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2016/4/15

WhyEvolutionIsTrue|Notes&Review|vialogue

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WhyEvolutionIsTrue|Notes&Review PostedonMay6,2012 10 JerryCoyne.WhyEvolutionIsTrue(h氀฀p://www.amazon.com/Why‑Evolution‑True‑Jerry‑Coyne/dp/B002ZNJWJU/ref=sr_1_1? ie=UTF8&qid=1336256470&sr=8‑1).Penguin,2009.(282pages)

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Preface …whiletheDovertrialisanAmericanstory,creationismisn’tauniquelyAmericanproblem.Creationists—whoaren’tnecessarily Christians—areestablishingfootholdsinotherpartsoftheworld,especiallytheUnitedKingdom,Australia,andTurkey.Theba氀฀lefor evolutionseemsnever‑ending.Andtheba氀฀leispartofawiderwar,awarbetweenrationalityandsuperstition.(xiii) Butevolutionisfarmorethana“theory,”letaloneatheoryincrisis.Evolutionisafact.(xiii)

Introduction Darwinma氀฀ersbecauseevolutionma氀฀ers.Evolutionma氀฀ersbecausesciencema氀฀ers.Sciencema氀฀ersbecauseitisthepreeminentstoryof anepicsagaaboutwhoweare,wherewecamefrom,andwherewearegoing.–MichaelShermer Tomany,evolutiongnawsattheirsenseofself.(xvii) Youcanfindreligionswithoutcreationism,butyouneverfindcreationismwithoutreligion.(xvii) Whyteachadiscredited,religiouslybasedtheory,evenonewidelybelieved,alongsideatheorysoobviouslytrue?It’slikeaskingthat shamanismbetaughtinmedicalschoolalongsideWesternmedicine,orastrologybepresentedinpsychologyclassasanalternative theoryofhumanbehavior.(xix) Acceptingevolutionneedn’tturnyouintoadespairingnihilistorrobyourlifeofpurposeandmeaning.Itwon’tmakeyouimmoral,or giveyouthesentimentsofaStalinorHitler.Norneeditpromoteatheism,forenlightenedreligionhasalwaysfoundawayto accommodatetheadvancesofscience.Infact,understandingevolutionshouldsurelydeepenandenrichourappreciationoftheliving worldandourplaceinit.(xx) https://vialogue.wordpress.com/2012/05/06/whyevolutionistruenotesreview/

