Writing in science.

1. Writing in science. Report & Journal Articles The Kenyon College Biology webpage was the source material for much of this tutorial.

2. Parts of a scientific paper. • Title • Introduction • Materials & Methods • Results • Discussion • Acknowledgments (perhaps) • References • Appendices (for this paper)

3. General rules • You are NOT writing for the professor. Real scientists write for an audience who is smart, but who was not involved in the experiment. • Don’t refer to the work being done as part of a class, or to your group. Write as if you were a real scientist who did an experiment • Past tense everywhere: you already did the experiment

4. Rules of scientific writing • Headings (Introduction, Methods & Materials, etc.) at the top of each section. • Use precise language; avoid vague, uninformative terms. • The active voice should be used as much as possible.

5. General writing tips • Tell a story with a plot and make it interesting • Plan how to order sections within the paper, paragraphs within the section, and sentences within the paragraph • Group all information about a topic together in a paragraph or consecutive paragraphs. • Don’t waste a sentence: “There are many kinds of college students. They can be young, old, male…” should read, “College students can be young, old, male…” • Define jargon smoothly • Bad: “The humpback chub is endemic to Colorado. Endemic is defined as a species that it occurs in one location but nowhere else.” • Better: “The humpback chub is endemic to Colorado, occurring there but nowhere else.

6. General writing tips • Paragraphs start with topic sentence. • Start each sentence with old information. • Avoid “this, those, these.” • Define new words; remind reader of previously defined words not mentioned for a while. • Join separate clauses with linking words: but, therefore, etc. • Conclude sentences with most important new thought. • Use concluding thought of previous sentence to begin next sentence.

7. Parts of a scientific report: the title • Self explanatory: casual reader should be able to tell what you did without reading the paper. Bad Title: Human Genome Report Better Title: An Investigation of Inheritance Patterns in the Family of Elsa Falls. Best Title: An Investigation of Inheritance Patterns in Eye Color, Male-Pattern Baldness, and High Blood Pressure in Three Generations of Elsa Falls’ Family

8. Avoid excessively long titles • Titles should be self contained but not excessively detailed. This title has too much of a good thing: “The effect of zero, five, and ten pound weights on the electromyograph of the extensor muscle of the human forearm, a study done as part of the Integrative Biology course at Randolph Macon College on twenty student volunteers during the week of February 7th in 2006.”

9. Purpose of introduction • Explains the reasoning behind your work. • Describes the context of your work and how it relates to existing work (such as providing new information to the field of study). • Clearly states the purpose of your work.

10. What are the basic things that you should ask before you write your introduction? • What is the existing knowledge about this subject? • Why did you undertake this study? • What specifically were you going to do?

11. What is the existing state of knowledge about this topic? • You should synthesize information from the literature. • Should be an account that traces the development of knowledge on the problem and summarizes its current state. • The gaps and inadequacies of current knowledge should be identified.

12. Why did you undertake this study? • A good initial statement may be a description of an observation in nature. • A conclusion drawn from a survey from the literature that stimulated the your interest.

13. What specifically, were you going to do? • Indicate the specific objectives or testable hypothesis that will be considered. • These should be as specific as possible. • In the case of hypotheses: These should be statements that are clearly capable of being either supported or refuted by the work.

14. Structure of the Introduction • Follow a logical outline. • One strategy that works well is the “funnel approach” • Begin with a “global problem” statement that describes the large problem to which your work is related. • End with a clear statement of the specific goal or goals of your specific work. • Connect the two statements with a series of logical steps that describe the published information related to your work and build a logical case for the importance of your work

15. Additional Notes • Restrict background material to that which is directly pertinent to the problem. • An author of a scientific report should always be prepared to answer the question: Why did you include this material in the introduction?

16. Purpose of Methods & Materials • Allows replication of your work by others. • Allows others to assess the validity of your techniques and adequacy of your equipment. • Provides the sources of key equipment, reagents, & supplies.

