Africa in the Age of Biology docx

AFRICA฀IN฀THE฀AGE฀OF฀BIOLOGY Wilmot฀James฀ HSRC฀ Publishers SCI 5_Africa Biology 007 8/25/04, 11:22 AM1 Free download from www.hsrcpublishers.ac.za Social฀Cohesion฀and฀Integration฀Research฀Programme,฀Africa฀Human฀Genome฀Initiative฀Occasional฀Paper฀Series฀No.฀3 Series฀Editor:฀Prof.฀Wilmot฀James,฀Executive฀Director:฀Social฀Cohesion฀and฀Integration฀Research฀Programme฀of฀the฀ Human฀Sciences฀Research฀Council Published฀by฀HSRC฀Publishers Private฀Bag฀X9182,฀Cape฀Town,฀8000,฀South฀Africa www.hsrcpublishers.ac.za ©฀2004฀Human฀Sciences฀Research฀Council฀ First฀published฀2004 All฀rights฀reserved.฀No฀part฀of฀this฀book฀may฀be฀reprinted฀or฀reproduced฀or฀utilised฀in฀any฀form฀or฀by฀any฀electronic,฀ mechanical,฀or฀other฀means,฀including฀photocopying฀and฀recording,฀or฀in฀any฀information฀storage฀or฀retrieval฀system,฀ without฀permission฀in฀writing฀from฀the฀publishers. ISBN฀0฀7969฀2073฀7 Production฀by฀comPress Distributed฀in฀Africa฀by฀Blue฀Weaver฀Marketing฀and฀Distribution,฀ PO฀Box฀30370,฀Tokai,฀Cape฀Town,฀7966,฀South฀Africa. Tel:฀+27฀+21-701-4477 Fax:฀+27฀+21-701-7302 email:฀orders@blueweaver.co.za Distributed฀worldwide,฀except฀Africa,฀by฀Independent฀Publishers฀Group, 814฀North฀Franklin฀Street,฀Chicago,฀IL฀60610,฀USA. www.ipgbook.com฀ To฀order,฀call฀toll-free:฀1-800-888-4741 All฀other฀inquiries,฀Tel:฀+1฀+312-337-0747฀ Fax:฀+1฀+312-337-5985 email:฀Frontdesk@ipgbook.com SCI 5_Africa Biology 007 8/25/04, 11:22 AM2 Free download from www.hsrcpublishers.ac.za 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,฀or฀they฀may฀be฀finished,฀publication-ready฀works.฀Authors฀invite฀comments฀ and฀suggestions฀from฀readers. This฀paper฀was฀presented฀as฀the฀first฀annual฀John฀Gerhart฀Memorial฀Lecture฀at฀ the฀conference฀of฀the฀Africa฀Genome฀Initiative฀held฀in฀Cairo฀from฀March฀26฀to฀29,฀ 2004.฀Considerations฀of฀Egyptian฀science฀and฀arts฀and฀their฀lasting฀impact฀on฀Africa฀ are฀a฀fitting฀tribute฀to฀the฀roundedness฀of฀John฀Gerhart,฀himself฀an฀art฀collector฀of฀ some฀note,฀a฀gifted฀story-teller,฀an฀enthusiastic฀birder,฀an฀economist฀by฀training฀and฀ a฀scientist฀by฀inclination,฀a฀philanthropist฀of฀great฀empathy฀and฀skill,฀and฀a฀university฀ president฀with฀vision฀and฀leadership.฀One฀of฀the฀last฀things฀John฀Gerhart฀did฀before฀ he฀died฀was฀ to฀visit฀ that฀birder’s฀dream,฀ the฀Galapagos฀ Islands,฀once฀described฀in฀ the฀title฀of฀a฀book฀as฀Evolution’s฀workshop฀(Larson฀2001).฀It฀was฀here฀that฀Charles฀ Darwin฀spent฀a฀great฀deal฀of฀time฀observing฀the฀behaviour฀of฀species฀of฀beings฀that฀ had฀evolved฀over฀hundreds฀of฀thousands฀of฀years฀in฀isolation฀and฀in฀the฀absence฀of฀ natural฀predators.฀If฀you฀approached฀and฀touched฀those฀birds,฀they฀did฀not฀fly฀away.