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Studies on Molecular Mechanisms of Prebiotic Systems

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Abstract

Lately there has been a growing interest in evolutionary studies concerning how the regularities and patterns found in the living cell could have emerged spontaneously by way of self-assembly and self-organization. It is reasonable to postulate that the chemical compounds found in the primitive Earth would have mostly been very simple in nature, and would have been immersed in the natural dynamics of the physical world, some of which would have involved self-organization. It seems likely that some molecular processes self-organized spontaneously into a hierarchy of complex behaviours. Our conceptual search herein reaches back to the time when prebiotic phenomena began to take shape. This was before the origin of life, so in this paper we hope to shed new light on some of the theoretical issues that surround the ways in which cellular organization might have evolved without the aid of replicated information.

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References

  • Assis R., Kondrashov A. S. (2009) Rapid repetitive element-mediated expansion of piRNA clusters in mammalian evolution. Proceedings of the National Academy of Sciences 106(17): 7079–7082

    Article  Google Scholar 

  • Bachmann P. A., Luisi P. L., Lang J. (1992) Autocatalytic self-replicating micelles as models for prebiotic structures. Nature 357: 57–59

    Article  Google Scholar 

  • Barabási A. L., Oltvai Z. N. (2004) Network biology: Understanding the cell’s functional organization. Nature Reviews Genetics 5: 101–113

    Article  Google Scholar 

  • Ben-Jacob E. (2009) Learning from bacteria about natural information processing. Annals of the New York Academy of Sciences 1178: 78–90

    Article  Google Scholar 

  • Boccaletti S., Latora V., Moreno Y. (2009) Handbook on biological networks (lecture notes in complex systems). World Scientific, Singapore

    Google Scholar 

  • Boto L. (2009) Horizontal gene transfer in evolution: Facts and challenges. Philosophical Transactions of the Royal Society B 277: 819–827

    Google Scholar 

  • Brosius J. (2003) The contribution of RNAs and retroposition to evolutionary novelties. Genetica 118: 99–115

    Article  Google Scholar 

  • Cardelli L. (2005) Abstract machines of systems biology. In: Priami C. (eds) Transactions on computational systems biology, III. Springer, New York, pp 145–168

    Chapter  Google Scholar 

  • Carletti T., Serra R., Poli I., Villani M., Filisetti A. (2008) Sufficient conditions for emergent synchronization in protocell models. Journal of Theoretical Biology 254: 741–751

    Article  Google Scholar 

  • Davies D. G., Parsek M. R., Pearson J. P., Iglewski B. H., Costerton J. W., Greenberg E. P. (1998) The involvement of cell-to-cell signals in the development of a bacterial biofilm. Science 280: 295–298

    Article  Google Scholar 

  • Denning P. J. (2007) Computing is a natural science. Communications of the ACM 50(7): 13–18

    Article  Google Scholar 

  • Edwards R. A., Rohwer F. (2005) Opinion: Viral metagenomics. Nature Reviews Microbiology 3: 504–510

    Article  Google Scholar 

  • Filée J., Forterre P. (2005) Viral proteins functioning in organelles: A cryptic origin?. Trends in Microbiology 13: 510–513

    Article  Google Scholar 

  • Fisher J., Piterman N. (2010) The executable pathway to biological networks. Briefings in Functional Genomics and Proteomics 9(1): 79–92

    Google Scholar 

  • Fisher J., Henzinger T. A. (2007) Executable cell biology. Nature Biotechnology 25: 1239–1249

    Article  Google Scholar 

  • Forterre P. (2002) The origin of DNA genomes and DNA replication proteins. Current Opinion in Microbiology 5: 525–532

    Article  Google Scholar 

  • Foster K., Parkinson K., Thompson C. (2007) What can microbial genetics teach sociobiology?. Trends in Genetics 23: 74–80

    Article  Google Scholar 

  • Fox S. (1988) The emergence of life: Darwinian evolution from the inside. Basic Books, New York

    Google Scholar 

  • Frost L. S., Leplae R., Summers A. O., Toussaint A. (2005) Mobile genetic elements: The agents of open source evolution. Nature Reviews Microbiology 3: 722–732

    Article  Google Scholar 

  • Gleiser M., Walker S. I. (2008) An extended model for the evolution of prebiotic homochirality: A bottom-up approach to the origin of life. Origins of Life and Evolution of Biospheres 38: 293–315

