PEERREVIEWED&PEEREDITEDSCIENTIFICPUBLICATIONS SUPPORTINGTHETHEORYOFINTELLIGENTDESIGN(ANNOTATED)

By:Staff DiscoveryInstitute February1,2012

EditorsNote:Whileintelligentdesign(ID)researchisanewscientificfield,recentyearshavebeena periodofencouraginggrowth,producingastrongrecordofpeerreviewedscientificpublications. In2011,theIDmovementcountedits50thpeerreviewedscientificpaperandnewpublications continuetoappear.Thecurrentboomgoesbackto2004,whenDiscoveryInstituteseniorfellow StephenMeyerpublishedagroundbreakingpaperadvocatingIDinthejournalProceedingsofthe BiologicalSocietyofWashington.TherearemultiplehubsofIDrelatedresearch. BiologicInstitute,ledbymolecularbiologistDougAxe,is"developingandtestingthescientificcasefor intelligentdesigninbiology."Biologicconductslaboratoryandtheoreticalresearchontheoriginand roleofinformationinbiology,thefinetuningoftheuniverseforlife,andmethodsofdetectingdesignin nature. AnotherIDresearchgroupistheEvolutionaryInformaticsLab,foundedbyseniorDiscoveryInstitute fellowWilliamDembskialongwithRobertMarks,DistinguishedProfessorofElectricalandComputer EngineeringatBaylorUniversity.Theirlabhasattractedgraduatestudentresearchersandpublished multiplepeerreviewedarticlesintechnicalscienceandengineeringjournalsshowingthatcomputer programming"pointstotheneedforanultimateinformationsourcequaintelligentdesigner." OtherproIDscientistsaroundtheworldarepublishingpeerreviewedproIDscientificpapers.These includebiologistRalphSeelkeattheUniversityofWisconsinSuperior,WolfEkkehardLnnigwho recentlyretiredfromtheMaxPlanckInstituteforPlantBreedingResearchinGermany,andLehigh UniversitybiochemistMichaelBehe. Theseandotherlabsandresearchershavepublishedtheirworkinavarietyofappropriatetechnical venues,includingpeerreviewedscientificjournals,peerreviewedscientificbooks(somepublishedby mainstreamuniversitypresses),tradepressbooks,peereditedscientificanthologies,peeredited scientificconferenceproceedingsandpeerreviewedphilosophyofsciencejournalsandbooks.These papershaveappearedinscientificjournalssuchasProteinScience,JournalofMolecularBiology, TheoreticalBiologyandMedicalModelling,JournalofAdvancedComputationalIntelligenceand IntelligentInformatics,QuarterlyReviewofBiology,CellBiologyInternational,Rivistadi Biologia/BiologyForum,PhysicsofLifeReviews,AnnualReviewofGenetics,andmanyothers.Atthe

sametime,proIDscientistshavepresentedtheirresearchatconferencesworldwideinfieldssuchas genetics,biochemistry,engineering,andcomputerscience. Collectively,thisbodyofresearchisconvergingonaconsensus:complexbiologicalfeaturescannot arisebyunguidedDarwinianmechanisms,butrequireanintelligentcause. DespiteIDspublicationrecord,wenoteparentheticallythatrecognitioninpeerreviewedliteratureis notanabsoluterequirementtodemonstrateanideasscientificmerit.Darwinsowntheoryofevolution wasfirstpublishedinabookforageneralandscientificaudiencehisOriginofSpeciesnotina peerreviewedpaper.Nonetheless,ID'speerreviewedpublicationrecordshowsthatitdeservesandis receivingseriousconsiderationbythescientificcommunity. ThepurposeofID'sresearchprogramisnottoconvincetheunconvinciblecriticswhorepeatover andoverinthemediathatthereisnosuchthingasIDresearch,thatIDhasnotproducedasinglepeer reviewedpaper.Rather,IDresearchseekstoengageopenmindedscientistsandthoughtfullaypersons withcredible,persuasive,peerreviewed,empiricaldatasupportingintelligentdesign. Andthisishappening.IDhasalreadygainedthekindofscientificrecognitionyouwouldexpectfroma young(andvastlyunderfunded)butpromisingscientificfield.ThescientificprogressofIDhaswonthe seriousattentionofskepticsinthescientificcommunity,whoengageinscientificdebatewithIDand attendprivatescientificconferencesallowingofftherecorddiscussionwithIDproponents. Weprovidebelowanannotatedbibliographyoftechnicalpublicationsofvariouskindsthatsupport, developorapplythetheoryofintelligentdesign.Thearticlesaregroupedaccordingtothetypeof publication. ScientificPublicationsSupportiveofIntelligentDesignPublishedinPeerReviewedScientific Journals,ConferenceProceedings,orAcademicAnthologies JosephA.Kuhn,DissectingDarwinism,BaylorUniversityMedicalCenterProceedings, Vol.25(1):4147(2012). ThisarticlebyDr.JosephKuhnoftheDepartmentofSurgeryatBaylorUniversityMedical CenterappearedinthepeerreviewedjournalBaylorUniversityMedicalCenterProceedings.It posesanumberofchallengestobothchemicalandbiologicalevolution,including: 1.LimitationsofthechemicaloriginoflifedatatoexplaintheoriginofDNA 2.Limitationsofmutationandnaturalselectiontheoriestoaddresstheirreducible complexityofthecell 3.Limitationsoftransitionalspeciesdatatoaccountforthemultitudeofchanges involvedinthetransition. Regardingthechemicaloriginoflife,KuhnpointstotheMillerUreyexperimentsandcorrectly observesthat"theexperimentalconditionsofalowoxygen,nitrogenrichreducingenvironment havebeenrefuted."CitingStephenMeyer'sSignatureintheCell,hecontendsthat"the fundamentalandinsurmountableproblemwithDarwinianevolutionliesintheremarkable complexityandinherentinformationcontainedwithinDNA."Kuhnalsoexplainsthat "Darwinianevolutionandnaturalselectioncouldnothavebeencausesoftheoriginoflife, becausetheyrequirereplicationtooperate,andtherewasnoreplicationpriortotheoriginoflife," butnootherknowncausecanorganizetheinformationinlife.

Dr.Kuhnthenturnstoexplainingtheconceptofirreduciblecomplexity,citingMichaelBehe's bookDarwin'sBlackBoxandnotingthat"irreduciblecomplexitysuggeststhatallelementsofa systemmustbepresentsimultaneouslyratherthanevolvethroughastepwise,sequential improvement,astheorizedbyDarwinianevolution."Further,"Thefactthattheseirreducibly complexsystemsarespecificallycodedthroughDNAaddsanotherlayerofcomplexitycalled 'specifiedcomplexity.'"Asamedicaldoctor,Kuhnproposesthatirreduciblycomplexsystems withinthehumanbodyinclude"vision,balance,therespiratorysystem,thecirculatorysystem, theimmunesystem,thegastrointestinalsystem,theskin,theendocrinesystem,andtaste."He concludesthat"thehumanbodyrepresentsanirreduciblycomplexsystemonacellularandan organ/systembasis." Kuhnalsoexploresthequestionofhuman/apecommonancestry,citingJonathanWells'sbook TheMythofJunkDNAandarguing: DNAhomologybetweenapeandmanhasbeenreportedtobe96%when consideringonlythecurrentproteinmappingsequences,whichrepresentonly2%of thetotalgenome.However,theactualsimilarityoftheDNAisapproximately70% to75%whenconsideringthefullgenome,includingthepreviouslypresumed"junk DNA,"whichhasnowbeendemonstratedtocodeforsupportingelementsin transcriptionorexpression.The25%differencerepresentsalmost35millionsingle nucleotidechangesand5millioninsertionsordeletions. InDr.Kuhn'sview,thisposesaproblemforDarwinianevolutionbecausethe"[t]heapeto humanspecieschangewouldrequireanincrediblyrapidrateofmutationleadingtoformationof newDNA,thousandsofnewproteins,anduntoldcellular,neural,digestive,andimmunerelated changesinDNA,whichwouldcodeforthethousandsofnewfunctioningproteins." KuhnalsoobservesthatachallengetoneoDarwinismcomesfromtheCambrianexplosion: ThousandsofspecimenswereavailableatthetimeofDarwin.Millionsofspecimens havebeenclassifiedandstudiedinthepast50years.Itisremarkabletonotethat eachoftheseshowsavirtualexplosionofnearlyallphyla(35/40)oftheanimal kingdomoverarelativelyshortperiodduringtheCambrianera525to530million yearsago.Sincethattime,therehasbeenoccasionalspeciesextinction,butonlyrare newphylahavebeenconvincinglyidentified.Theseminalpaperfrom paleoanthropologistsJ.ValentineandD.H.Erwinnotesthattheabsenceof transitionalspeciesforanyoftheCambrianphylalimitstheneoDarwinian explanationforevolution. DespiteTexas'scallfordiscussingthescientificstrengthsandweaknessesofDarwinian evolution,Kuhnclosesbynoting,"In2011,whennewtextbookswerepresentedtotheState BoardofEducation,9outof10failedtoprovidethemandatedsupplementarycurricula,which wouldincludebothpositiveandnegativeaspectsofevolution(44)."CitingDiscoveryInstitute's ReportontheTexasTextbooks,helaments: [S]everalofthetextbookscontinuedtoincorrectlypromotethedebunkedMiller Ureyoriginoflifeexperiment,thelongdiscreditedclaimsaboutnonfunctional appendixandtonsils,andthefraudulentembryodrawingsfromErnstHaeckel.In essence,currentbiologystudents,aspiringmedicalstudents,andfuturescientistsare

notbeingtaughtthewholestory.Rather,evidencesuggeststhattheycontinueto receiveincorrectandincompletematerialthatexaggeratestheeffectofrandom mutationandnaturalselectiontoaccountforDNA,thecell,orthetransitionfrom speciestospecies. Kuhnconcludes,"Itisthereforetimetosharpenthemindsofstudents,biologists,andphysicians forthepossibilityofanewparadigm." DavidL.Abel,IsLifeUnique?,Life,Vol.2:106134(2012). Whatisitthatdistinguisheslifefromnonlivingentities?Thispeerreviewedpaperattemptsto answerthatquestion,notingthatLifepursuesthousandsofbiofunctionalgoals,whereas Neitherphysicodynamics,norevolution,pursuegoals.Isitpossiblethatunguidedevolution andstrictlymaterialcausesproducedlifespurposefulprocesses?Accordingtothispaper,the answerisno.Lifesgoalsincludetheuseofsymbolsystemstomaintainhomeostasisfarfrom equilibriumintheharshestofenvironments,positiveandnegativefeedbackmechanisms, preventionandcorrectionofitsownerrors,andorganizationofitscomponentsintoSustained FunctionalSystems.Butthearticlenotesthattheintegrationandregulationofbiochemical pathwaysandcyclesintohomeostaticmetabolismisprogrammaticallycontrolled,notjust physicodynamicallyconstrained.Thisprogrammingistermedcyberneticyetaccordingto thepapercyberneticcontrolflowsonlyfromthenonphysicalworldofformalismintothe physicalworldthroughtheinstantiationofpurposefulchoices.Indeed,Onlypurposefulchoice contingencyatbonafidedecisionnodescanrescuefromeventualdeteriorationtheorganization andfunctionpreviouslyprogrammedintophysicality.Lifethuscannotbetheresultofunguided materialprocessessomecausecapableofprogrammingpurposefulchoicesisnecessary. DouglasD.Axe,PhilipLu,andStephanieFlatau,AStylusGeneratedArtificialGenome withAnalogytoMinimalBacterialGenomes,BIOComplexity,Vol.2011(3)(2011). Thispeerreviewedpaperisafollowupuptothe2008PLoSOnepapercoauthoredbyAxeand LuonStylus,acomputersimulationofevolutionwhichismorefaithfultobiologicalrealitythan manyothers.This2011paperexplainsthatthefunctionsofthedigitalorganismsinother simulationsareoftendivorcedfromrealworldmeaning.TheydesignedStylustopresentamore accuratepicture: ThemotivationforStyluswastherecognitionthatpriormodelsusedtostudy evolutionaryinnovationdidnotadequatelyrepresentthecomplexcausalconnection betweengenotypesandphenotypes. StylusaimstocorrectthesedeficienciesbysimulatingDarwinianevolutioninamannerthatmore accuratelyreflectsthebiologicalrelationshipbetweengenotypeandphenotype.Itisalsomore realisticbecauseitsolvesrealworldproblems.Asthepaperexplains,Functionalspecificity thereforehasastructuralbasisintheStylusworld,justasitdoesintherealworld.Stylus manipulatesdigitalobjectsthathaverealworldmeaning:thetargetsofevolutioninStylusare Chinesecharacters.Asthepaperexplains: Thesetranslationproducts,calledvectorproteins,arefunctionlessunlesstheyform legibleChinesecharacters,inwhichcasetheyservetherealfunctionofwriting.This couplingofartificialgeneticcausationtotherealworldoflanguagemakes

evolutionaryexperimentationpossibleinacontextwhereinnovationcanhavea richnessofvarietyandadepthofcausalcomplexitythatatleasthintsatwhatis neededtoexplainthecomplexityofbacterialproteomes. Thesecharactersnotonlyhaverealworldmeaning,buttheirfunctionrelatedshapesbear interestinganalogiestoproteins.AnadditionalsimilaritybetweenChinesecharactersandproteins isthatjustasproteindomainsarereusedthroughoutmanyproteins,soparticularshapes,called strokes,arefoundcommonlythroughoutChinesecharacters. Basictolifeisaninformationconversion,wheretheinformationcarriedingenes(thegenotype)is convertedintoanorganism'sobservabletraits(thephenotype).Thosebiologicalstructuresthen performvariousfunctions.Anotherwayofframingthisinformationconversionistherefore: sequencestructurefunction.Axe,LuandFlatauexplainthatmanypreviouscomputer programsattemptingtosimulateevolutionachievepartofthisconversion,butnotthewhole thing. Forexample,Conway'sfamousGameofLifestartswithastructure,andinsomeinstancesthat structurecanperformafunction.Butthereisnosequenceinvolvedintheconversion.Avidastarts withasequenceofprogrammingcommands,andwhensuccessfulperformscertainlogic functions.ButinAvidathereisnostructuretomediatebetweensequenceandfunction.Stylus,on theotherhand,ismoreadvancedinthatitsimulatesthefullsequencestructurefunction informationtransfer.Itdoesthisbystartingwithaprogrammedgenome.Asthepaperexplains: [The]Stylusgenomeencodesaspecialkindoftext,namely,onethatdescribeshow todecodethegenome.Thatis,thedesiredgenomewillencodeasequenceof Chinesecharacters(intheformofvectorproteins)thattellsareaderofChinesehow Stylusgenesaretranslatedintovectorsequences,andhowthosesequencesare processedtomakereadablevectorproteins. Thepaperexplains:WhatStylusoffersthatnoothermodeloffers,toourknowledge,isan artificialversionofgenetoproteingeneticcausationthatparallelstherealthing. IntheworldofStylus,aChinesecharacterislikeaprotein.Sohowcanwedetermineifa functional"protein"hasevolved?Accordingtothepaper,"AtthecoreofStylussoftwareisan algorithmthatquantifiesthelikenessofagivenvectorproteintoaspecifiedChinesecharacter." Thiscomplicatedalgorithmisdescribedasfollows: Stylusendowsthesegraphicalconstructswithinterestingsimilaritiestotheir molecularcounterpartsbyuncoveringandexploitingapreexistinganalogythe analogybetweenthesetofcharactersusedinChinesewritingandthesetofprotein structuresusedinlife.Specifically,vectorproteinsaredrawnobjectsthatmay functionaslegibleChinesecharactersiftheyaresuitablyformed....Stylusisunique initsuseofrealfunctionthatmapswelltomolecularbiology.Itthereforerepresents asignificantadvanceinthefieldofevolutionarymodeling.(internalcitations omitted) ThepaperpresentsasetofChinesecharactersthatcanbeusedforsimulatingtheevolutionary processintheStylusworld.ButcantheseChinesecharactergroups,whichhavemanyqualities thatparallelrealworldproteinfamilies,evolvebyrandommutationandnaturalselection?That's

