Download pdf - Chapter Language and Communication as Universal ... · Language and Communication as Universal Requirements for Life Guenther Witzany Contents 16.1 Introduction and Objectives 350

349

C h a p t e r 16

Language and Communication as Universal Requirements for Life

Guenther Witzany

Contents16.1 IntroductionandObjectives 35016.2 SummaryofCurrentKnowledgeaboutNaturalLanguages/Codesand

Communication 35016.2.1 LanguageIsaNaturalLanguageOnlyIfLivingAgentsUseIt 35116.2.2 MathematicalTheoriesofLanguagevs.PragmaticsofLanguages 35116.2.3 HowtoGenerateCorrectScientificSentences:ResultsofthePhilosophy

ofScienceDebateintheTwentiethCentury 35216.2.4 MeaningofMessagesDependsonContextualUse(Pragmatics),NotSyntax 354

16.3 KeyLevelsofBiocommunicationin ProkaryotesandEukaryotes 35616.3.1 Prokaryotes 35616.3.2 Eukaryotes 356

16.3.2.1Fungi 35616.3.2.2Animals 35816.3.2.3Plants 359

16.4 NucleicAcidLanguageasNaturalCode 36016.5 AgentsofNaturalGenomeEditing 362

16.5.1 BiocommunicationintheRNAWorld:RNASociology 36316.5.2 BiocommunicationattheLeveloftheRNAGroupMembership 36316.5.3 CooperationOutcompetesSelfishness 365

16.6 Conclusion 366Glossary 367ReviewQuestions 367RecommendedReadings 368

K19048_C016.indd 349 4/15/2014 11:19:06 AM

350 ◾ Astrobiology

16.1 IntroduCtIon And objeCtIvesNowadays,weknowthat it isanempirical fact that if cells, tissues,organs,andorgan-ismscoordinatetheirbehavior,thisneedssignals.Bioticsignalingservesasaprimarytooltocoordinategroupsofindividuallivingagentssuchascellsandorganisms,thatis,thewholeprocesswetermcommunication.Currentknowledgeindicatescommunicationasabasicinteractionwithinandbetweenorganismsinalldomainsoflife.Communicativeinteractions are necessary within organisms—intraorganismic—to coordinate cell–cellinteractions,similartotissue–tissueandorgan–organcoordinationsespeciallyincomplexbodies.Thisincludesalsotheinterpretationofabioticenvironmentalindicessuchaslight,temperature,gravity,water,andnutrientavailabilityassensing,monitoring,andfeedbackcontrolagainststoredbackgroundmemories.Wefindinterorganismiccommunicationinallsignal-mediatedinteractionsbetweensameandrelatedspecies.Ifspeciescommunicatewithnonmembers,wetermthis transorganismiccommunication.Throughoutallking-domsoflife,wedonotfindanycoordinationandorganizationthatdoesnotdependoncommunication.Inthischapter,Iwillshortlysummarizethesecommunicativelevelsinvariousdomainsoflife.

Additionally, all that protein-based life we investigate in cells, tissues, organs, andorganismsthroughoutalldomainsoflifedependsonstoredinformationaboutstructure,processing,development,andregulation.Thegeneticcodehas4kindsofnucleicacidcom-ponentsthatserveascharactersofanalphabet(guanine,adenine,thymine,andcytosine)thatcontinuouslyistranslatedintoaminoacidlanguagewith20aminoacidsthatformthewholevarietyofproteinbodiesand,additionally,anabundanceofribonucleicacids(RNAs)(withonevaryingcharacter inthealphabet;uracil insteadof thymine)thatregulateallfine-tunedprocessesofcellreplication,transcription,translation,andrepair.Thenucleo-tidesequencesofthegeneticcodearebasepairingaccordingtotheChargaffrules(adaptedbyWatsonandCrickintheirdoublehelix)inwhichtheybuildcomplementarysequencestructuresandserveasinformationstoragemedium.WewilllookatsomeagentsthatarecompetenttoeditthegeneticcodesuchasvirusesandsubviralRNAs.

First of all, let us have a look at the current background knowledge on natural lan-guages/codesandonthebasicbiologicalfeaturesofcommunicationprocesses.Becauseofitsempiricalsignificance,wecaneasilyadaptthisbiocommunicationapproachtononhu-manorganismsaswellasthenaturalgenome-editingcompetencesofvirusesandsubviralagentstotheevolutionandcontentorderofthegeneticcode.

16.2 summAry of Current KnoWledGe About nAturAl lAnGuAGes/Codes And CommunICAtIon

Current knowledge in linguistics and communication theory identified three basic fea-turesthatareessentialcharacteristicstoallnaturallanguages/codes:

1.Nonaturallanguagespeaksitselfasnonaturalcodecodesitself.Innaturallanguagesorcodes,living agentsthatarecompetenttogeneratesignsequencesaretheultimateprerequisitefortheexistenceandoccurrenceofnaturallanguagesandcodes.

AQ1

K19048_C016.indd 350 4/15/2014 11:19:06 AM

language and Communication as universal requirements for life ◾ 351

2.Theemergenceofnaturallanguagesandcodesdependsonpopulationsoflivingagents.This means that natural languages/codes in communication processes are primarilysocial interactions.Concretesocialinteractionsaretheessentialexperienceforsocializ-ingchildrentolearntheconnectionsbetweenlinguisticutterancesandtheirmeaning.(Utterancesaresentenceswithwhichwedosomething:convincesomeone,explainsome-thing,implementsomething,andsimilar.Wedonotthinkandthenformulatesentences:wethinkinlanguageandsentences.Also,everynonverbalexpressionisanutterance.)

3.Livingagentsthatusenaturallanguages/codestoinitiatesocialinteractionsmustbecompetenttofollowthree levels of rulesthatareobligatoryandareinherentinanynatural languageorcode: (a) competence tocorrectly combine signs to sequences(syntactic rules), (b) competence to correctly initiate communicative interactionsaccordingtothecontextspecificity(pragmaticrules),and(c)competencetocorrectlydesignateobjectsbyappropriatesigns(semanticrules).Ifonelevelofrulesismissing,onecannotseriouslyspeakaboutarealnaturallanguageorcode.

16.2.1 language Is a natural language only If living Agents use It

Languageusedependsoncommunities,ahistoricallygrowngroupofmembersthatsharethesethreelevelsofrules.Languageuseisasocialactionandisaprioriintersubjective.Ifthetimewindowofchildhoodlearningandtraininginlanguagewordsandsentencesin social interactions is disturbed, linguistic and communicative competences can bedeformedandevenbelifelong.Fromthisperspective,wecanavoidmonologicalconceptsoflanguage,allofwhichshareanessentialproblem:howtomakethemovefromastateofprivateconsciousnesstoastateofmutualagreementandcooperation.Monologicalcon-cepts includemetaphysical,philosophyofmind,orother solipsistic approaches suchassender–receiverorcoding–decodingnarratives.

