5.2 Functional Analysiss: aster Function and Helper Functions 83The onset of DNA‐based technologies such as transfection of viral DNA into
cells [19] and genetic engineering [15], associated with recognition that horizon
tal gene transfer made a considerable fraction of bacterial genomes [20], and
finally whole genome transplantation [21] was a turning point. They established
that the machine and the program are indeed separate entities, exactly as the
operating system (OS), and the computer can be physically told from one another
[10, 12]. It has been now possible to synthesize viral genomes in such a way that
they comply with a man‐made design [22, 23]. The statement found in rearguard
discussions that the comparison between cells and computers is not valid because
there is a considerable amount of information in the cell beside its genome can
not be retained as a final argument. Indeed, the situation is exactly the same in
computers, human artifacts that fare well. Nobody would argue that the tablet or
the PC do not carry a considerable body of information. The proof is that a CD
carrying an OS is useless in the absence of the information carried by the machine
that runs it. Yet nobody would argue against the fact that computers work, pro
vided they can read a support carrying a matching OS.
Of course, this is not the whole story: besides program and machine (the “chas
sis” of SynBio specialists [24]), the cell, as the computer, needs to process energy,
a feature that is not implemented in the abstract ancestor of the computer, the
Turing machine. Furthermore, there is a need for construction and maintenance,
which implies fluxes of matter, a currency of reality that is also absent from the
purely informational Turing machine. In living organisms these essential func
tions are fulfilled by metabolism. Life can be witnessed only when metabolic
fluxes can be measured, with “dormancy” labeling the limbo between life and
death. In summary, life combines a program, a machine reading and expressing
the program, and a metabolism managing matter and energy fluxes to run the
program in the machine. Finally, a living organism works through an ultimate
constraint: it must produce a progeny. Functions pertaining to that particular
process make the core of the present chapter. Using functional analysis to under
stand the making of life, with emphasis on the processes just summarized, we
propose here a set of developments that emphasize the mutual interaction
between the program and the chassis, a setup essential to master for the future of
SynBio.
5.2 Functional Analysis: Master Function and Helper Functions
Functions
The success of genome transplantation into recipient hosts – the founding exper
iment of next‐generation SynBio [25] – is allowing scholars to look into biology
with new eyes. To go further, we apply here the agenda of functional analysis
[4, 5] to cells considered as “machines” or “automata,” where a program can be
explicitly told from the machine that runs it (Figure 5.1). When trying to under
stand how an organism can be fit for a particular niche, we first split its biological
functions into two functional categories, at least one master function and associ
ated helper functions meant to achieve the target of the master function [26].