La biología sintética como desafío para comprender la autonomía de lo vivo

  1. Sara Murillo-Sánchez
  2. Kepa Ruiz-Mirazo
Revista:
Isegoría: Revista de filosofía moral y política

ISSN: 1130-2097

Año de publicación: 2016

Número: 55

Páginas: 551-575

Tipo: Artículo

DOI: 10.3989/ISEGORIA.2016.055.08 DIALNET GOOGLE SCHOLAR lock_openAcceso abierto editor

Otras publicaciones en: Isegoría: Revista de filosofía moral y política

Resumen

En este artículo se ofrece una visión de la biología sintética alternativa a los planteamientos ingenieriles que marcan gran parte de la agenda de investigación del campo. Nuestro análisis se centra en enfoques, teóricos y experimentales, cuyo objetivo fundamental es la comprensión del fenómeno de la vida per se. Una revisión detallada de varios casos de implementación artificial, in vitro, de sistemas químicos ‘auto-productivos’ nos ayudará a reflexionar sobre el enorme reto que supone transformar una disciplina científica eminentemente descriptiva, como la biología, en un proyecto que incluya y potencie líneas de investigación basadas en la idea de síntesis o fabricación. El reto es mayúsculo debido al carácter intrínsecamente metabólico de los sistemas biológicos, lo cual hace que nuestro empeño en controlarlos o en construirlos de novo sea mucho más dificultoso, forzándonos a desarrollar plataformas de intervención/implementación a nivel molecular que no pongan en compromiso esa inherente dimensión autónoma de lo vivo.

