Re: [Fis] Informatics of DNA (Sungchul Ji)

[Karl Javorszky]

Dear Professor Sungchul Ji,



Thank you for your discussion of the matter of information transmission by
means of the DNA. You point out that men and mice have differing gene
sequences. Then you work on results obtained by using microscopes and
solvents. Your chain of thought is based on empirical facts.

We have explored a different approach to the same question. The search for
a consistent explanation happens in our case less on observed facts, but
uses pencil and paper.

We assume that a sequence and a multidimensional entity interact. The main
problem appears to be that the sequence is longitudinal to a line of a
temporal nature, while the organism happens concurrently, like across the
time flow dimension. The logical symbols that describe the DNA are
sequenced consecutively, while the logical symbols that describe the
organism are commutative.

The information theoretical problem is that with capacity and
differentiation. Obviously, the information content that is contained in
the sequence is copied unto the information receptors in the set that is
contemporary. This is true in both directions, as we know that the organism
is able to replicate itself by copying its logical description unto a
sequence which stores the information content of her or his genetic
material. We have two processes of copying a content from a medium of
storage unto a different medium of storage and back again. The target of
the copy process must possess at least such a capacity of storage as the
source sends, otherwise something would get lost. We observe a dyade here,
of which both partners have to be bigger than the other: this unusual
requirement merits a closer study.

To answer this question, it was necessary to count, how many sequences can
exist at all. This would give the number of all possible creatures
generated by our idealised understanding of genetics. The next step is to
count how many multi-dimensional entities can exist in the same moment, at
the most. The answer to this is taught in the books about test theory: as
many ways are there to segment a population according to test results as
there are ways to validate a test on a population.  The idea is to count
the ways symbols can be attached to objects, and of course there are as
many ways to partition a collection from – to as there are to – from.

When looking at a collection of *n* objects, there are a number of ways to
look a *sequence *into the objects, and there are a number of ways to look
a *commutative collection *into the same objects. These two upper limits
determine, how many different sequences can point out how many organisms,
in dependence of how many objects are used to simulate the interactions.
Sometimes one set is bigger than the other, sometimes it is the other one
that is bigger. So far, the riddle of being copied and containing the copy
is solved.

The main innovation is however that we can use the fine filaments that
connect the past with the present and the present with the future. Cycles
have been found to play an extremely important role, by non-empiric
methods. There is a property to natural numbers which has not been utilised
so far. The natural numbers order themselves in filaments during changes
affecting the set, and the web these filaments weave is the stage on which
the action of exchanging information into spatial-chemical arrangements is
being performed.

The profession of number theoreticians would have died out long ago, if
there did not come up from time to time someone from that trade with a
really useful algorithm. We have developed numeric tables using which the
methods of producing differing more-dimensional commutative assemblies
quasi-bijective to changes in sequences can be easily read off. The tool
you may find practical for your further research is at your disposal,
esteemed Professor.

2017-11-29 20:15 GMT+01:00 Karl Javorszky :

> Dear Professor Sungchul Ji,
>
>
>
> Thank you for your discussion of the matter of information transmission by
> means of the DNA. You point out that men and mice have differing gene
> sequences. Then you work on results obtained by using microscopes and
> solvents. Your chain of thought is based on empirical facts.
>
>
> We have explored a different approach to the same question. The search for
> a consistent explanation happens in our case less on observed facts, but
> uses pencil and paper.
>
>
> We assume that a sequence and a multidimensional entity interact. The main
> problem appears to be that the sequence is longitudinal to a line of a
> temporal nature, while the organism happens concurrently, like across the
> time flow dimension. The logical symbols that describe the DNA are
> sequenced consecutively, while the logical symbols that describe the
> organism are commutative.
>
>
> The information theoretical problem is that with capacity and
> differentiation. Obviously, the information content that is contained in
> the sequence is copied unto the 

[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:


*12 3  45
   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 

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