Skip to main content

A Gallery of Organic Codes

  • 1198 Accesses

Abstract

The discovery of the genetic code has revealed the existence of a deep parallel between protein synthesis and language. In both cases, a small set of units is used to create an unlimited variety of objects by arranging the units in countless different combinations. In technical terms this process is called recursion, and the presence of recursion at the molecular level raised the possibility that there is a molecular language at the basis of life (Beadle and Beadle 1966). At the same time, however, the first models of the genetic code were all based on the stereochemical hypothesis, the idea that the coding rules are dictated by chemical relationships in three dimensions, whereas language is made of arbitrary conventions. Eventually, however, the stereochemical hypothesis had to be abandoned because it became clear that the rules of the genetic code are not the result of chemical necessity. In this sense they are as arbitrary as the rules of language, and this makes us realize that at the molecular level there is not only recursion but also arbitrariness.

Keywords

  • Histone Modification
  • Genetic Code
  • Stable Microtubule
  • Histone Code
  • Organic Code

These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

This is a preview of subscription content, access via your institution.

Buying options

Chapter
USD   29.95
Price excludes VAT (USA)
  • DOI: 10.1007/978-3-319-14535-8_3
  • Chapter length: 20 pages
  • Instant PDF download
  • Readable on all devices
  • Own it forever
  • Exclusive offer for individuals only
  • Tax calculation will be finalised during checkout
eBook
USD   109.00
Price excludes VAT (USA)
  • ISBN: 978-3-319-14535-8
  • Instant PDF download
  • Readable on all devices
  • Own it forever
  • Exclusive offer for individuals only
  • Tax calculation will be finalised during checkout
Hardcover Book
USD   199.99
Price excludes VAT (USA)

References

  • Agalioti T, Chen G, Thanos D (2002) Deciphering the transcriptional histone acetylation code for a human gene. Cell 111(3):381–392

    CAS  PubMed  CrossRef  Google Scholar 

  • Alberts B, Johnson A, Lewis J, Raff M, Roberts K, Walter P (2007) Molecular biology of the cell, 5th edn. Garland, New York

    Google Scholar 

  • Avery OT, Macleod CM, McCarty M (1944) Studies on the chemical nature of the substance inducing transformation of pneumococcal types: induction of transformation by a desoxyribonucleic acid fraction isolated from pneumococcus Type III. J Exp Med 79:137–158

    CAS  PubMed Central  PubMed  CrossRef  Google Scholar 

  • Barash Y, Calarco JA, Gao W, Pan Q, Wang X, Shai O, Blencow BJ, Frey BJ (2010) Deciphering the splicing code. Nature 465:53–59

    CAS  PubMed  CrossRef  Google Scholar 

  • Barbieri M (1998) The organic codes: the basic mechanism of macroevolution. Riv Biol Biol Forum 91:481–514

    CAS  Google Scholar 

  • Barbieri M (2003) The organic codes: an introduction to semantic biology. Cambridge University Press, Cambridge

    Google Scholar 

  • Beadle G, Beadle M (1966) The language of life: an introduction to the science of genetics. Doubleday and Co, New York

    Google Scholar 

  • Berger SL (2007) The complex language of chromatin regulation during transcription. Nature 447:407–412

    CAS  PubMed  CrossRef  Google Scholar 

  • Berridge M (1985) The molecular basis of communication within the cell. Sci Am 253:142–152

    CAS  PubMed  CrossRef  Google Scholar 

  • Boivin A, Vendrely R (1947) Sur le rôle possible deux acides nucleic dans la cellule vivant. Experientia 3:32–34

    CAS  PubMed  CrossRef  Google Scholar 

  • Bollenbach T, Kalin Vetsigian K, Kishony R (2007) Evolution and multilevel optimization of the genetic code. Genome Res 17:401–404

    CAS  PubMed  CrossRef  Google Scholar 

  • 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 18:8379–8386

    CrossRef  Google Scholar 

  • Boyd WC (1954) The proteins of immune reactions. In: Neurath H, Bayley K (eds) The proteins, Part 2, vol 2. Academic, New York, pp 756–844

