The "Grammar Hammer": Common Mistakes in Scientific Writing

1. GRAMMAR Myron The "Grammar Hammer":Common Mistakes in Scientific Writing Myron L. Toews, Ph.D., Professor Pharmacology and Experimental Neuroscience CU Biomed Sci Seminar October 9, 2012

2. Scientific Writing • Things we write • Papers • Grants • Review articles • Meeting abstracts • Posters • Seminar slides • Lecture slides • Manuscript and grant reviews • Letters (requests, recommendations, complaints) • Committee reports, meeting minutes • Emails • Same "grammar" applies to all • There are "rules" • We are "academics" and "scholars"-- WE should FOR SURE get it right!

3. Aspects of good scientific writing • Science: data, quality, controls, rationale, thoroughness • Significance: why should we care, was it worth doing • Sexiness: exciting, attention-getting, memorable, broad interest • Style: organization, consistency, clarity • what belongs where--Methods, Results, Figures, Discussion • effective figures, graphs, tables • proper referencing and bibliography styles • Good grammar • hyphens, commas, plurals, abbreviations • verb forms, tense, voice, person • proper words used correctly, clearly, concisely • Applies to EVERY SECTION of a manuscript • and all other scientific writing • Good writing can make a bad paper seem good • More often, bad grammar can get in the way of an otherwise good paper

4. Grammar Matters! • Grammar issues • hyphens, commas, plurals, abbreviations • verb forms, tense, voice, person • proper words used correctly, clearly, concisely • Applies to EVERY SECTION of a manuscript • and all other scientific writing • Good writing can make a bad paper seem good • Bad grammar can get in the way of an otherwise good paper

5. A typical "Myron Mark-Up"

6. GRAMMAR GRAMMAR Pounded by the Grammar Hammer Locked up in the Grammar Slammer Cursed commas!

7. My Qualifications • I'm old • Grammar mattered back when I went to school • and I diagrammed sentences • Papers used to be type-set and printed, not electronic • and "editors" edited my writing • and that annoyed me, so I learned the rules • I'm a reviewer and judge of lots of scientific writing • Manuscripts, grant proposals, dissertations, posters • And I so much wish that people would write right!! • I now teach about half of UNMC Scientific Writing course • I'm obsessive-compulsive • I like things done right • Little stuff matters to me • I like making lists

8. My Current(and Growing) List ofCommon Complaints and Corrections • Spaces and hyphens between numbers and units • Hyphens in compound words • Proper plurals • Too many significant figures • Correct commas • Inappropriate use of "time" words • Which/that • Person, voice and tense • Abbreviations • Setting up sentences • Misused words and professional wording • A number of other small things • Good old rules My examples are mostly from phys/pharm

9. #1a. Space between numbers and units!! • A space must be used between numbers and their units! • Simple and obvious • Now shows up in almost everything I review • Only in the last few years • Text-messaging and email generation "shortcut"? • Regardless of the reason…… • Use that space bar!! Do it right!! - ^

10. Space between numbers and units • Temperatures need spaces • between value and degree sign: 37 °C, not 37° C or 37°C • but the degree sign for angles goes with the number: 90º angle • Centrifugal forces need spaces • on both sides of the "x" • 10,000 x g, not 10,000g or 10,000xg • Other "places for spaces" • around equals sign: n = 3, not n=3 • also around >, <, ~, etc • around plus/minus: 29 ± 7, not 29±7 • Percentages may be the only exception • 5% serum, 0.01%bromophenol blue • This is because % is not really a unit, just an indication that the value is presented as the "ratio to 100"

11. #1b. Hyphens between numbers and units • Hyphenate if the number-plus-units is used as an adjective • Space if the number is an adjective and the unit is a noun • 35 mm or 35-mm?? • Cells were grown in 35-mmdishes. • "35-mm" is a compound adjective modifyingthe noun"dishes" • The diameter of the dish was 35mm. • Here "35" is the adjective and "mm" is the noun • a 2-ml reaction volume; 2 ml were added to each tube • The average 60-kg man weighs about 60 kg. • The one exception is concentrations, which are not hyphenated • a 50 mM buffer • The 10 μM concentration inhibited but the 1μM samples were unchanged. • But a space is required: 10 mM or 6 M, never 10mM or 6M!!

