Skip to main content Accessibility help

Understanding Life: A Bioinformatics Perspective

  • Natalia Szostak (a1) (a2), Szymon Wasik (a1) (a3) (a2) and Jacek Blazewicz (a1) (a3) (a2)


According to some hypotheses, from a statistical perspective the origin of life seems to be a highly improbable event. Although there is no rigid definition of life itself, life as it is, is a fact. One of the most recognized hypotheses for the origins of life is the RNA world hypothesis. Laboratory experiments have been conducted to prove some assumptions of the RNA world hypothesis. However, despite some success in the ‘wet-lab’, we are still far from a complete explanation. Bioinformatics, supported by biomathematics, appears to provide the perfect tools to model and test various scenarios of the origins of life where wet-lab experiments cannot reflect the true complexity of the problem. Bioinformatics simulations of early pre-living systems may give us clues to the mechanisms of evolution. Whether or not this approach succeeds is still an open question. However, it seems likely that linking efforts and knowledge from the various fields of science into a holistic bioinformatics perspective offers the opportunity to come one step closer to a solution to the question of the origin of life, which is one of the greatest mysteries of humankind. This paper illustrates some recent advancements in this area and points out possible directions for further research.



Hide All
1. Wang, J., Gu, J., Nguyen, M.T., Springsteen, G. and Leszczynski, J. (2013) From formamide to adenine: a self-catalytic mechanism for an abiotic approach. Journal of Physical Chemistry B, 117, pp. 1403914045.
2. Markvoort, A.J., Sinai, S. and Nowak, M.A. (2014) Computer simulations of cellular group selection reveal mechanism for sustaining cooperation. Journal of Theoretical Biology, 357, pp. 123133.
3. Takeuchi, N. and Hogeweg, P. (2012) Evolutionary dynamics of RNA-like replicator systems: a bioinformatic approach to the origin of life. Physics of Life Review, 9, pp. 219263.
4. Shay, J.A., Huynh, C. and Higgs, P.G. (2015) The origin and spread of a cooperative replicase in a prebiotic chemical system. Journal of Theoretical Biology, 364, pp. 249259.
5. Ma, W. and Hu, J. (2012) Computer simulation on the cooperation of functional molecules during the early stages of evolution. PloS One, 7, e35454.
6. Benner, S.A. (2010) Defining life. Astrobiology, 10, pp. 10211030 (2010).
7. Fenomen życia w ujęciu interdyscyplinarnym: teksty wykładów wygłoszonych na sympozjum naukowym zorganizowanym przez Oddział Polskiej Akademii Nauk i Wydział Teologiczny UAM w Poznaniu dnia 2 grudnia 2003 roku. (Ośrodek Wydawnictw Naukowych, 2004).
8. Shannon, C.E. (1948) A mathematical theory of communication. Bell Systems Technology Journal, 27, pp. 379423.
9. Axe, D.D. (200$0) Estimating the prevalence of protein sequences adopting functional enzyme folds. Journal of Molecular Biology, 341, pp. 12951315.
10. Meyer, S.C. (2010) Signature in the Cell: DNA and the Evidence for Intelligent Design (San Francisco: HarperOne).
11. Bowie, J.U., Reidhaar-Olson, J.F., Lim, W.A. and Sauer, R.T. (1990) Deciphering the message in protein sequences: tolerance to amino acid substitutions. Science, 247, pp. 13061310.
12. Dembski, W.A. (2006) The Design Inference: Eliminating Chance through Small Probabilities (Cambridge, UK: Cambridge University Press).