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1.WhatIsEvolution? Acuriousaspectofthetheoryofevolutionisthateverybodythinksheunderstandsit.–JacquesMonod Inessence,themoderntheoryofevolutioniseasytograsp.itcanbesummarizedinasingle(albeitslightlylong)sentence:Lifeonearth evolvedgraduallybeginningwithoneprimitivespecies—perhapsaself‑replicatingmolecule—thatlivedmorethan3.5billionyears ago;itthenbranchedoutovertie,throwingoffmanynewanddiversespecies;andthemechanismformost(butnotall)ofevolutionary changeisnaturalselection.|Whenyoubreakthatstatementdown,youfindthatitreallyconsistsofsixcomponents:evolution, gradualism,speciation,commonancestry,naturalselection,andnonselectivemechanismsofevolutionarychange.(3) Thefirstistheideaofevolutionitself.Thissimplymeansthataspeciesundergoesgeneticchangeovertime.Thatis,overmany generationsaspeciescanevolveintosomethingquitedifferent,andthosedifferencesarebasedonchangesintheDNA,whichoriginate asmutations.(3) Thesecondpartofevolutionarytheoryistheideaofgradualism.Ittakesmanygenerationstoproduceasubstantialevolutionarychange, suchastheevolutionofbirdsfromreptiles.(4) Thenexttwotenetsareflipsidesofthesamecoin.Itisaremarkablefactthatwhiletherearemanylivingspecies,allofus—you,me,the elephant,andthepo氀฀edcactus—sharefundamentaltraits.Amongthesearethebiochemicalpathwaysthatweusetoproduceenergy, ourstandardfour‑le氀฀erDNAcode,andhowthatcodeisreadandtranslatedintoproteins.Thistellsusthateveryspeciesgoesbacktoa singlecommonancestor,anancestorwhohadthosecommontraitsandpassedthemontoitsdescendants.Butifevolutionmeantonly gradualgeneticchangewithinaspecies,we’dhaveonlyonespeciestoday—asinglehighlyevolveddescendantofthefirstspecies.Yet wehavemany:wellovertenmillionspeciesinhabitourplanettoday,andweknowofafurtherquartermillionasfossils.Lifeisdiverse. Howdoesthisdiversityarisefromoneancestralform?Thisrequiresthethirdideaofevolution:thatofspli氀฀ing,or,moreaccurately, speciation.(4‑5) …speciationsimplymeanstheevolutionofdifferentgroupsthatcan’tinterbreed—thatis,groupsthatcan’texchangegenes.(6) …speciesdon’thavetosplit.Whethertheydodepends,aswe’llsee,onwhethercircumstancesallowpopulationstoevolveenough differencesthattheyarenolongerabletointerbreed.Thevastmajorityofspecies—morethan99percentofthem—goextinctwithout leavinganydescendants.(7) …theideaofcommonancestry—thefourthtenetofDarwinism—istheflipsideofspeciation.Itsimplymeansthatwecanalwayslook backintime,usingeitherDNAsequencesorfossils,andfinddescendantsjoiningattheirancestors.(8) BysequencingtheDNAofvariousspeciesandmeasuringhowsimilarthesesequencesare,wecanreconstructtheirevolutionary relationships.(10) ThefifthpartofevolutionarytheoryiswhatDarwinclearlysawashisgreatestintellectualachievement:theideaofnaturalselection.… Selectionisbothrevolutionaryanddisturbingforthesamereason:itexplainsapparentdesigninnaturebyapurelymaterialisticprocess thatdoesn’trequirecreationorguidancebysupernaturalforces.(10‑11) Overtime,thepopulationwillgraduallybecomemoreandmoresuitedtoitsenvironmentashelpfulmutationsariseandspreadthrough thepopulation,whiledeleteriousonesareweededout.…Itrequiresonlythatindividualsofaspeciesvarygeneticallyintheirabilityto surviveandreproduceintheirenvironment.(11) Naturalselectionisnotamasterengineer,butatinkerer.Itdoesn’tproducetheabsoluteperfectionachievablebyadesignerstarting fromscratch,butmerelythebestitcandowithwhatithastoworkwith.(12) Evolutionislikeanarchitectwhocannotdesignabuildingfromscratch,butmustbuildeverynewstructurebyadaptingapreexisting building,keepingthestructurehabitableallthewhile.(13) Sonaturalselectiondoesnotyieldperfection—onlyimprovementsoverwhatcamebefore.Itproducesfi氀฀er,notthefi氀฀est.(13) Thisbringsustothelastofevolutionarytheory’ssixpoints:processesotherthannaturalselectioncancauseevolutionarychange.(13) AccordingtotheOxfordEnglishDictionary,ascientifictheoryis astatementofwhatareheldtobethegenerallaws,principles,orcausesofsomethingknownorobserved. TherearetwopointsIwanttoemphasizehere.First,inscience,atheoryismuchmorethanjustaspeculationabouthowthingsare:itisa well‑thought‑outgroupofpropositionsmeanttoexplainfactsabouttherealworld.…Foratheorytobeconsideredscientific,itmustbe testableandmakeverifiablepredictions.(15) Becauseatheoryisacceptedas“true”onlywhenitsassertionsandpredictionsaretestedoverandoveragain,andconfirmedrepeatedly, thereisnoonemomentwhenascientifictheorysuddenlybecomesascientificfact.Atheorybecomesafact(ora“truth”)whensomuch evidencehasaccumulatedinitsfavor—andthereisnodecisiveevidenceagainstit—thatvirtuallyallreasonablepeoplewillacceptit. Thisdoesnotmeanthata“true”theorywillneverbefalsified.Allscientifictruthisprovisional,subjecttomodificationinlightofnew evidence.(16)

