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PROCEEDINGSOFTHEBIOLOGICALSOCIETYOFWASHINGTON 117(2):213-239.2004. The originofbiologicalinformationandthe highertaxonomiccategories StephenC.Meyer PalmBeachAtlanticUniversity,901S.FlaglerDr,WestPalmBeach,Florida33401 e-mail:[email protected] Introduction haveprovenadequateformappingandun- derstanding quantitative variability and InarecentvolumeoftheViennaSeries populational changes in organisms. Yet in Theoretical Biology (2003), Gerd B. MiillerandNewmaninsistthatpopulation MiillerandStuartNewmanarguethatwhat genetics,andthusevolutionarybiology,has they call the "origination of organismal not identified a specifically causal expla- form" remains an unsolved problem. In nationfortheoriginoftruemorphological making this claim, Miiller and Newman novelty during the history oflife. Central (2003:3-10)distinguishtwodistinctissues, totheirconcerniswhattheyseeasthein- namely, (1)thecausesofformgeneration adequacy ofthe variationofgenetic traits intheindividualorganismduringembryo- asasourceofnewformandstructure.They logicaldevelopmentand(2)thecausesre- note, following Darwin himself, that the sponsible for the production ofnovel or- sourcesofnewformandstructuremustpre- ganismalformsinthefirstplaceduringthe ce—detheactionofnatural selection(2003: historyoflife.Todistinguishthelattercase 3) thatselectionmustactonwhatalready (phylogeny) from the former (ontogeny), exists.Yet,intheirview,the"genocentric- Miillerand Newman usetheterm "origi- ity"and"incrementalism"oftheneo-Dar- nation"todesignatethecausalprocessesby winianmechanismhasmeantthatanade- whichbiologicalformfirstaroseduringthe quatesourceofnewformandstructurehas evolutionoflife.Theyinsistthat"themo- yettobeidentifiedbytheoreticalbiologists. lecularmechanismsthatbringaboutbiolog- Instead,MiillerandNewmanseetheneed ical form in modem day embryos should to identify epigenetic sources ofmorpho- notbe confused" with the causes respon- logical innovation during the evolution of sible for the origin (or "origination") of life. Inthemeantime,however,theyinsist novelbiologicalformsduringthehistoryof neo-Darwinism lacks any "theory of the life(p.3).Theyfurtherarguethatweknow generative" (p.7). moreaboutthecausesofontogenesis,due Asithappens, MiillerandNewman are toadvancesinmolecularbiology,molecu- notaloneinthisjudgment. Inthelastde- lar genetics and developmental biology, cade or so ahostofscientific essays and than—wedoaboutthecausesofphylogen- books have questionedthe efficacy ofse- esis the ultimate origination ofnewbio- lection and mutation as a mechanism for logicalformsduringtheremotepast. generatingmorphological novelty, aseven In makingthis claim, MiillerandNew- a brief literature survey will establish. manarecarefultoaffirmthatevolutionary Thomson (1992:107) expresseddoubtthat biology has succeeded in explaining how large-scale morphological changes could pre-existingformsdiversifyunderthetwin accumulate via minorphenotypic changes influencesofnaturalselectionandvariation at the population genetic level. Miklos ofgenetic traits. Sophisticatedmathemati- (1993:29)arguedthatneo-Darwinismfails cally-based models ofpopulation genetics to provide amechanismthatcan produce PROCEEDINGSOFTHEBIOLOGICALSOCIETYOFWASHINGTON large-scale innovations in form and com- corresponding emergence of higher taxa) plexity. Gilbert et al. (1996) attempted to from a particular theoretical standpoint. develop a new theory of evolutionary Specifically,itwilltreattheproblemofthe mechanisms to supplement classical neo- originationofthehighertaxonomicgroups Darwinism,which, theyargued,couldnot as a manifestation of a deeper problem, adequatelyexplainmacroevolution.Asthey namely, the problem ofthe origin ofthe putitinamemorablesummaryofthesit- information(whethergeneticorepigenetic) uation: "starting inthe 1970s, manybiol- that, as it will be argued, is necessary to ogists began questioning its [neo-Darwin- generatemorphologicalnovelty. ism's] adequacy in explaining evolution. Inordertoperformthisanalysis,andto Geneticsmightbeadequateforexplaining make itrelevantandtractableto systema- microevolution, but microevolutionary tistsandpaleontologists,thispaperwillex- changesingenefrequencywerenotseenas amineaparadigmaticexampleoftheorigin abletoturnareptileintoamammalorto ofbiologicalform andinformationduring convertafishintoanamphibian.Microevo- thehistoryoflife:theCambrianexplosion. lutionlooksatadaptationsthatconcernthe During the Cambrian, many novel animal survivalofthefittest,notthearrivalofthe forms and body plans (representing new fittest.AsGoodwi—n(1995)pointsout,—'the phyla, sub-phyla and classes) arose in a origin of species Darwin's problem re- geologicallybriefperiodoftime. Thefol- mainsunsolved'"(p.361).ThoughGilbert lowing information-based analysis of the etal.