Cellular Computing (Genomics and Bioinformatics)

239 Pages·2004·6.17 MB·English

by  Martyn Amos

Cellular Computing
Martyn Amos,
Editor
OXFORD UNIVERSITY PRESS
Cellular Computing
SeriesinSystemsBiology
EditedbyDennisShasha,NewYorkUniversity
EditorialBoard
MichaelAshburner,UniversityofCambridge
AmosBairoch,SwissInstituteofBioinformatics
DavidBotstein,PrincetonUniversity
CharlesCantor,Sequenom,Inc.
LeroyHood,InstituteforSystemsBiology
MinoruKanehisa,KyotoUniversity
RajuKucherlapati,HarvardMedicalSchool
Systems Biology describes the discipline that seeks to understand biological
phenomenaonalargescale:theassociationofgenewithfunction,thedetailed
modelingoftheinteractionamongproteinsandmetabolites,andthefunctionof
cells.SystemsBiologyhaswide-rangingapplication,asitisinformedbysev-
eralunderlyingdisciplines,includingbiology,computerscience,mathematics,
physics, chemistry, and the social sciences. The goal of the series is to help
practitioners and researchers understand the ideas and technologies underly-
ingSystemsBiology.Theseriesvolumeswillcombinebiologicalinsightwith
principlesandmethodsofcomputationaldataanalysis.
CellularComputing
MartynAmos,UniversityofExeter
Cellular Computing
Editedby
Martyn Amos
2004
Oxford NewYork
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LibraryofCongressCataloging-in-PublicationData
Cellularcomputing/editedbyMartynAmos.
p. cm.—(SeriesinSystemsBiology)
Includesbibliographicalreferencesandindex.
ISBN0-19-515539-4;0-19-515540-8(pbk)
1.Bioinformatics. 2.Cellularautomata. 3.Molecularcomputers. 4.Nanotechnology.
I.Amos,Martyn. II.Series.
QH324.2.C35 2004
571.6—dc22 2003058013
SerieslogoconceptbyCloeL.Shasha.
9 8 7 6 5 4 3 2 1
PrintedintheUnitedStatesofAmerica
onacid-freepaper
Preface
The field of cellular computing is a novel and exciting development at the
intersectionofbiology,computerscience,mathematics,andengineering.Prac-
titionersinthisemergingdisciplineareconcernedwiththeanalysis,modeling,
andengineeringofinter-andintra-cellularprocessesforthepurposesofcom-
putation.Developmentsinthefieldhavepotentiallyhugesignificance,ranging
fromnewbiologicalsensorsandmethodsforinterfacinglivingmaterialwith
siliconsubstrates,throughintelligentdrugdeliveryandnanotechnologyandon
toward a deeper understanding of the fundamental mechanisms of life itself.
Thisbookprovidesbothanintroductiontosomeoftheearlyfundamentalwork
andadescriptionofongoingcutting-edgeresearchinthefield.
Thisvolumeisorganizedintothreeparts.
PARTI:THEORETICALANDENGINEERINGPRINCIPLES
PartIisconcernedwiththetheoreticalfoundationsofthefield;initwedefinethe
engineeringprinciplesuponwhichthesecondpartisfounded.Chapter1(Amos
andOwenson)introducesthefieldofcellularcomputing,placingitinhistorical
contextandhighlightingsomeofthemoresignificantearlypapersinthefield.
Abriefintroductiontosomeunderlyingbiologicalprinciplesissuppliedforthe
benefitofthenonspecialistbiologist.Chapter2(Paton,Fisher,Malcolm,and
Matsuno)reviewscomputationalmethodsthatmaybeusefultobiologistsseek-
ingtomodeltheinteractionofproteinsinspatiallyheterogenousandchanging
vi PREFACE
environments. Chapter 3 (Lones and Tyrell) describes enzyme genetic pro-
gramming,anewoptimizationmethodthatdrawsinspirationfrombiological
representationsofinformation.InChapter4(Weiss,Knight,andSussman)the
idea of genetic process engineering is introduced. This is a methodology for
mappingdigitalcircuitryontogeneticelementsinarigorousandrobustfashion.
Thefundamentalengineeringprinciplesareestablished,andsoftwaretosup-
portdevelopmentisdescribed.PartIcloseswithChapter5(Simpsonetal.),in
whichwholecellsareconsideredasanalogoustosemiconductorcomponents.
Communicationbetweencells,andbetweencellsandsyntheticdevices,isdis-
cussed,aswellastheirintegrationwithnano-andmicro-structuredsubstrates
andthemodelingandsimulationofrelevantcellularprocesses.
PARTII:LABORATORYEXPERIMENTS
Part II is concerned with reporting the results of laboratory experiments in
cellularcomputing.InChapter6(WakabayashiandYamamura),theconstruc-
tion of a bacterial logical inverter is described. This is developed further in
Chapter7,whereWeiss,Knight,andSussmandescribethefeasibilityofdigital
computationincellsbybuildingseveralinvivodigitallogiccircuits.Engineered
intercellularcommunication,whichmaybecrucialtothelarge-scalescalability
ofcellularcomputing,isalsodescribed.Chapter8(Simpsonetal.)describes
excitingworkontheintegrationoflivingcellswithmicro-andnano-scalesys-
tems.Thischapterincludesstate-of-the-artresultsconcerningtheincorporation
ofnanofibersintolivingcells.
PARTIII:COMPUTATIONINCILIATES
PartIIIcoversanintriguingsubfieldofcellularcomputingconcernedwiththe
classoforganismsknownasciliates.Theseorganismsareparticularlyinterest-
ingbecausethey“encrypt”theirgenomicinformation.Althoughstudiesofthis
phenomenonhavenotyetsuggestedobviouspotentialforhumanengineering
ofciliates,elucidationoftheunderlyingcellularprocesseswillbeofgreatuse
inthefuture.InChapter9,PrescottandRozenbergbothdescribetheassembly
of ciliate genes from a biological perspective and consider its computational
implications.ThelatterthemeisdevelopedfurtherinChapter10,whereKari
and Landweber study the decryption of ciliate DNA from a computational
perspective.
ACKNOWLEDGMENTS
Firstthanksmustgotothecontributors.Theirtimeliness,flexibility,andhelpful-
nessmadeeditingthisvolumeanenjoyableandrewardingexperience.Thanks
PREFACE vii
goalsotoDennisShasha,theserieseditor,andtoKirkJensenatOUPfortheir
adviceandcarefulstewardshipoftheproject.IamalsogratefultoRobertHeller
forinvaluabletypesettingadvice.
MartynAmos
Exeter
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Contents
Contributors xi
PartI TheoreticalandEngineeringPrinciples
1 AnIntroductiontoCellularComputing 3
MartynAmosandGeraldOwenson
2 ProteinsandInformationProcessing 11
RayPaton,MichaelFisher,GrantMalcolm,andKoichiroMatsuno
3 EnzymeGeneticProgramming 19
MichaelA.LonesandAndyM.Tyrell
4 GeneticProcessEngineering 43
RonWeiss,ThomasF.KnightJr.,andGeraldSussman
5 TheDeviceScienceofWholeCellsasComponentsinMicroscale
andNanoscaleSystems 74
MichaelL.Simpson,GaryS.Sayler,JamesT.Fleming,
JohnSanseverino,andChrisD.Cox