Skip to main content

Disorder to Order, Nonlife to Life: In the Beginning There Was a Mistake

  • Chapter
  • First Online:
Genesis - In The Beginning

Abstract

Living matter is solemnly perceived as an embodiment of ultimate order that neither centuries long studies nor imagination can fully grasp. Yet, disorder is its necessary component in an intricate interplay between life’s actors from the highest level of populations, all the way to molecules. An intriguing thought is that life emerged from disorder. Reasoning around this starting point, the authors, however, come to a rather dialectic picture of never-ending alternations of the order and disorder, all the way from simple molecules to self-reproduction and evolution. A long series of the likely steps is described, from monomers to informational molecules, with reference to hard data enriched by cautious speculations, outlining the likely route from mere chemistry to the magic of life. An uncertainty, almost a principle, emerges in trying to pinpoint when and at which particular moment the magic transition occurred. The uncertainty is aggravated by the lack of a clear definition of what exactly “life is.” At the same time, the authors share the excitement of a strong feeling that the answer is very closely, if not already, explained.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 169.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 219.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 219.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Similar content being viewed by others

References

  • Alberty RA (2006) Thermodynamic properties of enzyme-catalyzed reactions involving guanine, xanthine, and their nucleosides and nucleotides. Biophys Chem 121:157–162

    Article  PubMed  CAS  Google Scholar 

  • Barks H, Buckley R, Grieves GA, Di Mauro E, Hud N, Orlando T (2010) Guanine, adenine, and hypoxanthine production in UV-irradiated formamide solutions: relaxation of the requirements for prebiotic purine nucleobase formation. Chembiochem 11:1240–1243

    Article  PubMed  CAS  Google Scholar 

  • Bean HD, Sheng Y, Collins JP, Anet FA, Leszczynski J, Hud NV (2007) Formation of a beta-pyrimidine nucleoside by a free pyrimidine base and ribose in a plausible prebiotic reaction. J Am Chem Soc 129:9556–9557

    Article  PubMed  CAS  Google Scholar 

  • Bloomfield VA, Crothers DM, Tinoco I (2000) Nucleic acids: structures, properties, and functions. University Science, Sausalito

    Google Scholar 

  • Brahms J, Michelson AM, Van Holde KE (1966) Adenylate oligomers in single- and double-strand conformation. J Mol Biol 15:467–488

    Article  PubMed  CAS  Google Scholar 

  • Brenner S (1988) The molecular evolution of genes and proteins: a tale of two serines. Nature 334:528–530

    Article  PubMed  CAS  Google Scholar 

  • Campen A, Williams RM, Brown CJ, Meng J, Uversky VN, Dunker AK (2008) TOP-IDP-scale: a new amino acid scale measuring propensity for intrinsic disorder. Protein Pept Lett 15:956–963

    Article  PubMed  CAS  Google Scholar 

  • Carny O, Gazit E (2005) A model for the role of short self-assembled peptides in the very early stages of the origin of life. FASEB J 19L:1051–1055

    Article  Google Scholar 

  • Carroll L (1865) Alice’s adventures in Wonderland. Macmillan, London

    Google Scholar 

  • Cech TR (2009) Crawling out of the RNA world. Cell 136:599–602

    Article  PubMed  CAS  Google Scholar 

  • Ciciriello F, Costanzo G, Pino S, Crestini C, Saladino R, Di Mauro E (2008) Molecular complexity favors the evolution of ribopolymers. Biochemistry 47:2732–2742

    Article  PubMed  CAS  Google Scholar 

  • Ciciriello F, Costanzo G, Pino S, Di Mauro E (2009) Spontaneous generation revisited at the molecular level. In: Pontarotti P (ed) Evolutionary biology: concept, modeling and application. Springer, Berlin/Heidelberg, pp 3–22

    Google Scholar 

  • Costanzo G, Saladino R, Crestini C, Ciciriello F, Di Mauro E (2007) Nucleoside phosphorylation by phosphate minerals. J Biol Chem 282:16729–16735

    Article  PubMed  CAS  Google Scholar 

  • Costanzo G, Pino S, Ciciriello F, Di Mauro E (2009) Generation of long RNA chains in water. J Biol Chem 284:33206–33216

    Article  PubMed  CAS  Google Scholar 

  • Damiano L, Luisi PL (2010) Towards an autopoietic redefinition of life. Orig Life Evol Biosph 40:145–149

