Cell Language Theory, The: Connecting Mind And Matter

352 The Cell Language Theory: Connecting Mind and Matter

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

A visual inspection of Figure 8.6(g) (reproduced from Figure 1 in [480])

indicates that the number of the 7-mers that occurred only once in the

genome is about 0.002 × 16,384 = 33, while the number of those that

occurred about 20 times in the genome numbered 0.025 × 16,384 = 410.

As evident in Figure 8.6(g), the 7-mer frequency distribution in P. abyssi

fits PDE, again indicating the molecular mechanisms underlying the fre-

quency determination of the 7-mers in P. abyssi are nonrandom but regu-

lated to the extent of 0.87 bits (Table 8.1) of Planckian information (see

Section 8.5 for the definition of the Planckian Information, IP) was utilized

per the frequency-determining action, equivalent to selecting 1 out 20.87 =

1.84 choices or 100 out of 184 (see Table 8.1, row g, last column).

The 7-mer (i.e., DNA words consisting of seven nucleotides [480])

frequency distribution in P. abyssi fits PDE (Figure 8.6(g)), indicating that

the nucleotide sequences of the 7-mers are nonrandom and hence are the

results of some selection processes.

8.3.8 Codon Usage Profile in the Human Genome (Figure 8.6(h))

There are 64 codons in all organisms, of which 61 code for 20 amino

acids. Hence, on average, about three codons encode one amino acid,

although the actual numbers vary from one to six in the human genome.

In addition, not all the codons encoding an amino acid are utilized with

equal probability — some are utilized more frequently than others, thus

giving rise to the phenomenon of the “codon usage bias” (see the left-most

two columns in Table 8.2). A codon profile is a record of the preferred use

of the four bases at the three positions inside the codon [347] (see the four

columns on the right-hand side of Table 8.2).

As shown in Figure 8.6(h), the codon profile distances of transcripts

from average codon bias is distributed nonrandomly [347] and fits PDE,

indicating that the codon profile is determined by some as-yet-unidentified

selection mechanisms in the living cell.

8.3.9 Protein-Length Frequency Distribution in H. influenza

(Figure 8.6(i))

The protein size (i.e., length) frequency distribution [481] is Planckian,

indicating that the protein lengths in living cells are determined not

b2861_Ch-08.indd 352 17-10-2017 12:09:15 PM