Table Of ContentAdvances in Experimental Medicine and Biology
Volume751
EditorialBoard:
IRUNR.COHEN,TheWeizmannInstituteofScience
ABELLAJTHA,N.S.KlineInstituteforPsychiatricResearch
JOHND.LAMBRIS,UniversityofPennsylvania
RODOLFOPAOLETTI,UniversityofMilan
Forfurthervolumes:
www.springer.com/series/5584
Orkun S. Soyer
Editor
Evolutionary Systems
Biology
123
Editor
OrkunS.Soyer
UniversityofExeter
Exeter,Devon,UK
ISSN0065-2598
ISBN978-1-4614-3566-2 ISBN978-1-4614-3567-9(eBook)
DOI10.1007/978-1-4614-3567-9
SpringerNewYorkHeidelbergDordrechtLondon
LibraryofCongressControlNumber:2012940413
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Preface
EvolutionarySystemsBiologyisanemergingfieldandascientificsynthesisinthe
making.Thereiscurrentlynosingledefinitionthatcapturesallthefacetsofthisfast-
developingfield (as discussed below, there may neverbe one).There is, however,
one binding aim at the core of this synthesis to understand better the genotype–
phenotypemappingatthecellularlevelanditsevolution.
Theabstractnotionsofgenotypeandphenotypewerefirstproposedbygeneticist
WilhelmJohannsentodescribebroadlythelow-levelmechanismsandtheirhigher
level manifestations in biological systems. These abstract notions became highly
usefultostudytheevolutionaryprocessatdifferentbiologicallevels.Forexample,
in the context of macromoleculessuch as RNA, primary sequence and secondary
structurecan be taken as the genotypeand phenotype,while in a cellular context,
one can define all the genes and their interactions in a given cell as the genotype
and physiological behavior of the cell as the phenotype. Construction of such
biologically meaningful genotype–phenotypedefinitions immediately leads to the
natural formulation of several challenging questions: which phenotype a given
genotype leads to and vice versa? What are the key features of the genotype–
phenotype mapping, is it, for example, a one-to-one mapping or one-to-many?
Which evolutionaryprocesses have shaped the genotype–phenotypemapping and
how?Howdoesevolutionsteerinthegenotype–phenotypemap?
Theanswerstothesequestionsholdthekeytomanymorespecificquestionsin
the context of particular biological systems both at the cellular and higher levels.
For example, a full understanding of the genotype–phenotype map in metabolic
networkswouldallowustopredictwhichenvironmentsacellcansurvivein,which
newenvironmentsitcanadaptto,andwhichperturbationswouldalteritsmetabolic
state(i.e.,howrobustitistoperturbations).Similarly,understandinghowevolution,
underspecificenvironmentalconditions,shapesthegenotype–phenotypemapmight
allowustoinfergeneticstructuresandphysiologicalcapabilitiesinmicrobeswith
differentlifestyles.Thus,adetailedunderstandingofthegenotype–phenotypemap
andhowevolutionsteersinitandshapesitatthesametimeisdirectlylinkedtoour
abilitytounderstandandmanipulatebiologicalsystems.
v
vi Preface
Evolutionary Systems Biology, with its focus on better understanding the
genotype–phenotype map, is thus bound to be an overarching field linking to
several existing fields including systems biology, population and quantitative ge-
netics,systemsmedicine,andsyntheticbiology.ResearchinEvolutionarySystems
Biology either uses techniques, concepts, and data generated in these fields, or
makessignificantcontributionstothembyprovidingconceptualandsystem-specific
insights.ThisisthereasonEvolutionarySystemsBiologyhasmanyfacets,employs
diverse research techniques, integrates different data sets, and eludes, so far, a
compact self-description. The last feature might remain so, even when the field
matures,asitmightwellbethatacompleteunderstandingofgenotype–phenotype
mapsrequiresanumbrellafieldsuchasEvolutionarySystemsBiology.
Theopeningchapterofthisbookaimstodefinethemanyfacetsofthisumbrella
fromphilosophicalandhistoricalperspectives.Theinsightfultreatmentthereinalso
identifies the centrality of the genotype–phenotypemap in Evolutionary Systems
Biology.A significant part of the currentresearch in the field, coveredin the first
partof thebook,isaimedat understandingthe shapeof these maps.Chapters2–7
presentseveraldifferentapproachesforachievingthisgoalandtheirfindingsinthe
context of different genotype–phenotype maps. While a full description of these
maps might be difficult to achieve, especially due to high dimensionality of the
genotypic spaces considered, it might be possible to identify unique genotypic
features that underlie specific phenotypes. Deciphering such potential features
(which one might call “design principles”) is discussed in Chaps.8 and 9. As
withanybiologicalproperty,such featuresandtheoverallshapeofthe genotype–
phenotypemapsaretheresultofevolutionitself.Thus,asignificantresearcheffortis
devotedtounderstandinghowcombinationsofevolutionaryprocesses(adaptiveor
neutral),environmentalconditions(fluctuatingenvironments,speciesinteractions),
and biophysical constraints/realities (e.g., noise, multilevel nature of biological
systems)shapethegenotypesandgenotype–phenotypemaps.Thesecondpartofthe
book,comprisingChaps.10–16,givesa detailedsummaryofthefindingsofthese
effortstodate.Asillustratedinthesetwoparts,EvolutionarySystemsBiologyasa
fieldalreadypossessesastrongintegrativenature,makinguseofdiverseapproaches
including mechanistic models, experimental measurements at pathway and cell-
scale, comparative analysis of genomic data, in silico evolution, experimental
evolution,reverseengineering,andsystemdynamicsanalyses.Chapters17and18
indicatethatcombiningsomeoftheseapproacheswithquantitativeandpopulation
geneticsmightpresentahighlysignificantanduniquefacetofEvolutionarySystems
Biology. It is expected that this combination would allow novel findings that
would not be possible by employing population genetics and systems biology
in isolation. The combination of understanding the key features of genotype–
phenotypemaps, and the evolutionaryforcesresulting in these, is already making
significantcontributionstoourunderstandingofbiologicalsystemsandourability
tomanipulatethem.Thesecontributionsareexemplifiedinthecontextofsynthetic
biologyinChap.19andintheinsightfuldiscussionofrobustnessinChap.20.