    Google Scholar 

  • Brachet J (1944) Embriologie Chimique. Masson et Cie, Paris

    Google Scholar 

  • Brachet J (1946) Nucleic acids in the cell and the embryo. Symp Soc Exp Biol 1:213–215 and 222

    Google Scholar 

  • Buckeridge MS, De Souza AP (2014) Breaking the “Glycomic Code” of cell wall polysaccharides may improve second-generation bioenergy production from biomass. Bioenergy Res. doi:10.1007/s12155-014-9460-6

  • Buckeridge MS, Crombie HJ, Mendes CJM, Reid JSG, Gidley MJ, Vieira CCJ (1997) A new family of oligosaccharides from the xyloglucan of Hymenaea courbaril L. (Leguminosae) cotyledons. Carbohydr Res 303(2):233–237

    CAS  PubMed  CrossRef  Google Scholar 

  • Buratti E, Baralle M, Baralle FE (2006) Defective splicing, disease and therapy: searching for master checkpoints in exon definition. Nucleic Acids Res 34:3494–3510

    CAS  PubMed Central  PubMed  CrossRef  Google Scholar 

  • Cavalli G, Paro R (1998) Chromo-domain proteins: linking chromatin structure to epigenetic regulation. Curr Opin Cell Biol 10(3):354–360

    CAS  PubMed  CrossRef  Google Scholar 

  • Charbon G, Breunig KD, Wattiez R, Vandenhaute J, Noël-Georis I (2004) Key role of Ser562/661 in Snf1-dependent regulation of Cat8p in Saccharomyces cerevisiae and Kluyveromyces lactis. Mol Cell Biol 24:4083–4091

    CAS  PubMed Central  PubMed  CrossRef  Google Scholar 

  • Cooper TA, Wan L, Dreyfuss G (2009) RNA and disease. Cell 136:777–793

    CAS  PubMed Central  PubMed  CrossRef  Google Scholar 

  • Crick FHC (1957) The structure of nucleic acids and their role in protein synthesis. Biochemical Society symposium, 14. Cambridge University Press, Cambridge, pp 25–26

    Google Scholar 

  • Crick FHC (1958) On protein synthesis. Symp Soc Exp Biol 12:138–163

    CAS  PubMed  Google Scholar 

  • Crick FHC (1966) Codon–anticodon pairing: the wobble hypothesis. J Mol Biol 19:548–555

    CAS  PubMed  CrossRef  Google Scholar 

  • Dhir A, Buratti E, van Santen MA, Lührmann R, Baralle FE (2010) The intronic splicing code: multiple factors involved in ATM pseudoexon definition. EMBO J 29:749–760

    CAS  PubMed Central  PubMed  CrossRef  Google Scholar 

  • Dounce AL (1952) Duplicating mechanism for peptide chain and nucleic acid synthesis. Enzymologia 15:251–258

    CAS  PubMed  Google Scholar 

  • Dounce AL (1953) Nucleic acid template hypothesis. Nature 172:541

    CAS  PubMed  CrossRef  Google Scholar 

  • Fischle W, Wang Y, Jacobs SA, Kim Y, Allis CD, Khorasanizadeh S (2003) Molecular basis for the discrimination of repressive methyl-lysine marks in histone H3 by Polycomb and HP1 chromodomains. Genes Dev 17(15):1870–1881

    CAS  PubMed Central  PubMed  CrossRef  Google Scholar 

  • Freeland SJ, Hurst LD (1998) The genetic code is one in a million. J Mol Evol 47:238–248

    CAS  PubMed  CrossRef  Google Scholar 

  • Fu XD (2004) Towards a splicing code. Cell 119:736–738

    CAS  PubMed  CrossRef  Google Scholar 

  • Gabius H-J (2000) Biological information transfer beyond the genetic code: the sugar code. Naturwissenschaften 87:108–121

