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MereTheisticEvolutionCannotBe(andNeverWas)MereAResponsetoJohnChurchillandMichaelMurray

PaulA.Nelson

DiscoveryInstituteandBiolaUniversity

ABSTRACT:Churchill andMurray (2019) criticizemy chapter on common descent inTheisticEvolution(2017)forwhattheyargueisitsillicitextensionofdoubtsaboutuniversalcommon descent (UCD) to the theory of evolution itself. This criticism isgroundless. I takepains todistinguishUCDfrom“evolution,”becausethe latter isdefined in 2019 not by a univocal or canonical scientific theory, but by aphilosophical boundary, namely, naturalism (whether philosophical ormethodologicalisirrelevant). “Evolution”inthissensesurvivesempiricalcritique.It isaparadigmaticcommitment toaparticular formofcausalexplanation,not toanybiologicaltheory.I.ACriticismReadilyDispatched–YettheDeeperPuzzleBehindIt..............1II.BackintheDay,“Evolution”MeantSomething.................................3III.Non-OrthologousGeneDisplacementasaCaseStudy..........................6IV.Naturalism,MethodologicalorOtherwise,GuaranteesEvolution’sSurvival....10References&Appendix..........................................................13

“WithoutGod.WeareexcludingGod.”

BiologistEvaJablonkaofTelAvivUniversity,attheNovember2016RoyalSocietymeetingonrevisingtheNeo-DarwinianSynthesisi

I.ACriticismReadilyDispatched–YettheDeeperPuzzleBehindItIntheirreviewofTheisticEvolution:AScientific,Philosophical,andTheologicalCritique[abbreviatedSPTC],JohnChurchillandMichaelMurray(hereafter,C&M)arguethatmychapter,“FiveQuestionsEveryoneShouldAskAboutCommoniWhiletheaudiorecordingrevealsscatteredlaughter,italsorevealsthatnooneattheRoyalSocietymeetingchallengedthisstatement.Jablonka’sremarkoccurredduringtheroundtablediscussionontheafternoonofTuesday,8November2016.ShehadaskedevolutionarybiologistDouglasFutuyma,oneoftheplenaryspeakers,whathewouldconsiderabonafide,ratherthanonlycosmetic,revisionofneo-Darwiniantheory.Jablonka’squestionbeginsat29:39ofthisRoyalSocietymp3file,withthe“WeareexcludingGod”remarkoccurringat30:29:http://downloads.royalsociety.org/events/2016/11/evolutionary-biology/panel-tues.mp3

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Descent,”misrepresentedthestatusoftheisticevolution,bylinkingdoubtsaboutthetheoryofuniversalcommondescent(UCD)totheconceptofevolutionitself.C&Mwrite:

Itisfairtoconcludefromthis,asPaulA.Nelsondoes...that“thetheoryofcommonancestryisintrouble;possiblyveryserioustrouble,fromwhichitmayneverescape.”Butdoesthismeanthatevolutionarytheoryortheisticevolutionisintrouble,asisalsoimpliedinNelson’schapter?Notatall.Evolutionarybiologistswereinfactquitekeentoadoptthisinsight,andtorevisetheirunderstandingofthenaturalprocessesthatgovernedthedevelopmentofearlylifeonourplanet.Thekeydiscoverydidnotunderminetheevolutionaryaccountoflifebutratherprovidedanevidence-drivensupplementtoit....Thelessonhereisthatinsomecases,theargumentsinSPTCthatattempttoprovidescientificevidenceagainstevolutionortheisticevolutionmisstheirmark.Doubtlessitistruethatsomeofthesescientificfindingsshowthatearlieraccountsofevolutionwereincorrect.Butratherthanunderminingthetheory,theyprovideusefulcomplementstoit.(emphasisadded)

