[Fis] I salute to Sungchul
Sungchul Ji
sji at pharmacy.rutgers.edu
Sun Jan 14 04:37:11 CET 2018
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 <alexhankey at gmail.com>
Sent: Saturday, January 13, 2018 12:24 AM
To: Sungchul Ji
Cc: Emanuel Diamant; fis at 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 <sji at pharmacy.rutgers.edu<mailto:sji at 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-bounces at listas.unizar.es<mailto:fis-bounces at listas.unizar.es>> on behalf of Emanuel Diamant <emanl.245 at gmail.com<mailto:emanl.245 at gmail.com>>
Sent: Friday, January 12, 2018 11:20 AM
To: fis at listas.unizar.es<mailto:fis at 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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