7.021--Introduction to Experimental Biology/Writing

1. 7.021--Introduction to Experimental Biology/Writing Section C (Tue 9-11 a.m.in 14N-0637) Section D (Tue 1-3 p.m. in E53-220) Neal Lerner Office: 68-580a; x2-2939; nlerner@mit.edu

2. Meeting 1: Introduction

3. What is the Plan for 7.021? • See Course web site: http://mit.edu/7.021/www/ • Course goals--by the end of the semester, you will: • Understand the seven components (title, abstract, introduction, methods, results, discussion/conclusion, tables/figures) of a laboratory research paper. • Understand the writing process and its application to scientific writing. • Understand the importance of communicating in writing as a scientist. • Understand the relationship between audience, purpose, and content. • Use writing both as a means of expressing content knowledge and of learningcontent. • Give and receive peer feedback in order to improve your writing. • Apply an understanding of scientific writing to your subsequent independent research.

4. Course Schedule • Meeting dates vary! Check dates for your section and mark your calendars. • Six Meetings focus on seven components of a research paper (Intro, Methods, Results, Figures/Legends, Discussion/Conclusion, Title and Abstract): • In-class exercises: Use discussion board and Star office. Make a hard copy of Star office docs and save files in course locker. • Please find Discussion Board http://mit.edu/7.021/www/ • Please load Star Office on Athena machines. • Out-of-class exercises: Use MS word on your own machines or Star Office on Athena, turn in hard copy and save file in course locker. • Long-term project: 3 choices - This follows an iterative process. Something needs to be turned in at each class meeting.(Use MS word on your own machines or Star Office on Athena, turn in hard copy and save file in course locker.)

5. Grading • In-class exercises = 30% • Out-of-class exercises = 30% • Long-term project = 40%

6. A Brief History of the Research Articlefrom Swales (1990) • Mid-17th century: Robert Boyle presents his pneumatic experiments to the Royal Society, public presentations before “witnesses” in order to seek agreement on the results. • 1665: The Philosophical Transactions of the Royal Society is established, the first scientific periodical. • By 1800 “the definition of experiment moves from any made or done thing, to an intentional investigation, to a test of theory, to finally a proof of evidence for a claim” (Bazerman 1983). • By 1900, the current format of research article is largely established.

7. Macrostructure of a Research Article • Hourglass diagram of Hill et al. • Introduction provides general field or context. • Methods follows a particularized path. • Discussion moves from specific findings to wider implications.

8. What’s an Introduction? • An introduction is a method to familiarize and orient your readers. • The content of an introduction depends on its purpose and theaudience. • All models share a direct approach. Don’t hide your main point or save it until the end of the paper.

9. What’s the Purpose of an Introduction in Scientific Writing? • Provide the contextof your work(create your research space, define gap in knowledge). • State your focus(hypothesis, question). • Provide justificationfor your work (how your work can answer the question).

10. What do we mean by Context, Focus, and Justification? • Context: Orient your reader to the published literature related to the study you are presenting. • Focus: Define your research space, stake out territory. What question are you addressing? What is your hypothesis. • Justification: Show how your work fits into and extends previous work. Argue for the importance of your work. • Your introduction sets up the direction you’ll take in the Discussion Section.

11. What are the Goals of an Introduction Section? • State the a) question/focus, b) context, and c) justification clearly and concisely to orient your readers to the purposeof the work. • Define your research space (stake out your territory, show how your work fits in to and potentially extends previous work). • Set up the direction you’ll take in the discussion section.

12. CARS Model • Create aResearch Space • 1. Re-establish significance of research field. • 2. Situate actual research in these terms. • 3. Show how this niche will be occupied and defended.

13. What are Some Common Pitfalls of an Introduction Section? • Including unnecessary backgroundor being repetitive. • Exaggerating (or understating) the importance of your work. • Using lackluster openers and weakfollow-through in the body of your introduction. • Including new results in the introduction section.