฀ Like฀John฀Gerhart,฀they฀lacked฀the฀biochemistry฀of฀trepidation. SCI 5_Africa Biology 007 8/25/04, 11:22 AM3 Free download from www.hsrcpublishers.ac.za 1 SCI 5_Africa Biology 007 8/25/04, 11:22 AM4 Free download from www.hsrcpublishers.ac.za 1 Africa฀in฀the฀Age฀of฀Biology Harvard฀ University’s฀ Richard฀Lewontin฀in฀his฀ book฀ Human฀ diversity฀ explains฀the฀ meaning฀ of฀what฀is฀ known฀ in฀ the฀world฀of฀ mathematics฀ as฀Markovian฀properties฀ operating฀as฀part฀of฀the฀dynamics฀of฀physical฀and฀natural฀systems.฀ The฀ properties฀ were฀ named฀ after฀ the฀ St฀ Petersburg฀ University฀ trained฀ Russian฀ mathematician฀ who฀first฀studied฀ them.฀Andrei฀Markov฀ (n.d.)฀ is฀best฀ remembered฀ for฀his฀study฀of฀sequences฀of฀random฀variables฀where฀the฀future฀state฀of฀a฀variable฀is฀ determined฀by฀a฀current฀variable฀but฀is฀independent฀of฀the฀way฀in฀which฀the฀present฀ state฀arose฀from฀its฀predecessors.฀So,฀for฀example,฀in฀demography,฀information฀about฀ the฀size฀of,฀say,฀the฀Egyptian฀population฀in฀2004฀depends฀only฀on฀how฀many฀people฀ were฀alive฀in฀2003฀and฀on฀the฀birth฀and฀death฀rates฀among฀the฀various฀age฀and฀sex฀ cohorts,฀without฀having฀ to฀know฀for฀purposes฀ of฀prediction฀how฀they฀ came฀to฀be฀ so. Lewontin฀talks฀ about฀Markovian฀properties฀ in฀reference฀ to฀an฀understanding฀ of฀ species฀evolution฀and฀particularly฀that฀of฀hominids,฀where฀all฀we฀need฀to฀know฀in฀ our฀endeavour฀to฀predict฀our฀future฀biological฀trajectory฀is฀the฀present฀state฀of฀our฀ genes.฀Our฀genes฀are,฀no฀doubt,฀as฀Lewontin฀put฀it,฀‘a฀consequence฀of฀their฀history’,฀ but฀he฀also฀says฀that฀‘the฀genes฀currently฀possessed฀by฀the฀species฀are฀all฀that฀matters฀ for฀ its฀evolutionary฀ future,฀ irrespective฀of฀ how฀it฀acquired฀ those฀genes’฀(Lewontin฀ 1995:฀147). Processes฀of฀biological฀evolution฀work฀like฀Markov’s฀mathematical฀chains,฀where฀ memory฀is฀interesting฀but฀irrelevant;฀for฀there฀is,฀as฀Lewontin฀puts฀it,฀no฀‘memory฀in฀ biology,฀only฀in฀books’฀(Lewontin฀1995:฀148).฀After฀the฀sequencing฀of฀the฀human฀ genome,฀he฀might฀not฀be฀quite฀so฀categorical฀about฀the฀apparently฀ahistorical฀quality฀ of฀ genetic฀ material,฀ as฀ molecular฀ geneticists฀ would฀ certainly฀ attribute฀ ‘time’฀ to฀ SCI 5_Africa Biology 007 8/25/04, 11:22 AM1 Free download from www.hsrcpublishers.ac.za Wilmot฀James 2 Africa฀in฀the฀Age฀of฀Biology 3 mutational฀events฀that฀are฀recorded฀there฀as฀junk฀or฀rubbish฀or฀the฀real฀thing;฀but฀ then฀again฀this฀matters฀not,฀for฀it฀is฀about฀what฀one฀needs฀to฀know฀in฀order฀to฀predict฀ the฀future.