Acta Biotheoretica

, Volume 56, Issue 3, pp 205–232 | Cite as

DNA Codes and Information: Formal Structures and Relational Causes

  • Richard v. SternbergEmail author
Regular Article


Recently the terms “codes” and “information” as used in the context of molecular biology have been the subject of much discussion. Here I propose that a variety of structural realism can assist us in rethinking the concepts of DNA codes and information apart from semantic criteria. Using the genetic code as a theoretical backdrop, a necessary distinction is made between codes qua symbolic representations and information qua structure that accords with data. Structural attractors are also shown to be entailed by the mapping relation that any DNA code is a part of (as the domain). In this framework, these attractors are higher-order informational structures that obviate any “DNA-centric” reductionism. In addition to the implications that are discussed, this approach validates the array of coding systems now recognized in molecular biology.


DNA Genome Code Information Structural realism Structural attractors Mathematical structures 



I thank the two anonymous reviewers for their comments on the initial manuscript and for all of their constructive suggestions.


  1. Anderson JC, Wu N, Santoro SW, Lakshman V, King DS, Schultz PG (2004) An expanded genetic code with a functional quadruplet codon. Proc Natl Acad Sci USA 101:7566–7571CrossRefGoogle Scholar
  2. Barnsley MF (2006) Superfractals. Cambridge University PressGoogle Scholar
  3. Biro JC (2006) Protein folding information in nucleic acids which is not present in the genetic code. Ann N Y Acad Sci 1091:399–411CrossRefGoogle Scholar
  4. Bollenbach T, Vetsigian K, Kishony R (2007) Evolution and multilevel optimization of the genetic code. Genome Res 17(4):401–404CrossRefGoogle Scholar
  5. Boutanaev AM, Mikhaylova LM, Nurminsky DI (2005) The pattern of chromosome folding in interphase is outlined by the linear gene density profile. Mol Cell Biol 18:8379–8386CrossRefGoogle Scholar
  6. Castresana J, Feldmaier-Fuchs G, Paäbo S (1998) Codon reassignment and amino acid composition in hemichordate mitochondria. Proc Natl Acad Sci USA 95:3703–3707CrossRefGoogle Scholar
  7. Collins FS (2006) The language of God. Free Press. Google Scholar
  8. Denton MJ, Marshall CJ, Legge M (2002) The protein folds as platonic forms: new support for the pre-Darwinian conception of evolution by natural law. J Theor Biol 219:325–342CrossRefGoogle Scholar
  9. Du Y, Davisson MT, Kafadar K, Gardiner K (2006) A-to-I pre-mRNA editing of the serotonin 2C receptor: comparisons among inbred mouse strains. Gene 382:39–46CrossRefGoogle Scholar
  10. Ehresmann AC, Vanbremeersch J-P (1987) Hierarchical evolutive systems: a mathematical model for complex systems. Bull Math Biol 49:13–50Google Scholar
  11. El-Hani CN, Queiroz J, Emmeche C (2006) A semiotic analysis of the genetic information system. Semiotica 160:1–68CrossRefGoogle Scholar
  12. Fernández MR, Porté S, Crosas E, Barberà N, Farrés J, Biosca JA, Parés X (2007) Human and yeast ξ-crystallins bind AU-rich elements in RNA. Cell Mol Life Sci 64:1419–1427CrossRefGoogle Scholar
  13. Fox Keller E (2000a) The century of the gene. Harvard University Press, CambridgeGoogle Scholar
  14. Fox Keller E (2000b) Decoding the genetic program: or, some circular logic in the logic of circularity. In: Beurton HJ, Falk R, Rheinberger H (eds) The concept of the gene in development and evolution. Cambridge University Press, Cambridge, pp 159–177Google Scholar
  15. Freeland SJ, Hurst LD (1998) The genetic code is one in a million. J Mol Evol 47:238–248CrossRefGoogle Scholar
  16. Gerstein MB, Bruce C, Rozowsky JS, Zheng D, Du J, Korbel JO, Emanuelsson O, Zhang ZD, Weissman S, Snyder M (2007) What is a gene, post-ENCODE? History and updated definition. Genome Res 17:669–681CrossRefGoogle Scholar
  17. Gilis D, Massar S, Cerf NJ, Rooman M (2001) Optimality of the genetic code with respect to protein stability and amino-acid frequencies. Genome Biol 2:RESEARCH0049Google Scholar
  18. Goodarzi H, Nejad HA, Torabi N (2004) On the optimality of the genetic code, with the consideration of termination codons. Biosystems 77:163–173CrossRefGoogle Scholar
  19. Goodwin B (2001) How the leopard changed its spots. Princeton University Press, PrincetonGoogle Scholar
  20. Griffiths PE (2001) Genetic information: a metaphor in search of a theory. Philos Sci 68:394–412CrossRefGoogle Scholar
  21. Griffiths PE, Stotz K (2006) Genes in the postgenomic era. Theor Med Bioeth 27:499–521CrossRefGoogle Scholar
  22. Gu W, Zhou T, Ma J, Sun X, Lu Z (2003) Folding type specific secondary structure propensities of synonymous codons. IEEE Trans Nanobioscience 2:150–157CrossRefGoogle Scholar
  23. Hoffmann PR, Hoge SC, Li PA, Hoffmann FW, Hashimoto AC, Berry MJ (2007) The selenoproteome exhibits widely varying, tissue-specific dependence on selenoprotein P for selenium supply. Nucleic Acids Res 35:3963–3973CrossRefGoogle Scholar