thesortofquestionthecreatorsofStylushopetoanswer.Theresultsofsuchsimulationswill probablybefleshedoutinfuturepapers.Butthecurrentpaperleavesuswithastrongsenseof wherethisisallheading: Evolutionarycausationisintrinsicallytiedtotherelationshipbetweengenotypeand phenotype,whichdependsonlowlevelgeneticcausation.Itfollowsthat evolutionaryexplanationsoftheoriginoffunctionalproteinsystemsmust subordinatethemselvestoourunderstandingofhowthosesystemsoperate.Inother words,thestudyofevolutionarycausationcannotenjoythedisciplinaryautonomy thatstudiesofgeneticcausationcan. Inviewofthis,thecontributionofStylusistomakeevolutionaryexperimentation possibleinamodelworldwherelowlevelgeneticcausationhastheessentialrole thatithasintherealworld.CombinedwiththefreeStylussoftware,thecomplete Stylusgenomemadefreelyavailablewiththispaperpavesthewayforanalogybased studiesonawidevarietyofimportantsubjects,manyofwhicharedifficulttostudy bydirectexperimentation.Amongthesearetheevolutionofnewproteinfoldsby combiningexistingparts,theoptimalityandevolutionaryoptimizationofthegenetic code,thesignificanceofselectivethresholdsfortheoriginandoptimizationof proteinfunctions,andthereliabilityofmethodsusedforhomologydetectionand phylogenetictreeconstruction. Thereprobablywillneverbeaperfectcomputersimulationofbiologicalevolution,butStylus bringsnewandimprovedmethodstothefieldofevolutionarymodeling.Thistoolwillhelpthose interestedintestingtheviabilityofDarwinianclaimstoassesswhethercomplexfeaturescanbe createdbyrandommutationsatthemolecularlevel. StephenC.MeyerandPaulA.Nelson,CantheOriginoftheGeneticCodeBeExplained byDirectRNATemplating?,BIOComplexity,Vol.2011(2)(2011). ThispeerreviewedpaperhaditsoriginsinadebateatBiolaUniversityin2009whereStephen Meyerdebatedtwocriticalbiologists.OneofthosescientistswasArthurHuntfromthe UniversityofKentucky,whohadpreviouslycitedtheresearchofMichaelYaruswhichproposed thatcertainchemicalaffinitiesbetweenRNAtripletsandaminoacidscouldhaveformeda chemicalbasisfortheoriginofthegeneticcode.AccordingtoHunt,Yarussresearchshowed thatchemistryandphysicscanaccountfortheoriginofthegeneticcodeandthusthevery heartofMeyersthesis(andhisbook[SignatureintheCell])iswrong.MeyerandNelsons BIOComplexitypaperrespondstoYarussclaims,showingthatwhenchallenged,IDproponents canproducecompellingtechnicalrebuttals.Accordingtotheirdetailedresponse,Yaruss(and Hunts)claimsfailduetoselectiveuseofdata,incorrectnullmodels,aweaksignalevenfrom positiveresults,andunsupportedassumptionsabouttheprebioticavailabilityofaminoacids. Ratherthanrefutingdesign,theresearchshowstheneedforanintelligentlydirectedoriginof thecode. AnnK.GaugerandDouglasD.Axe,TheEvolutionaryAccessibilityofNewEnzyme Functions:ACaseStudyfromtheBiotinPathway,BIOComplexity,Vol.2011(1)(2011). ThispaperreportsresearchconductedbyBiologicInstitutescientistsAnnGaugerandDouglas Axeonthenumberofminimumchangesthatwouldberequiredtoevolveoneproteininto

anotherproteinwithadifferentfunction.Theinvestigatorsstudiedtwoproteins,KblandBioF, withdifferentfunctionsbuthighlysimilarstructuresthoughtbyevolutioniststobeveryclosely related.Throughmutationalanalysis,GaugerandAxefoundthataminimumofseven independentmutationsandprobablymanymorewouldbenecessarytoconvertKblto performthefunctionofitsallegedlyclosegeneticrelative,BioF.PerAxes2010BIOComplexity paper,"TheLimitsofComplexAdaptation:AnAnalysisBasedonaSimpleModelofStructured BacterialPopulations,"theyreportthatthisisbeyondthelimitsofDarwinianevolution: TheextenttowhichDarwinianevolutioncanexplainenzymaticinnovationseems, oncarefulinspection,tobeverylimited.Largescaleinnovationsthatresultinnew proteinfoldsappeartobewelloutsideitsrange.Thispaperarguesthatatleastsome smallscaleinnovationsmayalsobebeyonditsreach.Ifstudiesofthiskindcontinue toimplythatthisistypicalratherthanexceptional,thenanswerstothemost interestingoriginsquestionswillprobablyremainelusiveuntilthefullrangeof explanatoryalternativesisconsidered. AnnK.Gauger,StephanieEbnet,PamelaF.Fahey,andRalphSeelke,Reductive EvolutionCanPreventPopulationsfromTakingSimpleAdaptivePathstoHighFitness, BIOComplexity,Vol.2010(2)(2010). Thisresearch,publishedbymolecularbiologistAnnGaugeroftheBiologicInstitute,Ralph SeelkeattheUniversityofWisconsinSuperiorstartedbybreakingageneinthebacterium Escherichiacolirequiredforsynthesizingtheaminoacidtryptophan.Whenthegenewasbroken injustoneplace,randommutationsinthebacteriasgenomewerecapableoffixingthegene. Butwhentwomutationswererequiredtorestorefunction,Darwinianevolutioncouldnotdothe job.SuchresultsshowthatitisextremelyunlikelyforblindandunguidedDarwinianprocessesto findrareaminoacidsequencesthatyieldfunctionalproteins.Inessence,functionalproteinsare multimutationfeaturesintheextreme. MichaelJ.Behe,ExperimentalEvolution,LossofFunctionMutations,andTheFirst RuleofAdaptiveEvolution,TheQuarterlyReviewofBiology,Vol.85(4):127(December 2010). ThispeerreviewedpaperbyMichaelBeheinthejournalQuarterlyReviewofBiologyhelps explainwhywedontobservetheevolutionofnewproteinfunctions.Afterreviewingmany studiesonbacterialandviralevolution,heconcludedthatmostadaptationsatthemolecularlevel areduetothelossormodificationofapreexistingmolecularfunction.Inotherwords,since Darwinianevolutionproceedsalongthepathofleastresistance,Behefoundthatorganismsare farmorelikelytoevolvebyalosingabiochemicalfunctionthanbygainingone.Hethus concludedthattherateofappearanceofanadaptivemutationthatwouldarisefromthe diminishmentoreliminationoftheactivityofaproteinisexpectedtobe1001000timestherate ofappearanceofanadaptivemutationthatrequiresspecificchangestoagene.IfBeheiscorrect, thenmolecularevolutionfacesasevereproblem.Ifaloss(ordecrease)offunctionismuchmore likelythanagainoffunction,logicdictatesthateventuallyanevolvingpopulationwillrunoutof molecularfunctionstoloseordiminish.BehespapersuggeststhatifDarwinianevolutionisat work,somethingelsemustbegeneratingtheinformationfornewmolecularfunctions. DouglasD.Axe,TheLimitsofComplexAdaptation:AnAnalysisBasedonaSimple ModelofStructuredBacterialPopulations,BIOComplexity,Vol.2010(4):1(2010).

TheabilityofDarwinianevolutiontoproducefeaturesthatrequiremultiplemutationsbefore gainingabenefithasbeenanissuelongdebatedbetweenproponentsofintelligentdesignand proponentsofneoDarwinism.ThispaperrespondstoargumentsfromMichaelLynchandAdam Abegg,findingthattheymadeamistakeactuallytwomistakesintheircalculationofthelength oftimerequiredformultiplemutationstooccurwhenthereisnoadaptivebenefituntilall mutationsareinplace. ThepurposeofAxespaperisthentomathematicallydeterminehowmuchtimeisneededto evolvetraitsthatrequiremultiplemutationsbeforeanyadaptivebenefitisconferredonthe organism.Henotesthatthereareessentiallythreemodelsthatmightbeinvokedtoexplainthe originofthesecomplexfeatures:molecularsaltation,sequentialfixation,andstochastictunneling. Axespapertacklesstochastictunneling,amodelthatisinasensemidwaybetweenthemolecular saltationandsequentialfixationmodels.AccordingtoAxe,stochastictunneling"differsfrom sequentialfixationonlyinthatitdependsoneachsuccessivepointmutationappearingwithoutthe prioronehavingbecomefixed."However,becausethepriormutationsarenotyetfixedinthe largerpopulation,thismeansthatthenumberoforganismsthathavethepriormutationsmaybe small.Thus,thismechanism"mustinsteadrelyonthenecessarymutationsappearingwithinmuch smallersubpopulations,"orasAxemodelsit,bacteriallines.Thismodelresemblesmolecular saltationinthatitdependsonallrequiredmutationseventuallyappearingbychancebut anticipatesthiswillhappenaftermutationsarefixedinsmallersubpopulations.Axeexplainswhy allofthesemodelsfaceunavoidablestatisticalimprobabilities:"inviewofthefactthatthe underlyinglimitationisanunavoidableaspectofstatisticsthatindependentrareeventsonly veryrarelyoccurincombinationitseemscertainthatallchancebasedmechanismsmust encounterit." Axethusaimstoaccuratelymodeltheevolutionofamultimutationfeature.Heinvestigatestwo cases:(1)whenintermediatemutationsareslightlydisadvantageous,and(2)whenintermediate mutationsareselectivelyneutral.AxeseekstogiveneoDarwinianevolutionageneroushelping ofprobabilisticresourcesbymodelingtheevolutionofbacteriaasexualorganismsthat reproducequicklyandhaveverylargeeffectivepopulationsizes.Unsurprisingly,Axefoundthat Darwinianevolutionhasgreatdifficultyfixingmultiplemutationswhenthosemutationshave negativeselectioncoefficients(i.e.,theyaredisadvantageous,ormaladaptive).Neutralmutations haveabettershotatbecomingfixed,butevenhereAxefindsthattheabilityofneoDarwinian evolutiontoproducemultimutationfeaturesisseverelylimited.Theimplicationsofthisanalysis forDarwinianevolutionarelargeandnegative.Axe'smodelmadeassumptionswhichwerevery generoustowardsDarwinianevolution.Heassumedtheexistenceofahugepopulationof asexuallyreproducingbacteriathatcouldreplicatequicklyperhapsnearlythreetimesperday overthecourseofbillionsofyears.Inthesecircumstances,complexadaptationsrequiringupto sixmutationswithneutralintermediatescanbecomefixed.Beyondthat,thingsbecome implausible.Ifonlyslightlymaladaptiveintermediatemutationsarerequiredforacomplex adaptation,onlyacoupleofmutations(atmosttwo)couldbefixed.Ifhighlymaladaptive mutationsarerequired,thetraitwillneverappear.Axediscussestheimplicationsofhiswork: Intheend,theconclusionthatcomplexadaptationscannotbeverycomplexwithout runningintofeasibilityproblemsappearstoberobust....Althoughstudiesofthis kindtendtobeinterpretedassupportingtheDarwinianparadigm,thepresentstudy indicatesotherwise,underscoringtheimportanceofcombiningcarefulmeasurements withtheappropriatepopulationmodels.

Axe'spaper,becauseitfocusesonbacteria,doesnotmodeltheevolutionofsexuallyreproducing organisms.Insexuallyreproducingeukaryoticorganisms,thelongergenerationtimesandlower effectivepopulationsizeswoulddramaticallylowerthenumberofmutationsthatcouldbefixed beforeacquiringsomeadaptivebenefit.Invertebrateevolution,theprobabilisticresources availabletoDarwinianevolutionwouldbemuchsmallerthanthoseavailabletobacteria,andthe resultproportionatelydifficulttoexplainalongDarwinianlines.Someothermechanismmustbe generatingcomplexmultimutationfeatures. WolfEkkehardLnnig,MutagenesisinPhysalispubescensL.ssp.floridana:Somefurther researchonDollosLawandtheLawofRecurrentVariation,Floricultureand OrnamentalBiotechnology,121(2010). Thisoriginalresearchpaperonmutagenesisinplantsfavorablycites"intelligentdesign proponents,"includingMichaelBehe,WilliamDembski,JonathanWells,andStephenMeyer,as advocatingoneofvariouslegitimate"scientifictheoriesontheoriginofspecies."Citingskeptics ofneoDarwinismsuchasBeheand"thealmost900scientistsoftheScientificDissentfrom Darwinism,"thepapernotesthat: Manyoftheseresearchersalsoraisethequestion(amongothers),whyevenafter inducingliterallybillionsofinducedmutationsand(further)chromosome rearrangementsalltheimportantmutationbreedingprogramshavecometoanend intheWesternworldinsteadofelicitingarevolutioninplantbreeding,eitherby successiveroundsofselective"micromutations"(cumulativeselectioninthesenseof themodernsynthesis),orby"largermutations"...andwhythelawofrecurrent variationisendlesslycorroboratedbythealmostinfiniterepetitionofthespectraof mutantphenotypesineachandanynewextensivemutagenesisexperiment(as predicted)insteadofregularlyproducingarangeofnewsystematicspecies... Lnnigfocusesontheoriginofaparticulartraitfoundinsomeangiosperms,wherelongersepals formashelterfordevelopingfruitcalledinflatedcalyxsyndrome,or"ICS."AccordingtoLnnig, phylogeneticdataindicatethatunderaneoDarwinianinterpretation,thistraitwaseitherlostin multiplelineagesorevolvedindependentlymultipletimes.Ifthetraitevolvedmultipletimes independently,thenwhydosomanyplantsstilllacksucha"lantern"protectiveshelter?After notingthatsomeproponentsofneoDarwinismmakeunfalsifiableappealstounknownselective advantages,heconcludesthatneoDarwinismisnotmakingfalsifiablepredictionsandfindsthat this"infinityofmostlynontestableexplanations(oftenjustsostories)itselfmayputthetheory outsidescience." However,thereisanotherpossibility,namelythescientifichypothesisofintelligentdesign.In contrasttoneoDarwinism,theauthornotestheIDviewcan"befalsifiedbyproving(among otherpoints)thattheprobabilitytoformanICSbypurelynaturalprocessesishigh,thatspecified complexityislow,andfinally,bygeneratinganICSbyrandommutationsinaspeciesdisplaying none."LnnigrecountsthemanyphrasesDarwinusedtoexplainthathistheoryofevolution requires"innumerableslightvariations,"andarguesthattheICScouldnotevolveinsucha stepwisefashion.AfterreviewingthemultiplecomplexstepsinvolvedinforminganICS,he statesthathisresearch"appearstobeinagreementwithBehe'sstudies(2007):itseemstobevery improbablethatthecurrentevolutionarytheorieslikethemodernsynthesis(continuousevolution) orthehopefulmonsterapproach(inoneorveryfewsteps)cansatisfactorilyexplaintheoriginof theICS."Inclosing,LnnigcitesfurtherBehe'sconceptofirreduciblecomplexityandDembski's

argumentsregardingtheuniversalprobabilitybound,contendingthattheICSmaybebeyondthe edgeofevolution.Nevertheless,heleavesthepresentquestionopenforfurtherresearch,which heenthusiasticallyinvites.Yet,citingtheworkofStephenMeyer,WilliamDembski,andRobert Marks,heconcludesthat"itappearstobemorethanunlikelytogeneratethewholeworldof livingorganismsbytheneoDarwinianmethod." GeorgeMontaez,WinstonEwert,WilliamA.Dembski,andRobertJ.MarksII,A VivisectionoftheevComputerOrganism:IdentifyingSourcesofActiveInformation, BIOComplexity,Vol.2010(3)(2010). ThispapercontinuestheworkoftheEvolutionaryInformaticsLabshowingthatsomecause otherthanDarwinianmechanismsisrequiredtoproducenewinformation.ThomasSchneider's "ev"programhasbeenwidelycitedasshowingthatDarwinianprocessescanincrease information.Inthispeerreviewedpaper,WilliamDembskiandhiscoauthorsdemonstratethat, contrarytosuchclaims,theevprogramisinfactriggedtoproduceaparticularoutcome. Accordingtothepaperev"exploit[s]oneormoresourcesofknowledgetomakethe [evolutionary]searchsuccessful"andthisknowledge"predisposesthesearchtowardsitstarget." Theyexplainhowtheprogramsmugglesinactiveinformation: ThesuccessofevislargelyduetoactiveinformationintroducedbytheHamming oracleandfromtheperceptronstructure.Itisnotduetotheevolutionaryalgorithm usedtoperformthesearch.Indeed,otheralgorithmsareshowntomineactive informationmoreefficientlyfromtheknowledgesourcesprovidedbyev. Schneiderclaimsthatevdemonstratesthatnaturallyoccurringgeneticsystemsgain informationbyevolutionaryprocessesandthat"informationgaincanoccurby punctuatedequilibrium."Ourresultsshowthat,contrarytotheseclaims,evdoesnot demonstrate"thatbiologicalinformation...canrapidlyappearingeneticcontrol systemssubjectedtoreplication,mutation,andselection."Weshowthisby demonstratingthatthereareatleastfivesourcesofactiveinformationinev. 1.Theperceptronstructure.Theperceptronstructureispredisposedtogenerating stringsofonessprinkledbyzerosorstringsofzerossprinkledbyones.Sincethe bindingsitetargetismostlyzeroswithafewones,thereisagreaterpredispositionto generatethetargetthanifitwere,forexample,asetofonesandzerosproducedby theflippingofafaircoin. 2.TheHammingOracle.Whensomeoffspringarecorrectlyannouncedasmorefit thanothers,externalknowledgeisbeingappliedtothesearchandactiveinformation isintroduced.Aswiththechild'sgame,wearebeingtoldwithrespecttothesolution whetherwearegetting"colder"or"warmer." 3.RepeatedQueries.Twoqueriescontainmoreinformationthanone.Repeated queriescancontributeactiveinformation. 4.OptimizationbyMutation.Thisprocessdiscardsmutationswithlowfitnessand propagatesthosewithhighfitness.Whenthemutationrateissmall,thisprocess resemblesasimpleMarkovbirthprocessthatconvergestothetarget. 5.DegreeofMutation.AsseeninFigure3,thedegreeofmutationforevmustbe

