Biology Reference
In-Depth Information
Table 6.3 A
formal
comparison between human and cell languages (Ji 1997a, 1999b)
Human language (
humanese
)
Cell language (
cellese
)
1. Alphabet (L)
Letters
4 Nucleotides (or 20 amino acids)
2. Lexicon (W)
Words
Genes (or polypeptides)
3. Sentences (S)
Strings of words
Sets of genes (or polypeptides)
expressed (or synthesized)
coordinately in space and time
dictated by DNA folds
a
(cell states)
4. Grammar (G)
Rules of sentence formation
The
physical laws
and
biological rules
mapping DNA sequences to
folding patterns of DNA
(polypeptides) under biological
conditions
b
5. Phonetics (P)
Physiological structures and
processes underlying
phonation, audition, and
interpretation, etc.
Concentration and mechanical waves
responsible for information and
energy transfer and transduction
driven by
conformons
c
and
intracellular dissipative structures
(IDSs)
d
6. Semantics (M)
Meaning of words and
sentences
Codes
mapping molecular signs to
gene-directed cell processes
7. First articulation
Formation of sentences
from words
Organization of gene expression
events in space and time through
non-covalent interactions
e
between
DNA and proteins (or Space- and
time-dependent non-covalent
interactions among proteins, DNA,
and RNA molecules). Thus,
macromolecular complexes can be
viewed as molecular analogs of
sentences
8. Second
articulation
Formation of words from
letters
Organization of nucleotides (or amino
acids) into genes (or polypeptides)
through covalent interactions
f
9. Third articulation
Organization of chemical
concentration gradients in space
and time called
dissipative
structures
(Babloyantz 1986;
Kondepudi and Prigogine 1998)
order to “reason” and “compute”
g
a
Just as verbal sentences (as written) are strings of words arranged linearly in the Euclidean space,
so the cell-linguistic (or molecular) sentences are visualized as series of gene expression events
b
Of all the folds of DNA and polypeptides allowed for by the laws of physics and chemistry, only
small subsets have been selected by evolution (thereby giving rise to
biological information
)to
constitute the gernome of a cell
c
Sequence-specific conformational strains that carry both free energy (to do work) and genetic
information (to control work) (Ji 1974a, 2000) (Chap.
8
). Conformons are thought to provide
immediate driving force (or serve as the force generators) for all nonrandom molecular processes
inside the cell. Experimental evidence for conformons is discussed in Sect.
8.3
Formation of texts from
sentences
(continued)
