Cell Language Theory, The: Connecting Mind And Matter

Applications of the Cell Language Theory to Biomedical Sciences 299

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

and c are constant for the yeast genome and b is a function of individual

mRNA molecules (reflecting the peculiarities of the experimental method

for measuring TR, known as the nuclear run-on technique [315]), then Eq.

(7.7) can be converted into

d(fTL)/dt = A(fTR) - B(fTD) (7.8)

where A = b/a and B = c/a and “fX” indicates “fold changes in X” as

defined in the legend to Figure 7.5. Integrating Eq. (7.8) leads to

fTL =

∫

[A(fTR) - B(fTD)]dt (7.9)

We can draw two important conclusions from Eq. (7.9):

(1) Since there are three variables in Eq. (7.9), it is impossible to deter-

mine any one of them without also measuring one of the remaining

two. For example, it would be impossible to determine A(fTR) by

measuring fTL alone (because of the B(fTD) term), contrary to

what has been routinely assumed in the field of microarray data

analysis, and

(2) Since there are at least three possibilities for the direction of changes

in d(fTL)/dt in Eq. (7.8) — increase (+), no change (0), or decrease

(-) — and, for each one of which, there are again three possible

mechanisms for the term [A(fTR) - B(fTD)] to be (+), (0), or (-) [25,

Table 12.4], there are nine possible mechanisms for regulating

d(fTL)/dt and hence the TL values [273, 317].

Each of the nine possible mechanisms inferred above is associated

with a unique RNA turnover mechanism involving a system of enzymes

(e.g., RNA polymerase, ribonucleases, other regulatory factors), and hence

it is logical to refer to it as an RNA turnover module or simply RNA mod-

ules [273, 317]. It should be pointed out that RNA modules invoked here

are examples of IDSs (see Sections 6.1.2 and 6.1.3), since they are not

permanent equilibrium structures such as RNA polymerases and electron-

transfer complexes but are transient ones that are called into action (or

excited or activated) by appropriate signals when needed and dissolve into

their components when their biological function is accomplished, very

similar to what Norris et al. referred to as “hyperstructures” [69]. Related

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