82 5 Functional Requirements in the Program and the Cell Chassis for Next-Generation Synthetic Biology
land, and of the city were written down, drawn, and discussed. This led some to
witness recurrent events within the records. Using repeated observations as
marks led our forefathers to derive useful applications, in computation and in
understanding and predicting how the world would fare. In parallel and in a
reciprocal activity, making tools, buildings, and machines resulted from accumu
lated understanding of repeated features (e.g., in using metals, in particular, iron,
at some point). In turn, this brought forth further understanding via all kinds of
explorations, both in the concrete world and in abstraction. Engineering allowed
those who ruled the city to tag events in time (including the regularity of days
and seasons) and to measure the flow of time, in parallel with measuring posi
tions in maps and lengths in space. The way we collect huge amounts of data
today is not without similarity with the situation in this ancient era, making it,
again, quite fit for the development of engineering.
Still, this activity was applied essentially to inanimate objects. Apart from
the domestication of plants and animals, life mostly escaped the engineer’s
hands because it was so natural: it appeared everywhere, independent of man.
Spontaneous generation was not the exception – it was the rule. You just had to
let a broth stand in the air to see it losing its transparency and becoming full of
worms. The consequence is that it took very long to think that life could also be
open to engineering. We witness a follow‐up of this attitude in today’s reluctance
of some to accept SynBio as the continuation of this prescientific attitude: after
all, rational plant breeding has but two centuries of age (at most [8]), and we still
witness sequels of the ancient idea that the moon directly influenced plant
growth (see [9] for reference). Pasteur discovered that life was associated with
dissymmetry. This led scientists to begin to see biology as a particular develop
ment of chemistry, at a time when the frontier between organic and inorganic
matters had begun to vanish. La dissymétrie, c’est la vie (dissymmetry, this is life!)
declared Pasteur. Indeed this claim pointed out the existence of some efficient
and somehow easy selection process that would trap and carry over, within living
organisms, some of the physical dissymmetry present in the universe. Pasteur
remained a vitalist, but Justus Liebig and Claude Bernard, each one in his own
way, propagated the idea that chemical processes were at the root of life. In short,
their works asked for some definition of life that would be useful for an engineer
wishing to (re)construct a living entity. It also, unobtrusively, pointed out a role
for information, an overlooked currency of reality. It is high time today to put
biology in the light of engineering.
The most successful engineering paradigm of cells and organisms is that they
behave as machines running a program [10–14]. The basis for genetic engi
neering has been the development of techniques that allow investigators to
synthesize pieces of genetic programs meant, oftentimes, to express genes into
proteins of industrial interest [15]. In an early work, James Danielli saw that
engineering could extend to the synthesis of life by combining individual bits
and pieces into a functional entity [16, 17]. Despite this deconstruction/recon
struction procedure, it was long asserted that machine and program were inti
mately linked together and inseparable (see [18] for a justification of this
negative view).