5.4 Helper Functions 87
(like trunk, branches, and leaves of a tree). To take this hierarchical view into
account, the functional part of the gene ontology effort has endeavored to
organize functional data as well as structural data [30]. The outcome of this
remarkable effort has still to be considerably improved, and it is likely that
much innovation will appear there in the near future [31].
Just to name a few helper functions, we find excerpts from an unlimited list: a
way to go forward and uncover unexpected functions would be to use the list of
all the verbs present in a particular language:
Making a progeny, with associated functions:
Construction of biomass
Replication of the program
Division (separating the progeny from the parent organism)
Maintenance
Making the progeny young, that is, separating between young and aged entities
Exploration is the function that could also be considered as a master function
for all living organisms, as life is doomed to explore its environment. It implies
either harnessing movements of the environment (spores or seeds propagated by
wind), constructing appendices allowing the organism to move (flagella in
microbes, limbs in animals), or harnessing features of the environment to move
ments (light with phycobilisomes, magnetic field with magnetosomes, etc.).
Each one of these functions is achieved using a lower level of helper functions,
some of them universally required for replication and reproduction, while others
are used by the organism for moving and occupying a particular niche [32]:
Transport (in and out): Extraction of chemical compounds from the environment,
and getting rid of waste
Circulation
Sensing
Management of energy
Storing
Shaping and maintenance of the cell structures
Degradation/resynthesis
Protection
To make this analysis explicit and concrete, we explore now some of the topics
that are central to place the genome in the cell’s context. Let us split some of
these helper functions along the dominating contribution of each of the five uni
versal currencies of reality: matter, energy, space, time, and information, with
emphasis on constraints on the genome (including its assembly).
5.4.1 Matter: Building Blocks and Structures (with Emphasis on DNA)
Formation of a cell begins with metabolism. For decades, this topic was consid
ered as a boring haphazard collection of chemicals. It was taught in classes where
students tried to remember by heart the lists of compounds, not really under
stood as following much logic. Yet, there is a clear logic of metabolism that begins
to be deciphered [33]. This logic is consistent in terms of the physics of matter.