Referencias bibliográficas

  • Adrianantoandro, E., Basu, S., Karig, D.K., Weiss, R., "Synthetic biology: new engineering rules for an emerging discipline", Mol. Syst. Biol. 2006, 2.
  • Annaluru, N. et al., "Total synthesis of a functional designer eukaryotic chromosome", 2014, Science, 344, pp. 55-58. https://doi.org/10.1126/science.1249252 PMid:24674868 PMCid:PMC4033833
  • Ashkenasy, G., Jagasia, R., Yadav, M., Ghadiri, M.R., "Design of a directed molecular network", 2004, PnAs, 101, pp. 10872-10877. https://doi.org/10.1073/pnas.0402674101 PMid:15256596 PMCid:PMC503713
  • Bachmann, P. A., Luisi, P.L. & Lang, J., "Autocatalytic self-replicating micelles as models for prebiotic structures", 1992, Nature 357, pp. 57-59. https://doi.org/10.1038/357057a0
  • Benner, S.A., Sismour, A.M., "Synthetic biology", 2005, Nat Rev Genet, 6, pp. 533–543. https://doi.org/10.1038/nrg1637 PMid:15995697
  • Bishop, R.C., "Fluid convection, constraint and causation", Interface Focus, 2012, 2, pp. 4-12. https://doi.org/10.1098/rsfs.2011.0065 PMid:23386955 PMCid:PMC3262306
  • Bissette, A.J. & Fletcher, S.P., "Mechanisms of autocatalysis", 2013, Angew. Chem, Int. ed, 52, pp. 12800–12826. https://doi.org/10.1002/anie.201303822 PMid:24127341
  • Bissette, A.J., Odell, B., Fletcher, S.P., "Physical autocatalysis driven by a bond-forming thiol-ene reaction", 2014, Nature Communications, 5, pp. 4607. https://doi.org/10.1038/ncomms5607 PMid:25178358
  • Cameron, D.E., Bashor, C.J., Collins, J.J., "A brief history of synthetic biology", 2014, Nature Reviews Microbiology, 12, pp. 381-390. https://doi.org/10.1038/nrmicro3239 PMid:24686414
  • Canton, B., Labno, A. & Endy, D., "Refinement and standardization of synthetic biological parts and devices", 2008, Nature Biotech., 26, pp. 787–793. https://doi.org/10.1038/nbt1413 PMid:18612302
  • Dadon, Z., Wagner, N., Ashkenasy, G., "The Road to Non-Enzymatic Molecular Networks", 2008, Angew. Chem. Int. Ed., 47, pp. 6128-6136. https://doi.org/10.1002/anie.200702552 PMid:18613152
  • De la Escosura, A., Briones, C. & Ruiz-Mirazo, K., "The systems perspective at the crossroads between chemistry and biology", 2015, Journal of Theoretical Biology, 381, pp. 11-22. https://doi.org/10.1016/j.jtbi.2015.04.036 PMid:25983045
  • Endy, D., "Foundations for engineering biology", 2005, Nature, 438, pp. 449–453. https://doi.org/10.1038/nature04342 PMid:16306983
  • Epstein, I.R., "Coupled Chemical Oscillators and Emergent System Properties", 2014, Chem. Commun., 50, pp. 10758-10767. https://doi.org/10.1039/C4CC00290C PMid:24835430
  • Fontana, W. & Buss, L.W., "The arrival of the fittest: Toward a theory of biological organization", 1994, Bull. Math. Biol, 56, pp. 1-64.
  • Fry, I., "The emergence of life on Earth: A historical and scientific overview", 2000, Rutgers Univ. Press, London.
  • Ganti, T., "The Principle of Life", 1987, omIKK, Budapest.
  • Ganti, T., "On the early evolutionary origin of biological periodicity", 2002, Cell Biol. Int., 26, pp. 729–735. https://doi.org/10.1006/cbir.2000.0668 PMid:12175676
  • Gibson, D.G., Glass, J.I., Lartigue, C., Noskov, V.N., Chuang, R-Y et al., "Creation of a bacterial cell controlled by a chemically synthesized genome", 2010, Science, 329, pp. 52–56. https://doi.org/10.1126/science.1190719 PMid:20488990
  • Hardy, M. D., Yang, J., Selimkhanov, J., Cole, C. M., Tsimring, L. S., Devara, N. K., "Selfreproducing catalyst drives repeated phospholipid synthesis and membrane growth", 2015, PnAs, 112, pp. 8187-8192. https://doi.org/10.1073/pnas.1506704112 PMid:26100914 PMCid:PMC4500204