(1996)attemptedtosolvetheproblem Cambrianexplosionwillsupporttheclaim oftheoriginofformbyproposingagreater ofrecentauthorssuchasMiillerandNew- role for developmental genetics within an man that the mechanism ofselection and otherwise neo-Darwinian framework,' nu- geneticmutationdoesnotconstituteanad- merous recent authors have continued to equatecausalexplanationoftheorigination raisequestions aboutthe adequacy ofthat ofbiologicalforminthehighertaxonomic framework itselfor about the problem of groups.Itwillalsosuggesttheneedtoex- theoriginationofformgenerally(Webster plore otherpossible causal factors forthe & Goodwin 1996; Shubin & Marshall originofformandinformationduringthe 2000; Erwin 2000; Conway Morris 2000, evolution of life and will examine some 2003b;Carrol2000;Wagner2001;Becker otherpossibilitiesthathavebeenproposed. &Lonnig2001;Stadleretal.2001;Lonnig & Saedler2002; Wagner & Stadler2003; TheCambrianExplosion Valentine2004:189-194). What lies behind this skepticism? Is it The "Cambrianexplosion" referstothe warranted?Isanewandspecificallycausal geologically sudden appearance of many theoryneededtoexplaintheoriginationof new animalbody plans about530 million biologicalform? years ago. At this time, at least nineteen, Thisreviewwilladdressthesequestions. andperhapsasmanyasthirty-fivephylaof Itwilldo soby analyzingtheproblemof fortytotal (Meyeretal. 2003),madetheir theoriginationoforganismalform(andthe first appearance on Earth within a narrow five-toten-million-yearwindowofgeolog- 'Specifically, Gilbert et al. (1996) argued that ic time (Bowring et al. 1993, 1998a:l, changesinmorphogeneticfieldsmightproducelarge- 1998b:40; Ken- 1993; Monastersky 1993; scalechangesinthedevelopmentalprogramsand,ul- Aris-Brosou&Yang2003).Manynewsub- timately,bodyplansofor—ganisms.Yettheyoffer—edno phyla,between32and48of56total(Mey- ebveiadletnecreedtthoatprsoudcuhcefiaelddvsantiafgienoduesedvartihaetyioenxsisitnbocdayn eretal.2003),andclassesofanimalsalso plan,thoughthisisanecessaryconditionofanysuc- arose at this time with representatives of cessfulcausaltheoryofmacroevolution. these new highertaxamanifesting signifi- VOLUME117,NUMBER2 cantmorphologicalinnovations.TheCam- tation and selection, or otherprocesses of brian explosion thus marked a majorepi- evolutionarychange,cangeneratetheform sodeofmorphogenesisinwhichmanynew and information necessary to produce the anddisparateorganismalforms aroseina animals that arise in the Cambrian. This geologicallybriefperiodoftime. analysis will, forthe mostpart,^therefore, To say that the fauna ofthe Cambrian not depend upon assumptions of either a period appeared in a geologically sudden longorshortfusefortheCambrianexplo- manner also implies the absence ofclear sion,oruponamonophyleticorpolyphyletic transitional intermediate forms connecting viewoftheearlyhistoryoflife. Cambrian animals with simpler pre-Cam- brianforms.And,indeed,inalmostallcas- DefiningBiologicalFormandInformation es, the Cambrian animals have no clear morphological antecedents in earlier Ven- Form,likelifeitself,iseasytorecognize dian or Precambrian fauna (Miklos 1993, butoftenhardtodefineprecisely.Yet,area- E20r0w1i,nCeotnwala.y1M9o9r7r:1i3s22,00S3tbe:in5e1r0,&ValReenittinneer fsiocneabfloerwoourrkpirnegsednetfipniutripoonseosf.fFoormrmwiclalnsubfe- ectental.di2s0c0o3v:er5i1e9s-5a2n0d).anFaulrytsheesr,susgegveersatlthrae-t rdeelfaitnieodnsaosftahneatfoomuirc-adlipmaerntssi.oTnhailstmoepaolnosgitchaalt thesemorphologicalgapsmaynotbemere- onecanunderstandformasaunifiedarrange- lyanartifactofincompletesamplingofthe mentofbodypartsormaterialcompo—nents fossilrecord(Foote1997,Footeetal.1999, inadistinctshapeorpattern(topology) one Benton&Ayala2003,Meyeretal.2003), that exists in three spatial dimensions and suggestingthatthefossilrecordisatleast whicharisesintimeduringontogeny. approximately reliable (Conway Morris Insofarasanyparticularbiologicalform 2003b:505). constitutes something like a distinct ar- Asaresult, debatenowexistsaboutthe rangementofconstituentbodyparts, form extent to which this pattern of evidence canbeseenasarisingfromconstraintsthat comportswithastrictlymonophyleticview limit the possible arrangements ofmatter. ofevolution(ConwayMorris1998a,2003a, Specifically, organismal form arises (both 2003b:510; Willmer 1990, 2003). Further, inphylogenyandontogeny)aspossiblear- among those who accept a monophyletic rangements