Whole Cells - Molecular Theory of the Living Cell - page 419

for the operation of the principle of “rule-governed creativity (RGC)” in the
genome-wide metabolism of RNAs, i.e., transcriptomics. (The principle of RGC is
discussed in detail in Sect. 6.1.4 . ) This conclusion is consistent with the postulate
that living cells use language, cellese , which is isomorphic with the human language,
humanese characterized by RGC (see Sects. 6.1.2 and 6.1.3 ) .

12.11 Genes as Molecular Machines

The experimental data presented Sect. 12.9 indicate that most structural genes of
budding yeast co-regulate their own transcript levels in the cell in cooperation with
other genes under the experimental condition of glucose-galactose shift. The extent
of such co-regulation may vary from one experimental condition to another. This
goes against the commonly held views that structural genes simply act as passive
templates for transcription and replication with their rates controlled by other
regions of DNA such as promoters, enhancers, and silencers (Fig. 12.22 ). The idea
that structural genes possess the capacity to regulate the intracellular concentration
of their own transcripts (as proposed in Sect. 12.9 ) is novel to the best of my
knowledge (Ji et al. 2009c).
If structural genes are to regulate their own transcript levels (through mechanisms
discussed in Table 12.8 ), they must dissipate free energy, since no control of any kind
is possible without dissipating free energy (Hess 1975). This means that structural
genes must be able to store energy as well as control information . Structural genes,
being DNA segments, can store mechanical energy in the form of conformational
strains as exemplified by DNA supercoils (Benham 1996a), which are examples of
conformons (Sect. 8.3 ). Since any material entity possessing both the control

Table 12.8 The energy-dependent self-regulatory powers of structural genes of budding yeast
observed during glucose-galactose shift. The slopes were read off from the diagonal lines of
the first six plots in Fig. 12.21 . The self-regulatory powers were calculated from the slopes using
Eq. 12.22

Self-regulatory
power ( 100) Function of RNA Slope

1. Drug resistance Early 5.53 18.1 90% "

Late 2.91 34.4

2. Endocytosis Early 3.96 25.3 162% "

Late 1.51 66.2

3. Lysine biosynthesis Early 16.18 6.2 53% "

Late 10.49 9.5

4. Autophagy Early 12.47 8.0 128% "

Late 5.48 18.2

5. Glucose repression Early 40.20 2.5 92% "

Late 20.91 4.8

6. Heme biosynthesis Early 13.88 7.2 28% #

Late 19.29 5.2