Scientific writing masterclass 2011


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Scientific writing masterclass 2011

  1. 1. Scientific Writing Masterclass Infectious Diseases Module MMLS November 2011 Calvin & Hobbes, copyright Bill Watterson
  2. 2. Introduction• Students – Master level, non-native English.• Masterclass – Apply advanced theory – Intense and practical
  3. 3. • …the purpose of writing is to inflate weak ideas, obscure poor reasoning, and inhibit clarity. With a little practise, writing can be an intimidating and impenetrable fog!
  4. 4. Masterclass outline• What is scientific writing?• The grind – Rules & conventions – Punctuation & grammar• The style – Learn to recognise and have it!• Get intimate – Writing with intent, know your audience
  5. 5. What is scientific writing• Form of formal academic writing.• Primary purpose is to disseminate information to a defined audience.• Three major factors influencing scientific writing ! Grammatical rules ! Scientific conventions ! Audience
  6. 6. The Grind Rules versus Style Correct English (spelling, Flexibility in expression (grammar,punctuation, grammar) should personal style). ALWAYS be used.Foundation for brilliant writing! Defined by: House styles, context, purpose, audience
  7. 7. The Grind: PunctuationWhich is correct (A or B)?Periods A. Dr. Prof. B.Sc Mr. B. Dr Prof BSc MrBoth- be consistent. Abbreviations & suspensions
  8. 8. Quick Lesson
  9. 9. The Grind: Punctuation• CommasA. Neutralising antibodies are not measured in convalescent patients, nor in patients in the acute phase.B. Neutralising antibodies are not measured in convalescent patients nor in patients in the acute phase.Before coordinating conjunctions (for, and, nor, but, or, yet etc) joining two independent clauses.
  10. 10. The Grind: Punctuation• CommasA. The human immunodeficiency virus, one of the simplest of viral constructs still evades true understanding.B. The human immunodeficiency virus, one of the simplest of viral constructs, still evades true understanding.Commas instead of parenthetical elements
  11. 11. The Grind: Punctuation• CommasA. Currently, infectious diseases remain the leading cause of deaths worldwide.B. Currently infectious diseases remain the leading cause of deaths, worldwide.After introductory elements(However, Unfortunately, Surprisingly, Finally, In conclusion, To summarise etc).
  12. 12. (A) , (B) ;You did your best , / ; let’s hope you pass the exam.Separating independent clauses. You did your best. Let’s hope you pass the exam.An effect of the Ebola virus is bleeding , / ; especially in the mucosa.Not independent clauses. Use a comma!Is the following usage of semicolons A. Correct or B. Incorrect ?Combine 6.7 ml 30 % acrylamide (60:1); 10 ml 5X tris/glycine buffer; 33.3 ml H2O; 250 μl 10% ammonium persulfate and lastly, 60 μl TEMED.Both are acceptable – using the colon as a supercomma
  13. 13. The Grind: Grammar• Adverbs: A. Correct or B. Incorrect?The bacteria were harvested quick. ly.B. Incorrect. An adverb requires inflection.Adverb position- which is correct?A. The virus rapidly multiplied.B. The virus multiplied rapidly.Answer: both. Changing adverb position changes the emphasis
  14. 14. Quick LessonAdverb position• Front position: links to previous sentence, or is not the main focus. – However, the virus multiplied.• Mid position – The virus rapidly multiplied.• End position – The virus multiplied rapidly.  Words in the last position generally receive the most emphasis.
  15. 15. Quick LessonAdverbs: Be aware of the placement to avoid ambiguities• The patient failed almost all the tests.(failed most but passed a few)• The patient almost failed all the tests. (but just passed the tests)• Children who laugh, rarely are shy.• Children who laugh rarely are shy.
  16. 16. The Grind: Commonly misused wordsThere were about/approximately 200 participants in the study.However, ‘approximately’ is more suited to formal writing.The level of IL-6 was about/approximately 4.0 g/L.Answer: B. Use approximately for mass nouns.
  17. 17. •If a bacterial culture is spilled, theaffected/effected area must be disinfectedimmediately.•The affects/effects of contamination are healthrelated.•Affect= verb (to influence)•Effect= noun (the result)•A virus that/which has lost virulency isharmless.
