Biology Reference
In-Depth Information
Table 11.5 An analysis of
the DNA-book-of-life
metaphor. The symbols p-, r-,
and d- in the last row stand for
protein, RNA, and DNA,
respectively
Ordering
information
Information
processor
Words
Book
Dictionary
Author's brain
Author/reader
DNA
Coding
regions:
”Lexical
Genes”
(Ji 1999b,
2002a)
drp-genes
(this topic)
Noncoding
regions:
Semantic genes
(Ji 1999b, 2002a)
dr- and d-genes
(this topic)
The cell
absent in the topic he produced. In other words, what are necessary to produce a
topic are words and the author's literary skills , since words alone cannot self-
arrange into a topic. The interesting question that arises is: What in DNA
corresponds to the author's literary skills? Based on then-available data it was
conjectured in Ji (1991, 1997a, b, 1999b, 2002b) that the information required to
order gene expression in time and space is encoded in the so-called noncoding (or
silent) regions of DNA that do not code for proteins. It should be pointed out that
space and time are postulated to be inseparably linked on the molecular level in
cells due to Brownian motions and the operation of the generalized Franck-Condon
principle discussed in Sect. 2.2.3 and in Ji (1991, pp. 52-56). These and related
ideas are summarized in Table 11.5 .
The so-called regulatory RNA molecules recently reviewed by Mattick (2003,
2004) can be viewed as indirectly supporting the concept of spatiotemporal genes
that was postulated in 1991 to be located in non-protein-coding DNA (Ji 1991),
although I was not aware then that at least a part of such non-protein-coding DNA
could code for regulatory RNAs (cf. dr-genes). The spatiotemporal gene hypothesis
formulated in Ji (1991) can now be updated as follows:
DNA molecules contain drp-, dr-, and d-genes that are located, respectively, in:
(1) Protein coding regions (1-3% of the total DNA mass in humans [Mattick 2004])
(2) RNA coding regions (~30% of the total human DNA mass)
(3) DNA-coding regions (the total human DNA mass)
The term “DNA-coding genes,” or d-genes, is self-referential, since DNA itself, without
being first transduced to RNA, is postulated to transmit genetic information as during the
replication step of the cell cycle. The d-genes include cis-regulatory regions, enhancers, and
silencers as already indicated above (Tjian 1995). It is further postulated that drp- and dr-
genes primarily encode equilibrium structures and d-genes primarily encode dissipative
structures consisting of conformationally deformed DNA.
(11.4)
Statement 11.4 will be referred to as the postulate of the “triadic overlapping
genomic architecture TOGA),” the triadicity stemming from the trichotomy
of the drp-, dr-, and d-genes and “overlapping” referring to the fact that drp genes
code for DNA, RNA, and proteins and dr genes code for DNA and RNA. Statement
11.4 clearly is a “spatiotemporal gene” hypothesis, because the drp- and dr-genes
carry spatial (or geometric) information specifying protein and RNA structures,
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