The Living Cell - Molecular Theory of the Living Cell - page 284

on the other. Hence, Gnergy can be geometrically represented as the center of a
body-centered tetrahedron with four vertices occupied by energy (E), matter (M),
information (I), and life (L) as shown in Fig. 10.7 . The model of computation , mind,
and signs constructed on the basis of BCT (body-centered tetrahedron) has been
referred to as the Tarragonator (Row 12) (Ji 2003a, b; Appendix A ).
The body-centered tetrahedron (BCT) was found to provide a useful topological
template to organize the various sets of related ideas in many fields of inquiries,
as summarized in Table 10.5 , which has led me to suggest that BCT may represent a
universal code (Ji 2004b).
10.7 Evolving Models of the Living Cell
It appears that one of the first theoretical models of the living cell was proposed by
J. Watson when he described a model of protein synthesis in cells diagrammati-
cally (see Fig. 10.8a ) in a letter to Crick in 1954, 1 year after the publication
of their historic paper announcing the double-helical structure of DNA (Judson
1979, pp. 262-270). Watson's model of protein synthesis consists of three nodes
(DNA, RNA, and proteins) and four edges. The main point of the model was
the idea that protein synthesis occurs not on the DNA double-helix as suggested
earlier by Gamow (Judson 1979) but on RNA molecules (see the vertical line in
Fig. 10.8a ), which idea was later superseded by the Crick's notion of the adaptor
molecule subsequently identified as transfer RNA. The Watson mechanism of
protein synthesis contained a deficiency - namely, the idea of chemically
transforming one of the two strands of DNA double helix into an RNA molecule
in the nucleus, which was then exported to the cytosol for protein synthesis (see
the horizontal edge connecting DNA and RNA in Fig. 10.8a ). Despite this short-
coming in mechanistic details, the Watson model of protein synthesis may be
accorded a great historical significance because it is one of the first theoretical
models of the cell ever proposed on the molecular level based on then available
experimental data.
In contrast to the Watson model of 1954, which contained three types of objects
(i.e., DNA, RNA, and proteins), the Bhopalator model of the cell proposed in 1982
at a conference held in Bhopal, India (and published 3 years later in [Ji 1985a, b])
contains two additional types of biological objects, i.e., dissipative structures of
Prigogine, also called Intracellular Dissipative Structures (IDSs) in Ji (1985a, b) or
dissipatons in Sect. 3.1 ) and conformons , conformational strains of biopolymers
carrying mechanical energy to drive goal-directed molecular motions (Chap. 8 ) .
IDSs (a species or token of dissipations ) are dynamic structures (also called
“attractors” in nonlinear dynamics [Scott 2005]) consisting of chemical concentra-
tion and mechanical stress gradients within the cell, whereas conformons are
dynamic mechanical deformations that are postulated to be localized to sequence-
specific sites within biopolymers (Ji 1974b, 2000).