    Article  PubMed  Google Scholar 

  • Darwin C (1859) Origin of species. John Murray, London, Chapter 4

    Google Scholar 

  • Daughdrill GW, Pielak GJ, Uversky VN, Cortese MS, Dunker AK (2004) Natively disordered proteins. In: Buchner J, Kiefhaber T (eds) Protein folding handbook. Wiley-VCH, Weinheim, pp 271–353

    Google Scholar 

  • Davidson AR, Sauer RT (1994) Folded proteins occur frequently in libraries of random amino acid sequences. Proc Natl Acad Sci USA 91:2146–2150

    Article  PubMed  CAS  Google Scholar 

  • Di Giulio M (1997) On the RNA world: evidence in favor of an early ribonucleoprotein world. J Mol Evol 45:571–578

    Article  PubMed  Google Scholar 

  • Dolgikh DA, Gilmanshin RI, Brazhnikov EV, Bychkova VE, Semisotnov GV, Venyaminov SYu, Ptitsyn OB (1981) Alpha-lactalbumin: compact state with fluctuating tertiary structure? FEBS Lett 136:311–315

    Article  PubMed  CAS  Google Scholar 

  • Dolgikh DA, Kolomiets AP, Bolotina IA, Ptitsyn OB (1984) ‘Molten-globule’ state accumulates in carbonic anhydrase folding. FEBS Lett 165:88–92

    Article  PubMed  CAS  Google Scholar 

  • Doudna JA, Cech T (2002) The chemical repertoire of natural ribozymes. Nature 418:222

    Article  PubMed  CAS  Google Scholar 

  • Dunker AK, Garner E, Guilliot S, Romero P, Albrecht K, Hart J, Obradovic Z, Kissinger C, Villafranca JE (1998) Evolution of molecular recognition. Pac Symp Biocomput 3:473–484

    Article  Google Scholar 

  • Dunker AK, Chan WS, Karn SHB, Uversky VN, Brooks DJ, Oldfield CJ, White J, Perumal N, Romero P (2009) Protein folding as a transition step from ancient to modern life forms. Biophys J 96:318a

    Article  Google Scholar 

  • Gabdank I, Barash D, Trifonov EN (2006) Tracing ancient mRNA hairpins. J Biomol Struct Dyn 24:163–170

    PubMed  CAS  Google Scholar 

  • Ivanyi-Nagy R, Davidovic L, Khandjian EW, Darlix JL (2005) Disordered RNA chaperone proteins from functions to disease. Cell Mol Life Sci 62:1409–1417

    Article  PubMed  CAS  Google Scholar 

  • Joyce J (1994) In: Deamer DW, Fleischaker GR (eds) The foreword of ‘Origins of Life: The Central Concepts’. Jones and Bartlett, Boston. The original reference is a 1992 internal NASA document entitled ‘Exobiology: Discipline Science Plan’.

    Google Scholar 

  • Kacian DL, Spiegelman S, Mills DR, Kramer FR (1972) Replicating RNA molecule suitable for a detailed analysis of extracellular evolution and replication. Proc Natl Acad Sci USA 69:3038–3042

    Article  PubMed  CAS  Google Scholar 

  • Kelly DR, Roberts SM (2006) Oligopeptides as catalysts for asymmetric epoxidation. Pept Sci 84:74–89

    Article  CAS  Google Scholar 

  • Klein DJ, Moore PB, Steitz TA (2004) The roles of ribosomal proteins in the structure assembly and evolution of the large ribosomal subunit. J Mol Biol 340:141–177

    Article  PubMed  CAS  Google Scholar 

  • Lahav N, White D, Chang S (1978) Peptide formation in prebiotic era – thermal condensation of glycine in fluctuating clay environments. Science 201:67–69

    Article  PubMed  CAS  Google Scholar 

  • Lopez-Alonso JP, Pardo-Cea MA, Gomez-Pinto I, Fernandez I, Chakrabarty A, Pedroso E, Gonzalez C, Laurents DV (2010) Putative one-pot prebiotic polypeptides with ribonuclease activity. Chem Eur J 16:5314–5323

    PubMed  CAS  Google Scholar 

  • Luisi PL (1998) About various definitions of life. Orig Life Evol Biosph 28:613–622

    Article  PubMed  CAS  Google Scholar 

  • Nissen BN, Hansen J, Moore PB, Steitz TA (2000) The complete atomic structure of the large ribosomal subunit at 2.4 A resolution. Science 289:905–920

    Article  PubMed  Google Scholar 

  • Noller HF (2004) The driving force for the evolution of translation. RNA 10:1833–1837

    Article  PubMed  CAS  Google Scholar 

  • Oparin AI (1952) The origin of life. Dover, New York

    Google Scholar 

  • Pauling L (1946) Molecular architecture and biological reactions. Chem Eng News 24:1375–1377