17. Structure of Methods & Materials • Follow logical outline. • Use past tense. • Use genus and species name of experimental organism unless common (Human, Lab Mouse, Lab Rat) • Describe basic experimental design: number of treatments replicates andwhat are the controls. • Rationale for the methods

18. Structure of Methods & Materials cont. • Concentration and quantities of reagents used. • Types and method of measurements made. • Statistical test used and justification. • In field studies, the description of study site and location. • Definition of new terms or abbreviations. • Conditions of experiment: Temperature, light, pH, etc.

19. Methods & Materials Do’s & Don’ts • Omit details that are not essential for the replication of the experiment by others. e.g. I stuck the electrodes on my lab partners forearm but one fell off and we had to stick it on again. e.g. Subjects lifted 10 lb weights bought at Jane’s Sporting Goods on Broad Street. e.g. We wrote all the data down in our lab books so we could remember it later.

20. Methods & Materials Do’s & Don’ts • Use precise language. Vague: We measured the electric discharge of the our fish several times during the study. Precise: The frequency of the electric discharge of the Black Ghost fish was measured twice per day for three consecutive days.

21. Methods & Materials Do’s & Don’ts • Tell reader what was done using past tense rather than how to do it using present or future tense. Incorrect: First , lower the electrodes in the aquarium. Then record the EOD for 1 sec. Afterward count the number of discharges in the voltage-time plot. Correct: The frequency of the EOD was determined by counting the discharges on a 1 sec voltage-time plot of the amplified signal from the aquarium electrodes.

22. Purpose of Results • Concisely presents the data using text, graphs, figures, and tables. • Guides the reader through the data without interpretation so they can formulate their own opinion.

23. Structure of Results • Use concise and direct style that summarizes data in an objective and clear manner. • First sentence of each paragraph puts data in context or introduces aspects of data detailed in body of paragraph. • Body of the paragraph describes major tends or patterns illustrated by comparison between experimental groups and controls. • Refer parenthetically to each Table and Figure in paper.

24. Results Do’s and Don’ts • Avoid including all of the raw data in a table or figure or making all possible comparisons. • Usually means (averages) and a measure of variability such as the “standard error of the mean” are reported instead of raw data. • Use graphs and tables to supplement the text.

25. Figures • Pedigrees, graphs and other types of illustrative material are referred to as figures. • Graphs are used to illustrate trends in the data; include X and Y axis labels with units. • Numbered consecutively (Figure 1, 2, 3…). • Have caption at bottom stating source of data, type of variability measure (error bars), sample size, and statistics.

26. Figures • Note number identifying figure. • Note statement of figure contents. • Note types of statistics. • Note sample size provided. • Note axes are labeled and units shown.

27. Figures When to use a figure? Use figure when you need to illustrate pattern or trend in data. Use figure when data are too complex to summarize as a simple statement in text.

28. Figures What type of figure to use? Use bar graphs to illustrate data sorted in discrete categories eg. Types of E-fish Use X-Y graph to illustrate continuous data, e.g. Frequency of electric discharge vs time.

29. Figures What features should be included: • X-axis with label and units of independent variable. • Y-axis with label and units of dependent variable. • When means are graphed some indication of variation must be included: eg. “error bars.”

30. Figures Error Bars The mean, or some other measure of central tendency of the data, is often plotted in graphs along with the mean value plus and minus some measure of variability. This range, shown with a line, is called an “error bar.” The most common types of variability used in error bars are: • Standard Error of the Mean (S.E.M. or S.E.) • Standard Deviation (S.D.) • 95% or 99% Confidence Limits or Confidence Interval (C.I). Excel can calculate any of these from your raw data.

31. Figures Bar Charts: • Note axes labels with units. • Note information in caption about what statistic is plotted and what the error bars indicate. • Note use of bar chart for categorical independent variable. • Note use of sans serif font (Helvetica) in chart. • Note ~ 2/3 proportion of height to width. Error bars Figure 9. The maximum EMG output of different muscle types under medium load (mean + S.E.M., n = 5).

32. Figures What is wrong here? • Note lack of units for Y-axis • Note lack of caption. • Note lack of variability measure. • Note gratuitous use of three dimensional chart for two dimensional data. • Note unnecessary use of color (Only use color when it adds information!) • Note unpleasing proportion of height to width.