12. Hyphens between numbers and units • Allcompound adjectives with numbers MUST be hyphenated • numbers as words, just like numbers as numerals • Numbers written out, but only when used as adjective • two-site competition curve • The data were best fit by a two-componentcurve. • The data indicated that the reaction had twocomponents. • four-steppathway • but "a pathway with foursteps" • a six-sided pentagon cannot be drawn • Note that this includes both"number plus adjective" (six-sided) and "number plus noun" (four-step) • But only when the combination is used as an adjective in the sentence

13. Hyphens between numbers and units • Most other "quantity-related"words are also hyphenated • semi-transparent plastic tubes • bi-directional reaction • multi-component signaling complex • "Her half-finished manuscript lay beside her pillow". • Some of these can be written as one word--no clear "rules" • bidirectional, monophasic

14. More on hyphens with numbers • Compound numbersare hyphenated if written as words • Fifty-four patients were enrolled in the study. • One-hundred percent of the knock-out animals survived the injury. • Average cost per run was over three-thousand dollars.

15. #2. Hyphens in compound words- terms with verbs used as adjectives 2a. A noun-verb combination used as an adjective is always hyphenated!!—Myron's most frequent serious complaint!! "The drug induced side effects" • Is this a sentence by itself? • "The druginducedside effects. These included headache, nausea, gas, …" • Here drug is the subject, induced is the verb (predicate), side effects is the object of the verb • Or is this only the subject of a sentence? • "The drug-induced side effects of aspirin includeGI distress." • Here drug-induced is a compound adjective modifying side effects which is the subject • It's the HYPHEN that lets me know without having to read the whole sentence first!

16. Using "noun-verb as adjective" terms in biomedical science writing • Common examples • receptor-mediated • Beta receptor-mediatedresponsesare blocked by propranolol. • The beta receptormediated the response, because the response was blocked by propranolol. • concentration-dependenteffects; ligand-independenttransactivation • drug-metabolizingenzyme; rate-limitingstep • ligand-bindingdomain • but not in "receptors were measured by ligandbinding" • RNA-dependentDNA synthesis, exercise-inducedasthma • site-directedmutagenesis, FDA-approveddrug • Note this includes most forms of the verb: ed, ing, ent • But only when used as an adjective

17. Other compound adjectives • Adjective-verb combinations are hyphenated when used as compound adjectives • fast-thinking graduate student; long-winded professor • high-minded journal editors; heavy-handed administrators • The part of speech for the words determines the hyphen • "blue-labeled" tubes • if the labels on the tubes are blue • but "blue labeled tubes" • if the tubes are blue and also labeled (but labeled in red?) • the red-labeled blue tubes= the blue tubes with red labels

18. Other compound adjectives • Preposition-verb combinations used as adjectives are usually hyphenated • over-utilized phrases • under-developed sexual organs in Turner's syndrome • often written as one word--overlooked, upturned, inbred • Prepositionsoften come after the verb form • clearly spelled-out expectations • but "expectations were spelled out clearly from the start" • laced-up shoes, tightened-down fasteners, wrap-around insulation

19. Other compound adjectives • Adverb-verbcombinations used as adjectives are NOT hyphenated • Adverbs always modify verbs or adjectives, so they don't need special treatment when used that way • Words ending in "-ly" are adverbs and not hyphenated • a newly established pathway • a highly regarded expert in the field • Also "too", "very", and "much" combos are usually not hyphenated • a very limited interaction • a much appreciated faculty member • It may not be wrong to hyphenate these, but it is not required

20. Other compound adjectives • Adjective-nouncombinations used as adjectives are seldom hyphenated • centrifuge tube rack • graduate student meeting • side effect profile • But they can be hyphenated and often are • open-door policy, closed-door meeting • fixed-rate insurance • long-term effects

21. Other compound adjectives • Don't hyphenate if both words modify the same word • a weak organic acid: a weak acid, an organic acid • weekly planning meeting: a weekly meeting, a planning meeting • strategy-planning meeting • strategy modifies planning here, doesn't modify meeting • an insulated Styrofoam container • the container is insulated and it is made of Styrofoam • the Styrofoam is not insulated, the container is • a Styrofoam-insulated container • the container is insulated, and the insulation is by Styrofoam

22. Other compound adjectives • Hyphenate BOTH terms if they modify the same word • Two modifiers before the verb form • the Ca2+- and phospholipid-dependent enzyme PKC • The epinephrine- and isoproterenol-induced responses were…. • Two modifiers after the verb form • The drug-sensitive and -insensitive cells were compared for…