    Article  Google Scholar 

  • Goldenfeld N., Woese C. (2007) Biology’s next revolution. Nature 445: 369

    Article  Google Scholar 

  • Gribaldo S., Poole M. A., Daubin V., Forterre P., Brochier-Armanet C. (2010) The origin of eukaryotes and their relationship with the Archaea: Are we at a phylogenomic impasse?. Nature Reviews Microbiology 8: 743–752

    Article  Google Scholar 

  • Hammer B., Bassler B. (2003) Quorum sensing controls biofilm formation in Vibrio cholerae. Molecular Microbiology 50: 101–104

    Article  Google Scholar 

  • Jablonka E., Lamb M. J. (2005) Evolution in four dimensions: Genetic, epigenetic, behavioral, and symbolic variation in the history of life. MIT Press, Cambridge, MA

    Google Scholar 

  • Karatan E., Watnick P. (2009) Signals, regulatory networks, and materials that build and break bacterial biofilms. Microbiology and Molecular Biology Reviews 73(2): 310–347

    Article  Google Scholar 

  • Kauffman S. (1993) The origins of order: Self-organization and selection in evolution. Oxford University Press, Oxford

    Google Scholar 

  • Kauffman S. (2000) Investigations. Oxford University Press, Oxford

    Google Scholar 

  • Kleinberg J. M. (2000) Navigation in a small world. Nature 406: 845

    Article  Google Scholar 

  • Koonin E. V., Wolf Y. I. (2009) Is evolution Darwinian or/and Lamarckian?. Biology Direct 4: 42

    Article  Google Scholar 

  • Kosztin I., Schulten K. (2004) Fluctuation-driven molecular transport through an asymmetric membrane channel. Physical Review Letters 93: 238102

    Article  Google Scholar 

  • Kristensen D. M., Mushegian A. R., Dolja V. V., Koonin E. V. (2010) New dimensions of the virus world discovered through metagenomics. Trends in Microbiology 18(1): 11–19

    Article  Google Scholar 

  • Lederberg J., Tatum E. L. (1946) Novel genotypes in mixed cultures of biochemical mutants of bacteria. Cold Spring Harbor Symposia on Quantitative Biology 11: 113–114

    Article  Google Scholar 

  • Leman L. J., Orgel L. E., Ghadiri M. R. (2004) Carbonyl sulfide-mediated prebiotic formation of peptides. Science 306(5694): 283–286

    Article  Google Scholar 

  • Leman L. J., Orgel L. E., Ghadiri M. R. (2006) Amino acid dependent formation of phosphate anhydrides in water mediated by carbonyl sulfide. Journal of the American Chemical Society 128: 20–21

    Article  Google Scholar 

  • Levine R. D. (2005) Molecular reaction dynamics. Cambridge University Press, Cambridge

    Book  Google Scholar 

  • Luisi P. L., Stano P., Rasi S., Mavelli F. (2004) A possible route to prebiotic vesicle reproduction. Artificial Life 10(3): 297–308

    Article  Google Scholar 

  • Makarova K. S., Grishin N. V., Shabalina S. A., Wolf Y. I., Koonin E. V. (2006) A putative RNA-interference-based immune system in prokaryotes: Computational analysis of the predicted enzymatic machinery, functional analogies with eukaryotic RNAi, and hypothetical mechanisms of action. Biology Direct 1: 7

    Article  Google Scholar 

  • Mansy S. S., Schrum J. P., Krishnamurthy M., Tobé S., Treco D. A., Szostak J. W. (2008) Template-directed synthesis of a genetic polymer in a model protocell. Nature 454: 122–125

    Article  Google Scholar 

  • Masuda N., Aihara K. (2004) Global and local synchrony of coupled neurons in small-world networks. Biological Cybernetics 90(4): 302–309

    Article  Google Scholar 

  • McDaniel L. D., Young E., Delaney J., Ruhnau F., Ritchie K. B., Paul J. H. (2010) High frequency of horizontal gene transfer in the Oceans. Science 330: 50

    Article  Google Scholar 

  • Mitchell M. (2009) Complexity: A guided tour. Oxford University Press, Oxford

    Google Scholar 

  • Mitchell, M. (2011). Biological computation. ACM Ubiquity Symposium on “What is Computation?”. Ubiquity, Issue February, Article No. 3, pp. 1–7. doi:10.1145/1940721.1944826.