฀History,฀however฀one฀may฀wish฀to฀conceive฀of฀it,฀does฀not฀count฀in฀the฀ case฀of฀Markovian฀properties. By฀ contrast,฀ cultural฀ systems฀ such฀ as฀ modes฀ of฀ production,฀ counting฀ systems,฀ language,฀writing,฀buildings,฀art,฀and฀so฀on,฀all฀depend฀vitally฀on฀an฀accumulation฀ of฀ memory฀ and฀ well-functioning฀ means฀ of฀ their฀ transmission฀ from฀ generation฀ to฀ generation.฀ Indeed,฀human฀progress฀in฀our฀styles฀of฀material฀and฀cultural฀manner฀of฀life฀relies฀ on฀our฀ability฀to฀store฀and฀pass฀on฀memory.฀Here฀the฀library,฀the฀architectural฀store฀ of฀written฀human฀memory,฀in฀books฀principally,฀or฀scrolls฀at฀that฀time฀more฀likely,฀ played฀a฀central,฀indisputable฀role.฀ And฀ it฀ is฀ in฀ illustrating฀ the฀ non-Markovian฀ principle฀ of฀ much฀of฀our฀cultural- historical฀processes฀that฀Lewontin฀talks฀about฀the฀libraries฀of฀Alexandria:฀‘[T]he฀low฀ state฀of฀European฀culture,’฀he฀writes,฀‘that฀continued฀long฀after฀the฀disintegration฀ of฀Rome฀was฀in฀part฀a฀consequence฀of฀the฀immense฀loss฀from฀the฀fund฀of฀technical฀ and฀humanistic฀knowledge฀that฀occurred฀at฀the฀final฀destruction฀of฀the฀libraries฀of฀ Alexandria฀in฀391.’฀He฀then฀adds:฀‘In฀contrast,฀Muslim฀culture฀grew฀at฀a฀prodigious฀ rate฀beginning฀in฀the฀seventh฀century฀partly฀because฀the฀knowledge฀of฀classical฀times฀ –฀ knowledge฀ then฀ unavailable฀ to฀ the฀ Latin฀ and฀ Greek฀ scholars฀ of฀ Europe฀ –฀ was฀ preserved฀in฀Arabic฀manuscripts’฀(Lewontin฀1995:฀148). ฀There฀is฀no฀question฀that฀the฀libraries฀of฀Alexandria฀were฀central฀to฀the฀city฀and฀ the฀broad฀region฀including฀what฀today฀is฀the฀Middle-East,฀North฀Africa฀and฀much฀of฀ Central฀and฀Western฀Europe;฀that฀they฀were฀not฀the฀only฀ones฀to฀exist฀but฀were฀part฀ of฀a฀larger฀set฀of฀institutions฀to฀emerge฀from฀the฀concatenations฀of฀cultural,฀scholarly฀ and฀other฀areas฀of฀learning฀and฀application฀of฀what฀were฀then฀the฀advanced฀societies฀ of฀this฀part฀of฀the฀world. The฀agency฀of฀their฀ruin฀is฀not฀so฀certain,฀neither฀is฀it฀clear฀what฀it฀was฀in฀volume฀ and฀substance฀ that฀the฀libraries฀actually฀ contained.฀The฀institution฀was฀created฀by฀ Ptolemy฀I฀Soter฀first฀as฀a฀museum฀to฀which฀his฀son฀Ptolemy฀Philadelphus฀added฀a฀ library.฀It฀was฀Julius฀Caesar,฀some฀claimed,฀who฀destroyed฀the฀library,฀others฀put฀the฀ blame฀on฀Christian฀mobs,฀and฀yet฀others฀peddle฀the฀story฀that฀it฀was฀‘[o]n฀the฀orders฀ of฀Omar,฀Caliph฀ of฀Baghdad,฀[that]฀the฀entire฀collection฀ of฀books฀(except฀for฀the฀ works฀of฀Aristotle)฀stored฀at฀the฀Library฀of฀Alexandria฀were฀removed฀and฀used฀as฀fuel฀ to฀heat฀water฀for฀the฀city’s฀public฀baths’฀(Libraries฀n.d.฀Accessed฀2004a฀+฀2004b).฀ The฀evidence฀for฀what฀happened฀is฀thin,฀and฀James฀Hannan’s฀assessment,฀balanced฀ it฀would฀seem,฀is฀that฀‘Caesar฀was฀most฀probably฀responsible฀for฀the฀loss฀of฀the฀Royal฀ SCI 5_Africa Biology 007 8/25/04, 11:22 AM2 Free download from www.hsrcpublishers.ac.za Wilmot฀James 2 Africa฀in฀the฀Age฀of฀Biology 3 Library’;฀a฀second฀library฀called฀the฀Serapeum฀‘ceased฀to฀be฀when฀a฀Christian฀mob฀ tore฀ it฀ down฀ to฀ the฀ foundations฀ under฀ the฀ leadership฀ of฀ the฀ orthodox฀ patriarch฀ Theophilus฀after฀he฀had฀received฀word฀from฀the฀Emperor฀Theodosius’฀(Libraries฀n.d.