  • Harold, F., "The way of the cell", 2001, Oxford University Press, Oxford.
  • Hordijk, W., & Steel, M., "Detecting autocatalytic, self-sustaining sets in chemical reaction systems", 2004, J Theor Biol, 227(4), pp. 451–461. https://doi.org/10.1016/j.jtbi.2003.11.020 PMid:15038982
  • Hutchison, C.A. et al., "Design and synthesis of a minimal bacterial genome", 2016, Science, 351, aad6253. https://doi.org/10.1126/science.aad6253 PMid:27013737
  • Ichihashi, N., Aita, T., Motooka, D., Nakamura, S., Yomo, T., "Periodic pattern of genetic and fitness diversity during evolution of an artificial cell-like system", 2015, Molecular Biology and Evolution. https://doi.org/10.1093/molbev/msv189 PMid:26342111
  • Issac, R., Chmielewski, J., "Approaching Exponential Growth with a Self Replicating Peptide", 2002, J. Am. Chem. Soc, 124, pp. 6808-6809. https://doi.org/10.1021/ja026024i PMid:12059185
  • Jonas, H., "The phenomenon of life. Toward a philosophical biology", 1966 (2000), Harper and Row, New York. (El principio vida. Hacia una biología filosófica. Editorial Trotta).
  • Joyce, G., "The antiquity of RNA-based evolution", Nature, 2002, 418, pp. 214–221. https://doi.org/10.1038/418214a PMid:12110897
  • Kauffman, S., "Autocatalytic Sets of Proteins", 1986, Journal of Theoretical Biology, 119, pp. 1-24. https://doi.org/10.1016/S0022-5193(86)80047-9
  • Kauffman, S., "Investigations", 2000, Oxford University Press, Oxford.
  • Keasling, J. D., "Synthetic biology for synthetic chemistry", 2008, ACs Chem. Biol., 3(1), pp. 64-76. https://doi.org/10.1021/cb7002434 PMid:18205292
  • Kiedrowski, G. von, "A self-replicating hexadeoxy nucleotide", 1986, Angew. Chem. Int. Ed. Engl, 25, pp. 932-935. https://doi.org/10.1002/anie.198609322
  • Kiedrowski,G. von, "Public Communication in Systems Chemistry Workshop", 2005, Venice International University, pp. 3–4.
  • King, G.A.M., "Recycling, reproduction and life's origins", 1982, Biosystems, 15, pp. 89– 97. https://doi.org/10.1016/0303-2647(82)90022-3
  • Kittleson, J.T., Wu, G.C., Anderson, J.C., "Successes and failures in modular genetic engineering", 2012, Current Opinion in Chemical Biology, 16, pp. 329-336. https://doi.org/10.1016/j.cbpa.2012.06.009 PMid:22818777
  • Kurihara, K. et al., "Self-reproduction of supramolecular giant vesicles combined with the amplification of encapsulated DNA", 2011, Nat. Chem., 3, pp. 775–781. https://doi.org/10.1038/nchem.1127 PMid:21941249
  • Kurihara, K. et al. (2015). A recursive, vesicle-based model protocell with a primitive model cell cycle. Nature Communications 6, pp. 8352. https://doi.org/10.1038/ncomms9352 PMid:26418735 PMCid:PMC4598553
  • Kwok, R., "Five hard truths for synthetic biology", 2010, Nature, 463, pp. 288-290. https://doi.org/10.1038/463288a PMid:20090726
  • Langton, C.G., "Artificial Life", 1989, Artificial Life I (Proceedings of the First Conference on Artificial Life, Los Alamos, september, 1987), pp. 1-47. PMid:2786419
  • Lee, D.H., Granja, J.R., Martínez, J.A., Severin, K. & Ghadiri, M.R., "A self-replicating peptide", 1996, Nature, 382, pp. 525-528. https://doi.org/10.1038/382525a0 PMid:8700225
  • Letelier, J. C., Marín, G., Mpodozis, J., "Autopoietic and (M,R) Systems", 2003, Journal of Theoretical Biology, 222(2), pp. 261-72. https://doi.org/10.1016/S0022-5193(03)00034-1
  • Ludlow, R.F., Otto,S., "Systems chemistry", 2008, Chem. Soc. Rev., 37, pp. 101–108. https://doi.org/10.1039/B611921M PMid:18197336