https://vialogue.wordpress.com/2012/05/06/whyevolutionistruenotesreview/

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Intheprocessofbecomingtruths,orfacts,scientifictheoriesareusuallytestedagainstalternativetheories.(16) Sohowdowetestevolutionarytheoryagainstthestillpopularalternativeviewthatlifewascreatedandremainedunchangedthereafter? Thereareactuallytwokindsofevidence.ThefirstcomesformusingthesixtenetsofDarwinismtomaketestablepredictions.By predictions,Idon’tmeanthatDarwinismcanpredicthowthingswillevolveinthefuture.Rather,itpredictswhatweshouldfindin livingorancientspecieswhenwestudythem.(17) Sincetherearefossilremainsofancientlife,weshouldbeabletofindsomeevidenceforevolutionarychangeinthefossilrecord.The deepest(andoldest)layersofrockwouldcontinathefossilsofmoreprimitivespecies,andsomefossilsshouldbecomemorecomplex asthelayersofrockbecomeyounger,withorganismsresemblingpresent‑dayspeciesfoundinthemostrecentlayers.Andweshould beabletoseesomespecieschangingovertime,forminglineagesshowing“descentwithmodification”(adaptation) Weshouldbeabletofindsomecasesofspeciationinthefossilrecord,withonelineofdescentdividingintotwoormore.Andwe shouldbeabletofindnewspeciesforminginthewild. Weshouldbeabletofindexamplesofspeciesthatlinktogethermajorgroupssuspectedtohavecommonancestry,likebirdswith reptilesandfishwithamphibians.Moreover,these“missinglinks”(moreaptlycalled“transitionalforms”)shouldoccurinlayersof rockthatdatetothetimewhenthegroupsaresupposedtohavediverged. Weshouldexpectthatspeciesshowgeneticvariationformanytraits(otherwisetherewouldbenopossibilityofevolution happening). Imperfectionisthemarkofevolution,notofconsciousdesign.Weshouldthenbeabletofindcasesofimperfectadaptation,inwhich evolutionhasnotbeenabletoachievethesamedegreeofoptimalityaswouldacreator. Weshouldbeabletoseenaturalselectionactinginthewild. Inadditiontothesepredictions,DarwinismcanalsobesupportedbywhatIcallretrodictions:factsanddatathataren’tnecessarily predictedbythetheoryofevolutionbutmakesenseonlyinlightofthetheoryofevolution.(18) Aswe’llsee,alltheevidence—botholdandnew—leadsineluctablytotheconclusionthatevolutionistrue.(19)

2.WrittenintheRocks Thecrustoftheearthisavastmuseum;butthenaturalcollectionshavebeenmadeonlyatintervalsoftimeimmenselyremote.–CharlesDarwin, OntheOriginofSpecies Fossilshavebeenknownsinceancienttimes:Aristotlediscussedthem,andfossilsofthebeakeddinosaurProtoceratops (h氀฀p://en.wikipedia.org/wiki/Protoceratops)mayhavegivenrisetothemythologicalgriffin(h氀฀p://en.wikipedia.org/wiki/Griffin)ofthe ancientGreeks.(21) Theformationoffossilsisstraightforward,butrequiresaveryspecificsetofcircumstances.First,theremainsofananimalorplantmust findtheirwayintowater,sinktothebo氀฀om,andgetquicklycoveredbysedimentsothattheydon’tdecayorgetsca氀฀eredbyscavengers (21) Takingintoaccountalloftheserequirements,it’sclearthatthefossilrecordmustbeincomplete.Howincomplete?Thetotalnumberof speciesthateverlivedonearthhasbeenestimatedtorangebetween17million(probablyadrasticunderestimategiventhatatleast10 millionspeciesarealivetoday)and4billion.Sincewehavediscoveredaround250,000differentfossilspecies,wecanestimatethatwe havefossilevidenceofonly0.1percentto1percentofallspecies—hardlyagoodsampleofthehistoryoflife!…Nevertheless,wehave enoughfossilstogiveusagoodideaofhowevolutionproceeded,andtodiscernhowmajorgroupssplitoffformoneanother.(22)

(h氀฀ps://vialogue.files.wordpress.com/2012/05/screen‑shot‑2012‑05‑05‑at‑4‑49‑49‑pm.png) https://vialogue.wordpress.com/2012/05/06/whyevolutionistruenotesreview/