13. Dembski, W.A. (2006) No Free Lunch: Why Specified Complexity Cannot Be Purchased Without Intelligence (Lanham, Maryland, Stany Zjednoczone: Rowman & Littlefield).
14. Abel, D.L. (2009) The Universal Plausibility Metric (UPM) & Principle (UPP). Theoretical Biology and Medical Modelling, 6, p. 27.
15. Eddington, A.S. (2005) The Nature of the Physical World (Whitefish, Montana, USA: Kessinger Publishing, LLC).
16. Kenyon, D.H. (1969) Biochemical Predestination (New York: McGraw Hill Text).
17. Nicolis, G. and Prigogine, I. (1977) Self-Organization in Nonequilibrium Systems: From Dissipative Structures to Order through Fluctuations (New York: Wiley).
18. Kauffman, S.A. (1993) The Origins of Order: Self-Organization and Selection in Evolution (Oxford, UK: Oxford University Press).
19. Cech, T.R. (2012) The RNA Worlds in Context. Cold Spring Harbor Perspectives on Biology, 4, a006742.
20. Crick, F.H. (1968) The origin of the genetic code. Journal of Molecular Biology, 38, pp. 367379.
21. Orgel, L.E. (1968) Evolution of the genetic apparatus. Journal of Molecular Biology, 38, pp. 381393.
22. Boyer, S.H. (1968) The genetic code: the molecular basis for genetic expression. American Journal of Human Genetics, 20, pp. 403404.
23. Gesteland, R.F., Cech, T. and Atkins, J.F. (2006) The RNA World: The Nature of Modern RNA Suggests a Prebiotic RNA World (New York: Cold Spring Harbor Laboratory Press).
24. Woese, C.R. (1967) The Genetic Code: the Molecular Basis for Genetic Expression (New York: Harper & Row).
25. Gesteland, R.F. (1993) The RNA World: The Nature of Modern Rna Suggests a Prebiotic RNA World (New York: Cold Spring Harbor Laboratory Press).
26. Neveu, M., Kim, H.-J. and Benner, S.A. (2013) The ‘strong’ RNA world hypothesis: fifty years old. Astrobiology, 13, pp. 391403.
27. The Nobel Foundation (2015) The Nobel Prize in Chemistry 1989. at <>.
28. Forster, A.C. and Symons, R.H. (1987) Self-cleavage of plus and minus RNAs of a virusoid and a structural model for the active sites. Cell, 49, pp. 211220.
29. Johnston, W.K., Unrau, P.J., Lawrence, M.S., Glasner, M.E. and Bartel, D.P. (2001) RNA-catalyzed RNA polymerization: accurate and general RNA-templated primer extension. Science, 292, pp. 13191325.
30. Diener, T.O. (1971) Potato spindle tuber ‘virus’: IV. A replicating, low molecular weight RNA. Virology, 45, pp. 411428.
31. Flores, R., Gago-Zachert, S., Serra, P., Sanjuán, R. and Elena, S.F. (2014) Viroids: Survivors from the RNA World? Annual Review of Microbioogy, 68, pp. 395414.
32. Ruiz-Mirazo, K., Briones, C. and de la Escosura, A. (2014) Prebiotic systems chemistry: new perspectives for the origins of life. Chemical Reviews, 114, pp. 285366.
33. Eigen, M. and Schuster, P. (1979) The Hypercycle (Berlin, Heidelberg: Springer)
34. Schuster, P. (2011) Mathematical modeling of evolution. Solved and open problems. Theory in Biosciences, 130, pp. 7189.
35. Miller, S.L. (1953) A production of amino acids under possible primitive earth conditions. Science, 117, pp. 528529.
36. Miller, S.L. and Urey, H.C. (1959) Organic compound synthesis on the primitive earth. Science, 130, pp. 245251.
37. McCollom, T.M., Ritter, G. and Simoneit, B.R. (1999) Lipid synthesis under hydrothermal conditions by Fischer-Tropsch-type reactions. Origins of Life and Evolutions of Biospheres, 29, pp. 153166.
38. Lawless, J.G. and Yuen, G.U. (1979) Quantification of monocarboxylic acids in the Murchison carbonaceous meteorite. Nature, 282, pp. 396398.