tunedtoabandofworkablevalues. AcriticmightclaimthatsomeoftheseitemsrepresentapropermodelingofDarwinianevolution. However,thewaythatevusestheseprocessesisunlikeDarwinianevolution.Forexample,in (1),weseethattheprogram'suseofa"perceptron"causestheoutputtobehighlybiasedtowards matchingthetarget.It'sawayofcheatingtoensuretheprogramreachesitstargetsequence. Likewise,in(2)and(4),theprogramcaneffectivelylookaheadandmarchintherightdirection towardsthetarget,whereasunguidedDarwinianevolutionwouldhaveno"lookahead" capability.TheactiveinformationintheHammingOraclemakesasharpcontrastwiththe evolutionofrealbindingsiteswheretheremaybenobindingcapabilityuntilmultiplemutations arefixed. Mutationandselectionarenotthecausesofsuccessinthesegeneticalgorithms.Yes,random mutationoccursandyes,thereisselection.Butselectionisperformedbyafitnessfunctionthatis encodedbytheprogrammer.Andinprogramslikeev,theprogrammerintentionallyshapesthe fitnessfunctiontobeamenabletostepwiseDarwinianevolution.Thiseffectivelyassumesthe truthofDarwinianevolution.Butintherealworldofbiology,fitnessfunctionsmightlookvery different:theremightbelonelyislandsoffunctioninavastseaofnonfunctionalsequences. Indeed,ifoneusesarandomizedfitnessfunction,thesearchperformspoorlyandmightnoteven outperformablindsearch. Thuschoosingtherightfitnessfunction(fromthesetofpossiblefitnessfunctions)requiresas muchormoreinformationthanchoosingtherightstringfromthesetofpossiblestringsinyour searchspace.Thefitnessfunctionitselfisaninformationrichstructure.Theprogramstartswith thisinformationrichfitnessfunction,andthenproducessomethingmuchlessinformationrich thetargetsequence.Andasthepapershows,evdoesthisinarelativelyinefficientway:usingthe sameinformationrichfitnessfunction,youcanfindthetarget700timesmoreefficientlythanby usingsimplesingleagentstochastichillclimbing.Activeinformationissmuggledintothefitness function.RatherthanshowingthatinformationcanarisebyDarwinianevolution,evshowsthat intelligenceisrequired. WilliamA.DembskiandRobertJ.MarksII,TheSearchforaSearch:Measuringthe InformationCostofHigherLevelSearch,JournalofAdvancedComputationalIntelligence andIntelligentInformatics,Vol.14(5):475486(2010). ThispaperbyleadingIDtheoristsWilliamDembskiandRobertMarksarguesthatwithout informationaboutatarget,anythinggreaterthanatrivialsearchisboundtofail:Needleinthe haystackproblemslookforsmalltargetsinlargespaces.Insuchcases,blindsearchstandsno hopeofsuccess.TheyciteNoFreeLunchtheorems,accordingtowhichanysearch techniquewillwork,onaverage,aswellasablindsearch.However,insuchacase,Success requiresanassistedsearch.Butwhencetheassistancerequiredforasearchtobesuccessful? DembskiandMarksthusarguethatsuccessfulsearchesdonotemergespontaneouslybutneed themselvestobediscoveredviaasearch.However,withoutinformationaboutthetarget,the searchforasearchitselfisstillnobetterthanablindsearch:Weprovetworesults:(1)The HorizontalNoFreeLunchTheorem,whichshowsthataveragerelativeperformanceofsearches neverexceedsunassistedorblindsearches,and(2)TheVerticalNoFreeLunchTheorem,which showsthatthedifficultyofsearchingforasuccessfulsearchincreasesexponentiallywithrespect totheminimumallowableactiveinformationbeingsought.Theimplication,ofcourse,isthat withouttheultimateinputfromanintelligentagentactiveinformationsuchsearcheswillfail.

DouglasD.Axe,TheCaseAgainstaDarwinianOriginofProteinFolds,BIO Complexity,Vol.2010(1)(2010). ThispaperbyBiologicInstitutedirectorDouglasAxearguesthataminoacidsequencesthat producefunctionalproteinfoldsaretooraretobediscoveredbythetrialanderrorprocessesof Darwinianevolution.Itbeginsbyobservingthatwhenthegeneticcodewasfirstdiscovered, Thecodehadmadeitclearthatthevastsetofpossibleproteinsthatcouldconceivablybe constructedbygeneticmutationsisfartoolargetohaveactuallybeensampledtoanysignificant extentinthehistoryoflife.Yethowcouldthehighlyincompletesamplingthathasoccurredhave beensosuccessful?Howcouldithavelocatedtheimpressivearrayofproteinfunctionsrequired forlifeinallitsforms,orthecomparablyimpressivearrayofproteinstructuresthatperformthose functions?Thisconcernwasraisedrepeatedlyintheearlydaysofthegeneticcode[14],butit receivedlittleattentionfromthebiologicalcommunity.Afterreviewingtheproblem,Axe concludesthatWithnodiscernableshortcuttonewproteinfolds,weconcludethatthesampling problemreallyisaproblemforevolutionaryaccountsoftheirorigins.Hearguesthatasearch mechanismunabletolocateasmallpatchonagrainoflevel14sandisnotapttoprovidethe explanationoffoldoriginsthatweseek.Clearly,ifthisconclusioniscorrectitcallsforaserious rethinkofhowweexplainproteinorigins,andthatmeansarethinkofbiologicaloriginsasa whole. WinstonEwert,GeorgeMontaez,WilliamDembskiandRobertJ.MarksII,Efficient PerQueryInformationExtractionfromaHammingOracle,42ndSouthEastern SymposiumonSystemTheory,pp.290297(March,2010). ThispapercontinuesthepeerreviewedworkcopublishedbyWilliamDembski,RobertMarks, andothersaffiliatedwiththeEvolutionaryInformaticsLab.Here,theauthorsarguethatRichard DawkinssMETHINKSITISLIKEAWEASELevolutionaryalgorithmstartsoffwithlarge amountsofactiveinformationthatis,informationintelligentlyinsertedbytheprogrammerto aidthesearch.ThispapercoversalloftheknownclaimsofoperationoftheWEASELalgorithm andshowsthatinallcases,activeinformationisused.Dawkinssalgorithmcanbestbe understoodasusingaHammingoracleasfollows:Whenasequenceoflettersispresentedtoa Hammingoracle,theoraclerespondswiththeHammingdistanceequaltothenumberofletter mismatchesinthesequence.Theauthorsfindthatthisformofasearchisveryefficientatfinding itstargetbutthatisonlybecauseitispreprogrammedwithlargeamountsofactiveinformation neededtoquicklyfindthetarget.Thispreprogrammedactiveinformationmakesitfarremoved fromatrueDarwinianevolutionarysearchalgorithm.Anonlinetoolkitofprogramscalled WeaselWareaccompaniesthepaperandcanbefoundathttp://evoinfo.org/weasel. DavidL.Abel,ConstraintsvsControls,TheOpenCyberneticsandSystemicsJournal, Vol.4:1427(January20,2010). Thisarticleexplainsthattheorganizationofmatterinliferequiresnonmaterialcausessuchas "mentalchoiceoftokens(physicalsymbolvehicles)inamaterialsymbolsystemwhichthen "instantiatesnonphysicalformalPrescriptiveInformation(PI)intophysicality."Italso acknowledgesthatlifeisfundamentallybaseduponinformation:"Life,ontheotherhand,is highlyinformational.Metabolicorganizationandcontrolishighlyprogrammed.Lifeismarkedby theintegrationoflargenumbersofcomputationalsolutionsintooneholisticmetasystem.Noas ofyetundiscoveredlawwilleverbeabletoexplainthehighlyinformationalorganizationof livingorganisms."Thearticleexplainsthat"choicecontingency"isaconceptwheretheoutcome

isdeterminedbythechoiceofanintelligentagent: Whereaschancecontingencycannotcauseanyphysicaleffects,choicecontingency can.Butchoicecontingency,likechancecontingency,isformal,notphysical.So howcouldnonphysicalchoicecontingencypossiblybecomeacauseofphysical effects?Theanswerliesinourabilitytoinstantiateformalchoicesintophysical media.Asweshallseebelow,formalchoicescanberepresentedandrecordedinto physicalityusingpurposefullychosenphysicalsymbolvehiclesinanarbitrarily assignedmaterialsymbolsystem.Choicescanalsoberecordedthroughthesettingof configurableswitches.Configurableswitchesarephysicodynamicallyindeterminate (inertdecoupledfromandincoherentwithphysicodynamiccausation).Thismeans thatphysicodynamicsplaysnoroleinhowtheswitchisset.Physicodynamicfactors areequalintheflippingofabinaryswitchregardlessofwhichoptionisformally chosen.Configurableswitchesrepresentdecisionnodesandlogicgates.Theyareset accordingtoarbitraryrules,notlaws.Herearbitrarydoesnotmeanrandom. Arbitrarymeansnotphysicodynamicallydetermined.Rulesarenotconstrainedby physicalnature.Arbitrarymeansfreelyselectablechoicecontingent. Onlyanintelligentcauseanagentcouldimplementsuchchoicecontingency.Thearticle furtherexplainsthatphysicalconstraintsarenotwhatgovernlife,butratherchoicecontrols, whichcannotbeexplainedbymetaphysicalnaturalism: Volition(choicecontingency)iseverybitasrepeatedlyobservable,predictable (givenanyformoftrueorganization),andaspotentiallyfalsifiableasanynaturalistic hypothesis.Volitionandcontrolarenomoremetaphysicalthanacceleration, wave/particleduality,weight,height,quarks,andlight.Wecannotlabelvolitionand controlmetaphysical,andquantummechanicsandstatisticalmechanicsphysical. Mathematicsandthescientificmethodthemselvesarenonphysical.Volitional controls(asopposedtomereconstraints)areafactofobjectivereality.Ifthisfact doesnotfitwithintheperimeterofourprizedlifelongworldview,perhapsitistime toopenourmindsandreconsiderthepurelymetaphysicalpresuppositionsthat shapedthatinadequateworldview.Philosophicnaturalismcannotempiricallyor logicallygenerateorganizationalbonafidecontrols.Itcanonlygenerateself ordering,lowinformational,unimaginativeconstraintswithnoformalcybernetic capabilities.Metaphysicalnaturalismistoosmallaperimetertocontainallofthe pieces.Naturalismistooinadequateametanarrativetobeabletoincorporateallof theobservablescientificdata. Thearticleconcludesthattheformalismsweseeinlifeariseonlyinthemindsofagents. DavidL.Abel,TheGS(geneticselection)Principle,FrontiersinBioscience,Vol.14:2959 2969(January1,2010). Thispaperstudiesthegeneticcode,observingthatNucleotidesfunctionasphysicalsymbol vehiclesinamaterialsymbolsystem.Butitarguesthatteleologyisnecessarytoexplainthe choicecontrolsinsuchsystems:Thechallengeoffindinganaturalmechanismforlineardigital programmingextendsfromprimordialgeneticsintothemuchlargerrealmofsemanticsand semioticsingeneral.SaysBarham:Themainchallengeforinformationscienceistonaturalize thesemanticcontentofinformation.Thiscanonlybeachievedinthecontextofanaturalized

teleology(byteleologyismeantthecoherenceandthecoordinationofthephysicalforces whichconstitutethelivingstate).Thealternativetermteleonomyhasbeenusedtoattributeto naturalprocesstheappearanceofteleology(4345).Eitherway,thebottomlineofsuch phenomenaisselectionforhigherfunctionatthelogicgateprogramminglevel.Thearticle explainswhynaturalselectionisinadequatetoexplainmanyfeaturesweobserveinbiology,and whyinsteadwerequireacausethatcananticipatefunction:Programmingselectionsat successivedecisionnodesrequiresanticipationofwhatselectionsandwhatsequenceswouldbe functional.Selectionmustbeforpotentialfunction.Naturecannotanticipate,letaloneplanor pursueformalfunction.Naturalselectioncanonlypreservethefittestalreadyexistingholistic life. D.Halsmer,J.Asper,N.Roman,andT.Todd,TheCoherenceofanEngineeredWorld, InternationalJournalofDesign&NatureandEcodynamics,Vol.4(1):4765(2009). Thispeerreviewedscientificpaperarguesthatweliveinan"engineeredworld."Itobservesthat "Humanengineeredsystemsarecharacterizedbystability,predictability,reliability,transparency, controllability,efficiency,and(ideally)optimality.Thesefeaturesarealsoprevalentthroughout thenaturalsystemsthatmakeupthecosmos.However,thelevelofengineeringappearstobefar aboveandbeyond,ortranscendentof,currenthumancapabilities."Thepapercitesthefinetuning oftheuniverseforlife,suchasthespecialpropertiesofwater,theprevalenceofelementsneeded forlife(e.g.hydrogen,oxygen,andcarbon),theexpansionrateoftheuniverse,aswellasthe GalacticHabitableZone,aconceptdevelopedbyDiscoveryInstituteseniorfellowGuillermo Gonzalez: Ontheuniversalscale,however,onecanseethatourplanetisinacomparatively narrowregionofspaceknownasthe"GalacticHabitableZone.Thiszoneallows fortherightsurfacetemperature,stableclimatemetallicity,abilitytoholdliquid water,andmanyotherconditionsnecessaryforlife.Thereisnopracticalreasonwhy theuniversehastocontainlife,butthefactthatitdoesgivesgreatimportancetothis zoneforthebenefitofourexistence. TheauthorsthenexplainGonzalezandJayRichards'sPrivilegedPlanetargument: Notonlydoesthiszonesatisfytherequirementsoflifebutalsoitendowedhumans withaprimepositiontoviewthewondersoftheuniverse.Therearemanyqualities thatmaketheearthanexcellentplacefromwhichtostudytheuniverse.Firstofallis thetransparencyoftheatmosphere.Ouratmosphereadmitstheradiationnecessary forlifewhileblockingmostofitslethalenergy.Thistransparencyalsoallows humanstoseeintospacewithoutthedistortionscausedbyathickatmosphereas wouldbethecaseonVenus.Secondly,theregularityofoursolarsystem'sorbits makestimecalculationofplanetaryeventsmorepredictable,evenallowingfor estimationsofplanetaryorbitsmillionsofyearsago.Finally,thegasanddustinour regionoftheMilkyWayarediffusecomparedtootherregionsinthelocalmid plane.Thisallowshumanstoview80%oftheuniversewithoutblockage.Ifour solarsystemwasmovedfartheraway,perpendicularlytothemidplane,wewould beabletoseetheother20%.However,thiswouldcausealargepercentageofour currentviewtobeblockedbydustaswellastheluminosityofstarsinclose proximity.Humanity'splaceintheuniverseisamazinglyuniquewhenitcomesto discovery.Planetearthisinprimepositionforthegleaningofknowledgefromthe