    CAS  PubMed  CrossRef  Google Scholar 

  • Gabius H-J (ed) (2009) The sugar code: fundamentals of glycosciences. Wiley-Blackwell, Weinheim

    Google Scholar 

  • Gamow G (1954) Possible relation between deoxyribonucleic acid and protein structures. Nature 173:318

    CAS  CrossRef  Google Scholar 

  • Gräff J, Mansuy IM (2008) Epigenetic codes in cognition and behavior. Behav Brain Res 192:70–87

    PubMed  CrossRef  Google Scholar 

  • Haig D, Hurst LD (1991) A quantitative measure of error minimization in the genetic code. J Mol Evol 33:412–417

    CAS  PubMed  CrossRef  Google Scholar 

  • Hansen JC, Tse C, Wolfe AP (1998) Structure and function of the core histone N-termini: more than meets the eye. Biochemistry 37:17637–17641

    CAS  PubMed  CrossRef  Google Scholar 

  • Hoagland MB, Zamecnik PC, Stephenson ML (1957) Intermediate reactions in protein biosynthesis. Biochim Biophys Acta 24:215–216

    CAS  PubMed  CrossRef  Google Scholar 

  • Hou Y-M, Schimmel P (1988) A simple structural feature is a major determinant of the identity of a transfer RNA. Nature 333:140–145

    CAS  PubMed  CrossRef  Google Scholar 

  • Jacob F, Monod J (1961) Genetic regulatory mechanisms in the synthesis of proteins. J Mol Biol 3:318–356

    CAS  PubMed  CrossRef  Google Scholar 

  • Jenuwein T, Allis CD (2001) Translating the histone code. Science 293:1074–1080

    CAS  PubMed  CrossRef  Google Scholar 

  • Jeppesen P (1997) Histone acetylation: a possible mechanism for the inheritance of cell memory at mitosis. BioEssays 19:67–74

    CAS  PubMed  CrossRef  Google Scholar 

  • Jukes TH, Osawa S (1990) The genetic code in mitochondria and chloroplasts. Experientia 46:1149–1157

    CAS  PubMed  CrossRef  Google Scholar 

  • Jukes TH, Osawa S (1993) Evolutionary changes in the genetic code. Comp Biochem Physiol 106B:489–494

    CAS  Google Scholar 

  • Khorana HG, Büchi H, Ghosh H, Gupta N, Jacob TM, Kössel H et al (1966) Polynucleotide synthesis and the genetic code. Cold Spring Harb Symp Quant Biol 31:39–49

    CAS  PubMed  CrossRef  Google Scholar 

  • Kim J, Daniel J, Espejo A, Lake A, Krishna M, Li X, Yi Z, Bedford MT (2006) Tudor, MBT and chromo domains gauge the degree of lysine methylation. EMBO Rep 7(4):397–403

    CAS  PubMed Central  PubMed  Google Scholar 

  • Kirschner MW, Mitchison T (1986) Microtubule dynamics. Nature 324:621

    CAS  PubMed  CrossRef  Google Scholar 

  • Kornberg RD, Lorch Y (1999) Twenty-five years of the nucleosome, fundamental particle of the eukaryote chromosome. Cell 98:285–294

    CAS  PubMed  CrossRef  Google Scholar 

  • Kühn S, Hofmeyr J-HS (2014) Is the “Histone Code” an organic code? Biosemiotics 7(2):203–222

    CrossRef  Google Scholar 

  • Laine RA (1977) The information-storing potential of the sugar code. In: Gabius H-J, Gabius S (eds) Glycosciences: status and perspectives. Chapman & Hall, London, pp 1–14

    Google Scholar 

  • Levenson JM, Sweatt JD (2005) Epigenetic mechanisms in memory formation. Nat Rev Neurosci 6(2):108–118

    CAS  PubMed  CrossRef  Google Scholar 

  • Lyko F, Paro R (1999) Chromosomal elements conferring epigenetic inheritance. BioEssays 21:824–832

