Beforeyoubegin:somegeneraladvice

Readingascientificpaperisacompletelydifferentprocessthanreadinganarticleabout
scienceinablogornewspaper.Notonlydoyoureadthesectionsinadifferentorderthan
theyrepresented,butyoualsohavetotakenotes,readitmultipletimes,andprobablygo
lookupotherpapersforsomeofthedetails.Readingasinglepapermaytakeyouavery
longtimeatfirst.Bepatientwithyourself.Theprocesswillgomuchfasterasyougain
experience.

Mostprimaryresearchpaperswillbedividedintothefollowingsections:Abstract,
Introduction,Methods,Results,andConclusions/Interpretations/Discussion.Theorder
willdependonwhichjournalitspublishedin.Somejournalshaveadditionalfiles(called
SupplementaryOnlineInformation)whichcontainimportantdetailsoftheresearch,but
arepublishedonlineinsteadofinthearticleitself(makesureyoudontskipthesefiles).

Beforeyoubeginreading,takenoteoftheauthorsandtheirinstitutionalaffiliations.Some
institutions(e.g.UniversityofTexas)arewellrespectedothers(e.g.theDiscovery
Institute)mayappeartobelegitimateresearchinstitutionsbutareactuallyagendadriven.
Tip:googleDiscoveryInstitutetoseewhyyoudontwanttouseitasascientific
authorityonevolutionarytheory.

Alsotakenoteofthejournalinwhichitspublished.Reputable(biomedical)journalswillbe
indexedbyPubmed.Bewareofquestionablejournals.

Asyouread,writedowneverysinglewordthatyoudontunderstand.Youregoingto
havetolookthemallup(yes,everyone.Iknowitsatotalpain.Butyouwontunderstand

thepaperifyoudontunderstandthevocabulary.Scientificwordshaveextremelyprecise
meanings).

Stepbystepinstructionsforreadingaprimaryresearcharticle

1.Beginbyreadingtheintroduction,nottheabstract.

Theabstractisthatdensefirstparagraphattheverybeginningofapaper.Infact,thats
oftentheonlypartofapaperthatmanynonscientistsreadwhentheyretryingtobuilda
scientificargument.(Thisisaterriblepracticedontdoit.).WhenImchoosingpapersto
read,Idecidewhatsrelevanttomyinterestsbasedonacombinationofthetitleand
abstract.ButwhenIvegotacollectionofpapersassembledfordeepreading,Ialways
readtheabstractlast.Idothisbecauseabstractscontainasuccinctsummaryoftheentire
paper,andImconcernedaboutinadvertentlybecomingbiasedbytheauthors
interpretationoftheresults.

2.IdentifytheBIGQUESTION.

NotWhatisthispaperabout,butWhatproblemisthisentirefieldtryingtosolve?

Thishelpsyoufocusonwhythisresearchisbeingdone.Lookcloselyforevidenceof
agendamotivatedresearch.

3.Summarizethebackgroundinfivesentencesorless.

Herearesomequestionstoguideyou:

WhatworkhasbeendonebeforeinthisfieldtoanswertheBIGQUESTION?Whatarethe
limitationsofthatwork?What,accordingtotheauthors,needstobedonenext?

Thefivesentencespartisalittlearbitrary,butitforcesyoutobeconciseandreallythink
aboutthecontextofthisresearch.Youneedtobeabletoexplainwhythisresearchhas
beendoneinordertounderstandit.

4.IdentifytheSPECIFICQUESTION(S)
Whatexactlyaretheauthorstryingtoanswerwiththeirresearch?Theremaybemultiple
questions,orjustone.Writethemdown.Ifitsthekindofresearchthattestsoneormore
nullhypotheses,identifyit/them.

Notsurewhatanullhypothesisis?Goreadthis,thengobacktomylastpostandreadone
ofthepapersthatIlinkedto(likethisone)andtrytoidentifythenullhypothesesinit.
Keepinmindthatnoteverypaperwilltestanullhypothesis.

5.Identifytheapproach

WhataretheauthorsgoingtodotoanswertheSPECIFICQUESTION(S)?

6.Nowreadthemethodssection.Drawadiagramforeachexperiment,
showingexactlywhattheauthorsdid.

Imeanliterallydrawit.Includeasmuchdetailasyouneedtofullyunderstandthework.
Asanexample,hereiswhatIdrewtosortoutthemethodsforapaperIreadtoday
(Battagliaetal.2013:ThefirstpeoplingofSouthAmerica:Newevidencefrom
YchromosomehaplogroupQ).Thisismuchlessdetailthanyoudprobablyneed,because

itsapaperinmyspecialtyandIusethesemethodsallthetime.Butifyouwerereading
this,anddidnthappentoknowwhatprocessdatawithreducedmedianmethodusing
Networkmeans,youdneedtolookthatup.

Youdontneedtounderstandthemethodsinenoughdetailtoreplicatethe
experimentthatssomethingreviewershavetodobutyourenotreadytomoveonto
theresultsuntilyoucanexplainthebasicsofthemethodstosomeoneelse.

7.Readtheresultssection.Writeoneormoreparagraphstosummarizethe
resultsforeachexperiment,eachfigure,andeachtable.Dontyettrytodecide
whattheresultsmean,justwritedownwhattheyare.

Youllfindthat,particularlyingoodpapers,themajorityoftheresultsaresummarizedin
thefiguresandtables.Paycarefulattentiontothem!Youmayalsoneedtogotothe
SupplementaryOnlineInformationfiletofindsomeoftheresults.

Itisatthispointwheredifficultiescanariseifstatisticaltestsareemployedinthepaper
andyoudonthaveenoughofabackgroundtounderstandthem.Icantteachyoustatsin
thispost,buthere,here,andherearesomebasicresourcestohelpyou.ISTRONGLY
adviseyoutobecomefamiliarwiththem.

