Hi Alex,

Thanks for raising the thought-provoking question.


According to the dual theory of information (i.e, the physical vs. semantic 
information theory (PSIT)) [1] as I understand it, there is no  "Information 
that you cannot put in a data set ".  That is, all the information discussed in 
natural and human sciences must be grounded in the physical upon which the 
semanticity (or functionality) of any structure must arise.  For example, all 
heritable traits (including the kind of sensory experiences you described) must 
be grounded in DNA structures as clearly pointed out by Petoukhov [2, 3], for 
instance.   Unlike the current textbook version of DNA viewed as a set of 
linear sequences of genes composed of just one alphabet of 4 letters, A, C. G 
and T,  my interpretation of the mathematical analyses of DNA-sequences (as 
summarized in the concept of the tetra-groups of DNA sequences [4]) carried out 
by Petoukhov [2, 3] indicates that DNA is a linear sequences of the 4 
nucleotides structured (or partitioned) into n alphabets (or languages), each 
consisting of 4^n letters, where n = 1, 2, 3, 4, 5, etc., of which we may 
currently be aware of only the simplest alphabet with n = 1.  The n = 5 
alphabet (i.e., the n^th alphabet or the n^th cell language) should consist of 
4^5 = 1,024 letters, and the n = 6 alphabet should contain 4,096 letters, etc.  
Having these multiple alphabets or molecular languages may have been beneficial 
for biological evolution, probably because they increased the information 
storage and processing capacities of the cell.   I am not a computer scientist 
but it seems to me that the situation is similar to computer scientists using 
two different alphabets -- one with 2 digits (i.e., o, 1) and the other with 
2^3 = 8 digits (i.e., 00000000, 10000000, 11000000, 11110011, . . .) in order 
to increase the information storage and processing capacities of computers.

All biological communications including cell-cell, cell-organ, cell-human, 
humnan-human communications must be mediated by messages (or signs) (i) written 
in an alphabet with n letters, where n can be 2, 3, 4, 5, 6, . . . .10^6?, thus 
having varying information storage and processing capacities, and (ii) obeying 
a set of syntactic rules  so that (iii) the sender and the receiver can 
understand the messages using a common set (or dictionary) of rules of 
interpretation.


In conlusion, my breif answer to Alex's question would be that human brains 
have evolved to perform the kind of sensory functions you describe based on 
"molecular data", not necessarily macroscopic physical or linguistic data 
employed in macrosciences and engineering.


All the best.


Sung



References:

  [1] Emanuel Diamant, The brain is processing information, not data. Does 
anybody care?, ISIS Summit Vienna 2015, Extended Abstract. 
http://sciforum.net/conference/isis-summit-vienna-2015/paper/2842<https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fsciforum.net%2Fconference%2Fisis-summit-vienna-2015%2Fpaper%2F2842&data=02%7C01%7Csji%40pharmacy.rutgers.edu%7C89f81861ee684f05e46b08d559d86fe1%7Cb92d2b234d35447093ff69aca6632ffe%7C1%7C1%7C636513708497810284&sdata=bMlZ324OoEHA5XMQibKiEFsm75NhcpkfIcSRUJbQZNg%3D&reserved=0>
<https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fsciforum.net%2Fconference%2Fisis-summit-vienna-2015%2Fpaper%2F2842&data=02%7C01%7Csji%40pharmacy.rutgers.edu%7C89f81861ee684f05e46b08d559d86fe1%7Cb92d2b234d35447093ff69aca6632ffe%7C1%7C1%7C636513708497810284&sdata=bMlZ324OoEHA5XMQibKiEFsm75NhcpkfIcSRUJbQZNg%3D&reserved=0>
  [2] Petoukhov, S. (2017).  Genetic coding and united-hypercomplex systems in 
the models of algebraic biology.BioSystems 158: 31-46.                    [3] 
Petoukhov, S. (2016).  The system-resonance approach in modeling genetic 
structures. BiosySystems 139:1-11.
   [4] Petoukhov, S. (2018). The rules of long DNA-sequences and tetra-groups 
of oligonucleotides. arXiv:1709.04943v4 [q-bio.OT]






