Writing

1. Writing Be concise!

2. What makes a good writer? • Inborn talent? • Years of English and humanities classes? • An artistic nature? • The influence of alcohol and drugs? • Divine inspiration? • Having something to say • Logical and clear thinking • Knowing a few simple, learnable rules of style

3. Clear writing starts with clear thinking Before you start writing, ask: “What am I trying to say?” When you finish writing, ask: “Have I said it?”

4. Make every word tell “Vigorous writing is concise. A sentence should contain no unnecessary words, a paragraph no unnecessary sentences, for the same reason that a drawing should have no unnecessary lines and a machine no unnecessary parts. This requires not that the writer make all his sentences short, or that he avoid all detail and treat his subjects only in outline, but that every word tell.” The Elements of Style, William Strunk Jr. (available online at: http://www.bartleby.com/141/)

5. FDR’s response: “Tell them that in the buildings where they have to keep the work going to put something across the windows.” Make every word tell “Such preparations 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.” (from a US government blackout order in 1942)

6. Words and sentences Words 1. Reduce dead weight 2. Cut, cut, cut 3. Be specific Sentences 4. Include subject + verb + object 5. Use strong verbs 6. Eliminate negatives; use positive constructions

7. Dead weight • Very, really, quite, basically, generally • Watch out for the verb “to be” (e.g., “there are”) There are many students who like writing. Many students like writing

8. Dead weight • In the event that • In the nature of • It has been estimated that • It seems that • It may be argued that • It can be shown that • It is believed that • For the most part • For the purpose of • In the case of • In the final analysis

9. Dead weight Clunky phraseEquivalent • A majority of • A number of • Are of the same opinion • At the present moment • By means of Most Many Agree Now By

10. Dead weight Clunky phrase Equivalent • All three of the • Fewer in number • Give rise to • In all cases • In a position to • In close proximity to • In order to The three Fewer Cause Always Can Near To

11. Dead weight Beware of Use instead • Assistance • Utilize • Numerous • Facilitate • Remainder • Due to the fact that • Is indicative of • Sufficient • For the purpose of Help Use Many Help Rest Because Shows Enough For/to

12. Choosing the right words • Reduce dead weight words and phrases • Cut, cut, cut • Is a word or phrase necessary? • What happens if I take it out? • Don’t get attached!

13. Cutting words I would like to assert that the author should be considered to be a buffoon. The author is a buffoon. The expected prevalence of mental retardation, based on the assumption of a normal distribution of intelligence in the population, is stated to be theoretically about 2.5%.” The expected prevalence of mental retardation, if intelligence is normally distributed, is 2.5%

14. Cutting words To control infection with Mycobacterium tuberculosis (M. tb), a robust T-cell-mediated immune response is necessary, and deficiency in this response predisposes an individual towards active TB. Deficiency in T-cell-mediated immune response predisposes an individual to active TB.

15. Cutting words This paper provides a review of the basic tenets of cancer biology study design, using as examples studies that illustrate the methodologic challenges or that demonstrate successful solutions to the difficulties inherent in biological research. S and This paper reviews cancer biology study design, using examples that illustrate specific challenges and solutions.

16. Choosing the right words • Reduce dead weight words and phrases • Cut, cut, cut: learn to part with your words • Be specific Use specific nouns and specific verbs and specific details….

17. Specific: It rained every day for a week. Be specific Vague nouns Problem, situation, approach, method, reaction, period, component, technique, solution, challenge, difficulty Vague: A period of unfavorable weather set in.

18. Building sentences Sentences 4. Subject + verb + object 5. Use strong verbs and don’t turn verbs into nouns 6. Eliminate negatives; use positive constructions

19. Active vs. passive voice In the passive voice, the actor is AWOL… President Kennedy was shot in 1963. Who shot him? Cigarette ads were designed to appeal to children. Who is responsible?

20. Building sentences 4. Subject + verb + object 5. Use strong verbs and don’t turn verbs into nouns

21. Weak verbs The useful bits Active verbs Obtain estimates of Has seen an expansion in Provides a methodologic emphasis Take an assessment of estimate has expanded emphasizes assess

22. More active verbs Provide a review of Offer confirmation of Make a decision Shows a peak Exhibits a dependence upon review confirm decide peaks depends

23. Building sentences 4. Subject + verb + object 5. Use strong verbs and don’t turn verbs into nouns 6. Eliminate negatives; use positive constructions

24. Be positive • Not honest dishonest • Does not have lacks • Did not remember forgot • Did not pay attention to ignored • Did not have much confidence distrusted • Did not succeed failed

25. Subject very long! Negatives Passive Dead weight Boring verb Example The fear expressed by some teachers that students would not learn statistics well if they were permitted to use canned computer programs has not been realized in our experience. A careful monitoring of achievement levels before and after the introduction of computers in the teaching of our course revealed no appreciable change in students’ performances. 55 words

26. Example Many teachers feared that the use of canned computer programs would prevent students from learning statistics. We monitored student achievement levels before and after the introduction of computers in our course and found no decrease in performance. 37 words

27. Dangling participles & misplaced modifiers Participles modify the nearest noun Walking along the beach, the sun rose majestically over the ocean.  Using tissue isolation protocol, mtDNA was isolated from dried skins. Ivory samples were taken from tusks using a drill.