of material parts are con- view of the history of life, debate exists strainedtoestablishaspecificorparticular aboutwhethertoprivilegefossilormolec- arrangement with an—identifiable three di- ulardataandanalyses.Thosewhothinkthe mensionaltopography onethatwewould ftohsesilordiagtianporfovtihdeeaMemtoarzeoarenliatbelnedpitcot—utrheionkf roregcaong,nibzoedayspalapnarotricourlagranpirsomt.einA,pcaelrltitcyuplea,r theseanimalsaroserelativelyquickly that theCambrianexplosionhada"shortfuse." -Ifonetakesthefossilrecordatfacevalueand (ConwayMorris 2003b:505-506, Valentine assumesthattheCambrianexplosiontookplacewithin &Jablonski2003).Some(Wrayetal.1996), arelativelynarrow5-10millionyearwindow,explain- bthuattnmootleaclulla(rAypahlyaloegtenali.es19e9st8a)b,liwshhoreltihaibnlke nbineegcwatuphsreeotoemriiungtsia,ntifooofrntehrxaeatmeispnlfwoeor,umblatedicononomtensheacmevsoesrabereyeacntuotsuepfrfioindcpiuaecrnett divergencetimesfrompre-Cambrianances- togeneratethenumberofchangesinthegenomenec- torsthinkthattheCambriananimal—sevolved essarytobuildthenewproteinsformorecomplex over a very long period oftime thatthe Cambriananimals(Ohno 1996:8475-8478).Thisre- Cambrianexplosionhada"longfuse."This viewwillarguethat,evenifoneallowsseveralhun- review will not address these questions of ndirfeidcamnitlplrioobnabyielairsstifcorantdheotohreirgidnifoffictuhletiemsetraezmoaainn,wsiitgh- historical pattern. Instead, it will analyze theneo-Darwinianexplanationoftheoriginofform whethertheneo-Darwinianprocessofmu- andinformation. PROCEEDINGSOFTHEBIOLOGICALSOCIETYOFWASHINGTON "form,"therefore,representsahighlyspe- cleotidebases.Sinceeachofthefourbases cificandconstrainedarrangementofmate- hasaroughlyequalchanceofoccurringat rialcomponents(amongamuchlargerset eachsitealongthespineoftheDNAmol- ofpossiblearrangements). ecule,biologistscancalculatetheprobabil- Understandingforminthiswaysuggests ity, and thus the information-carrying ca- aconnectiontothenotionofinformationin pacity, ofany particularsequencenbases its mosttheoretically general sense.When long. Shannon (1948) first developed a mathe- Theeasewithwhichinformationtheory matical theory of information he equated applies to molecular biology has created theamountofinformationtransmittedwith confusionaboutthetypeofinformationthat theamountofuncertaintyreducedorelim- DNA and proteins possess. Sequences of inatedinaseriesofsymbolsorcharacters. nucleotidebasesinDNA,oraminoacidsin Information, in Shannon's theory, is thus a protein, are highly improbable and thus impartedassomeoptionsareexcludedand havelargeinformation-carryingcapacities. othersareactualized.Thegreaterthenum- But, like meaningful sentences orlinesof ber of options excluded, the greater the computercode,genesandproteinsarealso amount ofinformation conveyed. Further, specified with respect to function. Just as constraining a set ofpossible material ar- themeaningofasentencedependsuponthe rangementsbywhateverprocessormeans specificarrangementofthelettersinasen- involvesexcludingsomeoptionsandactu- tence, so too does the function ofagene alizing others. Thus, to constrain a setof sequencedependuponthespecificarrange- possiblematerialstatesistogenerateinfor- ment of the nucleotide bases in a gene. mationin Shannon's sense. Itfollowsthat Thus, molecularbiologists beginning with theconstraintsthatproducebiologicalform Crick equated information not only with alsoimpartin/ormation.Orconversely,one complexity but also with "specificity," mightsaythatproducingorganismalform where "specificity" or "specified" has bydefinitionrequiresthegenerationofin- meant "necessary to function" (Crick formation. 1958:144, 153; Sarkar, 1996:191).^Molec- InclassicalShannoninformationtheory, ular biologists such as Monod a—nd Crick tahlesoaimnovuernsteloyfrielnaftoerdmattoiotnheinproabasbyisltiteymoifs ufonrdmeartsitoonodstboiroeldogiincaDlNinAfoarnmdatpiroonteitnhse—ians- thearrangementofconstituentsinasystem something morethan merecomplexity (or or the characters along a communication improbability).Theirnotionofinformation channel(Shannon1948).Themoreimprob- associated both biochemical contingency able (or complex) the arrangement, the and combinatorial complexity with DNA moreShannoninformation,orinformation- sequences(allowingDNA'scarryingcapac- carrying capacity, a string or system pos- ity to be calculated), but it also affirmed sesses. thatsequencesofnucleotidesandaminoac- Sincethe 1960s,mathematicalbiologists ids in functioning macromolecules pos- haverealizedthat Shannon'stheory could sessedahighdegreeofspecificityrelative beappliedtotheanalysisofDNAandpro- tothemaintenanceofcellularfunction. teins