Can life be standardized?current challenges in biological standardization

  1. Juli Peretó
  2. Manuel Porcar
Journal:
Mètode Science Studies Journal: Annual Review

ISSN: 2174-3487 2174-9221

Year of publication: 2021

Issue Title: Science's structure

Issue: 11

Pages: 74-81

Type: Article

DOI: 10.7203/METODE.11.15981 DIALNET GOOGLE SCHOLAR lock_openOpen access editor

More publications in: Mètode Science Studies Journal: Annual Review

Abstract

The concept of standard strongly evokes machines, industries, electric or mechanical devices, vehicles, or furniture. Indeed, our technological civilization would not be possible – at least in the terms it is structured today – without universal, reliable components, whose acknowledged use results in competitive costs, robustness and interchangeability. For example, an Ikea screw can be used in a wide set of structurally dissimilar furniture and an app can be run on many different smartphones. The very concept of standardization is linked to the industrial revolution and mass production of goods through assembly lines. The question we will try to answer in the present paper is the extent to which standards and the standardization process can be accomplished in the biological realm.

Bibliographic References

  • Amos, M., & Goñi-Moreno, A. (2018). Cellular computing and synthetic biology. In S. Stepney, S. Rasmussen, & M. Amos (Eds.), Computational Matter (pp. 93–110). Springer.
  • Arnold, F. H. (2019). Innovation by evolution: Bringing new chemistry to life (Nobel acceptance speech). Angewandte Chemie International Edition, 58(41), 14420–14426. http://doi.org/10.1002/anie.201907729
  • D’Ari, R., & Casadesús, J. (1998). Underground metabolism. BioEssays, 20(2), 181–186. http://doi.org/10.1002/(SICI)1521-1878(199802)20:2%3C181::AID-BIES10%3E3.0.CO;2-0
  • De Crécy-Lagard, V., Haas, D., & Hanson, A. D. (2018). Newly-discovered enzymes that function in metabolite damage-control. Current Opinion in Chemical Biology, 47, 101–108. http://doi.org/10.1016/j.cbpa.2018.09.014
  • Ellens, K. W., Christian, N., Singh, C., Satagopam, V. P., May, P., & Linster, C. L. (2017). Confronting the catalytic dark matter encoded by sequenced genomes. Nucleic Acids Research, 45(20), 11495–11514. http://doi.org/10.1093/nar/gkx937
  • Elowitz, M. B., & Leibler, S. (2000). A synthetic oscillatory network of transcriptional regulators. Nature, 403(6767), 335–338. http://doi.org/10.1038/35002125
  • Elowitz, M. B., Levine, A. J., Siggia, E. D., & Swain, P. S. (2002). Stochastic gene expression in a single cell. Science, 297(5584), 1183–1186. http://doi.org/10.1126/science.1070919
  • Khersonsky, O., & Tawfik, D. S. (2010). Enzyme promiscuity: A mechanistic and evolutionary perspective. Annual Review of Biochemistry, 79, 471–505. http://doi.org/10.1146/annurev-biochem-030409-143718
  • Kittleson, J. T., Wu, G. C., & Anderson, J. C. (2012). Successes and failures in modular genetic engineering. Current Opinion in Chemical Biology, 16(3-4), 329–336. http://doi.org/10.1016/j.cbpa.2012.06.009
  • Kizer, L., Pitera, D. J., Pfleger, B. F., & Keasling, J. D. (2008). Application of functional genomics to pathway optimization for increased isoprenoid production. Applied and Environmental Microbiology, 74(10), 3229–3241. http://doi.org/10.1128/AEM.02750-07
  • Martínez-García, E., Goñi-Moreno, A., Bartley, B., McLaughlin, J., Sánchez-Sampedro, L., Pascual del Pozo, H., Prieto Hernández, C., Marletta, A. S., De Lucrezia, D., Sánchez-Fernández, G., Fraile, S., & de Lorenzo, V. (2019). SEVA 3.0: An update of the Standard European Vector Architecture for enabling portability of genetic constructs among diverse bacterial hosts. Nucleic Acids Research, 48(D1), D1164–D1170. http://doi.org/10.1093/nar/gkz1024
  • Moradigaravand, D., Palm, M., Farewell, A., Mustonen, V., Warringer, J., & Parts, L. (2018). Prediction of antibiotic resistance in Escherichia coli from large-scale pan-genome data. PLOS Computational Biology, 14(12), e1006258. http://doi.org/10.1371/journal.pcbi.1006258
  • Nicholson, D. J. (2019). Is the cell really a machine? Journal of Theoretical Biology, 477, 108–126. http://doi.org/10.1016/j.jtbi.2019.06.002
  • Porcar, M., Latorre, A., & Moya, A. (2013). What symbionts teach us about modularity. Frontiers in Bioengineering and Biotechnology, 1, 14. http://doi.org/10.3389/fbioe.2013.00014
  • Vilanova, C., & Porcar, M. (2014). iGEM 2.0–refoundations for engineering biology. Nature Biotechnology, 32, 420–424. http://doi.org/10.1038/nbt.2899
  • Vilanova, C., & Porcar, M. (2019). Synthetic microbiology as a source of new enterprises and job creation: A Mediterranean perspective. Microbial Biotechnology, 12, 8–10. http://doi.org/10.1111/1751-7915.13326
  • Vilanova, C., Tanner, K., Dorado-Morales, P., Villaescusa, P., Chugani, D., Frías, A., Segredo, E., Molero, X., Fritschi, M., Morales, L., Ramón, D., Peña, C., Peretó, J., & Porcar, M. (2015). Standards not that standard. Journal of Biological Engineering, 9, 17. http://doi.org/10.1186/s13036-015-0017-9