  • Maturana, H. & Varela, F.J., "De Máquinas y Seres Vivos: Una teoría sobre la organización biológica", 1973, Editorial Universitaria S.A., Santiago de Chile.
  • Mavelli, F. & Ruiz-Mirazo, K., "Theoretical conditions for the stationary reproduction of model protocells", 2013, Integrative Biology, 5, pp. 324-341. https://doi.org/10.1039/C2IB20222K PMid:23233152
  • Moreno, A. & Ruiz-Mirazo, K., "Metabolism and the problem of its universalization", 1999, Biosystems, 49(1), pp. 45-61. https://doi.org/10.1016/S0303-2647(98)00034-3
  • Morowitz, H.J., "Energy flow in Biology", 1968, Academic Press, New York.
  • Morowitz, H.J., "Beginnings of Cellular Life", 1992, Yale University Press, Binghamton, New York.
  • Mossio, M., Saborido, C., Moreno, A., "An organisational account of biological functions", 2009, Brit J Philo Sci., 60, pp. 813–841. https://doi.org/10.1093/bjps/axp036
  • Nicolis, G., "Physics of far-from-equilibrium systems and self-organisation", 1989, The New Physics, Cambridge Univ. Press, Cambridge, pp. 316-347.
  • Orgel, L.E., "Prebiotic chemistry and the origin of the RNA world", 2004, Crit. Rev. Biochem. Mol. Biol., 39, pp. 99–123. https://doi.org/10.1080/10409230490460765 PMid:15217990
  • Patel, B.H., Percivalle, C., Ritson, D.J., Duffy, C.D. & Sutherland, J. D., "Common origins of RNA, protein and lipid precursors in a cyanosulfidic protometabolism", 2015, Nature Chemistry, 7, pp. 301-307. https://doi.org/10.1038/nchem.2202 PMid:25803468 PMCid:PMC4568310
  • Piedrafita, G., Ruiz-Mirazo, K., Monnard, P.-A., Cornish-Bowden, A. & Montero, F., "Viability conditions for a compartmentalized proto-metabolic system: a semi-empirical approach", 2012, PLos One, 7(6), e39480. https://doi.org/10.1371/journal.pone.0039480 PMid:22761803 PMCid:PMC3384665
  • Pinheiro, V.B., Holliger, P., "The XNA world: progress towards replication and evolution of synthetic genetic polymers", 2012, Current Opinion in Chemical Biology, 16 (3), pp. 245-252. https://doi.org/10.1016/j.cbpa.2012.05.198 PMid:22704981
  • Purnick, P.E. & Weiss, R., "The second wave of synthetic biology: from modules to systems", 2009, Nature Rev. Mol. Cell Biol., 10, pp. 410–422. https://doi.org/10.1038/nrm2698 PMid:19461664
  • Rao, C.V., Wolf, D.N., Arkin, A.P., "Control, exploitation and tolerance of intracellular noise", 2002, Nature, 420, pp. 231–237. https://doi.org/10.1038/nature01258 PMid:12432408
  • Rosen, R., "Life itself: A comprehensive inquiry into the nature, origin and fabrication of life", 1991, Columbia Univ. Press, New York.
  • Rosenfeld, N., Young, J.W., Alon, U., Swain, P.S. & Elowitz, M.B., "Gene regulation at the single-cell level", 2005, Science, 307, pp. 1962–1965. https://doi.org/10.1126/science.1106914 PMid:15790856
  • Ruiz-Mirazo, K., Briones, C., de la Escosura, A., "Prebiotic systems chemistry: New perspectives for the origins of life", 2014, Chem. Rev., 114, pp. 285–366. https://doi.org/10.1021/cr2004844 PMid:24171674
  • Ruiz-Mirazo, K. & Mavelli, F., "On the way towards 'basic autonomous agents': stochastic simulations of minimal lipid-peptide cells", 2008, Biosystems, 91(2), pp. 374-387. https://doi.org/10.1016/j.biosystems.2007.05.013 PMid:17714858
  • Ruiz-Mirazo, K. & Moreno, A., "Basic autonomy as a fundamental step in the synthesis of life", 2004, Artificial Life, 10(3), pp. 235-259. https://doi.org/10.1162/1064546041255584 PMid:15245626
  • Ruiz-Mirazo, K. & Moreno, A., "Autonomy in evolution: from minimal to complex life", 2012, Synthese, 185 (1), pp. 21-52. https://doi.org/10.1007/s11229-011-9874-z