to measure the information-carrying Theeasewithwhichinformationtheory capacity of these macromolecules. Since appliesto molecularbiology has alsocre- DNAcontainstheassemblyinstructionsfor atedconfusionaboutthelocationofinfor- building proteins, the information-process- ingsysteminthecellrepresentsakindof communication channel (Yockey 1992: 'AsCrickputit."informationmeansherethepre- 110). Further, DNA conveys information cniuscelediectearcimdinoartioonnaomfisneoquaecnicder,eseiidthueersoifntbhaesepsroitneitnh"e via specifically arranged sequences ofnu- (Crick1958:144,153). — 8 VOLUME117,NUMBER2 mation in organisms. Perhapsbecausethe geret al. 1995). Forty millionyearslater, information carrying capacity ofthe gene theCambrianexplosionoccurred(Bowring could be so easily measured, it has been et al. 1993). The emergence of the Edi- easytotreatDNA,RNAandproteinsasthe acaranbiota(570mya),andthentoamuch solerepositoriesofbiologicalinformation. greaterextenttheCambrianexplosion(530 Neo-Darwinistsinparticularhaveassumed mya),representedsteepclimbsupthebio- thattheoriginationofbiologicalformcould logicalcomplexitygradient. beexplainedbyrecoursetoprocessesofge- Onewaytoestimatetheamountofnew netic variationandmutationalone (Levin- CSIthatappeared withtheCambrianani- ton 1988:485). Yet ifone understands or- mals is to count the number ofnew cell ganismalformasresultingfromconstraints types that emerged with them (Valentine on the possible arrangements ofmatterat 1995:91-93). Studies of modern animals many levels in the biological hierarchy suggest that the sponges that appeared in from genes andproteins tocell typ—es and the late Precambrian, for example, would tissues to organs and body plans then have required five cell types, whereas the clearly biological organisms exhibit many morecomplexanimalsthatappearedinthe levelsofinformation-richstructure. Cambrian(e.g.,arthropods)wouldhavere- Thus, wecanpose aquestion, notonly quiredfiftyormorecelltypes.Functionally abouttheoriginofgeneticinformation,but more complex animals require more cell alsoabouttheoriginoftheinformationnec- types to perform theirmore diversefunc- essarytogenerateformandstructureatlev- tions.Newcelltypesrequiremanynewand els higher than that present in individual specializedproteins.Newproteins,inturn, proteins.Wemustalsoaskabouttheorigin require new genetic information. Thus an ofthe "specifiedcomplexity," asopposed increaseinthenumberofcelltypesimplies to mere complexity, that characterizesthe (ataminimum) aconsiderableincreasein new genes, proteins, cell types and body the amount of specified genetic informa- plansthataroseintheCambrianexplosion. tion.Molecularbiologistshaverecentlyes- Dembski (2002) hasusedtheterm "com- timated that a minimally complex single- polneyxmspfeocrifi"esdpeicniffoiremdatcioomnp"le(xCiStIy)"astoahseynl-p caenldle5d6o2rgkailnoibsamsewopuailrdsroefquDirNeAbettowpereond3uc1e distinguish functional biological inf—orma- the proteins necessary to maintain life tionfrommereShannoninformation that (Koonin2000).Morecomplexsinglecells is, specified complexity from mere com- might require upward of a million base plexity. This review will use this term as pairs.Yettobuildtheproteinsnecessaryto well. sustainacomplexarthropodsuchasatri- lobite would require orders ofmagnitude TheCambrianInformationExplosion morecodinginstructions.Thegenomesize of a modern arthropod, the fruitfly Dro- marTkhaeblCeamjburmipaninextphelosspieocnifrieepdrecsoemnptlseaxirtey- smoilplhiiolnambealsaenogpaaisrtser,(Giesrhaaprptrox&imaKtierlsych1n8e0r or "complex specifiedinformation" (CSI) 1997:121, Adams etal. 2000). Transitions ofthebiologicalworld.Foroverthreebil- from a single cell to colonies ofcells to lionyears,thebiologicalrealmincludedlit- complexanimalsrepresentsignificant(and, tlemorethanbacteriaandalgae(Brockset inprinciple,measurable)increasesinCSI. al. 1999).Then,beginningabout570-565 Building a new animal from a single- millionyearsago(mya),thefirstcomplex celledorganismrequires avastamountof mruolctkicsetlrlautla,arinocrlguadinnigsmsspoangpepse,arecndidairniatnhse, wneawy—goefnetaircrainngfiornmgatgioenn.eItpraolsdoucrtesqu—irperso-a andthepeculiarEdiacaranbiota(Grotzin- teins into higher levels of organization. PROCEEDINGSOFTHEBIOLOGICALSOCIETYOFWASHINGTON New proteins are required to service new hasshownthatmeaningfulwordsandsen- celltypes.Butnewproteinsmustbeorga- tencesareextremelyrareamongthesetof nizedintonewsystemswithinthecell;new possiblecombinationsofEnglishletters,es- celltypesmustbeorganizedintonewtis- peciallyassequencelengthgrows.