<https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fsciforum.net%2Fconference%2Fisis-summit-vienna-2015%2Fpaper%2F2842&data=02%7C01%7Csji%40pharmacy.rutgers.edu%7C89f81861ee684f05e46b08d559d86fe1%7Cb92d2b234d35447093ff69aca6632ffe%7C1%7C1%7C636513708497810284&sdata=bMlZ324OoEHA5XMQibKiEFsm75NhcpkfIcSRUJbQZNg%3D&reserved=0>


   [4] Ji, S. (2017).Neo-Semiotics: Introducing Zeroness into Peircean 
Semiotics May Bridge the Knowable and the Unknowable. Prog. Biophys. Mol. Biol. 
 131:387-401. PDF at 
http://www.sciencedirect.com/science/article/pii/S0079610717300858?via%3Dihub<https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.sciencedirect.com%2Fscience%2Farticle%2Fpii%2FS0079610717300858%3Fvia%253Dihub&data=02%7C01%7Csji%40pharmacy.rutgers.edu%7Cd3662883d79442bc279b08d55a45ef3e%7Cb92d2b234d35447093ff69aca6632ffe%7C1%7C1%7C636514178788801408&sdata=afKjg3GrB3JRHkESNqHxOOhhjn9C%2F9%2FuJAFx6OX7%2FVs%3D&reserved=0>
   [5] Ji, S. (1997). Isomorphism between cell and human languages: molecualr 
biological, bioinformatic and linguistic implications. 
<https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.conformon.net%2Fwp-content%2Fuploads%2F2012%2F05%2FIsomorphism1.pdf&data=02%7C01%7Csji%40pharmacy.rutgers.edu%7Cd3662883d79442bc279b08d55a45ef3e%7Cb92d2b234d35447093ff69aca6632ffe%7C1%7C1%7C636514178788801408&sdata=RaGj9cNFqT4nLwPh%2BllpEgryPeou9Dm%2F6MZGEOXqA18%3D&reserved=0>
 BioSystems 44:17-39.  PDF at 
http://www.conformon.net/wp-content/uploads/2012/05/Isomorphism1.pdf<https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.conformon.net%2Fwp-content%2Fuploads%2F2012%2F05%2FIsomorphism1.pdf&data=02%7C01%7Csji%40pharmacy.rutgers.edu%7Cd3662883d79442bc279b08d55a45ef3e%7Cb92d2b234d35447093ff69aca6632ffe%7C1%7C1%7C636514178788801408&sdata=RaGj9cNFqT4nLwPh%2BllpEgryPeou9Dm%2F6MZGEOXqA18%3D&reserved=0>

    [6] Ji, S. (2017).  The Cell Language Theory: Connecting Mind and Matter.  
World Scientific, New Jersey.  Chapter 5.








________________________________
From: Alex Hankey <alexhan...@gmail.com>
Sent: Saturday, January 13, 2018 12:24 AM
To: Sungchul Ji
Cc: Emanuel Diamant; fis@listas.unizar.es
Subject: Re: [Fis] I salute to Sungchul

And what about the Kinds of Information that you cannot put in a data set?
The information that makes you turn your head and meet the gaze of someone 
staring at you.
No one could do that, which we humans and all animals do constantly,
unless we had received such information at a subliminal level in the brain.
We all have that capacity, it is vital for survival in the wild. All animals do 
it.
The 'Sense of Being Stared At' is a common experience for most animals,
how far down the tree of life no one yet knows.

Whatever triggers it is definitely 'A Difference that Makes a Difference',
so fits in your definition of 'Meaningful Information' - it has to!
BUT IT CANNOT BE DIGITAL INFORMATION.
Please Face Up to This Fact.

All best wishes,

Alex


On 13 January 2018 at 07:30, Sungchul Ji 
<s...@pharmacy.rutgers.edu<mailto:s...@pharmacy.rutgers.edu>> wrote:

Hi Emmanuel and FISers,


Thank you, Emmanuel, for your generous remarks.  It is heartening to know that 
our ideas converge, although we carried out our research independently of each 
other, a clear example of consilience.


