[Fis] Fwd: Re: Informatics of DNA (From Sungchul)
Pedro C. Marijuan
pcmarijuan.iacs at aragon.es
Fri Dec 1 09:04:00 CET 2017
Asunto: Re: [Fis] Informatics of DNA
Fecha: Thu, 30 Nov 2017 23:33:09 +0000
De: Sungchul Ji <sji at pharmacy.rutgers.edu>
Para: FIS Group <fis at listas.unizar.es>, yxs at pku.edu.cn <yxs at pku.edu.cn>
Hi Xueshan,
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.
The concept of the third articulation that emerged in cell biology
around 2012 (the reference to be provided upon request) is useful in
understanding cell metabolism and hence perhaps in linguistics too:
1st articulation = words ----> sentences;
2nd articulation = letters ----> words;
3rd articulation = sentences ----> texts (e.g., the syllogism)
*Table 1.* The isomorphism between the human and cell languages
*Human Language *
*Cell Language *
*Function*
Letters
A. C, G, T or U
to build
Words
genes/mRNA/proteins
to denote
Sentences
metabolic pathways
to decide and judge
Texts
functional networks of metabolic pathways
to reason and compute
We recently discovered that what we came to refer to as the
"*Planck-Shannon plot*" can be used to identify the
cell-linguistic counter-parts of *sentences*and *texts*based on mRNA
data measured from, e.g., human breast tissues. I will be detailing
this finding shortly in a later post.
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?
A good question. We have not yet extended our cell-linguistic approach
to neural network. When we do, we may find evidence for higher-order
articulations such as the fourth, fifth, sixth articulations, etc.
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?
An excellent point.
I often wonder if I do understand cell information biologically but not
linguistically, i.e., I feel and communicate with every cell in my body
but cannot articulate that experience due to the limited expressive
power of human language. The study of the phenomenon of
such communication that can occur without linguistic signs has
recently been referred to as "neo-semiotics" that was formulated by
extending Peirce's semiotics by including a new category called
"Zeroness" (see the attached).
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?
According to Peirce (1839-1914), communication is irreducibly triadic.
I have found ti useful to use this definition of communication in my
research in biology. So I am currently of the opinion that whenever
there is an irreducible triadic relation, there is communication: i.e.,
f g
A ------> B ------> C
| ^
| |
|_________________|
h
*Figure 1*. A diagrammatic representation of the *irreducible triadic
relation*(ITR) or *communication.* A = source; B = message; C =
receiver; f = encoding; g = decoding; h = grouding or information flow.
There is no reason why A, B and C cannot be all molecules, e.g., A =
DNA/RNA, B = proteins, and C = chemical reactions, but this does not
mean that molecules A is communicating with molecule C, because without
the third and the rest of the communication system, no communication
would be possible.
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?
I don't think so, because all genes carry information but not all
information carriers are genes.
All the best.
Sung
------------------------------------------------------------------------
*From:* Fis <fis-bounces at listas.unizar.es> on behalf of Xueshan Yan
<yxs at pku.edu.cn>
*Sent:* Thursday, November 30, 2017 8:35 AM
*To:* FIS Group
*Subject:* Re: [Fis] Informatics of DNA
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 INFORMATIONfrom 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
<https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.thisisinsider.com%2Fcomparing-genetic-similarity-between-humans-and-other-things-2016-5&data=02%7C01%7Csji%40pharmacy.rutgers.edu%7C65e6d35da38f42a35c0608d537f75fe4%7Cb92d2b234d35447093ff69aca6632ffe%7C1%7C0%7C636476457988945872&sdata=jpAs7QGzTxeIP6qyqUV1jcjOk1OWwKERTNK8V%2FHrg0E%3D&reserved=0>
(*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 /In//tracellular
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
<https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.quora.com%2FWhy-are-ribosomes-so-important-in-plant-cells&data=02%7C01%7Csji%40pharmacy.rutgers.edu%7C65e6d35da38f42a35c0608d537f75fe4%7Cb92d2b234d35447093ff69aca6632ffe%7C1%7C0%7C636476457988945872&sdata=JWXFYri%2BEXQzF3%2B2nfzklANJlXbKYoP2sEmgk9l%2BUs8%3D&reserved=0>).
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 <sji.conformon at gmail.com> <mailto: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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