(Thera- sues,organs,andbodyparts.These,inturn, tioofmeaningful12-letterwordsto12-letter mustbeorganizedtoformbodyplans.New sequences is I/IO'"*; the ratio of 100-letter animals, therefore, embody hierarchically sentences to possible 100-letter strings is organized systems of lower-level parts 1/10'°°.) Further, Denton shows that most withinafunctionalwhole. Suchhierarchi- meaningful sentences are highly isolated calorganization itselfrepresentsatypeof from one another in the space ofpossible information, since body plans comprise combinations, so that random substitutions both highly improbable and functionally ofletterswill,afteraveryfewchanges,in- specifiedarrangementsoflower-levelparts. evitablydegrademeaning.Apartfromafew The specified complexity of new body closely clustered sentences accessible by plansrequiresexplanationinanyaccountof randomsubstitution,theoverwhelmingma- theCambrianexplosion. jorityofmeaningful sentenceslie,probabi- Can neo-Darwinismexplainthediscon- listicallyspeaking,beyondthereachofran- tinuousincreaseinC—SIthatappearsinthe domsearch. Cambrianexplosion eitherintheformof Denton(1986:301-324)andothershave newgenetic informationorintheformof argued that similar constraints apply to hierarchically organized systems ofparts? genes andproteins. Theyhave questioned Wewillnowexaminethetwopartsofthis whetheranundirectedsearchviamutation question. and selection would have a reasonable chan—ce of locating new islands of func- NovelGenesandProteins tion representin—g fundamentally new genes or proteins within the time avail- Manyscientistsandmathematicianshave able (Eden 1967, Shutzenberger 1967, questioned the ability ofmutationandse- L0vtrup 1979).Somehavealsoarguedthat lectiontogenerateinformationintheform alterationsinsequencingwouldlikelyresult ofnovel genes andproteins. Such skepti- in loss of protein function before funda- cism often derives from consideration of mentally new function could arise (Eden theextremeimprobability (andspecificity) 1967, Denton 1986). Nevertheless, neither offunctionalgenesandproteins. theextenttowhichgenesandproteinsare Atypicalgenecontainsoveronethousand sensitive to functional loss as a result of preciselyarrangedbases.Foranyspecificcir- sequence change, northe extent to which rangementoffournucleotidebasesoflength functional proteins are isolated within se- n, thereisacorrespondingnumberofpos- quencespace,hasbeenfullyknown. siblearrangementsofbases,4".Foranypro- Recently, experimentsinmolecularbiol- tein,thereare20"possiblearrangementsof ogy have shed lighton these questions. A protein-forming amino acids. A gene 999 variety of mutagenesis techniques have basesinlengthrepresentsoneof4'^'*'^possi- shownthatproteins(andthusthegenesthat ble nucleotide sequences; aprotein of333 produce them) aie indeed highly specified aminoacidsisoneof20^'*''possibilities. relative to biological function (Bowie & Since the 1960s, some biologists have Sauer 1989,Reidhaai-Olson&Sauer 1990, thoughtfunctionalproteinstoberareamong Taylor et al. 2001). Mutagenesis research the set of possible amino acid sequences. teststhesensitivityofproteins(and,byim- Somehaveusedananalogywithhumanlan- plication,DNA)tofunctionallossasaresult guage to illustrate why this should be the ofalterationsinsequencing.Studiesofpro- case.Denton(1986,309-311),forexample. teinshavelongshownthataminoacidres- VOLUME117,NUMBER2 iduesatmany activepositionscannotvary chancealonecannotaccomplishblindlyor withoutfunctionalloss(Perutz&Lehmann inoneleap,selection(actingonmutations) 1968).Morerecentproteinstudies(oftenus- canaccomplishthroughthecumulativeef- ing mutagenesis experiments) have shown fectofmanyslightsuccessivesteps. thatfunctionalrequirementsplacesignificant Yettheextremespecificityandcomplex- constraintsonsequencingevenatnon-active ityofproteinspresentsadifficulty,notonly sitepositions (Bowie& Sauer 1989,Reid- forthechanceoriginofspecifiedbiological haar-Olson & Sauer 1990, Chothia et al. information(i.e.,forrandommutationsact- 1998,Axe2000,Tayloretal.2001).Inpar- ingalone),butalsoforselectionandmuta- ticular.Axe(2000)hasshownthatmultiple tionactinginconcert. Indeed,mutagenesis as opposed to single position amino acid experimentscastdoubtoneachofthetwo substitutionsinevitablyresultinlossofpro- scenariosbywhichneo-Darwinistsenvision teinfunction,evenwhenthesechangesoc- newinformationarisingfromthemutation/ curatsitesthatallowvariationwhenaltered selectionmechanism(forreview,seeLonnig inisolation.Cumulatively,theseconstraints 2001). For neo-Darwinism, new functional imply that proteins are highly sensitive to geneseitherarisefromnon-codingsections