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Part of the book series: Lecture Notes in Computer Science ((TCSB,volume 3380))

Abstract

Systems Biology constitutes tools and approaches aimed at deciphering complex biological entities. It is assumed that such complexity arose gradually, beginning from a few relatively simple molecules at life’s inception, and culminating with the emergence of composite multicellular organisms billions of years later. The main point of the present paper is that very early in the evolution of life, molecular ensembles with high complexity may have arisen, which are best described and analyzed by the tools of Systems Biology. We show that modeled prebiotic mutually catalytic pathways have network attributes similar to those of present-day living cells. This includes network motifs and robustness attributes. We point out that early networks are weighted (graded), but that using a cutoff formalism one may probe their degree distribution and show that it approximate that of a random network. A question is then posed regarding the potential evolutionary mechanisms that may have led to the emergence of scale-free networks in modern cells.

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References

  1. Gilbert, W.: The RNA world. Nature 319, 618 (1986)

    Article  Google Scholar 

  2. Gesteland, R.F., Cech, T.R., Atkins, J.F.: The RNA World, 2nd edn. Cold Spring Harbor Laboratory (2000)

    Google Scholar 

  3. Joyce, G.F.: The antiquity of RNA-based evolution. Nature 418, 214–221 (2002)

    Article  Google Scholar 

  4. Luisi, P.L.: Introduction (to COST27 special issue). Origins of Life and Evolution of the Biosphere 34, 1–2 (2004)

    Article  Google Scholar 

  5. Eigen, M.: Selforganization of matter and the evolution of biological macromolecules. Naturwissenschaften 58, 465–523 (1971)

    Article  Google Scholar 

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

    Google Scholar 

  7. Jeong, H., Tombor, B., Albert, R., Oltvai, Z.N., Barabasi, A.L.: The large-scale organization of metabolic networks. Nature 407, 651–654 (2000)

    Article  Google Scholar 

  8. Jeong, H., Mason, S.P., Barabasi, A.L., Oltvai, Z.N.: Lethality and centrality in protein networks. Nature 411, 41–42 (2001)

    Article  Google Scholar 

  9. Wagner, A.: The yeast protein interaction network evolves rapidly and contains few redundant duplicate genes. Mol. Biol. Evol. 18, 1283–1292 (2001)

    Google Scholar 

  10. Wagner, A., Fell, D.A.: The small world inside large metabolic networks. In: Proc. R. Soc. Lond. B. Biol. Sci., vol. 268, pp. 1803–1810 (2001)

    Google Scholar 

  11. Giot, L., Bader, J.S., Brouwer, C., Chaudhuri, A., Kuang, B., Li, Y., Hao, Y.L., Ooi, C.E., Godwin, B., Vitols, E., Vijayadamodar, G., Pochart, P., Machineni, H., Welsh, M., Kong, Y., Zerhusen, B., Malcolm, R., Varrone, Z., Collis, A., Minto, M., Burgess, S., McDaniel, L., Stimpson, E., Spriggs, F., Williams, J., Neurath, K., Ioime, N., Agee, M., Voss, E., Furtak, K., Renzulli, R., Aanensen, N., Carrolla, S., Bickelhaupt, E., Lazovatsky, Y., DaSilva, A., Zhong, J., Stanyon, C.A., Finley Jr., R.L., White, K.P., Braverman, M., Jarvie, T., Gold, S., Leach, M., Knight, J., Shimkets, R.A., McKenna, M.P., Chant, J., Rothberg, J.M.: A protein interaction map of Drosophila melanogaster. Science 302, 1727–1736 (2003)

    Article  Google Scholar 

  12. Barabasi, A.L., Oltvai, Z.N.: Network biology: understanding the cell’s functional organization. Nat. Rev. Genet. 5, 101–113 (2004)

    Article  Google Scholar 

  13. Li, S., Armstrong, C.M., Bertin, N., Ge, H., Milstein, S., Boxem, M., Vidalain, P.O., Han, J.D., Chesneau, A., Hao, T., Goldberg, D.S., Li, N., Martinez, M., Rual, J.F., Lamesch, P., Xu, L., Tewari, M., Wong, S.L., Zhang, L.V., Berriz, G.F., Jacotot, L., Vaglio, P., Reboul, J., Hirozane-Kishikawa, T., Li, Q., Gabel, H.W., Elewa, A., Baumgartner, B., Rose, D.J., Yu, H., Bosak, S., Sequerra, R., Fraser, A., Mango, S.E., Saxton, W.M., Strome, S., Van Den Heuvel, S., Piano, F., Vandenhaute, J., Sardet, C., Gerstein, M., Doucette-Stamm, L., Gunsalus, K.C., Harper, J.W., Cusick, M.E., Roth, F.P., Hill, D.E., Vidal, M.: A map of the interactome network of the metazoan C. elegans. Science 303, 540–543 (2004)

    Article  Google Scholar 

  14. Kunin, V., Pereira-Leal, J.B., Ouzounis, C.A.: Functional evolution of the yeast protein interaction network. Mol. Biol. Evol. 21, 1171–1176 (2004)