16.2.2 mathematical theories of language vs. Pragmatics of languages

Themathematicaltheoryoflanguageanditsderivatives(systemstheory,informationtheory,gametheory,bioinformatics,syntheticbiology,biolinguistics)triedtheotherwayaround:thereisalogicofrelationswithinmaterialrealitythatisinherentalsoinbiologicalmatter.Inthecaseofhumanevolution,thislogicdeterminesfinallythearchitectureofneuronalbrainconstruc-tion.Ifthebrainusesalanguagethatdepictsthislogic,itmustbepossibletodepictmaterialrealitywiththislanguage.Theonlylanguagethatisabletodepictmaterialrealityisaformaliz-able,algorithm-basedlanguage,thatis,mathematics.Therefore,thehumanbrainmustusefor-malizedmathematicallanguagesothatitcanscientificallydepictandexplainmaterialreality.

Thecrucialdeficit in thismethodis thatonecannotexplaineveryday languagewithit.Everydaylanguageistheultimatemetalanguage.Thismeansthattherecannotbeanylanguage that couldgobeyondeveryday language.Since it servesasaprimary tool foreveryday life communication and socializationofhumans, it is the sourceof theorigi-nalmeaningofwordsinsentences.Everydaylanguagecannotbeformalized:wecannotexplaindeepgrammarsandillocutionaryactsweuseprimarilytotransportavarietyofmeaningswithidenticalsuperficialsyntacticstructures.

K19048_C016.indd 351 4/15/2014 11:19:07 AM


Forthebenefitofthereaders,Iwouldliketoexplainthetermslocutionary,illocution-ary, and perlocutionary, which are used in this chapter. Locutionary speech act is rep-resentedby thesuperficial syntaxof thesentence. Incontrast, illocutionaryspeechactstransportcontext-dependentmeaning.Forexample,“Iwillcometomorrow”isillocution-ary,whichcouldbeapromise,athreat,asecretcode,etc.,dependingonthecircumstancesand intentions. With perlocutionary speech acts, someone fulfills a complete action. IfsomeoneasksyouifyouarewillingtotakeXYasyourwifeandyouanswer“yes,”thentheyesisaperlocutionaryspeechact.

The same holds true for information theory: in a recently published article, SydneyBrennerstatesthatbiologyis,inhisopinion,physicswithcomputation.Thefundamen-talconceptthatintegratesbiologicalinformationwithmatterandenergyistheuniversalTuringmachineandvonNeumann’sself-reproducingmachines.However,nosingleself-reproducingmachinehadeverbeenobservedwithinthelast80 yearssincetheypresentedtheirconcept.Therearegoodreasonsforthis,becausemachinescannotcreatenewpro-gramswithoutalgorithms. Incontrast to theartificialmachines that cannot reproducethemselves,thelivingcellsandorganismscanreproducethemselvesandadditionallygen-erateanabundanceofbehavioralmotifsforwhichnoalgorithmcanbeconstructed,suchasdenovogenerationofcoherentnucleotidesequences.

16.2.3 How to Generate Correct scientific sentences: results of the Philosophy of science debate in the twentieth Century

To get things methodologically straight, we have to remind ourselves of the discussionbetween1920and1980inthehistoryofphilosophyofscienceandthetransitionofmeta-physicstothelinguistic turnandafterwardtothefoundationandjustificationofscientificsentencesinthepragmatic turn.

1.Thelinguistic turnwastheresultofanattempttodelimitthelogicofsciencefromphi-losophyandothernonscientificmethods.Thetermdelimitgenerallymeanstodefinetheconditionsthatmustbefulfilledasvalidityclaimsofexactsciences.Specifically,thelogicofsciencetriedtofindalanguagewhosesentencesarestrictlyscientificincontrast to the sentences from poetry, theology, astrology, and other nonscientificfields.Basedongoodreasons,thelinguisticturnstatesthatwedonotunderstandperse objects, relations, structures, intelligence, mind, consciousness, cognition, con-struction,matter,energy,information,system,andnaturallaws,butonlylinguisticsentencesinutterances.(Utterancesaresentenceswithwhichwedosomething:trytoconvincesomeone,explainsomethingtosomeone,callsomeonetodosomething,andsimilar.)Untillinguisticturn,itwasassumedinphilosophyandsciencesingen-eralthatsentencessomehowdepictreality.

Onlyprotocolpropositionsofobservationsthatarereproducibleinexperimentalsetupsarecapableofdepictingrealityona1:1basis,thusadirectcorrespondence.Thisisalsovalidforpropositionsofalanguageoftheorythatwouldhavetobebroughtintoagreementwiththeseprotocolpropositions.Whatisrequiredforalanguageisthatitcanbeformalized,asinlogicalcalculations,algorithms.This languagewould

K19048_C016.indd 352 4/15/2014 11:19:07 AM


representauniversalsyntaxthatwouldbeuniversallyvalid(a)inthethingsoftheexternalworld,(b)inthephysical laws,and(c)inthematerialrealityofthebrainof humans speaking in formalizable propositions. But after several unsuccessfulattempts,logicalempiricismhadtoabandonitseffortstoachievetheultimatevalid-ityclaimofauniversalscientificlanguage.

2.Asaresultofthis,thepragmatic turnreferstothecommunicativeeverydayinterac-tionsofhistoricallyevolvedgroupsandcommunitiesthatarethebasisforlearningandtraining linguisticandcommunicativecompetences.Historicallygrowncom-municative practice of linguistic communities is the prerequisite for organizationand coordination of social interactions, and later of linguistic abstractions, suchas scientific languages in communities of specialized disciplines (see Figure 16.1).

fIGure 16.1 In his early thinking, which was outlined in the Tractatus Logico-Philosophicus,LudwigWittgensteinledthefoundationsfortheprojectexact scientific language,thatis,formaliz-ablesentencesthatdepictrealityina1:1manner.Thisservedascommonfoundationofthelinguis-tic turn.InhislatePhilosophical Investigations,Wittgensteinrefutedhisearlythoughtscompletely.Thebasicfeaturesofnaturallanguagesarethereal-lifeworldsofsocialgroupsthatusesignsystemsineverydayuse.Thecontextofusedeterminesthemeaningofsignsequences.Naturallanguagesserveasanessential tool in social interactions.Thiswas the startof thepragmatic turn. (FromBlackwellPublishing,2001.Withpermission.)

AQ2

K19048_C016.indd 353 4/15/2014 11:19:07 AM


The pragmaticturnfoundedandjustifiedtheintersubjective–communicative charac-ter of thought, experience, and research.