functional loss as aresultofalterations in in the genome or from preexisting genes. sequencing,andthatfunctionalproteinsrep- Bothscenariosareproblematic. resent highly isolated and—improbable ar- Inthe firstscenario,neo-Darwinistsen- rangements of amino acids arrangements visionnewgeneticinformationarisingfrom thatare farmore improbable, infact, than those sections ofthe genetic textthatcan wouldbelikelytoarisebychancealonein presumably vary freely without conse- thetimeavailable(Reidhaar-Olson&Sauer quencetotheorganism. Accordingtothis 1990; Behe 1992; Kauffman 1995:44; scenario, non-coding sections of the ge- Dembski 1998:175-223; Axe 2000, 2004). nome,orduplicatedsectionsofcodingre- (Seebelowthediscussionoftheneutralthe- gions,canexperienceaprotractedperiodof ory ofevolution for a precise quantitative "neutralevolution" (Kimura 1983)during assessment.) which alterations in nucleotide sequences Ofcourse, neo-Darwinists do not envi- have nodiscernibleeffectonthe function sion a completely random search through of the organism. Eventually, however, a the—setofall possible nucleotide sequenc- newgenesequencewillarisethatcancode es so-called "sequencespace." Theyen- for a novel protein. Atthat point, natural vision natural selection acting to preserve selection can favor the new gene and its smalladvantageousvariationsingeneticse- functional protein product, thus securing quences and their corresponding protein thepreservationandheritabilityofboth. products.Dawkins(1996),forexample,lik- Thisscenariohastheadvantageofallow- ensanorganismtoahighmountainpeak. ingthegenometovarythroughmanygen- Hecompares climbing the sheerprecipice erations, as mutations "search" the space upthefrontsideofthemountaintobuild- of possible base sequences. The scenario ing a new organism by chance. He ac- has an overriding problem, however: the knowledgesthatthisapproachup "Mount size of the combinatorial space (i.e., the Improbable" will not succeed. Neverthe- numberofpossibleaminoacidsequences) less, he suggests that there is a gradual andtheextremerarityandisolationofthe slopeupthebacksideofthemountainthat functional sequences within that space of could be climbed in small incremental possibilities.Sincenaturalselectioncando steps.Inhisanalogy,thebacksideclimbup nothingtohelpgeneratenewfunctionalse- "Mount Improbable" corresponds to the quences,butrathercanonlypreservesuch processofnatural selection actingonran- seque—nces once they have—arisen, chance dom changes in the genetic text. What alone random variation must do the 220 PROCEEDINGSOFTHEBIOLOGICALSOCIETYOFWASHINGTON — workofinformationgeneration thatis,of tant organisms comprise over 400 amino findingtheexceedinglyrarefunctionalse- acids. These molecules are both highly quences within the set of combinatorial complex (non-repetitive) and functionally possibilities.Yettheprobabilityofrandom- specified. Reasonable extrapolation from lyassembling(or"finding,"intheprevious mutagenesis experiments done on shorter sense) a functional sequence is extremely protein molecules suggeststhattheproba- small. bilityofproducingfunctionally sequenced Cassette mutagenesis experiments per- proteinsofthislengthatrandomissosmall formedduringtheearly 1990ssuggestthat astomakeappealstochanceabsurd,even theprobabilityofattaining(atrandom)the grantingthedurationoftheentireuniverse. correctsequencingforashortprotein 100 (SeeDembski1998:175-223forarigorous haamairn-oOlascoinds&loSnagueisra1b9o9u0t,1Beinhe10^1^99(2R:e6i5d-- cBaolucnulda"t;ioSneeofaltshoisAx"Ueni2v0e0r4s.a)lYePtr,obsaebciolnidt,y 69).Thisresultagreedcloselywithearlier fossil data (Bowring etal. 1993, 1998a:1, calculations that Yockey (1978) had per- 1998b:40; Kerr 1993; Monastersky 1993), formed based upon the known sequence and even molecular analyses supporting variabilityofcytochromecindifferentspe- deepdivergence(Wrayetal.1996),suggest cies and other theoretical considerations. thatthedurationoftheCambrianexplosion Morerecentmutagenesisresearchhaspro- (between5-10X 10^and,atmost,7X 10^ vthiadtedfunacdtdiiotinoanlaplrostuepipnosrtarfeorextcheeedcionngcllyusriaorne yuenairvse)rsies(f1a.r3s-m2alXle1r0't°hayneatrhsa)t.oTfhitrhde,eDntNirAe amongpossibleaminoacidsequences(Axe mutationrates arefartoolowtogenerate 2000,2004).Axe(2004)hasperformedsite the novelgenes andproteinsnecessaryto directedmutagenesisexperimentsona150- building the Cambrian animals, given the residueprotein-foldingdomainwithinap- mostprobabledurationoftheexplosionas lactamaseenzyme.Hisexperimentalmeth- determinedbyfossilstudies(ConwayMor- odimprovesuponearliermutagenesistech- ris 1998b). As Ohno (1996:8475) notes, peOnsoisinzstqesiutime(hbase1lt5eeab0danesdrstiethsseicimoodrrafaurtteetiischoo)tenssotefehfraeo(rtarxo)prpseepeirrrvniofehmtoreeerarinlmentnssats.oosufiApnrxetccyteeiphsfiehcimaoae.sldf pntmesieioveoltrqenlunayieleoenaxnadcprimleyvuareeiteoarsnafrugtslea.ittnoshgcnTeieihvnruoeoasfornt,neipglsrhioyeenefc-atei1axo0o1irf"n%sg't'uotiecfhnpsehgeDartgnCNhebgaanaAtemesbsemiirnuncpitataaa1nhin--0er fwuhnoclteiosnetvioafapnosysifbolledeadmistnroucatcuirdestsoe(qbu)entch-e formsinthattime."