From research to manuscript: A guide to scientific writing

158 Pages·2006·2.639 MB·English

by  Michael J. Katz

FROM RESEARCH TO MANUSCRIPT
From Research to Manuscript
A Guide to Scientific Writing
by
MICHAEL JAY KATZ
Case Western Reserve University,
Cleveland OH, U.S.A.
A C.I.P. Catalogue record for this book is available from the Library of Congress.
ISBN-10 1-4020-4045-8 (PB)
ISBN-13 978-1-4020-4045-0 (PB)
ISBN-10 1-4020-4071-7 ( e-book)
ISBN-13 978-1-4020-4071-9 (e-book)
Published by Springer,
P.O. Box 17, 3300 AADordrecht, The Netherlands.
www.springer.com
Printed on acid-free paper
All Rights Reserved
© 2006 Michael Jay Katz. The exclusive exploitation and distribution
rights remain with Springer.
No part of this work may be reproduced, stored in a retrieval system, or transmitted
in any form or by any means, electronic, mechanical, photocopying, microfilming, recording
or otherwise, without written permission from the Publisher, with the exception
of any material supplied specifically for the purpose of being entered
and executed on a computer system, for exclusive use by the purchaser of the work.
Printed in the Netherlands.
Contents
ACKNOWLEDGEMENTS................................................................ vii
INTRODUCTION............................................................................ ix
SCIENTIFICPAPERSUSEDASEXAMPLES....................................... xi
1. TOOLSANDTECHNIQUES......................................................... 1
1. TheStandards......................................................................... 1
1.1. AStereotypedFormat........................................................ 1
1.2. PreciseLanguage.............................................................. 1
1.3. ASingle,ClearDirection.................................................... 2
1.4. ReviewedandMadeAvailabletoOthers.................................. 2
2. WordsandText...................................................................... 3
2.1. WritewithExactnessandClarity........................................... 3
2.2. HowtoWriteText............................................................. 6
2.3. AdvicetoSpeakersofOtherLanguages.................................. 24
3. Numbers............................................................................... 25
3.1. Tables............................................................................ 27
3.2. Statistics......................................................................... 30
4. Figures................................................................................. 41
4.1. BasicGuidelines............................................................... 41
4.2. FigureLegends................................................................. 43
4.3. Graphs........................................................................... 43
4.4. AestheticsofNumericalFigures............................................ 48
5. ScientificPatterns.................................................................... 49
2. THESCIENTIFICPAPER............................................................. 51
1. ResearchandWriting............................................................... 51
1.1. DailyLabNotebook........................................................... 51
1.2. ABeginningDraft............................................................. 52
2. WritingtheSectionsofaScientificPaper....................................... 53
2.1. MaterialsandMethods....................................................... 54
v
vi Contents
2.2. Appendix........................................................................ 66
2.3. Results........................................................................... 68
2.4. Discussion....................................................................... 85
2.5. Conclusion...................................................................... 101
2.6. Introduction..................................................................... 104
2.7. Title.............................................................................. 113
2.8. Abstract.......................................................................... 115
2.9. References...................................................................... 121
2.10. Footnotes...................................................................... 123
2.11. Acknowledgements.......................................................... 124
3. PREPARINGTOPUBLISH........................................................... 125
1. GestationandRewriting............................................................ 125
1.1. DetailsofStyle................................................................. 125
1.2. Rewrite.......................................................................... 126
1.3. AFriendlyCritique............................................................ 127
1.4. ReadthePaperBackwards................................................... 127
1.5. Spelling.......................................................................... 128
2. FinalManuscriptPreparation...................................................... 129
3. RespondingtoEditorsandReferees.............................................. 132
3.1. APrecritiqueRewrite......................................................... 132
3.2. TheComment-by-CommentLetter........................................ 132
3.3. StayCalm ...................................................................... 133
APPENDIXES................................................................................ 135
A. WordsThatAreOftenMisused............................................... 135
B. SimplifyingWordy,Redundant,andAwkwardPhrases................. 141
C. StandardScientificAbbreviations............................................ 143
D. TypicalBibliographicFormats............................................... 147
E. AdditionalReading.............................................................. 149
INDEX......................................................................................... 151
Acknowledgements
I thank journal editors Olaf Andersen, John Bennett, Lynn Enquist, David
Fastovsky, Robert Genco, William Giannobile, Kathryn Harden, Theodore Harman,
William Koros, James Olds, David Rosenbaum, Catharine Ross, and George Schatz
forsuggestingspecificwell-writtenscientificpapers.Permissionstoquotefromtheir
papersweregrantedby:DanielaBerg,DavidFastovsky,JacquelineGeraudie,David
Rosenbaum, and Benjamin Widom. Permissions to reproduce the first page of their
articlesforthebookcoverweregrantedby:DanielaBergandJacquelineGeraudie.
