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The Genetic Code and Zipf's Law Author(s): M. L.

Bender and Pritmohinder Gill Reviewed work(s): Source: Current Anthropology, Vol. 27, No. 3 (Jun., 1986), pp. 280-283 Published by: The University of Chicago Press on behalf of Wenner-Gren Foundation for Anthropological Research Stable URL: http://www.jstor.org/stable/2742889 . Accessed: 29/06/2012 06:12
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are currently unableto identify indigenous groups oversuchan extendedperiod,and thisforcesus to be cautiousin our ethnographic interpretations (Michielli1984). Indigenousgroups in South America tended to be migratory, with few settlements, and itis to thispreurban phase thatthemajority rock of art belongs, beginning 17,000 B.P. in easternBrazil and at 9,000 B.P. in southern Argentina (Guidon 1981, Gradinet al. 1977). The San Luis rock art, which includesboth painting and engraving, generally is in geometric design.This does not simplyrepresent influence Andean art but is consistent the of withthebroadertraditions SouthAmericanart as a whole. of Four pictographic fivepetroglyphic and styles, earliest the dating to 4000 B.C., have been identified. Some of themreflect influence fromas far away as the Chilean Andes, the ArgentineNorthwest, and Patagonia (Consens 1985). We considerit wrong,withfewexceptions, correlate to art styles artefact or typeswithethnicgroups.Nor are terms such as "hunter's art"or "pastoralist art"helpful, sincethey confuse conceptsof subsistence withsemiotic relationships. The varietyoftheenvironment, from sierras thepampas,and the the to utilisation the area as a traditional of migration routeallowed San Luis artists draw on a vast repertoire sourceswhich to of never amalgamatedto forma distinctive regionalstyle.San Luis is therefore particularly well-suited the testing hyto of on potheses influence, diffusion, adaptationbetweenareas and thatdiffer geographical in and archaeological character.

ReferencesCited
ALVAREZ, 1985. "Metodologia del tratamiento E. de estadfstico los in datos de la investigaci6n arte rupestre," "Utilizaci6nde la de inform6tica la determinaci6n estilosde arterupestre: ejemen de Un plo de analisis factorial correspondencia." de Actas de las Primeras Jornadas de Arte y Arqueologia, Santiago de Chile, 1983. In press. de CONSENS, 1980. "Sobrealgunosaspectosfisico-tecnicos la invesM. tigaci6nde arte rupestre."Programsand Abstracts, 43d International Congress Americanists, A25. of p. . 1985. San Luis: El arte rupestre sus sierras. San Luis: de Direcci6nde Culturade la Provinciade San Luis. GAMBIER, M. 1981. Instalaci6nhumana prehispanica la region en de de Cuyo. Instituto Investigaciones Arqueol6gicas Museo, Univery sidad de San Juan, Publicaciones9:1-5. GRADIN, J., et al. 1977 Investigaciones C. arqueol6gicasen la Cueva de las Manos, Estancia AltoRio Pinturas. Relacionesde la Sociedad Argentina Antropologia, de n.s., 10:3-52. GUIDON, M. 1981. Datao6es pelo C-14 de sitiosarqueol6gicos em Sao RaimundoNonato, sudestedo Piaui (Brasil). Clio 4:35-38. MICHIELLI,C. T. 1984. La regi6n Cuyo y sus naturales travesde de a la cr6nica de Ger6nimode Bibar y su confrontaci6n con otras fuentes.Institutode Investigaciones Arqueol6gicas Museo, Uny iversidadNacional de San Juan, Publicaciones 10:1-16. H. PAGER, 1976a. The rating superimposed of rockpaintings. Almogaren 5-6:205-18. . 1976b. Quantitativeanalysis elucidates the motivesof the SouthAfrican rockpainters.Almogaren 5-6:219-26.