* esofthat size. Basedonhis experiments. ApTrhxouetse,hinatshaeempsortonibmgaabttiehldeittpyhoiosssfrifabitlineodiatnomgibaneofu1natccotiid1o0ns^ae^l-. etsoxeis"pssTtreoeodndcsvueiocrletvoueftahltlaehyinshayelpplworttobhhbeeoltdeigymceanplOelthaianncnsoceiosnhftfiromtarshlmeealftfCoiaorpmnmrbornpteiohcaasetenssspaaotnrshiy-e- quences corresponding to a 150-residue mals.Heassertsthatthisancestorandits "panani- proOttehineriscsoinmsiildaerlryat1ioinns10i^m^p.ly additional mmiallliiaonngyeeanrosmbee"formeigthhteChaavmebrairainseenxpsleovseiroanl.hOunndtrheids immaplrsobawboiullitdierse.quFiirrest,prnoteewinsCammubcrhianlonagnei-r cvhoianevswei,dpeeorsaascbehlsesoefldattvheienrttduiaaflnfldeyreiundnteentxCipacrmaelbsrgsieeadnnomcaeanpsia,cmiaatllbyseiwitnowuitlthdhe than 100residuestoperformmanyneces- caseofeachindividualform(Ohno1996:8475-8478). saryspecializedfunctions.Ohno(1996)has Whilethisproposalmighthelpexplaintheoriginof noted that Cambrian animals would have theCambriananimalformsbyreferencetopre-exist- requiredcomplexproteinssuchaslysylox- imnegregleynedtiiscpliancfeosr,matthieonp,roibtldeomesofnotthesoolrvieg,inbuotftihnestgeea-d idase in orderto supporttheir stoutbody netic information necessary to produce these new structures. Lysyl oxidasemolecules in ex- — VOLUME117,NUMBER2 Theselection/mutationmechanismfaces bility) ofany scenariofortheorigination anotherprobabilisticobstacle.Theanimals ofCambriangeneticinformationthatrelies that arise in the Cambrian exhibit struc- uponrandomvariationaloneunassistedby turesthatwouldhaverequiredmanynew naturalselection. typesofcells, each ofwhich wouldhave Yet the neutral theory —requires novel required many novel proteins to perform genes and proteins to arise essentially their specialized functions. Further, new byrandommutationalone.Adaptiveadvan- celltypesrequiresystemsofproteinsthat tage accrues after the generation of new must,asaconditionoffunctioning,actin functionalgenesandproteins.Thus,natural close coordination with one another. The selection cannot play arole until new in- unitofselection in such systems ascends formation-bearingmoleculeshaveindepen- tothesystemasawhole.Naturalselection dently arisen. Thus neutral theorists envi- selects forfunctional advantage. Butnew sionthe needto scale the steepfaceofa cell types require whole systems ofpro- Dawkins-style precipice ofwh—ich there is teinstoperformtheirdistinctivefunctions. nograduallyslopingbackside asituation Insuchcases,naturalselectioncannotcon- that,byDawkins' ownlogic,isprobabilis- tributetotheprocessofinformationgen- ticallyuntenable. eration until afterthe information neces- In the second scenario, neo-Darwinists sary to build therequisitesystem ofpro- envision novel genes andproteins arising teins has arisen. Thus random variations by numerous successive mutations in the must, agai—n, do the work of information preexistinggenetictextthatcodesforpro- generation and now not simply for one teins. To adapt Dawkins's metaphor, this protein, but for many proteins arising at scenario envisions gradually climbing nearlythesametime.Yettheoddsofthis down one functional peak and then as- occurringby chancealoneare, ofcourse, cending another. Yet mutagenesis experi- farsmallerthantheoddsofthe—chanceor- ments again suggest a difficulty. Recent iginofasinglegeneorprotein sosmall experimentsshowthat,evenwhenexplor- infactastorenderthechanceoriginofthe ing aregionofsequence spacepopulated genetic information necessary to build a byproteins ofasinglefoldandfunction, new cell type (a necessary but not suffi- most multiple-position changes quickly cient condition of building a new body leadtolossoffunction(Axe2000).Yetto plan)problematicgiveneventhemostop- turnoneproteinintoanotherwithacom- timistic estimates for the duration ofthe pletely novel structure and function re- Cambrianexplosion. quiresspecifiedchangesatmanysites.In- Dawkins(1986:139)hasnotedthatsci- deed,thenumberofchangesnecessaryto entific theories canrely on only somuch produceanewproteingreatlyexceedsthe "luck" before they cease to be