[Fis] Informatics of DNA

Thu Nov 30 14:35:50 CET 2017

Dear Sungchul,

1. I highly appreciate your informational parsing on cell language and the comparative study of cell language and human language. By the end of last century, the main topics of (Human) Linguistics have been basically completed. It is not known whether human language study can get any inspiration from cell language study.

2. What kind of information definition and principle(s) have you got from the cell language study? To what extent are they applicable to other information fields? Exactly, your conclusions are mainly from the analysis of genetic cell. Among the biological information, the second major field of information application is neural cell. Are they effective in Neuroscience?

3. At the macro level, in your seven (six) steps of information flow scheme, we can consider all the content as "cell information / genetic information". But on the step 6, what you call it: Cell Functions→Human Behaviors, they transform cell information / genetic information into human information. If some information can be understood by a cell, it must not be understood by a (human) brain, and vice versa. How do you think of it?

4. In your information flow scheme of DNA→pre-mRNA→mRNA→proteins→IDS→Cell Functions→Human Behaviors, should the leftmost DNA be molecule? So far, we have seen that many researches thought that there are communication between molecules. From your research experience, are there any real examples of information communication took place between molecules?

5. Before 1952, the concept of "information" was rarely used in the works of Genetics. After Molecular Genetics, or after Crick's "central dogma", in Genetics research, many places used to use "gene" were replaced by "information". Do you think is it feasible to replace all "gene" with "information" completely at last?

Best wishes,

Xueshan

From: fis-bounces at listas.unizar.es [mailto:fis-bounces at listas.unizar.es] On Behalf Of Pedro C. Marijuan
Sent: Wednesday, November 29, 2017 9:41 PM
To: 'fis' <fis at listas.unizar.es>
Subject: [Fis] Informatics of DNA (Sungchul Ji)

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> 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  conservedtranscriptional response to adversity (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 anti-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 acid in 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 Table 1. 

.....

Sungchul Ji  <mailto:sji.conformon at gmail.com> <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

-------------------------------------------------
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 <mailto:pcmarijuan.iacs at aragon.es> 
http://sites.google.com/site/pedrocmarijuan/
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