[Fis] Informatics of DNA (Sungchul Ji)

[Pedro C. Marijuan]

Message from Sungchul Ji

It was too heavy for the list server. You can see the complete version at:
http://fis.sciforum.net/wp-content/uploads/sites/2/2014/11/Sung_informatics-of-DNA.pdf 


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Hi FISers,


We may have in DNA a golden opportunity to define what *information* is.

*(1)*We now know that we are different from mice because our 
DNA sequences are different from those of mice [1].  That is, we are 
different from mice because our DNA carries different kinds (both 
with respect to /quality/ and /quantity/) of INFORMATION from the mouse DNA:

           ”When it comes to protein-encoding genes, mice are 85% 
similar to humans.  For non-coding genes, it's only about 50%. The 
National Human Genome  Research Institute attributes

   this similarity to a shared ancestor about 80 million years ago.” 
http://www.thisisinsider.com/comparing-genetic-similarity-between-humans-and-other-things-2016-5

(*2*)  We also know that our properties or behaviors are at least 
in part determined by both DNA sequences (i.e., /genetics/) and the way 
they are turned on or off by environment-sensitive cells constituting 
our body (i.e., /epigenetics/): We are the products of both our 
/genes/ and our /environment/.  The causal link between DNA and our 
behaviors can be briefly summarized as follows:

*1                2                     3  4                5            
                        6***

*DNA ----> pre-mRNA -----> mRNA -----> proteins ----->  IDS -----> Cell 
Functions  -----> Human Behaviors
^ |
| |
| 
                                                                               |
| 
                                                                                         |
    |_________________________________________________________________________________|*

*7*

**

*Figure A. *The flow of genetic and epigenetic informations between 
DNA and the human behavior. IDS stands for the /Intracellular 
Dissipative Structures /(also called the /Dissipative Structures of 
Prigogine/) such as ion gradients across cell membranes and within the 
cytoplasm without any membrane barriers.  According to the Bhopalator, a 
molecular model of the living cell proposed in 1985 in a meeting held 
in Bhopal, India, IDS's are postulated to be the immediate or the 
proximal causes for all cell functions [2].  The seven steps in the 
scheme are

*1* = transcription

*2* = splicing

*3* = translation (explained in (3) in more detail.)

*4* = enzyme catalysis

*5* = cell motions

*6* = body motions
*7* = the effect of human behavior or emotion on gene expression, e.g., 
see the phenomenon of the /c//onserved//t//ranscriptional //r//esponse 
to //a//dversity/ (CTRA) [3].

I hope that the /information flow scheme/ shown in* Figure A* can 
serve as a concrete example of information inaction as 
information scientists strive to come up with a generally acceptable 
definition of what INFORMATIONis.


(*3*)  Unlike in Steps 1 and 2 where the same kinds of molecules, i.e., 
the nucleic acids, DNA and RNA, directly interact (or contact or touch 
each other) via the Watson-Crick base-paring mechanism (see the second 
row in *Figure 1* below), in Step 3, there is no such direct interaction 
between mRNA and amino acids, but rather their interactions are mediated 
by tRNA which recognizes mRNA  at  its /a//nti-codon arm/ and amino 
acids at its 3/'-acceptor stem/, about 60 angstroms away (see the blue 
region in the mechanism of translation shown at 
https://www.quora.com/Why-are-ribosomes-so-important-in-plant-cells). 
The universality of the wave-particle duality demonstrated in [4] 
suggest that the tripartite coupling  among codon, anticodon, and amino 
acidin the ribosome-mRNA-tRNA complex may be mediated by /resonant 
vibrations/ or /standing waves/ (also called /resonance/ or /resonant 
waves/) generated within the complex, just as the vibratioal patterns 
located at distant regions on the Chladni (1756-1827)  plate [5, 6] are 
coordinated via resonance.

The Chladni plate [5, 6] is an ideal model for illustrating the role of 
resonance in molecular biology.  At a given resonance frequency, the 
particles on remote regions of the Chaldni plate are coordinated without 
any direct interactions between them and yet form ordered patterns.  To 
me this is similar to what happens in the ribosome system when a peptide 
molecule is synthesized; i.e, different components of the 
ribosome-mRNA-tRNA complex execute their motions that are so coordinated 
as to achieve the peptide synthesis.   The ribosome and the Chladni 
plate are compared at several levels in*T**able 1.*

.....

Sungchul Ji <sji.conformon at gmail.com>

The message continues at:
http://fis.sciforum.net/wp-content/uploads/sites/2/2014/11/Sung_informatics-of-DNA.pdf 


-- 
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Pedro C. Marijuán
Grupo de Bioinformación / Bioinformation Group
Instituto Aragonés de Ciencias de la Salud
Centro de Investigación Biomédica de Aragón (CIBA)
Avda. San Juan Bosco, 13, planta 0
50009 Zaragoza, Spain
Tfno. +34 976 71 3526 (& 6818)
pcmarijuan.iacs at aragon.es
http://sites.google.com/site/pedrocmarijuan/
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