From: <complex-science@necsi.org> (val bykovsky)
Sender: <y3list1@necsi.org> (Yaneer Bar-Yam)
To: complex-science
Date: Mon, 18 Aug 2008 01:32:40 -0400
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Subject: Re: Watson-Crick and Prigoginian forms of genetic information
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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.