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AFRICAINTHEAGEOFBIOLOGY
WilmotJames
HSRC
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SocialCohesionandIntegrationResearchProgramme,AfricaHumanGenomeInitiativeOccasionalPaperSeriesNo.3
SeriesEditor:Prof.WilmotJames,ExecutiveDirector:SocialCohesionandIntegrationResearchProgrammeofthe
HumanSciencesResearchCouncil
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©2004HumanSciencesResearchCouncil
Firstpublished2004
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Preface
The Human Sciences Research Council (HSRC) has established an occasional
paper series. The occasional papers are designed to be quick, convenient vehicles
for making timely contributions to debates or for disseminating interim research
findings,ortheymaybefinished,publication-readyworks.Authorsinvitecomments
andsuggestionsfromreaders.
ThispaperwaspresentedasthefirstannualJohnGerhartMemorialLectureat
theconferenceoftheAfricaGenomeInitiativeheldinCairofromMarch26to29,
2004.ConsiderationsofEgyptianscienceandartsandtheirlastingimpactonAfrica
areafittingtributetotheroundednessofJohnGerhart,himselfanartcollectorof
somenote,agiftedstory-teller,anenthusiasticbirder,aneconomistbytrainingand
ascientistbyinclination,aphilanthropistofgreatempathyandskill,andauniversity
presidentwithvisionandleadership.OneofthelastthingsJohnGerhartdidbefore
hediedwas tovisit thatbirder’sdream, theGalapagos Islands,oncedescribedin
thetitleofabookasEvolution’sworkshop(Larson2001).ItwasherethatCharles
Darwinspentagreatdealoftimeobservingthebehaviourofspeciesofbeingsthat
hadevolvedoverhundredsofthousandsofyearsinisolationandintheabsenceof
naturalpredators.Ifyouapproachedandtouchedthosebirds,theydidnotflyaway.
LikeJohnGerhart,theylackedthebiochemistryoftrepidation.
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AfricaintheAgeofBiology
Harvard University’s RichardLewontininhis book Human diversity explainsthe
meaning ofwhatis known in theworldof mathematics asMarkovianproperties
operatingaspartofthedynamicsofphysicalandnaturalsystems.
The properties were named after the St Petersburg University trained Russian
mathematician whofirststudied them.AndreiMarkov (n.d.) isbest remembered
forhisstudyofsequencesofrandomvariableswherethefuturestateofavariableis
determinedbyacurrentvariablebutisindependentofthewayinwhichthepresent
statearosefromitspredecessors.So,forexample,indemography,informationabout
thesizeof,say,theEgyptianpopulationin2004dependsonlyonhowmanypeople
werealivein2003andonthebirthanddeathratesamongthevariousageandsex
cohorts,withouthaving toknowforpurposes ofpredictionhowthey cametobe
so.
Lewontintalks aboutMarkovianproperties inreference toanunderstanding of
speciesevolutionandparticularlythatofhominids,whereallweneedtoknowin
ourendeavourtopredictourfuturebiologicaltrajectoryisthepresentstateofour
genes.Ourgenesare,nodoubt,asLewontinputit,‘aconsequenceoftheirhistory’,
buthealsosaysthat‘thegenescurrentlypossessedbythespeciesareallthatmatters
for itsevolutionary future, irrespectiveof howitacquired thosegenes’(Lewontin
1995:147).
ProcessesofbiologicalevolutionworklikeMarkov’smathematicalchains,where
memoryisinterestingbutirrelevant;forthereis,asLewontinputsit,no‘memoryin
biology,onlyinbooks’(Lewontin1995:148).Afterthesequencingofthehuman
genome,hemightnotbequitesocategoricalabouttheapparentlyahistoricalquality
of genetic material, as molecular geneticists would certainly attribute ‘time’ to
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mutationaleventsthatarerecordedthereasjunkorrubbishortherealthing;but
thenagainthismattersnot,foritisaboutwhatoneneedstoknowinordertopredict
thefuture.History,howeveronemaywishtoconceiveofit,doesnotcountinthe
caseofMarkovianproperties.