฀ Accessed฀2004b).฀The฀story฀about฀Arab฀destruction,฀by฀the฀Caliph฀of฀Baghdad,฀is฀a฀ myth,฀without฀any฀evidence฀it฀would฀seem.฀And,฀of฀course,฀it฀is฀not฀the฀first฀time฀ that฀Baghdad฀has฀been฀blamed฀for฀something฀it฀did฀not฀do฀or฀not฀blamed฀for฀what฀ it฀did฀do. This฀paper฀starts฀with฀this฀story฀in฀part฀because฀some,฀if฀not฀most,฀of฀Aristotle’s฀ work฀was฀housed฀in฀the฀Alexandria฀library;฀and฀this฀great฀figure,฀principally฀known฀for฀ his฀philosophical฀scholarship,฀was฀also,฀as฀things฀tended฀to฀be฀then,฀one฀of฀the฀world’s฀ first฀embryologists฀and฀developmental฀biologists.฀This฀same฀Aristotle,฀who฀collected฀ and฀ dissected฀ embryos,฀ and฀ observed฀ them฀ closely,฀ got฀ the฀ sex฀ determination฀ of฀ human฀beings,฀we฀now฀know,฀terribly฀wrong.฀He฀claimed฀that฀the฀sex฀of฀a฀person฀was฀ determined฀by฀the฀heat฀of฀the฀male฀partner฀during฀intercourse.฀The฀more฀heated฀the฀ passion,฀the฀greater฀the฀probability฀of฀male฀offspring.฀He฀had฀counselled฀elderly฀men฀ to฀conceive฀in฀the฀summer฀if฀they฀wished฀to฀have฀male฀heirs.฀Scott฀Gilbert฀in฀his฀text฀ Developmental฀biology฀says฀about฀Aristotle฀that฀he฀‘promulgated฀a฀very฀straightforward฀ hypothesis฀of฀sex฀determination.฀Women฀were฀men฀whose฀development฀was฀arrested฀ too฀ early’฀(Gilbert฀ 2000:฀523).฀With฀ no฀sense฀at฀ all฀of฀the฀ microbiological,฀never฀ mind฀the฀molecular฀biological,฀Aristotle฀and฀many฀since฀then฀had฀not฀a฀clue฀about฀ the฀role฀of฀X฀and฀Y฀chromosomes,฀genetic฀heredity฀and฀the฀boost฀to฀human฀survival฀ of฀sexual฀as฀opposed฀to฀asexual฀reproduction.฀ Still,฀Aristotle฀was฀crucial฀in฀the฀history฀of฀biology฀and฀medicine฀for฀his฀painstaking฀ observations,฀his฀method฀ of฀pursuing฀ some฀key฀ questions฀about฀humanity฀ and฀its฀ evolution,฀and฀his฀unusual฀preoccupation฀with฀embryology,฀even฀though฀he฀could฀ not฀recognise฀that฀sexual฀as฀opposed฀to฀asexual฀reproduction฀was฀nature’s฀masterful฀ secret฀to฀human฀variety฀and฀survival.฀ Egypt฀and฀its฀history฀are฀what฀lie฀at฀the฀heart฀of฀the฀early฀history฀of฀medical฀biology,฀ engineering,฀physics,฀mathematics,฀architecture,฀art฀and฀literature.฀Although฀scholars฀ today฀tend฀to฀ think฀only฀ of฀early฀ Egyptians’฀knowledge฀of฀the฀medical฀biology฀ of฀ mummification฀and฀their฀understanding฀of฀anatomy,฀the฀biochemistry฀of฀soft฀and฀ hard฀ tissue,฀decay฀ and฀ preservation,฀it฀ is฀ clear฀as฀ Sameh฀ Arab,฀Associate฀Professor฀ of฀ Cardiology฀ at฀Alexandria฀University฀ writes,฀ that฀ ‘[s]ome฀kind฀of฀medicine฀ was฀ already฀practiced฀in฀Egypt฀in฀the฀earliest฀prehistoric฀days’.