(1)  I like and agree with the Kolomogorov quote you cited in [1]:


"Information is a linguistic description of structures in a given data set."

It seems to me that there are 4 key concepts embedded in the above quote, which 
we may view as the definition of what may be called the "Komogorov information" 
or the "Kolmogorov-Bateson information" for  the convenience of reference:

i)   data set (e.g., ACAGTCAACGGTCCAA)
ii)  linguistic description (e.g., Threonine, Valine, Asparagine, Glycine)
iii) structure (e.g., 16 mononucdotide, 8 dinucldotides, 5 trinucleotides plus 
1)
iv) mathematical description (e.g., tensor product of two 2x2 matrices of 4 
nucleotides) [2, 3].

The first three elements are obvious, but the 4th is not so obvious but 
justified in view of the recent work of Petoukhov [2, 3].

(2) Based on these ideas, I have constructed Table 1 below of the various names 
applied to the two kinds of information which I described as I(-) and I(+) in 
my previous post.







Table 1.  The arbitrariness of the signs referring to ‘information’. It doesn’t 
matter what you call it, as long as your chosen label refers to the right 
reality, thing, process, mechanisms, etc.


1


Type I Information


Type II information


2


Physical Information


Sematic information


3


Shannon information


Kolmogorov information, or

Kolmogorov-Bateson information


4


‘Meaningless’ information


‘Meaningful’ information


5


I(-) information, or simply I(-)


I(+) information, or simply I(+)


6


Quantitative information


Qualitative information


7


Mathematical information


Linguistic information (see Statement (1))


8


Formal information


Phenomenological information


9


Interpretant-less sign [4]


Triadic sign [4]




(3)  One practical application of the dual theory of information under 
discussion is in deducing the structure of cell language, or the structure of 
the linguistics of DNA, in a much more rigorous manner than was possible in 
1997 [5].

   It is the common practice in biology to use the terms "letters", "words", 
"sentences", and "texts" without any rigorous definitions.  The general rule is 
to follow the rules of concatenations used in linguistics literally and say that

i) just as 26 letters in the English alphabet are combined to form words (the 
process being called the second articulation [5]), so the 4 letters of the 
genetic alphabets, A, C, G and T/U,  combine in triplets to form genetic 
codons.  Similarly, just as words form sentences and sentences form texts by 
the same concatenation procedure (or tensor multiplication, mathematically 
speaking , i.e, linearly arranging words and sentences, respectively (see the 
second column in Table 2), so the 64 nucleotide triplets combine to form 
proteins and proteins combine to form metabolic pathways by continuing the 
concatenation process, or the tensor multiplication of matrices of larger and 
larger sizes (see the fourth column, which is based on the physical theory of 
information, i.e., without any involvement of semantics or the first 
articulation).

ii)   In contrast to the fourth column just described, we can justify an 
alternative structural assignments based on the semantic theory of information 
as shown in the fifth column of Table 2.  Here the letters of the cell language 
alphabet are not always mononucloetoides but thought to be n-nucleotides, such 
as dinucleotides (when n = 2), trinucleotides (when n =3), tetranucleotides 
(when n = 4), penta-nucelotides (when n = 5), etc.  That is, unlike in human 
language where the letters of an alphabet usually consist of one symbol, e.g., 
A, B, C, D, E, . . . , I am claiming that in cell language, the letters can be 
mononucloetides (i.e., A, G, C, T/U), dinucloeotides (i.e., AG, AC, . . . .) , 
trinucleotides (i.e., ACT, GTA,  . . . ), tetranucleotides (i.e., ACTG, CCGT, . 
. . .), pentanucleotides (i.e., ACCTG, TCGAT, . . .) and, up to n-nucleotides 
(also called n-plets [2, 3]), where n is an unknown number whose upper limit is 
not yet known (at least to me).  If this conjecture turns out to be true, then 
the size of the cell language alphabet can be much larger (10^3 - 10^9 ?) than 
the size of a typical human linguistic alphabet which is usually less than 
10^2, probably due to the limitation of the memory capacity of the human brain.