23. Hyphenation summary • Always hyphenate • All noun-verb combinations if used as adjective • All number-verb, number-noun, number-adverb combinations used as adjectives • Sometimes hyphenate • Some adverb-verb combinations if used as adjectives • A few adjective-noun combinations if used as adjectives • Don't hyphenate • Adverbs, including –ly words and others • Two adjectives that modify the same noun

24. Singular cell hypothesis Plural cells hypotheses #3. Proper plurals The hypothesis (singular) that PKC is involved was only one of several equally likely hypotheses (plural) that we could have proposed. Separate hypothesesare proposed for each specific aim. A separate hypothesisis proposed for each specific aim. Know which is singular and which is plural…. …and then use the correctly matched verb form!!

25. Singular drug datum Plural drugs data Proper plurals • The use of "data is/was…" vs. "data are/were…." is no doubt the most frequently mis-used example • The word "data " is absolutely and always plural !!! • No matter how many smart people use it improperly !!! • There is no doubt that "datum" is the singular and "data" is the plural, and I can think of no other example where "is/was" is used with a clearly plural noun. Always use the plural form of the verb (are/were) with this plural noun. • Some argue that data is a "collective" noun like "family" or "class" or "group" or "committee" and that singular can be used. But collective nouns are singular forms used to describe a group and therefore use a plural form of the verb, NOTplural forms of the noun used as if they were singular.

26. Singular drug datum Plural drugs data Proper plurals Correct: "All data were obtained by my technician, because I don't even remember how to hold a Pipetman anymore." "Data presented are the averages of at least three experiments". Incorrect: "The data is clinically important because it shows a difference between the drug responses of the two groups of patients." "The data was best fit by a single-site model." Correct: "The datum at 5 min, but only that specific data point, that onesingle value, was obtained with help from the last author."

27. Singular cell medium Plural cells media Proper plurals • Dulbecco's is one growth medium(singular),even though it has many components • RPMI and Weymouth's are two different media(plural), each of which has multiple different components • "Just because one type of growth mediumworks well for your cells does not mean that any of several other media might not work equally well. • "Growth media were obtained from Gibco" • only if more than one kind of medium was used!

28. Singular forms all end in consonants; plural forms (almost) all end in vowels The "-is" vs. "-es" forms are the only exceptions "Most graphs have two axes—one x-axis and one y-axis." "There are threeloci for drug intervention: the most common locusis the cell surface receptor, a second important locusis the intracellular signaling pathway, and the newest locus istargeting the nucleus with gene therapy."

29. #4. Too many significant figures All of your "significant figures" should be "believable" Looking at your error bars is a good way to decide Instruments and spreadsheets give you lots of numbers that are meaningless; don't use them unless you believe them!! 94 ± 14 3060 ± 310 700 ± 130 4470 ± 500

30. Proper use of numbers And remember spaces too!!! 94 ± 14 3060 ± 310 700 ± 130 4470 ± 500

31. #5a. Correct commasin parenthetical statements • "Parenthetical" loosely means that it could also be put in parentheses, or that it is an "aside" or an "addition"; the sentence would be complete without it. • Commas always come in pairs when in the middle of a sentence! • The inhibitor genistein, which is supposed to be selective for tyrosine kinases, inhibited this serine kinase-mediated response. • Propranolol, the prototypical beta antagonist, has many dangerous side effects. • One comma is OK only if the parenthetical statement ends the sentence. • The reaction was inhibited by C3 toxin, a selective blocker of Rho. • The reaction was inhibited by C3 toxin, a selective blocker of Rho, and also by the Rho kinase inhibitor Y25632.

32. Commas in parenthetical statements • One-word and simple multi-word parenthetical statements do not NEED commas, and I strongly prefer that they NOT be used. • The protein kinase inhibitor genistein did not alter the response. • preferred • The protein kinase inhibitor,genistein, did not alter the response. • less appropriate • The Ca2+- and phospholipid-dependent enzyme protein kinase C mediates many of the effects of PI hydrolysis. • preferred • The Ca2+- and phospholipid-dependent enzyme,protein kinase C, mediates many of the effects of PI hydrolysis. • less appropriate

33. Commas in parenthetical statements • "and" and "but" go outside the parenthetical statement commas • The control cells, contrary to our hypothesis, showed less internalization. • The control cells showed modest internalization but,contrary to our hypothesis,drug-treated cells showed less internalization. • NOT: The control cells showed modest internalization,but contrary to our hypothesis,drug-treated cells showed less internalization. • "… in males but, in contrast, not in females …" • NOT "… in males, but in contrast,not in females …" • "Treated animals survived longer and, as a result, produced more progeny.