  18. 18. Quick Lesson: That/Which• That introduces restrictive clauses (essential) while which introduces non-restrictive (non- essential) clauses.• If the information is left out, is the meaning of the sentence changed?• A virus that/which has lost virulency is harmlessEssential information: use THATUnessential information: use WHICHThrow out the ‘which’ and it will not be missed.
  19. 19. The Grind: Commonly misused words• Since/Because chocolate is so delicious, I can eat an entire block.• Why is editing important? Since/Because it produces higher quality work.• There are so many exercises since/because grammar is an important skill.• Since/Because can be used at the beginning of sentences• Because – in the middle of sentences.• Because- to introduce new information
  20. 20. The Grind: Commonly misused words• The actual/current figures from the report.• You might lose/loose your pants.• If your pants are too lose/loose you might lose your pants.The monkey realised he was bigger than/then the dog.The monkey than/then threatened the dog• The diagnostic test had been applied since/from 2008.• The gel was run since/from two o’clock.
  21. 21. Quick Lesson- Since/From/ForDescribe an event with a point in time reference.• Since – perfect tenses: „has had, have been, has been, had been.‟• From – other tenses (past, future): ‘was, will be‟. – For periods of time with a defined start and end.• The vaccine had been commercially available since 1998.• The vaccine was produced in chickens from 2000
  22. 22. Quick Lesson: Since/From/For• Period of time: use ‘For’ for all tenses – „This class runs for 2 hours. – The masterclass ran for longer than expected. – The writing course had been given for two years.
  23. 23. END OF PUNCTUATION!• See study guide.• Use reference books.• Don’t trust all that you read!• Practise punctuating.--PAUSE--
  24. 24. Good Scientific Writing
  25. 25. StyleRecognise Edit Write, write,good style ↓ write & edit, ↓ Read, take edit, editLearn to initiative. ↓identify it. Be your ownUnderstand strictest critic.what makes itgood, or bad. Vaccine adviseMasterclass Masterclass & own report & own initiative initiative
  26. 26. Good Scientific Writing • Plain languageSix key movement: ‘To improvefeatures communication by*Understandable eliminating* Clear and unnecessarily complexsimple language from* Credible academia,* Efficient government, law and business.’* Follows • Encouraged by manyconvention journals.
  27. 27. Style Guide Document & House Style Define your Audience Personal Writing StyleFlexibility,
  28. 28. Type of Document & House Style• Type of document.• Employer, journal, association, university.• Font, layout, UK/US English, abbreviations.
  29. 29. American vs British Spelling• „Though the tough cough and hiccough plough him through’• British English is irregular – Borrowed words – Shift in pronunciation – Spelling reform not successful• Webster’s American Dictionary of the English language.
  30. 30. British Spelling American SpellingFlavour FlavorColour ColorNeighbour NeighborMetre MeterLitre LiterTitre TiterOrganise OrganizeAnalyse AnalyzeHydrolyse HydrolyzeAmoeba AmebaFoetal FetalPaediatric PediatricAnalogue AnalogDialogue DialogPedagogue PedagogPersonal preference, geographic location,employer preference, publisher’sinstructions.
  31. 31. Have a purpose when writing• Identify your motivation Explain, inform, argue, educate, justify, request, report, document, investigate, debate, summarise, evaluate, recommend, propose, review, advise.• What is the context? Essay, literature review, abstract, research report, project proposal.• Combine the motivation and the context to clarify for yourself WHY you are writing
  32. 32. Jargon ∝ Audience Efficient Fog of communication impenetrability• Define your audience• The audience and context determines the amount of jargon• Jargon is only a problem when it is inappropriate for the intended audience.