Journalpermissionsforquotations:
– Augspurger et al. 2005. J Nutrition 135: 1712–1717 [copyright 2005, permission
fromtheAmericanSocietyforNutrionalSciences].
– Bohm et al. 2005. Leukemia Res 29: 609–615 [copyright 2005, permission from
ElsevierLtd.].
– Borgensetal.2004.JNeurosciRes76:141–154[copyright2004,permissionfrom
Wiley-Liss,Inc.,asubsidiaryofJohnWiley&Sons,Inc.].
– FastovskyandSheehan.2005.GSAToday15:4–10[permissionfromtheGeological
SocietyofAmerica].
– Gapski et al. 2004. J Periodontol 75: 441–452 [permission from the American
AcademyofPeriodontology].
– GlaunsingerandGanem.2004.JExpMed200:391–398[copyright2004,permission
fromTheRockefellerUniversityPress].
– Milneretal.1968.Sci161:184–186[copyright1968,permissionfromAAAS].
– ReadingerandMohney.2005.JElectronicMaterials34:375–381[permissionfrom
theMinerals,Metals&MaterialsSociety].
– Sugimori et al. 1994. Biol Bull 187: 300–303 [permission from The Biological
Bulletin].
– SundarandWidom.1987.JPhysChem91:4802–4809[copyright1987,permission
fromtheAmericanChemicalSociety].
– Williams CM. 1961. Biol Bull 121: 572–585 [permission from The Biological
Bulletin].
vii
Introduction
ObservationsPlusRecipes
Itissometimessaidthatscienceistheorderlycollectionoffactsaboutthenatural
world.Scientists,though,havebeenincreasinglywaryofusingtheword‘fact.’‘Fact’
hasthefeelingofabsolutenessanduniversality.“Childrenhave20deciduous(baby)
teeth”isanobservationabouttherealworld,butscientistswouldnotcallitafactor
evenacompletescientificstatement.Somechildrenhavefewerdeciduousteeth,and
somehavemore.Moreover,thosechildrenwhodohave20deciduousteethusetheir
full complement of deciduous teeth during only a brief part of their childhood. As
babiesandtoddlers,theyhavefewerteeth.Asolderchildren,notalltheirdeciduous
teeth are still in place because the deciduous teeth are being replaced by permanent
teeth. In addition, the statement “children have 20 deciduous teeth” does not tell us
whatwemeanby“teeth.”Are“teeth”onlythosethatcanseenbewiththeunaidedeye
ordowealsoincludethehidden,uneruptedteeth?
Anobservationsuchas“childrenhave20deciduousteeth”isnotafact,anditonly
becomes a scientific observation when it comes with definitions and qualifiers. The
simplestandmostthoroughwaytoaddtheneededscientificdepthtoanobservationis
todescribehowtheobservationwasmade.Theobservation“childrenhave20deciduous
teeth”canbemadescientificallymeaningfulbydescribingtherecipethatgeneratedit,
arecipesuchas:“Ilookedinthemouthsof25five-year-oldboysand25five-year-old
girlsintheGardenDayNurserySchoolinCleveland,OH,onMonday,May24,2005,
andfoundthat23oftheboysand25ofthegirlshad20visibleteeth.”