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Figure3.Thefossilrecordshowingfirstappearanceofvariousformsoflifethatarosesincetheearthformed4,600millionyearsago (MYA).Notethatmulticellularlifeoriginatedanddiversifiedonlyinthelast15percentoflife’shistory.Groupsappearonthesceneinan orderlyevolutionaryfashion,withmanyarisingafterknownfossiltransitionsfromancestors. …thefossilrecordgivesnoevidenceforthecreationistpredictionthatallspeciesappearsuddenlyandthenremainunchanged.Instead, formsoflifeappearintherecordinevolutionarysequence,andthenevolveandsplit.(32) Whatreallyexcitespeople—biologistsandpaleontologistsamongthem—aretransitionalforms:thosefossilsthatspanthegapbetween twoverydifferentkindsoflivingorganisms.(32) Showingcommonancestryoftwogroups,then,doesnotrequirethatweproducefossilsoftheprecisesinglespeciesthatwastheir commonancestor,orevenspeciesonthedirectlineofdescentfromanancestortodescendant.Rather,weneedonlyproducefossils havingthetypesoftraitsthatlinktwogroupstogether,and,importantly,wemustalsohavethedatingevidenceshowingthatthose fossilsoccurattherighttimeinthegeologicalrecord.A“transitionalspecies”isnotequivalentto“anancestralspecies”;itissimplya speciesshowingamixtureoftraitsfromorganismsthatlivedbothbeforeandafterit.935) Oneofthegreatestfulfilledpredictionsofevolutionarybiologyisthediscovery,in2004,ofatransitionalformbetweenfishand amphibians.ThisisthefossilsspeciesTiktaalikroseae(h氀฀p://tiktaalik.uchicago.edu/),whichtellsusalotabouthowvertebratescameto liveontheland.(35)[VIA:seeNOVAvideo(h氀฀p://www‑tc.pbs.org/wgbh/nova/rss/media/nova‑v‑20071109.m4v),andYourInnerFish] (h氀฀p://www.amazon.com/Your‑Inner‑Fish‑Journey‑3‑5‑Billion‑Year/dp/0307277453/ref=sr_1_1?ie=UTF8&qid=1336263162&sr=8‑1)

(h氀฀ps://vialogue.files.wordpress.com/2012/05/screen‑shot‑2012‑05‑05‑at‑5‑22‑21‑pm.png) Tiktaalikshowsthatourancestorswereflat‑headedpredatoryfishwholurkedintheshallowwatersofstreams.Itisafossilthat marvelouslyconnectsfishwithamphibians.Andequallymarvelousisthatitsdiscoverywasnotonlyanticipated,butpredictedtooccur inrocksofacertainageandinacertainplace.(38) ThefirstlinkbetweenbirdsandreptileswasactuallyknowntoDarwin,who,curiously,mentioneditonlybrieflyinlatereditionsofThe Origin,andthenonlyasanoddity.Itisperhapsthemostfamousofalltransitionalforms:thecrow‑sizedArchaeopteryxlithographica (h氀฀p://en.wikipedia.org/wiki/Archaeopteryx),discoveredinalimestonequarryinGermanyin1860.(ThenameArchaeopteryxmeans “ancientwing,”and“lithographica”comesfromtheSolnhofenlimestone,fine‑grainedenoughtomakelithographicplatesandpreserve theimpressionsofsoftfeathers.)(39‑40)

(h氀฀ps://vialogue.files.wordpress.com/2012/05/archie2.jpg) Asthesefossilsgetyounger,weseethereptiliantailshrinking,theteethdisappearing,theclawsfusingtogether,andtheappearanceofa largebreastbonetoanchortheflightmuscles.(44) Whilewemayspeculateaboutthedetails,theexistenceoftransitionalfossils—andtheevolutionofbirdsfromreptiles—isfact.Fossils likeArchaeopteryxanditslaterrelativesshowamixtureofbirdlikeandearlyreptiliantraits,andtheyoccurattherighttimeinthefossil record.Scientistspredicatedthatbirdsevolvedfromtheropoddinosaurs,and,sureenough,wefindtheropoddinosaurswithfeathers. Weseeaprogressionintimefromearlytheropodshavingthin,filamentousbodycoveringstolateroneswithdistinctfeathers,probably adeptgliders.Whatweseeinbirdevolutionistherefashioningofoldfeatures(forelimbswithfingersandthinfilamentsontheskin)into newones(fingerlesswingsandfeathers)—justasevolutionarytheorypredicts.(47)

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WhyEvolutionIsTrue|Notes&Review|vialogue