    CAS  PubMed  CrossRef  Google Scholar 

  • Margueron R, Trojer P, Reinberg D (2005) The key to development: interpreting the histone code? Curr Opin Genet Dev 15:163–176

    CAS  PubMed  CrossRef  Google Scholar 

  • Maruta H, Greer K, Rosenbaum JL (1986) The acetylation of alpha-tubulin and its relationship to the assembly and disassembly of microtubules. J Cell Biol 103:571–579

    CAS  PubMed  CrossRef  Google Scholar 

  • Matlin A, Clark F, Smith C (2005) Understanding alternative splicing: towards a cellular code. Nat Rev Mol Cell Biol 6:386–398

    CAS  PubMed  CrossRef  Google Scholar 

  • Maurer-Stroh S, Dickens NJ, Hughes-Davies L, Kouzarides T, Eisenhaber F, Ponting CP (2003) The Tudor domain ‘Royal Family’: tudor, plant agenet, chromo, PWWP and MBT domains. Trends Biochem Sci 28(2):69–74

    CAS  PubMed  CrossRef  Google Scholar 

  • Melcher G (1974) Stereospecificity and the genetic code. J Mol Evol 3:121–141

    CAS  PubMed  CrossRef  Google Scholar 

  • Mellor J (2006) It takes a PHD to read the histone code. Cell 126(1):22–24

    CAS  PubMed  CrossRef  Google Scholar 

  • Monod J (1970) Le Hasard et la Necessité. Seuil, Paris. English edition: (1971) Chance and Necessity. A Knopf, New York

    Google Scholar 

  • Mujtaba S, Zeng L, Zhou MM (2007) Structure and acetyl-lysine recognition of the bromodomain. Oncogene 26(37):5521–5527

    CAS  PubMed  CrossRef  Google Scholar 

  • Niremberg M, Leder P (1964) RNA codewords and protein synthesis. Science 145:1399–1407

    CrossRef  Google Scholar 

  • Niremberg M, Matthaei H (1961) The dependence of cell-free protein synthesis in E. coli upon naturally occurring or synthetic polyribonucleotides. Proc Natl Acad Sci U S A 47:1588–1602

    CrossRef  Google Scholar 

  • Niremberg M, Caskey T, Marshal R, Brimacombe R, Kellogg D, Doctor B et al (1966) The RNA code and protein synthesis. Cold Spring Harb Symp Quant Biol 31:11–24

    CrossRef  Google Scholar 

  • Nishimura S, Jones DS, Khorana HG (1965) The in vitro synthesis of a co-polypeptide containing two amino acids in alternating sequence dependent upon a DNA-like polymer containing two nucleotides in alternating sequence. J Mol Biol 13:302–324

    CAS  PubMed  CrossRef  Google Scholar 

  • Nomura M, Tissières A, Lengyel P (1974) Ribosomes. Cold Spring Harbor monograph series. Cold Spring Harbor Laboratory, New York

    Google Scholar 

  • Owen DJ, Ornaghi P, Yang J-C, Lowe N, Evans PR, Ballario P, Neuhaus D, Filetici P, Travers AA (2000) The structural basis for the recognition of acetylated histone H4 by the bromodomain of histone acetyltransferase Gcn5p. EMBO J 19(22):6141–6149

    CAS  PubMed Central  PubMed  CrossRef  Google Scholar 

  • Pelc SR, Weldon MGE (1966) Stereochemical relationship between coding triplets and amino-acids. Nature 209:868–870

    CAS  PubMed  CrossRef  Google Scholar 

  • Pertea M, Mount SM, Salzberg SL (2007) A computational survey of candidate exonic splicing enhancer motifs in the model plant Arabidopsis thaliana. BMC Bioinf 8:159

    CrossRef  Google Scholar 

  • Peterson CL, Laniel M-A (2004) Histones and histone modifications. Curr Biol 14:546–551

    CrossRef  Google Scholar 

  • Roberts RB (1958) Microsomal particles and protein synthesis. Pergamon Press, Washington, DC