    Article  CAS  Google Scholar 

  • Pino S, Ciciriello F, Costanzo G, Di Mauro E (2008) Nonenzymatic RNA ligation in water. J Biol Chem 283:36494–36503

    Article  PubMed  CAS  Google Scholar 

  • Polanyi M (1921) On adsorption catalysis. Z Eleckrochem 27:142–150

    CAS  Google Scholar 

  • Poole AM, Jeffares DC, Penny D (1998) The path from the RNA world. J Mol Evol 46:1–17

    Article  PubMed  CAS  Google Scholar 

  • Powner MW, Gerland B, Sutherland JD (2009) Synthesis of activated pyrimidine ribonucleotides in prebiotically plausible conditions. Nature 459:239–422

    Article  PubMed  CAS  Google Scholar 

  • Rich A (1994) Pauling Linus (1901–1994) – Obituary. Nature 371:285

    Article  PubMed  CAS  Google Scholar 

  • Saladino R, Crestini C, Busiello V, Ciciriello F, Costanzo G, Di Mauro E (2005a) Origin of informational polymers. Differential stability of 3′- and 5′-phosphoester bonds in deoxy monomers and oligomers. J Biol Chem 280:35658–35669

    Article  PubMed  CAS  Google Scholar 

  • Saladino R, Crestini C, Neri V, Brucato JR, Colangeli L, Ciciriello F, Di Mauro E, Costanzo G (2005b) Synthesis and degradation of nucleic Acid components by formamide and cosmic dust analogues. Chembiochem 6:1368–1374

    Article  PubMed  CAS  Google Scholar 

  • Saladino R, Crestini C, Costanzo G, Di Mauro E (2005c) On the prebiotic synthesis of nucleobases, nucleotides, oligonucleotides, pre-RNA and pre-DNA molecules. In: Walde P (ed) Topics in current chemistry, “Prebiotic chemistry”, vol 259. Springer, Berlin, pp 29–68R

    Google Scholar 

  • Saladino R, Crestini C, Ciciriello F, Di Mauro E, Costanzo G (2006a) Origin of informational polymers: differential stability of phosphoester bonds in ribomonomers and ribooligomers. J Biol Chem 281:5790–5796

    Article  PubMed  CAS  Google Scholar 

  • Saladino R, Crestini C, Neri V, Ciciriello F, Costanzo G, Di Mauro E (2006b) Origin of informational polymers: the concurrent roles of formamide and phosphates. Chembiochem 711:1707–1714

    Article  Google Scholar 

  • Saladino R, Crestini C, Ciciriello F, Costanzo G, Di Mauro E (2007) Formamide chemistry and the origin of informational polymers chemistry & biodiversity. Helvetica Chimica Acta 4:694–720

    CAS  Google Scholar 

  • Saladino R, Neri V, Crestini C, Costanzo G, Graciotti M, Di Mauro E (2008) Synthesis and degradation of nucleic acid components by formamide and iron sulfur minerals. J Am Chem Soc 130:15512–15518

    Article  PubMed  CAS  Google Scholar 

  • Saladino R, Crestini C, Ciciriello F, Pino S, Costanzo G, Di Mauro E (2009) From formamide to RNA: the roles of formamide and water in the evolution of chemical information. Special issue on “the origin of life and microbiology”. Res Microbiol 160:441–448

    Article  PubMed  CAS  Google Scholar 

  • Saladino R, Neri V, Crestini C, Costanzo G, Graciotti M, Di Mauro E (2010) The role of the formamide/zirconia system in the synthesis of nucleobases and biogenic carboxylic acid derivatives. J Mol Evol 71:100–110

    Article  PubMed  CAS  Google Scholar 

  • Saladino R, Barontini M, Cosetti C, Di Mauro E, Crestini C (2011) The effects of borate minerals on the synthesis of nucleic acid bases, amino acids and biogenic carboxylic acids from formamide. Orig Life Evol Biosph 41:317–330

    Article  PubMed  CAS  Google Scholar 

  • Schulz GE (1979) Nucleic acid binding proteins. In: Balaban M (ed) Molecular mechanisms of biological recognition. Elsevier/North Holland Biomedical Press, Amsterdam, pp 79–94

    Article  PubMed  CAS  Google Scholar 

  • Sobolevsky Y, Frenkel ZM, Trifonov EN (2007) Combinations of ancestral modules in proteins. J Mol Evol 65:640–650

