The Living Cell - Molecular Theory of the Living Cell - page 266

5. Through the two mechanisms described in (4), the environment of the cell can
cause the two types of changes in DNA - (1) changes in nucleotide sequences
( genetics ), and (2) changes in the three-dimensional structure of DNA includ-
ing covalent modification of bases and DNA-binding proteins without changing
its nucleotide sequence ( epigenetics ; Riddihough and Zahn 2010; Bonasio et al.
2010).
6. There are two types of environment-induced genetic and epigenetic changes
described in (5) - (1) heritable from one cell generation to the next, and (2)
nonheritable . Heritable genetic changes are well known in biomedical sciences
(Mundios and Olsen 1997; Chu and Tsuda 2004). Environment-induced heri-
table epigenetic changes (EIHEC), well established experimentally, is known
as Lamarckism or lamarckian (Ji 1991, p. 178, Jablonka 2006, 2009) and may
play a fundamental role in both phenotypic plasticity and evolution itself
(West-Eberhard 2003).
7. There are two types of environment-induced heritable epigenetic changes
(EIHEC) - (1) rapid with the time constant , comparable to or less than the

life span of organisms, and (2) slow with the time constant

t

', comparable to the

t

lifespan of species (say, 10 2

or greater) and to geological times. The study
of rapid EIHEC constitutes a major part of developmental biology and pheno-
typic plasticity, whereas the study of slow EIHEC is a newly emerging aspect
of biological evolution (West-Eberhard 2003).
8. The causes of cell functions, that is, the factors that affect cell functions directly
or indirectly, can be identified with the directed arrows in Fig. 10.1 , either
singly or as groups of two or more arrows.
9. The causes of cell functions divide into two types - (1) external causes or
environment (e.g., temperature, humidity, salinity, pressure, radiation, environ-
mental chemicals including nutrients), and (2) internal causes , namely, DNA,
RNA, proteins, and/or IDSs.
10. The internal causes of cell functions may be divided into at least three groups -
(1) the proximal (IDSs in Fig. 10.1 ), (2) the intermediate (proteins and RNA),
and (3) the distal causes (DNA). The external causes of cell functions may be
similarly divided. Thus, the living cell, as modeled in the Bhopalator 2011,
embodies a complex web of both internal and external causes that interact with
one another. Such complex systems of interactions may be difficult to analyze
and discuss without the aid of the visual diagram provided by the Bhopalator
2011, that is, Fig. 10.1 .
11. The system of the unidirectional arrows constituting the Bhopalator model
of the living cell symbolizes orderly, nonrandom motions/movements of
biopolymers and their associated small molecules inside the living cell (e.g.,
active transport of ions across cell membrane mediated by membrane ion
pumps, RNA polymerse movement along DNA, myosin movement along
actin filament, kinesin and dynein movement along microtubules, and chromo-
some remodeling). According to the Second Law of Thermodynamics (Sect.
2.1.4 ) , no orderly motions such as these are possible without dissipating
requisite free energy, and this free energy dissipation is postulated to be

t