  • Morowitz H. J. (1992) Beginnings of cellular life: Metabolism recapitulates biogenesis. Yale University Press, New Haven, CT

    Google Scholar 

  • Morowitz H. J., Srinivasan V., Smith E. (2010) Ligand field theory and the origin of life as an emergent feature of the periodic table of elements. Biological Bulletin 219(1): 1–6

    Google Scholar 

  • Morowitz H., Smith E. (2007) Energy flow and the organization of life. Complexity 13(1): 51–59

    Article  Google Scholar 

  • Nadell C. D., Xavier J. B., Levin S. A., Foster K. R. (2008) The evolution of quorum sensing in bacterial biofilms. PLoS Biology 6(1): e14. doi:10.1371/journal.pbio.0060014

    Article  Google Scholar 

  • Newman S. A., Bhat R. (2008) Dynamical patterning molecules: Physico-genetic determinants of morphological development and evolution. Physical Biology 5(1): 015008

    Article  Google Scholar 

  • Nowak M.A., Ohtsuki H. (2008) Prevolutionary dynamics and the origin of evolution. Proceedings of the National Academy of Sciences 105(39): 14924–14927

    Article  Google Scholar 

  • Oberholzer T., Wick R., Luisi P. L., Biebricher C. K. (1995) Enzymatic RNA replication in self-reproducing vesicles: An approach to a minimal cell. Biochemical and Biophysical Research Communications 207(1): 250–257

    Article  Google Scholar 

  • Ochman H., Lawrence J. G., Groisman E. A. (2000) Lateral gene transfer and the nature of bacterial innovation. Nature 405: 299–304

    Article  Google Scholar 

  • Paton, R., Bolouri, H., Holcombe, W. M. L., Parish, J. H., Tateson, R. (eds) (2004) Computation in cells and tissues: Perspectives and tools of thought (natural computing series). Springer, Heidelberg

    Google Scholar 

  • Peak D., West J. D., Messinger S.A., Mott K.A. (2004) Evidence for complex, collective dynamics and emergent, distributed computation in plants. Proceedings of the National Academy of Sciences, USA 101(4): 918–922

    Article  Google Scholar 

  • Portillo M. C., Gonzalez J. M. (2010) Differential effects of distinct bacterial biofilms in a cave environment. Current Microbiology 60(6): 435–438

    Article  Google Scholar 

  • Ragan M. A., Beiko R. G. (2009) Lateral genetic transfer: Open issues. Philosophical Transactions of the Royal Society B 364(1527): 2241–2251

    Article  Google Scholar 

  • Rasmussen S., Chen L., Stadler B. M. R., Stadler P. F. (2004) Proto-organism kinetics: Evolutionary dynamics of lipid aggregates with genes and metabolism. Origins of Life and Evolution of the Biosphere 34(1–2): 171–180

    Google Scholar 

  • Remis J. P., Costerton J. W., Auer M. (2010) Biofilms: Structures that may facilitate cell–cell interactions. Multidisciplinary Journal of Microbial Ecology 4(9): 1085–1087

    Google Scholar 

  • Riofrio W. (2007) Informational dynamic systems: Autonomy, information, function. In: Gershenson C., Aerts D., Edmonds B. (eds) Worldviews, science, and us: Philosophy and complexity. World Scientific, Singapore, pp 232–249

    Chapter  Google Scholar 

  • Riofrio W. (2008) Understanding the emergence of cellular organization. Biosemiotics 1(3): 361–377

    Article  Google Scholar 

  • Riofrio W. (2010) On biological computing, information and molecular networks. In: Vallverdú J. (eds) Thinking machines and the philosophy of computer science: Concepts and principles. IGI, Global, pp 53–65

    Chapter  Google Scholar 

  • Riofrio, W. (2011). A molecular dynamic network: Minimal properties and evolutionary implications. In M. Burgin & G. Dodig-Crnkovic (Eds.), Information and computation (pp. 307–330). Singapore: World Scientific. Forthcoming.

  • Rocheleau T., Rasmussen S., Nielsen P. E., Jacobi M. N., Ziock H. (2007) Emergence of protocellular growth laws. Philosophical Transactions of the Royal Society B 362: 1841–1845

    Article  Google Scholar 

  • Ruden D., Jamison D., Zeeberg B., Garfinkel M., Weinstein J., Rasouli P., Lu X. (2008) The EDGE hypothesis: Epigenetically directed genetic errors in repeat-containing proteins (RCPs) involved in evolution, neuroendocrine signaling, and cancer. Frontiers in Neuroendocrinology 29(3): 428–444

    Article  Google Scholar 

  • Ryan R. F. (2007) Viruses as symbionts. Symbiosis 44: 11–22

    Google Scholar 

  • Sadot A., Fisher J., Barak D., Admanit Y., Stern M. J., Hubbard E. J., Harel D. (2008) Toward verified biological models. IEEE/ACM Transactions on Computational Biology and Bioinformatics 5(2): 223–234

    Article  Google Scholar 

  • Sakuragi Y., Kolter R. (2007) Quorum-sensing regulation of the biofilm matrix genes (pel) of Pseudomonas aeruginosa. Journal of Bacteriology 189: 5383–5386

    Article  Google Scholar 

  • Salthe S. N. (1975) Evolutionary biology. Holt, Rinehart and Winston, New York

    Google Scholar 

  • Salthe S. N. (1985) Evolving hierarchical systems. Columbia University Press, New York

    Google Scholar 

  • Salthe S. N. (2002) Summary of the principles of hierarchy theory. General Systems Bulletin 31: 13–17

    Google Scholar 

  • Schnitzer M. J. (2002) Biological computation: Amazing algorithms. Nature 416: 683

    Article  Google Scholar 

  • Shin C. W., Kim S. (2006) Self-organized criticality and scale-free properties in emergent functional neural networks. Physical Review E 74(4): 45101

    Article  Google Scholar 

  • Siefert J. L. (2009) Defining the mobilome. In: Gogarten M. B., Gogarten J. P., Olendzenski L. C. (eds) Horizontal gene transfer: Genomes in flux. Humana Press, New York, pp 13–27

    Chapter  Google Scholar 

  • Singh P.K., Schaefer A.L., Parsek M.R., Moninger T.O., Welsh M.J. et al (2000) Quorum-sensing signals indicate that cystic fibrosis lungs are infected with bacterial biofilms. Nature 407: 762–764

    Article  Google Scholar 

  • Solé R. V. (2009) Evolution and self-assembly of protocells. International Journal of Biochemistry and Cell Biology 41: 274–284

    Article  Google Scholar 

  • Sorek R., Kunin V., Hugenholtz P. (2008) CRISPR—A widespread system that provides acquired resistance against phages in bacteria and archaea. Nature Reviews Microbiology 6(3): 181–186

    Article  Google Scholar 

  • Sporns O., Honey C. J. (2006) Small worlds inside big brains. Proceedings of the National Academic Science USA 103(51): 19219–19220

    Article  Google Scholar 

  • Suttle C. A. (2007) Marine viruses—Major players in the global ecosystem. Nature Reviews Microbiology 5: 801–812

    Article  Google Scholar 

  • Szostak D., Bartel P. B., Luisi P. L. (2001) Synthesizing life. Nature 409: 387–390

    Article  Google Scholar 

  • Thomas C. M., Nielsen K. M. (2005) Mechanisms of, and barriers to, horizontal gene transfer between bacteria. Nature Reviews Microbiology 3: 711–721

    Article  Google Scholar 

  • Velicer G. J. (2003) Social strife in the microbial world. Trends in Microbiology 11: 330–337

    Article  Google Scholar 

  • Villarreal L. P., DeFilippis V. R. (2000) A hypothesis for DNA viruses as the origin of eukaryotic replication proteins. Journal of Virology 74: 7079–7084

    Article  Google Scholar 

  • Watts D. J., Strogatz S. H. (1998) Collective dynamics of ‘small-world’ networks. Nature 393: 40–442

    Article  Google Scholar 

  • West S. A., Griffin A. S., Gardner A., Diggle S. P. (2006) Social evolution theory for microorganisms. Nature Reviews Microbiology 4: 597–607

    Article  Google Scholar 

  • Woese C. (1998) The universal ancestor. Proceedings of the National Academy of Sciences 95: 6854–6859

    Article  Google Scholar 

  • Woese C. (2000) Interpreting the universal phylogenetic tree. Proceedings of the National Academy of Sciences 97(15): 8392–8396

    Article  Google Scholar 

  • Woese C. (2002) On the evolution of cells. Proceedings of the National Academy of Sciences 99(13): 8742–8747

    Article  Google Scholar 

  • Woese C. (2004) A new biology for a new century. Microbiology and Molecular Biology Reviews 68(2): 173–186

    Article  Google Scholar 

  • Zimmer C. (2005) How and where did life on earth arise?. Science 309: 89

    Article  Google Scholar 

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  1. Complex Thought Institute Edgar Morin, University Ricardo Palma, Av. Arequipa, 5198, Miraflores, Lima 18, Peru

    Walter Riofrio

  2. Institut des Systèmes Complexes, ParisÎle-de-France (ISC-PIF), 57-59 rue Lhomond, 75005, Paris, France

    Walter Riofrio

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Riofrio, W. Studies on Molecular Mechanisms of Prebiotic Systems. Found Sci 17, 277–289 (2012). https://doi.org/10.1007/s10699-011-9236-9

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