Everydaylanguageanalysisshowsspeechactsorhow to do things with words.Asweareboth,inparallel,subjectsandobjectsofourutterances,weareinaprivilegedpositiontotake intoaccount,at thesametime,ourhistoricallyevolvedeverydaylanguage. We understand utterances as participants in the communicative, rep-resentative, imperative, and constitutive speech acts, rather than acting as lonely(solus ipse) isolatedobservers.Thisenablesus toexplaincentralmarksof speechactsasthereare

• Simultaneousunderstandingofidenticalmeaningsintwointeractingpartners,asexpressedinsuccessfullycoordinatedactivity

• Differentiationbetweendeepandsuperficialgrammarofastatementalongwithdifferentiationbetweenlocutionary,illocutionary,andperlocutionaryspeechactswithwhichthestatementsaremade

Thepragmaticturnreplacesallmonological subjectsofknowledgebytheprimacyoflin-guisticcommunities.Thisistheendforamethodologicalidealthatlastednearly2000 yearsand that maintained as a principle that one subject alone could—monologically—get knowledge and construct a language/code in a process that Thomas McCarthy hasdescribedasfollows:“Themonologicalapproachpreordainedcertainwaysofposingthebasicproblemsofthoughtandaction:subjectvs.object,reasonvs.sense,reasonvs.desire,mindvs.body,selfvs.other,andsoon.”

16.2.4 meaning of messages depends on Contextual use (Pragmatics), not syntax

It isadeepgrammar,orasoutlined ingreatdetailby JohnAustinand JohnSearle,itistheillocutionaryactweundertakewithwhatwesay.So,besidesthelocutionaryaspect,whichisrepresentedbythesuperficialsyntaxofthesentence,thereisavarietyof(hidden)possibilitiesofwhatwewanttodo(intend)withthissentence,namely,theillocutionaryact.Inextremecases,wecanintendcontradictorygoalswiththesamesyntacticstructure.Thisistherealityofeverydaylanguagethatisimpossibletocap-ture in the formalized languages that cannot representboth locutionaryand illocu-tionaryaspects.

Animportantconsequenceofthisisthatpurelanguageanalysesthatwanttoextractdeepgrammar/illocutionaryactionoutofavailablesyntacticsequencesmustnecessar-ilyfail.Thisisbecausetheanalysesofsyntacticalrulescannotexplainpragmaticinter-actionalcontexts thatfinallydeterminethemeaningofsyntacticstructures.Thishasseriousconsequences:

1.Thevarietyofwordscombinedtoformsentencesineverydaylanguagesanddia-lectsarenottheresultofcopyingerrorsordamageofpreexistingsentencesoravail-ablesentences.AccordingtoGödel,naturallanguageusersareprincipallycapabletoproducenewsequencesthathaveneverbeengeneratedbefore(seeFigure16.2).

K19048_C016.indd 354 4/15/2014 11:19:07 AM


Itisaninherentfeatureofallnaturallanguagesthatlivingagentsthatusethemcanproducenewones.Theymaybeunpredictableandthusincalculable.Assuch,theycannotbededucedoutofformeronesoravailableones.

2.Innatural languages/codes, there isnosyntaxbasedonauniversalgrammarthattransportsidenticalmeanings(e.g.,withauniquepositioninaformalizablesequencespaceassuggestedbyManfredEigen).

3.Tolearnanaturallanguagemeanstocommunicatebasiceverydayneedswithcom-munitymembers.Thisishowwelearnwhatawordmeans(“Themeaningofawordis itsuse”—LudwigWittgenstein).Wecanunderstandwordsand their sequences,becausewehavelearnedapracticeofinteraction,whichincludeslearningfromthecommunitywhichwordsarecombinedwithwhichinteractionalpatterns;wethenmemorizethose.

fIGure 16.2 Gödeldiscoveredthecrucialdeficitof the linguistic turn: inhis investigation,heconvincinglyprovedthefactthatinopensystems,thereisthepossibilitytocreatenewsentencesthathaveneverbeencreatedbeforeandcannotbepredictedoutofpreexistingonesinprinciple.This was the end of Hilbert’s program of a self-consistent axiomatic system (Hilbert space) astheultimatefoundationandjustificationofmathematics.(FromDoverPublications,1992.Withpermission.)

K19048_C016.indd 355 4/15/2014 11:19:09 AM


16.3 Key levels of bIoCommunICAtIon In ProKAryotes And euKAryotes

Communicationprocesseswithinandbetweenorganismsarerathercomplexsign-mediatedinteractionsthatsignificantlydifferinprokaryotes(unicellularorganismswithoutatruenucleus)andeukaryotes(uni-andmulticellularorganismswithtruenucleus).Prokaryotesrepresentasuccessstoryinevolutionandexistsincenearly3.8billionyears.However,thetransitiontoeukaryoteswasarealrevolutionbecauseitincorporatesavarietyofformerfree-livingprokaryoteswithinadouble-layeredcellanditsinformation-bearingnucleus.Thelatterwasmostprobablyderivedfromalargedouble-strandedDNAvirus.Thismeansthatthebasiccomponentsofeukaryoticcellsarebothcellularandviralsymbiontsthataregeneticallyconservedintoasocialorganism.

16.3.1 Prokaryotes

Thebacterialworldisasocialandcommunicativeone.Theproductionandthe exchangeof messenger molecules enable unicellular organisms to coordinate their behaviorlikeamulticellularorganism.Thebiocommunicationinbacteriacommunities isnotrestricted to species-specific levels but represents a clear multilevel communicationthatenableshundredsofdifferentbacteriagroupstoco-occupyoneandthesameeco-logicalniche.

Ithasbeenproventhatbacteriagroupsusequorumsensingtodeterminetheirstrengthandtoreactbycoordinatingtheirbehaviorsuchasinbiofilmformation.

Studiesofquorumsensingsystemsdemonstratethatbacteriahaveevolvedmultiplelanguagesforcommunicatingwithinandbetweenspecies.Intra-andinterspeciescell–cellcommunicationallowsbacteriatocoordinatevariousbiologicalactivitiesinordertobehavelikemulticellularorganisms.

SCHAUDERANDBASSLER(2001)

Figure16.3demonstratesthisasasnapshotfromavideoinwhichagroupofbacteriasenseavailablenutrientsandcoordinateredirectedgroupmovementsinthecorrectdirection.Recently,allkeylevelsofbiocommunicationofsoilbacteriahavebeencategorized.

16.3.2 eukaryotes16.3.2.1 FungiFungialsocommunicateandthereforeareabletoorganizeandcoordinatetheirbehavior.Coordinationandorganizationprocessesinfungiareseenattheintraorganismiclevel,forexample,duringtheformationoffruitingbodies,betweenspeciesofthesamekind(inter-organismic),andbetweenfungalandnonfungalorganisms(transorganismic).

Thesemiochemicals(fromtheGreekwordsemeion,meaningsign)usedareofbioticori-gin,incontrasttoabioticindicatorsthattriggerthefungalorganismtoreactinaspecificmanner.Therolesofsomeofthesesignalingmoleculesareasfollows:(1)Mitogen-activatedprotein kinase signaling (MAPK) is involved in cell integrity, cell wall construction,

K19048_C016.indd 356 4/15/2014 11:19:09 AM


pheromones/mating, andosmoregulation; (2) thecyclic adenosinemonophosphate/pro-teinkinaseA(cAMP/PKA)systemisinvolvedinfungaldevelopmentandvirulence;(3)theRAS(proteinfamilymembersthatbelongtoaclassofsmallGTPase)proteinisinvolvedinthecrosstalkbetweensignalingcascades;(4)calcium,calmodulin,andcalcineurinareinvolvedincellsurvivalunderoxidativestress,hightemperature,andmembrane/cellwallperturbation; (5) rapamycin is involved in the control of cell growth and proliferation;(6) aromaticalcoholstryptopholandphenylethylalcoholareusedasquorumsensingmol-ecules;and(7)avarietyofvolatile(alcohols,esters,ketones,acids,lipids)andnonvolatileinhibitorycompounds(farnesol,H2O2).