฀He฀refers฀to฀the฀Kahung฀ gynaecology฀ papyrus฀ dating฀ to฀ 1825฀ BC฀ which฀ ‘describes฀ methods฀ of฀ diagnosing฀ pregnancy฀and฀the฀sex฀of฀the฀fetus,฀toothache฀during฀pregnancy,฀diseases฀of฀women,฀ as฀well฀as฀feminine฀drugs’฀and฀to฀the฀Edwin฀Smith฀papyrus฀of฀1600฀BC,฀which฀can฀be฀ SCI 5_Africa Biology 007 8/25/04, 11:22 AM3 Free download from www.hsrcpublishers.ac.za Wilmot฀James 4 Africa฀in฀the฀Age฀of฀Biology 5 described฀as฀a฀reference฀work฀on฀internal฀medicine,฀dealing฀as฀it฀does฀with฀‘diseases฀of฀ the฀eye,฀skin,฀extremities,฀gynecology฀and฀some฀surgical฀diseases’฀(Arab฀n.d.).฀There฀ is,฀of฀course,฀much฀more฀to฀be฀said฀about฀ancient฀Egyptian฀medicine฀and฀its฀link฀with฀ modern฀biology,฀but฀that฀will฀have฀to฀be฀left฀for฀another฀time,฀another฀place. .฀.฀. Among฀ some฀ recently฀found฀fossils฀ left฀ in฀ the฀ Still฀Bay฀area฀ along฀ South฀ Africa’s฀ southernmost฀coastline฀by฀ what฀must฀ have฀been฀ ancestral฀Khoi฀ or฀San฀ people฀is฀ a฀ piece฀of฀decorated฀ochre,฀a฀form฀of฀iron฀ore.฀It฀is฀named฀in฀Afrikaans฀the฀blombos฀ (flower-bush)฀ochre฀after฀the฀cave฀where฀the฀fossil฀discoveries฀were฀found.฀The฀name฀ is฀an฀odd฀linguistic฀construction,฀being฀part฀of฀the฀vocabulary฀used฀to฀describe฀the฀ indigenous฀fauna฀variety฀of฀the฀south-western฀Cape฀known฀as฀fynbos฀(fine-bush),฀to฀ be฀found฀only฀there฀in฀all฀of฀its฀splendid฀variety฀and฀age. Christopher฀Henshilwood฀of฀the฀State฀University฀of฀New฀York,฀the฀archaeologist฀ digging฀at฀this฀site,฀describes฀the฀red฀ochre฀as฀‘measuring฀two฀and฀three฀inches฀long’,฀ ‘first฀scraped฀and฀ground฀smooth฀to฀create฀flat฀surfaces’,฀and฀‘then฀marked฀with฀cross฀ hatches฀and฀lines฀to฀create฀a฀consistent฀complex฀geometric฀motif’(Highfield฀n.d.).฀ What฀these฀markings฀mean฀is฀open฀to฀debate.฀One฀more฀cautious฀interpretation฀is฀ that฀ they฀are฀‘tally฀ marks’,฀‘making฀them฀ the฀ oldest฀form฀ of฀recorded฀ counting฀ever฀ found’฀[Blombos฀Cave฀n.d.].฀There฀is฀no฀independent฀source฀of฀proof฀as฀to฀what฀it฀is฀ these฀ancestors฀were฀counting.฀It฀could฀have฀had฀something฀to฀do฀with฀the฀ordinary฀ material฀ habits฀ of฀ hunters฀ and฀ gatherers,฀ and฀ likely฀ the฀ tallying฀ of฀ animal฀ kills.฀ Or,฀ perhaps,฀it฀related฀to฀trading฀with฀neighbours,฀or,฀more฀on฀a฀deeply฀existential฀level,฀ observing฀the฀astronomical,฀with,฀as฀Georges฀Ifrah฀puts฀it฀so฀beautifully฀in฀the฀Universal฀ history฀of฀numbers,฀a฀fascination฀with฀the฀regularity฀of฀‘the฀phases฀of฀the฀moon,฀the฀eternal฀ return฀of฀day฀and฀night,฀the฀cycle฀of฀the฀seasons’฀or,฀we฀might฀add,฀given฀the฀context,฀the฀ elliptical฀phases฀of฀the฀tides฀of฀great฀and฀marvellous฀oceans฀(Ifrah฀2000:฀xvi). In฀the฀history฀of฀counting,฀the฀San฀and฀Khoi฀perhaps฀joined฀other฀human฀beings฀and,฀ in฀observing฀that฀birds฀have฀two฀wings,฀animals฀four฀legs,฀and฀they฀ten฀fingers฀to฀their฀ hands฀and฀ten฀toes฀to฀their฀feet,฀developed฀a฀numbering฀system฀using฀their฀fingers฀or฀toes฀ as฀the฀base฀ten,฀the฀most฀common฀type฀of฀counting฀found฀among฀earlier฀peoples.