    Google Scholar 

  • Schimmel P (1987) Aminoacyl tRNA synthetases: general scheme of structure-function relationship in the polypeptides and recognition of tRNAs. Annu Rev Biochem 56:125–158

    CAS  PubMed  CrossRef  Google Scholar 

  • Schimmel P, Giegé R, Moras D, Yokoyama S (1993) An operational RNA code for amino acids and possible relationship to genetic code. Proc Natl Acad Sci U S A 90:8763–8768

    CAS  PubMed Central  PubMed  CrossRef  Google Scholar 

  • Schreiber SL, Bernstein BE (2002) Signaling network model of chromatin. Cell 111:771–778

    CAS  PubMed  CrossRef  Google Scholar 

  • Segal E, Fondufe-Mittendorf Y, Chen L, Thåström A, Fiels Y, Moore IK, Wang JP, Widom J (2006) A genomic code for nucleosome positioning. Nature 442:772–778

    CAS  PubMed Central  PubMed  CrossRef  Google Scholar 

  • Shimizu M (1982) Molecular basis for the genetic code. J Mol Evol 18:297–303

    CAS  PubMed  CrossRef  Google Scholar 

  • Solis AS, Shariat N, Patton JG (2008) Splicing fidelity, enhancers, and disease. Front Biosci 13:1926–1942

    CAS  PubMed  CrossRef  Google Scholar 

  • Speyer J, Lengyel P, Basilio C, Wahba A, Gardner R, Ochoa S (1963) Synthetic polynucleotides and the amino acid code. Cold Spring Harb Symp Quant Biol 28:559–567

    CAS  CrossRef  Google Scholar 

  • Sporn MB, Roberts AB (1988) Peptide growth factors are multifunctional. Nature 332:217–219

    CAS  PubMed  CrossRef  Google Scholar 

  • Stergachis AB, Haugen E, Shafer A, Fu W, Vernot B, Reynolds A, Raubitschek A, Ziegler S, LeProust EM, Akey JM, Stamatoyannopoulos JA (2013) Exonic transcription factor binding directs codon choice and affects protein evolution. Science 342:1367–1372

    CAS  PubMed Central  PubMed  CrossRef  Google Scholar 

  • Strahl BD, Allis D (2000) The language of covalent histone modifications. Nature 403:41–45

    CAS  PubMed  CrossRef  Google Scholar 

  • Sutherland EW (1972) Studies on the mechanism of hormone action. Science 177:401–408

    CAS  PubMed  CrossRef  Google Scholar 

  • Swan LS, Goldberg LJ (2010) Biosymbols: symbols in life and mind. Biosemiotics 3(1):17–31

    CrossRef  Google Scholar 

  • Tazi J, Bakkour N, Stamm S (2009) Alternative splicing and disease. Biochim Biophys Acta 1792:14–26

    CAS  PubMed  CrossRef  Google Scholar 

  • Tiné MAS, Silva CO, Lima DU, Carita NC, Buckeridge MS (2006) Fine structure of a mixed-oligomer storage xyloglucan from seeds of Hymenaea courbaril. Carbohydr Polym 66:444–454

    CrossRef  Google Scholar 

  • Tomkins MG (1975) The metabolic code. Science 189:760–763

    CAS  PubMed  CrossRef  Google Scholar 

  • Trifonov EN (1989) The multiple codes of nucleotide sequences. Bull Math Biol 51:417–432

    CAS  PubMed  CrossRef  Google Scholar 

  • Trifonov EN (1999) Elucidating sequence codes: three codes for evolution. Ann N Y Acad Sci 870:330–338

    CAS  PubMed  CrossRef  Google Scholar 

  • Turner BM (2000) Histone acetylation and an epigenetic code. BioEssays 22:836–845