stars. Thepaperalsofocusesonfinetuninginbiologyasevidenceofbiologicaldesign,citingthework ofavarietyofnoteworthyproponentsofintelligentdesign,includingWalterBradley,Michael Behe,JonathanWells,andWilliamDembski.Thepaperexaminestheengineeringoflife,noting that"[b]iologicalsystemsareconstantlyundergoingprocessesthatexhibitmodularity,specificity, adaptability,durability,andmanyotheraspectsofengineeredsystems."ItquotesfromWilliam DembskiandJonathanWells'sbookTheDesignofLife,stating:"Manyofthesystemsinsidethe cellrepresentnanotechnologyatascaleandsophisticationthatdwarfshumanengineering. Moreover,ourabilitytounderstandthestructureandfunctionofthesesystemsdependsdirectly onourfacilitywithengineeringprinciples."TheauthorsfurthercitetheworkofMichaelBehe's, suchasDarwin'sBlackBoxandTheEdgeofEvolution,explainingthatbiologicalsystems display"irreduciblecomplexity"whichrequiresagoaldirectedprocessor"'bottomuptopdown' design".Afterexaminingtheengineeringofouruniversefromthemacrotomicroscopescales, theyconclude:"Aninterdisciplinarystudyofthecosmossuggeststhatatranscendently engineeredworldmaybethemostcoherentexplanationfortherealityweexperienceashuman beings." WinstonEwert,WilliamA.Dembski,andRobertJ.MarksII,EvolutionarySynthesisof NandLogic:DissectingaDigitalOrganism,Proceedingsofthe2009IEEEInternational ConferenceonSystems,Man,andCybernetics,pp.30473053(October,2009). In2003,researchersattheUniversityofMichiganpublishedinNaturetheresultsofacomputer simulationofevolutioncalledAvida.ThepapersauthorsexpresslyframedAvidaasa refutationofintelligentdesign(ID)arguments,claimingtheprogramshowsthatcomplex adaptivetraitsdoemergeviastandardDarwinianmechanisms.ButdoesAvidatrulymodel standardDarwinianmechanisms?In2009,fourresearchersattheproIDEvolutionary InformaticsLabfurtheredthisscientificdebateinapeerreviewedpapertitled,Evolutionary SynthesisofNandLogic:DissectingaDigitalOrganism.Buildinguponconceptspreviously establishedbyWilliamDembskiandRobertJ.Marks,thepaperarguesthatAvidasprogrammers smuggleinactiveinformationtoallowtheirsimulationtofinditsevolutionarytargets. Accordingtothepaper,sourcesofintelligentlyprogrammedactiveinformationinAvida includethefollowing: ActiveinformationfromAvidasinitializationwhere[t]heinitializationinAvida recognizestheessentialroleofthenopCinstructioninfindingtheEQU. Mutation,fitness,andchoosingthefittestofanumberofmutatedoffspring. Mostimportantly,thereisStairstepactiveinformationwherethedigitalmutationsin Avidaareessentiallypreprogrammedtoperformausefulfunction,andarerewardedfor doingso. Ewert,Dembski,andMarksfocusonthisthirdpoint,notingthat,Theimportanceofstairstep activeinformationisevidentfromtheinabilitytogenerateasingleEQU[thetargetfunction]in Avidawithoutusingit.Theyask,Whathappenswhennostairstepactiveinformationis applied?andnotewhattheoriginalauthorsoftheAvidapaperinNaturereveal: Attheotherextreme,50populationsevolvedinanenvironmentwhereonlyEQU wasrewarded,andnosimplerfunctionyieldedenergy.WeexpectedthatEQU wouldevolvemuchlessoftenbecauseselectionwouldnotpreservethesimpler

functionsthatprovidefoundationstobuildmorecomplexfeatures.Indeed,noneof thesepopulationsevolvedEQU,ahighlysignificantdifferencefromthefractionthat didsointherewardallenvironment. ButdoesrealbiologyrewardmutationstotheextentthatAvidadoes?Thepassagequoted aboveshowsthatwhenAvidaiscalibratedtomodelactualbiologywheremanychangesmay benecessarybeforethereisanybeneficialfunctiontoselectfor(irreduciblecomplexity)none ofthesepopulationsevolvedthetargetfunction.Avidascreatorstrumpetitssuccess,butEwert, Dembski,andMarksshowthatAvidausesstairstepactiveinformationbyrewardingformsof digitalmutationsthatarepreprogrammedtoyieldthedesiredoutcome.Itdoesnotmodeltrue Darwinianevolution,whichisblindtofutureoutcomesandcannotuseactiveinformation.The implicationsmaybeunsettlingforproponentsofneoDarwiniantheory:NotonlyisDarwinian evolutiononaveragenobetterthanblindsearch,butAvidaisriggedbyitsprogrammersto succeed,showingthatintelligenceisinfactnecessarytogeneratecomplexbiologicalfeatures.An onlinetoolkitofprogramscalledMiniVidaaccompaniesthepaperandcanbefoundat http://evoinfo.org/minivida. WilliamA.DembskiandRobertJ.MarksII,BernoullisPrincipleofInsufficientReason andConservationofInformationinComputerSearch,Proceedingsofthe2009IEEE InternationalConferenceonSystems,Man,andCybernetics,pp.26472652(October, 2009). Inhis2001bookNoFreeLunch,WilliamDembskiarguedthatDarwinianevolutionarysearches cannotproducenewcomplexandspecifiedinformation,andinformationthatisfoundby Darwiniansearchesactuallyreflectsinformationthatwassmuggledinbyanintelligenceexternal tothesearch.ThispeerreviewedpapercowrittenwithRobertJ.MarksfurthersDembskis arguments,contendingthatinallsearchesincludingDarwinianonesinformationisconserved suchthatonaveragenosearchoutperformsanyother.Theimplicationoftheirprincipleof ConservationofInformation(COI)isthatDarwinianevolution,atbase,isactuallynobetter thanarandomsearch.Tomaketheirargument,thepaperdevelopsamethodologyformeasuring theinformationsmuggledintoasearchalgorithmbyintelligence.ExogenousInformation(I) representsthedifficultyasearchinfindingitstargetwithnopriorinformationaboutitslocation. ActiveInformation(I+ )istheamountofinformationsmuggledinbyintelligencetoaidthesearch algorithminfindingitstarget.EndogenousInformation(Is)thenmeasuresthedifficultythesearch willhaveinfindingitstargetaftertheadditionofActiveInformation.Thus,I+ =IIs.Having laidthistheoreticalgroundwork,DembskiandMarksbegintoapplytheirideastoevolutionary algorithmswhichclaimtoproducenewinformation.Theyarguethatcomputersimulationsoften donotproperlymodeltrulyunguidedDarwinianevolution:COIhasledtotheformulationof activeinformationasameasurethatneedstobeintroducedtorenderanevolutionarysearch successful.Likeanathleteonsteroids,manysuchprogramsaredoctored,intentionallyornot,to succeed,andthusCOIputstoresttheinflatedclaimsfortheinformationgeneratingpowerof evolutionarysimulationssuchasAvidaandev.Theyconcludethatwhentryingtogeneratenew complexandspecifiedinformation,inbiology,asincomputing,thereisnofreelunch,and thereforesomeassistancefromintelligenceisrequiredtoaidDarwinianevolutionfindunlikely targetsinsearchspace. WilliamA.DembskiandRobertJ.MarksII,ConservationofInformationinSearch: MeasuringtheCostofSuccess,IEEETransactionsonSystems,Man,andCyberneticsPart

A:SystemsandHumans,Vol.39(5):10511061(September,2009). ThispeerreviewedarticlebyWilliamA.DembskiandRobertJ.MarksIIchallengestheability ofDarwinianprocessestocreatenewfunctionalgeneticinformation.Darwinianevolutionis,at itsheart,asearchalgorithmthatusesatrialanderrorprocessofrandommutationandunguided naturalselectiontofindgenotypes(i.e.,DNAsequences)thatleadtophenotypes(i.e., biomoleculesandbodyplans)thathavehighfitness(i.e.,fostersurvivalandreproduction). DembskiandMarks'sarticleexplainsthatunlessyoustartwithsomeinformationaboutwhere peaksinafitnesslandscapemaylie,anysearchincludingDarwiniansearchesareonaverage nobetterthanarandomsearch.Afterassessingvariousexamplesofevolutionarysearches, DembskiandMarksshowthatattemptstomodelDarwinianevolutionviacomputersimulations, suchRichardDawkinsfamous"METHINKSITISLIKEAWEASEL"exercise,startoffwith,as DembskiandMarksputit,"problemspecificinformationaboutthesearchtargetorthesearch spacestructure."Accordingtothepaper,suchsimulationsonlyreachtheirevolutionarytargets becausethereisprespecified"accurateinformationtoguidethem,"orwhattheycall"active information."Theimplication,ofcourse,isthatsomeintelligentprogrammerisrequiredtofront loadasearchwithactiveinformationifthesearchistosuccessfullyfindrarefunctionalgenetic sequences.Theyconcludethat"Activeinformationisclearlyrequiredinevenmodestlysized searches."ThispaperisinmanywaysavalidationofsomeofDembski'scoreideasinhis2001 bookNoFreeLunch:WhySpecifiedComplexityCannotBePurchasedwithoutIntelligence, whicharguedthatsomeintelligentinputisrequiredtoproducenovelcomplexandspecified information.DembskihaswrittenaboutthisarticleatUncommonDescent,explaininghowit supportsID:OurcriticswillimmediatelysaythatthisreallyisntaproIDarticlebutthatits aboutsomethingelse(IveseenthislinenowforoveradecadeonceworkonIDstarted encroachingintopeerreviewterritory).Beforeyoubelievethis,havealookatthearticle.Initwe critique,forinstance,RichardDawkinsMETHINKS*IT*IS*LIKE*A*WEASEL(p.1055). Question:WhenDawkinsintroducedthisexample,washearguingproDarwinism?Yeshewas. Incritiquinghisexampleandarguingthatinformationisnotcreatedbyunguidedevolutionary processes,weareindeedmakinganargumentthatsupportsID. DavidL.Abel,TheUniversalPlausibilityMetric(UPM)&Principle(UPP),Theoretical BiologyandMedicalModelling,Vol.6(27)(2009). Materialistsoftenvaguelyappealtovastperiodsoftimeandboundlessprobabilisticresourcesin theuniversetomaketheirscenariossoundplausible.Butismerepossibilitysufficient justificationtoassertscientificplausibility?ThispeerreviewedarticleinTheoreticalBiology andMedicalModellinganswersthatquestion,arguingthat[m]erepossibilityisnotanadequate basisforassertingscientificplausibilitybecause[a]preciselydefineduniversalboundisneeded beyondwhichtheassertionofplausibility,particularlyinlifeoriginmodels,canbeconsidered operationallyfalsified.ThepaperobservesthatCombinatorialimaginingsandhypothetical scenarioscanbeendlesslyarguedsimplyonthegroundsthattheyaretheoreticallypossible,but thenarguesthattheunwillingnessofmaterialiststoconsidercertainoriginoflifemodelstobe falseisactuallystoppingtheprogressofscience,sinceatsomepointourreluctancetoexclude anypossibilitybecomesstultifyingtooperationalscience.ThepaperobservesthatJustbecause ahypothesisispossibleshouldnotgrantthathypothesisscientificrespectability,animportant rejoindertomaterialistswhoproposespeculativestoriesaboutselforganizationorcooptionto explaintheoriginofbiologicalcomplexity.TheauthorthenrigorouslycalculatestheUniversal PlausibilityMetric(UPM),incorporatingthemaximumprobabilisticresourcesavailableforthe

universe,galaxy,solarsystem,andtheearth:
c =Universe=1013reactions/secX1017secsX1078atoms=10108 u c =Galaxy=1013X1017X1066=1096 g c =SolarSystem=1013X1017X1055=1085 s c =Earth=1013X1017X1040=1070 e

TheauthorconcludesthatconsiderationofUniversalPlausibilityMetricsallowforfalsificationof speculativeoriginoflifescenarios:TheapplicationofTheUniversalPlausibilityPrinciple(UPP) precludestheinclusioninscientificliteratureofwildmetaphysicalconjecturesthatconveniently ignoreorillegitimatelyinflateprobabilisticresourcestobeyondthelimitsofobservational science.Whenhypothesesrequireprobabilisticresourcesthatexceedthesemetrics,theauthor arguesthattheyshouldbeconsiderednotonlyoperationallyfalsifiedhypotheses,butbad metaphysicsonaplaneequivalenttoblindfaithandsuperstition.Itconcludesthatthecomplexity weseeinliferequiresanagentbasedcausethatcanmakechoices:Symbolsystemsand configurableswitchsettingscanonlybeprogrammedwithchoicecontingency,notchance contingencyorfixedlaw,ifnontrivialcoordinationandformalorganizationareexpected. DavidL.Abel,TheCapabilitiesofChaosandComplexity,InternationalJournalof MolecularSciences,Vol.10:247291(2009). Thispaperseekstoaddressthequestion,Ifallknownlifedependsupongeneticinstructions, howwasthefirstlineardigitalprescriptivegeneticinformationgeneratedbynaturalprocess? Theauthorwarnsmaterialiststhatthereisaneasysolutiontothechallengesposedbyintelligent design:TostemthegrowingswellofIntelligentDesignintrusions,itisimperativethatwe providestandalonenaturalprocessevidenceofnontrivialselforganizationattheedgeofchaos. Wemustdemonstrateonsoundscientificgroundstheformalcapabilitiesofnaturallyoccurring physicodynamiccomplexity.However,whiletheauthornotesthatmuchefforthasbeenspent arguingtothelaycommunitythatwehaveprovedthecurrentbiologicalparadigm,he concludesthattheactualevidenceforselforganizationissorelylackingandhasbeen inflated.Theauthoremphasizesadistinctionbetweenorderandorganization,arguingthat selforderedstructureslikewhirlpoolsarereadilyconstructedbynaturalprocesses,buthave neverbeenobservedtoachieve1)programming,2)computationalhalting,3)creative engineering,4)symbolsystems,5)language,or6)bonafideorganizationallhallmarksof livingorganisms.Incontrast,livingorganismsarebuiltuponprogrammingandarehighly organized,butphysicodynamicsalonecannotorganizeitselfintoformallyfunctionalsystems requiringalgorithmicoptimization,computationalhalting,andcircuitintegration.Hissolution offersapositiveargumentfordesign:Noknownnaturalprocessexiststhatspontaneouslywrites meaningfulorfunctionalsyntax.Onlyagentshavebeenknowntowritemeaningfuland pragmaticsyntax.Henotesthatthekindofsophisticatedformalfunctionfoundinlife consistentlyrequiresregulationandcontrol,butControlalwaysemanatesfromchoice contingencyandintentionality,notfromspontaneousmolecularchaos. DavidL.Abel,Thebiosemiosisofprescriptiveinformation,Semiotica,Vol.174(1/4):119 (2009). Thisarticleexplainsthatclassicalmeasuresofinformation,suchasShannonInformation,are inadequatetoexplainbiologicalfunction,suggestingthatfunctionalbiologicalinformationbe

measuredasprescriptiveinformation(PI).Itarguesthatthechoiceofanintelligentagentis necessarytoproducePI:"PIarisesfromexpedientchoicecommitmentsatbonafidedecision nodes.Suchdecisionssteereventstowardpragmaticresultsthatarevaluedbyagents.Empirical evidenceofPIarisingspontaneouslyfrominanimatenatureissorelylacking.Neitherchancenor necessityhasbeenshowntogenerateprescriptiveinformation(TrevorsandAbel2004).Choice contingency,notchancecontingency,prescribesnontrivialfunction."Accordingtothearticle, agentchoiceisrequiredtogeneratetheformalismsfoundinlivingorganism:Formalismsofall kindsinvolveabstractideasandagentmediatedpurposefulchoices.Inanimatephysicsand chemistryhaveneverbeenshowntogeneratelifeorformalchoicebasedsystems. A.C.McIntosh,InformationandEntropyTopDownorBottomUpDevelopmentin LivingSystems,InternationalJournalofDesign&NatureandEcodynamics,Vol.4(4):351 385(2009). Thispaperexpresslyendorsesintelligentdesign(ID)afterexploringakeyquestioninID thinking.Theultimatequestioninoriginsmustbe:Caninformationincreaseinapurely materialisticornaturalisticway?Itisnotsatisfactorytosimplyassumethatinformationhasto haveariseninthisway.Thealternativeoforiginaldesignmustbeallowedandalloptions examinedcarefully.Aprofessorofthermodynamicsandcombustiontheory,McIntoshiswell acquaintedwiththeworkingsofmachinery.Hisargumentisessentiallytwofold:(1)First,he definestheterm"machine"(adevicewhichlocallyraisesthefreeenergy)andobservesthatthe cellisfullofmachines.SuchmachinesposeachallengetoneoDarwinianevolutionduetotheir irreduciblycomplexnature.(2)Second,hearguesthattheinformationinlivingsystems(similarto computersoftware)usessuchmachinesandinfactrequiresmachinestooperate(whatgoodisa programwithoutacomputertorunit?).AnexampleisthegenomeintheDNAmolecule.Froma thermodynamicsperspective,theonlywaytomakesenseofthisistounderstandthatthe informationisnonmaterialandconstrainsthethermodynamicssothatthelocalmatterandenergy areinanonequilibriumstate.McIntoshaddressestheobjectionthat,thermodynamically speaking,highlyorganizedlowentropystructurescanbeformedattheexpenseofanincreasein entropyelsewhereintheuniverse.However,henotesthatthisargumentfailswhenappliedtothe originofbiologicalinformation: whilstthisargumentworksforstructuressuchassnowflakesthatareformedby naturalforces,itdoesnotworkforgeneticinformationbecausetheinformation systemiscomposedofmachinerywhichrequirespreciseandnonspontaneousraised freeenergylevelsandcrystalslikesnowflakeshavezerofreeenergyasthephase transitionoccurs. McIntoshthentacklesthepredominantreductionistviewofbiologicalinformationwhich"regards thecodingandlanguageofDNAasessentiallyaphenomenonofthephysicsandchemistryofthe nucleotidesthemselves."Hearguesthatthisclassicalviewiswrong,for"biologicalstructures containcodedinstructionswhich...arenotdefinedbythematterandenergyofthemolecules carryingthisinformation."AccordingtoMcIntosh,Shannoninformationisnotagoodmeasureof biologicalinformationsinceitis"largelynotrelevanttofunctionalinformationatthephenotype level."Inhisview,"[t]oconsiderbiologicalinformationassimplya'byproduct'ofnatural selectiveforcesoperatingonrandommutationsisnotonlycounterintuitive,butscientifically wrong."AccordingtoMcIntosh,onemajorreasonforthisis"theirreduciblycomplexnatureof themachineryinvolvedincreatingtheDNA/mRNA/ribosome/aminoacid/protein/DNA polymeraseconnections."Hecontinues:

