Sung,
It is always a pleasure to read your very logical comments.
Let's try to place your logic in a "wider" context though.
(Sungchul Ji) wrote:
There is no doubt that cells are capable of transmitting information in
space (e.g.,from the nucleus to the cytosol and to the adjacent cells) and
in time (e.g., from one cell generation to the next in developing
organisms or from one population of organisms to next in evolution).
The molecular mechanisms underlying the information transmission in time
(i.e., through transfer of DNA sequences) has been well established
throughout the latter half of the 20th century following the discoveries
of the double helical structure of DNA by Watson and Crick in 1953 and
the genetic code in the 1960's. But the mechanisms responsible for the
information transmission through space has not been widely discussed in the
biological literature, despite the fact that the relevant experiments have
been vigorously persued, for example, in the fields of cell-cell
communications and signal transduction pathways in individual cells.
Consequently, the contemporary concept of genetic information (i.e., genes) has been, it seems to me, unjustifiably biased in favor of the time
dimension at the sacrifice of the spatial dimension. The main purpose of
this post is to contribute to righting this bias, with the hope of
defining genes in a more realistic manner for the post-ENCODE
(Encyclopedia of DNA elements) genomics.
It seems to me that even within that *highly simplistic* model there were both temporal *and* spatial components; indeed, the gene-controlled synthesis of proteins is the *sequence* of events in time *and* in space - as any synthesis of mol. structures in chemistry. So, to me, the "information transmission" in chemistry is always a process in space and in time.
In 1988 [1] I proposed that there are two types of genetic information in
the cell -- the traditional sequence-centered information (referred to as
the Watson-Crick form) and the new, dynamic information encoded in
concentration waves such as ion gradients and time-dependent RNA levels in
the cell (referred to as the Prigoginian form). The Prigoginian form of
genetic information (or Prigoginian genes, for short) can be identified with "intracellular dissipative structures" (IDSs), the final form of
gene expression according to the Bhopalator model of the cell [2]. In [1]
I have proposed the following ideas:
1) Watson-Crick genes => information transmission in time
2) Prigoginian genes => information transmission in space,
where "=>" means "is responsible for" or "can mediate".
Examples of information transmission in space and time are familiar to us
through music and languages:.
1) Information transmission in time = Sheet music; written languages
2) Information transmission in space = Audio music; spoken languages
We can summarize all these ideas in a tabular form:
Table 1. The duality of the mechanisms of information transmission
in linguistics, musicology, and cell biology.
_____________________________________________________________________
Information Transmission in
____________________________________________________
Information Space Time
Carriers
(or Signs)
______________________________________________________________________
Macroscopic Audio music Sheet music
Spoken language Written language
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Microscopic Dissipative structures Equilibrium structures
(e.g., concentration waves) (e.g., DNA segments)
(Prigoginian genes) (Watson-Crick genes)
_______________________________________________________________________
It is interesting to note that the information transmission in space
utilizes waves of sounds or concentrations, whereas the information in
space utilizes discrete material objects of either microscopic (e.g., DNA
sequences) or macroscopic (e.g., words, musical notes) dimensions. Thus,
it appears that the duality of spatial and temporal mechanisms of
information transfer ultimately depends on the duality of waves and
particles. Since DNA is a quantum mechanical object, it is not surprising
that it should exhibit both particle and wave properties.
Does anybody on this list know if a similar relation between the
space-time duality and the wave-particle duality is observed in physics?
Well, in (quantum) physics, a process, for example, a photo-induced chemical reaction of dissociation (or association) is always a spatio-temporal *and* wave-particle (quantum) phenomenon, say, the dissociation of polar molecules by slow electrons (AB+e-->A+B-).
As to your introduction of process(P) genes, in addition to structural(S) ones, well, a gene seems to be an inseparable structure *and* function - in terms of chemistry and biology. So, a gene cannot be purely S-gene as well as it cannot be purely P-gene. Correct me if im missing something here.
Sung, your analogy with sheet music is indeed nice and instructive, demonstrating implicitly the critical/creative role of the *interpretive environment*, the musician/performer. To me, in a cell, the DNA/genome is a "dead stuff", a hi-tech punch-card, being (continuously) *interpreted* by the cellular environment in terms of the spatio-temporal tune ("protein expression") which is life. [feel free to correct this speculation]
spatio-temporal-ly y'rs, val
With all the best.
Sung
Reference:
[1] Ji, S. (1988). Watson-Crick and Prigoginian forms of Genetic
Information. J.
theoretical Biology 130:239-245.
[2] Ji, S. (1985). The Bhopalator--a molecular model of the living cell
based on
the concepts of conformons and dissipative structures. J. theoret. Biol.
116:399-426.
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