28. Paragraphs • Avoid a succession of loose sentences 2. Paragraph flow is helped by: • logical flow of ideas • if necessary, transition words • 3. First and last sentences should be really good

30. Abstract • Summary of research • At beginning of paper (write last!) • Conference proceedings • Short! (150-250 words) • Give max information in min space Weissman 2008

31. Abstract structure • Purpose (1-2 sentences) • Procedures (very abbreviated) • Findings • Conclusions (1-2 sentences of discussion; 1 sentence about general importance)

32. Mori et al. Circadian clock protein KaiC forms ATP-dependent hexameric rings and binds DNA. PNAS 99: 17203-17208 KaiC from Synechococcus elongatus PCC 7942 (KaiC) is an essential circadian clock protein in cyanobacteria. Previous sequence analyses suggested its inclusion in the RecA/DnaB superfamily. A characteristic of the proteins of this superfamily is that they form homohexameric complexes that bind DNA. We show here that KaiC also forms ring complexes with a central pore that can be visualized by electron microscopy. A combination of analytical ultracentrifugation and chromatographic analyses demonstrates that these complexes are hexameric. The association of KaiC molecules into hexamers depends on the presence of ATP. The KaiC sequence does not include the obvious DNA-binding motifs found in RecA or a DnaB. Nevertheless, KaiC binds forked DNA substrates. These data support the inclusion of KaiC into the RecA/DnaB superfamily and have important implications for enzymatic activity of KaiC in these circadian clock mechanism that regulates global changes in gene expression patterns. 143 words

33. Mori et al. Circadian clock protein KaiC forms ATP-dependent hexameric rings and binds DNA. PNAS 99: 17203-17208 KaiC from Synechococcus elongatus PCC 7942 (KaiC) is an essential circadian clock protein in cyanobacteria. Previous sequence analyses suggested its inclusion in the RecA/DnaB superfamily. A characteristic of the proteins of this superfamily is that they form homohexameric complexes that bind DNA. We show here that KaiC also forms ring complexes with a central pore that can be visualized by electron microscopy. A combination of analytical ultracentrifugation and chromatographic analyses demonstrates that these complexes are hexameric. The association of KaiC molecules into hexamers depends on the presence of ATP. The KaiC sequence does not include the obvious DNA-binding motifs found in RecA or a DnaB. Nevertheless, KaiC binds forked DNA substrates. These data support the inclusion of KaiC into the RecA/DnaB superfamily and have important implications for enzymatic activity of KaiC in these circadian clock mechanism that regulates global changes in gene expression patterns. 143 words

34. Mori et al. Circadian clock protein KaiC forms ATP-dependent hexameric rings and binds DNA. PNAS 99: 17203-17208 KaiC from Synechococcus elongatus PCC 7942 (KaiC) is an essential circadian clock protein in cyanobacteria. Previous sequence analyses suggested its inclusion in the RecA/DnaB superfamily. A characteristic of the proteins of this superfamily is that they form homohexameric complexes that bind DNA. We show here that KaiC also forms ring complexes with a central pore that can be visualized by electron microscopy.A combination of analytical ultracentrifugation and chromatographic analyses demonstrates that these complexes are hexameric. The association of KaiC molecules into hexamers depends on the presence of ATP. The KaiC sequence does not include the obvious DNA-binding motifs found in RecA or a DnaB. Nevertheless, KaiC binds forked DNA substrates. These data support the inclusion of KaiC into the RecA/DnaB superfamily and have important implications for enzymatic activity of KaiC in these circadian clock mechanism that regulates global changes in gene expression patterns. 143 words