Thiscriticismisreadilydispatched.MychapteronUCDcarefullydistinguishedUCDfromevolutionitself,inawaywhichnoattentivereadercouldmiss.(SeetheAppendixforfullcitations.)Iexplainedinthechapter’sintroductionthatevolutionarybiologistswhohaveabandonedUCDhavenotabandonedthemoregeneralthesisofevolution,orturnedtointelligentdesign(ID).Toensurethatthisimportantdistinctionwasnotoverlooked,IincludedadiagramfromthehistorianofbiologyPeterBowler,depictingthepolyphyleticgeometrysuggestedbyLamarck’sevolutionaryideas.iiIalsoincludedatableshowingafour-quadrantmatrixofscientificopinion,whereleadingevolutionarybiologistslandedonbothsidesoftheUCDversus~UCDquestion.(Again,seetheAppendix.)C&MclaimthatIimpliedevolutionwas“introuble”becauseofthechangingfortunesofUCD.Thepagestheycite,however,406and421,donotsupporttheirclaim,nordotheyquotemedirectly.MaybeduringourdiscussiononNovember20theycanexplain,withspecificquotationsfromchapter12,whereIsaidthatdoubtsaboutUCDentailedskepticismaboutevolutionitself.“Butsurely,”thereadermaybewondering,“NelsonmustthinkthatcastingdoubtonUCDalsocastssomedoubtontheisticevolution?”Otherwise,whyincludethe“FiveQuestions”chapterintheSPTCvolume?

iiPolyphyly(adj.polyphyletic;Gk:“multiplebranches”ororigins)yieldsthecontrastclasstomonophyly(adj.monophyletic;Gk:“singlebranch”ororigin).Darwin’s(1859)TreeofLifeismonophyletic,asistheneo-Darwiniangeometryofuniversalcommondescent(UCD);otherevolutionarygeometries,suchasLamarck’s,orHaeckel’s,arepolyphyletic.

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Funnyyoushouldask.There’sanimportantbackstorythatneedstelling,whichIlackedthespacetotreatinSPTC.Hereistheshortversion:Theempiricalcontentof“evolution”hasshiftedsoradicallyoverthepastfivedecadesthatthetermnowlargelymeans“theoriginanddiversificationoflivingthingsbyanycauseotherthanintelligentdesign”(ID).Thus,doubtsaboutUCDdonotentailtherejectionofevolutionitself,becauseevolutioncanmeanalmostanything–except,ofcourse,ID.Onthisview,evolutionisnotsomuchascientifictheoryasitisaphilosophicalcommitmenttotellinganaturalisticstoryaboutorigins.AndthatiswhyIdidnottrytoargueinthe“FiveQuestions”chapteragainstevolutionsimpliciter.Rather,IexplainedhownewlinesofevidencehaveraiseddoubtsaboutUCD,whichrepresentsonlyoneofmanypossibleevolutionarytopologiesorgeometriesforlifeonEarth.UCDisthemostwidely-acceptedsuchgeometrytoday,butevenifUCDshouldtopple,evolutionitselfwouldremainstanding.ThatiswhythoseevolutionarybiologistswhohavejettisonedUCDcanremainfirmlycommittedtothemoregeneralevolutionaryproject.Theyarecommitted,however,nottoaspecificscientifictheory,buttoananswerofaparticularphilosophicalkind.“Nevermindaboutphilosophyrightnow,”objectsthereader.“Ifevolution,howeverweconceiveit,remainsstanding,isn’tthatpreciselyC&M’spoint?–namely,thatevolutionhappilyaccommodatesnewdata,withbiologistsrevisingandexpandingthetheoryasbiologicalknowledgegrows?”Timeforthelongerversionofthebackstory.Here’sapreview:ContraC&M,itisnotastrengthofevolutionasascientifictheory(althoughthismovemaysustaintheideaindefinitelyasaphilosophicalposition)that,whenitscorepropositionsarecontradictedbynewfindings,thetheoryembracesthosefindings,whileatthesametimetossingtheerstwhilecorepropositionsoverthestarboardrailingoftheship.Thatisaproblemforevolution–andhardlyasmallone.Weshouldconsidertheempiricaldetailsnext.II.BackintheDay,“Evolution”MeantSomethingIn1985,evolutionarygeneticistFranciscoAyala(whoin1995wastobecomethepresidentoftheAAAS)publishedanarticleonwhathecalledthe“fact”ofevolution(Ayala1985).Undertheheadingof“evolutionasfact,”Ayalasaidthatthesingleproposition“mostfundamental”and“mostdefinitelycorroboratedbyscience,”undergirdingthetheory’sfactualstanding,wasthecommonancestryofalllifeonEarth.Thisisthegeometryofhistoricalrelatedness,Darwin’sTreeofLife,