(iii) From linguistics, we learn that there are at least 4 levels of 
organization, each level characterized by a unique function (see the second 
column).  Without presenting any detailed argument, I just wish to suggest that 
the linguistic structures deduced based on the semantic information theory 
(i.e., the fifth column) agree with the human linguistic structures (i.e., the 
second column) better than does the linguistic structures based on the 
physical/mathematical/quantitative information theory (i.e., the fourth 
column), when the functional hierarchy given in the third column is taken into 
account.



Table 2.  Two versions of the linguistics of DNA based on (i) the physical 
information theory, and (ii) the semantic information theory [1]. M stands for 
a 2x2 matrix whose elements are the 4 genetic nucleotides, A, C, G and T/U, 
i.e., M = [C A; T G] (see Figure 16 in [2]). The symbol, (x), indicates tensor 
multiplication [2, 3].  The I to II transition is known in linguistics as the 
second articulation; the II to III transition as the first articulation [4]; 
the III to IV transition was referred to as the third articulation [5].


Organization  level


Human Language


Cell Language





Structure


Function/Semantics


Structure based on the Physical Information Theory (PIT) [1]


Structure based on the Semantic Information Theory (SIT) [1]


I


Letters


Basic building

blocks or basic physical signals


4 Nucleotides (A, C, G, T/U);

M = [C A;T G]*


mono-, di-, trinucleotides, 4-plets, 5-plets, . . . , n-plets of nucleotides,  
. . .


II


Words


To denote


16 dinucleotides;

M(x)M or M^2


Any combinations of the n-plets/ genes/proteins


III


Sentences


To decide


64 trinucleotides /amino acids;
M(x)M(x)M or M^3




Assembly of  genes/proteins; or metabolic pathways (MP)


IV


Texts


To argue/compute/

reason (e.g., syllogism)


254 tetranucleotides;

Metabolic pathways (?); M(x)M(x)M(x)M or M^4


Networks of MP’s


characterized by a unique function (see the second column).  Without presenting 
any detailed argument, I would like to suggest that the linguistic structures 
deduced based on the semantic information theory (i.e., the fifth column) agree 
with the human linguistic structures (i.e., the second column) better than does 
the linguistic structures based on the physical/mathematical/quantitative 
information theory (i.e., the fourth column).
In other words, the structure of cell language deduced based on the semantic 
information theory agrees better, functionally, with that of the human language 
than the structure of cell language deduced based on the physical information 
theory, thus further supporting the 1997 postulate that cell and human 
languages are isomorphic [5, 6].

If you have any questions or suggestions for improvements on the above tables, 
I would appreciate hearing from you.

All the best.

Sung

References:
   [1] Emanuel Diamant, The brain is processing information, not data. Does 
anybody care?, ISIS Summit Vienna 2015, Extended Abstract. 
http://sciforum.net/conference/isis-summit-vienna-2015/paper/2842<https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fsciforum.net%2Fconference%2Fisis-summit-vienna-2015%2Fpaper%2F2842&data=02%7C01%7Csji%40pharmacy.rutgers.edu%7C89f81861ee684f05e46b08d559d86fe1%7Cb92d2b234d35447093ff69aca6632ffe%7C1%7C1%7C636513708497810284&sdata=bMlZ324OoEHA5XMQibKiEFsm75NhcpkfIcSRUJbQZNg%3D&reserved=0>
  [2] Petoukhov, S. (2017).  Genetic coding and united-hypercomplex systems in 
the models of algebraic biology. BioSystems 158: 31-46.

  [3] Petoukhov, S. (2016).  The system-resonance approach in modeling genetic
structures. BiosySystems 139:1-11.