Thestandardformforrecordingmeaningfulscientificobservations—observations
withtheirrecipes—isthescientificpaper.
WritingaScientificPaper
Science is the orderly collection of observations about the natural world made
viawell-definedprocedures,andmodernscienceisanarchiveofscientificpapers.A
ix
x Introduction
researchprojecthasnotcontributedtoscienceuntilitsresultshavebeenreportedina
paper,theobservationsinwhichareaccompaniedbycompleterecipes.
Asacontributingscientist,youmustwritescientificpapers.Writingagoodscien-
tific paper takes time. On the other hand, the writing will seem endless if you begin
withthetitleandslogstraightthroughtothelastreference.Thisapproachisdifficult,
wearing,andinefficient.Thereisamuchmoreeffectivewaytowrite.
Isuggestthatyouwriteyourpaperfromtheinsideout.Beginwiththeall-important
recipes, the Materials and Methods. Next collect your data and draft the Results. As
your experiments end, formulate the outlines of a Discussion. Then write a working
Conclusion.Nowgobackandwritethehistoricalcontext,theIntroduction.Onlyafter
allelsehasbeenwrittenandtidiedup,willyouhavesufficientperspectivetowritethe
TitleandtheAbstract.
Throughoutyourwriting,yourtoolsandtechniqueswillbethesame.Youshould
useprecisewordsand,wheneverpossible,numbers.Youshouldwritedirectsentences
thatfollowastraightlinefrompointAtopointB.And,youshouldthoroughlycomplete
everysectionofthestereotypedformatofastandardscientificpaper.
Writing a paper should be an active part of your research. If you wait until your
studiesarefinishedbeforeyoubegintowrite,youwillmissapowerfultool.Research
is iterative—you do, you assess, and you redo. Writing a paper is a way for you to
continuallymaketheassessmentsnecessaryforcriticalandperceptiveresearch.
Yourmanuscriptcanbeablueprintforyourexperiments.Theemptyskeletonof
a scientific paper poses a set of research questions. As you fill in the skeleton, you
automatically carry out an orderly analysis of your data and observations. And, by
continuallysettingnewdataintothedraftofyourpaper,youcanmaintainperspective.
Youwillfilterouttheshineof“newness,”asyourresults—evenunusualresults—are
putintothecontextofyourfullresearchplan.
Asascientist,youmustwrite,andasanexperimentalist,writingwhileyouwork
strengthensyourresearch.
Scientific Papers Used as Examples
Inthetextofthisbook,IrebuildapaperthatIwrotein1985,entitled“Intensifier
ForBodianStainingofTissueSectionsandCellCultures.”Iusethispaperbecauseit
isbrief,simple,andwell-knowntome.
Just as a picture is worth a thousand words, an actual example of a well-written
scientific paragraph is worth a dozen descriptions of one. To illustrate the craft of
scientific writing, I have included excerpts from far better scientific papers than my
own.Theexcerptsarefromarticlesacrosstherangeofscientificstudies.Thesepapers
are lean, logical, and cleanly-written. They are examples of especially good science
writing and have, for the most part, been recommended to me by the editors of the
journalsinwhichtheyappeared.Inthetext,Irefertothepapersbyauthor(s)anddate.
Herearethefullbibliographiccitations:
AbercrombieM,HeaysmanJEM.1954.Observationsonthesocialbehaviourofcells.
II.“Monolayering”offibroblasts.ExpCellRes6:293–306.
Augspurger NR, Scherer CS, Garrow TA, Baker DH. 2005. Dietary s-
methylmethionine,acomponentoffoods,hascholine-sparingactivityinchickens.
JNutrition135:1712–1717
BergD,SiefkerC,BeckerG.2001.EchogenicityofthesubstantianigrainParkinson’s
diseaseanditsrelationtoclinicalfindings.JNeurol248:684–689.