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designatedaboveasuniversalcommondescent,orUCD.Thistheory,Ayala(1985,59-60)continued,

isascientificconclusionestablishedwithacertaintysimilartothatofnotionssuchastheroundnessoftheearth,themotionsoftheplanets,andthemolecularcompositionofmatter.Thisdegreeofcertaintybeyondreasonabledoubtiswhatisimpliedbyscientistswhentheysaythattheevolutionoforganismsisa“fact.”

Sixyearslater,NationalAcademyofSciencesmolecularbiologistRussellDoolittlewrotethat"itiswidelyacceptedthatalllifeonEarthtodayisdescendedfromacommonancestralcellularorganismthatexistedsometimebetween1.5and3.0billionyearsago”(1991,165)–i.e.,UCD,ortheTreeofLife,rootedintheLastUniversalCommonAncestor(LUCA).ThiscanonicalstandingofUCD,“beyondreasonabledoubt,”canbeseeninanybiologytextbookfromthe1960stotheearly1990s.Itremainsthedefaultpositionofmostworkingbiologiststoday.CentraltothecanonicalepistemicstandingofUCDduringthisperiodwastheapparentuniversalconservationofthekeymolecularfeaturesoflife:DNA,RNA,proteinsassembledfromthesamesetof20[now22]aminoacids,theuniversalgeneticcode,theribosome,andsoon.“Ifthereisaunityoflifebasedonevolution[i.e.,UCD],”arguedevolutionarybiologistJohnMoore(1984,509),“thatshouldbereflectedinthemolecularprocessesoforganisms.”Let’scallthisacorepropositionofevolutioninthe20thcentury.Theexplanatoryrationalefortheexpectationofuniversalmolecularconservationwasfunctional.Oncethesebasiccellularfeatureswereinventedbywhatevernaturalprocessescausedthem,andestablishedinLUCA,organismswouldnottoleratetheirmodification–lethalitybeingtheinevitableconsequenceofanymodification.Therecouldbenocrossing(orsoitwaswidelyheld)sucha“‘DeathValley’intheadaptivelandscape”(Lehman2001,R63).Hence,theobserveduniversalityofthosekeyfeaturestoday.

Consider,forinstance,theapparentuniversality–circatheearly1980s–ofthegeneticcode.AsJamesWatsonetal.(1987,453)expressedthepoint,

Considerwhatmighthappenifamutationchangedthegeneticcode.Suchamutationmight,forexample,alterthesequenceoftheserinetRNAmoleculeoftheclassthatcorrespondstoUCU,causingthemtorecognizeUUUsequencesinstead.ThiswouldbealethalmutationinhaploidcellscontainingonlyonegenedirectingtheproductionoftRNAser,forserinewouldnotbeinsertedintomanyofitsnormalpositionsinproteins.Evenifthereweremorethanonegene...thistypeofmutationwouldstillbelethal,sinceitwouldcausethesimultaneousreplacementofmanyphenylalanineresiduesbyserineincellproteins.

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Thefollowingschemacapturesthelogicalstructureofthisargument,which,again,wecancallacoreproposition:

(1)Evolution⊃ UCD+thecodecannotvary! universalgeneticcodeiii Now,ifyouarereadingthisonline,clickonthislinkattheNationalCenterforBiotechnologyInformation:

https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi

Hereiswhatyouwillfindthere,ifyouarenotonline:

Everyyear,thislistofvariantornon-universalgeneticcodesgrowslonger.Butwhataboutourcoreproposition,(1),above?–which,untilrecently,couldbefoundinnearlyanybiologytextbook,startingfromthelate1960s.(Theuniversalityofthecodewaspredictedin1963,inthejournalScience,byRalphHinegardnerandJosephEngelberg.Theyusedschemaorproposition[1].)Itseemsproposition(1)needssomeadjusting:(2)Evolution⊃UCD+guesswhat,thecodedoesvary→variantgeneticcodesWithaminortweakwehave“savedthephenomena.”Eraseproposition(1);wewillrevisethosetextbooks,andincorporateproposition(2).

iiiReadthe“⊃”symbolasmaterialimplication:if,then.

