Biology Reference
In-Depth Information
Proteins are related to their objects
iconically
due to their complementary
molecular shapes and
indexically
due to the postulated requirement for converting
virtual conformons to real conformons during binding processes, as required by
illustrated by the arbitrary relation between the primary and tertiary structure of a
protein as summarized in the
postulate of the unpredictability of the 3-D protein
is provided by the arbitrariness of the rate constants of the chemical reaction
catalyzed by an enzyme, as exemplified by the single-molecule enzyme kinetics
of cholesterol oxidase discussed in Sect.
11.3
(see Fig.
11.18
).
In the
biochemicalese
, biochemicals are viewed as molecular signs (also called
first messengers) and their objects can be receptors, second messengers, or gene-
directed molecular processes that they trigger. The iconicity and the indexicality of
the relations between first messengers and their cognate receptors are clear from the
previous examples given in connection with the proteinese. The symbolicity of the
relation between first messengers and the gene-directed intracellular processes is
exemplified by the two opposite processes triggered by the same ligands, depending
on cell types, as shown in the bottom four rows in Table
11.3
.
When, say, a smooth muscle cell chooses to contract rather than relax when
acetylcholine binds to its cell membrane receptors, what dictate the choice is not
any thermodynamic changes resulting from ligand-receptor interactions but rather
the cell states; smooth muscle cells contract while cardiac muscle cells relax, which
reflects the history of biological evolution. Thus physical systems follow the laws of
physics and chemistry (including thermodynamics) but living systems follow in
addition the rules of biological evolution, most likely to increase the probability of
reproduction. This is consistent with what H. Pattee (2001, 2008) refers to as the
principle of matter-symbol complementarity.
Table
11.3
exemplifies the utility of Peircean semiotics in differentiating
between physical systems and biological ones:
1. Molecules in physical systems act as iconic and/or indexical signs, whereas those
in living systems act as symbolic signs in addition to iconic and indexical signs.
2. Iconic and indexical signs obey the laws of physics and chemistry.
3. Symbolic signs obey the rules (or codes) forged by evolution, which allows
arbitrariness or
freedom within
(not beyond) the constraints of the laws of
physics and chemistry (e.g., see “phenotypic freedom with genotypic
constraints” discussed in Sect.
12.10
).
11.2.4 Three Kinds of Genes: drp-, dr-, and d-Genes
The new concept of genes (as dissipatons and functions as defined in Fig.
11.5
and
Statement 11.1) views the traditional conception of genes (as protein-coding DNA
segments) as projections of the functional genes onto the three-dimensional Euclid-
ean space. Since DNA can serve as the template for self-replication, the DNA