35. Mori et al. Circadian clock protein KaiC forms ATP-dependent hexameric rings and binds DNA. PNAS 99: 17203-17208 KaiC from Synechococcus elongatus PCC 7942 (KaiC) is an essential circadian clock protein in cyanobacteria. Previous sequence analyses suggested its inclusion in the RecA/DnaB superfamily. A characteristic of the proteins of this superfamily is that they form homohexameric complexes that bind DNA. We show here that KaiC also forms ring complexes with a central pore that can be visualized by electron microscopy. A combination of analytical ultracentrifugation and chromatographic analyses demonstrates that these complexes are hexameric. The association of KaiC molecules into hexamers depends on the presence of ATP. The KaiC sequence does not include the obvious DNA-binding motifs found in RecA or a DnaB. Nevertheless, KaiC binds forked DNA substrates. These data support the inclusion of KaiC into the RecA/DnaB superfamily and have important implications for enzymatic activity of KaiC in these circadian clock mechanism that regulates global changes in gene expression patterns. 143 words

36. Mori et al. Circadian clock protein KaiC forms ATP-dependent hexameric rings and binds DNA. PNAS 99: 17203-17208 KaiC from Synechococcus elongatus PCC 7942 (KaiC) is an essential circadian clock protein in cyanobacteria. Previous sequence analyses suggested its inclusion in the RecA/DnaB superfamily. A characteristic of the proteins of this superfamily is that they form homohexameric complexes that bind DNA. We show here that KaiC also forms ring complexes with a central pore that can be visualized by electron microscopy. A combination of analytical ultracentrifugation and chromatographic analyses demonstrates that these complexes are hexameric. The association of KaiC molecules into hexamers depends on the presence of ATP. The KaiC sequence does not include the obvious DNA-binding motifs found in RecA or a DnaB. Nevertheless, KaiC binds forked DNA substrates. These data support the inclusion of KaiC into the RecA/DnaB superfamily and have important implications for enzymatic activity of KaiC in these circadian clock mechanism that regulates global changes in gene expression patterns. 143 words

37. Assignment • Write an abstract of paper provided • Max: 150 words • Due: Monday, November 15 (by email)

38. Introductions BIG picture General background, i.e., what is known The gap: what is not known Your question/ goals Your approach

39. First paragraph Diabetes mellitus is an increasingly important global public health problem that threatens to reach pandemic levels by 2030.As some randomised trials have consistently shown, increased physical activity and weight loss are efficient approaches for the control and prevention of type 2 diabetes. Diet has also long been believed to be an important risk factor for diabetes. Introduction structure Martínez-González et al. (2008) Adherence to Mediterranean diet and risk of developing diabetes: prospective cohort study. BMJ : What is known about risk factors for diabetes

40. Second paragraph : What is known about the Mediterranean diet and diabetes Many studies have shown that the Mediterranean food pattern has a role in prevention of cardiovascular disease.The similarity of some risk factors and some empirical and mechanistic evidence suggest that the Mediterranean diet can also protect against diabetes. The major protective characteristics include a high intake of fibre, a high intake of vegetable fat, a low intake of trans fatty acids, and a moderate intake of alcohol. Moreover, a particular feature of the diet is the abundant use of virgin olive oil for cooking, frying, spreading on bread, or dressing salads.This leads to a high ratio of monounsaturated fatty acids to saturated fatty acids. This ratio can be used to score adherence to a Mediterranean diet as the traditional diet. Despite having a relatively high total fat content, this food pattern is rich in monounsaturated fatty acids (from olive oil) and poor in saturated fatty acids. Diets rich in monounsaturated fatty acids improve lipid profiles and glycaemic control in people with diabetes, suggesting that a high intake improves insulin sensitivity.Together these associations suggest the hypothesis that following an overall pattern of Mediterranean diet can protect against diabetes. In addition to having a long tradition of use without evidence of harm, a Mediterranean diet is highly palatable, and people are likely to comply with it.

41. Fourth paragraph We evaluated the association between adherence to a Mediterranean diet and the incidence of diabetes using a full validated food frequency questionnaire to measure the entire diet. Third paragraph : What is not known about the Mediterranean diet and diabetes Few prospective studies have evaluated the specific role of the Mediterranean diet on the risk of developing diabetes in initially healthy Mediterranean populations. A prospective follow-up study recently reported an inverse association between adherence to the diet and the incidence of diabetes. All members of that study, however, had survived a previous myocardial infarction and the tool to assess dietary habits had inherent limitations because it included only a short list of items, and the authors did not attempt to measure the entire diet. : What this study did and why it’s better than previous studies

42. Plagiarism of structure = bad Point B Point A Point C Point D

43. Emulation = good Model/ system Problem Question Your approach

44. Assignment • Write a 1-1.5 page Introduction for a NSERC Discovery Grant • single-spaced, 12 pt font, with 2.5 cm margins • Use two major headings: (1) Objectives and (2) Background.  You may also use subheadings within these major headings. • Include references (not included in the space limit). • Due: Monday, November 22 (by email, as Word document)