The Genetic Code and Zipf's Lawl


byM. L. BENDER and PRITMOHINDER GILL Department Anthropology, of SouthernIllinois University at Carbondale,Carbondale,Ill. 62901, U.S.A. 19 VII 85 As a powerful and versatileinformation-carrying system, the genetic code is a testcase fordisplaying necessary the propertiesofsuchsystems. Most fundamental perhapsis therelationship known as Zipf's Law: the productof rank order and frequencyof elementsin a code is a constant.A second relationship discovered Zipfis thatmorefrequent by itemsin a code are more highlypolysemous than less frequent ones in accordancewitha simplemathematical formula. Bothofthese properties are examined here for several organismswhose DNA structures have been completely workedout. The genetic code, as itsnameimplies, a system elements is of which communicates in information the formalsense of the term(Cherry1978, Shannon and Weaver 1949). As such, it shows interesting parallels with other codes, e.g., human speech. At the lowest structural level, the nitrogen bases of nucleotides (adenine [A], cytosine [C], guanine[G], thymine [T], uracil [U]) can be seen as parallel to phoneticfeatures (about 40 in number,including presenceor absence of nasalization or vocalization,degree of aspiration,etc.). Stringsof three nucleotides make up codons(43 or 64 in number) parallel to phones(sets of phonetic features, probablyfewerthan300 forany given language). Of the 64 codons, equivalence sets exist,withtheresult thatthereare 20 distinct aminoacids and a boundary signal(e.g., alanineis represented GCA, GCC, by GCG, or GCT in thegenetic code formessenger RNA) parallel to the naturalclasses of phones makingup phonemes(12-70

1?

to happy acknowledge comments JackParker, from DuWayne Englert, Robert and Corruccini aidwith and statistical from computations Robert Corruccini. ofthem responsible anyerrors None is for herein.
280

search, all rights reserved 0011-3204/86/2703-0008$1.00. are We

1986 TheWenner-Gren by for ReFoundation Anthropological

forany language). (For moredetails on the geneticcode, see standard sources such as Crick 1966 or Dobzhansky et al. 1977.) The parallelcould be takenfarther Doerfler (see 1982), but forpresent purposeswe shall restrict attention the our to levelsjust mentioned. Statisticalproperties codes have been studiedin depth of (Cherry1978). One of the pioneering is findings Zipf's(1949) R x F = C; whereR is rankorderand F is frequency an of element a code, C is a constant thecode in question.Zipf in for shows that this relationship holds for the words of James Joyce's Ulyssesand formanyotherinformation-conveying systems(Cherry1978, Zipf 1949). In logarithmic terms, thisbecomeslogR + log F = log C, or in other terms + y = c, i.e., x a straight line of slope - 1 and y-intercept on log paper, c (logarithm any convenient to base). Zipf also investigated questionof meaningsper token, the finding thatmorefrequent itemsare morehighly polysemous than less frequentones-for example, more frequentphonemes have more allophones, more frequentwords have morehomophones (suchas bear[animal],bear[carry], bare).In fact,therelationship thiscase is thatofa straight 2y + x in line = c (wherey is log F and x is log R). The only difference betweenthisand thefirst Zipffinding, then,is thattheslopeis - 1/2 insteadof - 1. This means thatthereis a moregradual off falling of frequency than in the first case. Given that the geneticcode is an information-transmitting system excellence, Zipf'srelationships reallyuniverpar if are sal, theyshouldhold forit. As faras we are aware, no one has presented testof thisexpectation, a thoughseveralhave discussedtheDNA-languageparallel(e.g., Doerfier 1982,Jakobson 1970). We examinedthe codon structure the 5,375-nucleotide of DNA of the bacterialvirus4X 174 the completesequenceof whichhas been publishedby Fiddes (1977). The sequenceincludes nineidentified genes(labelledA, B, C, D, E, F, G, H, J). B is includedin A, E is includedin D, C overlapswithA and D, and J overlapswithD; F, G, and H are disjointfrom theothers.Each gene encodesa protein witha givenfunction (e.g., E forlysis-disrupting a hostcell'soutermembrane, for G part of the production spikes in the virus's proteincoat). of
CURRENT ANTHROPOLOGY