THINGSTOPAYATTENTIONTOINTHERESULTSSECTION:

Anytimethewordssignificantornonsignificantareused.Thesehaveprecise
statisticalmeanings.Readmoreaboutthishere.

Iftherearegraphs,dotheyhaveerrorbarsonthem?Forcertaintypesofstudies,alackof
confidenceintervalsisamajorredflag.

Thesamplesize.Hasthestudybeenconductedon10,or10,000people?(Forsome
researchpurposes,asamplesizeof10issufficient,butformoststudieslargerisbetter).

8.DotheresultsanswertheSPECIFICQUESTION(S)?Whatdoyouthinkthey
mean?

Dontmoveonuntilyouhavethoughtaboutthis.Itsokaytochangeyourmindinlightof
theauthorsinterpretationinfactyouprobablywillifyourestillabeginneratthiskind
ofanalysisbutitsareallygoodhabittostartformingyourowninterpretationsbefore
youreadthoseofothers.

9.Readtheconclusion/discussion/Interpretationsection.

Whatdotheauthorsthinktheresultsmean?Doyouagreewiththem?Canyoucomeup
withanyalternativewayofinterpretingthem?Dotheauthorsidentifyanyweaknessesin
theirownstudy?Doyouseeanythattheauthorsmissed?(Dontassumetheyreinfallible!)
Whatdotheyproposetodoasanextstep?Doyouagreewiththat?

10.Now,gobacktothebeginningandreadtheabstract.

Doesitmatchwhattheauthorssaidinthepaper?Doesitfitwithyourinterpretationofthe
paper?

11.FINALSTEP:(Dontneglectdoingthis)Whatdootherresearcherssay
aboutthispaper?

Whoarethe(acknowledgedorselfproclaimed)expertsinthisparticularfield?Dothey
havecriticismsofthestudythatyouhaventthoughtof,ordotheygenerallysupportit?

HeresaplacewhereIdorecommendyouusegoogle!Butdoitlast,soyouarebetter
preparedtothinkcriticallyaboutwhatotherpeoplesay.

(12.Thisstepmaybeoptionalforyou,dependingonwhyyourereadingaparticularpaper.
Butforme,itscritical!IgothroughtheLiteraturecitedsectiontoseewhatotherpapers
theauthorscited.Thisallowsmetobetteridentifytheimportantpapersinaparticularfield,
seeiftheauthorscitedmyownpapers(KIDDING!.mostly),andfindsourcesofuseful
ideasortechniques.)

10bigquestionstodissectsciencepapers
1. Whatisthecentralpointtheauthorsaretryingtoprove?Readcarefullyto
determinewhethertheauthorsactuallygetthereorfallshortand/or
overinterpretresults.
2. Doesitmatterhowoftenanexperimentisrepeated?Generallyifyougeta
specificresultonce,itcouldbeamistake.Ifyougetthesameresulttwice,it
couldbeacoincidence.Ifyougetthesameresultthreetimes,thenmaybeyou
haveaninterestingstory.
3. Arethereanycontrols?Anexperimentisusuallyonlyasgoodasitscontrols,
whichshouldaddressmultipleaspectsoftheexperimentincludingsensitivityof
assaysused,whatapositiveresultshouldlooklike,andwhatanegative
resultshouldlooklike.Thisallowsanexperimenttobeevaluatedbycomparing
experimentalfindingstomultiplestandards.
4. Dotheyusethebestmethodsavailable?Thisbringsupseveralrelatedquestions.
Checkwhethertheyusedmethodsthatarequalitative(i.e.,issomethingthereor
not)versusquantitative(i.e.,ifitsthere,howabundantisit?).Considerwhether
theyuserigorousandcomplementaryapproachessuchascellular

lineagetracing,clonalanalysis,and/orfunctionalassays.Dotheyoverlyrelyon
asimplephenotype(i.e.,somethingsortoflookslikeX,sotheycallitX)?
5. Alwaysaskyourself,Whatexperimentdidnttheydothatcouldmakethedata
moreconvincing?Forexample,ifapapershowsthatagivencellexpresses
musclespecificgenesthatlooklikemusclecellsunderthemicroscope,andthat
whentransplantedintoamousesdamagedmuscleintegrateandsurvive,what
additionalexperimentwouldbetterconvinceyouthattheyareinfactbonafide
muscle?
6. Didtheyperformenrichment(i.e.,itismostlythis)vs.purification(i.e.,itis
onlythis)vs.noideawhattheyused?Iftheyknockout/downagene,isthere
alsoaknockoutmodel?Dotheyagreeordisagree?Onewouldhopethatthey
wouldproducesimilareffects.Ifso,whatphenotypedoesithave?Istheresultin
ananimalmodelthesameasforthecognatehumancondition?Ifno,itmay
actuallynotbeaveryusefulmodelofthehumandisease.
7. Didtheyincreaseconfidenceintheoutcomebyprovingtheirresultsinmultiple
ways?Didtheytakethetimetotrytodisprovetheirfindings?
8. Isthepaperdescriptive/hypothesisgeneratingorisithypothesisdrivenwith
multipleexamplestobackupthebottomline?
9. Whatdootherarticlessayaboutthetopic?Ifthepaperisfarafieldfromwhat
othershavepublished,areitsbigclaimsbackedupbyconvincingdata?How
goodisthebibliography?Agoodresearchpapershouldnotcitetoomany
revieworopinionpapersoverpeerreviewed,primaryresearcharticlesfrom
highimpactjournals.
10.Havethedatabeenreproducedbyotherlabs?Reproducibilityisakeyfeatureof
goodscienceandwithabrandnewfinding,onlytimewilltellifothersareable
togetittoworkthesameway.