Allofthesefunctioningpartsareneededtomakethebasicformsoflivingcellsto work....This,itmaybeargued,isarepeatoftheirreduciblecomplexityargumentof Behe[67],andmanythinkthatthatdebatehasbeensettledbytheworkofPallen andMatzke[68]whereanattempttoexplaintheoriginofthebacterialflagellum rotarymotorasadevelopmentoftheType3secretorysystemhasbeenmade. However,thisargumentisnotrobustsimplybecauseitisevidentthatthereare featuresofbothmechanismswhichareclearlynotwithinthegeneticframeworkof theother.Thatis,theevidence,farfrompointingtoonebeingtheancestorofthe other,actuallypointstothembothbeingirreduciblycomplex.Intheviewofthe authorthisargumentisstillaverypowerfulone. FurthercitingSignatureintheCell,McIntoshstates:Whatisevidentisthattheinitial informationcontentinDNAandlivingproteinsratherthanbeingsmallmustinfactbelarge,and isinfactvitalforanyprocesstoworktobeginwith.Theissueoffunctionalcomplexityand informationisconsideredexhaustivelybyMeyer[93,94]whoarguesthattheneoDarwinist modelcannotexplainalltheappearancesofdesigninbiology.Sohowdobiologicalsystems achievetheirhighlyordered,lowentropystates?McIntosh'sargumentiscomplementarytothatof StephenMeyer's,butittakesamorethermodynamicapproach.AccordingtoMcIntosh, informationiswhatallowsbiologicalsystemstoattaintheirhighdegreesoforder:thepresence ofinformationisthecauseofloweredlogicalentropyinagivensystem,ratherthanthe consequence.Inlivingsystemstheprincipleisalwaysthattheinformationistranscendentto,but usingraisedfreeenergychemicalbondingsites.McIntoshsolvestheproblemoftheoriginof informationbyarguingthatitmustariseina"topdown"fashionrequiringtheinputof intelligence: [T]hereisaperfectlyconsistentviewwhichisatopdownapproachwherebiological informationalreadypresentinthephenotypiccreature(andnotemergentasclaimed inthetraditionalbottomupapproach)constrainsthesystemofmatterandenergy constitutingthelivingentitytofollowintricatenonequilibriumchemicalpathways. Thesepathwayswhilstobeyingallthelawsofthermodynamicsareconstantly supportingthecodedsoftwarewhichispresentwithin...Withouttheadditionof outsideintelligence,rawmatterandenergywillnotproduceautoorganizationand machinery.Thislatterassertionisactuallyrepeatedlyborneoutbyexperimental observationnewmachineryrequiresintelligence.Andintelligenceinbiological systemsisfromthenonmaterialinstructionsofDNA. ThisthinkingcanbeappliedtoDNA:since"thebasiccodingisthecause(andthusreflectsan initialpurpose)ratherthantheconsequence,[thetopdownapproach]givesamuchbetter paradigmforunderstandingthemolecularmachinerywhichisnowconsistentwithknown thermodynamicprinciples."McIntoshexplainsthatthelowentropystateofbiologicalsystemsis theresultoftheworkingsofmachines,whichmustbebuiltbyintelligence:Ithasoftenbeen assertedthatthelogicalentropyofanonisolatedsystemcouldreduce,andtherebynew informationcouldoccurattheexpenseofincreasingentropyelsewhere,andwithoutthe involvementofintelligence.Inthispaper,wehavesoughttorefutethisclaimonthebasisthatthis isnotasufficientconditiontoachieveariseinlocalorder.Onealwaysneedsamachineinplace tomakeuseofaninfluxofnewenergyandanewmachineinevitablyinvolvesthesystematic raisingoffreeenergiesforsuchmachinestowork.Intelligenceisaprerequisite.Heconcludes hispaperwithanexpressendorsementofintelligentdesign:"theimplicationofthispaperisthatit

supportsthesocalledintelligentdesignthesisthatanintelligentdesignerisneededtoputthe informationintothebiologicalsystem." A.C.McIntosh,Evidenceofdesigninbirdfeathersandavianrespiration,International JournalofDesign&NatureandEcodynamics,Vol.4(2):154169(2009). Inthispeerreviewedpaper,LeedsUniversityprofessorAndyMcIntosharguesthattwosystems vitaltobirdflightfeathersandtheavianrespiratorysystemexhibitirreduciblecomplexity. ThepaperdescribesthesesystemsusingtheexactsortofdefinitionsthatMichaelBeheusesto describeirreduciblecomplexity: [F]unctionalsystems,inordertooperateasworkingmachines,musthaveallthe requiredpartsinplaceinordertobeeffective.Ifonepartismissing,thenthewhole systemisuseless.Theinferenceofdesignisthemostnaturalstepwhenpresented withevidencesuchasinthispaper,thatisevidenceconcerningavianfeathersand respiration. Regardingthestructureoffeathers,hearguesthattheyrequiremanyfeaturestobepresentin ordertoproperlyfunctionandallowflight: [I]tisnotsufficienttosimplyhavebarbulestoappearfromthebarbsbutthat opposingbarbulesmusthaveoppositecharacteristicsthatis,hooksononesideof thebarbandridgesontheothersothatadjacentbarbsbecomeattachedbyhooked barbulesfromonebarbattachingthemselvestoridgedbarbulesfromthenextbarb (Fig.4).ItmaywellbethatasYuetal.[18]suggested,acriticalproteinisindeed presentinsuchlivingsystems(birds)whichhavefeathersinordertoformfeather branching,butthatdoesnotsolvethearrangementissueconcerninglefthandedand righthandedbarbules.Itisthatvitalnetworkofbarbuleswhichisnecessarilya functionoftheencodedinformation(software)inthegenes.Functionalinformation isvitaltosuchsystems. Hefurthernotesthatmanyevolutionaryauthorslookforevidencethattruefeathersdeveloped firstinsmallnonflyingdinosaursbeforetheadventofflight,possiblyasameansofincreasing insulationforthewarmbloodedspeciesthatwereemerging.However,hefindsthatwhenit comestofossilevidencefortheevolutionoffeathers,Noneofthefossilevidenceshowsany evidenceofsuchtransitions. Regardingtheavianrespiratorysystem,McIntoshcontendsthatafunctionaltransitionfroma purportedreptilianrespiratorysystemtotheaviandesignwouldleadtononfunctional intermediatestages.HequotesJohnRubenstating,Theearlieststagesinthederivationofthe avianabdominalairsacsystemfromadiaphragmventilatingancestorwouldhavenecessitated selectionforadiaphragmaticherniaintaxatransitionalbetweentheropodsandbirds.Sucha debilitatingconditionwouldhaveimmedi atelycompromisedtheentirepulmonaryventilatory apparatusandseemsunlikelytohavebeenofanyselectiveadvantage.Withsuchunique constraintsinmind,McIntosharguesthatevenifonedoestakethefossilevidenceastherecord ofdevelopment,theevidenceisinfactmuchmoreconsistentwithanabinitiodesignposition thatthebreathingmechanismofbirdsisinfacttheproductofintelligentdesign. McIntoshspaperarguesthatsciencemustremainatleastopentothepossibilityofdetecting

designinnature,sincetodenythepossibilityoftheinvolvementofexternalintelligenceis effectivelyanassumptioninthereligiouscategory.Sincefeathersandtheavianrespiratory systemexhibitirreduciblecomplexity,heexpresslyarguesthatsciencemustconsiderthedesign hypothesis: Asexamplesofirreduciblecomplexity,theyshowthatnaturalsystemshaveintricate machinerywhichdoesnotariseinabottomupapproach,wherebysomenatural selectivemethodofgainingsmallscalechangescouldgivetheintermediarycreature someadvantage.Thiswillnotworksince,first,thereisnoadvantageunlessallthe partsofthenewmachineareavailabletogetherand,second,inthecaseoftheavian lungtheintermediarycreaturewouldnotbeabletobreathe,andthereislittle selectiveadvantageifthecreatureisnolongeralive.Asstatedintheintroduction,the possibilityofanintelligentcauseisbothavalidscientificassump tion,andborneout bytheevidenceitself. DavidL.Abel,TheCyberneticCut:ProgressingfromDescriptiontoPrescriptionin SystemsTheory,TheOpenCyberneticsandSystemicsJournal,Vol.2:252262(2008). Thisarticletriestoexplainhowscientistscanproduceartificialintelligenceandbridgethe cyberneticcutfromprogrammedreactionstorealchoices.Itthusstates:Howdidinanimate naturegiverisetoanalgorithmicallyorganized,semioticandcyberneticlife?Boththepracticeof physicsandlifeitselfrequiretraversingnotonlyanepistemiccut,butaCyberneticCut.A fundamentaldichotomyofrealityisdelineated.Thedynamicsofphysicality(chanceand necessity)lieononeside.Ontheothersideliestheabilitytochoosewithintentwhataspectsof ontologicalbeingwillbepreferred,pursued,selected,rearranged,integrated,organized, preserved,andused(cyberneticformalism).Thearticlecontendsthatchoicecontingencyis necessarytoproducefunctionalbiologicallifeforms,for:Choicecontingency,ontheother hand,involvespurposefulselectionfromamongrealoptions.Unlikechancecontingency,with choicecontingencyaninternalizedgoalmotivateseachselection.Thepaperfurthernotesthat Thecapabilitiesofchancecontingencyareoftengreatlyinflated,suggestingthatagent steerageisnecessarytoexplainbiologicalfeatures.AccordingtothepaperPurposefulchoices areneededtoachievesophisticatedformalutility.Thechanceand/ornecessityof physicodynamicsalonehaveneverbeenobservedtogenerateanontrivialformalcontrolsystem. Richardv.Sternberg,DNACodesandInformation:FormalStructuresandRelational Causes,ActaBiotheoretica,Vol.56(3):205232(September,2008). ThisarticlebyproIDevolutionarybiologistRichardSternbergcomparestheinformation processingabilityofthecelltocomputerprogramming.Sternbergobservesthatnonphysical symbolsandcodesunderliebiology,statingthatTherearenochemicalconstraintsorlawsthat explainthe64to20mappingofcodonstoaminoacidsandstopsitestherelationsare arbitrarywithrespecttothemolecularcomponentsinthesensethatmappingscanbe reassigned.AccordingtoSternberg,thegeneticcodeislikecomputercodesinthatitcontainsthe followingproperties:Redundancy,Errordampeningcapability,Symbolicandsemantic flexibility,Outputversatility,Multiplerealizability,andTextediting.Thereisalsoacomputer likeformofrecursivityinmolecularbiology,asaproteinproductcaninturnbepartofthe transcriptional,RNAprocessing,ortranslationalapparatusevenbindingtoitsownmRNA. HeexplainstheinterdependentnatureofDNAandotherbiomolecules,statingAnyDNAcode isbutthedomainofalargersystemthelargersysteminturndependsonDNAcodes(atleastin

part).Theauthorsconclusionisthattheworkingsofbiology,fundamentally,arenotreducible tomaterialmoleculesbutratherresidesininformation,symbols,andsetsofmathematicallylogical rules:Themathematicalstructuresthatproteins(andRNAs!)aretheresultofarenotinagene. Instead,theDNAsequenceisthematerialplatformforthesymbolstringsthatallowinformation tobeaccessed.Inthissense,then,DNAislessthanitsCentralDogmainterpretationbecauseitis notonticallyinformational.YetDNAenablesmanymorecodesystemstha[n]commonly acknowledgedandinthiswayismorethanjustacollectionofcodons. DouglasD.Axe,BrendanW.Dixon,PhilipLu,Stylus:ASystemforEvolutionary ExperimentationBasedonaProtein/ProteomeModelwithNonArbitraryFunctional Constraints,PLoSOne,Vol.3(6):e2246(June2008). ComputersimulationsofevolutionsuchasAvidahavebeenwidelytoutedashavingrefuted intelligentdesign.Butclosescrutinyofthesesimulationsrevealthattheydonotmodeltrue Darwinianprocessesbecausetheyareessentiallypreprogrammedtoevolvecomplexsystems. ThispeerreviewedpaperbyIDproponentsattemptstopresentacomputersimulationthatfixes thesedefectsbymodelingDarwinianevolutioninabiologicallyaccuratemanner,superiortothat usedbyotherevolutionarysimulationssuchasAvida. MichaelSherman,UniversalGenomeintheOriginofMetazoa:ThoughtsAbout Evolution,CellCycle,Vol.6(15):18731877(August1,2007). Thisstrikingpapersupportsintelligentdesignadvocateswhoviewlifeasbeingfrontloadedto allowforbiologicalevolution.Forexample,thepaperstates,Thismodelhastwomajor predictions,firstthatasignificantfractionofgeneticinformationinlowertaxonsmustbe functionallyuselessbutbecomesusefulinhighertaxons,andsecondthatoneshouldbeableto turnoninlowertaxonssomeofthecomplexlatentdevelopmentalprograms,e.g.,aprogramof eyedevelopmentorantibodysynthesisinseaurchin.Inotherwords,lowertaxasomehowhave thegenetictoolstoproducesystemsthattheydonothave,butthatdoexistinhighertaxa.Asthe articlestates:"Genesthatareseeminglyuselessinseaurchinbutareveryusefulinhighertaxons exemplifyexcessivegeneticinformationinlowertaxons.Itisunclearhowsuchgenetic complexitycouldhaveevolved."Whendiscussingtheconvergentuseofpax6inwidelydiverse organisms,itstates:"So,howdoesithappenthatconvergentlyevolvedsystemshavethesame developmentalswitches?Thesefindingsareverydifficulttoexplainwithinthecontextof Darwinianideas."TheauthorproposesahypothesiswheresomepreCambrianancestorthathad "aUniversalGenomethatencodesallmajordevelopmentalprogramsessentialforeveryphylum ofMetazoaemergedinaunicellularoraprimitivemulticellularorganism."Thiscommonancestor thenlostmuchgeneticinformationinmanylineages:TheproposedmodelofaUniversal Genomeimpliesthatalotofinformationencodedingenomesisnotutilizedineachindividual taxon,andthereforeiseffectivelyuseless.Thearticlesuggeststhatmicroevolutionisatwork,but thatDarwinianmacroevolutioncannotbecreditedwithmajorinnovations:Furthermore,genetic evolutionincombinationwithnaturalselectioncoulddefinemicroevolution,however,withinthis modelitisnotresponsiblefortheemergenceofthemajordevelopmentalprograms.Thisisan evolutionarymodel,butitchallengesthesortofunguidedandrandomevolutioninherenttoneo Darwinism,andsupportsanintelligentdesignmodel. KirkK.Durston,DavidK.Y.Chiu,DavidL.Abel,JackT.Trevors,Measuringthe functionalsequencecomplexityofproteins,TheoreticalBiologyandMedicalModelling, Vol.4:47(2007).