Todate,400differentsecondarymetaboliteshavebeendocumented.Developmentandgrowth of fungal organisms depend upon successful communication processes within,andbetween,cellsoffungalorganisms.

In order to generate an appropriate behavioral response, fungal organisms addition-ally must be able to sense, interpret, and memorize important indices from the abioticenvironmentandadapttothemappropriately(seeFigure16.4).Interestingly,certainrulesoffungalcommunicationareverysimilartothoseofanimals,whileothersmorecloselyresemblethoseofplants.

AQ4

(b)(a)

(c) (d)

fIGure 16.3 Swarming intelligence inbacteria: someextracellular foodwaspositionednearabacteriacolony.Aftersensingofthefood,thecolonyswarmmovedtowardtheresource.Intra-andintercellularsignalingisnecessarytosense, interpret,andcoordinatecommonmotilebehavior.(FromBen-Jacob,E.,Ann. N.Y. Acad. Sci.,1178,78,2009.Withpermission.)

AQ3

K19048_C016.indd 357 4/15/2014 11:19:10 AM


16.3.2.2 AnimalsAnimals also depend primarily on volatile substances such as pheromones to identifygroupidentityofselfandnonself.However,inaddition,theydependonavarietyofsignsthatconveymeaningviavocalsoundsandvisualgestures.Thisopensupavarietyofcom-binatorialpossibilitiesandbroadensthecommunicativecompetencies.Suchcomplexityincreasesexponentiallyincomparisontobiocommunicationofbacteria,fungi,andplants.Thesignalingmolecules,vocalandtactilesigns,gestures,andtheircombinationsdifferthroughoutallspeciesaccordingtotheirevolutionaryoriginsandvarietyofadaptationprocesses.However,certainlevelsofbiocommunicationcanbefoundinallanimalspecies:

1.Abiotic environmental indices such as temperature, light, water, and gravity thataffectthelocalecosphereofanorganismaresensedandinterpreted(againststoredbackground memory). Then they are being used for organization of behavioralresponsetoadaptaccordingly(takingintoaccountalsooptimalenergycost).

2.Trans-specificcommunicationwithnonrelatedorganismsasfoundinattack,defense,andsymbiotic(evenendosymbiotic)sign-mediatedinteractions.

Neighboringcells

Interspeciesinboundsignaling

Intraspeciessignaling

Metabolites

RNA

DNA

HO

H3CO

O

O

OH

O

CH3

CH3

Protein

Interspeciesoutboundsignaling

Epig

enom

eEp

igenome Epigenome

Epigenome Epigenome

Epig

enom

e

fIGure 16.4 Dependingonthereal-lifecontextoffungalorganisms,epigeneticregulationcansuppressoramplifyincomingortransmittedsecondarymetabolites,animportantsignalresourceof fungal organisms. Therefore, not for every message, a novel sequence has to be produced(multiplemeaningsofidenticalsyntaxstructures).(FromCichewicz,R.,Epigenetic Regulation of Secondary Metabolite Biosynthetic Genes in Fungi,SpringerScience+BusinessMedia,Dordrecht,theNetherlands,2012.Withpermission.)

K19048_C016.indd 358 4/15/2014 11:19:10 AM


3. Interorganismiccommunicationbetweensameorrelatedspecies.

4.Intraorganismic communication, that is, sign-mediated coordination within thebodyof theorganism.Thismeans twosublevels, suchascell–cell communicationandintracellularsignalingbetweencellularparts.

16.3.2.3 PlantsPlantsaresessileorganismsthatactivelycompeteforenvironmentalresourcesbothaboveandbelowtheground.Theyassess theirsurroundings,estimatehowmuchenergytheyneedforparticulargoals,andthenrealizetheoptimumvariant.Theytakemeasurestocontrol certain environmental resources. They perceive themselves and can distinguishbetween self andnonself.Theyprocessandevaluate informationand thenmodify theirbehavioraccordingly(seeFigure16.5).Plantcommunicationcentersarethestemandtherhizosphere(theentireareaofinteractionswithintherootzone).Therhizosphereofplantsis a realm of overlapping communicative interactions and a dynamic environment fea-turing dense microbiological life, high growth rates and metabolic activities, as well asrapidlychangingphysicalconditions.Thecommunicationprocessesbetweentissuesandcellsinplantsareincrediblycomplexandencompassnucleicacids,oligonucleotides,pro-teinsandpeptides,minerals,oxidativesignals,gases,mechanicalsignals,electricalsignals,fattyacids,andoligosaccharides,growthfactors,severalaminoacids,varioussecondarymetaboliteproducts,andsimplesugars.

Biocommunicationin

plants

Interpretation ofabiotic in uences

Transorganismiccommunication

Interorganismiccommunication

Intraorganismiccommunication

(sign-mediatedinteractions withbacteria, protists,fungi, insects, and

other animals)

(sign-mediatedinteractions withsame, related, andnonrelated plant

species)

(intercellular andintracellular sign-

mediatedinteractions, andviral symbioticinteractions)

(e.g., lightsensing,gravisensing,waterpressure

sensing, and woundsensing of

mechanical damage)

fIGure 16.5 Key levels of biocommunication in plants. (From Witzany, G., Key Levels of Biocommunication in Plants,Springer-Verlag,Berlin,Germany,2012.Withpermission.)

K19048_C016.indd 359 4/15/2014 11:19:11 AM


Asineverybiocommunicationprocessofreallifeworld(pragmatic)situations,contextdeterminessemanticmeaningofsignals.Auxin,forexample,isanancientsignalingmol-ecule in plants. It functions in differenthormonal,morphogen, and transmitter signal-ingpathways.Thus,itisverydifficulttodeciphertheactualsemanticsofauxin,sinceitdependsonwhetheritisusedashormonalormorphogenortransmittersignal.Thesamesignalcantakeondifferentmeaningsandtriggerdifferenteffects,dependingonwhetheritreachesthewholeplant,atissue,oracell.Becauseofthis,therespectivedevelopmentalstatusoftheorganismservesasamemoryforeachindividualplant.

16.4 nuCleIC ACId lAnGuAGe As nAturAl CodeConceptssuchasgenetic code,nucleic acid language,recognition sequences,translation process,amino acid language,immune responses,andcell–cell communicationrepresentirreplaceablecore concepts in molecular biology. These concepts were not introduced into biochemis-tryandmolecularbiologybylinguists,communicationexperts,orlanguagephilosophers.Rather, theywere independentlycoinedbymolecularbiologists toexplainobservedphe-nomenaandwereclearlyinvokedduetothestronganalogytoprocessesofhumancommu-nication.FrancisCricktermedthegeneticcodeacode without commas.However,ManfredEigeninvestigatedthegeneticcodeasreallanguageandnotjustasametaphor,asrevealedbythefollowingcitations:“Therelativearrangementoftheindividualgenes,thegenemap,aswellasthesyntaxandsemanticsofthismolecularlanguageare(…)largelyknowntoday”(EigenandWinkler,1983,p.207).“Allthewordsofthemolecularlanguagearecombinedtoameaningfultext,whichcanbebrokendownintosentences”(p.305).“Atanyrateonecansaythattheprerequisiteforbothgreatevolutionaryprocessesofnature—theoriginofallformsoflifeandtheevolutionofthemind—wastheexistenceofalanguage”(p.314).

