From: <complex-science@necsi.org> (Sungchul Ji)
Sender: <y3list1@necsi.org> (Yaneer Bar-Yam)
To: complex-science
Date: Wed, 06 Aug 2008 23:27:43 -0400
Message-ID: <redirect-22520615@necsi.org>
Subject: Watson-Crick and Prigoginian forms of genetic information
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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.

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?

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.