Thisarticledevisesamethodofmeasuringthefunctionalsequencecomplexityofproteins,which inturnpermitsdistinguishingbetweenorder,randomness,andbiologicalfunction.Theauthors suggestthatIfgenescanbethoughtofasinformationprocessingsubroutines,thenproteinscan beanalyzedintermsoftheproductsofinformationinteractingwithlawsofphysics.Themetric offunctionalsequencecomplexityadvancedbytheseauthorsishighlysimilartothenotionof complexandspecifiedinformation. WolfEkkehardLnnigandHeinzAlbertBecker,"CarnivorousPlants,"inHandbookof PlantScience,Vol2:14931498(editedbyKeithRoberts,JohnWiley&Sons,2007). This2007chapteroncarnivorousplantsbyLnnigandBeckerintheJohnWiley&Sonsvolume HandbookofPlantSciencesnotesthatitappearstobehardeventoimaginetheclearcut selectiveadvantagesforallthethousandsofpostulatedintermediatestepsinagradualscenario, nottomentiontheformulationandexaminationofscientific(i.e.testable)hypothesesforthe originofthecomplexcarnivorousplantstructuresexaminedabove.Theygoontofavorablycite theworkofMichaelBehe,stating: Thereaderisfurtherinvitedtoconsiderthefollowingproblem.CharlesDarwin providedasufficiencytestforhistheory(1859,p.219):"Ifitcouldbedemonstrated thatanycomplexorganexisted,whichcouldnotpossiblyhavebeenformedby numerous,successive,slightmodifications,mytheorywouldabsolutelybreak down."Darwin,however,statedthathecould"notfindsuchacase."Biochemist MichaelJ.Behe(1996,p.39)hasrefinedDarwin'sstatementbyintroducingand defininghisconceptof"irreduciblecomplexity",specifying:"Byirreducibly complexImeanasinglesystemcomposedofseveralwellmatchedinteractingparts thatcontributetothebasicfunction,whereintheremovalofanyoneoftheparts causesthesystemtoeffectivelyceasefunctioning."Somebiologistsbelievethetrap mechanism(s)ofUtriculariaandseveralothercarnivorousplantgenera(Dionaea, Aldrovanda,Genlisea)comeatleastverynearto"suchacase"ofirreducible complexity. DavidL.Abel,Complexity,selforganization,andemergenceattheedgeofchaosinlife originmodels,JournaloftheWashingtonAcademyofSciences,Vol.93:120(2007). Thisarticlesuggeststhatintelligentmindisresponsibleforthecomplexityoflife,stating:In computerscience,onlytheprogrammer'sminddetermineswhichwaytheswitchknobispushed. Inevolutionsciencewesaythatenvironmentalselectionfavorsthefittestsmallgroups.But selectionisstillthekeyfactor,notchanceandnecessity.Ifphysicodynamicssettheswitches,the switcheswouldeitherbesetrandomlybyheatagitation,ortheywouldbesetbyforce relationshipsandconstants.Neitherchancenornecessity,noranycombinationofthetwo,can program.Chanceproducesonlynoiseandjunkcode.Lawwouldsetalloftheswitchesthesame way.Configurableswitchesmustbesetusingchoicewithintentifcomputationalhaltingis expected. FelipeHouatdeBrito,ArturNouraTeixeira,OtvioNouraTeixeira,RobertoC.L. Oliveira,AFuzzyIntelligentControllerforGeneticAlgorithmParameters,inAdvances inNaturalComputation(LichengJiao,LipoWang,XinboGao,JingLiu,FengWu,eds, SpringerVerlag,2006)FelipeHouatdeBrito,ArturNouraTeixeira,OtvioNoura Teixeira,RobertoC.L.Oliveira,AFuzzyApproachtoControlGeneticAlgorithm

Parameters,SADIOElectronicJournalofInformaticsandOperationsResearch,Vol. 7(1):1223(2007). Thispaper(publishedintwodifferentvenues)usesgeneticalgorithmsthatarecontrolledbyan intelligentagentbasedonfuzzylogicandfindsthatsuchamethodismoreefficientthana randomsearchtypicalofDarwinism.CitingtheIntelligentDesignandEvolutionAwareness (IDEA)Center,itstates:Thesuccessachievedintheimplementationofanintelligentagent controllingtheevolutionaryprocessissomewhatsimilartothecontroversialapproachofthe IntelligentDesignTheory[14],whichisdefendedbymanyscientistsasananswertoseveral aspectsthatarenotwellexplainedbytheneoDarwinistTheory. WolfEkkehardLnnig,KurtStber,HeinzSaedler,JeongHeeKim,Biodiversityand DollosLaw:ToWhatExtentcanthePhenotypicDifferencesbetweenMisopatesorontium andAntirrhinummajusbeBridgedbyMutagenesis,Bioremediation,Biodiversityand Bioavailability,Vol.1(1):130(2007). Thisstudyattemptstotracetheevolutionaryhistoryoftwotaxaoffloweringplantsthat evolutionarybiologistsbelievetobecloselyrelated.Theauthorstriedtousemutagenesis experimentstocausetheplantstraitstoreverttoamoreprimitiveform,butfoundthatsuch basicmutagenesisexperimentswereunabletocausethereversionofthetaxatotheprimitive state.Theauthorshaveanexplanationfortheirobservationsthatexplainsalongstandinglawof evolution,andsupportsthebasictenetsofintelligentdesign:sincemostnewcharactersarise,not bysimpleadditionsbutbyintegrationofcomplexnetworksofgenefunctionsrenderingmany systemstobeirreduciblycomplex(Behe1996,2004forareview,seeLnnig2004),such systemscannotinagreementwithDolloslawsimplyreverttotheoriginalstatewithout destroyingtheentireintegrationpatternguaranteeingthesurvivalofaspecies.Theyconclude that,fortheriseofthesetaxaaswellasfortheinceptionofirreduciblecomplexsystems,the debatecontinueswhethermutationsandselectionalonewillbesufficienttoproduceallthenew geneticfunctionsandinnovationsnecessaryforthecytoplasm,membranes,andcellwalls.The articlefavorablycitesworksfromIDfriendlyscientistssuchasDougAxe'sarticlesinJournalof MolecularBiologyMichaelBehe'sDarwin'sBlackBoxBeheandSnoke's2004articlein ProteinScienceDavidBerlinski'swritingsinCommentaryWilliamDembski'sbooksThe DesignInference,NoFreeLunch,andTheDesignRevolutionStephenC.Meyer'sarticlein ProceedingsoftheBiologicalSocietyofWashington,andhisworkinDarwinism,Design,and PublicEducationandalsocitesproIDentriesfromDebatingDesign. WolfEkkehardLnnig,Mutations:TheLawofRecurrentVariation,Floriculture, OrnamentalandPlantBiotechnology,Vol.1:601607(2006). CitingDarwinsBlackBoxandotherarticlesbyMichaelBeheaboutirreduciblecomplexity,as wellastheworkofWilliamDembskiandStephenMeyer,thisarticlestates:allthemodelsand datarecentlyadvancedtosolvetheproblemofcompletelynewfunctionalsequencesandthe originofneworgansandorgansystemsbyrandommutationshaveprovedtobegrossly insufficientintheeyesofmanyresearchersuponcloseinspectionandcarefulscientific examination.CitingtheworkofMeyer,itfurthernotesthelimitsoftheoriginofspeciesby mutations. DavidL.AbelandJackT.Trevors,Selforganizationvs.selforderingeventsinlifeorigin models,PhysicsofLifeReviews,Vol.3:211228(2006).

Thisarticle,coauthoredbyatheoreticalbiologistandanenvironmentalbiologist,explicitly challengestheabilityofDarwinianmechanismsorselforganizationalmodelstoaccountforthe originofthelanguagebasedchemicalcodeunderlyinglife.Theyexplainthat"evolutionary algorithms,neuralnets,andcellularautomatahavenotbeenshowntoselforganizespontaneously intonontrivialfunctions."Theauthorsobservethatlife,"typicallycontainslargequantitiesof prescriptiveinformation."Theyfurtherarguethat"[p]rescriptionrequireschoicecontingency ratherthanchancecontingencyornecessity,"entailinganecessaryappealtoanintelligentcause. Throughoutthepaper,theauthorsusepositiveargumentsreferencingthecreativepowerof "agents"astheycitetheworkofDiscoveryInstitutefellowsandIDtheoristsWilliamDembski, CharlesThaxton,andWalterBradley.Critiquingmodelsofselforganization,theyconcludethat" [t]heonlyselfthatcanorganizeitsownactivitiesisalivingcognitiveagent." DavidL.AbelandJackT.Trevors,MorethanMetaphor:GenomesAreObjectiveSign Systems,JournalofBioSemiotics,Vol.1(2):253267(2006). Thisarticlearguesforintelligentdesign,observingthatonlyintelligencecapableofmaking choicescancreatethecomplexityweseeinhumanbeings.Theauthorsstate:"Neitherchance contingency(quantifiedbyShannontheory)noranyyettobediscoveredlawofnaturecan generateselectioncontingency(TrevorsandAbel,2004).Yetselectioncontingencyisabundantly evidentthroughoutnature."Thesortofcausethatisneededlookslikethis:"Ifthebrainsdecision nodeswereconstrainedbynaturallaw,ourdecisionswouldnotbereal.Ifourchoiceswere constrainedbychanceornecessity,weshouldstopholdingengineersresponsibleforbuilding collapses,andstopholdingcriminalsresponsiblefortheirbehavior.Realselection/choice contingencynotonlypredatestheexistenceofhumanmetaphorandheuristicuseofanalogy,it producedhumanmentation."Accordingtotheauthors,Signsystemsinhumanexperiencearise onlyfromchoicecontingencyatsuccessivedecisionnodes,notchancecontingencyornecessity. yvindAlbertVoie,Biologicalfunctionandthegeneticcodeareinterdependent,Chaos, SolitonsandFractals,Vol.28:10001004(2006). Inthisarticle,NorwegianscientistyvindAlbertVoieexaminesanimplicationofGdel's incompletenesstheoremfortheoriesabouttheoriginoflife.Gdel'sfirstincompletenesstheorem statesthatcertaintruestatementswithinaformalsystemareunprovablefromtheaxiomsofthe formalsystem.Voiethenarguesthattheinformationprocessingsysteminthecellconstitutesa kindofformalsystembecauseit"expressesbothfunctionandsignsystems."Assuch,byGdel's theoremitpossessesmanypropertiesthatarenotdeduciblefromtheaxiomswhichunderliethe formalsystem,inthiscase,thelawsofnature.HecitesMichaelPolanyi'sseminalessayLife's IrreducibleStructureinsupportofthisclaim.AsPolanyiputit,"thestructureoflifeisasetof boundaryconditionsthatharnessthelawsofphysicsandchemistrytheir(theboundary conditions)structurecannotbedefinedintermsofthelawsthattheyharness."Ashefurther explained,"Asthearrangementofaprintedpageisextraneoustothechemistryoftheprinted page,soisthebasesequenceinaDNAmoleculeextraneoustothechemicalforcesatworkinthe DNAmolecule."LikePolanyi,VoiearguesthattheinformationandfunctionofDNAandthe cellularreplicationmachinerymustoriginatefromasourcethattranscendsphysicsandchemistry. Inparticular,sinceasVoieargues,"chanceandnecessitycannotexplainsignsystems,meaning, purpose,andgoals,"andsince"mindpossessesotherpropertiesthatdonothavethese limitations,"itis"thereforeverynaturalthatmanyscientistsbelievethatlifeisratherasubsystem ofsomeMindgreaterthanhumans."

KirkDurstonandDavidK.Y.Chiu,AFunctionalEntropyModelforBiological Sequences,DynamicsofContinuous,Discrete&ImpulsiveSystems:SeriesBSupplement (2005). ThispeerreviewedarticlebyIDproponentsseekstoofferdefinitionsofinformationthatmeasure informationintermsoffunctionality.Theauthorssapproachmirrorstheconceptofspecified complexity.TheyexplainthatThepurposeofthispaperistoshowthatShannonentropycan alsoberedefinedasafunctionofthejointpatternsbetweendataandfunctionality,thus incorporatingafunctionalinterpretationintothemeasure.Theyexplainthattheirmethodscan alsobeusedtomeasurethedegreeofmutationalchangesnecessarytoconvertonefunctional proteinintoanother:Thedifferenceinfunctionalentropybetweenthetwodifferentsequences notonlyprovidesanestimatefortheamountofinformationrequiredtochangethestarting sequenceintothefinalsequence,butitalsocalculatestheestimatednumberoftrialstoachievethe finalsequenceinevolutionandthusThefunctionalentropychangecalculatedcanbe interpretedasaquantifierofevolutionarychange.Theirpaperexperimentallyteststheirmethods, calculatingdifferenceinfunctionalentropybetweenahoxenzymefoundininsectsand crustaceans,thoughttobehomolagous.Theywrite:Sincethenovelfunctionasexpresseddid notcomeintoeffectuntilall6mutationswereinplace,theevolutionarypathwasmodeledasa randomwalkandyieldedachangeof~26bits.AccordingtoAxe(2010),thisofcoursepushes thelimitofwhatcanbeproducedbyDarwinianevolution. DavidL.AbelandJackT.Trevors,Threesubsetsofsequencecomplexityandtheir relevancetobiopolymericinformation,TheoreticalBiologyandMedicalModeling,Vol. 2(29):115(August11,2005). Thisarticlerecognizestheimportantpointthatbiologicalinformationmustbedefinedintermsof thespecifictypeofinformationitrepresents.ShannoninformationandKomologorovinformation aresaidtobeinadequatemeasuresofinformation.Instead,theauthorsrecommendusing functionalsequencecomplexity,aconceptessentiallyidenticaltospecifiedcomplexity,to measurebiologicalinformation.Thearticlealsoreferstochoicecontingencyentailingan arbitraryintelligentchoiceasaknowncause:Compressionoflanguageispossiblebecauseof repetitiveuseofletterandwordcombinations.Wordscorrespondtoreusableprogramming modules.Theletterfrequenciesandsyntaxpatternsofanylanguageconstrainawriter'savailable choicesfromamongsequencespace.Buttheseconstraintsarethesoleproductofarbitrary intelligentchoicewithinthecontextofthatlanguage.Sourceanddestinationreachaconsensusof communicativemethodologybeforeanymessageissentorreceived.Thismethodologyiscalleda languageoranoperatingsystem.Abstractconcept('choicecontingency')determinesthelanguage system,not'chancecontingency,'andnotnecessity(theorderedpatterningofphysical'laws.')"It thenarguesthattrueorganization,suchasthatstudiedinbiology,requiresthis"choice contingency,"implyingintelligentdesign:"Selforderingphenomenaareobserveddailyinaccord withchaostheory.Butundernoknowncircumstancescanselforderingphenomenalike hurricanes,sandpiles,crystallization,orfractalsproducealgorithmicorganization.Algorithmic 'selforganization'hasneverbeenobserveddespitenumerouspublicationsthathavemisusedthe term.Bonefideorganizationalwaysarisesfromchoicecontingency,notchancecontingencyor necessity." JohnA.Davison,APrescribedEvolutionaryHypothesis,RivistadiBiologia/Biology Forum,Vol.98:155166(2005).

OttoSchindewolfoncewrotethatevolutionpostulates"aunique,historicalcourseofeventsthat tookplaceinthepast,isnotrepeatableexperimentallyandcannotbeinvestigatedinthatway."In thispeerreviewedarticlefromanItalianbiologyjournal,JohnA.Davisonagreeswith Schindewolf.Since"[o]necanhardlyexpecttodemonstrateamechanismthatsimplydoesnot anddidnotexist,"Davisonattemptstofindnewexplanationsfortheoriginofconvergence amongbiologicalforms.Davisoncontendsthat"[t]hesocalledphenomenonofconvergent evolutionmaynotbethatatall,butsimplytheexpressionofthesamepreformed'blueprints'by unrelatedorganisms."Whilediscussingmanyremarkableexamplesof"convergentevolution," particularlythemarsupialandplacentalsabertoothedcats,Davisonisunmistakableinhis meaning.Theevidence,hewrites,"bears,notonlyonthequestionsraisedhere,butalso,onthe wholeissueofIntelligentDesign."Davisonclearlyimpliesthatthisevidenceisexpectedunderan intelligentdesignmodel,butnotunderaNeoDarwinianone. DouglasD.Axe,EstimatingthePrevalenceofProteinSequencesAdoptingFunctional EnzymeFolds,JournalofMolecularBiology,Vol.341:12951315(2004). Thisexperimentalstudyshowsthatfunctionalproteinfoldsareextremelyrare,findingthat "roughlyonein1064signatureconsistentsequencesformsaworkingdomain"andthatthe "overallprevalenceofsequencesperformingaspecificfunctionbyanydomainsizedfoldmaybe aslowas1in1077."Axeconcludesthat"functionalfoldsrequirehighlyextraordinary sequences."SinceDarwinianevolutiononlypreservesbiologicalstructuresthatconfera functionaladvantage,itwouldbeverydifficultforsuchablindmechanismtoproducefunctional proteinfolds.Thisresearchalsoshowsthattherearehighlevelsofspecifiedcomplexityin enzymes,ahallmarkindicatorofintelligentdesign.Axehimselfhasconfirmedthatthisstudy addstotheevidenceforintelligentdesign:"Inthe2004paperIreportedexperimentaldatausedto putanumberontherarityofsequencesexpectedtoformworkingenzymes.Thereportedfigure islessthanoneinatrilliontrilliontrilliontrilliontrilliontrillion.Again,yes,thisfindingdoesseem tocallintoquestiontheadequacyofchance,andthatcertainlyaddstothecaseforintelligent design."SeeScientistSaysHisPeerReviewedResearchintheJournalofMolecularBiology "AddstotheCaseforIntelligentDesign". MichaelBeheandDavidW.Snoke,Simulatingevolutionbygeneduplicationofprotein featuresthatrequiremultipleaminoacidresidues,ProteinScience,Vol.13(2004). Inthisarticle,LehighUniversitybiochemistMichaelBeheandUniversityofPittsburghphysicist Snokeshowhowdifficultitisforunguidedevolutionaryprocessestotakeexistingprotein structuresandaddnovelproteinswhoseinterfacecompatibilityissuchthattheycouldcombine functionallywiththeoriginalproteins.Accordingtotheiranalysis,mechanismsinadditionto standardDarwinianprocessesarerequiredtogeneratemanyproteinproteininteractions: Thefactthatverylargepopulationsizes109orgreaterarerequiredtobuildeven aminimalMRfeaturerequiringtwonucleotidealterationswithin108generationsby theprocessesdescribedinourmodel,andthatenormouspopulationsizesare requiredformorecomplexfeaturesorshortertimes,seemstoindicatethatthe mechanismofgeneduplicationandpointmutationalonewouldbeineffective,at leastformulticellulardiploidspecies,becausefewmulticellularspeciesreachthe requiredpopulationsizes.Thus,mechanismsinadditiontogeneduplicationand pointmutationmaybenecessarytoexplainthedevelopmentofMRfeaturesin

