Intracellular Dissipative Structures (IDSs) - Molecular Theory of the Living Cell - page 257

Table 9.1 The cell interactome as a five-dimensional hypernetwork. Cis-interactions occur
through direct physical contact between interacting entities, whereas trans-interactions occur
through the mediation of diffusible molecules
d n (node) e (edge) f (function)

1 Genes cis-Interactions Preservation and evolution

of genetic information

trans-Interactions

2 RNAs cis-Interactions Transfer of information from DNA

to proteins

trans-Interactions Complexification of genetic

information

3 Proteins cis-Interactions Execution of genetic information

by catalyzing those chemical reactions
selected by genetic information

trans-Interactions

4 Chemical

reactions

cis-Interactions Source of free energy needed for life

trans-Interactions Mediators of trans-interactions

5 Functions trans-Interactions Survival

Evolution

that it is an additive relation (i.e., the top node of the inverted T is equal to the sum
of the two lower nodes) unlike the complementarity relation which is nonadditive
(Ji 1995). Thus, just as when a large number of quanta is concentrated into a small
volume matter emerges, sowhen a large number of molecular mechanisms (which can
be viewed as examples of “dissipatons” since their operations require dissipating free
energy) are spatiotemporally organized inside the cell through the mechanism of
evolution (i.e., a complex of coupled processes between the variation of genotypes
and the selection of the fittest phenotypes by environmental conditions), living
processes (including chemotaxis) emerge. If this interpretation is correct, emergence
of living processes from molecular mechanisms (i.e., material processes) can be
viewed as a token of the supplementarity relation viewed as a type reified over
the spatiotemporal scales appropriate for the biological evolution . In a similar manner,
the emergence of the collective properties of matter such as rigidity, fluidity, super-
conductivity, superfluidity, etc. of nonliving matter may be looked upon as a token
of the supplementarity relation type that has been instantiated or reified over the
spatiotemporal scales appropriate for macroscopic and cosmological processes.
In Sect. 2.4.1 , a biological network (or bionetwork) was defined in terms of
three parameters, that is, nodes (n), edges (e), and functions or emergent properties
(f) (see Eq. 2.56 ). The complexity of the structure and function of the living cell
as depicted in Fig. 9.3 entails expanding the definition of a bionetwork given by
Eq. 2.56 by including two more parameters, namely, the dimensionality, d, of the
network and the level, l, of the of the hypernetwork under consideration:

BN ¼ (n ; e ; d ; l ; f) (9.2)

The cell hypernetwork characterized in Eq. 9.2 as a five-dimensional
hypernetwork is further detailed in Table 9.1 . As indicated in Table 9.1 ,the cell
hypernetwork can be alternatively referred to as the cell interactome which highlights
the complex molecular interactions underlying the cell hypernetwork.