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“Listen,Paul,”thereaderobjects,“thishappensallthetimewithmaturescientifictheories.Newfindingsmaychallengetheirauxiliaryhypotheses,suchas–inthisinstance–thenecessaryfunctionalinvarianceofthegeneticcode.Nevertheless,thecorepropositions,suchasUCD,orevolutionitself,stillhold.”Well,yes:evolutionstillholds.AsIhavebeenarguing,however,thatisdecidedlynotagoodoutcomeforevolution,ifwewishtoseeitasascientifictheory,ratherthanaphilosophicalcommitment.SoweshouldconsidernextwhymanyleadingevolutionarybiologistshavenowdumpedUCD–onecannot,afterall,findamorecorepropositionthanUCD–toseeifevolutionitselfwaseverthreatened.Theanswerisno.III.Non-OrthologousGeneDisplacement(NOGD)asaCaseStudy

Rollthetapeaheadto2007,andamajorpaperbyNationalAcademyofSciencesmoleculargeneticistandNCBIlabdirectorEugeneKoonin:

...itisgenerallyassumedthat,inprinciple,theTOL[TreeofLife,UCD]existsandisresolvable...Here,Iargueforafundamentallydifferentsolution,i.e.,thatasingle,uninterruptedTOLdoesnotexist,althoughtheevolutionoflargedivisionsoflifeforextendedtimeintervalscanbeadequatelydescribedbytrees.Isuggestthatevolutionarytransitionsfollowageneralprinciplethatisdistinctfromtheregularcladogenesis[evolutionarybranching].IdenotethisprincipletheBiologicalBigBang(BBB)Model.(2007,3;emphasisinoriginal)

Whathappened?Evolution’scorepropositionofuniversalcommondescent,whichAyala(1985)saidwasasindubitableas“theroundnessoftheearth,”isbeingjettisoned.OvertherailinggoesUCD,intothewater.Why?

Whathappenedwasthebirthofanewmethodofmoleculardatagatheringinbiology,ashistoricallyimportanttothatscience,itturnsout,astheinventionofthetelescopewastoastronomy.Fromstagerightinthemid-1990s,rapidandincreasinglyinexpensiveDNAsequencingenteredbiology,andquicklybecameawidely-usedresearchtechnology.Forthefirsttime,biologistscouldsurveyvastlymore,andinmanycases,genomicallycompleteDNAsequencesfromamultitudeofspecies.Before1995,molecularcomparisonsamongspecies,basedonsinglegeneorproteinsequences,wereakintotryingtomaptheentiretyofNewYorkCitybymeasuring10inchesofcurbinBrooklynandManhattan,afootortwoinStatenIsland,andanothersmallsectionofcurbstoneinQueensandtheBronx.

Inbrief,wholegenomeDNAsequencinghasoverturnedthegenetic“unityoflife”describedbyMoore(1984)andprominentinbiologytextbooksforthelastfiftyyears.Oneremarkablefindinginthisrespecthasbeentermed“non-orthologousgenedisplacement”(NOGD),anawkwardphrasewhichmeanssimplythatthe

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expectedconservation(orthology)ofgenesandproteins,whenassessedacrosstheTreeofLife,andaspredictedbyuniversalcommondescent,isnotobserved.Rather,inthecentralinformation-processingandmetabolicpathwaysinferredtohavebeenpresentinLUCA,different(non-orthologous)genesandtheirproteinproductshave“displaced”whatbiologistsexpectedtofind.