TABLE

FREQUENCIES AND RANKS OF AMINO ACIDS AND CODONS IN THE NINE GENES OF THE BACTERIAL VIRUS 4X 174 AMINO ACID AND CODONS Alanine ............ GCA ............ GCC ............ GCG ............ GCT ............ Arginine ........... CGA ............ CGC ............ CGG ............ CGT ............ AGA ............ AGG ............ Asparagine ......... AAC ............ AAT ............ Aspartic acid ....... GAC ............ GAT ............ Cysteine ........... TGC ............ TGT ............ Giutamic acid ...... GAA ............ GAG ............ Glutamine ......... CAA ............ CAG ............ Giycine ............ GGA ............ GGC ............ GGG ............ GGT ............ Histidine .......... CAC ............ CAT ............ Isoleucine .......... ATA ............ ATC ............ ATT ............ Leucine ............ CTA ............ CTC ............ CTG ............ FREQUENCY 168 17 29 19 103 114 6 36 8 49 11 2 91 35 56 123 52 71 26 12 14 88 32 56 92 45 47 126 18 41 4 63 35 9 26 88 6 15 67 167 7 17 25 In FREQUENCY 5.12 2.83 3.37 2.94 4.64 4.74 1.79 3.64 2.08 3.89 2.40 .69 4.51 3.55 4.02 4.81 3.95 4.26 3.26 2.48 2.64 4.48 3.47 4.02 4.52 3.81 3.85 4.84 2.89 3.71 1.39 4.14 3.55 2.20 3.26 4.48 1.79 2.71 4.20 5.12 1.96 2.83 3.22 RANK 1 41 27 36 1 9 59 23 55 16 51 63 12 24 11 6 14 3 19 50 47 13 25 12 10 19 17 4 37 20 61 6 18 52 29 14 58 43 5 2 57 40 30 In RANK 0 3.71 3.30 3.58 0 2.20 4.06 3.14 4.01 2.77 3.93 4.14 2.48 3.18 2.40 1.79 2.64 1.10 2.94 3.91 3.85 2.56 3.22 2.48 2.30 2.94 2.83 1.39 3.61 3.00 4.11 1.79 2.89 3.95 3.37 2.64 4.08 3.76 1.61 .69 4.04 3.69 3.40 AMINO ACID AND CODONS CTT ............ TTA ............ TTG ............ Lysine ............. AAA ............ AAG ............ Methionine (also initiator) ....... ATG ............ ...... Phenylalanine TTC ............ TTT ............ Proiine ............ CCA ............ CCC ............ CCG ............ CCT ............ Serine ............. AGC ............ AGT ............ TCA ............ TCC ............ TCG ............ TCT ............ Threonine ......... ACA ............ ACC ............ ACG ............ ACT ............ Tryptophan TGG ............ Tyrosine ........... TAC ............ TAT ............ Vaiine ............. GTA ............ GTC ............ GTG ............ GTT ............ Terminators ........ TAA ............ TAG ............ TGA ............ FREQUENCY 55 24 39 115 69 46 58 58 91 32 59 78 8 9 22 39 134 7 12 22 15 18 60 126 14 24 28 60 23 23 67 17 50 116 12 18 14 72 10 3 1 6 In FREQUENCY 4.01 3.18 3.66 4.75 4.23 3.83 4.06 4.06 4.51 3.47 4.08 4.36 2.08 2.20 3.09 3.66 4.89 1.96 2.48 3.09 2.71 2.89 4.09 4.84 2.64 3.18 3.33 4.09 3.14 3.14 4.21 2.83 3.91 4.75 2.48 2.89 2.64 4.28 2.30 1.10 0 1.79 RANK 13 32 22 8 4 18 17 10 11 26 9 15 54 53 34 21 3 56 48 35 44 39 8 5 45 31 28 7 20 33 16 42 15 7 49 38 46 2 21 62 64 60 In RANK 2.56 3.47 3.09 2.08 1.39 2.89 2.83 2.30 2.40 3.26 2.20 2.71 3.99 3.97 3.53 3.04 1.10 4.03 3.87 3.56 3.78 3.66 2.08 1.61 3.81 3.43 3.33 1.95 3.00 3.50 2.77 3.74 2.71 1.95 3.89 3.64 3.83 .69 3.04 4.13 4.16 4.09

NOTE: Orderofcodonsis alphabetical.Ties are listedin alphabetical order(e.g., ACT is 7th,TCT is 8th).Aminoacids are listedalphabetically exceptfor terminators (last).

