Biophysics: Searching for Principles

653 Pages·2012·8.767 MB·English

by  William Bialek

Biophysics
Searching for Principles
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Biophysics
Searching for Principles
William Bialek
PRINCETON UNIVERSITY PRESS
PrincetonandOxford
Copyright©2012byPrincetonUniversityPress
PublishedbyPrincetonUniversityPress,41WilliamStreet,Princeton,NewJersey08540
IntheUnitedKingdom:PrincetonUniversityPress,6OxfordStreet,Woodstock,
OxfordshireOX201TW
press.princeton.edu
AllRightsReserved
ISBN978-0-691-13891-6
LibraryofCongressCataloging-in-PublicationData
Bialek,WilliamS.
Biophysics:searchingforprinciples/WilliamBialek.
p. cm.
Includesbibliographicalreferencesandindex.
ISBN978-0-691-13891-6(hardback:alk.paper)
1. Biophysics. I. Title.
QH505.B455 2012
571.4—dc23 2012014443
BritishLibraryCataloging-in-PublicationDataisavailable
ThisbookhasbeencomposedinBirkawithMyriadProdisplayusingZzTEX
byPrincetonEditorialAssociatesInc.,Scottsdale,Arizona.
Printedonacid-freepaper.
PrintedintheUnitedStatesofAmerica
10 9 8 7 6 5 4 3 2 1
Inmemoryofmyparents,whoseimprobablejourneys
madepossiblesomanywonderfulthings.
This page intentionally left blank
Contents
Acknowledgments ix
PART I EXPLORINGTHEPHENOMENA
1. Introduction 3
1.1 AboutOurSubject 3
1.2 AboutThisBook 11
2. PhotonCountinginVision 17
2.1 AFirstLook 17
2.2 DynamicsofSingleMolecules 51
2.3 BiochemicalAmplification 68
2.4 TheFirstSynapseandBeyond 97
2.5 Coda 115
3. Lessons,Problems,Principles 117
PART II CANDIDATEPRINCIPLES
4. NoiseIsNotNegligible 127
4.1 FluctuationsandChemicalReactions 127
4.2 MotilityandChemotaxisinBacteria 149
4.3 MoleculeCounting,MoreGenerally 172
4.4 MoreaboutNoiseinPerception 192
4.5 ProofreadingandActiveNoiseReduction 218
4.6 Perspectives 245
vii
viii
Contents
5. NoFineTuning 247
5.1 SequenceEnsembles 248
5.2 IonChannelsandNeuronalDynamics 279
5.3 TheStatesofCells 299
5.4 LongTimeScalesinNeuralNetworks 329
5.5 Perspectives 349
6. EfficientRepresentation 353
6.1 EntropyandInformation 354
6.2 NoiseandInformationFlow 369
6.3 DoesBiologyCareaboutBits? 395
6.4 OptimizingInformationFlow 421
6.5 GatheringInformationandMakingModels 449
6.6 Perspectives 467
7. Outlook 469
Appendix SomeFurtherTopics 473
A.1 PoissonProcesses 473
A.2 Correlations,PowerSpectra,andAllThat 484
A.3 DiffractionandBiomolecularStructure 495
A.4 ElectronicTransitionsinLargeMolecules 503
A.5 TheKramersProblem 512
A.6 BergandPurcell,Revisited 521
A.7 MaximumEntropy 533
A.8 MeasuringInformationTransmission 545
AnnotatedBibliography 557
Index 625
Acknowledgments
A four-page paper in Physical Review Letters typically includes a full paragraph of
acknowledgments.AnaivescalingargumentsuggeststhatImayneedupwardofone
hundredparagraphsinwhichtogivethankstothemanypeoplewhohavehelpedmake
thisbookpossible.Idon’tproposetousequitethatmuchspace,butthisbook,andthe
ideasonwhichitisbased,haveoccupiedasubstantialpartofmylifeovermanyyears,
andIhaveaccumulatedmanyintellectualdebts.
AsIsuspectwillbecomeclearrathersoonuponenteringthemaintext,theviews
of the field that I present here are very personal, and I don’t want anyone else held
responsible for my foibles. However, these views did not emerge in isolation. I am
especiallygratefultoRobdeRuytervanSteveninck,whointroducedmetothewonders
ofclosecollaborationbetweentheoryandexperiment.Whatbeganasabriefdiscussion
aboutthepossibilityofmeasuringtheprecisionofcomputationinasmallcornerof
thefly’sbrainhasbecomehalfalifetime(sofar!)offriendshipandsharedintellectual
adventure.
MygoodfortuneinfindingwonderfulexperimentalcollaboratorsbeganwithRob
but certainly did not end with him. A decade of conversations with Michael Berry,
Allison Doupe, Steve Lisberger, and Leslie Osborne—sometimes reflected in joint
papersandsometimesnot—hasinfluencedimportantpartsofthisbookinwaysIhope
they will recognize. Special thanks to Michael and his group for the beautiful image
thatservesasthebackgroundofthechapterlogos.AfterImovedtoPrinceton,David
Tank,EricWieschaus,andIbeganaverydifferentadventure,soonjoinedbyThomas
Gregor.Ihavebeenamazedbyhowtheseinteractionshavesoquicklyreshapedmyown
thinking, leavingtheirmarkonmyviewofthesubjectasawholeandhenceonthis
text.
Theory itself is more fun in collaboration with others, even when not engaged
withexperimentalistfriends.Differentpartsofthetexttracetheiroriginstojointwork
and discussions with Blaise Agu¨era y Arcas, Gurinder S. Atwal, Feraz Azhar, Naama
Brenner, William J. Bruno, Curtis G. Callan, Jr., Andrea Cavagna, Denis Chigirev,
Michael C. Crair, Michael DeWeese, Adrienne Fairhall, Irene Giardina, Robert F.
Goldstein, Julian S. Joseph, Steven Kivelson, Roland Koberle, Dmitry Krotov, Leonid
Kruglyak,ThierryMora,IlyaNemenman,Jose´NelsonOnuchic,W.GeoffreyOwen,
StephaniePalmer, FernandoPereira, MarcPotters, KanakaRajan, FredRieke, Daniel
Ruderman, Elad Schneidman, Sima Setayeshgar, Tatyana Sharpee, Spyros Skourtis,
ix