By contrast, cultural systems such as modes of production, counting systems,
language,writing,buildings,art,andsoon,alldependvitallyonanaccumulation
of memory and well-functioning means of their transmission from generation to
generation.
Indeed,humanprogressinourstylesofmaterialandculturalmannerofliferelies
onourabilitytostoreandpassonmemory.Herethelibrary,thearchitecturalstore
ofwrittenhumanmemory,inbooksprincipally,orscrollsatthattimemorelikely,
playedacentral,indisputablerole.
And it is in illustrating the non-Markovian principle of muchofourcultural-
historicalprocessesthatLewontintalksaboutthelibrariesofAlexandria:‘[T]helow
stateofEuropeanculture,’hewrites,‘thatcontinuedlongafterthedisintegration
ofRomewasinpartaconsequenceoftheimmenselossfromthefundoftechnical
andhumanisticknowledgethatoccurredatthefinaldestructionofthelibrariesof
Alexandriain391.’Hethenadds:‘Incontrast,Muslimculturegrewataprodigious
ratebeginningintheseventhcenturypartlybecausetheknowledgeofclassicaltimes
– knowledge then unavailable to the Latin and Greek scholars of Europe – was
preservedinArabicmanuscripts’(Lewontin1995:148).
ThereisnoquestionthatthelibrariesofAlexandriawerecentraltothecityand
thebroadregionincludingwhattodayistheMiddle-East,NorthAfricaandmuchof
CentralandWesternEurope;thattheywerenottheonlyonestoexistbutwerepart
ofalargersetofinstitutionstoemergefromtheconcatenationsofcultural,scholarly
andotherareasoflearningandapplicationofwhatwerethentheadvancedsocieties
ofthispartoftheworld.
Theagencyoftheirruinisnotsocertain,neitherisitclearwhatitwasinvolume
andsubstance thatthelibrariesactually contained.Theinstitutionwascreatedby
PtolemyISoterfirstasamuseumtowhichhissonPtolemyPhiladelphusaddeda
library.ItwasJuliusCaesar,someclaimed,whodestroyedthelibrary,othersputthe
blameonChristianmobs,andyetotherspeddlethestorythatitwas‘[o]ntheorders
ofOmar,Caliph ofBaghdad,[that]theentirecollection ofbooks(exceptforthe
worksofAristotle)storedattheLibraryofAlexandriawereremovedandusedasfuel
toheatwaterforthecity’spublicbaths’(Librariesn.d.Accessed2004a+2004b).
Theevidenceforwhathappenedisthin,andJamesHannan’sassessment,balanced
itwouldseem,isthat‘CaesarwasmostprobablyresponsibleforthelossoftheRoyal
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Library’;asecondlibrarycalledtheSerapeum‘ceasedtobewhenaChristianmob
tore it down to the foundations under the leadership of the orthodox patriarch
TheophilusafterhehadreceivedwordfromtheEmperorTheodosius’(Librariesn.d.
Accessed2004b).ThestoryaboutArabdestruction,bytheCaliphofBaghdad,isa
myth,withoutanyevidenceitwouldseem.And,ofcourse,itisnotthefirsttime
thatBaghdadhasbeenblamedforsomethingitdidnotdoornotblamedforwhat
itdiddo.
