe further qualitative results if possible.
  • Inform the reader of any ignored data or “runs” that would otherwise alter conclusions (i.e., have you chosen, improperly, to present the only run out of 10 that showed a significant result?).
  • In another paragraph, begin presentation of data analysis that more specifically addresses your hypothesis.
  • Include leading zeros on all numbers with values less than 1 (e.g., p = 0.034).
  • Include spaces before and after “=” to improve readability of statistics (e.g., p = 0.023).
  • Opt for figures whenever possible. Tables put readers to sleep.
  • Refer to figures and tables parenthetically. For example, write “…the mean running speed of rats on fire was higher than that of control rats (t = 23.84, p < 0.0005, df = 19; figure 7a)”.
  • Use significant, correlated, and normal according to their statistical meanings.
  • Avoid discussion of the results in this section.
  • Below are tips on graphs.  Make your graphs look really nice.

Use line plots (below) to show means (=averages). Much better than bar graphs because you can easily see the variation around the mean; also removes the temptation to fill bars with different colors for no reason! Error bars can be standard errors, standard deviations, etc., so be sure to specify which in figure legend. Also specify the sample sizes for each treatment. Comparison of means can be done with unpaired Student’s t-test, analysis of variance (ANOVA), etc.

Use box plots (below) to displays medians (when one or more groups have non-normally distributed data). The “box” contains 50% of the data points, and the middle line of the box is the median. The tips of the projecting bars show minimum and maximum values. There are ways ways to make these, so it is critical to explain graph elements in the figure legend. List sample sizes, too. Comparisons of medians can be done with Wilcoxon rank sum tests, Wilcoxon signed rank tests, and Kruskal-Wallis tests, among many others.

Use scatterplots (below left) and regression plots (below right) to show relationships between continuous variables. Regression assumes causality (X causes Y, e.g.).

Use bar graphs (below) to show count (=discrete, discontinuous) data. Statistically compare counts with goodness of fit tests and contingency chi-square tests, for example.

  • Craft figure legends that stand on their own. A figure legend should be able to convey the general result to a reader if the reader were to look at figures only.
  • Label both axes of charts using sentence-style capitalization (e.g., “Mean running speed (m/s)”).
  • Remove extraneous boxes, tick-marks, lines, and symbols in graphs. Rarely should you be satisfied with the “default” graphs of standard charting software.
  • Figure captions (=legends) for graphs should not contain “Results” sentences. I.e., do not give statistics in your captions. If you really, really, want to give readers a sense of statistical results, then put some asterisks or p-values directly onto the graph, perhaps accompanied by arrows. Then you could say, in the caption, “asterisks refer to post-hoc tests” (or whatever).
  • Include sample sizes in figure legends.

Discussion

  • Remind (without sounding like you are reminding) the reader of hypothesis and results, and quickly state whether your hypothesis was supported.
  • Discuss why your results are conclusive and interesting. Be sure to convince the reader, not just yourself.
  • Lead the reader through the logic of all of your conclusions.
  • State relevance of your findings to other published work.
  • State relevance to real world.
  • Detail future directions that are possible, especially experiments that could expand or confirm your conclusions. (Repeating the experiment with a larger sample size is too boring of a future experiment, however.)
  • Do not use p-values and t-values, and do not refer to figures or tables in this section.

Acknowledgements

  • Thank individuals for specific contributions to project (e.g., equipment donation, statistical advice, laboratory assistance, editorial comments on earlier versions).
  • Mention the individuals, companies, programs, and government agencies that have provided funding.
  • Be sincere but do not lapse too much into informality.
  • Include people’s names only, using abbreviations for first names (e.g., C. Darwin). Omit titles such as “professor,” “Writing Associate,” Mrs., and Dr.

Literature cited

  • Follow format described by The Council of Biology Editors. E.g., if you have cited a scholarly article in a journal, then you go this site and click on the “article in a scholarly journal” link, and it will tell you exactly how to format the citation.Use initials for first and middle names of authors.
  • Include all authors’ names for multi-authored papers.
  • Format titles of articles and book chapters in sentence case. Note that many journals use “title case” for journal article titles…but you should not copy that style!
  • Spell out journal names fully.
  • Web citations for research results and facts are extremely undesirable. In most of the cases there is primary literature that can be used, and you should go to great efforts to find this literature (e.g., use all the databases to search for journal articles.
  • Note that most journals are available online. But if you read an article on your computer, you should site the article as a journal article, not as a web site.
  • Cite only sources that you have actually read. Reading only the abstract of an article (e.g., on an online database of primary literature) does not qualify.

General

  • Do not use text quotations in scientific writing, even if you have been allowed to do this in other science courses or in high school. Rephrase with your own words.
  • Make absolutely sure that you have properly attributed others’ ideas and facts. Using phrases from your source material without quotations is plagiarism even if you cite the source at the end of the sentence. Mixing your own words with short fragments from your sources is called “patchwork plagiarism.”
  • Check for spelling errors with spell-checking software and by rereading manuscript manually (to catch “their/there” and related errors).
  • Include page numbers at the bottom of all pages.
  • Refer to your experiments and all cited experiments in the past tense.
  • Attempt to vary sentence length to improve readability.
  • Make sure all sentences fit logically within a paragraph, and that all paragraphs belong in the order that they appear. Take great care to use linking phrases between paragraphs so that your reader knows why a new paragraph has been started.
  • Italicize the Latin binomials of all organisms (e.g., Cuscuta salina).
  • After you have introduced the species’ scientific name, refer to it thereafter in an abbreviated form to conserve space (e.g., C. salina).
  • Fully spell out the genus name when a sentence begins with a scientific name, even if you have introduced the beast earlier in the manuscript.
  • Use a serif font (e.g., Palatino, Times) for your text and tables. Non-serif fonts (e.g., Helvetica, Verdana) are fine, indeed desirable, for figures.
  • Delete any ext ra spaces within and __between words, especially before and after   italicized   text.

Word choice

  • Pair all instances of data with plural verbs. Datum is the singular. You therefore should write, “data are”, never “data is.” It is of course true that many people, including some scientists, often say “data is”, but the frequency of the error does not make it less of an error.
  • Use “whether” and “if” appropriately. “If” means “in the event that” (a hypothetical scenario) and is rarely the appropriate word in scientific writing.
  • Use “that” to specify a particular item. “Which” is used when you want to provide information that is not absolutely critical in defining the previous phrase of the sentence.
  • Use “because” to indicate causality (e.g., “the cat purred because she was being fed”). Use “since” to indicate a timing issue (e.g., “the cat had not purred since the tragic boating accident in July”).
  • Use “e.g.” (which is generally italicized because it is a foreign word, but not here because italics looks awful on the web) when you want to provide an example. Use “i.e.” when you want to rephrase (i.e., to state more explicitly). These abbreviations are not interchangeable.
  • Keep your manuscript completely free of slang, cliches, and contractions.
  • Avoid, when possible, the ambiguous words “their,” “they,” “it,” and “this.”
  • Avoid using “etc.” Instead opt for more complete listings of items.
  • “Et cetera” is abbreviated “etc.”  I feel foolish saying that, but it’s a common mistake.
  • Resist the strange trend to use “woman” as an adjective (it’s a noun). Say, “female scientist” instead of “woman scientist.” Or, if you can’t resist, be consistent and write, “man scientist,” and brace yourself for the derisive laughter. Note, however, that a scientist who studies women might, I guess, be called a “woman scientist.”
  • If you don’t know the difference between “effect” and “affect,” then never, ever use either of those words. I could explain the difference right here, but I’d much rather send you to The Oatmeal’s “10 words you need to stop misspelling” (scroll down to appropriate section).

Useful literature

Alley, M. 1996. The Craft of Scientific Writing, 3rd ed. Springer-Verlag, New York.

Briscoe, M.H. 1996. Preparing Scientific Illustrations: A Guide to Better Posters, Presentations, and Publications, 2nd ed. Springer-Verlag, New York.

Day, R.A. 1994. How To Write and Publish a Scientific Paper, 4th ed. Oryx Press, Phoenix.

Matthews, J.R., J.M. Bowen, and R.W. Matthews. 1996. Successful Science Writing: A Step-by-Step Guide for the Biological and Medical Sciences. Cambridge University Press, Cambridge.

Moore, R. 1994. Writing as a tool for learning biology. BioScience 44:613-617.

Pechenik, J.A. 2010. A Short Guide to Writing about Biology, 7th ed. Pearson, New York.

Schlenker, R.M. 1990. Student research report writing. The American Biology Teacher 52:491-492.

Strunk, W., Jr., and E.B. White. 1979. The Elements of Style, 3rd ed.

Style Manual Committee, Council of Biology Editors. 1994. Scientific Style and Format: the CBE Manual for Authors, Editors, and Publishers, 6th ed. University of Cambridge, New York.

Tufte, E.R. 1983. The Visual Display of Quantitative Information. Graphics Press, Connecticut.

Internet links

Using this site

Anyone is allowed to link to this page, but please don’t download the darn thing and keep it on your site.  I can’t believe I have to say that.

Purrington, C.B. Writing science papers. Retrieved <today’s date>, 2011, from http://colinpurrington.com/tips/academic/labwriteups.

Copyright Colin Purrington

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