Towards a Category Theory of Everything (cTOE) - Molecular Theory of the Living Cell - page 619

Table 21.1 A comparison among different theories of life
Self-
reproducing
system

Generalized
Franck-Condon
principle

Molecular
machine

Genetic
information

Chemical
reaction

1. Schr odinger

(1943)

€ + +

2. Prigogine (1977) + +

3. Blumenfeld and
Tikhonov (1994)

+ + + +

4. Alberts (1998) + +

5. This topic (2011) + + + + +

The meaning of the symbols: + ¼ “is included at least implicitly,” ¼ “is not included explicitly

or implicitly”

If I had to summarize my own answer to the question “What Is Life?” in one
sentence, I would suggest that the following is one possibility:
Life is the property of self-reproducing systems composed of molecular machines driven by
chemical reactions under the control of genetic information.

(21.1)

There are five key concepts in Statement 21.1, i.e., (i) self-reproduction , (ii)
molecular machines (Alberts 1998), (iii) chemical reactions (Prigogine 1977, 1980,
1991), (iv) genetic information , and (v) one fundamental principle, the generalized
Franck-Condon principle , which enables molecular machines to utilize the free
energy supplied by chemical reactions (see Sect. 2.2 ). Not all of these five items
appear in any of the contemporary theories of life listed in Table 21.1 , to the best of
my knowledge.
The theory of life presented in this topic contains all of the five items in
Table 21.1 and the theory proposed by Blumenfeld and Tikhonov (1994) contains
four of the five items. One difference between the theory of Blumenfeld and
Tokhonov and that proposed in this topic is the generalized Franck-Condon princi-
ple (GFCP) with the discussion of which this topic began (see Sect. 2.2 ). Please
recall that it is this principle that enables proteins to transduce chemical energy into
mechanical energy of enzymes, called conformons (Chap. 8 ) which then drive all
the functions of molecular machines including DNAs and RNAs (see Sects. 11.3 ,
11.4 , 11.5 ).
In the following excerpt, Blumenfeld and Tikhonov (1994) point out that, to
explain the functioning of molecular machines (Alberts 1998), it is necessary to
apply principles other than those of classical statistical physics, although the
authors did not indicate the nature of such new principles.
... It has become fashionable today to speak of the machine-like behavior of enzymes,
intracellular particles (e.g., ribosomes), etc., during their functioning. The phrases “a protein
is a machine”, “an enzyme is a machine” are now trivial clich´s, and at the same time remain
vague. The main reason for this is the very approach used by the majority of scientists in the
treatment of the chemical properties of biopolymers. In spite of speculation regarding
the “machineness” of proteins, they apply, as a rule, to the conventional approaches of
chemical thermodynamics and chemical kinetics that have been developed for the reactions
of low-molecular (weight; my addition) compounds in gaseous phases and dilute solutions.