39. Oro, J. and Kimball, A.P. (1961) Synthesis of purines under possible primitive earth conditions. I. Adenine from hydrogen cyanide. Archives of Biochemistry and Biophysics, 94, pp. 217227.
40. Powner, M.W., Gerland, B. and Sutherland, J.D. (2009) Synthesis of activated pyrimidine ribonucleotides in prebiotically plausible conditions. Nature, 459, pp. 239242.
41. Saladino, R., Crestini, C., Pino, S., Costanzo, G. and Di Mauro, E. (2012) Formamide and the origin of life. Physics of Life Reviews, 9, pp. 84104.
42. Despois, D., Crovisier, J., Bockelée-Morvan, D. and Biver, N. (2002) Comets and prebiotic chemistry: the volatile component. In: H. Lacoste (Ed.), Proceedings of the First European Workshop on Exo-Astrobiology, ESA SP-518, Noordwijk, the Netherlands, pp. 123–127.
43. Adande, G.R., Woolf, N.J. and Ziurys, L.M. (2013) Observations of interstellar formamide: availability of a prebiotic precursor in the galactic habitable zone. Astrobiology, 13, pp. 439453.
44. Wang, J., Gu, J., Nguyen, M.T., Springsteen, G. and Leszczynski, J. (2013) From formamide to adenine: a self-catalytic mechanism for an abiotic approach. Journal of Physics and Chemistry B, 117, pp. 1403914045.
45. Zaher, H.S. and Unrau, P.J. (2007) Selection of an improved RNA polymerase ribozyme with superior extension and fidelity. RNA New York, 13, pp. 10171026.
46. Ferris, J.P., Hill, A.R., Liu, R. and Orgel, L.E. (1996) Synthesis of long prebiotic oligomers on mineral surfaces. Nature, 381, pp. 5961.
47. Costanzo, G., Pino, S., Ciciriello, F. and Di Mauro, E. (2009) Generation of Long RNA Chains in Water. Journal of Biological Chemistry, 284, pp. 3320633216.
48. Adamala, K. and Szostak, J.W. (2013) Non-enzymatic template-directed RNA synthesis inside model protocells. Science, 342, pp. 10981100.
49. Szostak, J.W., et al. (2015) Szostak’s Lab Publications.
50. Budin, I. and Szostak, J.W. (2011) Physical effects underlying the transition from primitive to modern cell membranes. Proceedings of the National Academy of Science, 108, pp. 52495254.
51. Zhang, B. and Cech, T.R. (1997) Peptide bond formation by in vitro selected ribozymes. Nature, 390, pp. 96100.
52. Robertson, M.P., Hesselberth, J.R. and Ellington, A.D. (2001) Optimization and optimality of a short ribozyme ligase that joins non-Watson-Crick base pairings. RNA New York, 7, pp. 513523.
53. Paul, N. and Joyce, G.F. (2002) A self-replicating ligase ribozyme. Proceedings of the National Academy of Sciences, 99, pp. 1273312740.
54. Unrau, P.J. and Bartel, D.P. (1998) RNA-catalysed nucleotide synthesis. Nature, 395, pp. 260263.
55. Turk, R.M., Chumachenko, N.V. and Yarus, M. (2010) Multiple translational products from a five-nucleotide ribozyme. Proceedings of the National Academy of Sciences USA, 107, pp. 45854589.
56. Gebicki, J.M. and Hicks, M. (1973) Ufasomes are stable particles surrounded by unsaturated fatty acid membranes. Nature, 243, pp. 232234.
57. Gebicki, J.M. and Hicks, M. (1976) Preparation and properties of vesicles enclosed by fatty acid membranes. Chemical Physics Lipids, 16, pp. 142160.
58. Hargreaves, W.R. and Deamer, D.W. (1978) Liposomes from ionic, single-chain amphiphiles. Biochemistry (Mosc.), 17, pp. 37593768.
59. Eigen, M. and Schuster, P. (1977) The hypercycle. A principle of natural self-organization. Part A: Emergence of the hypercycle. Naturwissenschaften, 64, pp. 541565.
60. Eigen, M. (1971) Selforganization of matter and the evolution of biological macromolecules. Naturwissenschaften, 58, pp. 465523.