Table1andFigure1show(respectively)soberbiologicalversushomespunanalogicalrepresentationsofNOGD.ConsideranespeciallystrikingexampleofNOGD:themolecularstructureofreleasefactor,anessentialplayerinproteinassemblywithintheribosome.Ribosomesareunquestionablythemostfundamentalmolecularmachineinanyfree-livingcell(virusesaredefinedbylackingribosomes),thelocusofactionforturningDNAsequenceinformation,viamessengerRNA(mRNA),intofunctioningproteins.Ifyouareacell,oracollectionofcells,onEarth,youmusthaveribosomes.

Table1.Examplesofnon-orthologousgenedisplacement(Koonin2012,70)

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Figure1.“Non-orthologous”automobileenginesatacarshow:keyoperatingcomponentsdifferfundamentally.

DuringtranslationofmRNAintheribosome,mostcodonsarerecognizedby"charged"transferRNA(tRNA)molecules,calledaminoacyl-tRNAsbecausetheyconnecttospecificaminoacidscorrespondingtoeachtRNA'santicodon,thethree-nucleotidesignalonthemRNA-bindingstemofthetRNA.But“stop,”orterminationcodons,arehandleddifferently.Intheso-called“universal”geneticcode,therearethreemRNAstopcodons:UAG,UAA,andUGA.Whilethesestopcodonsrepresenttriplets,likeordinaryamino-acidspecifyingcodons,tRNAsdonotdecodethem.Instead,in1967,MarioCapecchifoundthattRNAsdonotrecognizestopcodonsatall.ivRather,proteinshenamed"releasefactors"performedthattask.

Briefly,whentheribosome,movingalonganmRNAstrand,arrivesatastopcodon,releasefactorenterstheribosomeandhydrolyzes(cuts)thechemicalbondholdingthelastaminoacidinthenewly-synthesizedproteintoitscorrespondingtRNA.This“releases”thenascentproteintoexitthelargesubunitoftheribosome,andfold–hence,thenameforthefamilyofproteinsperformingthisessentialtask.

Now,mini-thoughtexperiment.IfLUCAexisted,andpossessedaDNAgenome,ribosomes,andreleasefactors–andifthesefeatureswerefunctionallyessentialwithinLUCA,andthereforeinheritedbyallitsdescendants–whatshouldoneexpecttofind,whensurveyingtheproteinfolds(three-dimensionalstructures)ofreleasefactorsacrosstheTreeofLife?Inotherwords:assumeUCD,couplethatmonophyleticgeometrytoourknowledgeofribosomalfunction,andmakeaprediction.ivExcepttheydo–ifthespeciesinquestion,suchastheciliatedprotozoanTetrahymena,carriesavariantgeneticcode.Tetrahymenapossessesasinglestop(UGA)andassignsUAAandUAG,stopsintheuniversalcode,totheaminoacidglutamine.In1967,however,thesediscoverieslaymorethan20yearsinthefuture.

A B C C D E G X

A M

The essential parts of these engines are

not the same.

C

B

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Figure2depictsthethree-dimensionalstructureofreleasefactorfromthebacteriumEscherichiacoli(domainBacteria;Vestergaardetal.2001):

Figure2.CrystalstructureofE.colireleasefactor.Figure3isthethree-dimensionalstructureofreleasefactorinHomosapiens(domainEukarya;Frolovaetal.2000)

Figure3:CrystalstructureofH.sapiensreleasefactor.Thesearenotthesameproteins.Theyarenon-orthologous:rotatethemasyoulike,theirthree-dimensionalstructuresremaintopologicallyincongruent.Althoughthereleasefactorsperformthesamefunctionaltaskintheribosome,theydifferatthemolecularlevel,inthesamewayabutterfly’swingdiffersfromabird’swingattheanatomicallevel:totalabsenceofhomology.ThisraiseswhatBaranovetal.(2006,7)call“severalunsolvedpuzzles”:

Sincethereisnostrongevidenceforanevolutionaryrelationshipbetweenbacterialclass-IRFs[releasefactors]andtheircounterpartsfromarchaeaandeukaryotes,itisunknownhowterminationwasmediatedinthelastcommonancestor.