14. From the International Committee of Medical Journal Editors: State the purpose of the article and summarize the rationale for the study or observation. Give only strictly pertinent references and do not include data or conclusions from the work being reported. From the American Society for Microbiology: The introduction should supply sufficient background information to allow the reader to understand and evaluate the results of the present study without referring to previous publications on the topic. The introduction should also provide the hypothesis that was addressed or the rationale for the present study. Use only those references required to provide the most salient background rather than an exhaustive review of the topic. Guidelines for Introductions from Two Scientific Organizations

15. context/focus context justification hypothesis/focus An Example from the NEJM • Morbidity and mortality among patients with chronic obstructive pulmonary disease are related in large part to acute exacerbations, which occur one to three times per year.1,2,3,4,5,6 Our understanding of the cause and pathogenesis of these exacerbations is incomplete, and the role of bacterial pathogens is controversial.7,8,9,10 • In studies performed decades ago, investigators followed patients with chronic obstructive pulmonary disease longitudinally, with periodic collection of sputum samples for culture, to determine whether there was an association between the isolation of bacterial pathogens in sputum and the occurrence of exacerbations.5,6,11 In these studies, the rate of isolation of potential bacterial pathogens from sputum samples during stable disease was identical to the rate during acute exacerbations. This finding led to the conclusion that bacterial pathogens do not cause exacerbations and that their presence in sputum is due to chronic colonization.7,12 • An increased understanding of the genetic heterogeneity among strains of a bacterial species exposes a major limitations of the older cohort studies.13 At the time of these studies, it was not possible to differentiate among strains of a pathogenic bacterial species. Therefore, all strains isolated from sputum over the course of the study were regarded as identical if they belonged to the same species. This approach did not allow for the detection of changes in strains over time. More recent studies have shown that the immune response to bacterial pathogens after exacerbations of chronic obstructive pulmonary disease is characterized by considerable strain specificity, suggesting the importance of differentiation among strains of bacterial pathogens isolated over time from patients with chronic obstructive pulmonary disease.14,15,16 • We hypothesized that the acquisition of a new strain of pathogenic bacterial species in a patient with chronic obstructive pulmonary disease who has no preexisting immunity to the strain leads to an exacerbation. To test this hypothesis, we conducted a study in which we obtained sputum samples monthly and during exacerbations in a cohort of patients with chronic obstructive pulmonary disease. Bacterial strains isolated from sputum obtained during periods of stable disease and during exacerbations were subjected to molecular typing. This report represents the results from the first 56 months of this study. • New Strains of Bacteria and Exacerbations of Chronic Obstructive Pulmonary Diseas Sanjay Sethi, M.D., Nancy Evans, R.N., Brydon J.B. Grant, M.D., and Timothy F. Murphy, M.D.NEJM Previous Volume 347:465-471 August 5, 2002

16. Today’s In-Class Exercises • On the class discussion board (from http://web.mit.edu/7.021/www/), write a brief biographical blurb for your department web page (about 100 words). • Use Star Office to write brief biographical sketches (about 100 words each) for the following audiences: a) a dating service, b) a foreign relative, c) a potential summer employer. • Three research articles will be distributed in class. Review the introductions and break into small groups to discuss the features they share and the differences between them. What general properties of introductions can you distill? • Go to the discussion board and state three things you learned and three questions you have about your work in 7.02. Then, respond to someone else’s question. This will be the first thing you do each time you come to 7.021. • Please review Exercise 2 Meeting 2 before the next meeting so you can bring props if needed.

17. Instructions for setting up your work directory in the 7.021 course locker • Launch Star Office on your Athena machine. • Choose “Save As…” from the File menu. • Click on “move up directory” button to get to the 7.021 locker: /afs/athena.mit.edu/course/7/7.021/ • Open your section’s directory. • Open the directory with your name. • Create a new folder labeled “Meeting 1.” • Inside the Meeting 1 folder, create three folders: • In-class exercises • Out-of-class exercises • Long-term project • Save your work in the appropriate folder.

18. Today’s Out-of-Class ExercisesDue by Next Class Meeting 1. Write a plain language summary (about 250 words) of an introduction to the research article provided. 2. Find two published research papers in a print or on-line journal that interest you (e.g., New England Journal of Medicine,Cell, Journal of Bacteriology, Genes and Development). Print or photocopy the introduction and label the main parts (question/focus, context, and justification). Be prepared to discuss your observations at the beginning of the next class meeting. 3. Long-term Project (See more detailed explanation in Course Description): • Choice #1.Write a few paragraphs describing yourself as a student entering 7.02 laboratory, e.g., what you know, what you expect to learn, how you will approach the class. • Choice #2. Write an introduction to a paper by Gregor Mendel introducing the experiments with pea plants that were used to establish the laws of segregation and independent assortment. • Choice #3: Propose an independent project for instructor approval.