Science Writing for Research

1. Science Writing for Research Instructor: Richard Rothenberg MD Office: 140 Decatur St. Atlanta GA 30302-3995 Phone: 404-413-1144 Email: rrothenberg@gsu.edu, rrothen@emory.edu

2. Overview Part 1: Language as dialect Part 2: Macrostructure of scientific articles Part 3: Microstructure: form and function in language

3. Language as dialect • Regional dialects • A dialect is a language without an army. • Dialects within a “standard” language • Pulp fiction • Literature • Bureaucratese • Computerese • Scientific language • Language of the underclass (Ebonics, Cockney, Verlan, Argot, Espaňol de Tepito [Cantinflas])

4. Pulp fiction Jack Python walked through the lobby of the Beverly Hills Hotel with every eye upon him. He had money, charisma, a certain kind of power, razor-sharp wit, and fame. It all showed. He was six feet tall with virile good looks. Thick black hair worn just a tad too long, penetrating green eyes, a two-day stubble on a deep suntan, and a hard body.

5. Literature (i) …Miss Coldfield in the eternal black which she had worn for forty-three years now, whether for sister, father, or nothusband none knew, sitting so bolt upright in the straight hard chair that was so tall for her that her legs hung straight and rigid as if she had iron shinbones and ankles, clear of the floor with that air of impotent and static rage like children’s feet, and talking in that grim haggard amazed voice until at last listening would renege and hearing-sense self-confound and the long-dead object of her impotent yet indomitable frustration would appear, as though by outraged recapitulation evoked, quiet inattentive and harmless, out of the biding and dreamy and victorious dust.

6. Literature (ii) Today, mama died. Or maybe yesterday; I don’t know. I received a telegram from the Home: “Mother deceased. Burial tomorrow. Deepest sympathies.” That leaves the matter in doubt. Perhaps it was yesterday.

7. Bureaucratese Original Such preparation shall be made as will completely obscure all Federal buildings and non-Federal buildings occupied by the Federal Government during an air raid for any period of time from visibility by reason of internal or external illumination. Such obscuration may be obtained by blackout construction or by termination of the illumination. Translation In buildings where they have to keep the work going, cover the windows. If the work can stop for a while, turn out the lights.

8. Computerese Older: FS/NOFS temporarily overrides the FS/NOFS system option to specify whether HELP information is displayed in full screen format on the display terminal Newer: You can correct common typing errors automatically as you work by using the AutoCorrect command on the Tools menu. This feature automatically capitalizes the first word of a sentence and the names of days, changes two capital letters at the beginning of a word to a single capital letter, and corrects capitalization errors caused by accidental use of the CAPS LOCK key.

9. Scientific language In 1990, the percentage of adults who reported having had their cholesterol checked ranged from 48% in the District of Columbia to 70% in Rhode Island (median: 63%) (Table 1). The percentage of adults who had been told their cholesterol level ranged from 29% in the District of Columbia to 58% in Washington and New Hampshire (median: 48%), and the percentage of adults who knew their level ranged from 12% in the District of Columbia to 37% in Rhodes Island and New Hampshire (median: 29%).

10. The Challenge of Scientific Writing (i) Content

11. The Challenge of Scientific Writing (ii) Content Writing

12. The Challenge of Scientific Writing (iii) Concise Coherent Clear Complex Unambiguous Non-self-referential Nonintrusive

13. The Challenge of Scientific Writing (iv) Concise Coherent Clear Complex Unambiguous Non-self-referential Unintrusive Content

14. The Challenge of Scientific Writing (v) To stay within the required format and still say something interesting.

15. The Scope of Scientific Presentation • Original contributions • Brief Reports • Methodological contributions • Reviews • Commentary • Hypotheses • Editorials • Letters

16. Je n'ai fait celle-ci plus longue que parce que je n'ai pas eu le loisir de la faire plus courte. I have written a long letter because I do not have time to write a short one. - Blaise Pascal, "Lettres provinciales", Letter 16, December 4, 1656 http://www.ac-nice.fr/philo/textes/Pascal-Provinciales.htm

17. Original contributions Usual Format Size (text): 2,500 to 5,000 words Size (abstract): 150 to 250 words Illustrations: 3 to 6 Tables, Figures, Graphics

18. Original contributions Overall Structure I Introduction (Why did you do it?) M Methods (How did you do it?) R Results (What did you learn?) D Discussion (Who cares?)

