Information theory, evolution, and the origin of life

272 Pages·2005·1.941 MB·English

by  Hubert P. Yockey

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Information theory, evolution, and the origin of life
Information Theory, Evolution, and the Origin of Life presents a timely
introductiontotheuseofinformationtheoryandcodingtheoryinmolecular
biology.Thegeneticalinformationsystem,becauseitislinearanddigital,
resemblesthealgorithmiclanguageofcomputers.GeorgeGamowpointed
outthattheapplicationofShannon’sinformationtheorybreaksgeneticsand
molecularbiologyoutofthedescriptivemodeintothequantitativemode,
andDr.Yockeydevelopsthistheme,discussinghowinformationtheoryand
codingtheorycanbeappliedtomolecularbiology.Hediscusseshowthese
toolsformeasuringtheinformationinthesequencesofthegenomeandthe
proteome are essential for our complete understanding of the nature and
originoflife.Theauthorwritesforthecomputercompetentreaderwhois
interestedinevolutionandtheoriginsoflife.
Hubert P. Yockey is a former director of the Pulsed Radiation Facility at
the US Army’s Aberdeen Proving Ground, Maryland. He is the author of
InformationTheoryandMolecularBiology(1992).
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Information theory, evolution,
and the origin of life
HUBERT P. YOCKEY
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  
Cambridge, New York, Melbourne, Madrid, Cape Town, Singapore, São Paulo
Cambridge University Press
TheEdinburghBuilding,Cambridge,UK
Published in the United States of America by Cambridge University Press, New York
www.cambridge.org
Information on this title: www.cambridg e.org /9780521802932
©HubertP.Yockey2005
Thisbookisincopyright.Subjecttostatutoryexceptionandtotheprovisionof
relevantcollectivelicensingagreements,noreproductionofanypartmaytakeplace
withoutthewrittenpermissionofCambridgeUniversityPress.
Firstpublishedinprintformat 2005
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CambridgeUniversityPresshasnoresponsibilityforthepersistenceoraccuracyof
sforexternalorthird-partyinternetwebsitesreferredtointhisbook,anddoesnot
guaranteethatanycontentonsuchwebsitesis,orwillremain,accurateorappropriate.
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It must be considered that there is nothing more difficult to carry out nor
moredoubtfulofsuccess,normoredangeroustohandle,thantoinitiatea
new order of things. For the reformer has enemies in all those who profit
by the old order, and only lukewarm defenders in all those who would
profit by the new order, this lukewarmness arising partly for fear of their
adversaries,whohavethelawsintheirfavor;andpartlyfromtheincredulity
ofmen,whodonottrulybelieveinanythingnewuntiltheyhavehadactual
experienceofit.
Niccolo` Machiavelli(1469–1519),ThePrince,Chapter6.
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Contents
Preface page ix
1 Thegeneticinformationsystem 1
2 JamesWatson,FrancisCrick,GeorgeGamow,and
thegeneticcode 8
3 TheCentralDogmaofmolecularbiology 20
4 Themeasureoftheinformationcontentinthe
geneticmessage 27
5 Communicationofinformationfromthegenometothe
proteome 33
6 Theinformationcontentorcomplexityof
proteinfamilies 57
7 Evolutionofthegeneticcodeanditsmodern
characteristics 93
8 Haeckel’sUrschleimandtheroleoftheCentralDogma
intheoriginoflife 114
9 Philosophicalapproachestotheoriginoflife 149
10 TheerrorcatastropheandthehypercyclesofEigenand
Schuster 158
11 Randomness,complexity,theunknowable,
andtheimpossible 164
12 Doesevolutionneedanintelligentdesigner? 176
13 Epilogue 182
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Contents viii
Mathematicalappendix 191
Glossary 213
References 219
Index 251
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Preface
Thisbookintroducesthegeneralreaderandthespecialisttotheneworder
ofthingsinevolution,theoriginoflifeonEarth,andthequestionoflifeon
MarsandEuropaandelsewhereintheuniverse.Althoughtherearemany
fieldsofbiologythatareessentiallydescriptive,withtheapplicationofin-
formationtheory,theoreticalbiologycannowtakeitsplacewiththeoretical
physicswithoutapology.Thusbiologyhasbecomeaquantitativeandcom-
putationalscienceasGeorgeGamow(1904–68)suggested.Byemploying
informationtheory,comparisonsbetweenthegeneticsoforganismscannow
bemadequantitativelywiththesameaccuracythatistypicalofastronomy,
physics,andchemistry.
SpacecraftsendmessagestoEarthastheypasstheouterplanets–Mars,
Jupiter,Saturn,Uranus,Neptune,andPluto–inspiteofthesmallamountof
energyavailable.Enormousamountsofdataandinformationflowabouton
theInternet.Hugesumsofmoneyaretransferredeveryday.Errorsinthese
communicationscannotbetolerated.ClaudeShannon(1916–2001)showed
thatthisisaccomplishedbecausecommunicationissegregated,linear,and
digital so that sufficient redundance can be introduced in communication
codestoovercomeerrors.Furthermore,heshowedthatthesesignals,which
containmessages,canbemeasuredinbitsandbytes,termsthatarefamiliar
tocomputerusers.
WatsonandCrickdiscoveredthatthereisageneticmessage,recordedin
thedigitalsequenceofnucleotidesinDNA,thatcontrolstheformationof
proteinandofcourseallbiologicalprocesses.Themessageinthegenetic
informationsystemissegregated,linear,anddigitalandcanbemeasured
inbitsandbytes.Computeruserswillnoticetheisomorphismbetweenthe
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