multicellularorganisms. Bydemonstratinginherentlimitationstounguidedevolutionaryprocesses,thisworkgivesindirect scientificsupporttointelligentdesignandbolstersBehe'scaseforintelligentdesigninanswerto someofhiscritics. WolfEkkehardLnnig,Dynamicgenomes,morphologicalstasis,andtheoriginof irreduciblecomplexity,inValerioParisi,ValeriaDeFonzo,andFilippoAluffiPentini eds.,DynamicalGenetics(2004). Biologyexhibitsnumerousinvariantsaspectsofthebiologicalworldthatdonotchangeover time.Theseincludebasicgeneticprocessesthathavepersistedunchangedformorethanthree andahalfbillionyearsandmolecularmechanismsofanimalontogenesisthathavebeenconstant formorethanonebillionyears.Suchinvariants,however,aredifficulttosquarewithdynamic genomesinlightofconventionalevolutionarytheory.Indeed,ErnstMayrregardedthisasoneof thegreatunsolvedproblemsofbiology.InthispaperDr.WolfEkkehardLnnig,SeniorScientist intheDepartmentofMolecularPlantGeneticsattheMaxPlanckInstituteforPlantBreeding Research(nowretired),employsthedesigntheoreticconceptsofirreduciblecomplexity(as developedbyMichaelBehe)andspecifiedcomplexity(asdevelopedbyWilliamDembski)to elucidatetheseinvariants,accountingforthemintermsofanexplicitintelligentdesign(ID) hypothesis. StephenC.Meyer,Theoriginofbiologicalinformationandthehighertaxonomic categories,ProceedingsoftheBiologicalSocietyofWashington,Vol.117(2):213239(2004) (HTML). ThisarticlearguesforintelligentdesignasanexplanationfortheoriginoftheCambrianfauna. Notsurprisingly,itcreatedaninternationalfirestormwithinthescientificcommunitywhenitwas published.(SeeDavidKlinghoffer,TheBrandingofaHeretic,WallStreetJournal,Jan.28, 2005,aswellasthefollowingwebsitebytheeditorwhooversawthearticle'speerreview process:http://www.richardsternberg.net/.)ThetreatmentoftheeditorwhosentMeyer'sarticle outforpeerreviewisastrikingillustrationofthesociologicalobstaclesthatproponentsof intelligentdesignencounterinpublishingarticlesthatexplicitlydefendthetheoryofintelligent design. JohnAngusCampbellandStephenC.Meyer,Darwinism,Design,andPublicEducation (DDPE)(EastLansing,Michigan:MichiganStateUniversityPress,2003publishedas partofthepeerreviewedRhetoricandPublicAffairsSeries). Thisisacollectionofinterdisciplinaryessaysthataddressesthescientific,philosophical,and educationalcontroversiesconcerningthetheoryofintelligentdesign.AccordingtoMichigan StateUniversityPress'soriginaldescriptionofthebook:"Darwinism,Design,andPublic EducationexaminesIDasascience,aphilosophy,andamovementforeducationalreform.In thisbook,leadingdesigntheoristspresenttheirscientificcaseforintelligentdesign,theircriticisms ofcontemporaryDarwinismandtheirargumentsforapluralisticcontroversybasedmodelof scienceeducation."Thebookwaspeerreviewedbyaphilosopherofscience,arhetoricianof science,andaprofessorinthebiologicalsciencesfromanIvyLeagueuniversity.Thebook includesfivescientificarticlesadvancingthecaseforthetheoryofintelligentdesign,thecontents ofwhicharesummarizedbelow.

S.C.Meyer,DnaandtheOriginofLife:Information,Specificationand Explanation,DDPE,pp.223285. Meyercontendsthatintelligentdesignprovidesabetterexplanationthancompeting chemicalevolutionarymodelsfortheoriginoftheinformationpresentinlargebio macromoleculessuchasDNA,RNA,andproteins.Meyershowsthattheterminformation asappliedtoDNAconnotesnotonlyimprobabilityorcomplexitybutalsospecificityof function.Hethenarguesthatneitherchancenornecessity,northecombinationofthetwo, canexplaintheoriginofinformationstartingfrompurelyphysicalchemicalantecedents. Instead,hearguesthatourknowledgeofthecausalpowersofbothnaturalentitiesand intelligentagencysuggestsintelligentdesignasthebestexplanationfortheoriginofthe informationnecessarytobuildacellinthefirstplace. M.J.Behe,DesignintheDetails:TheOriginofBiomolecularMachines,DDPE, pp.287302. Behesetsforthacentralconceptofthecontemporarydesignargument,thenotionof "irreduciblecomplexity."Behebaseshisargumentonaconsiderationofphenomena studiedinhisfield,biochemistry,includingsystemsandmechanismsthatdisplaycomplex, interdependent,andcoordinatedfunctions.Suchintricacy,Beheargues,defiesthecausal powerofnaturalselectionactingonrandomvariation,the"noendinview"mechanismof neoDarwinism.Ontheotherhand,henotesthatirreduciblecomplexityisafeatureof systemsthatareknowntobedesignedbyintelligentagents.Hethusconcludesthat, comparedtoDarwiniantheory,intelligentdesignprovidesabetterexplanationforthe presenceofirreduciblecomplexityinthemolecularmachinesofthecell. P.NelsonandJ.Wells,HomologyinBiology:ProblemforNaturalisticScienceand ProspectforIntelligentDesign,DDPE,pp.303322. PaulNelsonandJonathanWellsreexaminethephenomenonofhomology,thestructural identityofpartsindistinctspeciessuchasthepentadactylplanofthehumanhand,thewing ofabird,andtheflipperofaseal,onwhichDarwinwaswillingtoresthisentireargument. NelsonandWellscontendthatnaturalselectionexplainssomeofthefactsofhomologybut leavesimportantanomalies(includingmanysocalledmolecularsequencehomologies) unexplained.Theyarguethatintelligentdesignexplainstheoriginofhomologybetterthan domechanismscitedbyadvocatesofneoDarwinism. S.C.Meyer,M.Ross,P.Nelson,P.Chien,TheCambrianExplosion:Biology'sBig Bang,DDPE,pp.323402. Meyer,Ross,Nelson,andChienshowthatthepatternoffossilappearanceintheCambrian periodcontradictsthepredictionsorempiricalexpectationsofneoDarwinian(and punctuationalist)evolutionarytheory.Theyarguethatthefossilrecorddisplaysseveral featuresahierarchicaltopdownpatternofappearance,themorphologicalisolationof disparatebodyplans,andadiscontinuousincreaseininformationcontentthatare stronglyreminiscentofthepatternofevidencefoundinthehistoryofhumantechnology. Thus,theyconcludethatintelligentdesignprovidesabetter,morecausallyadequate explanationoftheoriginofthenovelanimalformspresentintheCambrianexplosion.

W.A.Dembski,ReinstatingDesignWithinScience,DDPE,pp.403418. Dembskiarguesthatadvancesintheinformationscienceshaveprovidedatheoreticalbasis fordetectingtheprioractionofanintelligentagent.Startingfromthecommonsense observationthatwemakedesigninferencesallthetime,Dembskishowsthatwedosoon thebasisofclearcriteria.Hethenshowshowthosecriteria,complexityandspecification, reliablyindicateintelligentcausation.Hegivesarationalreconstructionofamethodby whichrationalagentsdecidebetweencompetingtypesofexplanation,thosebasedon chance,physicalchemicalnecessity,orintelligentdesign.Sinceheassertswecandetect designbyreferencetoobjectivecriteria,Dembskialsoarguesforthescientificlegitimacyof inferencestointelligentdesign. FrankJ.Tipler,IntelligentLifeinCosmology,InternationalJournalofAstrobiology,Vol. 2(2):141148(2003). ThispaperbyTulanemathematicianandcosmologistFrankTiplerobservesthatteleological explanationsarelivepossibilitieswithinphysics.Tipleralsocontendsthattheuniverseissetupto permittheexistenceoflife,andthattheuniverseseemsguidedbyanultimategoalinherentit.The implication,asTiplerwrites,isthattheevolutionoflifehasbeenguidedbythatgoal,ratherthan beingentirelyrandom. DavidL.Abel,IsLifereducibletocomplexity?,FundamentalsofLife,Chapter1.2 (2002). Thisarticlesuggeststhatexplainingthefunctionalcomplexityinliferequiresaforcethatcan makechoices:Progressinunderstandingthederivationofbioinformationthroughnatural processeswillcomeonlythroughelucidatingmoredetailedmechanismsofselectionpressure 'choices'inbiofunctionaldecisionnodesequences.Thelatteristhesubjectofboth'BioFunction theory'andthemoreinterdisciplinary'instructiontheory'.Life,then,isnotonlynotreducible tocomplexityitisnotevenreducibletoFSC!Lifeisasymphonyofdynamic,highlyintegrated, algorithmicprocessesyieldinghomeostaticmetabolism,development,growth,andreproduction (ignoringthemisgivingsofthosefewlifeorigintheoristswithmulefixations!).ButasYockey argues,itremainstobeseenwhethersuchhighlysophisticatedalgorithmicprocessescanexist apartfromthelinear,segregatable,digital,FSCinstructionsobservedatthehelmofallknown empiricallife.TheauthorarguesthatThekeytolifeoriginresearchliesinuncoveringthe mechanismswherebytheseproductivealgorithmicprogrammingchoicesweremadeandrecorded innucleicacid.Hecomparestheprocessesthatgeneratedlifetothosethatgeneratecomputer programming:Selectionisexactlywhatisfoundincomputeralgorithms.Correctchoicesateach successivedecisionnodealoneproducesophisticatedsoftware.RSCstringsarepragmatically distinguishedfromFSCstringsbyvirtueofthefactthatRSCstringsarealmostneverobservedto doanythingusefulinanycontext.FSCstrings,ontheotherhand,canbecountedontocontribute specificutility. DavidK.Y.ChiuandThomasW.H.Lui,IntegratedUseofMultipleInterdependent PatternsforBiomolecularSequenceAnalysis,InternationalJournalofFuzzySystems,Vol. 4(3):766775(September2002). CitingtheworkofWilliamDembski,theopeningparagraphofthisarticlereads:Detectionof complexspecifiedinformationisintroducedtoinferunknownunderlyingcausesforobserved

patterns.Bycomplexinformation,itreferstoinformationobtainedfromobservedpatternor patternsthatarehighlyimprobablebyrandomchancealone.Weevaluateherethecomplex patterncorrespondingtomultipleobservationsofstatisticalinterdependencysuchthattheyall deviatesignificantlyfromthepriorornullhypothesis.Suchmultipleinterdependentpatternswhen consistentlyobservedcanbeapowerfulindicationofcommonunderlyingcauses.Thatis, detectionofsignificantmultipleinterdependentpatternsinaconsistentwaycanleadtothe discoveryofpossibleneworhiddenknowledge. MichaelJ.Denton,CraigJ.Marshall,andMichaelLegge,TheProteinFoldsasPlatonic Forms:NewSupportforthepreDarwinianConceptionofEvolutionbyNaturalLaw, JournalofTheoreticalBiology,Vol.219:325342(2002). TheseresearchersreachaconclusionthatisthoroughlyteleologicalandnonDarwinian.The authorslooktolawsofformembeddedinnatureaspossessingthepowertoguidetheformation ofbiologicalstructures.Theintelligentdesignresearchprogramreflectedhereisbroadyet certainlyrecognizable,positingdesignasafeatureprogrammedintonature. WolfEkkehardLnnigandHeinzSaedler,ChromosomeRearrangementand TransposableElements,AnnualReviewofGenetics,Vol.36:389410(2002). Thisarticleexaminestheroleoftransposonsintheabruptoriginofnewspeciesandthe possibilityofapartlypredeterminedgenerationofbiodiversityandnewspecies.Theauthors' approachisnonDarwinian,andtheycitefavorablytheworkofdesigntheoristsMichaelBehe andWilliamDembski,acknowledgingthatsomebiologicalsystemsareirreduciblycomplex. DouglasD.Axe,ExtremeFunctionalSensitivitytoConservativeAminoAcidChangeson EnzymeExteriors,JournalofMolecularBiology,Vol.301:585595(2000). ThisstudypublishedbymolecularbiologistDouglasAxe,nowattheBiologicInstitute, challengesthewidespreadideathathighspeciestospeciesvariationintheaminoacidsequence ofanenzymeimpliesmodestfunctionalconstraints.Darwinistscommonlyassumethatsuch variationindicateslowselectionpressureatthevariableaminoacidsites,allowingmany mutationswithlittleeffect.Axe'sresearchshowsthatevenwhenmutationsarerestrictedtothese sites,theyareseverelydisruptive,implyingthatproteinsarehighlyspecifiedevenatvariablesites. Accordingtothiswork,sequencesdivergenotbecausesubstantialregionsarefreefrom functionalconstraints,butbecauseselectionfiltersmostmutations,leavingonlytheharmless minority.Byshowingfunctionalconstraintstobetheruleratherthantheexception,itraisesthe questionofwhetherchancecaneverproducesequencesthatmeettheseconstraintsinthefirst place.Axehimselfhasconfirmedthatthisstudyaddstotheevidenceforintelligentdesign:"I concludedinthe2000JMBpaperthatenzymaticcatalysisentails'severesequenceconstraints.' Themoreseveretheseconstraintsare,thelesslikelyitisthattheycanbemetbychance.So,yes, thatfindingisveryrelevanttothequestionoftheadequacyofchance,whichisveryrelevantto thecasefordesign."SeeScientistSaysHisPeerReviewedResearchintheJournalofMolecular Biology"AddstotheCaseforIntelligentDesign". SolomonVictorandVijayaM.Nayak,Evolutionaryanticipationofthehumanheart, AnnalsoftheRoyalCollegeofSurgeonsofEngland,Vol.82:297302(2000). Thisarticlearguesthatintelligentdesignisrecognizableinthehumanheart,stating:Comparative

anatomypointstoadesignandaDesigner.Surgeons,anatomistsandanyonestudyingthehuman formandfunctionhaveanunsurpassedopportunitytoponderoverthewondersofcreationand contemplatethebasicquestions:wheredidwecomefrom?whyarewehere?andwherearewe going? SolomonVictor,VljayaM.Nayek,andRaveenRajasingh,EvolutionoftheVentricles, TexasHeartInstituteJournal,Vol.26:168175(1999). Thisarticleconcludesthatthereisadesignintheevolutionofthevenousconnectionsofthe heart,pectinatemuscles,atrioventricularvalves,leftventriculartendons,outflowtracts,andgreat arteries.ButtheversionofevolutionitpresentsisdecidedlynonDarwinian,asitnotesthat evolutionappearstobegoaldirectedbyadesigner:Oneneglectedaspectinthestudyof evolutionisthatofanticipation.Fishatriaandventriclesappeartohaveabuiltinprovisionfor becomingupdatedtothehuman4chamberedstructure.Thistransformationisachievedinstages: thetruncusyieldsthegreatarteries,appropriateshiftingtakesplaceinthegreatarteries,theleft ventricledecreasesinsponginessandincreasesinthesizeofitslumen,thechordopapillary apparatusbecomesmoresophisticated,thecoronarycirculationundergoeschanges,andthe ventricularseptaldefectcloses.Thearticleclosesbystating,"Thisevolutionaryprogression pointstoamasterdesignandplanforcountlessmillennia." W.A.Dembski,TheDesignInference:EliminatingChancethroughSmallProbabilities (Cambridge:CambridgeUniversityPress,1998). ThisbookwaspublishedbyCambridgeUniversityPressandpeerreviewedaspartofa distinguishedmonographseries,CambridgeStudiesinProbability,Induction,andDecision Theory.TheeditorialboardoftheseriesincludesmembersoftheNationalAcademyofSciences aswellasaNobellaureate,JohnHarsanyi,whosharedtheprizein1994withJohnNash, protagonistofthefilmABeautifulMind.CommentingontheideasinTheDesignInference,well knownphysicistandsciencewriterPaulDaviesremarked:"Dembski'sattempttoquantifydesign, orprovidemathematicalcriteriafordesign,isextremelyuseful.I'mconcernedthatthesuspicion ofahiddenagendaisgoingtopreventthatsortofworkfromreceivingtherecognitionit deserves."QuotedinLarryWitham,ByDesign(SanFrancisco:EncounterBooks,2003),p.149. R.Kunze,H.Saedler,andW.E.Lnnig,PlantTransposableElements,inAdvancesin BotanicalResearch,Vol.27:331470(AcademicPress,1997). ThispeerreviewedchapterfromanacademicbookonplantresearchfavorablyreferencesMichel Behesconceptofirreduciblecomplexity.Afternotingthatsomemajorproblemshavetobe solvedforgeneduplicationstobeoffundamentalevolutionarysignificance,itcitestoBehe's 1996bookDarwin'sBlackBoxtojustifythequestion:Whatcouldbetheselectiveadvantageof theintermediate(stillunfinished)reactionchains?Theauthorsfurtherstatethatexamplesof irreduciblycomplexsystemsarefoundinbiology. MichaelBehe,Darwin'sBlackBox:TheBiochemicalChallengetoEvolution(NewYork: TheFreePress,1996). InthisbookBehedevelopsacritiqueofthemechanismofnaturalselectionandapositivecasefor thetheoryofintelligentdesignbaseduponthepresenceof"irreduciblycomplexmolecular machines"andcircuitsinsidecells.ThoughthisbookwaspublishedbyTheFreePress,atrade