BohmA,PiribauerM,WimazalF,GeisslerW,GisslingerH,KnoblP,JagerU,Fonatsch
C,KyrlePA,ValentP,LechnerK,SperrWR.2005.HighdoseintermittentARA-C
(HiDAC)forconsolidationofpatientswithdenovoAML:asinglecenterexperience.
LeukemiaRes29:609–615.
BorgensRB,BohnertD,DuerstockB,SpomarD,LeeRC.2004.Tri-blockcopolymer
producesrecoveryfromspinalcordinjury.JNeurosciRes76:141–154.
Fastovsky DE, Sheehan P. 2005. The extinction of the dinosaurs in North America.
GSAToday15:4–10.
Gapski R, Barr JL, Sarment DP, Layher MG, Socransky SS, Giannobile WV. 2004.
Effectofsystemicmatrixmetalloproteinaseinhibitiononperiodontalwoundrepair:
aproofofconcepttrial.JPeriodontol75:441–452.
xi
xii ScientificPapersUsedasExamples
Glaunsinger B, Ganem D. 2004. Highly selective escape from KSHV-mediated host
mRNAshutoffanditsimplicationsforviralpathogenesis.JExpMed200:391–398.
HaselerLJ,ArcinueE,Danielsen,ER,BlumlS,RossD.1997.EvidenceFromProton
MagneticResonanceSpectroscopyforaMetabolicCascadeofNeuronalDamagein
ShakenBabySyndrome.Pediatrics99:4–14.
JacobsonC-O.1959.Thelocalizationofthepresumptivecerebralregionsintheneural
plateoftheaxolotllarva.JEmbryolExpMorph7:1–21.
MilnerB,TaylorL,SperryRW.1968.Lateralizedsuppressionofdichoticallypresented
digitsaftercommissuralsectioninman.Sci161:184–186.
PaulDR,McSpaddenSK.1976.Diffusionalreleaseofasolutefromapolymermatrix.
JMembraneSci1:33–48.
PerezJF,SandersonMJ.2005.Thefrequencyofcalciumoscillationsinducedby5-HT,
ACH,andKCldeterminethecontractionofsmoothmusclecellsofintrapulmonary
bronchioles.JGenPhysiol125:535–553.
ReadingerED,MohneySE.2005.EnvironmentalsensitivityofAudiodesonn-AlGaN.
JElectronicMater34:375–381.
RichardsTW,LembertME.1914.Theatomicweightofleadofradioactiveorigin.J
AmChemSoc36:1329–1344.
Rosenbaum,DA.2005.TheCinderellaofpsychology.Theneglectofmotorcontrolin
thescienceofmentallifeandbehavior.AmPsychologist60:308–317.
RutherfordE.1919.Collisionsofalphaparticleswithlightatoms.IV.Ananomalous
effectinnitrogen.LondEdinbDublPhilMagJSci37:581.
SingerM,WeckesserEC,GeraudieJ,MaierCE,SingerJ.1987.Openfingertiphealing
andreplacementafterdistalamputationinRhesusmonkeywithcomparisontolimb
regenerationinlowervertebrates.AnatEmbryol177:29–36.
Speidel CC. 1932. Studies of living nerves. I. The movements of individual sheath
cells and nerve sprouts correlated with the process of myelin-sheath formation in
amphibianlarvae.JExpZool61:279–317.
SugimoriM,LangEJ,SilverRB,LlinasR.1994.High-resolutionmeasurementofthe
timecourseofcalcium-concentrationmicrodomainsatsquidpresynapticterminals.
BiolBull187:300–303.
SundarG,WidomB.1987.Interfacialtensionsonapproachtoatricriticalpoint.JPhys
Chem91:4802–4809.
Williams CM. 1961. The juvenile hormone. II. Its role in the endocrine control of
molting,pupation,andadultdevelopmentintheCecropiasilkworm.BiolBull121:
572–585.