฀ Or฀perhaps฀they฀joined฀the฀Mayans,฀Aztecs,฀Celts฀and฀Basques฀who฀looked฀down฀ at฀their฀feet฀and฀realised฀that฀their฀toes฀could฀be฀counted฀like฀fingers฀and฀chose฀the฀ much฀more฀unusual฀arithmetic฀base฀of฀20. SCI 5_Africa Biology 007 8/25/04, 11:22 AM4 Free download from www.hsrcpublishers.ac.za Wilmot฀James 4 Africa฀in฀the฀Age฀of฀Biology 5 Or฀ again,฀ perhaps,฀ they฀ joined฀ the฀ Sumerians฀and฀Babylonians,฀who฀chose฀for฀ reasons฀unknown฀to฀us฀today฀a฀base฀of฀60,฀which฀we฀use฀in฀respect฀of฀measuring฀time,฀ with฀an฀hour฀being฀60฀minutes฀and฀a฀minute฀being฀60฀seconds;฀or฀the฀measurement฀ of฀a฀circle฀into฀360฀degrees,฀each฀of฀60฀minutes฀divided฀into฀60฀seconds. Counting฀is,฀of฀course,฀the฀crucial฀first฀step;฀but฀it฀is฀not฀arithmetic฀and฀it฀certainly฀ does฀ not฀ approach฀ mathematics:฀ the฀ earliest฀ known฀ evidence฀ for฀ the฀ arithmetic฀ foundations฀of฀modern฀mathematics฀was฀found฀in฀Elam฀and฀Mesopotamia,฀Sumeria,฀ Ancient฀Egypt,฀Crete,฀Greece฀and฀Rome.฀ The฀ mathematics฀ of฀ Ancient฀ Egypt฀ were฀ quite฀ obviously฀ remarkable฀ in฀ their฀ sophistication฀ –฀proof฀of฀ this฀ are฀ the฀remains฀of฀ one฀ of฀ the฀great฀wonders฀ of฀ the฀ world:฀ the฀ pyramids,฀ which฀ were฀ engineered฀with฀extraordinary฀precision฀ and฀ on฀ a฀scale฀that฀stretches฀the฀mind.฀And,฀in฀confirmation฀of฀the฀test฀of฀all฀construction฀ tests,฀they฀still฀stand฀today,฀stripped฀perhaps,฀vandalised฀yes,฀looted฀certainly,฀but฀still฀ there฀in฀all฀of฀their฀beauty฀and฀grace.฀ Building฀the฀pyramids฀presumed฀expertise฀in฀stone฀cutting,฀engineering,฀mathematics฀ and฀physics,฀not฀to฀mention฀understanding฀and฀mastering฀the฀basics฀of฀the฀physics฀of฀ levers,฀ navigation฀ and฀ water฀ behaviour฀ in฀ moving฀ these฀ monstrous฀ blocks฀ of฀ stone฀ down฀the฀great฀river฀Nile.฀They฀are,฀in฀their฀practicality฀and฀complexity,฀stunning฀to฀ us;฀looking฀as฀we฀do฀in฀admiration,฀backwards฀at฀history. This฀ venture฀ into฀ biology฀ and฀ Africa฀ is฀ by฀ way฀ of฀ counting฀ and฀ arithmetic฀ then;฀ because฀it฀is฀an฀interesting฀digression฀into฀the฀epistemological฀lineage฀of฀mathematics฀and,฀ for฀reasons฀that฀will฀become฀clear,฀because฀there฀is฀a฀critical฀mathematical฀side฀to฀human฀ genetics฀which฀also฀indicates฀where฀Africa฀stands฀in฀relation฀to฀modern฀biology฀today. The฀mass฀media฀has฀over฀ the฀last฀ few฀years฀ been฀replete฀ with฀news฀ and฀feature฀ stories฀about฀deoxyribonucleic฀acid฀or฀DNA฀and฀what฀it฀means฀and฀might฀mean฀for฀ medicine,฀forensics,฀human฀origins฀and฀population฀ancestry.