19. Original contributions Introduction (i) Key point: SHORT State the issue (3-5 sentences) State the commonly held belief (4-6 sentences) State what you will do (2-4 sentences)

20. Original contributions Introduction (ii) Example: The rationale underlying contact investigation for tuberculosis (TB) is that certain clinical presentations pose a risk of infection to patient contacts through inhalation of airborne droplet nuclei containing Mycobacterium tuberculosis.1,2 This rationale has generated a set of priorities for contact tracing justified by the frequency of transmission of M. tuberculosis to close contacts of infectious patients. For example, contacts of patients with non-cavitary, or smear-negative pulmonary TB would have a lower priority than contacts of patients with sputum AFB smear-positive pulmonary disease. Contacts with evidence of latent TB infection (LTBI) can reduce their risk of progression to active disease by 60-70% upon completion of a 6 to 9 month course of isoniazid.3 In recent years, primarily as a result of the HIV and STD epidemics, interest has grown in the contribution that social network analysis can make to understanding disease transmission.3-5 Several examples of its application in the field of TB control suggest that a network-informed approach holds promise for improving both the understanding of transmission dynamics and the effectiveness with which secondary TB cases and contacts with LTBI may be discovered through the contact tracing process.6,7 The underlying hypothesis for a network-informed approach to contact investigations is that in areas of ongoing transmission, this strategy will provide access to a wider group of persons involved in a transmission milieu. An infectious person’s contacts may have TB or LTBI because of direct contact with him or her, or by having acquired it elsewhere. Thus, a network investigation, it might be predicted, would be able to uncover a group that is epidemiologically and biologically interconnected (that is, have social, sexual, or drug-using connections and have M. tuberculosis isolates with matching DNA fingerprint patterns) as well as persons with epidemiologic connections, but unique DNA fingerprint patterns. In this study, we explore the use of network-informed approaches, coupled with RFLP typing, in the investigation of a protracted TB outbreak in Wichita, Kansas in a group of 19 young persons (25-35 years of age) diagnosed with TB over a seven year period. The outbreak was first identified among women who worked as exotic dancers, and we investigated the role of social, sexual, and drug-using network relationships in understanding TB transmission

21. Original contributions Introduction (iii) Example: (The Issue)The rationale underlying contact investigation for tuberculosis (TB) is that certain clinical presentations pose a risk of infection to patient contacts through inhalation of airborne droplet nuclei containing Mycobacterium tuberculosis.1,2 This rationale has generated a set of priorities for contact tracing justified by the frequency of transmission of M. tuberculosis to close contacts of infectious patients. For example, contacts of patients with non-cavitary, or smear-negative pulmonary TB would have a lower priority than contacts of patients with sputum AFB smear-positive pulmonary disease. Contacts with evidence of latent TB infection (LTBI) can reduce their risk of progression to active disease by 60-70% upon completion of a 6 to 9 month course of isoniazid.3 (Common Beliefs) In recent years, primarily as a result of the HIV and STD epidemics, interest has grown in the contribution that social network analysis can make to understanding disease transmission.3-5 Several examples of its application in the field of TB control suggest that a network-informed approach holds promise for improving both the understanding of transmission dynamics and the effectiveness with which secondary TB cases and contacts with LTBI may be discovered through the contact tracing process.6,7 The underlying hypothesis for a network-informed approach to contact investigations is that in areas of ongoing transmission, this strategy will provide access to a wider group of persons involved in a transmission milieu. An infectious person’s contacts may have TB or LTBI because of direct contact with him or her, or by having acquired it elsewhere. Thus, a network investigation, it might be predicted, would be able to uncover a group that is epidemiologically and biologically interconnected (that is, have social, sexual, or drug-using connections and have M. tuberculosis isolates with matching DNA fingerprint patterns) as well as persons with epidemiologic connections, but unique DNA fingerprint patterns. (What you will do)In this study, we explore the use of network-informed approaches, coupled with RFLP typing, in the investigation of a protracted TB outbreak in Wichita, Kansas in a group of 19 young persons (25-35 years of age) diagnosed with TB over a seven year period. The outbreak was first identified among women who worked as exotic dancers, and we investigated the role of social, sexual, and drug-using network relationships in understanding TB transmission

22. Original contributions Methods (i) Key point: Stands alone

23. Original contributions Methods (ii) Overall structure:

24. Original contributions Methods (iii) Provide the context 1-2 paragraphs give general background for study describe setting in which study was done (do NOT provide justification)

25. Original contributions Methods (iv) Describe what you did: 7-10 paragraphs sample selection and ascertainment instruments used biologic measurements (procedures) analytic approaches (data management) (human subjects considerations)

26. Original contributions Methods (v) Reference standard methods: 1-2 paragraphs cite analytic methods cite statistical and computer tools cite standard data bases

27. Original contributions Methods (vi) Acknowledge Human Subjects issues: One paragraph mention use of informed consent mention IRB approval

28. Original contributions Methods (vii) • Some “don’ts”: • Do not include methods considered but abandoned (don’t recreate the thinking) • Do not justify the methodological choices • Do not discuss their implications • Do not offer results or opinion