Thispaperstartswiththisstoryinpartbecausesome,ifnotmost,ofAristotle’s
workwashousedintheAlexandrialibrary;andthisgreatfigure,principallyknownfor
hisphilosophicalscholarship,wasalso,asthingstendedtobethen,oneoftheworld’s
firstembryologistsanddevelopmentalbiologists.ThissameAristotle,whocollected
and dissected embryos, and observed them closely, got the sex determination of
humanbeings,wenowknow,terriblywrong.Heclaimedthatthesexofapersonwas
determinedbytheheatofthemalepartnerduringintercourse.Themoreheatedthe
passion,thegreatertheprobabilityofmaleoffspring.Hehadcounselledelderlymen
toconceiveinthesummeriftheywishedtohavemaleheirs.ScottGilbertinhistext
DevelopmentalbiologysaysaboutAristotlethathe‘promulgatedaverystraightforward
hypothesisofsexdetermination.Womenweremenwhosedevelopmentwasarrested
too early’(Gilbert 2000:523).With nosenseat allofthe microbiological,never
mindthemolecularbiological,Aristotleandmanysincethenhadnotaclueabout
theroleofXandYchromosomes,geneticheredityandtheboosttohumansurvival
ofsexualasopposedtoasexualreproduction.
Still,Aristotlewascrucialinthehistoryofbiologyandmedicineforhispainstaking
observations,hismethod ofpursuing somekey questionsabouthumanity andits
evolution,andhisunusualpreoccupationwithembryology,eventhoughhecould
notrecognisethatsexualasopposedtoasexualreproductionwasnature’smasterful
secrettohumanvarietyandsurvival.
Egyptanditshistoryarewhatlieattheheartoftheearlyhistoryofmedicalbiology,
engineering,physics,mathematics,architecture,artandliterature.Althoughscholars
todaytendto thinkonly ofearly Egyptians’knowledgeofthemedicalbiology of
mummificationandtheirunderstandingofanatomy,thebiochemistryofsoftand
hard tissue,decay and preservation,it is clearas Sameh Arab,AssociateProfessor
of Cardiology atAlexandriaUniversity writes, that ‘[s]omekindofmedicine was
alreadypracticedinEgyptintheearliestprehistoricdays’.HereferstotheKahung
gynaecology papyrus dating to 1825 BC which ‘describes methods of diagnosing
pregnancyandthesexofthefetus,toothacheduringpregnancy,diseasesofwomen,
aswellasfemininedrugs’andtotheEdwinSmithpapyrusof1600BC,whichcanbe
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describedasareferenceworkoninternalmedicine,dealingasitdoeswith‘diseasesof
theeye,skin,extremities,gynecologyandsomesurgicaldiseases’(Arabn.d.).There
is,ofcourse,muchmoretobesaidaboutancientEgyptianmedicineanditslinkwith
modernbiology,butthatwillhavetobeleftforanothertime,anotherplace.
...
Among some recentlyfoundfossils left in the StillBayarea along South Africa’s
southernmostcoastlineby whatmust havebeen ancestralKhoi orSan peopleis a
pieceofdecoratedochre,aformofironore.ItisnamedinAfrikaanstheblombos
(flower-bush)ochreafterthecavewherethefossildiscoverieswerefound.Thename
isanoddlinguisticconstruction,beingpartofthevocabularyusedtodescribethe
indigenousfaunavarietyofthesouth-westernCapeknownasfynbos(fine-bush),to
befoundonlythereinallofitssplendidvarietyandage.
ChristopherHenshilwoodoftheStateUniversityofNewYork,thearchaeologist
diggingatthissite,describestheredochreas‘measuringtwoandthreeincheslong’,
‘firstscrapedandgroundsmoothtocreateflatsurfaces’,and‘thenmarkedwithcross
hatchesandlinestocreateaconsistentcomplexgeometricmotif’(Highfieldn.d.).
Whatthesemarkingsmeanisopentodebate.Onemorecautiousinterpretationis
that theyare‘tally marks’,‘makingthem the oldestform ofrecorded countingever
found’[BlombosCaven.d.].Thereisnoindependentsourceofproofastowhatitis
theseancestorswerecounting.Itcouldhavehadsomethingtodowiththeordinary
material habits of hunters and gatherers, and likely the tallying of animal kills. Or,
perhaps,itrelatedtotradingwithneighbours,or,moreonadeeplyexistentiallevel,
observingtheastronomical,with,asGeorgesIfrahputsitsobeautifullyintheUniversal
historyofnumbers,afascinationwiththeregularityof‘thephasesofthemoon,theeternal
returnofdayandnight,thecycleoftheseasons’or,wemightadd,giventhecontext,the
ellipticalphasesofthetidesofgreatandmarvellousoceans(Ifrah2000:xvi).