฀In฀part,฀the฀media฀has฀ been฀celebrating฀because฀of฀the฀50฀years฀of฀progress฀that฀have฀passed฀since฀DNA฀was฀ first฀discovered฀as฀having฀a฀ double-helical฀architecture,฀ and฀in฀ part฀because฀ of฀the฀ sometimes฀over-dramatised฀advances฀in฀understanding฀and฀treating฀inherited฀disease฀ regimes฀made฀possible฀by฀the฀sequencing฀of฀the฀human฀genome,฀the฀full฀repertoire฀of฀ our฀biological฀instructions. Three฀billion฀base-pair฀nucleotides฀make฀up฀the฀human฀genome฀and฀these฀add฀up฀ to฀an฀unknown฀number฀of฀genes฀in฀the฀region,฀it฀is฀said,฀of฀about฀32฀000.฀Nucleotide฀ information฀is฀digital,฀in฀that฀two฀elements฀combine฀in฀a฀manner฀following฀the฀rule฀of฀ A฀(for฀adenine)฀combining฀with฀T฀(for฀thymine)฀and฀G฀(for฀guanine)฀and฀with฀C฀(for฀ cytosine),฀making฀up฀a฀chain฀–฀the฀full฀extent฀of฀which฀we฀have฀still฀to฀understand฀ fully฀from฀the฀point฀of฀view฀of฀function฀and฀purpose;฀but฀we฀do,฀of฀course,฀know฀the฀ SCI 5_Africa Biology 007 8/25/04, 11:22 AM5 Free download from www.hsrcpublishers.ac.za Wilmot฀James 6 Africa฀in฀the฀Age฀of฀Biology 7 exact฀sequence฀of฀all฀the฀genetic฀letters฀of฀the฀nucleotide฀alphabet.฀Indeed,฀genomes฀ are฀encyclopaedias฀of฀genetic฀materials฀collected฀quite฀mechanically,฀not฀to฀prove฀a฀ set฀of฀hypotheses฀but฀simply฀to฀document฀what฀there฀is฀–฀the฀hypotheses฀coming,฀as฀ it฀were,฀later.฀And฀they฀now฀come฀thick฀and฀fast. Mathematics฀was฀ required฀ to฀ count฀the฀ DNA.฀Mathematical฀molecular฀ biology,฀ called฀bioinformatics,฀is฀required฀to฀make฀sense฀of฀the฀DNA,฀identify฀and฀discover฀the฀ candidate฀genes฀that฀are฀the฀particular฀strings฀or฀chains฀of฀DNA฀and฀begin฀to฀ascertain฀ their฀function.฀Described฀once฀by฀the฀South฀African฀born฀Nobel฀Laureate,฀Sydney฀ Brenner,฀in฀typically฀sardonic฀and฀intellectually฀dismissive฀manner฀as฀a฀new฀brand฀of฀ library฀science,฀bioinformatics฀is฀part฀of฀the฀essential฀equipment฀of฀every฀gene฀hunter.฀ He฀or฀she฀is฀the฀person฀who฀can฀master฀the฀software฀and฀data฀management฀associated฀ with฀millions฀and฀billions฀of฀bits฀of฀digitised฀information฀that฀add฀up฀to฀genes฀and฀ combinations฀ of฀ genes฀ that฀ programme฀ the฀ various฀ parts฀ of฀ the฀ human฀ body,฀ its฀ maintenance,฀ the฀ death฀ of฀ cells฀ and฀ eventually฀ the฀ demise฀ of฀the฀ entire฀ organism.฀ It฀is฀quite฀a฀business,฀made฀possible฀by฀the฀exponential฀growth฀of฀computerisation,฀ and฀in฀particular฀the฀work฀of฀a฀person฀after฀whom฀the฀writer’s฀visiting฀professorship฀ at฀the฀California฀Institute฀of฀Technology฀is฀named,฀Gordon฀Moore.