    Article  PubMed  CAS  Google Scholar 

  • Solomatin SV, Greenfeld M, Chu S, Herschlag D (2010) Multiple native states reveal persistent ruggedness of an RNA folding landscape. Nature 463:681–684

    Article  PubMed  CAS  Google Scholar 

  • Stenger VJ (2006) The comprehensible cosmos: where do the laws of Physics come from? Prometheus, Amherst

    Google Scholar 

  • Tanaka T, Hayashi M, Kimura H, Oobatake M, Nakamura H (1994) De novo design and creation of a stable artificial protein. Biophys Chem 50:47–61

    Article  PubMed  CAS  Google Scholar 

  • Treiber DK, Williamson JR (1999) Exposing the kinetic traps in RNA folding. Curr Opin Struct Biol 9:339–345

    Article  PubMed  CAS  Google Scholar 

  • Treiber DK, Williamson JR (2001) Beyond kinetic traps in RNA folding. Curr Opin Struct Biol 11:309–314

    Article  PubMed  CAS  Google Scholar 

  • Trifonov EN (2000) Consensus temporal order of amino acids and evolution of the triplet code. Gene 261:139–151

    Article  PubMed  CAS  Google Scholar 

  • Trifonov EN (2004) The triplet code from first principles. J Biomol Struct Dyn 22:1–11

    PubMed  CAS  Google Scholar 

  • Trifonov EN (2006) Theory of early molecular evolution: predictions and confirmations. In: Eisenhaber F (ed) Discovering biomolecular mechanisms with computational biology. Landes Bioscience, Georgetown, pp 107–116

    Chapter  Google Scholar 

  • Trifonov EN (2009) Origin of the genetic code and of the earliest oligopeptides. Res Microbiol 160:481–486

    Article  PubMed  CAS  Google Scholar 

  • Trifonov EN, Bettecken T (1997) Sequence fossils, triplet expansion, and reconstruction of earliest codons. Gene 205:1–6

    Article  PubMed  CAS  Google Scholar 

  • Trifonov EN, Kirzhner A, Kirzhner VM, Berezovsky IN (2001) Distinct stages of protein evolution as suggested by protein sequence analysis. J Mol Evol 53:394–401

    Article  PubMed  CAS  Google Scholar 

  • Vamvaca K, Vogeli B, Kast P, Pervushin K, Hilvert D (2004) An enzymatic molten globule: efficient coupling of folding and catalysis. Proc Natl Acad Sci USA 101:12860–12864

    Article  PubMed  CAS  Google Scholar 

  • Van Holde K (1980) In: Halvorson HO, van Holde KE (eds) The origins of life and evolution. Alan R. Liss, Inc., New York, p 31

    Google Scholar 

  • Waldrop MM (1992) Finding RNA makes protein gives ‘RNA world’ a big boost. Science 256:1396–1397

    Article  PubMed  CAS  Google Scholar 

  • Watson JD, Crick FH (1953) Molecular structure of nucleic acids; a structure for deoxyribose nucleic acid. Nature 171:737–738

    Article  PubMed  CAS  Google Scholar 

  • Zalatan JG, Herschlag D (2009) The far reaches of enzymology. Nat Chem Biol 5:516–520

    Article  PubMed  CAS  Google Scholar 

Download references

Acknowledgments

Ernesto Di Mauro was supported by “Istituto Pasteur – Fondazione Cenci Bolognetti.” Thanks also to Silvia Lopizzo for helpful contributions. Keith Dunker was supported by: NIH 5R01GM071714-04 “Mining Structural Genomics Initiative for Disorder”; NIH 5R13LM006766-13 Pacific Symposium on Biocomputing; NIH 2R56LM007688-05A1 Bioinformatics – “Linkage of Protein Disorder and Function”; NSF 0849803 “DisProt Database: A Central Repository of Information on Intrinsically Disordered Proteins.”

Thanks also to Maya Wagle for helpful contributions. Edward N. Trifonov is supported by Czech Ministry of Education (grant SM0021622415) and by SoMoPro (South Moravia Project).

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Ernesto Di Mauro .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2012 Springer Science+Business Media B.V.

About this chapter

Cite this chapter

Di Mauro, E., Dunker, A.K., Trifonov, E.N. (2012). Disorder to Order, Nonlife to Life: In the Beginning There Was a Mistake. In: Seckbach, J. (eds) Genesis - In The Beginning. Cellular Origin, Life in Extreme Habitats and Astrobiology, vol 22. Springer, Dordrecht. https://doi.org/10.1007/978-94-007-2941-4_23

Download citation

Publish with us

Policies and ethics