Subcellular Systems - Molecular Theory of the Living Cell - page 292

at a time for the convenience of thought, but in reality they may all represent
different aspects of the one and the same phenomenon we refer to as protein
folding.
It is interesting to note that the triadic model of protein folding depicted in
Fig. 11.2 is consistent with the protein folding mechanism deduced from an entirely
different direction, namely, based on the principle of constrained freedom , the
molecular version of the linguistic principle known as the rule-governed creativity
(see Sect. 6.1.4 ).
11.2 What Is a Gene?
11.2.1 Historical Background
Prior to 2007, when the results of an international research effort known as the
ENCODE (Encyclopedia of DNA Elements) Project was announced, the definition
of gene was simple: DNA segments encoding RNAs leading to protein synthesis
(Gerstein et al. 2007). But the ENCODE project has revealed numerous findings that
cannot be readily accommodated by such a simple conception of a gene, and a new
definition of a gene is called for. The failure of the pre-ENCODE conception of a
gene may be traced ultimately to the following fact: Biologists have been measuring
the functions of genes (which belong to the class P of processes) and reduced the
results to nucleotide sequences of DNA (which belongs to the class S of static
structures) without specifying requisite mechanisms (which belongs to the class M
of mechanisms) . To stimulate discussions, such approaches in biological research
where P is erroneously inferred from S alone may be referred to as the P-to-S
reduction error . One way to resolve the problems revealed by the ENCODE project
is to postulate that there are two equally important classes of genes - the S-genes and
P-genes. The former is identified with the pre-ENCODE conception of genes (also
called the Watson-Crick genes [Ji 1988]) and the latter is a new class of genes called
the Prigoginian genes (Ji 1988). S-genes are analogous to sheet music (or written
language) and P-genes are analogous to audio music (or spoken language) (see
Fig. 11.3 ). Just as the sheet music is converted into audio music by a pianist, so
are the Watson-Crick genes postulated to be transduced into Prigoginian genes by
molecular motions driven by conformons, the sequence-specific conformational
strains of enzymes (Chap. 8 ) . Thus, conformons in biology may be analogous to
the de Broglie equation in quantum physics, since mechanisms based on conformons
can convert structure (S-genes) to processes (P-genes) in cells, just as the de Broglie
equation can convert the particle-like properties of moving objects to their wave-like
properties (Herbert 1987; Morrison 1990). If this analogy is true, it may be predicted
that conformons will resolve the structure-process paradox in molecular cell biology
in the twenty-first century just as the de Broglie equation resolved the wave-particle
paradox in particle physics in the twentieth century.