96 5 Functional Requirements in the Program and the Cell Chassis for Next-Generation Synthetic Biology
time. In general, the importance of time has been underestimated, in particular
because laboratory conditions are most often meant to provide steady‐state
invariable conditions. Time‐dependent pattern formation, a basis for multicel
lular body plan, must be explored with novel approaches [135]. Finally, the role
of ubiquitous transitions (shifts in temperature, light, metabolites supply, inter
actions with other organisms, and simply aging) will certainly need to be explored
much more in‐depth for large‐scale SynBio applications. The time scales of DNA
movements have not been explored in‐depth, and, if relevant, this missing
knowledge might become a limitation for the future of SynBio constructs.5.4.5 Information
SynBio uses cell factories that associate a program with a chassis. As previously
discussed, the transplantation experiment that implemented a program that did
not match the receiving host chassis [21] demonstrates the physical material
separability between machine and program [10, 12]. It also emphasizes another
point, where information is central: while, at the end of the experiment, the
donor’s program is identical to that at the beginning, the final machine
(Mycoplasma capricolum) differs from the initial host machine (Mycoplasma
mycoides) (Figure 5.2). This implies that some specific input of contextual infor
mation (gene expression in a particular environment, at a particular time), and
not directly related to the information carried over by the genetic program, has
been involved. In the same way, construction of a young progeny from aged cells
demonstrates that there is a specific management of information by cells, in a
way that is highly reminiscent of the way Maxwell’s demons operate [27, 136].
Briefly, creating a link between information and entropy, Maxwell introduced
the idea of a hypothetical being, later seen as a “demon” that uses an in‐built
information‐processing ability to reduce the entropy of a homogeneous gas (at a
given temperature). The demon is able to measure the speed of gas molecules
and open or close a door between two compartments as a function of the mole
cules’ speed, keeping them on one side if fast and on the other side if slow. This
behavior will build up two compartments, one hot and one cold, reversing time
and acting apparently against the second principle of thermodynamics. In the
same way, proteins such as septins prevent aged proteins to go from the mother
cell to the daughter cells [137] or organize cell division [138], using energy to
reset their state to ground level [27, 136].
Information is split into several components: a genetic memory, carried over
by DNA via faithful replication, epigenetic memory that reproduces a particular
state of the chassis, including a specific organization of gene expression, and a
variety of processes managing information transfers. DNA replication uses an
asymmetrical nanomachine that breaks the DNA double helix opened at a speci
fied origin and starts elongating a continuous strand in the 5′ to 3′ direction. The
process is straightforward in replication of the leading DNA strand. By contrast,
replication of the lagging strand poses major structural problems. Indeed, repli
cation of that strand requires a considerable length of single‐stranded DNA that
must be protected by specific complexes; it also requires management of multi
ple initiation complexes, in contrast to replication of the leading strand, which