Whole Cells - Molecular Theory of the Living Cell - page 462

Table 12.16 The
syntagmatic ( row )
and paradigmatic ( column )
in human language

Meaning Subject Verb Object

Sentence 1 He loves her

Sentence 2 I saw a play

Sentence 3 She adores him

Sentence 4 The university fired him

Table 12.17 The paradigmatic ( row ) and syntagmatic relations ( column ) in cell language. The
question mark indicates the protein predicted to exist in vertebrate cells in analogy to the protein
found in S. cerevisiae (Seger and Krebs 1995). See Fig. 12.36 for a more complete description of
the MAPK signaling cascade

Meaning (i.e., A, B, C or D
in Fig. 12.36 ) MAPKKK (or MAP3K) MAPKK (or MAP2K) MAPK

MEKK MEK 1/2 ERK 1/2 Growth, proliferation, etc.

Raf-1 MEK 1/2 ERK 1/2 Growth, proliferation, etc.

MOS MEK 1/2 ERK 1/2 Growth, proliferation, etc.

?? RKK RK Growth, proliferation, etc.

Table 12.18 Structural and functional comparison of protein language (p roteinese ) and human
language ( humanese )
Level of organization Proteinese (A) Humanese (B) Function (C)

1. Primary Amino acids Phonemes Units of communication

2. Secondary Functional domains Morphemes Units of meaning

3. Tertiary Folded polypeptides Words Units of denotation

4. Quaternary Protein complexes Sentences Units of judgment

5. Quintic Protein networks Texts Units of reasoning or computing

The paradigmatic relation is obtained between two or more words that can
occupy the same syntagmatic position in a sentence. Thus all the words appearing
within a column in Table 12.16 are related paradigmatically . Some examples of the
paradigmatic relation as applied to the MAP kinase signal transduction pathway are
given in the columns in Table 12.17 , along with examples showing the syntagmatic
relations given in the rows of the same table.
It is possible that, depending on the environmental conditions, an extracellular
signal (or a first messenger) can trigger more than one series of protein-protein
interactions (or molecular sentences) thereby activating a molecular text, which is
an example of a third articulation. The postulated biological functions of the first,
second, and third articulations are discussed in Table 12.18 in terms of the protein
molecular language.
Although proposed more than a decade before the cell language theory (Ji 1997a),
which has proven to provide a sound theoretical foundation for signal transduction ,
the Bhopalator model of the cell (Ji 1985a, b, 2002b) appears to be capable of acting as
the signal transduction machinery described in Fig. 12.36 . The 20 steps constituting
the Bhopalator can be roughly grouped into 6 steps of the signal transduction machin-
ery as shown in the lower right-hand corner of Fig. 12.37 .