34. #5b. Correct commasin compound sentences • If the compound sentence is so long that it needs a comma, then it needs two independent clauses, each with a "subject" (noun)anda "predicate" (verb) • Or it should be two separate sentences • Both sides of ", and" (with a comma) need to have a subject and a predicate (be independent clauses) • But "and" (without a comma) does NOTneed to have a second subject; but it can, if the sentence is not too long • Incorrect • The cellswere pretreated with pertussis toxin for 24 hr to inactivate Gi, and lysed by scraping in a hypotonic buffer. • How to fix • Take out the comma, or … • Add a subject to the second clause to make it independent, or… • Make it two separate sentences if "too long" is the problem

35. #6. Inappropriate use of "time words" • Don't use "while", "since" or "as"except to indicate the relationship of events in time • I only learned about this when journal style editors changed them in my papers, so I learned to do them right myself! • We often use "while" when we mean "whereas" or "although" • We often use "as" when we mean "because" • We often use "since" when we mean "because" • Use the proper word, not the time word, unless it is a time concept!

36. Inappropriate use of "time words" • "While" • Incorrect:Whilestaurosporine is a PKC inhibitor, it can also inhibit other kinases. (The intent is not to indicate that these two events are taking place at the same point in time.) • Better:Althoughstaurosporine is…. Whereasstaurosporine is.…. • Correct use of "while": "While the cells were being incubated in serum-free medium to induce cell cycle arrest, they were also being exposed to pertussis toxin to inactivate Gi. (Here the point is that the starvation and pertussis toxin treatments were going on simultaneously.)

37. Inappropriate use of "time words" • "As" • Incorrect:AsC3 toxin is a highly selective Rho inhibitor, our data implicate Rho as a mediator of synergism. (The intent is NOT to indicate that these two events are taking place at the same point in time.) • Better:BecauseC3 toxin is…. • Correct use of "as": "As the cells reached confluence, their shape changed from flattened to cuboidal. (Here the point is that the shape change coincided in time with the attainment of confluence.)

38. Inappropriate use of "time words" • "Since"--similar to "as", "because" is often what is meant • Incorrect:SinceC3 toxin is a highly selective Rho inhibitor, our data indicate Rho as a mediator of synergism. (The intent is not to indicate that one event is taking place at a later time point than the other.) • Better:BecauseC3 toxin is…. • Correct use of "since": "Since changing the HEPA filter in our hood, we have no further problems with cell contamination. (Here the word "since" is properly used to indicate that one thing has happened following another thing in time.)

39. #7. Which vs. That • A tough distinction, but with simple differences and rules of thumb! • "That" is used to "restrict" the meaning or to "identify" a specific entity • "Which" does not restrict but rather "elaborates" or "describes" • Examples • The estrogen that is present in most birth control pills is ethinyl estradiol. • The estrogen drug ethinyl estradiol, which is present in most birth control pills, is only slightly different from endogenous estradiol. • The estrogen that is present in most birth control pills, which has been modified for greater oral effectiveness, is ethinyl estradiol. • WRONG: The estrogen which is present in most birth control pills is ethinyl estradiol.

40. Which vs. That -- Rules of thumb • Rule of thumb #1: • If the phrase can be taken out without losing the meaning of the overall sentence, use "which" • If the phrase is vital to the point of the sentence, use "that" • Rule of thumb #2: • "Which" statements are almost always set off with commas • "That" statements should NOT be set off with commas • If commas seem needed or natural, use "which" • If commas are not needed or seem awkward, use "that" • Correct use of both: The car that hit my bicycle, which is a VW bug, is now in the body shop with a big dent in its hood. • Common incorrect use: The car whichhit my bicycle is now in the body shop.

41. Which vs. That -- more examples • Drug example • Tamoxifen, which is a so-called anti-estrogen, is the most appropriate drug for this patient. • "which is a so-called anti-estrogen" can be left out and the sentence is still complete and true and meaningful • this would not read well without the commas • The drug that is most appropriate for this patient is tamoxifen. • taking out "that is most appropriate for this patient" leaves a complete sentence but it has lost its meaning • it would seem awkward to use commas here • Most common kind of wrong use • The drug which we used to block redox signaling was tempol. • The drug that we used in to block redox signaling was tempol.