    CAS  PubMed  CrossRef  Google Scholar 

  • Turner BM (2002) Cellular memory and the histone code. Cell 111:285–291

    CAS  PubMed  CrossRef  Google Scholar 

  • Turner BM (2007) Defining an epigenetic code. Nat Cell Biol 9:2–6

    CAS  PubMed  CrossRef  Google Scholar 

  • Verhey KJ, Gaertig J (2007) The tubulin code. Cell Cycle 6(17):2152–2160

    CAS  PubMed  CrossRef  Google Scholar 

  • Wang Z, Burge C (2008) Splicing regulation: from a part list of regulatory elements to an integrated splicing code. RNA 14:802–813

    CAS  PubMed Central  PubMed  CrossRef  Google Scholar 

  • Wang GS, Cooper TA (2007) Splicing in disease: disruption of the splicing code and the decoding machinery. Nat Rev Genet 8:749–761

    CAS  PubMed  CrossRef  Google Scholar 

  • Wang GG, Cai L, Pasillas MP, Kamps MP (2007) NUP98–NSD1 links H3K36 methylation to Hox-A gene activation and leukaemogenesis. Nat Cell Biol 9:804–812

    CAS  PubMed  CrossRef  Google Scholar 

  • Watson JD, Crick FHC (1953) Molecular structure of nucleic acids: a structure for deoxyribose nucleic acid. Nature 171:737–738. Genetical implications of the structure of deoxyribose nucleic acid. Nature 171:964–967

    Google Scholar 

  • Webster DR, Wehland J, Weber K, Borisy GG (1990) Detyrosination of alpha tubulin does not stabilize microtubules in vivo. J Cell Biol 111:113–122

    CAS  PubMed  CrossRef  Google Scholar 

  • Wheatheritt RJ, Babu MM (2013) The hidden codes that shape protein evolution. Science 342:1325–1326

    CrossRef  Google Scholar 

  • Winterburn PJ, Phelps CF (1972) The significance of glycosylated proteins. Nature 236:147–151

    CAS  PubMed  CrossRef  Google Scholar 

  • Woese CR (1965) Order in the genetic code. Proc Natl Acad Sci U S A 54:71–75

    CAS  PubMed Central  PubMed  CrossRef  Google Scholar 

  • Woese CR, Dugre DH, Saxinger WC, Dugre SA (1966) The molecular basis for the genetic code. Proc Natl Acad Sci U S A 55:966–974

    CAS  PubMed Central  PubMed  CrossRef  Google Scholar 

  • Wolfe AP, Hayes JJ (1999) Chromatin disruption and modification. Nucleic Acid Res 27:711–720

    CrossRef  Google Scholar 

  • Wu J, Grunstein M (2000) 25 years after the nucleosome model: chromatin modifications. Trends Biochem Sci 25(12):619–623

    CAS  PubMed  CrossRef  Google Scholar 

  • Xin L, Zhou G-L, Song W, Wu X-S, Wei G-H, Hao D-L, Lv X, Liu D-P, Liang C-C (2007) Exploring cellular memory molecules marking competent and active transcriptions. BioMed Cent Mol Biol 8:31–40

    Google Scholar 

  • Yuan GC, Liu YJ, Dion MF, Slack MD, Wu LF, Altschuler SJ, Rando OJ (2005) Genome-scale identification of nucleosome positions in S. cerevisiae. Science 309:626–630

    CAS  PubMed  CrossRef  Google Scholar 

  • Zhu B, Zheng Y, Pham A-D, Mandal SS, Erdjument-Bromage H, Tempst P, Reinberg D (2005) Monoubiquitination of human histone H2B: the factors involved and their roles in HOX gene regulation. Mol Cell 20(4):601–611

    CAS  PubMed  CrossRef  Google Scholar 

  • Trifonov EN (1996) Interfering contexts of regulatory sequence elements. Cabios, 12: 423--429.

    Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Rights and permissions

Reprints and Permissions

Copyright information

© 2015 Springer International Publishing Switzerland

About this chapter

Cite this chapter

Barbieri, M. (2015). A Gallery of Organic Codes. In: Code Biology. Springer, Cham. https://doi.org/10.1007/978-3-319-14535-8_3

Download citation