    Article  Google Scholar 

  15. Alm, E., Arkin, A.P.: Biological networks. Current Opinion in Structural Biology 13, 193–202 (2003)

    Article  Google Scholar 

  16. Monk, N.A.M.: Unravelling nature’s networks. Biochemical Society Transactions 31, 1457–1461 (2003)

    Article  MathSciNet  Google Scholar 

  17. Newman, M.E.J.: The structure and function of complex networks. Siam Review 45, 167–256 (2003)

    Article  MATH  MathSciNet  Google Scholar 

  18. You, L.C.: Toward computational systems biology. Cell Biochemistry and Biophysics 40, 167–184 (2004)

    Article  Google Scholar 

  19. Wachtershauser, G.: Evolution of the first metabolic cycles. Proc. Natl. Acad. Sci. USA 87, 200–204 (1990)

    Article  Google Scholar 

  20. Dyson, F.J.: Origins of Life, 2nd edn. Cambridge University Press, Cambridge (1999)

    Book  Google Scholar 

  21. Segre, D., Lancet, D.: Composing life. Embo. Reports 1, 217–222 (2000)

    Article  Google Scholar 

  22. Segre, D., Ben-Eli, D., Deamer, D.W., Lancet, D.: The lipid world. Origins of Life and Evolution of the Biosphere 31, 119–145 (2001)

    Article  Google Scholar 

  23. Morowitz, H.J.: The Emergence of Everything: How the World Became Complex. Oxford University Press, Oxford (2002)

    Google Scholar 

  24. Segre, D., Lancet, D., Kedem, O., Pilpel, Y.: Graded autocatalysis replication domain (GARD): Kinetic analysis of self-replication in mutually catalytic sets. Origins of Life and Evolution of the Biosphere 28, 501–514 (1998)

    Google Scholar 

  25. Segre, D., Ben-Eli, D., Lancet, D.: Compositional genomes: Prebiotic information transfer in mutually catalytic noncovalent assemblies. In: Proceedings of the National Academy of Sciences of the United States of America, vol. 97, pp. 4112–4117 (2000)

    Google Scholar 

  26. Shenhav, B., Segre, D., Lancet, D.: Mesobiotic emergence: Molecular and ensemble complexity in early evolution. Advances in Complex Systems 6, 15–35 (2003)

    Article  Google Scholar 

  27. Shenhav, B., Kafri, R., Lancet, D.: Graded Artificial Chemistry in Restricted Boundaries. In: Proceedings of 9th International Conference on the Simulation and Synthesis of Living Systems (ALIFE9), Boston, Massachusetts, USA, pp. 501–506 (2004)

    Google Scholar 

  28. Lancet, D., Sadovsky, E., Seidemann, E.: Probability Model for Molecular Recognition in Biological Receptor Repertoires - Significance to the Olfactory System. Proceedings of the National Academy of Sciences of the United States of America 90, 3715–3719 (1993)

    Article  Google Scholar 

  29. Lancet, D., Kedem, O., Pilpel, Y.: Emergence of Order in Small Autocatalytic Sets Maintained Far from Equilibrium - Application of a Probabilistic Receptor Affinity Distribution (RAD) Model. Berichte Der Bunsen-Gesellschaft-Physical Chemistry Chemical Physics 98, 1166–1169 (1994)

    Google Scholar 

  30. Rosenwald, S., Kafri, R., Lancet, D.: Test of a statistical model for molecular recognition in biological repertoires. Journal of Theoretical Biology 216, 327–336 (2002)

    Article  Google Scholar 

  31. Han, J.D., Bertin, N., Hao, T., Goldberg, D.S., Berriz, G.F., Zhang, L.V., Dupuy, D., Walhout, A.J., Cusick, M.E., Roth, F.P., Vidal, M.: Evidence for dynamically organized modularity in the yeast protein-protein interaction network. Nature 430, 88–93 (2004)

    Article  Google Scholar 

  32. Shenhav, B., Bar-Even, A., Kafri, R., Lancet, D.: Polymer GARD: computer simulation of covalent bond formation in reproducing molecular assemblies. Origins of Life and Evolution of the Biosphere (2005)

    Google Scholar 

  33. Benko, G., Flamm, C., Stadler, P.F.: Generic properties of chemical networks: Artificial chemistry based on graph rewriting. In: Proceedings of Advances in Artificial Life, vol. 2801, pp. 10–19 (2003)

    Google Scholar 

  34. Milo, R., Itzkovitz, S., Kashtan, N., Levitt, R., Shen-Orr, S., Ayzenshtat, I., Sheffer, M., Alon, U.: Superfamilies of Evolved and Designed Networks. Science 303, 1538–1542 (2004)

    Article  Google Scholar 

  35. Waddington, C.H.: Canalization of development and the inheritance of acquired characters. Nature 150, 563–565 (1942)

    Article  Google Scholar 

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Shenhav, B., Solomon, A., Lancet, D., Kafri, R. (2005). Early Systems Biology and Prebiotic Networks. In: Priami, C. (eds) Transactions on Computational Systems Biology I. Lecture Notes in Computer Science(), vol 3380. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-32126-2_2

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  • DOI: https://doi.org/10.1007/978-3-540-32126-2_2

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-25422-5

  • Online ISBN: 978-3-540-32126-2

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