5.4 Helper Functions 95Another question that must be answered is the way the influx of protons is
distributed within the cell. As the membrane‐associated rotor of ATP synthase
or the flagella motor leaks in protons at a fast rate, their influx must be coupled
to a steady average amount of “free” protons in the cell that is extremely low
(typically, if there were such a pH as 7.6 in an E. coli cell, this would mean about
15 free protons per cell at any time). The way protons are disposed of so that on
average such a small number remains free is an entirely open question that
requires understanding the way water is organized in the extremely crowded
environment of the cytoplasm. This situation has considerable consequences in
particular for highly charged molecules such as nucleic acids. This is not yet
really understood [124, 125]. An alternative to safety valves is storage by polym
erization, a function fulfilled by a variety of structures and compartments [126],
and polymerization of nucleotides is a way, rarely considered, to buffer osmotic
pressure.
5.4.4 Time
The idea that time and transitions are essential in shaping molecules and organ
izing cells is also central to the understanding of the addressing, organization
and motion of proteins within the cell and its membrane. The role of time will be
one of the most important features of the development of SynBio in the next
decade. This is because in most research, studies of evolution and phylogeny
aside, there has been a tendency to account for life in synchronous terms. For
example, the recent descriptions of the way DNA is folded in cells provide us
with a fairly static view [127–129]. Yet, it is obvious that except in dormant states,
DNA is highly flexible and mobile, with movements triggered by transcription
and all related processes that maintain supercoiling, as opening up the double
helix locally will trigger a deformation that will propagate [127, 130, 131]. It is
likely that the organization into macrodomains is fit to coordinate gene expres
sion [113], including when transcription involves time‐dependent movements of
the DNA template.
Considering cells and organisms as computers, making computers exposes a
considerable possible limitation, where time plays a central role, resulting from
the fact that expression of the genetic program is highly parallel. Parallelism
implies that a variety of clocks allow synchronization of gene expression pro
cesses [27]. This need for synchronization is likely to be another constraint that
organizes the genome into macrodomains [89]. Indeed, clocks are found every
where in life: coupling of gene expression with seasons [131], circadian rhythms
[132], and many other kinds of clocks, unrelated to obvious environmental
parameters [133]. It has been known since the nineteenth century that circuits
with relevant feedback loops could end up with oscillating properties, de facto
creating clocks. It is therefore quite trivial to find clocks based on regulatory
gene expression circuits, an expected property that nevertheless became quite
fashionable several decades ago, hiding more interesting roles of time. By con
trast and more interestingly, other intrinsic clocks, for example, based on the
aging half‐life of macromolecules (such as resulting from isomerization of aspar
agine and aspartate in proteins [27, 134]) may bring about unexpected uses of