Thiscollectionofchaptersrepresentsthefirstsystematicattempttodemonstrate
all the different facets of the emerging field of Evolutionary Systems Biology.
Preface vii
Itbringstogetherthemanyaspectsofthefieldanddemonstratesitscurrentbreadth
and wealth. It is possible that some readers might find that certain areas are not
represented as much as they should have been or that are all together omitted.
I hope that such potential shortcomings are minimal and can be forgiven by the
considerationthattheprimarypurposeofthisbookistoexciteandinformthereader
abouttheemergingfieldofEvolutionarySystemsBiologyandfacilitateitsfurther
development.Letushopethatmanysuchvolumeswillfollowthisoneasthefield
matures.
Evolutionary Systems Biology increasingly takes shape as a key research
direction in our quest towards deciphering broad biological principles. For any
researcher who shares this aim, this book will provide a highly interesting and,
hopefully,thought-provokingread. Providingthe reader with an understandingof
the motivationbehindEvolutionarySystems Biology,its key findingsto date, and
thewiderangeofapproachesanddatasetsitdrawson,thisbookwouldalsoserve
asabasisforagraduatelevelcourseorundergraduatereadingclub.
Iwouldliketogivemysincerethankstoallcontributingauthorsfortheirtimely
andhardworkinputtingthisvolumetogetherandtoSpringerandtheeditorialteam
ledbyMelanieWilichinskyTuckerfortheircommitmentinmakingitareality.
Exeter,Devon OrkunS.Soyer
Contents
1 Evolutionary Systems Biology: Historical
and Philosophical Perspectives on an Emerging
Synthesis..................................................................... 1
MaureenA.O’Malley
2 MetabolicNetworksandTheirEvolution ............................... 29
AndreasWagner
3 OrganizationPrinciplesinGeneticInteractionNetworks............. 53
ChristopherJacobsandDanielSegre`
4 EvolutionofRegulatoryNetworks:NematodeVulva
InductionasanExampleofDevelopmentalSystemsDrift ............ 79
RalfJ.Sommer
5 Life’sAttractors ............................................................ 93
JohannesJaegerandAntonCrombach
6 EvolutionaryCharacteristicsofBacterial
Two-ComponentSystems.................................................. 121
XiaSheng,MaximeHuvet,JohnW.Pinney,
andMichaelP.H.Stumpf
7 ComparativeInteractionNetworks:BridgingGenotype
toPhenotype................................................................. 139
PedroBeltrao,ColmRyan,andNevanJ.Krogan
8 Evolution In Silico: From Network Structure
toBifurcationTheory...................................................... 157
PaulFranc¸ois
9 OntheSearchforDesignPrinciplesinBiologicalSystems............ 183
JuanF.Poyatos
ix
x Contents
10 TowardaTheoryofMultilevelEvolution:Long-Term
Information Integration Shapes the Mutational
LandscapeandEnhancesEvolvability................................... 195
PaulienHogeweg
11 Evolutionary Principles Underlying Structure
andResponseDynamicsofCellularNetworks.......................... 225
ArnoSteinacherandOrkunS.Soyer
12 Phenotypic Plasticityand Robustness: Evolutionary
StabilityTheory, Gene ExpressionDynamicsModel,
andLaboratoryExperiments ............................................. 249
KunihikoKaneko
13 GeneticRedundanciesandTheirEvolutionaryMaintenance......... 279
JianzhiZhang
14 EvolutionofResourceandEnergyManagement
inBiologicallyRealisticGeneRegulatoryNetworkModels ........... 301
DovJ.StekelandDafydJ.Jenkins
15 ReverseEcology:FromSystemstoEnvironmentsandBack.......... 329
RoieLevyandElhananBorenstein
16 Bacteria–VirusCoevolution............................................... 347
AngusBucklingandMichaelBrockhurst
17 The Genotype–PhenotypeMaps of Systems Biology
andQuantitativeGenetics:DistinctandComplementary............. 371
ChristianR.LandryandScottA.Rifkin
18 HowEvolutionarySystemsBiologyWillHelpUnderstand
AdaptiveLandscapesandDistributionsofMutationalEffects........ 399
LaurenceLoewe
19 BuildingSyntheticSystemstoLearnNature’sDesignPrinciples..... 411
EricA.Davidson,OliverP.F.Windram,andTravisS.Bayer
20 TheRobustnessContinuum............................................... 431
SashaF.LevyandMarkL.Siegal
Index............................................................................... 453