press,thepublishersubjectedthebooktostandardscientificpeerreviewbyseveralprominent biochemistsandbiologicalscientists. CharlesB.Thaxton,WalterL.Bradley,RogerL.Olsen,TheMysteryofLife'sOrigin: ReassessingCurrentTheories(NewYork:PhilosophicalLibrary,1984Dallas,Texas: Lewis&StanleyPublishing,4thed.,1992). InthisbookThaxton,BradleyandOlsendevelopaseminalcritiqueoforiginoflifestudiesand developacaseforthetheoryofintelligentdesignbasedupontheinformationcontentand"low configurationalentropy"oflivingsystems. StanleyL.Jaki,TeachingofTranscendenceinPhysics,AmericanJournalofPhysics, Vol.55(10):884888(October1987). ThisarticlefromtheAmericanJournalofPhysicsseekstohelpeducatorsunderstandhowthey canteachstudentsabouttheevidencefortranscendenceintheuniverse.Thearticleassumesthata transcendentrealmexistsbeyondtheuniverseandthattheuniversecanplausiblybesaidtoreflect design. GranvilleSewell,Postscript,inAnalysisofaFiniteElementMethod:PDE/PROTRAN (NewYork:SpringerVerlag,1985)(HTML). Inthisarticleappearingina1985technicalreferencebook,mathematicianGranvilleSewell comparesthecomplexityfoundinthegeneticcodeoflifetothatofacomputerprogram.He recognizesthatthefundamentalproblemforevolutionisthe"problemofnovelties"whichinturn raisesthequestion"Howcannaturalselectioncauseneworganstoariseandguidetheir developmentthroughtheinitialstagesduringwhichtheypresentnoselectiveadvantage?"Sewell explainshowatypicalDarwinistwilltrytobridgebothfunctionalandfossilgapsbetween biologicalstructuresthrough"alongchainoftinyimprovementsinhisimagination,"butthe authornotesthat"theanalogywithsoftwareputshisideasintoperspective."Majorchangestoa speciesrequiretheintelligentforesightofaprogrammer.Naturalselection,aprocessthatis "unabletoplanbeyondthenexttinymutation,"couldneverproducethecomplexityoflife. WilliamG.Pollard,Rumorsoftranscendenceinphysics,AmericanJournalofPhysics, Vol.52(10)(October1984). Inthispeerreviewedpaper,nuclearphysicistWilliamG.PollardnotesthatBigBangcosmology requiressomekindoftranscendentreality.Pollardarguesthatthescientificjustificationforthis transcendentdomaincanbefoundinquantummechanicsbecauseuniversallawsandconstants arefinelytunedtopermittheexistenceofadvancedlife,whichpointtoanintelligentsource,a mind,asdesigningtheuniverse. PeerEditedorEditorReviewedArticlesSupportiveofIntelligentDesignPublishedinScientific Journals,ScientificAnthologiesandConferenceProceedings A.C.McIntosh,FunctionalInformationandEntropyinLivingSystems,Designand NatureIII:ComparingDesigninNaturewithScienceandEngineering,Vol.87(Ashurt, Southampton,UnitedKindom:WITTransactionsonEcologyandtheEnvironment,WIT Press,2006).

Thispaperexplorestheproperwaytomeasureinformationandentropyinlivingorganisms. CitingtheworkofStephenMeyer,theauthorarguesthatrandommutationscannotincreaseorder inalivingsystem:[R]andommutationsalwayshavetheeffectofincreasingthedisorder(or whatwewillshortlydefineaslogicalentropy)ofanyparticularsystem,andconsequently decreasingtheinformationcontent.Whatisevidentisthattheinitialinformationcontentrather thanbeingsmallmustinfactbelarge,andisinfactvitalforanyprocesstoworktobeginwith. TheissueoffunctionalcomplexityandinformationisconsideredexhaustivelybyMeyerwho arguesthattheneoDarwinistmodelcannotexplainalltheappearancesofdesigninbiology. McIntoshcontinues,explainingthatonlyteleologyintelligentdesigncanexplainthe increasesininformationthatgenerateobservedbiologicalcomplexity:Evenwithintheneo Darwinistcamptheevidenceofconvergence(similarity)inthesuggestedevolutionary developmentofdisparatephylogenyhascausedsomewriterstoconsiderchannellingof evolution.Suchthinkingisatacitadmissionofateleologicalinfluence.Thatinformationdoesnot increasebyrandomchanges(contrarytoDawkinsassertion)isevidentwhenweconsiderinthe followingsection,thelogicalentropyofabiochemicalsystem.Heconcludesthatgoaldirected processes,orteleonomy,arerequired:Therehastobepreviouslywritteninformationororder (oftentermedteleonomy)forpassive,nonlivingchemicalstorespondandbecomeactive. JonathanWells,DoCentriolesGenerateaPolarEjectionForce?RivistadiBiologia /BiologyForum,Vol.98:7196(2005). MolecularbiologistJonathanWellswritesintheItalianbiologyjournalRivistadiBiologiathatthe cellmaybeviewedandstudiedasadesignedsystemwithengineeredmachines.Showingthe heuristicvalueofintelligentdesign,hewrites:Insteadofviewingcentriolesthroughthe spectaclesofmolecularreductionismandneoDarwinism,thishypothesisassumesthattheyare holisticallydesignedtobeturbines.Whatifcentriolesreallyaretinyturbines?Thisismuch easiertoconceiveifweadoptaholisticratherthanreductionisticapproach,andifweregard centriolesasdesignedstructuresratherthanaccidentalbyproductsofneoDarwinianevolution.If centriolesreallyareturbines,thenfluidexitingthroughthebladeswouldcausethemtorotate clockwisewhenviewedfromtheirproximalends.Wellshypothesizesthatsuchapproachesmay leadtounderstandingsoftheworkingsofcentrioles,perhapsevenuncoveringsomecausesof cancer. HeinzAlbertBeckerandWolfEkkehardLnnig,Transposons:Eukaryotic, EncyclopediaofLifeSciences(JohnWiley&Sons,2005). Thisencyclopediaentryrecountsthatsomebiologicalsystemsmaybeirreduciblycomplex, stating:"Ageneraldifficultytobementionedinthiscontext(butnotinherentintheselfishDNA hypothesis)isthatmutationandselectionmaynotbethefullexplanationfortheoriginofspecies i.e.thefactorsoftheneoDarwinianscenariomayfindtheirlimits,forexample,inthegeneration ofirreduciblycomplexstructures(Behe,1996).Thisisatermusedtodescribestructuresthat, accordingtoBeheandcoworkers,cannotbeexplainedbyapiecemealproductionvia intermediatesteps."ThearticleelaboratesonBehe'sargumentstating,"Amongtheexamples discussedbyBehearetheoriginsof(1)thecilium,(2)thebacterialflagellumwithfilament,hook andmotorembeddedinthemembranesandcellwalland(3)thebiochemistryofbloodclottingin humans."ThearticlethenproposesthatadditionalsystemsmaychallengeDarwinian explanations,stating:"Moreover,thetrapsofUtricularia(andsomeothercarnivorousplant genera)aswellasseveralfurtherapparatusesintheanimalandplantworldappeartoposesimilar problemsforthemodernsynthesis(joints,echolocation,deceptiveflowers,etc.).Uptonow,

noneofthesesystemshasbeensatisfactorilyexplainedbyneoDarwinism.Whetheraccelerated TEactivitieswithalltheabovenamedmutagenicconsequencescansolvethequestionsposed remainsdoubtful." ScottA.MinnichandStephenC.Meyer,Geneticanalysisofcoordinateflagellarandtype IIIregulatorycircuitsinpathogenicbacteria,ProceedingsoftheSecondInternational ConferenceonDesign&Nature,Rhodes,Greece,editedbyM.W.CollinsandC.A.Brebbia (Ashurst,Southampton,UnitedKingdom:WITPress,2004). Thisarticleunderwentconferencepeerreviewtobeincludedinthispeereditedvolumeof proceedings.MinnichandMeyerdothreeimportantthingsinthepaper.First,theyrefutea popularobjectiontoMichaelBehe'sargumentfortheirreduciblecomplexityofthebacterial flagellum.Second,theysuggestthattheTypeIIISecretorySystempresentinsomebacteria, ratherthanbeinganevolutionaryintermediatetothebacterialflagellum,probablyrepresentsa degenerateformofthesame.Finally,theyargueexplicitlythatcomparedtotheneoDarwinian mechanism,intelligentdesignbetterexplainstheoriginofthebacterialflagellum.Astheauthors explain,Inallirreduciblycomplexsystemsinwhichthecauseofthesystemisknownby experienceorobservation,intelligentdesignorengineeringplayedaroleintheoriginofthe system. FoursciencearticlesinWilliamA.DembskiandMichaelRuse,eds.,DebatingDesign: FromDarwintoDNA(Cambridge,UnitedKingdom:CambridgeUniversityPress,2004) (hereinafterDebatingDesign). WilliamA.Dembksi,TheLogicalUnderpinningsofIntelligentDesign,Debating Design,pp.311330. Inthisarticle,Dembskioutlineshismethodofdesigndetection.Heproposesarigorous wayofidentifyingtheeffectsofintelligentcausationanddistinguishingthemfromthe effectsofundirectednaturalcausesandmaterialmechanisms.Dembskishowshowthe presenceofspecifiedcomplexityor"complexspecifiedinformation"providesareliable markerofpriorintelligentactivity.Healsorespondstoacommoncriticismmadeagainst hismethodofdesigndetection,namelythatdesigninferencesconstitute"anargumentfrom ignorance." WalterL.Bradley,Information,Entropy,andtheOriginofLife,DebatingDesign, pp.331351. WalterBradleyisamechanicalengineerandpolymerscientist.Inthemid1980sheco authoredwhatsupportersconsideraseminalcritiqueoforiginoflifestudiesinthebook TheMysteryofLife'sOrigins.Bradleyandhiscoauthorsalsodevelopedacaseforthe theoryofintelligentdesignbasedupontheinformationcontentand"lowconfigurational entropy"oflivingsystems.Inthischapterheupdatesthatwork.Heclarifiesthedistinction betweenconfigurationalandthermalentropy,andshowswhymaterialistictheoriesof chemicalevolutionhavenotexplainedtheconfigurationalentropypresentinliving systems,afeaturethatBradleytakestobestrongevidenceofintelligentdesign. MichaelBehe,IrreducibleComplexity:ObstacletoDarwinianEvolution,Debating Design,Pp.352370.

InthisessayBehebrieflyexplainstheconceptofirreduciblecomplexityandreviewswhy hethinksitposesasevereproblemfortheDarwinianmechanismofnaturalselection.In addition,herespondstoseveralcriticismsofhisargumentforintelligentdesignfrom irreduciblecomplexityandseveralmisconceptionsabouthowthetheoryofintelligent designappliesinbiochemistry.Inparticularhediscussesseveralputativecounterexamples thatsomescientistshaveadvancedagainsthisclaimthatirreduciblycomplexbiochemical systemsdemonstrateintelligentdesign.Beheturnsthetableonhiscritics,arguingthatsuch examplesactuallyunderscorethebarrierthatirreduciblecomplexityposestoDarwinian explanations,and,ifanything,showtheneedforintelligentdesign. StephenC.Meyer,TheCambrianInformationExplosion:EvidenceforIntelligent Design,DebatingDesign,pp.371391. MeyerarguesfordesignonthebasisoftheCambrianexplosion,thegeologicallysudden appearanceofnewanimalbodyplansduringtheCambrianperiod.Meyernotesthatthis episodeinthehistoryofliferepresentsadramaticanddiscontinuousincreaseinthe complexspecifiedinformationofthebiologicalworld.Hearguesthatneitherthe Darwinianmechanismofnaturalselectionactingonrandommutationsnoralternativeself organizationalmechanismsaresufficienttoproducesuchanincreaseininformationinthe timeallowedbythefossilevidence.Instead,hesuggeststhatsuchincreasesinspecified complexinformationareinvariablyassociatedwithconsciousandrationalactivity,thatis, withintelligentdesign. GranvilleSewell,AMathematiciansViewofEvolution,TheMathematicalIntelligencer, Vol.22(4)(2000).(HTML). MathematicianGranvilleSewellexplainsthatMichaelBehe'sargumentsagainstneoDarwinism fromirreduciblecomplexityaresupportedbymathematicsandthequantitativesciences, especiallywhenappliedtotheproblemoftheoriginofnewgeneticinformation.Sewellnotesthat thereare"agoodmanymathematicians,physicistsandcomputerscientistswho...areappalledthat Darwin'sexplanationforthedevelopmentoflifeissowidelyacceptedinthelifesciences." Sewellcomparesthegeneticcodeoflifetoacomputerprogramacomparisonalsomadeby computergurussuchasBillGatesandevolutionarybiologistssuchasRichardDawkins.He notesthatexperienceteachesthatsoftwaredependsonmanyseparatefunctionallycoordinated elements.Forthisreason"[m]ajorimprovementstoacomputerprogramoftenrequiretheaddition ormodificationofhundredsofinterdependentlines,nooneofwhichmakesanysense,orresults inanyimprovement,whenaddedbyitself."Sinceindividualchangestopartofageneticprogram typicallyconfernofunctionaladvantage(inisolationfrommanyothernecessarychangestoother portionsofthegeneticcode),Sewellarguesthatimprovementstoageneticprogramrequirethe intelligentforesightofaprogrammer.Undirectedmutationandselectionwillnotsufficeto producethenecessaryinformation. ArticlesSupportiveofIntelligentDesignPublishedinPeerReviewedPhilosophyJournals,or PeerReviewedPhilosophyBooksSupportiveofIntelligentDesign MichaelC.Rea,WorldwithoutDesign:TheOntologicalConsequencesofNaturalism (OxfordUniversityPress,2004). WilliamLaneCraig,DesignandtheAnthropicFineTuningoftheUniverse,inGodand

Design:TheTeleologicalArgumentandModernScience,pp.155177.(NeilMansoned., London:Routledge,2003). MichaelBehe,ReplytomyCritic:AResponsetoReviewsofDarwinsBlackBox:The BiochemicalChallengetoEvolution,BiologyandPhilosophy,Vol.16,685709,(2001). InthisarticlepublishedinthemainstreamjournalBiologyandPhilosophy,MichaelBehedefends hisviewssupportingintelligentdesignasstatedDarwinsBlackBox. DelRatzsch,Nature,Design,andScience:TheStatusofDesigninNaturalScience(State UniversityofNewYorkPress,2001). WilliamLaneCraig,TheAnthropicPrinciple,inTheHistoryofScienceandReligionin theWesternTradition:AnEncyclopedia,pp.366368(GaryB.Ferngren,generaled., GarlandPublishing,2000). MichaelBehe,SelfOrganizationandIrreduciblyComplexSystems:AReplytoShanks andJoplin,PhilosophyofBiology,Vol.67(1):155162(March,2000). MichaelBehedefendshisargumentsforirreduciblecomplexityagainstthecriticismsofvarious Darwinianscientists. WilliamLaneCraig,BarrowandTiplerontheAnthropicPrinciplevs.DivineDesign, BritishJournalforthePhilosophyofScience,Vol.38:389395(1988). WilliamLaneCraig,God,Creation,andMr.Davies,BritishJournalforthePhilosophy ofScience,Vol.37:168175(1986).

TheworkofDiscoveryInstituteismadepossiblebythegenerosityofitsmembers.Clickheretodonate.

DiscoveryInstituteCenterforScienceandCulture 208ColumbiaSt.Seattle,WA98104 2062920401phone2066825320fax email:cscinfo@discovery.orgAlso:www.intelligentdesign.org