Overlapping worksbecause of"phase differences," Gene e.g., B beginswithATGGAA, whileGene A readsTGG as a codon in thisstretch. additionto thegenes,thereare intermediate In "untranslated" regionswhich deal with operationalmatters such as terminating transcription detailssee Fiddes 1977). (for In thisstudy,only the genes are dealt with. Their lengths varygreatly; codons involvednumberper gene as follows:A, 514; B, 121; C, 87; D, 153; E, 92; F, 425; G, 176; H, 329; J,39 (total 1,936). Table 1 tabulatesthe frequencies and ranks of aminoacids and their codons.In figures and 2 thetwosetsof 1 data are graphedon scales of ln (naturallogarithm) rank of (x-axis)vs. ln frequency (y-axis).For amino acids (fig.1) the goodnessof fitto a straight line is farfrom impressive; much better wouldbe a broken-line approximation witha segment of shallow negativeslope from(0, 5.12) to (2.64, 4.48) and a segmentof steep negative slope from(2.64, 4.48) to (3.04, 2.30). Even so, a least-squares approximation = -0. 64x + y 5.73 has a correlation coefficient -0.73. Not surprisingly, of forthe largerdata set, that of codons, a somewhatsharper result obtained;theconcavecurveoffigure can be approxiis 2
Vol. 27 * No. 3 * June 1986

matedby y = 0.80x + 5.62 withr = -0. 83. Finally,table 2 showsthe data forthecodon composition each aminoacid, of and figure displaysthemgraphically F, whereF is num3 (ln ber of codons per amino acid vs. ln R, whereR is rank).The straight joiningtheextreme line points(0, 1.79 vs. 3.04, 0) has equationy = - 0.59x + 1.79, whichis a fairapproximation to the expectedy = - 0.5x + c. A least-squares approximation givesy = - 0.59x + 2.31 (same slope, higher intercept) with r = -0.88. It maybe arguedthata major-axis regression is fit moreappropriate thana least-squares one, sincemeasurement error maybe involvedin bothx and y variates.Without taking a standon whichmethod prefer, foundthatthereducedto we major-axisslopes are -0.88 foramino acids and -0.956 for codons,whichare closerapproximations thetheoretical to expectation - 1.0 (see table 3). of of Since the human geneticcode carriesa description the humanlanguagemechanism (oral-aural organs,brainspecialiof zations, etc.), the geneticcode containsa description the languagecode and vice versa (sincehumanlanguagecan prethe sumably succeedin describing genetic code). If therelation281

45-_

TABLE
CODON COMPOSITIONS NUMBER OF CODONS

2
ACIDS

OF THE AMINO

In
NUMBER RANK

In
RANK

AMINO 40 35
____T+_

ACID

Arginine ..........
.......... Leucine Serine ............ Alanine .......... Glycine ........... Proline ........... ........ Threonine Valine ............ ......... Isoleucine ...... Terminators ....... Asparagine ...... Aspartic acid Cysteine .......... ..... Glutamic acid ........ Glutamine Histidine ......... ........... Lysine ..... Phenylalanine Tyrosine ..........

6
6 6 4 4 4 4 4 3 3 2 2 2 2 2 2 2 2 2 1 1

1.79
1.79 1.79 1.39 1.39 1.39 1.39 1.39 1.10 1.10 .69 .69 .69 .69 .69 .69 .69 .69 .69 0 0

1
2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21

0
.69 1.10 1.39 1.61 1.79 1.95 2.08 2.20 2.30 2.40 2.48 2.56 2.64 2.71 2.77 2.83 2.89 2.94 3.00 3.04

30

25 InF 20

10

15

20 InR

25

30

35

40

45

logarithm frequency of logarithm rank natural of vs. FIG. 1. Natural XX ofamino occurrencesnine in of virus 174. genes thebacterial acid
y Least-squaresapproximation = -0. 64x + 5. 73, r = -0. 73.