Asweknowtoday,Eigen followedtheopinionofhis time, that language follows thestructureofauniversalandcontext-free grammar(NoamChomsky)thatunderliesstrictnatural lawsas it represents the logicof thematerial reality.Thecore functionsof lan-guagesarelimited,formalizable,predicable,andcomputable.Theonlyreallanguagethatdepictsmaterialrealityismathematics.Therefore,themoleculargeneticcodecanbeinves-tigatedanddescribedsufficientlybyphysicsandchemistry.Eigenadaptedtheopinionofthelinguisticturnasdescribedearlier.

Several other derivatives of the linguistic turn and its mathematical theories of lan-guage,suchassystemstheory,cyberneticinformationtheory,syntheticbiology,andevenbiolinguistics,allsharethisdeficit.Noneofthemtakethefullrangeoflevelsofrulesintotheirtheoreticalassumptionsbutlettheselevelsofrulesberestrictedtosyntaxandseman-tics.Butthedemissionoftheprimaryrole,pragmatics,totheinvestigationsofnaturallan-guageshasafatalconsequence.Itinstallsapermanentdeficitintothesetheoreticalrealmsthatdeterminestheirfailuretoexplainsufficientlynaturallanguages.

Because natural language/code tools are limited, the information-bearing sequencesdenoteseveralindependentandevencontradictorycontexts.Onenucleotideword,suchasapseudoknot(atypeofthenucleicacidsecondarystructure),mayhaveseveraldifferentmeanings.Becauselivingagentscannotinventnewsignsforeverynewsituationordesig-nation(energycosts),thisevidentlymakessense.Similarorequalcombinationsofsigns,

AQ5

K19048_C016.indd 360 4/15/2014 11:19:11 AM


characters,andwordsthatresultinsentencescanbeusedasinformationaltoolstotrans-portdifferentmeaningsaboutawholegenome.Examplesincludeoverlappingepigeneticmarking (the genetic sequence is marked through environmental influences that deter-mine the context-relevant meaning/expression pattern) and silencing of transposons(DNAsequencesthatmove),whichinducerepressionofmaternalcytotype(havingdiffer-entchromosomalfactors)inanimals,amongothers.

From human communication, we know that different gestures or spelling may indi-catedifferentmeaningsofthesamewords.Withoutcontextualexplanation,thephrasethe shooting of the hunterscannotbeunderstoodunequivocably.Theidenticalsequencemaytransportcontradictingmessages(seeFigure16.6).Themarkingofsyntacticsequencesbymarkingtoolsiscommonuseinnaturallanguages/codesanddeterminessemanticcontentaccordingtotheneedsofthepragmaticinteractingagents.

To investigate syntactic sequences without knowing something about the real-lifecontext of code using agents is senseless because syntactic structures do not representunequivocable semantic meaning. Quantifiable analyses of signs, words, or sequencescannotextractcontext-dependentmeaning.Inarestrictedsense,thisispossiblethroughsequencecomparison,forexample,ifweknowwhichsequencesdeterminecertainfunc-tions.Butallthesefeaturesareabsentinnon-animatenature.Ifwaterfreezestoice,nolivingagentsnorsemioticrulesorsignsarenecessary.

fIGure 16.6 The shooting of the hunters: in natural languages/codes, the meaning of syntacti-calidenticalsequencesdependsonthereal-lifeworldcontextinwhichcompetentsignusersareinterwoven.Theuseofidenticalsyntaxstructurestotransportdifferent(andevencontradictory)meaningssavesenergycosts(BaluskaandWitzany2012).Algorithm-basedmachines(computers)thatmustextractthemeaningofgivensyntaxstructurescannotdecidebetweensuperficialgram-maranddeepgrammar(illocutionaryacts)intendedbysignusers.(ReprintedbypermissionfromMacmillanPublishersLtd.EMBO Reports,Witzany,G.andBaluška,F.,Life’scodescriptdoesnotcodeitself.Themachinemetaphorforlivingorganismsisoutdated,13,1054–1056,Copyright2012.)

AQ6

K19048_C016.indd 361 4/15/2014 11:19:13 AM


16.5 AGents of nAturAl Genome edItInGWithinthelastdecade,viewsonnaturalgeneticengineeringandnaturalgenomeeditinghavechangeddramatically.Inparticular,researchinvirologyhasopenedperspectivesonearlyevolutionoflife,aswellasonvirusesasessentialagentswithintherootsandstemofthetreeoflife.FromtheearlyRNA-worldperspective,thewholediversityofprocesseswithinandbetweenevolutionarily later-derivedcellular lifedependsonvariousRNAs.TheprecellularRNAworldmusthavebeendominatedbyquasi-speciesconsortia-basedevolution,asarecurrentRNAviruses.

Virusescanparasitizealmostanyreplicationsystem—evenprebioticones.RNAvirusesstorecrucialanddynamicinformation.Basedonthisandtheresultsofphylogeneticanal-ysesandcomparativegenomics, it ispossible toestablishviral linesofancestralorigin.Theselinesoforigincanalsobenonlinearbecausedifferentpartsofvirusescontaindif-ferentevolutionaryhistories.SinceviruseswithRNAgenomesaretheonlylivingbeingsthatuseRNAasastoragemedium,theyareconsideredtobewitnessesofanearlierRNAworld.CurrentnegativelystrandedRNAviruseshavegenomestructuresandreplicationpatternsthataredissimilartoallknowncelltypes.

NosimilaritybetweenRNA-viralreplicasesandthoseofanyknowncell typeshasbeenidentified.DNAviruses,too,donotgiveanyreferencetoacellularorigin.DNA-repairproteinsofDNAvirusesdonothaveanycounterpartsincells.Onemilliliterofseawatercontainsonemillionbacteriaand10timesmoreviralsequences.1031bacteriophagesinfect1024bacteriaeachsecond.Theenormousviralgeneticdiversityintheoceanhasestablishedpathwaysfortheinte-grationofcompleteandcomplexgeneticdatasetsintohostgenomes,forexample,acquisitionofcomplexnewphenotypes.Aprophagecanprovidetheacquisitionof>100newgenesinasin-glegenome-editingevent.Today,itisassumedthatthegenewordorderinbacterialgenomesisdeterminedbyviralsettlersofbacterialhostgenomes.Notonlybacteriallifeisdeterminedbynonlyticviralsettlements,butalsotheevolutionofeukaryoteshasstronglydependedonviralproperties.Incontrast tothemitochondriaandothereukaryoticpartsofbacterialdescent,theeukaryoticnucleuswasformerlyalargedouble-strandedDNAvirus.AllpropertiesoftheeukaryoticnucleusarelackinginbacteriallifeformsbutaretypicalfeaturesofDNAviruses.Evenlethallyirradiatedvirusescanoftenrepairthemselves.Theyarecompetenttorecombinecombinationsofdefectiveviralgenomesinordertoassembleintactviruses.Therefore,virusesaretheonlylivingagentscapableofmeaningfullyrecombiningtextfragmentsofadamagedgenomeintoafullyfunctionalviralgenomethatiscapableofself-replication.

