Subcellular Systems - Molecular Theory of the Living Cell - page 304

sublanguages is not entirely clear to me but may be for the same reason that
the computer language is hierarchically organized into multiple layers starting
from the machine language level to (a) the micro architecture level, to (b)
the instruction set architecture (ISA) level, to (c) the operating system machine
level, to (d) the assembly language level, and finally to (5) the problem-oriented
language level (Tanenbaum 2003). Just as all these computer languages are
necessary in the computer architecture to facilitate the communication between
humans and the computer, it is here postulated that the multiple sublanguages
in the cell are necessary to couple the molecular (i.e., microscopic) processes
(studied in molecular biology and enzymology) to the mesoscopic or macroscopic
processes (studied in cell biology and animal physiology, respectively) that span
spatial and temporal dimensions differing in scale by 5-15 orders of magnitude
(see Statement 11.3). According to the spatiotemporal scaling hypothesis (Ji 1991,
p. 56) quoted below, the generalized Franck-Condon principle may be ultimately
responsible for the number of levels into which cell metabolism is organized:
... Cellular metabolism implicates spatial structures ranging in size from 10 10 cm (diam-
eter of the proton) to 10 5 cm (diameter of a cell), spanning 5 orders of magnitude, and in
time from 10 9 s (electron transfer reactions) to 10 6 s (cellular differentiation), spanning
15 orders of magnitude. To organize the intracellular processes that span such wide ranges
of space and time, these processes may have to be “chunked” into manageable functional
units, to each of which the generalized Franck-Condon Principle may apply. Various
intracellular structures from DNA to enzymes to subcellular organelles may be viewed as
a part of the cell's tactics for subdividing the spatial and temporal scales into optimal sizes
for efficient control and regulation. (11.3)

We will refer to Statement 11.3 as the “Spatiotemporal Scaling Hypothesis
of Biology.”
Within each sublanguage, we can recognize iconic , indexical , and symbolic
signs as indicated in Rows (2a)-(2d). When DNA is viewed as a molecular sign,
its immediate object can be identified with either RNA for transcription or DNA
itself for self-replication. The relation between DNA and its objects is iconic due to
the structural similarity resulting from the Watson-Crick base paring, indexical due
to the causal role postulated to be played by the mechanical energy stored in DNA
supercoils in effectuating transcription factor binding (see the TF-conformon colli-
sion hypothesis discussed in Sect. 8.3 ), and symbolic due to the arbitrariness of the
relation between the structural genes and the DNA segments regulating their
expression (Ji et al. 2009b).
Similarly, within the RNese, mRNA is iconically related to tRNA through
Watson-Crick base paring, indexically through the postulated causal role of
conformons during the translation step catalyzed by ribosomes. The symbolicity
in the interaction between mRNA and tRNA is probably not present but the relation
between the anticodons located in the middle of a tRNA molecule and the
corresponding amino acyl group located at the amino acid attachment site at the
3 0 end of tRNA is clearly arbitrary and thus symbolic.
When proteins act as molecular signs, their objects can be identified with their
cognate ligands which can be small molecular-weight organic or inorganic species
or biopolymers such as DNA, RNA, carbohydrates, glycoproteins, or other proteins.