Methionine (initiator) Tryptophan

....... .......

of ships discoveredby Zipf are necessaryproperties efficient code shouldbe a it codingsystems, would seemthatthegenetic for In strong exemplarof thoserelationships. fact,the results as the bacterialvirus 4X 174 are not as impressive some of Zipf'sexamples,e.g., wordsin Ulysses(Zipf 1949:23-25). But since the numberof different this is not really surprising, words in Ulyssesis about 29,899, more than 467 timesthe to number tokensin our test.Because codonsare limited 64 of is and aminoacids to 20, theonlyway to sharpentheresults to examineotherorganisms, especiallymorecomplexones (e.g.,
5.5-

5.0

4.5

mammalson the order of 109). the orderof 106 nucleotides, of The first thesedealt Two such analyseswere undertaken. DNA (Bibb et al. 1981) and the with mouse mitochondrial the 1984). Interestingly, second withE. coli (Alff-Steinberger of pattern curveforaminoacids and codonsin thesetwoexamples was very similarto the one seen in figures1 and 2 for 4X 174. The statisticalresultsfor all three examples are summarizedin table 3. In all cases except for the smallest sample (amino acids of 4X 174), slope is nearerto - 1 than for -0.75, and the best resultsare generally the largersamall ples. Correlations hover around -0.7 or -0.8, and reE. duced major axis (exceptfor coli codons)is near - 1. Thus, lines well by straight fairly thecurvescan all be approximated would be obof slopes near - 1, but a betterapproximation tainedby a brokengraphhavinga line of shallowerslope for This and steeperslope forlowerfrequencies. highfrequencies versionof coding,a modified meansthatin thecase of genetic tokensare very Zipf's Law seems to hold in which frequent explatokensrare.A biological indeedand infrequent frequent nationshould be soughtforthissituation.

according to Dobzhansky et al. [197 7:72-74], bacteria have on

4.0-

InF
3.5

2.0

15

3.0

InF 1.

2.5

.5-

OI

(number codonsper amino of of logarithm frequency FIG. 3. Natural logarithm frequency of FIG. 2. Natural logarithm rank natural of vs. of acid) vs. natural logarithm rank of amino acids in termsof the virusfX 174. of codonoccurrences ninegenesof thebacterial in y= . approximation 0.59X + 2.31, r = - 0.88. y= above Least-squares Least-squares approximation -O. 80X + 5.62, r = -0. 83.
282

InR

.5

1.0

1.5 InR

2.0

2.5

3.0

3.5

CURRENT

ANTHROPOLOGY

TABLE
SUMMARY AMINO OF GRAPHIC ACIDS RESULTS

3
FOR THREE ORGANISMS CODONS ,X 174 Mouse Mitochondrial DNA E. coli

,X Slope (m) ......... Intercept (y) ..........5.737 Correlation (r) ........ Reduced major axis ..

174

Mouse Mitochondrial DNA - 0.846 6.75 -0.781 - 1.08

E. coli -0.751 8.05 - 0.742 - 1.01

(N = 1,936) 5.62 - 0.835 -0.956

(N = 3,816)

(N = 16,351) 7.93 - 0.706 - 1 238

- 0.644 - 0.732
.

- 0.798

- 0.839
6.45 - 0.799 - 1.05

- 0.874

-0.88

ReferencesCited
on C. 1984. Evidence fora codingpattern the strandof the E. coli genome. Nucleic Acid Research non-coding 12:2235-41. BIBB, M. J.,R. A. VAN ETTEN, C. T. WRIGHT, M. W. WALBERG. 1981. Sequence and gene organizationof mouse mitochondrial DNA. Cell 26:167-80. Cambridge: CHERRY, COLIN. 1978. 3d ed. On humancommunication. M.I.T. Press. American215 code. 3. Scientific CRICK, F. H. C. 1966. The genetic (4):55-62.
ALFF-STEINBERGER,

linguistics be a guide? Medical Hypotheses 9:563-79. J. C. 1977. The nucleotide sequence of a viral DNA. Scientific American237 (6):54-67. JAKOBSON, ROMAN. 1970. Main trendsin the science of language. New York: Harper and Row. SHANNON, CLAUDE E., and WARREN WEAVER. 1949. The mathematical theory of communication. Urbana: University of Illinois Press. ZIPF, GEORGE K. 1949. Human behaviorand the principleof least effort.Cambridge: Addison-Wesley.
FIDDES,

