Biology Reference
In-Depth Information
evidently species of IDSs (intracellular dissipative structures; see Sect.
3.1.2
). The
advantage and the utility of the term “ribons” derive from the fact that it is directly
connected to the rich results of the theories of
dissipative structures
formulated by
Prigogine and others in the 1980s (Babloyantz 1986; Kondepudi and Prigogine
1998; Kondepudi 2008).
Just as the atomic spectroscopic technique measures the electronic energy levels
in the atom, so
ribonoscopy
measures the RNA concentration levels (ascending,
descending, or staying steady) in the cell that appear to be quantized (see Sect.
12.13
) and are associated with target metabolic functions (Row 3). The former is
affected by the absorption of photons by the atom and the latter by the binding of
environmental signaling molecules by the cell (Row 4). The results of
measurements are
atomic line spectra
for the atom and the
time-dependent patterns
of the changes in RNA concentrations in the cell, namely,
ribons
or
r-dissipatons,
RNA trajectories, or RNA waves
(Row 5). An important lesson to be learned from
the atom-cell analogy is that, just as the atomic spectra are determined by (or
reflect) the internal structure of the whole atom including electrons, protons, and
neutrons, so the patterns of the RNA concentration profiles measured with DNA
arrays are determined by (or reflect) the functional state of the whole cell, including
the sate of enzymes, the cytoskeletons, and biochemical concentrations (Rows 6
and 7). Another lesson to be learned from the atom-cell analogy may be this: Just
as the atomic line spectra of the hydrogen atom were impossible to interpret
quantitatively before Bohr's model of the atom was formulated in 1913, so it
may be that the patterns of RNA levels measured with DNA arrays may be
impossible to interpret without a theoretical model of the living cell such as the
Bhopalator proposed in 1985 (Row 8). The basic theoretical concept embodied in
the model of the atom proposed was that of the quantum of action discovered by
Planck in 1900. The basic concepts underlying the Bhopalator model of the cell
include the conformon viewed as the quantum of biological communication (Ji 1991,
p. 122), IDSs, and SOWAWN machines (also called modules and hyperstructures)
(Row 9). Quantum mechanical principles such as the Franck-Condon principle are
necessary and sufficient to account for all atomic phenomena. Similarly, it is
suggested here that the conformon theory of molecular machines (which includes
or enfolds the generalized Franck-Condon principle), the cell language theory, and
the molecular information theory are necessary and sufficient to account for the
observable properties of the living cell (Row 10). It is of particular interest to note
that the same principle known as the
Principle of Slow and Fast Processes
(Ji 1991,
pp. 52-56) is postulated to operate at both the atomic and cellular levels in the form
of the Franck-Condon principle and the generalized Franck-Condon principle,
respectively (Row 10). Bohr developed the philosophy of complementarity begin-
ning in 1915 based on the principles of quantum mechanics (Murdoch 1987; Pais
1991; Plotnitsky 2006; Herbert 1987). The realization in the 1970s and 1980s that
Bohr's complementarity concept can be extended into enzymology in the form of the
information-energy complementarity, which in turn could be extended back to
physics in the form of the principle of
gnergy
, the ultimate driving force for all
self-organizing processes in the Universe (see Fig.
4.8
), led to the formulation of a
