Cell Language Theory, The: Connecting Mind And Matter

Cell Language 211

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

and that of the mind (see the discussion on micro- and macrosemi-

otics in Section 6.4).

(3) For the cell to be able to self-replicate, it must (i) utilize the free

energy provided by chemical reactions which do not proceed inside

the cell spontaneously without catalysis performed by molecular

machines (also called enzymes) and (ii) control the utilization of free

energy in accordance with the genetic information stored in DNA and

incoming environmental information.

(4) Molecular machines are capable of carrying out both the utilization

of the free energy generated from chemical reactions (called “rate-

dependent dynamics” by Pattee) and the control of free energy utili-

zation based on genetic information (called “rate-independent

genetic symbols”), ultimately because:

(i) biopolymers possess the right physical sizes/dimensions to be

thermally deformed, thereby transiently storing thermally derived

kinetic and potential energies in the form of “virtual confor-

mons” [65] (see also Section 3.4.4) and

(ii) the genetic information encoded in the internal structures of biopol-

ymers provide the necessary constraints to synchronize (or control

the timing of) the entrapping of virtual conformons at sequence-

specific loci and the catalysis triggered by the virtual conformons,

leading to the dissipation of the requisite chemical free energy into

heat (thus paying back the thermal energy borrowed from environ-

ment quickly enough to avoid violating the second law) [14, 65].

The combination of the synchronized partial processes (i) and

(ii) is necessary and sufficient to convert virtual conformons into real

conformons driven by exergonic chemical reactions catalyzed by

enzymes. As long as this conversion is completed within the cycling

time of the molecular machine, no laws of thermodynamics are violated

[227, 273]. It should be pointed out that realistic molecular mechanisms

for synchronizing processes (i) and (ii) were proposed almost three

decades ago based on the “generalized Franck–Condon principle”

(GFCP) [12, 65]. The critical role that thermal noise (also called ther-

mal activations or fluctuations) must play in the workings of molecular

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