Inthehistoryofcounting,theSanandKhoiperhapsjoinedotherhumanbeingsand,
inobservingthatbirdshavetwowings,animalsfourlegs,andtheytenfingerstotheir
handsandtentoestotheirfeet,developedanumberingsystemusingtheirfingersortoes
asthebaseten,themostcommontypeofcountingfoundamongearlierpeoples.
OrperhapstheyjoinedtheMayans,Aztecs,CeltsandBasqueswholookeddown
attheirfeetandrealisedthattheirtoescouldbecountedlikefingersandchosethe
muchmoreunusualarithmeticbaseof20.
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Or again, perhaps, they joined the SumeriansandBabylonians,whochosefor
reasonsunknowntoustodayabaseof60,whichweuseinrespectofmeasuringtime,
withanhourbeing60minutesandaminutebeing60seconds;orthemeasurement
ofacircleinto360degrees,eachof60minutesdividedinto60seconds.
Countingis,ofcourse,thecrucialfirststep;butitisnotarithmeticanditcertainly
does not approach mathematics: the earliest known evidence for the arithmetic
foundationsofmodernmathematicswasfoundinElamandMesopotamia,Sumeria,
AncientEgypt,Crete,GreeceandRome.
The mathematics of Ancient Egypt were quite obviously remarkable in their
sophistication –proofof this are theremainsof one of thegreatwonders of the
world: the pyramids, which were engineeredwithextraordinaryprecision and on
ascalethatstretchesthemind.And,inconfirmationofthetestofallconstruction
tests,theystillstandtoday,strippedperhaps,vandalisedyes,lootedcertainly,butstill
thereinalloftheirbeautyandgrace.
Buildingthepyramidspresumedexpertiseinstonecutting,engineering,mathematics
andphysics,nottomentionunderstandingandmasteringthebasicsofthephysicsof
levers, navigation and water behaviour in moving these monstrous blocks of stone
downthegreatriverNile.Theyare,intheirpracticalityandcomplexity,stunningto
us;lookingaswedoinadmiration,backwardsathistory.
This venture into biology and Africa is by way of counting and arithmetic then;
becauseitisaninterestingdigressionintotheepistemologicallineageofmathematicsand,
forreasonsthatwillbecomeclear,becausethereisacriticalmathematicalsidetohuman
geneticswhichalsoindicateswhereAfricastandsinrelationtomodernbiologytoday.
Themassmediahasover thelast fewyears beenreplete withnews andfeature
storiesaboutdeoxyribonucleicacidorDNAandwhatitmeansandmightmeanfor
medicine,forensics,humanoriginsandpopulationancestry.Inpart,themediahas
beencelebratingbecauseofthe50yearsofprogressthathavepassedsinceDNAwas
firstdiscoveredashavinga double-helicalarchitecture, andin partbecause ofthe
sometimesover-dramatisedadvancesinunderstandingandtreatinginheriteddisease
regimesmadepossiblebythesequencingofthehumangenome,thefullrepertoireof
ourbiologicalinstructions.
Threebillionbase-pairnucleotidesmakeupthehumangenomeandtheseaddup
toanunknownnumberofgenesintheregion,itissaid,ofabout32000.Nucleotide
informationisdigital,inthattwoelementscombineinamannerfollowingtheruleof
A(foradenine)combiningwithT(forthymine)andG(forguanine)andwithC(for
cytosine),makingupachain–thefullextentofwhichwehavestilltounderstand
fullyfromthepointofviewoffunctionandpurpose;butwedo,ofcourse,knowthe
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exactsequenceofallthegeneticlettersofthenucleotidealphabet.Indeed,genomes
areencyclopaediasofgeneticmaterialscollectedquitemechanically,nottoprovea
setofhypothesesbutsimplytodocumentwhatthereis–thehypothesescoming,as
itwere,later.Andtheynowcomethickandfast.
