Biology Reference
In-Depth Information
Biochemicals (B)
Environment (Env)
Proteins (P)
DNA (D)
RNA (R)
Fig. 10.2 A simple topological model of the living cell viewed as a
body-centered tetrahedron
(BCT).
The tetrahedron is the simplex of the three-dimensional space, an
n-dimensional simplex
being defined as the simplest polyhedron in an n dimensional space (Aleksandrov et al. 1984).
The six edges connecting the four vertices (B, D, R, and P) are not shown for brevity. One unique
feature of BCT is that all the nodes (including the center) are in simultaneous contact with
one another, a topological property suggestive of the physical situation where changing one
node affects all the others
2. We may distinguish two kinds of causalities - the
direct
and the
indirect
causalities. For example, if a perturbation causes mRNA levels to change, it
may be due to
direct
effects on any one or more of the apexes (i.e., biochemicals,
DNA, RNA and proteins), or indirect effects mediated by environment which are
affected by the perturbation, or due to indirect effects on DNA, proteins, or
biochemicals which affect mRNA levels through their actions on the environment.
3. Mutations in DNA may affect mRNA levels measured with DNA microarrays in
some but not all mutated cells, depending on the environmental conditions (e.g.,
tissue specificity, or microcirculatory variations within a given tissue).
The model of the cell depicted in Figure
10.2
reveals the material components of
the cell that determine the structure and function of the cell under a given environ-
mental condition. A similar
topological structure
of the cell can be constructed (see
Figure
10.2a
) wherein the nodes are occupied by
theoretical
(rather than
physical
)
components that have been proposed to account for the structure and function of the
living cell over a period of two and a half decades (1972-1997). It is interesting to
point out that the experimental evidence for the cell force concept was not
recognized until toward end of writing this topic as discussed in Section 12.13.
The theoretical components of the Bhopalator are collected in Table
10.2A
in the
order of their publication and with the experimental evidence supporting them.
The four theoretical components of the Bhopalator are all essential to account for
the phenomenon of life on the cellular level in molecular terms and inseparably
linked to one another mechanistically. The intimate relations among these
components can be diagrammatically represented as a
body-centered tetrahedron
(BCT) (Figure
10.2a
) wherein every node is in direct contact with all the other