  • Ruiz-Mirazo, K., Moreno, A., "Synthetic biology: challenging life in order to grasp, use or extend it", 2013, Biol. Theor., 8, pp. 376–382. https://doi.org/10.1007/s13752-013-0129-8
  • Schwille, P., "Bottom-up synthetic biology: engineering in a tinkerer's world", 2011, Science, 333(6047), pp. 1252-4. https://doi.org/10.1126/science.1211701 PMid:21885774
  • Semenov, S. N. et al. "Autocatalytic, bistable, oscillatory networks of biologically relevant organic reactions", 2016, Nature, 537, pp. 656-660. https://doi.org/10.1038/nature19776 PMid:27680939
  • Serrano, L., "Synthetic biology: promises and challenges", 2007, Mol Syst Biol, 3, pp. 158. https://doi.org/10.1038/msb4100202 PMid:18091727 PMCid:PMC2174633
  • Shirt-Ediss, B., Solé, R.V. & Ruiz-Mirazo, K., "Emergent chemical behavior in variablevolume protocells", 2015, Life, 5(1), pp. 181-211. https://doi.org/10.3390/life5010181 PMid:25590570 PMCid:PMC4390847
  • Shetty, R.P., Endy, D. & Knight, T.F. Jr., "Engineering BioBrick vectors from BioBrick parts", 2008, J. Biol. Eng., 2, pp. 5. https://doi.org/10.1186/1754-1611-2-5 PMid:18410688 PMCid:PMC2373286
  • Szathmáry, E., Santos, M., Fernando, C., "Evolutionary potential and requirements for minimal protocells", 2005, Top. Curr. Chem., 259, pp. 167-211. https://doi.org/10.1007/tcc001
  • Szostak, J.W., "The eightfold path to non-enzymatic RNA replication", 2012, J. Syst. Chem., 3, pp. 2. https://doi.org/10.1186/1759-2208-3-2
  • Terasawa, H., Nishimura, K., Suzuki, H., Matsuura, T.,Yomo, T., "Coupling of the fusion and budding of giant phospholipid vesicles containing macromolecules", 2012, PnAs, 109, pp. 5942-5947. https://doi.org/10.1073/pnas.1120327109 PMid:22474340 PMCid:PMC3340996
  • Turing, A. M., "The chemical basis of morphogenesis", 1952, Philos. Trans. R. Soc. London. Ser. b., 237, pp. 37-72. https://doi.org/10.1098/rstb.1952.0012
  • Varela, F. J., "Principles of Biological Autonomy", 1979, Elsevier, New York. PMCid:PMC1186669
  • Vaidya, N., Manapat, M.L., Chen, I.A., Xulvi-Brunet, R., Hayden, E.J., Lehman, N., "Spontaneous network formation among cooperative RNA replicators", 2012 Nature, 491, pp. 72–77. https://doi.org/10.1038/nature11549 PMid:23075853
  • Varios autores, "Life after the synthetic cell", 2010, Nature.
  • Vinson, V., Pennisi, E., "The allure of synthetic biology", 2011, Science, 333, pp. 1235. https://doi.org/10.1126/science.333.6047.1235 PMid:21885767
  • Virgo, N., Ikegami, T., "Autocatalysis before enzymes: the emergence of prebiotic chain reactions", 2013, Proceedings of the twelfth european Conference on Artificial Life, mIt Press, pp. 240-247.
  • Walde, P., "Building artificial cells and protocell models: Experimental approaches with lipid vesicles", 2010, Bioessays, 32, pp. 296–303. https://doi.org/10.1002/bies.200900141 PMid:20217842
  • Walde, P., Wick, R., Luisi. P.L., "Autopoietic self-reproduction of fatty acid vesicles" 1994, J. Am. Chem. Soc., 116, pp. 11649–11654. https://doi.org/10.1021/ja00105a004
  • Wang, H.-S., Wei, K. Y. & Smolke, C.D., "Synthetic biology: advancing the design of diverse genetic systems", 2013, Ann. Rev. Chem. Biomolec. Engineering, 4, pp. 69-102. https://doi.org/10.1146/annurev-chembioeng-061312-103351 PMid:23413816 PMCid:PMC3773533
  • Yao, S., Ghosh, I., Zutshi, R., Chmielewski, J., "Selective amplification by auto- and crosscatalysis in a replicating peptide system", 1998, Nature, 396, pp. 447-450. https://doi.org/10.1038/24814