Canwefindanymammalsthatliveonbothlandandwater,thekindofcreaturethatsupposedlycouldnothaveevolved?|Easily.A goodcandidateisthehippopotamus,which,althoughcloselyrelatedtoterrestrialmammals,isaboutasaquaticasalandmammalcan get.(48) Similarly,snakeshavelongbeensupposedtohaveevolvedfromlizard‑likereptilesthatlosttheirlegs,sincereptileswithlegsappearint hefossilrecordwellbeforesnakes.(53)[VIA:See“EvolutioninGenesis”(h氀฀ps://vialogue.wordpress.com/2008/08/06/evolution‑in‑ genesis/)] Thefossilrecordteachesusthreethings.First,itspeaksloudlyandeloquentlyofevolution.Therecordintherocksconfirmsseveral predictionsofevolutionarytheory:gradualchangewithinlineages,spli氀฀ingoflineages,andtheexistenceoftransitionalformsbetween verydifferentkindsoforganisms.…Second,whenwefindtransitionalforms,theyoccurinthefossilrecordpreciselywheretheyshould …Finally,evolutionarychange,evenofamajorsort,nearlyalwaysinvolvesremodelingtheoldintothenew.(53) Thereisnoreasonwhyacelestialdesigner,fashioningorganismsfromscratchlikeanarchitectdesignsbuildings,shouldmakenew speciesbyremodelingthefeaturesofexistingones.Eachspeciescouldbeconstructedfromthegroundup.Butnaturalselectioncanact onlybychangingwhatalreadyexists.Itcan’tproducenewtraitsoutofthinair.Darwinismpredicts,then,thatnewspecieswillbe modifiedversionsofolderones.Thefossilrecordamplyconfirmsthisprediction.(54)

3.Remnants:Vestiges,Embryos,andBadDesign Nothinginbiologymakessenseexceptinthelightofevolution.–TheodosiusDobzhansky InmedievalEurope,beforetherewaspaper,manuscriptsweremadebywritingonparchmentandvellum,thinsheetsofdriedanimal skins.Becausethesewerehardtoproduce,manymedievalwriterssimplyreusedearliertextsbyscrapingofftheoldwordsandwriting onthenewlycleanedpages.Theserecycledmanuscriptsarecalledpalimpsests(h氀฀p://en.wikipedia.org/wiki/Palimpsest),fromtheGreek palimpsestos,meaning“scrapedagain.”(55) Liketheseancienttexts,organismsarepalimpsestsofhistory—evolutionaryhistory.(56) Vestiges.…afeatureofaspeciesthatwasanadaptationinitsancestors,butthathaseitherlostitsusefulnesscompletelyor,asinthe ostrich,hasbeenco‑optedfornewuses.(57)Itisvestigialnotbecauseit’sfunctionless,butbecauseitnolongerperformsthefunctionfor whichitevolved.(58) Thelongandshortofitisthis:flightismetabolicallyexpensive,usingupalotofenergythatcouldotherwisebedivertedtoreproduction. (59) Inotherwords,ourappendixissimplytheremnantofanorganthatwascriticallyimportanttoourleaf‑eatingancestors,butofnoreal valuetous.(61) Wehaveavestigialtail:thecoccyx…(62) …vestigialtraitsmakesenseonlyinthelightofevolution.(64) Atavisms.Occasionallyanindividualcropsupwithananomalythatlookslikethereappearanceofanancestraltrait.Ahorsecanbeborn withextratoes,ahumanbabywithatail.Thesesporadicallyexpressedremnantsofancestralfeaturesarecalledatavisms,fromtheLatin atavus,or“ancestor.”Theydifferfromvestigialtraitsbecausetheyoccuronlyoccasionallyratherthanineveryindividual.(64) Themoststrikingatavisminourownspeciesiscalledthe“coccygealprojection,”be氀฀erknownasthehumantail.(65)

(h氀฀ps://vialogue.files.wordpress.com/2012/05/tail05.jpg) DeadGenes.Weexpecttofind,inthegenomesofmanyspecies,silenced,or“dead,”genes:genesthatoncewereusefulbutarenolonger intactorexpressed.Inotherwords,thereshouldbevestigialgenes.(67)Outofaboutthirtythousandgenes,forexample,wehumans carrymorethantwothousandpseudogenes.(67) Adeadgeneinonespeciesthatisactiveinitsrelativesisevidenceforevolution,butthere’smore.WhenyoulookatψGLOinliving primates,youfindoutthatitssequenceismoresimilarbetweencloserelativesthanbetweenmoredistantones.(68) Whydoesn’tnaturalselectionel...