References 9914 Yockey, H.P. (1992) Information Theory and Molecular Biology, Cambridge
University Press, Cambridge.
15 Cohen, S.N., Chang, A.C., Boyer, H.W., and Helling, R.B. (1973) Construction of
biologically functional bacterial plasmids in vitro. Proc. Natl. Acad. Sci. U.S.A.,
70 , 3240–3244.
16 Danielli, J.F. (1972) Context and future of cell synthesis. N. Y. State J. Med., 72 ,
2814–2815.
17 Danielli, J.F. (1974) Genetic engineering and life synthesis: an introduction to
the review by R. Widdus and C. Ault. Int. Rev. Cytol., 38 , 1–5.
18 Longo, G. (2009) Critique of computational reason in the natural sciences, in
Fundamental Concepts in Computer Science (eds E. Gelenbe and J.‐P. Kahane),
Imperial College Press/World Scientific, London, pp. 43–70.
19 Epstein, H.T. (1968) Factors affecting bacterial competence for transfection and
transfection enhancement. Bacteriol. Rev., 32 , 313–319.
20 Medigue, C., Rouxel, T., Vigier, P., Henaut, A. et al. (1991a) Evidence for
horizontal gene transfer in Escherichia coli speciation. J. Mol. Biol., 222 ,
851–856.
21 Lartigue, C., Glass, J.I., Alperovich, N., Pieper, R. et al. (2007) Genome
transplantation in bacteria: changing one species to another. Science, 317 ,
632–638.
22 Chan, L.Y., Kosuri, S., and Endy, D. (2005) Refactoring bacteriophage T7.
Mol. Syst. Biol., 1 (2005), 0018.
23 Jaschke, P.R., Lieberman, E.K., Rodriguez, J., Sierra, A. et al. (2012) A fully
decompressed synthetic bacteriophage øX174 genome assembled and archived
in yeast. Virology, 434 , 278–284.
24 de Lorenzo, V. (2011) Beware of metaphors: chasses and orthogonality in
synthetic biology. Bioeng. Bugs, 2 , 3–7.
25 Hutchison, C.A. 3rd, Chuang, R.Y., Noskov, V.N., Assad‐Garcia, N. et al. (2016)
Design and synthesis of a minimal bacterial genome. Science, 351 , aad6253.
26 Danchin, A. and Sekowska, A. (2013) Constraints in the design of the synthetic
bacterial chassis. Methods Microbiol., 40 , 39–68.
27 Danchin, A. (2012) Scaling up synthetic biology: do not forget the chassis.
FEBS Lett., 586 , 2129–2137.
28 Danchin, A. (2009) Natural selection and immortality. Biogerontology, 10 ,
503–516.
29 Dyson, F.J. (1985) Origins of Life, Cambridge University Press, Cambridge.
30 Blake, J.A. et al. (2015) Gene ontology consortium: going forward. Nucleic Acids
Res., 43 , D1049–D1056.
31 Ruch, P. (2017) Text mining to support gene ontology curation and vice versa.
Methods Mol. Biol., 1446 , 69–84.
32 Acevedo‐Rocha, C.G., Fang, G., Schmidt, M., Ussery, D.W. et al. (2013) From
essential to persistent genes: a functional approach to constructing synthetic life.
Trends Genet., 29 , 273–279.
33 Danchin, A. and Sekowska, A. (2014) The logic of metabolism and its fuzzy
consequences. Environ. Microbiol., 16 , 19–28.
34 Wachtershauser, G. (2007) On the chemistry and evolution of the pioneer
organism. Chem. Biodivers., 4 , 584–602.