  33. 33. Aspect Lay audiences Managerial audiences Expert audiences Focus/ Purpose Decision-making Reporting, dissemination purpose Human interest of information. > Informative, > real life application. >Accurate reporting Interpretive in the> Overall and reasoning. related context.features Explain specialised Use specialised termsJargon Limited terms, use glossary with minimal explanation Analogies, relate Intermediate level of Detailed, concepts can Information concepts to easily detail, explain the be explained using level relatable contexts concepts references Present selected results Present detailed results Scientific data Results are paraphrased and give summaries or and interpretation overviews Use illustrations to Use appropriate figures, Provide data in figures,Graphics explain concepts tables or graphs tables or graphs
  34. 34. Surgeons make cancer cells fluoresce for removal analogy, Intraoperative tumor-specific fluorescenceTrying to remove every last cancer cell during imaging in ovarian cancer by folate receptor-α recognisable Writing for non-scientistssurgery can be a bit like playing blind mans bluff: context targeting: first in-human resultsthey are often the same colour as healthy cells, sosurgeons risk leaving behind cancer cells which The prognosis in advanced-stage ovarian cancer simplifiedcan regrow. But that could change thanks to a remains poor. Tumor-specific intraoperativetechnique that makes ovarian cancer cells glow. fluorescence imaging may improve staging andCurrently, adding largely rely on touch toQuote, surgeons personality, varies debulking efforts in cytoreductive surgery anddetermine where an ovarian tumour starts andwriting style thereby improve prognosis. The overexpression ofends. "You have no real clue where the borders folate receptor-α (FR-α) in 90–95% of epithelial Simplifying data, recognisableare," says Gooitzen van Dam (...). ovarian cancers prompted the investigation of paraphrasing jargonVan Dam and his colleagues took advantage of the intraoperative tumor-specific fluorescence terminologyfact that the vast majority of ovarian cancer cells imaging in ovarian cancer surgery using an FR-α–over-express a receptor for folate on their cell targeted fluorescent agent. In patients withsurface while normal cells do not. They attached a ovarian cancer, intraoperative tumor-specificfluorescent label to folate molecules and fluorescence imaging with an FR-α–targetedadministered them to women via an intravenous fluorescent agent showcased the potentialdrip 2 hours before surgery to remove their applications in patients with ovarian cancer fortumours. improved intraoperative staging and more radicalHuman interest emphasis,the cancerThe labelled folate was taken up by cytoreductive surgery.cells but not normal cells, so surgeons could use abroader focuscamera that detects fluorescence to see thetumours. The team now plan to see whether themethod boosts patient survival rates.
  35. 35. Cancer drug thwarts malaria Activation of a PAK-MEK signalling pathway inIN THE wake of World Malaria Day on Monday Human interest, impact on society malaria parasite-infected erythrocytes Catchy titlecomes news that certain anti-cancer drugs might Merozoites of malaria parasites invade red bloodalso work against the malarial parasite.inhibitors cells (RBCs), where they multiply by schizogony, Kinase are a new class ofThere were 780,000 deaths and 225 milliondrugs undergoing development through ring, anticancercases of malaria in 2009. With resistance to trophozoite and schizont stages that areexisting anti-malarial drugs growing all the time, responsible for malaria pathogenesis. Here, weSelective informationnew weapons against the disease are a priority. report that a protein kinase-mediated signallingSimple language colleagues haveNow C. Doerig (...) and pathway involving host RBC PAK1 and MEK1,discovered that Plasmodium falciparum, the which do not have orthologues in theparasite that causes malaria, co-opts two red Plasmodium kinome, is selectively stimulated inblood cell proteins called kinases. Many new Plasmodium falciparum-infected (versuscancer treatments also target kinases, and when uninfected) RBCs, as determined by the use ofthe team exposed malaria-infected red blood phospho-specific antibodies directed against the Simple and catchy activated forms of these enzymes.cells and liver cells to some of these "kinaseinhibitors", they killed the bug but not the cells. Pharmacological interference with host MEK and"Our discovery opens up new ways to potentially PAK function using highly specific allostericcombat malaria," says Doerig, although he inhibitors in their known cellular IC50 rangescautions that the work is very preliminary. results in parasite death. Furthermore, MEKHowever, the team is in discussions with inhibitors have parasiticidal effects ...on thepharmaceutical companies to test more kinase rodent malaria parasite Plasmodium berghei,inhibitors, especially those that have proved safe indicating conservation of this subversivein clinical trials but didnt make the grade as strategy in malaria parasites. These findings havecancer drugs. profound implications for the development of novel strategies for antimalarial chemotherapy.
