98 5 Functional Requirements in the Program and the Cell Chassis for Next-Generation Synthetic Biology
transplant artificial genetic constructs, with outputs that work well. Indeed, the
proof of concept of this view has been repeatedly established, in constructing all
kinds of circuits or metabolic pathways, showing that the key idea of the cell as
a computer is at least conceptually viable. However, as industrial processes
require both stability in time and high production, it is important that the proof
of concept is followed by scaling up in making economically viable constructs.
We have delineated here some of the constraints that must be taken into account
to allow a smooth transition from the academic laboratory to the industrial
scale.Acknowledgments
Stanislas Noria is a network supported by the Fondation Fourmentin‐Guilbert.
The authors declare that they have no conflict of interest involved in this work.References
1 Potthast, T. (2009) Paradigm shifts versus fashion shifts? Systems and synthetic
biology as new epistemic entities in understanding and making ‘life’. EMBO Rep.,
10 (Suppl. 1), S42–S45.
2 Danchin, A. (1999) From protein sequence to function. Curr. Opin. Struct. Biol.,
9 , 363–367.
3 Galperin, M.Y., Walker, D.R., and Koonin, E.V. (1998) Analogous enzymes:
independent inventions in enzyme evolution. Genome Res., 8 , 779–790.
4 Cole, E.L. Jr. (1998) Functional analysis: a system conceptual design tool [and
application to ATC system]. IEEE Trans. Aerosp. Electron. Syst., 34 , 354–365.
5 Fantoni, G., Apreda, R., and Bonaccorsi, A. (2009) A theory of the constituent
elements of functions, in Proceedings of the 17th International Conference on
Engineering Design (ICED’09) (eds M. Norell Bergendahl, M. Grimheden, L.
Leifer, P. Skogstad, et al.), Design Society, Stanford University, San Francisco,
CA, pp. 179–190.
6 Endy, D. (2005) Foundations for engineering biology. Nature, 438 , 449–453.
7 Dyson, F.J. (2012) History of science. Is science mostly driven by ideas or by
tools? Science, 338 , 1426–1427.
8 Frängsmyr, T., Heilbron, J.L., and Rider, R.E. (eds) (1990) The Quantifying
Spirit in the 18th Century, University of California Press, Berkeley, Los Angeles,
Oxford.
9 Beeson, C.F. (1946) The moon and plant growth. Nature, 158 , 572.
10 Brenner, S. (2012) Turing centenary: life’s code script. Nature, 482 , 461.
11 Danchin, A. (2003) The Delphic Boat. What Genomes Tell us, Harvard
University Press, Cambridge, MA.
12 Danchin, A. (2009) Bacteria as computers making computers. FEMS Microbiol.
Rev., 33 , 3–26.
13 Quastler, H. (1953) Essays on the Use of Information Theory in Biology,
University of Illinois Press, Urbana.