Cell Language Theory, The: Connecting Mind And Matter

56 The Cell Language Theory: Connecting Mind and Matter

b2861 The Cell Language Theory: Connecting Mind and Matter “6x9”

and ion gradients, would disappear if free energy derived from metabo-

lism is not supplied continuously to maintain them.

The living cell can be viewed as a self-organizing chemical reac-

tion–diffusion system catalyzed by biopolymers (proteins, RNA, and

DNA). The arrows indicate molecular processes driven by free energy

under the control of genetic information. This is equivalent to saying that

the arrows indicate the actions of enzymes that use conformons to

change A to B, where A is the initial state of a molecular system and B

the final state, and conformons embody both energy and information,

i.e., gnergy, the complementary union of information (gn-) and energy

(-ergy) (see Section 2.9).

The cell can be represented as a system of nodes and arrows that

change with time. Such a system may be referred to as a dynamic molecu-

lar network or a cell machine. The basic components of the cell machine

are molecular machines (e.g., enzymes), driven by conformons.

Both molecular machines and cell machines may be identified as

examples of what mathematicians call categories (see Section 2.1). A cat-

egory is often represented diagrammatically as

(^) AB→f (3.2)
where A and B are nodes and f is the name of the arrow meaning that
A can be transformed into B while preserving some structure or a rule.
M. Burgin refers to Scheme 3.2 as the named triad or the fundamental
triad [37, pp. 566–568].
The cell machine receives an input from its environment (see step 19
in Figure 3.2) and processes it utilizing the genetic information stored in
DNA, and the cytosol driven by molecular machines, and produces an
output to the environment of the cell (see step 20).
3.2.1 The IDS-Cell Function Identity (ICFI) Hypothesis
Any structure inside the cell, e.g., the Ca^2 + ion gradient in the cytosol (see
Figure 3.3), that disappears when the cell runs out of energy can be defined
as IDSs (Intracellular Dissipative Structures). IDSs include any steady-
state levels or dynamic concentration patterns of metabolites and ions
inside the cell such as ATP, glucose, NADH, mRNA, Na+, Ca^2 +, and K+.
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