  36. 36. Inhibition of TLR8- and TLR4-induced Type I IFN induction by alcohol isdifferent from its effects on inflammatory cytokine production in monocytesProlonged alcohol consumption is a significant Alcoholco-factor in the progression of chronic viral isminfections including hepatitis C and HIV, which are Related to diseaseboth single-stranded RNA viruses. progressionToll like receptor 8 (TLR8), a pattern recognitionreceptor expressed in monocytes, senses viral Virus presencesingle stranded RNA as a danger signal andleads to the induction of Type I interferon (IFN) as Leads towell as the pro-inflammatory cytokine, tumor immune systemnecrosis factor alpha (TNF alpha) reponse AlcoholThese novel results suggest first, that alcohol has supressesa profound inhibitory effect on Type I IFN virusinduction regardless of intracellular (TLR8) or cell activated Alcohol immune (?bingesurface-derived (TLR4) danger signals. Second, system drinking &both acute and prolonged alcohol exposure can response chronicinhibit antiviral Type I IFN pathway activation. alcohol abuse)
  37. 37. Too much alcohol dulls more than your wits. It also weakens Alcohol your immune system and could make you much more ism vulnerable to viruses, including HIV. Related to To see how alcohol affects resistance to infection, Gyongyi disease Szabo (...) and colleagues exposed monocytes – white bloodprogression cells involved in the front-line defence against infection – to chemicals that mimic viruses and bacteria. Half of the cellsVirus presence were also soused in the levels of alcohol that a person might have in their blood after quaffing four or five alcoholic drinks daily for a week. Leads to Alcohol blunted the monocytes defences. When the over-the- immune limit cells were exposed to a virus mimic, they produced only a quarter as much of the virus-fighting signalling molecule called system type-1 interferon as teetotal monocytes made. reponse Alcohol "Interferon is pivotal, the first response to any viral infection," supresses says Szabo. "Theres no viral elimination without it." Szabo says that the results fit with evidence from medical virus records that chronic heavy drinkers with HIV die sooner than activated Alcohol non-drinkers. They also fit with earlier studies showing that the immune immune system of heavy drinkers might be less vigilant (?binge system against cancer. drinking & response Szabo says heavy drinkers should beware of damaging their chronic immune systems. alcohol
  38. 38. Style Guide Document & House Style Define your Audience Personal Writing StyleFlexibility,
  39. 39. Personal Writing Style• Learn the rules before playing with them!• There is often more than one correct way to say something.• Elements of style: use them as your weapons! – Simple sentences – Active Voice – Renovating long sentences – Writing paragraphs
  40. 40. Simple sentencesWHAT?• Strict definition: one independent clause (idea)• Practical definition: limit ideas, length Short Simple sentence (strict definition) We are studying. Simple long sentence (strict definition) We are studying punctuation, grammar, scientific writing, elements of style and paragraphs. Simple sentence (practical definition) We are learning about punctuation, grammar, scientific writing, elements of style and paragraphs.
  41. 41. Simple SentencesWHY?• Effective Communication• Punchy, Powerful, Energy.• Long sentences are difficult to write well.• Badly written sentences are confusing.
  42. 42. Simple SentencesHow?• Use punctuation• Split up sentences• Use active voice• Remove unnecessary words• Simplify terminology• Limit the number of ideas in one sentence
  43. 43. Remove unnecessary words• In order to write elegantly, you do not need many words.• It was reported that more girls were born in industrialised countries.• The fact that I have three boys undermines this finding.• My days, which are busy, are enjoyable.• My children who are energetic, are a handful.• Moreover,• Furthermore,• Indeed,
  44. 44. Activation of a PAK-MEK signalling pathway in malaria parasite-infected erythrocytesMerozoites of malaria parasites invade red blood cells (RBCs), wherethey multiply by schizogony, undergoing development through ring,trophozoite and schizont stages that are responsible for malariapathogenesis. Here, we report that a protein kinase-mediated signallingpathway involving host RBC PAK1 and MEK1, which do not haveorthologues in the Plasmodium kinome, is selectively stimulated inPlasmodium falciparum-infected (versus uninfected) RBCs, asdetermined by the use of phospho-specific antibodies directed againstthe activated forms of these enzymes. Pharmacological interference withhost MEK and PAK function using highly specific allosteric inhibitors intheir known cellular IC50 ranges results in parasite death. Furthermore,MEK inhibitors have parasiticidal effects ...on the rodent malaria parasitePlasmodium berghei, indicating conservation of this subversive strategyin malaria parasites. These findings have profound implications for thedevelopment of novel strategies for antimalarial chemotherapy.
  45. 45. Simple sentencesMerozoites of malaria parasites invade red blood cells(RBCs), where they multiply by schizogony, undergoingdevelopment through ring, trophozoite and schizontstages that are responsible for malaria pathogenesis. Too many ideas in one sentence: Redundancy – undergoing RBC invasion, multiplication, development development stages, pathogenesis Overload of terminology. * TRY TO EDIT THIS All relevant information? SENTENCE! Dangler Passive- undegoing developmentMerozoites of malaria parasites invade red blood cells(RBCs), where they reproduce by schizogony. Duringreproduction, they develop through the ring, trophozoiteand schizont stages that are responsible for malariapathogenesis.
  46. 46. • . Here, we report that a protein kinase-mediated signalling pathway involving host RBC PAK1 and MEK1, which do not have orthologues in the Plasmodium kinome, is selectively stimulated in Plasmodium falciparum-infected (versus uninfected) RBCs, as determined by the use of phospho-specific antibodies directed against the activated forms of these enzymes
  47. 47. Passive and Active VoiceSunflowers, a Vincent van Goghpainting by paintedVincent van SunflowersGogh Emphasis on the object Emphasis on the subject
  48. 48. Active Voice• Modern scientific writing embraces active voice!• Strong verbs• Clear meaning• Shorten sentenceSubject – Verb - Object
  49. 49. Active: Subject - verb - objectI shot the sheriffPassive: Object - verb (modified) - subjectThe sheriff was shot by me.
  50. 50. How to rescue passive sentences• Seek and change the adverb into the verb – Examination – Analysis The, an – Investigation – a The,Performance – Are going to … Investigation into the recent deaths is being carried out by private detectives. Investigate Private detectives are investigating the recent deaths
  51. 51. Renovating Long Sentences• Remove unnecessary words• Remove repetition• Keep subject and verb together• Avoid danglers• Punctuate• Reduce prepositions• Unstack wordy terminology
  52. 52. Rescuing long sentences• In patients with ovarian cancer, intraoperative redundan tumor-specific fluorescence imaging with an FR- simplify α–targeted fluorescent agent showcased the Vague, unsu potential applications in patients with ovarian Get to the p cancer for improved intraoperative staging and Ideas over more radical cytoreductive surgery.• Using an FR-α-specific fluorescent imaging system may benefit patients with ovarian cancer. Visual detection of cancerous cells during surgery may improve intraoperative staging and aid more radical cytoreductive surgery.
  53. 53. Paragraphs• the topic sentence comes at or near the beginning;• the succeeding sentences explain or establish or develop the statement made in the topic sentence; and• the final sentence either emphasizes the thought of the topic sentence or states some important consequence.• (strunk)
  54. 54. • Be positive, not negative.• Since Hemingway wasn’t the cheeriest guy in the world, what does he mean by be positive? Basically, you should say what something is rather than what it isn‟t.• This is what Michel Fortin calls using up words:• By stating what something isn‟t can be counterproductive since it is still directing the mind, albeit in the opposite way. If I told you that dental work is painless for example, you‟ll still focus on the word “pain” in “painless.”• • Instead of saying “inexpensive,” say “economical,” • Instead of saying “this procedure is painless,” say “there‟s little discomfort” or “it‟s relatively comfortable,” • And instead of saying “this software is error-free” or “foolproof,” say “this software is consistent” or “stable.”• He was not very often on time.He usually came late.He did not think that studying Latin was much use.He thought the study of Latin useless.The Taming of the Shrew is rather weak in spots. Shakespeare does not portray Katharine as a very admirable character, nor does Bianca remain long in memory as an important character in Shakespeares works.The women in The Taming of the Shrew are unattractive. Katharine is disagreeable, Bia
  55. 55. • Grammatical Variation• Don’t overuse any one element
  56. 56. Syntax• Elements of style Strunk•