Lyticdiseasesthatarecausedbyviralinfectionsaretheexceptioninvirallifestrategies,althoughtheymighthaveepidemicandpandemicandthereforecatastrophicconsequencesforinfectedpopulations.Themostdominantvirallifestrategyisthenonlyticbutpersistentviralsettlementofcytoplasmofcellularhostsandevenmoreofcellularhostgenomes.Addictionmodulesaretheresultofintegrationofformercompetingviralinfections.Assymbioticneu-tralizationandcounterpartregulation,theyrepresentnewhostphenotypicfeatures.Onefea-tureisregulatedexactlybytheantagonistaccordingtodevelopmentalstagesinthecellcycle,replication, and tissuegrowth.Should this suppressor functionbecomeunbalanced, thenthenormallydownregulatedpartmightbecomelyticagain.Wecanidentifyvirus-derived

K19048_C016.indd 362 4/15/2014 11:19:13 AM


addiction modules in every toxin/antitoxin, restriction/modification, or insertion/deletionmodules inwhichformercompetingviralcloudsarenowimmunologicallybalanced.Ifabalancedstatusisreached,thismeansachangedgeneticidentityofthehostorganismand,in consequence, a changing genetic identity of the viral settler. Current knowledge indi-catesthatmostevolutionarilynovelderivedspeciesaretheresultofchangedandexpandedgenomicidentitiescausedbypersistentviralcolonization.Researchresultsinvirologyhaveledtotheassumptionthat,besidescommunicativecompetencesofcellularorganisms,whichareinvolvedincoordinatingbehavior,therearelinguisticcompetencesofvirusesandvirus-derivedviralparts(e.g.,env,gag,pol),whichnotonlyregulateallcellularprocessesbuteditthegeneticcontentoflivingorganisms.Thisviralgenetictext-editingcompetencedependsonlivingorganismsthataredifferentfromeachother,anditthereforeneedsabioticmatrixtoexpandthiscompetence.Withoutlivingandinteractingorganismsandcells,genomiccre-ativitywouldonlybeapossibilitythatisrestrictedtomereRNAcombinatorialevents(inanearlyprecellularRNAworld),whichhasnorelevancetothegenerationofabiosphere.

16.5.1 biocommunication in the rnA World: rnA sociology

TheancientRNA-worldhypothesisiscurrentlyupdatedwithRNA-worldfactsandincreas-ingknowledgeabouttheabundanceofdifferentbutcompatibleRNAs.InthisworldoflifeprocessesactivelydominatedbyRNA,DNAisincreasinglycastintheroleofthehabitatofgeneticinformationstorage,whereastheinteractingRNAsseemtobetheinhabitantswithinthishabitat.Ifwelookatthesenetwork-likecooperatinginhabitants,wecanseeasecondarystructurethatissharedbyalltheseRNAnucleicacidsequences:itisthestem-loopstructureor,inthecaseofmorecomplexagentssuchastRNAorribosomalsubunits,theligatedconsortiaofsuchstemloops(seeFigure16.7).

TheratherastonishingresultofinvestigationsisthatrandomlyassociatedRNAsthathavenoevolutionaryhistory showthe samestructure-dependentcompositionalbiasasnaturalderived(ribosomal)RNAs.Thismeansthatthedifferencesdonotdependonselec-tionprocessesbutontheoverallcompositionoftheRNAconsortium.

16.5.2 biocommunication at the level of the rnA Group membership

RNAgroupmembershipcanneverbecompletelyspecified,sinceitcanalwaysbefurtherpar-asitizedbyasyettobeencounteredmembersorparasites.Thisessentialandmostimportantfeaturerenderstheabilitytoabsolutelyspecifymembership(absoluteimmunity)asbasicallyindefinable.Thus,anRNAgroupcanneverbefullysecurefromasyetundefinedparasiteagents.Butacrucialconsequencefromthisinsecurityisthatitprovidestheinherentcapacityfornovelty,thatis,thepreconditionforevolutionaryinnovationsuchasgreatercomplexity.

Tointroducesociologicalterms,wenowhavetoask:Howdoagentsemergefromchemi-calstoformidentityandthenformgroupsthatlearnmembership?SingleRNAstem-loopgenerationoccursbyphysicalchemicalpropertiessolelyasdemonstratedbynaturalandrandomizedRNAexperiments.Ifstem-loopconsortiabuildcomplexconsortia,they initiatesocialinteractionsnotpresentinapurechemicalworld,thatis,biologicalselectionemerges.Thisdesignatesthecrucialstepfrominanimateworldtolife(Figure16.8). AQ7

K19048_C016.indd 363 4/15/2014 11:19:13 AM


Stem

Loop

Bulge

Junction

End

Flexible

Total

S SS S

SS

SS

SS

SS

SS S

S

SS

S

SS L

L

LL L

LL L

LL

L

FF

EE

E

E E

S

JJ

J JJJ

B

5΄

3΄

BB

fIGure 16.7 TheRNAstemloopshaveseveraldistinctparts/subunits:stemsconsistingofbase-pairednucleicacidsandloops/bulges/junctionsconsistingofunpairedregionslimitedbystems.Important:anyRNAispartofsuchstemloops.

Consortialviral cloud

Addictedsurvivor

Edited: new code

New groupencounter

New viral group

Group protectionsurvival

Virus

Acute (toxic)group death

Acute (toxic)culling

Uncolonized

Uncolonizedpopulation

fIGure 16.8 Basicinteractionalmotifofinfection-derivedgroupidentities:theaddictionmod-ule as result of counterbalanced, infection-derived, and persistent genetic parasites that initiateevolutionary inventions by natural genetic engineering of host genetic identities, some we canfindastoxin/antitoxin,restriction/modification,orinsertion/deletionmodules.(FromVillarreal,L.P., Viruses and Host Evolution: Virus-Mediated Self Identity, Landes Bioscience and SpringerScience+BusinessMedia,2012b.Withpermission.)