29. Original contributions Results (i) Key point: Don’t tell them everything you know.

30. Original contributions Results (ii) • Overall structure: • Results should be parallel with Methods (roughly) • Proceed from simple to more complex • General description • Univariable (unadjusted) comparisons • Multivariable (adjusted) comparisons • More complex models and statistical approaches • Mention only: other approaches that were confirmatory or noncontributory

31. Original contributions Results (iii) • Illustrative material (i): • <7 Tables* • avoid tables if you can say it in the text • avoid “text tables” whenever possible • <4 Graphs and Figures* • avoid graphs if you can use tables • use legends to graphs instead of footnotes • Avoid duplication in tables and text *depending on overall length and specifications of the journal

32. Original contributions Results (iii) • Illustrative material (ii): • Do not use a table, graph, or figure that is not referred to (cited) in the text • Cite tabular content, not the table itself: • Wrong:The comparative heights of men and women are shown in Table 3. • Right:In general, men are taller than women (Table 3).

33. Original contributions Results (iii) • Illustrative material (iii): • Avoid appendices if possible • Do not include data tables, questionnaires • Include numerical examples, proofs, etc. • Avoid footnotes • Incorporate material into text

34. Original contributions Results (iv) • Illustrative material (iv): • Avoid graphs and figures with a low • Content:Ink ratio:

35. Original contributions Results (v) • General coherence • Do not use a technique in the Results that is not mentioned in the Methods • Do not mention something in the Results that you do not consider in the Discussion

36. Original contributions Discussion (i) Key point: Don’t go beyond the data.

37. Original contributions Discussion (i) • Overall structure (i) • First Paragraph • Use the first paragraph to restate the basic question and the major result(s) that illuminate the issue • Do not use the first paragraph to summarize the findings

38. Original contributions Discussion (i) Overall structure (ii) Discussion sections

39. Original contributions Discussion (i) • Overall structure (iii) • 3-5 Major points • Offset each point visually, using either a 2nd level header or by beginning a paragraph with an italicized phrase. • To the extent possible, maintain parallelism between the Discussion, the Results, and the Methods.

40. Original contributions Discussion (i) Overall structure (iv) Example: Discussion This is the opening paragraph that restates for the reader what the major research questions is and what the importance is of this study. A major point This is the first paragraph that discusses a major point. This is the second paragraph that discusses a major point. A second major point This is the first paragraph…. This is the second paragraph….

41. Original contributions Discussion (i) Overall structure (v) Alternative example: Discussion This is the opening paragraph that restates for the reader what the major research questions is and what the importance is of this study. A major point. This is the first paragraph that discusses a major point. It uses an italicized phrase at the beginning of the sentence to offset the point. This is the second paragraph that discusses a major point. A second major point. This is the first paragraph of second major point. It uses an italicized phrase at the beginning of the sentence to offset the point. This is the second paragraph that discusses a second major point

42. Original contributions Discussion (i) • Overall structure (iv) • Strengths and Limitations • Understate. Don’t break your arm patting yourself on the back. • Avoid phrases like: “This is the first study to do such-and-such.” • Include real limitations, not “strawmen” (items that sound like limitations but are really strengths). • Avoid phrases like: “This study has several limitations.” • Defend the methods used, as appropriate

43. Original contributions Discussion (i) • Overall structure (v) • Implications of the findings • Understate. Do not go beyond the data • Provide biological plausibility for findings, if appropriate • Point to parallels in other lines of inquiry, if appropriate

44. Original contributions Discussion (i) • Overall structure (vi) • Future directions • Try to say something that enhances the reader’s perspective on the issue, based on the presented findings. • Avoid saying: More research is needed. (If more research is needed, be more specific.) • Draw conclusions if warranted by the data

45. Original contributions Discussion (i) • Overall structure (vii) • Extraneous Sections • Do not include a separate section for Conclusions (these are integrated into the Discussion) • Do not include a section called Summary (that is what the Abstract is for)

46. Original contributions Discussion (ii) • General coherence (i) • Don’t include results that you do not discuss. • Don’t discuss findings that were not presented in results. (That is: do not introduce new material in the discussion.)

47. Original contributions Discussion (ii) • General coherence (ii) • Keep Methods, Results, and Discussion… • roughly parallel • mutually exclusive • Don’t put results or discussion in Methods • Don’t discuss the findings in the Results • Don’t put methods or results in the Discussion

48. Original contributions Structured abstract (i) • Key points: • Write the abstract AFTER you write the paper • Remember that is probably the only part of the paper that most people will read

49. Original contributions Structured abstract (ii) • Generally 150-250 words • Several alternative formats • Check the uniform guidelines and the specific instructions from the journal to which the manuscript will be submitted

50. Original contributions Structured abstract (iii) Example (i)(from Sexually Transmitted Diseases) : Background:… Goal:… Study Design:… Results: … Conclusions: …