Why Is the Cell So Complex? - Molecular Theory of the Living Cell - page 580

30% 30% 40%

S. cerevisiae

Coding DNA 'C/R Hybrid DNA' Regulatory DNA

3% 97%

H. sapiens

Fig. 17.2 A schematic representation of the hypothesis that 40% of the budding yeast genome is
both protein-coding and transcription - regulatory DNA , or the self-transcribing DNA. C ¼ coding;

R ¼ regulatory; C/R ¼ coding/regulatory hybrid

be provided if we assume that about 40% of the yeast genome has a dual role, that
is, protein-coding and transcription-regulatory (see Fig. 17.2 ). We may refer to
this assumption as the “Coding/Regulatory Hybrid DNA (CRHD) hypothesis” or
the “Self-Transcribing Structural Genes (STSG)” hypothesis, since “self-tran-
scribing” would require a structural gene to both encode RNA and control its
transcription level. The concept of the “structural genes regulating their own
transcript levels” (Sect. 12.9 ) was invoked in (Ji et al. 2009c) based on the
microarray evidence that nucleotide sequences of structural genes co-regulate
(with other regulatory regions of DNA) the intracellular levels of their transcripts
probably through Steps 4 and 5 in Fig. 12.22 . According to this view, the yeast
genome is 30% coding, 30% regulatory, and 40% both coding and self-regulating
(Fig. 17.2 ). In contrast, the human genome is 3% protein-coding and 97%
regulatory and coding, since the latter, although not coding for proteins, does
code for DNA for self-replication. Hence, most of the genomic DNA in humans
can be viewed as coding/regulatory hybrid regions.

17.3 The Fourfold Complexities in Physics and Biology

In Sect. 2.3.5 , we discussed two distinct types of complementarities in physics
as suggested by Murdoch (1987, p. 80). This idea is represented in the row
labeled Physics in Table 17.4 . The wave-particle complementarity is thought to
belong to ontology (the study of being) while the kinematics-dynamics complemen-
tarity belongs to epistemology (the study of knowledge). These dual complementary
relations are thought to reflect the well-known dual dichotomies of discontinuity
versus continuity and global versus local that contribute to the complexity of material
systems in physics. It is suggested here that the same set of dichotomous or comple-
mentary categories contribute to the complexity of living systems. Examples belong-
ing to these four categories of classification are given below the last row in
Table 17.4 .