Assuming,thatis,thattherewasalastuniversalcommonancestor(LUCA).Foragrowingcadreofevolutionarybiologists,thewideextentofNOGD,whenaddedtoothermolecularanomaliesrevealedbywhole-genomesequencing,renderthehypotheticalconstructofLUCAaproblematicalornon-existententity,which

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historicalbiologyisbetteroffwithout.Themolecularunityoflife,LUCA’soriginalclaimtofame,hasbeenerodedawaybyunanticipatedgeneticfindings:

Asthegenomedatabasegrows,itisbecomingclearthatNOGDreachesacrossmostofthefunctionalsystemsandpathwayssuchthatthereareveryfewfunctionsthataretruly“monomorphic”,i.e.representedbygenesfromthesameorthologouslineageinallorganismsthatareendowedwiththesefunctions.Accordingly,theuniversalcoreoflifehasshrunkalmosttothepointofvanishing.(Koonin2016,417)

Tobesure,UCDandtherealexistenceofLUCAremainthedefaultpositionformostworkingbiologists,iffornootherreasonthandisciplinaryinertia,orbecausetheydonotbothertothinkaboutthelarge-scalecomparativequestionsthatmotivatethegrowingcommunityofUCDskeptics,suchasthelateCarlWoese,EugeneKoonin,W.FordDoolittle,DidierRaoult,EricBapteste,ortheotherleadingevolutionarybiologistsdiscussedinthe“FiveQuestions”chapterofSPTC.ButnoonetodaywouldpublishaclaimaboutUCDsuchasAyala’s1985pronouncementofitsfactualcertitudeakintotheroundnessoftheEarth.Instead,eachnewgenomesequencedchipsawayatUCDandLUCA,inexorably.Nonetheless–evolutionsurvives.IV.Naturalism,MethodologicalorOtherwise,GuaranteesEvolution’sSurvival

Faust: Tellmewhomadetheworld.Mephistopheles: Iwillnot.Faust: SweetMephistopheles,tellme.Mephistopheles: Movemenot,forIwillnottellthee.Faust: Villain,haveInotboundtheetotellmeanything?Mephistopheles: Ay,thatisnotagainstourkingdom;butthisis.

ChristopherMarlowe,TheTragicalHistoryofDoctorFaustus

ToparaphrasethewriterofHebrews11:32,“timewouldfailme”ifIrecitedthemanyaspects–thecorepropositions–oftextbookneo-Darwiniantheorythathavebeenoverturnedorcastintodoubtwithinthelastfewdecades.Thecollapseofreceiveddefinitionsofhomology,theabandonmentofthestandardcausalroleofrandomvariationandnaturalselection,proposalsfornon-geneticformsofinheritance,radicallychangingfamilytreesofanimalrelationships:the17sciencecritiquechaptersofSPTCprovideanintroductiontotheevidence.FortheSPTCauthors,thesecontroversies,andtheirreversibletolltheyhavetakenontheexplanatoryadequacyofneo-Darwiniantheory,providemorethansufficientgroundstoabandonevolutioninsearchofsomethingbetter.YetattendeesattheNovember2016RoyalSocietygatheringtoamendneo-Darwiniantheory(includingseveraloftheSPTCauthors)couldnothavemissedthe