credible. numberofchangesthatwilltypicallypro- Theneutraltheoryofevolution,which,by duce functional losses. Given this, the its own logic, prevents natural selection probability of escaping total functional from playing arole in generating genetic lossduringarandomsearchforthechang- information until after the fact, relies on esneededtop—roduceanewfunctionisex- entirelytoomuchluck.Thesensitivityof tremelysmall andthisprobabilitydimin- proteins to functional loss, the need for ishes exponentially with each additional long proteinstobuildnewcelltypes and requisitechange (Axe2000).Thus,Axe's animals, the needforwhole new systems results imply that, in all probability, ran- ofproteins to service new celltypes, the dom searches fornovel proteins (through probable brevity of the Camb—rian explo- sequence space) will result in functional sionrelativetomutationrates allsuggest losslongbeforeanynovelfunctionalpro- theimmenseimprobability(andimplausi- teinwillemerge. 222 PROCEEDINGSOFTHEBIOLOGICALSOCIETYOFWASHINGTON Blancoetal.havecometoasimilarcon- gentlimitationsontheefficacyofmutation clusion. Using directed mutagenesis, they and selection. In the first case, function have determined thatresidues in both the mustarisefirst,beforenaturalselectioncan hydrophobiccoreandonthesurfaceofthe acttofavoranovelvariation.Inthesecond protein play essentialroles indetermining case,functionmustbecontinuouslymain- proteinstructure.Bysamplingintermediate tainedinordertopreventdeleterious(orle- sequencesbetweentwonaturallyoccurring thal)consequencestotheorganismandto sequences that adopt different folds, they allowfurtherevolution.Yetthecomplexity foundthattheintermediatesequences"lack and functional specificity ofproteins im- awelldefinedthree-dimensionalstructure." pliesthatboththeseconditionswillbeex- Thus,theyconcludethatitisunlikelythat tremely difficult to meet. Therefore, the a new protein fold would evolve from a neo-Darwinian mechanism appears to be pre-existingfoldviaaseriesoffoldedin- inadequatetogeneratethenewinformation termediatessequences(Blancoetal. 1999: presentinthenovelgenesandproteinsthat 741). arisewiththeCambriananimals. Thus,althoughthissecondneo-Darwin- ian scenario has the advantage ofstarting NovelBodyPlans with functional genes andproteins, italso has a lethal disadvantage: any process of The problems with the neo-Darwinian random mutation or rearrangement in the mechanismrundeeperstill.Inordertoex- genome would in all probability generate plain the origin ofthe Cambrian animals, nonfunctional intermediate sequences be- onemustaccountnotonlyfornewproteins forefundamentallynewfunctionalgenesor andcelltypes,butalsofortheoriginofnew proteinswouldarise.Clearly,nonfunctional bodyplans.Withinthepastdecade,devel- intermediate sequences conferno survival opmental biology has dramatically ad- advantageontheirhostorganisms.Natural vanced our understanding of how body selectionfavorsonlyfunctionaladvantage. plansarebuiltduringontogeny.Inthepro- It cannot select or favor nucleotide se- cess,ithasalsouncoveredaprofounddif- quences orpolypeptidechainsthatdo not ficultyforneo-Darwinism. yet perform biological functions, and still Significant morphological change in or- less will it favor sequences that efface or ganisms requires attention to timing. Mu- destroypreexistingfunction. tations in genes thatare expressedlate in Evolving genes and proteins will range the development ofan organism will not through aseriesofnonfunctionalinterme- affectthe body plan. Mutations expressed diate sequences that natural selection will earlyindevelopment,however,couldcon- notfavororpreservebutwill,inallprob- ceivablyproducesignificantmorphological ability,eliminate (Blancoetal. 1999,Axe change(Arthur 1997:21).Thus,eventsex- 2000).Whenthishappens,selection-driven pressedearlyinthedevelopmentoforgan- evolutionwillcease. Atthispoint,neutral ismshavetheonlyrealisticchanceofpro- evolutionofthegenome(unhingedfromse- ducing large-scale macroevolutionary lective pressure) may ensue, but, as we change(Thomson1992).AsJohnandMik- have seen, such a process mustovercome los (1988:309) explain, macroevolutionary immenseprobabilistichurdles,evengrant- changerequiresalterationsintheveryearly ingcosmictime. stagesofontogenesis. Thus, whetherone envisions the evolu- Yetrecentstudies indevelopmentalbi- tionaryprocessbeginningwithanoncoding ologymakeclearthatmutationsexpressed regionofthegenomeorapreexistingfunc- early in developmenttypically havedele- tional gene, the functional specificity and terious effects (Arthur 1997:21). For ex- complexity ofproteins impose very strin- ample, when early-acting body plan mol-