Mathematicswas required to countthe DNA.Mathematicalmolecular biology,
calledbioinformatics,isrequiredtomakesenseoftheDNA,identifyanddiscoverthe
candidategenesthataretheparticularstringsorchainsofDNAandbegintoascertain
theirfunction.DescribedoncebytheSouthAfricanbornNobelLaureate,Sydney
Brenner,intypicallysardonicandintellectuallydismissivemannerasanewbrandof
libraryscience,bioinformaticsispartoftheessentialequipmentofeverygenehunter.
Heorsheisthepersonwhocanmasterthesoftwareanddatamanagementassociated
withmillionsandbillionsofbitsofdigitisedinformationthatadduptogenesand
combinations of genes that programme the various parts of the human body, its
maintenance, the death of cells and eventually the demise ofthe entire organism.
Itisquiteabusiness,madepossiblebytheexponentialgrowthofcomputerisation,
andinparticulartheworkofapersonafterwhomthewriter’svisitingprofessorship
attheCaliforniaInstituteofTechnologyisnamed,GordonMoore.GordonMoore,
founderofIntel,predictedthatthenumberoftransistorsthatcouldbeplacedona
computerchipwoulddoubleevery18months,andsoithasbeenforover30years.
Butpeopleshould notbemisledby SydneyBrenner’slovely,dolorous senseof
humour:theinformationdemandsingenomicsarestaggering.Thegenomecontains
twokindsofdigitalinformation,onethatencodestheproteinandRNA‘molecular
machinesoflife’,andtheotherbeingtheregulatorynetworksthatspecifyhowthese
genesareexpressedintime,spaceandamplitude.
DNAinformationislayeredandarrangedinahierarchy,startingwiththegene,
then the RNA, then the protein, then the protein interactions, then the protein
complexes,thenthenetworksof proteincomplexes ina cell,then thetissues and
organs,thentheindividualorganism,followedbypopulationsandtheecosystemsin
whichtheylive.Inthiskindofdiscoveryscience,masteringsuchvastquantitiesof
informationtoanswerimportantquestionsisaskillandanart.
Andthehardware?Thefirstautomatedsequencingmachinetookaday,in1986,
tosequence250ofthethreebillionbasepairs.Ittookthehumangenomeproject
tenyearstosequencethehumangenome,twoyearsshorterthanpredicted;andthe
privatecompanyCelerawithitsso-calledshotgunapproachtooklessthanthepublic
consortium’s ten, using a warehouse of computers to do so. ‘With single-DNA-
molecule sequencing, we foresee a time’ say the inventors of the first sequencing
machine‘whentheentiregenomeofanindividualcouldbesequencedinasingle
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. sense of
humour: the informationdemands in genomicsarestaggering. The genomecontains
twokinds of digitalinformation,onethatencodes the proteinandRNA‘molecular
machines of life’,and the otherbeing the regulatorynetworksthatspecifyhowthese
genesareexpressed in time,spaceandamplitude.
DNAinformationislayeredandarranged in ahierarchy,startingwith the gene,
then the RNA, then the protein, then the protein interactions, then the protein
complexes,then the networks of . andnotonly in Africa, wherethereisastandingaccusation
fromcertainquartersthatAfricaninstitutionsaremereplatformsfor the interests of
the multinationalpharmaceuticalcompaniesanddonorcountryinterestsseekingless
restrictiveplacestobio-prospect,testandmarketnewbiotechnologyproducts.
Asatest of the integrity of whatitiswedo,weshouldaskhowbiotechnological
research in Africa feedsbackinto the teaching of modern biology atitsuniversities,
the training of the nextgeneration of researchscientists,and the establishmentand
maintenance of qualityresearchlaboratories–ararecommodityonthiscontinent.
We
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