K19048_C016.indd 364 4/15/2014 11:19:15 AM


Nowwehavemolecularstructurescoherentwithphysicallawsthatstoregeneticinfor-mation.Incontrasttoinanimatenature,theyactivelygeneratebehavioralmotifsandpat-ternsofinteraction,thatis,coordinatecommonbehavioraccordingtorulesthatleadtoconsortiaofselfandnonselfgroups.Thisresemblessomekindsofsocialgroupbehaviorwithsharedfeatures:

• De novo initiation of behavior that cannot be deduced from former behavioralpatterns

• Highlyadaptiveprocesses

• Lackingcentralorfittesttypecontrol

• Retainingacontextualhistory

• Smart(optimalenergycosts)

• Solvesproblemsbeyondthecapacityofitsindividualmembers

• Fast-changingreactionsagainstnonmembers

Togetherthesefeaturesareclearlyandexclusivelyatthefoundationofalllivingnature.Ifweweretoeliminatethesecomplementarycompetencesoutofthelifeprocesses,wouldthereremainalivingorganism,orwoulditnowsimplybeachemicalstate?Itseemsnot;thus,socialRNAgentsareessential.

16.5.3 Cooperation outcompetes selfishness

IfwelookatsomeinteractionalmotifsofRNAgentstoformconsortialbioticstructuresthatfollowbiologicalselectionprocessesandnotmerephysicalchemicalreactionpatterns,wemustlookatthegroupbuildingofRNAstem-loopstructures.

Recently,ithasbeenfoundthatsinglestemloopsinteractinapurephysicalchemicalmodewithoutselectiveforces,independentlywhethertheyarederivedrandomlyorarecon-structedunderinvitroconditions.Incontrasttothis,ifthesesingleRNAstemloopsbuildgroups,theytranscendpurephysicalchemical interactionpatternandemergebiologicalselectionforces,biologicalidentitiesofself/nonselfidentificationandpreclusion,immunefunctions,anddynamicallychanging(adapting)membershiproles.Asinglealterationinabase-pairingRNAstemthatleadstoanewbulgemaydynamicallyalternotsolelythissinglestemloopbutmaychangethewholegroupidentityofwhichthisstemloopispartof.

Simpleself-ligatingRNAstemloopscanbuildmuchlargergroupsofRNAstemloopsthatserveforincreaseofcomplexity(Figure16.9).

Significantly,RNAfragmentsthatself-ligateintoself-replicatingribozymesspontane-ouslyformcooperativenetworks.Forexample,three-memberednetworksshowedhighlycooperativegrowthdynamics.Whensuchcooperativenetworkscompetedirectlyagainstselfishautocatalyticcycles,theformergrowfaster,indicatingcompetenceofRNApopula-tionstoevolvegreatercomplexitythroughcooperation.Inthisrespect,cooperationclearlyoutcompetesselfishness.

K19048_C016.indd 365 4/15/2014 11:19:15 AM


16.6 ConClusIonWhatisthebenefitofthisconceptoflanguageandcommunicationasuniversalrequire-ments of life in contrast to mechanistic, holistic, objectivistic, mathematically derivedformalizable concepts such as system theoretical, bioinformatics, or synthetic biologyapproachesinmolecularbiology,genetics,epigenetics,andmicrobiology?Thebiocommu-nicationandnaturalgenome-editingapproachonprocessualrealityoflivingagentsbringssomeadvantagestotraditionalscholarlyconviction:

• Cleardistinctionbetweenlifeandnonlife.

• Empiricalnonmechanisticandnonreductionisticdescriptionmethodofbioticinter-actionalpatternsthroughoutallorganismickingdoms.

Step 1: Random RNA polymerization Step 2: Folding of RNA oligomers

Step 4: Toward the �rst RNA polymeraseStep 3: Ligation and modular evolution

+

+

fIGure 16.9 Schematicrepresentationofthestepwiseprocesstowardatemplate-dependentRNApolymerase.Ineverystep,wedepicttwopossibleandcompatiblescenarios:evolutiononmineralsurfaces(shownasbrownrectangles)inbulksolutionandevolutioninsidevesiclesthatcouldalsoencapsulate mineral particles. Functional hairpin structures (with ligase activity) are shown inred.Solidanddottedarrowsstandforthesurface-boundtoin-solutionequilibria.TheRNApoly-meraseemergingfromthisprocessisdepictedinblue.(FromBriones,C.et al.,RNA,15,743,2009.)

K19048_C016.indd 366 4/15/2014 11:19:16 AM


• Any observed coordination within and between organisms can be deciphered byresearchthatidentifiessignalingmoleculesandsyntactic,pragmatic,andsemanticrulesunderlyingthemodeofsignaluse.

• Biologicalresearchmustnotconcentrateanylongeronexperimentalsetupsandthe-oreticalapproachesthatwanttoelucidatelanguageandcommunicationinnonhu-manlivingnaturebymathematical(algorithm-based)modeling.

GlossAryBiochemically related terms: Pleaseconsultthefollowingrecommendedreadings.Biofilm: Bacterialgroupbuildingbysignalinginteractions.Communication: Interactionsviasignalsbetweenlivingorganismsaccordingtosyntac-

tic,pragmatic,andsemanticrules.Evolution: Genotype/phenotypenoveltyasaresultofvariation(mutation=replication

error)andselection.Language: Any repertoire of signs that is used according to syntactic, pragmatic, and

semanticrules.Linguistic turn: Wedonotunderstandtheouterandtheinnerworld,butsentencesaboutit.Natural genome editing: Evolutionarilyrelevantvariationresultsoutofdenovosequence

generation and recombination by competent RNA consortia, not of replicationerror.

Noncoding RNAs: RNAsthatshortlyaftertranscriptionoutofDNAarenottranslatedintoproteinsbutserveasgeneregulatorytools,increasingthemainpartofgeneticinformationineukaryotes.

Pragmatics: Levelofrulesthatdeterminehowtocorrectlycombinewords/sentenceswithreal-lifecontext.

Pragmatic turn: Languageuseisakindofsocialinteraction,thatis,needsusergroups.Semantics: Levelofrulesthatdeterminethecorrectdesignationofobjectswithwords/

sentences,thatis,meaning.Syntax: Levelofrulesthatdeterminehowpartsofanalphabetcanbecorrectlycombined.

revIeW QuestIons1. Ifwewouldfindextraterrestriallife,howdoyouthinkwewouldidentifycommunica-

tion within it? Suggest how the material on language and communication you havelearnedfromthischaptermayormaynotbehelpfulforansweringthisquestion.

2. Writeashortessayononewayofbiocommunicationinlife,suchasbacteriaandfungi,based on the material in this chapter. Research further a subtopic that you like, forexample,thewayplantscommunicate.

3. Why iscontextdependencycrucial for identifyingmeaningofwordsandsentences?Trytoformulateexamplesinwhichillocutionaryactsdeterminemeaningofsyntaxofsentences(e.g.,the shooting of the hunters).

K19048_C016.indd 367 4/15/2014 11:19:16 AM


4. Who was John Searle and how is his philosophy of language relevant to sufficientlyexplaincommunication?Explorethistopic;exemplifythedifferenceoflocutionary,illo-cutionary,andperlocutionaryspeechacts;andwriteashortessaytopresenttotheclass.

5. Whatarethebasicdifferencesofnaturallanguages/codesandmathematicalconceptsoflanguages?

6. What are the essential differences between single RNA stem loops and (self-)ligatedgroupsofRNAs?Isthereanyevolutionaryimportantdivergence?