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factthatnointelligentdesigntheorists,fromtheUnitedStates,theUnitedKingdom,Europe,orBrazil–alllocationswhereIDisactivelybeingdeveloped–wereinvitedtospeak.Andthatfactbringsustothedeepestissue:naturalism.“OfcourseIDpeopleweren’tinvited,”thereadermaybesaying.“They’renotintherightclub.Orlet’scallitthe‘relevantacademiccommunity’or‘socialcontextofdiscourse’or‘disciplinarymatrix’orwhatever.”Todescribetherelevantcommunity–withinwhichonemaypursueevolutionarytheory,evenwhilerejectingcorepropositionssuchasUCDornaturalselection,yetoutsideofwhichoneispursuingsomethingelse–wewillneedadefinition.C&Mprovideitintheirdiscussionpaper:Wedonotandcannotknow,asamatterofvalidempiricalinference,thatbiologicaldesign–meaningthedetectableactionwithinspaceandtimeofatranscendentintelligence–hasoccurred.vAnysuchproposition(i.e.,thepositiveinferenceofdivinedesignasanempiricalmatter)doesnotfallwithinnaturalscienceproper.IDtheoristsbydefinitionsayotherwise:designisdetectableasanempiricalfinding.Itisanear-certitudethattheRoyalSocietymeetingorganizers,toaperson,agreewithC&M.Whateverelseonewantstocallit,therefore,IDisnotscience.Sonooneshouldbesurprisedthat,from7to9November2016,thespeaker’spodiuminLondonlackedevenoneIDtheorist.C&Maffirmthatwemayknowdesigninallsortsofotherways,andindeedsaythattheirunderstandingof“meretheisticevolution”doesnotrequiremethodologicalnaturalism(MN).Butonecanholdtoarequirementinpracticeevenwhilenotaffirmingitexplicitly.NothinginC&M’spaperindicatesthattheythinkbiologicaldesignisempiricallydetectable.ThisisMNinpractice,ifnotinname.Venndiagramsclarifyreasoning.Figure4belowillustratestheregulativeroleofnaturalism(methodologicalorotherwise)insettingtheboundariesofdiscoursefor“evolution,”suchthatIDfallsoutsidethoseboundaries.SeveralofthecircleswithinthedomainofnaturalismwererepresentedonthepodiumattheRoyalSocietymeeting,andlatersuchgatherings,suchastheApril2019EvolutionEvolvingconferenceatCambridgeUniversity.Eachofthecirclesfindsregularpublicationinmainstreambiologyjournals.Theseideas,whetheroneendorsesthemornot,represent“science”in2019.

vC&Mdon’tsaythis,atleastnotasplainlyasIhave.Theydon’thaveto,however.Thewholethrustoftheirargumentpresupposesthepoint.Ifweknowbiologicaldesign,C&Mconsistentlyargue,weknowitviameansormethodsotherthaninferencefrombiologicalobservation.IfmybluntformulationdoesnotfitwithC&M’sunderstandingof“meretheisticevolution,”Iinvitecorrection.

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Figure4.Alternativeevolutionarytheorieswithinthedomainofnaturalism;IDliesoutsidethesamedomain.NowwhatmakesFigure4particularlypoignantistheisticevolutionitself.Ididnotsupplyacircle,orabox,fortheisticevolution,becauseIwanttoaskC&Mwheretheywouldplaceit.Thereadershouldtrythesamethoughtexperiment.WhywerenotheisticevolutionistsadvocatingforthatideaonthepodiumattheRoyalSociety?WhywerenotheisticevolutionistsspeakingupfortheisticevolutionattheApril2019EvolutionEvolvingmeetingatCambridgeUniversity?(Atleastonewasaplenaryspeakerandservedontheprogramcommittee,butthispersondidnotdefendorexplaintheisticevolutionintheirlecture.)Whywillnomainstreambiologyjournalpublishaprimaryresearchpaperdefendingorarticulatingtheisticevolution?Whydotheisticevolutionists,ontheirCVs,carefullydistinguish(i.e.,listseparately)theirsciencepublicationsfromtheirpublicationsabouttheisticevolution?Whycouldnobiologygraduatestudent,atanymajoruniversity,winapprovalforadoctoraldissertationproposalexploringtheisticevolutionasabiologicaltheory?Hereiswhy:Wedonotandcannotknow,asamatterofvalidempiricalinference,thatbiologicaldesign–meaningthedetectableactionwithinspaceandtimeofatranscendentintelligence–hasoccurred.Remove“theistic”from“theisticevolution,”andyoucanclimbinsidethebox.Attachthatadjective,however,andgiveitanydetectablecontentofitsown–outoftheboxyougo.Evolutionsurvives,despiteitsradicallychangingformasascientific