฀Gordon฀Moore,฀ founder฀of฀Intel,฀predicted฀that฀the฀number฀of฀transistors฀that฀could฀be฀placed฀on฀a฀ computer฀chip฀would฀double฀every฀18฀months,฀and฀so฀it฀has฀been฀for฀over฀30฀years. But฀people฀should฀ not฀be฀misled฀by฀ Sydney฀Brenner’s฀lovely,฀dolorous฀ sense฀of฀ humour:฀the฀information฀demands฀in฀genomics฀are฀staggering.฀The฀genome฀contains฀ two฀kinds฀of฀digital฀information,฀one฀that฀encodes฀the฀protein฀and฀RNA฀‘molecular฀ machines฀of฀life’,฀and฀the฀other฀being฀the฀regulatory฀networks฀that฀specify฀how฀these฀ genes฀are฀expressed฀in฀time,฀space฀and฀amplitude.฀ DNA฀information฀is฀layered฀and฀arranged฀in฀a฀hierarchy,฀starting฀with฀the฀gene,฀ then฀ the฀ RNA,฀ then฀ the฀ protein,฀ then฀ the฀ protein฀ interactions,฀ then฀ the฀ protein฀ complexes,฀then฀the฀networks฀of฀ protein฀complexes฀ in฀a฀ cell,฀then฀ the฀tissues฀ and฀ organs,฀then฀the฀individual฀organism,฀followed฀by฀populations฀and฀the฀ecosystems฀in฀ which฀they฀live.฀In฀this฀kind฀of฀discovery฀science,฀mastering฀such฀vast฀quantities฀of฀ information฀to฀answer฀important฀questions฀is฀a฀skill฀and฀an฀art. And฀the฀hardware?฀The฀first฀automated฀sequencing฀machine฀took฀a฀day,฀in฀1986,฀ to฀sequence฀250฀of฀the฀three฀billion฀base฀pairs.฀It฀took฀the฀human฀genome฀project฀ ten฀years฀to฀sequence฀the฀human฀genome,฀two฀years฀shorter฀than฀predicted;฀and฀the฀ private฀company฀Celera฀with฀its฀so-called฀shotgun฀approach฀took฀less฀than฀the฀public฀ 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฀‘when฀the฀entire฀genome฀of฀an฀individual฀could฀be฀sequenced฀in฀a฀single฀ SCI 5_Africa Biology 007 8/25/04, 11:22 AM6 Free download from www.hsrcpublishers.ac.za . sense of humour: the information฀demands in genomics฀are฀staggering. The genome฀contains฀ two฀kinds of digital฀information,฀one฀that฀encodes the protein฀and฀RNA฀‘molecular฀ machines of life’,฀and the other฀being the regulatory฀networks฀that฀specify฀how฀these฀ genes฀are฀expressed in time,฀space฀and฀amplitude.฀ DNA฀information฀is฀layered฀and฀arranged in a฀hierarchy,฀starting฀with the gene,฀ then฀ the RNA,฀ then฀ the protein,฀ then฀ the protein฀ interactions,฀ then฀ the protein฀ complexes,฀then the networks of . and฀not฀only in Africa, ฀where฀there฀is฀a฀standing฀accusation฀ from฀certain฀quarters฀that฀African฀institutions฀are฀mere฀platforms฀for the interests of the multinational฀pharmaceutical฀companies฀and฀donor฀country฀interests฀seeking฀less฀ restrictive฀places฀to฀bio-prospect,฀test฀and฀market฀new฀biotechnology฀products. As฀a฀test of the integrity of what฀it฀is฀we฀do,฀we฀should฀ask฀how฀biotechnological฀ research in Africa feeds฀back฀into the teaching of modern biology at฀its฀universities,฀ the training of the next฀generation of research฀scientists,฀and the establishment฀and฀ maintenance of quality฀research฀laboratories฀–฀a฀rare฀commodity฀on฀this฀continent. We฀