42. Which vs. That -- more examples • The drug that had the highest potency was RX-1040A. • RX1040A, which had the highest potency of all the drugs tested, was chosen for further clinical trials. • The receptor that is the subject of my NIH grant is the AT2 angiotensin receptor. • The AT2 angiotensin receptor, which is the subject of my NIH grant, is a Gq-coupled receptor. • The receptor that is the subject of my NIH grant, which is the AT2 angiotensin receptor, is a Gq-coupled receptor. • an example of that and which used properly in the same sentence

43. #8. Person, Voice and Tense • Person and voice • Historically recommended NOT to use first person in scientific writing • And I still very strongly prefer little or no first person! • But this does NOT mean that you need to use cumbersome third personpassive voice • Third person can be cumbersome, but it doesn't need to be • Third person can make writing seem "impersonal" • Passive voice can be very cumbersome • Passive voice removes all sense of "action", things "happening", "excitement" and "story" • I try to use third person but active voice

44. Person and Voice • Person and voice examples • First person active -- AVOID this • We noted that there were fewer endosomes in the inhibitor-treated cells. • Two VERY BAD ways of avoiding first person • The authors noted that there were fewer endosomes in the inhibitor-treated cells. • It was noted that there were fewer endosomes in the inhibitor-treated cells. • Simplest statement; maybe OK; but "boringly passive" • There were fewer endosomes in the inhibitor-treated cells. • Some good third person active voice statements • Treating cells with inhibitor reduced the number of endosomes. • Treated cells contained fewer endosomes than control cells. • The number of endosomes was reduced in inhibitor-treated cells. • These avoid "we", retain "action", are not cumbersome or passive

45. Person and Voice • More good and bad person and voice examples "It has been reported that ……. " "Smith et al. reported that ……. " or "Several groups have reported… " • State WHO reported it, which makes it active. "It is the hypothesis of this study that …… " "It is hypothesized that …… " "The authors of this study hypothesize that ……. " • Very cumbersome ways to avoid first person "The hypothesis of this study is that …… " • Active voice and very clear

46. Person, Voice and Tense • It is almost always easy to avoid first person • We tested the hypothesis that…. • The hypothesis guiding these studies was that…. • These studies tested the hypothesis that…. • It was hypothesized that…. (I do NOT like this wording) • We instilled saline or drug into mouse lungs … • Saline or drug was instilled into mouse lungs… • We further propose that ROS alter BBB by… • These data suggest that… • A likely possibility is that…

47. Person and Voice • Places I TOLERATE use of first person: • Introduction, only once! • "We hypothesize that …. " • Discussion, only once! • "We speculate that ….." or "We propose that these drugs,,,,,, " • Your hypothesis and speculation are quite "personal", not "facts" • LIMITED USE of first person possessive • "Our previous studies showed that ….. " • Places NEVER to use first person • Methods • "We obtained inhibitors from .."; "We grew cells in …." • Results • "We found that prestin …"; "We next used confocal to ……. "

48. Person and Voice • Almost always use "we" and "our" rather than "I" or "my" • Science is almost always a group effort! • Even if not, "I" sounds awkward and maybe egotistical • Students describing their own work is my one exception • I like to know what you (the student) did or observed • in contrast to what your lab did or observed or knows • In oral presentations, in posters, in grant proposals • in these places it is important to emphasize student's own work, plans, ideas • But not in a student's manuscript for publication

49. Tense • When to say what "happened" or "was observed" (past tense) vs. what "happens" or "is known" (present tense) • General guideline • Use past tense to state what you did in your experiments and what you observed that you are reporting in this paper • These are clearly observations of what happened(past tense) in your experiments but not necessarily what happens(present tense)in general. • "C3 toxin prevented synergism between LPA and EGF, as shown in Fig.3." • Use present tense to describe what is generally accepted or whatis "known" to occur from previous studies • "C3 toxin is(present tense)an inhibitor of Rho." • "Forskolinactivates(present tense)adenylyl cyclase."

50. Tense • Introduction • Mix of present and past tenses—what is known already, what was reported in previous studies, • "Prestinis an important protein for hearing (a fact), and Hallworthet al. showed it to be located in auditory hair cells(what they saw)." • Methods • Almost exclusively past tense—what was done in your studies • Results • Almost exclusively past tense—what was observed, what happened • Discussion • Again a mix of presentand past tenses • "Rhomediatesthis response (present tense conclusion), because it was inhibited by C3 toxin (what happened in a specific experiment)."