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theory,becausenaturalismsetstheboundaries.Thisisnot,andneverhasbeen,adifficultpuzzle.viReferencesAyala,F.J.1985.TheTheoryofEvolution:RecentSuccessesandChallenges.InErnanMcMullin,ed.,CreationandEvolution.NotreDame,IN:NotreDameUniversityPress.Baranov,Paveletal.2006.Diversebacterialgenomesencodeanoperonoftwogenes,oneofwhichisanunusualclass-IreleasefactorthatpotentiallyrecognizesatypicalmRNAsignalsotherthannormalstopcodons.BiologyDirect1:28.Brown,HaroldI.1979.Perception,Theory,andCommitment.Chicago:UniversityofChicagoPress.Doolittle,Russell.1991.NewPerspectivesonEvolutionProvidedbyProteinSequences.InNewPerspectivesonEvolution,eds.L.WarrenandH.Koprowski(TheWistarSymposiumSeriesVol.4),NewYork:Wiley-Liss;pp.165-173.Frolova,Ludmilaetal.2000.Translationterminationineukaryotes:PolypeptidereleasefactoreRF1iscomposedoffunctionallyandstructurallydistinctdomains.RNA6:381-90.Hinegardner,RalphandJosephEngelberg.1963.RationaleforaUniversalGeneticCode.Science142:1083-85.viAsizablephilosophicalliteratureexistsontheregulativeroleofwhatHaroldBrown(1979,105)calls“paradigmaticpropositions.” NaturalismasIhavedefineditplaysjustsuchaboundary-settingroleinthedebatesovertheisticevolutionandID.Thenaturalisticdictumisnotsomethingwehavelearnedfromobservation,butratherdetermineswhatwillcountasanobservation,aknowncause,anexplanation,oravalidinference.“[S]uchpropositions,”writesBrown,“arenotordinaryempiricalpropositions,exactlybecausetheyareprotectedfromstraightforwardempiricalrefutation.IwillborrowatermfromKuhnandrefertopropositionswhichexpresspresuppositionsandwhichareneitheranalytic,norempiricalintheusualsense,noreternaltruths,asparadigmaticpropositions.Theyconstituteanepistemicallydistinctclassinthattheydonotfitthetraditionaldivisionofallproposition[s]intoaprioriandempirical.Rather,theyarepropositionswhichareacceptedasaresultofscientificexperiencebutwhichcometohaveaconstitutiveroleinthestructureofscientificthought.Atvarioustimespropositionssuchasthatallcelestialmotionsarecircular,thatphysicalspaceisEuclidean,thateveryeventhasacause,ortheentirepanoplyofmodernconservationprincipleshasachievedthisstatus.”

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Koonin,Eugene.2007.TheBiologicalBigBangModelforthemajortransitionsinevolution.BiologyDirect2:21.Koonin,Eugene.2016.EvolutionoftheGenomicUniverse.InV.L.Korogodinaetal.,eds.,Genetics,EvolutionandRadiation.Basel:SpringerInternational,pp.413-40.Lehman,Niles.2001.Molecularevolution:Pleasereleaseme,geneticcode.CurrentBiology11:R63-R66.Moore,John.1984.ScienceasaWayofKnowing–EvolutionaryBiology.AmericanZoologist24:467-534.

Vestergaard,Benteetal.2001.BacterialPolypeptideReleaseFactorRF2IsStructurallyDistinctfromEukaryoticeRF1.MolecularCell8:1375-82.

Watson,James,NancyHopkins,JeffreyRoberts,JoanSteitz,andAlanWeiner.1987.MolecularBiologyoftheGene,4thed.MenloPark,CA:Benjamin/Cummings.

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AppendixBelowareexactreproductionsfromSPTCoftherelevantsectionsofchapter12,“FiveQuestionsEveryoneShouldAskAboutCommonDescent,”wherethedistinctionbetweenthetheoryofuniversalcommondescent(UCD)and“evolution”itselfismadeexplicit.FromtheIntroduction,page407:

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FromtheIntroduction,page408:

FromtheIntroduction,page410: