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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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
Bachmann P. A., Luisi P. L., Lang J. (1992) Autocatalytic self-replicating micelles as models for prebiotic structures. Nature 357: 57–59
Barabási A. L., Oltvai Z. N. (2004) Network biology: Understanding the cell’s functional organization. Nature Reviews Genetics 5: 101–113
Ben-Jacob E. (2009) Learning from bacteria about natural information processing. Annals of the New York Academy of Sciences 1178: 78–90
Boccaletti S., Latora V., Moreno Y. (2009) Handbook on biological networks (lecture notes in complex systems). World Scientific, Singapore
Boto L. (2009) Horizontal gene transfer in evolution: Facts and challenges. Philosophical Transactions of the Royal Society B 277: 819–827
Brosius J. (2003) The contribution of RNAs and retroposition to evolutionary novelties. Genetica 118: 99–115
Cardelli L. (2005) Abstract machines of systems biology. In: Priami C. (eds) Transactions on computational systems biology, III. Springer, New York, pp 145–168
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
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
Denning P. J. (2007) Computing is a natural science. Communications of the ACM 50(7): 13–18
Edwards R. A., Rohwer F. (2005) Opinion: Viral metagenomics. Nature Reviews Microbiology 3: 504–510
Filée J., Forterre P. (2005) Viral proteins functioning in organelles: A cryptic origin?. Trends in Microbiology 13: 510–513
Fisher J., Piterman N. (2010) The executable pathway to biological networks. Briefings in Functional Genomics and Proteomics 9(1): 79–92
Fisher J., Henzinger T. A. (2007) Executable cell biology. Nature Biotechnology 25: 1239–1249
Forterre P. (2002) The origin of DNA genomes and DNA replication proteins. Current Opinion in Microbiology 5: 525–532
Foster K., Parkinson K., Thompson C. (2007) What can microbial genetics teach sociobiology?. Trends in Genetics 23: 74–80
Fox S. (1988) The emergence of life: Darwinian evolution from the inside. Basic Books, New York
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
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
Goldenfeld N., Woese C. (2007) Biology’s next revolution. Nature 445: 369
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
Hammer B., Bassler B. (2003) Quorum sensing controls biofilm formation in Vibrio cholerae. Molecular Microbiology 50: 101–104
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
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
Kauffman S. (1993) The origins of order: Self-organization and selection in evolution. Oxford University Press, Oxford
Kauffman S. (2000) Investigations. Oxford University Press, Oxford
Kleinberg J. M. (2000) Navigation in a small world. Nature 406: 845
Koonin E. V., Wolf Y. I. (2009) Is evolution Darwinian or/and Lamarckian?. Biology Direct 4: 42
Kosztin I., Schulten K. (2004) Fluctuation-driven molecular transport through an asymmetric membrane channel. Physical Review Letters 93: 238102
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
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
Leman L. J., Orgel L. E., Ghadiri M. R. (2004) Carbonyl sulfide-mediated prebiotic formation of peptides. Science 306(5694): 283–286
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
Levine R. D. (2005) Molecular reaction dynamics. Cambridge University Press, Cambridge
Luisi P. L., Stano P., Rasi S., Mavelli F. (2004) A possible route to prebiotic vesicle reproduction. Artificial Life 10(3): 297–308
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
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
Masuda N., Aihara K. (2004) Global and local synchrony of coupled neurons in small-world networks. Biological Cybernetics 90(4): 302–309
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
Mitchell M. (2009) Complexity: A guided tour. Oxford University Press, Oxford
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
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
Morowitz H., Smith E. (2007) Energy flow and the organization of life. Complexity 13(1): 51–59
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
Newman S. A., Bhat R. (2008) Dynamical patterning molecules: Physico-genetic determinants of morphological development and evolution. Physical Biology 5(1): 015008
Nowak M.A., Ohtsuki H. (2008) Prevolutionary dynamics and the origin of evolution. Proceedings of the National Academy of Sciences 105(39): 14924–14927
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
Ochman H., Lawrence J. G., Groisman E. A. (2000) Lateral gene transfer and the nature of bacterial innovation. Nature 405: 299–304
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
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
Portillo M. C., Gonzalez J. M. (2010) Differential effects of distinct bacterial biofilms in a cave environment. Current Microbiology 60(6): 435–438
Ragan M. A., Beiko R. G. (2009) Lateral genetic transfer: Open issues. Philosophical Transactions of the Royal Society B 364(1527): 2241–2251
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
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
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
Riofrio W. (2008) Understanding the emergence of cellular organization. Biosemiotics 1(3): 361–377
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
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
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
Ryan R. F. (2007) Viruses as symbionts. Symbiosis 44: 11–22
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
Sakuragi Y., Kolter R. (2007) Quorum-sensing regulation of the biofilm matrix genes (pel) of Pseudomonas aeruginosa. Journal of Bacteriology 189: 5383–5386
Salthe S. N. (1975) Evolutionary biology. Holt, Rinehart and Winston, New York
Salthe S. N. (1985) Evolving hierarchical systems. Columbia University Press, New York
Salthe S. N. (2002) Summary of the principles of hierarchy theory. General Systems Bulletin 31: 13–17
Schnitzer M. J. (2002) Biological computation: Amazing algorithms. Nature 416: 683
Shin C. W., Kim S. (2006) Self-organized criticality and scale-free properties in emergent functional neural networks. Physical Review E 74(4): 45101
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
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
Solé R. V. (2009) Evolution and self-assembly of protocells. International Journal of Biochemistry and Cell Biology 41: 274–284
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
Sporns O., Honey C. J. (2006) Small worlds inside big brains. Proceedings of the National Academic Science USA 103(51): 19219–19220
Suttle C. A. (2007) Marine viruses—Major players in the global ecosystem. Nature Reviews Microbiology 5: 801–812
Szostak D., Bartel P. B., Luisi P. L. (2001) Synthesizing life. Nature 409: 387–390
Thomas C. M., Nielsen K. M. (2005) Mechanisms of, and barriers to, horizontal gene transfer between bacteria. Nature Reviews Microbiology 3: 711–721
Velicer G. J. (2003) Social strife in the microbial world. Trends in Microbiology 11: 330–337
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
Watts D. J., Strogatz S. H. (1998) Collective dynamics of ‘small-world’ networks. Nature 393: 40–442
West S. A., Griffin A. S., Gardner A., Diggle S. P. (2006) Social evolution theory for microorganisms. Nature Reviews Microbiology 4: 597–607
Woese C. (1998) The universal ancestor. Proceedings of the National Academy of Sciences 95: 6854–6859
Woese C. (2000) Interpreting the universal phylogenetic tree. Proceedings of the National Academy of Sciences 97(15): 8392–8396
Woese C. (2002) On the evolution of cells. Proceedings of the National Academy of Sciences 99(13): 8742–8747
Woese C. (2004) A new biology for a new century. Microbiology and Molecular Biology Reviews 68(2): 173–186
Zimmer C. (2005) How and where did life on earth arise?. Science 309: 89
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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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DOI: https://doi.org/10.1007/s10699-011-9236-9