   [4] Ji, S. (2017).Neo-Semiotics: Introducing Zeroness into Peircean 
Semiotics May Bridge the Knowable and the Unknowable. Prog. Biophys. Mol. Biol. 
 131:387-401. PDF at 
http://www.sciencedirect.com/science/article/pii/S0079610717300858?via%3Dihub<https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.sciencedirect.com%2Fscience%2Farticle%2Fpii%2FS0079610717300858%3Fvia%253Dihub&data=02%7C01%7Csji%40pharmacy.rutgers.edu%7Cd3662883d79442bc279b08d55a45ef3e%7Cb92d2b234d35447093ff69aca6632ffe%7C1%7C1%7C636514178788801408&sdata=afKjg3GrB3JRHkESNqHxOOhhjn9C%2F9%2FuJAFx6OX7%2FVs%3D&reserved=0>
   [5] Ji, S. (1997). Isomorphism between cell and human languages: molecualr 
biological, bioinformatic and linguistic implications. 
<https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.conformon.net%2Fwp-content%2Fuploads%2F2012%2F05%2FIsomorphism1.pdf&data=02%7C01%7Csji%40pharmacy.rutgers.edu%7Cd3662883d79442bc279b08d55a45ef3e%7Cb92d2b234d35447093ff69aca6632ffe%7C1%7C1%7C636514178788801408&sdata=RaGj9cNFqT4nLwPh%2BllpEgryPeou9Dm%2F6MZGEOXqA18%3D&reserved=0>
 BioSystems 44:17-39.  PDF at 
http://www.conformon.net/wp-content/uploads/2012/05/Isomorphism1.pdf<https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.conformon.net%2Fwp-content%2Fuploads%2F2012%2F05%2FIsomorphism1.pdf&data=02%7C01%7Csji%40pharmacy.rutgers.edu%7Cd3662883d79442bc279b08d55a45ef3e%7Cb92d2b234d35447093ff69aca6632ffe%7C1%7C1%7C636514178788801408&sdata=RaGj9cNFqT4nLwPh%2BllpEgryPeou9Dm%2F6MZGEOXqA18%3D&reserved=0>

    [6] Ji, S. (2017).  The Cell Language Theory: Connecting Mind and Matter.  
World Scientific, New Jersey.  Chapter 5.








________________________________
From: Fis <fis-boun...@listas.unizar.es<mailto:fis-boun...@listas.unizar.es>> 
on behalf of Emanuel Diamant <emanl....@gmail.com<mailto:emanl....@gmail.com>>
Sent: Friday, January 12, 2018 11:20 AM
To: fis@listas.unizar.es<mailto:fis@listas.unizar.es>
Subject: [Fis] I salute to Sungchul


Dear FISers,



I would like to express my pleasure with the current state of our discourse – 
an evident attempt to reach a more common understanding about information 
issues and to enrich preliminary given assessments.

In this regard, I would like to add my comment to Sungchul’s post of January 
12, 2018.



Sungchul proposes “to recognize two distinct types of information which, for 
the lack of better terms, may be referred to as the "meaningless information" 
or I(-)  and "meaningful information" or I(+)”.

That is exactly what I am trying to put forward for years, albeit under more 
historically rooted names: Physical and Semantic information [1]. Never mind, 
what is crucially important here is that the duality of information becomes 
publicly recognized and accepted by FIS community.



I salute to Sungchul’s suggestion!



Best regards, Emanuel.



[1] Emanuel Diamant, The brain is processing information, not data. Does 
anybody care?, ISIS Summit Vienna 2015, Extended Abstract. 
http://sciforum.net/conference/isis-summit-vienna-2015/paper/2842<https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fsciforum.net%2Fconference%2Fisis-summit-vienna-2015%2Fpaper%2F2842&data=02%7C01%7Csji%40pharmacy.rutgers.edu%7C89f81861ee684f05e46b08d559d86fe1%7Cb92d2b234d35447093ff69aca6632ffe%7C1%7C1%7C636513708497810284&sdata=bMlZ324OoEHA5XMQibKiEFsm75NhcpkfIcSRUJbQZNg%3D&reserved=0>







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--
Alex Hankey M.A. (Cantab.) PhD (M.I.T.)
Distinguished Professor of Yoga and Physical Science,
SVYASA, Eknath Bhavan, 19 Gavipuram Circle
Bangalore 560019, Karnataka, India
Mobile (Intn'l): +44 7710 534195
Mobile (India) +91 900 800 8789
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2015 JPBMB Special Issue on Integral Biomathics: Life Sciences, Mathematics and 
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