33. Tables When to use a table? • Use a table when the data are not appropriate for a graph. • Use a table when the data can’t, usually because of complexity, be included in the text of the results.

34. Tables Organization • Number each table separately from figures (Table 1, 2, 3…) • Caption goes above table. • Organize data in columns to be read down. • Include units in column names. • Use footnotes to add explanation of columns if needed.

35. Tables • Note table number and caption at top. • Note column format, column names, with units. • Note footnotes describing what values are. MacIver et al., 2001

36. Discussion: Purpose • The Discussion generally does two things: • it gives the “big lessons” that can be learned from the work 2. it compares the work to other similar research found in the literature.

37. Discussion: Do’s & Don’ts • The discussion is usually full of references • The discussion is not a summary • Emphasis should be on broadly applicable generalizations and principles • May use subheadings to separate major sections. (Only when necessary.) • End the discussion with a short summary of the significance of the work and conclusions drawn.

38. Discussion: Contents • Interpretations of the data. • Relate interpretations to the questions you posed in the introduction and the work of other researchers. • Clear up any discrepancies or ambiguities in your data or results. What further experiments might be performed to clear these up? • If necessary, make a new hypothesis that might be tested and that might explain why your results came out the way they did.

39. Discussion: Contents cont. • Did the results answer your question? • Did they support your hypothesis or not? • Draw some conclusions, supporting them with your data. • What is the significance of your results in the general area you studied? • What are the main principles demonstrated by your results?

40. Structure of the Discussion • Follow a logical outline. • Use a “reverse funnel approach”. - Begin with specifics - End globally - Fill in between with connecting statements or paragraphs

41. The Refereed Literature • What it isn’t: Wikipedia and other encyclopedias, newspapers, magazines, web pages, lecture notes… • What it is • Scientific studies written by practicing scientists • Peer reviewed: 30-70% of papers are rejected by expert reviewers who judge the information less-than-reliable • Expensive to produce: you won’t find it on Google • Published in “journals”

42. Finding Literature • Must have access to expensive databases • R-MC library pays thousands per database so that you can search for free! Link

43. Finding literature • Accessing databases in the Biology subject area: Start with this one

44. Developing a Search Strategy • Learn to develop good search terms and to string them together appropriately:

45. Saving your references • View and select good articles, then email the citations to yourself. ILL to get full article

46. Formatting References • Next section after Acknowledgements • Alphabetical order based on first author’s last name. • “Hanging” first line Peterman, R.M. 1982. Model of salmon age structure and its use in preseason forecasting and studies of marine survival. Canadian Journal of Fisheries and Aquatic Sciences 39: 1444-1452. Note: In MSWord, use “Format paragraph”, NOT tabs, spaces, returns, etc.

47. Formatting References • General format: • author(s), year, article title, journal name, volume, pages. • Exact format depends on the journal if publishing or professor if turning in for grade. Peterman, R.M. 1982. Model of salmon age structure and its use in preseason forecasting and studies of marine survival. Canadian Journal of Fisheries and Aquatic Sciences 39: 1444-1452.

48. Formatting References • Nit-picky rules are very important • No capitalization of article title. • No italics or underline (unless scientific name) • Pay attention to exact punctuation • Volume number, but not issue. Peterman, R.M. 1982. Model of salmon age structure and its use in preseason forecasting and studies of marine survival. Canadian Journal of Fisheries and Aquatic Sciences 39: 1444-1452.

49. Citing References • Refer to all sources of information that you used in your paper. • All sources in a reference list must be cited in the paper and vice versa. • Cite: books, journal articles, etc. (Refereed or peer reviewed) • Sometimes: Cite any persons from whom you obtained information as “personal communication”

50. Additional information about citing references • Citation of a reference does not entitle you to “lift” passages of text. • Direct quotations must be set off by quotation marks. • Minimize exact quotations; extended quotes in science papers are rare! • Best to digest the information and present it in your own words.