61. Boerlijst, M.C. and Hogeweg, P. (1995) Spatial gradients enhance persistence of hypercycles. Physics of Nonlinear Phenomena, 88, pp. 2939.
62. Hogeweg, P. and Takeuchi, N. (2003) Multilevel selection in models of prebiotic evolution: compartments and spatial self-organization. Origins of Life and Evolution of the Biospheres, 33, pp. 375403.
63. Takeuchi, N. and Hogeweg, P. (2009) Multilevel selection in models of prebiotic evolution II: a direct comparison of compartmentalization and spatial self-organization. PLoS Computational Biology, 5, e1000542.
64. Boerlijst, M.C. and Hogeweg, P. (1991) Spiral wave structure in pre-biotic evolution: hypercycles stable against parasites. Physics D, 48, pp. 1728.
65. Szathmáry, E. and Demeter, L. (1987) Group selection of early replicators and the origin of life. Journal of Theoretical Biology, 128, pp. 463486.
66. Vaidya, N., et al. (2012) Spontaneous network formation among cooperative RNA replicators. Nature, 491, pp. 7277.
67. May, R.M. (1991) Hypercycles spring to life. Nature, 353, pp. 607608.
68. Boerlijst, M. and Hogeweg, P. (1991) Self-structuring and selection: spiral waves as a substrate for prebiotic evolution. In: C.G. Langton, C. Taylor, J.D. Farmer, S. Rasmussen (Eds), Artificial Life II, Vol. 2, (Boston, USA: Addison-Wesley), pp. 255–276.
69. Nowak, M.A.. Evolutionary Dynamics: Exploring the Equations of Life (Belknap Press, 2006).
70. Mansy, S.S., et al. (2008) Template-directed synthesis of a genetic polymer in a model protocell. Nature, 454, pp. 122125.
71. Zhu, T.F. and Szostak, J.W. (2009) Coupled growth and division of model protocell membranes. Journal of the American Chemical Society, 131, pp. 57055713.
72. Schrum, J.P., Zhu, T.F. and Szostak, J.W. (2010) The origins of cellular life. Cold Spring Harbor Perspectives on Biology, 2, a002212.
73. Service, R.F. (2013) The life force. Science, 342, pp. 10321034.
74. Gelenbe, E., Seref, E. and Xu, Z. (2001) Simulation with learning agents. Proceedings of the IEEE, 89, pp. 148157.
75. Gelenbe, E. (2007) Dealing with software viruses: a biological paradigm. Information Security Technical Report, 12, pp. 242250.
76. Ören, T.L., Numrich, S.K., Uhrmacher, A.M., Wilson, L.F. and Gelenbe, E. (2000) Agent-directed simulation: challenges to meet defense and civilian requirements. in Proceedings of the 32nd conference on Winter simulation (Society for Computer Simulation International, San Diego, CA, USA), pp. 1757–1762.
77. Wasik, S., Jackowiak, P., Figlerowicz, M. and Blazewicz, J. (2014) Multi-agent model of hepatitis C virus infection. Artificial Intelligence Medicine, 60, pp. 123131.
78. Wasik, S., Prejzendanc, T. and Blazewicz, J. (2013) ModeLang – experts-friendly language for describing viral infection models. Computational and Mathematical Methods in Medicine, 8.
79. Wasik, S., et al. (2010) Towards prediction of HCV therapy efficiency. Computational and Mathematical Methods in Medicine, 11(2), pp. 185199.
80. Pietal, M.J., Szostak, N., Rother, K.M. and Bujnicki, J.M. (2012) RNAmap2D–calculation, visualization and analysis of contact and distance maps for RNA and protein-RNA complex structures. BMC Bioinformatics, 13, p. 333.


Full text views

Total number of HTML views: 0
Total number of PDF views: 0 *
Loading metrics...

Abstract views

Total abstract views: 0 *
Loading metrics...

* Views captured on Cambridge Core between <date>. This data will be updated every 24 hours.

Usage data cannot currently be displayed