DOBZHANSKY, T., F. J. AYALA, G. L. STEBBINS, and J. W. VALENTINE. 1977. Evolution. San Francisco: Freeman. DOERFLER, W. 1982. In search of more complex genetic codes: Can

volumeThe QuestforPeace, whichis theoutcomeof a multiof disciplinary meeting theInternational Social ScienceCouncil held at UNESCO headquartersin Paris last year. That meetingwas both cheeringand depressing-depressingbecause the 11 social sciencesrepresented there thepresidents (by by PETER WORSLEY or secretaries, usually,of theirinternational organizations) all 22 Northchurch Terrace,London Ni 4EG, England. 26 XI reported thatno serioussustainedworkon theissue ofnuclear 85 war had been developeduntilthelast couple ofyears.In conTwo years'workwiththeCommission theStudyofPeace of on trast,the naturalscienceshave played a major role-for inthe International Union of Anthropological Ethnological stance,in researching medicalconsequences nuclearwar and the of Sciences(IUAES) has convincedme thatthereis widespread or the prospectof a "nuclearwinter."Here, too, scenariosof receptivity any ideas that anthropologists able to conto are likelysocial responsesto nuclear devastationhave been left tribute the analysisof the major international to conflicts and largely social psychologists. to especiallyof the threatof nuclearwarfare. In theU.S.A., important contributions symposia interon to The sourcesof the armsrace lie in conflicts interests of and national conflicts the AmericanAssociationfor the Ad(at in "imagesof the Other"which are oftenbased on ignorance vancement Science in Los Angeleslast May and at theDeof and stereotypes similarin kindto thosewhichanthropologists cember1985 annual meeting theAmerican of Anthropological have so effectively analysedin studiesof interethnic relations. Association)have already been undertaken,and more are Beliefsabout an innate human propensity aggression, to for planned. The Soviet Academyof Sciences,similarly, invited instance,or Manichaean ideas about the intrinsic evil-ness of thePeace Commission a veryopen and rewarding to discussion believedenemies, whichhave beenstudiedin theanthropology in Moscow this August and has accepted its suggestion a of ofwitchcraft verysophisticated in ways,are highly relevant to conference involvingEast European and West European ansuspicions theintentions theU.S.S.R. or theU.S.A. The of of in thropologists London on the subject of urban ethnicity. studyof war making,and of peace making,by anthropoloand Conferences buildconfidence promote and interpersonal gists,in both state and acephalous societies,also points to institutional contactswithoutwhichwe remainignorant and mechanisms-of mediation,confidence building,alternatives usuallysuspiciousof colleaguesfrom whomwe are dividedby to war-which have theiranalogues in superpower other politicaland culturalbarriers. believethatanthropology, or I of kinds of international hostility. The institutional making of all disciplines,is best fitted do the following to even more war, includingmilitaryorganization,and the social forces important things: whichgenerate peace movements further are appropriate fields of research. (In the U.S.A., for example, Donna Brasset1. To multiply,on a greatlyincreased scale, fieldworkSheareris engaged in an anthropological studyof top U.S. based studiesbothby established and anthropologists by gradmilitary leaders.) uate students the kindCarolineHumphrey done in the of has The Peace Commission has now contributed severalmato U.S.S.R. and Jack Potterin China-which, so far, no East jor academic conferences. initialcollection papers from Europeanor Chineseanthropologist beenencouraged do An of has to the XIth International Congressof Anthropological Ethand in the West. nological Sciences at Vancouver in 1982 will come offthe 2. To embarkupon a program exchangesof teachersin of pressesas a book any minute(Peace and War: Cross-cultural whichtheywould equip themselves teach coursesin their to Perspectives, TransactionBooks). Carol Greenhouseof Corhome universities "The Peoples (plural) of the U.S.S.R." on nell University, of the cochairpersons the Peace Comone of (beforelong, an English-language textbook,preparedby an mission, is contributing behalf of our disciplineto the on American will anthropologist, be available) or "The Peoplesof the U.S.A./Western Europe." 1 ? 1986 by The Wenner-Gren 3. To exchange graduate students,trainedto first-degree FoundationforAnthropological Reall reserved search, rights 0011-3204/86/2703-0009$1.00. level in theirhome countries,who would pursue graduate Vol.27 * No. 3 - June 1986
283

Proposals forAnthropology the in Nuclear Agel