7. WhatismeantbyRNA sociology?Nominatethedifferencestoastrictphysical/chemicalvocabulary.

8. Fordecades,itwasassumedthaterrorsinreplication(mutations)arekeyforevolution,thatis,variationsthatthenaresubjecttobiologicalselection.NowitisrecognizedthatgeneticnoveltyisbetterexplainedbynaturalgeneticengineeringandnaturalgenomeeditinginitiatedbycompetentRNAagents.Whydoyouthinkwastheerror-basednar-rativeinsufficienttoexplaingeneticnovelty?

reCommended reAdInGsBooksAtkins,J.F.,Gesteland,R.F.,andCech,T.(eds.).RNA Worlds: From Life’s Origins to Diversity in Gene

Regulation.NewYork:ColdSpringHarborLaboratoryPress,2010.Austin,J.L.How to Do Things with Words.London,U.K.:HarvardUniversityPress,1975.Carter,J.B.andSaunders,V.A.Virology, Principles and Applications,2ndedn.Chichester,U.K.:Wiley,

2013.Cichewicz,R.Epigenetic Regulation of Secondary Metabolite Biosynthetic Genes in Fungi.Dordrecht,

theNetherlands:SpringerScience+BusinessMedia,2012.Eigen, M., and Winkler, R. The Laws of the Game: How the Principles of Nature Govern Chance.

Princeton,NJ:PrincetonUniversityPress,1983.Frisch, K. Bees: Their Vision, Chemical Senses and Language, revised edn. Ithaca, NY: Cornell

UniversityPress,1971.McCarthy,T.Translator’sintroduction.InThe Theory of Communicative Action,Vol.1.Boston,MA:

BeaconPress,p.ix,1984.Searle,J.Speech Acts: An Essay in the Philosophy of Language.Cambridge,U.K.:CambridgeUniversity

Press,1976.Shapiro,J.A.Evolution: A View from the 21st Century.Washington,DC:FTPress,2011.Tomasello,M.Origins of Human Communication.Cambridge,MA:MITPress,2008.Villarreal,L.P.Viruses and the Evolution of Life.Washington,DC:ASMPress,2005.Villarreal,L.P.Theaddictionmoduleassocialforce.InViruses: Essential Agents of Life.Dordrecht,

theNetherlands:Springer,pp.107–145,2012a.Villarreal, L.P. Viruses and Host Evolution: Virus-Mediated Self Identity. Landes Bioscience and

SpringerScience+BusinessMedia,2012b.Voet,D.andVoet,J.D.Biochemistry,4thedn.Hoboken,NJ:Wiley,2011.Witzany,G.(ed.).Natural Genetic Engineering and Natural Genome Editing.NewYork:Annalsofthe

NewYorkAcademyofSciences,2009.Witzany,G.(ed.).Biocommunication in Soil Microorganisms.Heidelberg,Germany:Springer,2011.Witzany,G.(ed.).Biocommunication of Fungi.Dordrecht,theNetherlands:Springer,2012.Witzany,G.(ed.).Viruses: Essential Agents of Life.Dordrecht,theNetherlands:Springer,2012a.

AQ8

AQ9

K19048_C016.indd 368 4/15/2014 11:19:17 AM


Witzany,G.Key Levels of Biocommunication in Plants.Berlin,Germany:Springer-Verlag,2012b.Witzany,G.(ed.).Biocommunication of Animals.Dordrecht,theNetherlands:Springer,2013.Witzany,G.andBaluška,F.(eds.).Biocommunication of Plants.Heidelberg,Germany:Springer,2012.

JournalsBen-Jacob,E. (2009)Learning frombacteriaaboutnatural informationprocessing.Annals of the

New York Academy of Sciences1178:78–90.Briones,C.,Stich,M.,andManrubia,S.C.(2009)ThedawnoftheRNAworld:Towardfunctional

complexitythroughligationofrandomRNAoligomers.RNA15:743–749.Gwiazda,S.,Salomon,K.,Appel,B.,andMüller,S.(2012)RNAselfligation:Fromoligonucleotides

tofulllengthribozymes.Biochimie94:1457–1463.Mercer,T.R.andMattick,J.(2013)StructureandfunctionoflongnoncodingRNAsinepigenetic

regulation.Nature Structural & Molecular Biology20:300–307.Schauder,S.andBassler,B.L.Thelanguagesofbacteria.Genes & Development15(2001):1468–1480.Smit,S.,Yarus,M.,andKnight,R.(2006)Naturalselectionisnotrequiredtoexplainuniversalcom-

positionalpatternsinrRNAsecondarystructurecategories.RNA12:1–14.Vaidya, N., Manapat, M.L., Chen, I.A., Xulvi-Brunet, R., Hayden, E.J., and Lehman, N. (2012)

SpontaneousnetworkformationamongcooperativeRNAreplicators.Nature49:72–77.Villarreal,L.P.andWitzany,G.(2010)Virusesareessentialagentswithintherootsandstemofthe

treeoflife.Journal of Theoretical Biology262:698–710.Villarreal,L.P.andWitzany,G.(2013)TheDNAhabitatanditsRNAinhabitants:Atthedawnof

RNAsociology.Genomics Insights6:1–12.Villarreal,L.P.andWitzany,G.Rethinkingquasispeciestheory:Fromfittesttypetocooperativecon-

sortia.World Journal of Biological Chemistry4(inpress).Witzany,G.(1995)Fromthe“logicofthemolecularsyntax”tomolecularpragmatism.Explanatory

deficitsinManfredEigen’sconceptoflanguageandcommunication.Evolution and Cognition1:148–168.

Witzany,G.(2011)Theagentsofnaturalgenomeediting.Journal of Molecular Cell Biology3:181–189.Witzany,G.andBaluška,F.(2012)Life’scodescriptdoesnotcodeitself.Themachinemetaphorfor

livingorganismsisoutdated.EMBO Reports13:1054–1056.

AQ10

AutHor QuerIes[AQ1]Pleasecheckifedittothesentencestarting“Wefindinterorganismic...”isokay.[AQ2]PleaseprovidecompletesourcedetailsforFigures16.1and16.2.[AQ3]Pleasespecifypartlabels“a”to“d”inthecaptionofFigure16.3.[AQ4]Pleasecheckifitem7shouldalsobeacompletesentence.[AQ5]Pleasecheckifedittothesentencestarting“Noneofthem...”isokay.[AQ6]ReferencecitationBaluskaandWitzany(2012)iscitedintextbutnotprovidedin

thereferencelist.Pleaseaddthereferencetothelistordeletethecitation.[AQ7]PleasecheckiftheinsertedcitationsforFigures16.8and16.9arecorrectasgiven.[AQ8]PleaseprovideeditorgroupforVillarreal(2012a).[AQ9]PleaseprovidelocationforVillarreal(2012b)andalsoupdatethesameinthesource

ofFigure16.8.[AQ10]PleaseupdateVillarrealandWitzany(inpress).

K19048_C016.indd 369 4/15/2014 11:19:17 AM

K19048_C016.indd 370 4/15/2014 11:19:17 AM