  24. Hohsaka T, Ashizuka Y, Murakami H, Sisido M (2001) Five-base codons for incorporation of nonnatural amino acids into proteins. Nucleic Acids Res 29:3646–3651CrossRefGoogle Scholar
  25. Itzkovitz S, Alon U (2007) The genetic code is nearly optimal for allowing additional information within protein-coding sequences. Genome Res 17:405–412CrossRefGoogle Scholar
  26. Kjosavik F (2007) From symbolism to information?—Decoding the gene code. Biol Philos 22:333–349CrossRefGoogle Scholar
  27. Ladyman J (1998) What is structural realism? Stud Hist Philos Sci 29:409–424CrossRefGoogle Scholar
  28. Lewin B (2007) Genes IX. Jones and Bartlett, BostonGoogle Scholar
  29. Link AJ, Tirrell DA (2005) Reassignment of sense codons in vivo. Methods 36:291–298CrossRefGoogle Scholar
  30. Moss L (2003) What genes can’t do. MIT Press, CambridgeGoogle Scholar
  31. Newman SA (2002) Developmental mechanisms: putting genes in their place. J Biosci 27:97–104CrossRefGoogle Scholar
  32. Ofran Y, Margalit H (2006) Proteins of the same fold and unrelated sequences have similar amino acid composition. Proteins 64:275–279CrossRefGoogle Scholar
  33. Ohlson J, Pedersen JS, Haussler D, Ohman M (2007) Editing modifies the GABA(A) subunit receptor alpha3. RNA 13:698–703CrossRefGoogle Scholar
  34. Oyama S (2000) The ontogeny of information: developmental systems and evolution, 2nd edn. Cambridge University Press, CambridgeGoogle Scholar
  35. Pattee H (2007) The necessity of biosemiotics: matter-symbol complementarity. In: Barbieri M (ed) Introduction to biosemiotics: the new biological synthesis. Springer, Netherlands, pp 115–132CrossRefGoogle Scholar
  36. Perry AJ, Hulett JM, Likić VA, Lithgow T, Gooley PR (2006) Convergent evolution of receptors for protein import into mitochondria. Curr Biol 16:221–229CrossRefGoogle Scholar
  37. Pertea M, Mount SM, Salzberg SL (2007) A computational survey of candidate exonic splicing enhancer motifs in the model plant Arabidopsis thaliana. BMC Bioinformatics 8:159. doi: 10.1186/1471-2105-8-159
  38. Ray A, van Naters WG, Shiraiwa T, Carlson JR (2007) Mechanisms of odor receptor gene choice in Drosophila. Neuron 53:353–369CrossRefGoogle Scholar
  39. Rinn JL, Kertesz M, Wang JK, Squazzo SL, Xu X, Brugmann SA, Goodnough LH, Helms JA, Farnham PJ, Segal E, Chang HY (2007) Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs. Cell 129:1311–1323CrossRefGoogle Scholar
  40. Salthe SN (1993) Development and evolution: complexity and change in biology. MIT Press, CambridgeGoogle Scholar
  41. Sarkar S (2000) Information in genetics and developmental biology. Philos Sci 67:208–213CrossRefGoogle Scholar
  42. Segal E, Fondufe-Mittendorf Y, Chen L, Thastrom A, Field Y, Moore IK, Wang JP, Widom J (2006) A genomic code for nucleosome positioning. Nature 442:772–778CrossRefGoogle Scholar
  43. Shea N (2007) Representation in the genome and in other inheritance systems. Biol Philos 22:313–331CrossRefGoogle Scholar
  44. Siorvanes L (1997) Proclus: neoplatonic philosophy and science. Yale University PressGoogle Scholar
  45. Small-Howard A, Morozova N, Stoytcheva Z, Forry EP, Mansell JB, Harney JW, Carlson BA, Xu XM, Hatfield DL, Berry MJ (2006) Supramolecular complexes mediate selenocysteine incorporation in vivo. Mol Cell Biol 26(6):2337–2346CrossRefGoogle Scholar
  46. Song W. Liu Z, Tan J, Nomura Y, Dong K (2004) RNA editing generates tissue-specific sodium channels with distinct gating properties. J Biol Chem 279:32554–32561CrossRefGoogle Scholar
  47. Taylor WR (2002) A ‘periodic table’ for protein structures. Nature 416:657–660CrossRefGoogle Scholar
  48. Tegmark M (1998) Is the ‘theory of everything’ merely the ultimate ensemble theory? Ann Phys 270:1–51CrossRefGoogle Scholar
  49. Washietl S, Pedersen JS, Korbel JO, Stocsits C, Gruber AR, Hackermuller J, Hertel J, Lindemeyer M, Reiche K, Tanzer A, Ucla C, Wyss C, Antonarakis SE, Denoeud F, Lagarde J, Drenkow J, Kapranov P, Gingeras TR, Guigo R, Snyder M, Gerstein MB, Reymond A, Hofacker IL, Stadler PF (2007) Structured RNAs in the ENCODE selected regions of the human genome. Genome Res 17:852–864CrossRefGoogle Scholar
  50. Waters K (2000) Molecules made biological. Revue Int Philos 4:539–564Google Scholar
  51. Xie X, Mikkelsen TS, Gnirke A, Lindblad-Toh K, Kellis M, Lander ES (2007) Systematic discovery of regulatory motifs in conserved regions of the human genome, including thousands of CTCF insulator sites. Proc Natl Acad Sci USA 104:7145–7150CrossRefGoogle Scholar
  52. Xin L, Zhou GL, Song W, Wu XS, Wei GH, Hao DL, Lv X, Liu DP, Liang CC (2007) Exploring cellular memory molecules marking competent and active transcriptions. BMC Mol Biol 8:31. doi: 10.1186/1471-2199-8-31

Copyright information

© Springer Science+Business Media B.V. 2008

Authors and Affiliations

  1. 1.Biologic InstituteRedmondUSA

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