Why Is the Cell So Complex? - Molecular Theory of the Living Cell - page 582

or, more accurately, the Liformation-Mattergy Complementarity (Sect. 2.3.1 ) .
Just as the early twentieth-century physics saw heated debates between the supporters
of the particle- versus the wave-views of light, which remains incompletely resolved
(Plotnitsky 2006; Bacciagaluppi and Valenti 2009), I predict that biology, as
it matures as a science, will experience similarly heated controversies surrounding
the definition of life between two complementary views - the cybernetic/informatic
(e.g., gene-centric) view of life and the thermodynamic/energetic (e.g., process-
centric) view. Again just as the wave-view of light was dominant throughout the
modern history of physics until the particle-view gained support from Einstein's
theory of photoelectric effect published in 1905, the gene-centric view of life has
been dominatingmolecular biology for over half a century now (since the discovery of
the DNA double helix in 1953) with little or no attention given to the alternative
process-centric view . The characteristics of the gene-centric view of biology is
that most, if not all, biological phenomena can be satisfactorily accounted for in
terms of genes, static nucleotide sequences in DNA (Sect. 11.2 ). In contrast, the
process-centric approach to biology (e.g., see Sect. 10.2 ) maintains that genes are
necessary but not sufficient to account for life and that genes and their RNA and
protein products must be coupled to exergonic chemical reactions (processes) through
thermal excitations (Sect. 12.12 ) and the Franck-Condon mechanisms (Sect. 2.2.3 )
before living phenomena can be completely explained (see Fig. 14.7 ).
One example of the conflict between the gene-centric and process-centric views
in biology is provided by the field of microarray data interpretation:
Most biologists believe that RNA levels in cells measured with microarrays can be used to
identify the genes of interest. But careful analyses (Ji et al. 2009a) have revealed that these
changes in RNA levels cannot be used to identify the genes of interest but reflect the
different ways in which transcription and transcript degradation processes are coupled or
interact in the cell. (17.6)
Statement 17.6 is reminiscent of the famous wave-particle debate or paradox in
physics in the early decades of the twentieth century and hence may be viewed as a
species of what may be referred to as the “structure-process paradox in biology”
(SPPB) or the “structure-process conflation in biology” (SPCB). My students at
Rutgers and I have examined over 100 prominent papers reporting the results of
DNA microarray experiments and found that over 90% of these papers have
committed SPCB, that is, the authors conflated transcripts (structures) and tran-
scription (processes) rates (Sect. 12.6 ). The structure-process conflation may be
related to the quality-quantity duality discussed in Sect. 17.7 below.
17.6 The Universal Law of Thermal Excitations
and Biocomplexity
In Sect. 12.12 , evidence was presented indicating that thermal excitations of
biopolymers are implicated in single-molecule enzymology, whole-cell metabolism,
and protein stability, thus establishing the fundamental role that thermal motions