Cari Emanuel, Loet, Sung, Alex, Terry,
tutti insieme costituite un bel coro. Siete un'armonia meravigliosa. La
musica è il paradigma della scienza della vita o della vita della scienza.
E' un vero piacere dell'anima leggerVi. Siete forti, chiari e
incontrovertibili. Credo che il regista Pedro sia molto contento. Questa è
la strada da seguire. Non bisogna inseguire chimere o illusioni. Tutto ciò
che si conosce esiste e tutto ciò che esiste si conosce (lo dedico a
Giuseppe Brenner). Grazie, grazie, grazie.
Da parte di un economista della felicità.
Un abbraccio affettuoso.
Francesco

2018-01-14 4:37 GMT+01:00 Sungchul Ji <s...@pharmacy.rutgers.edu>:

> 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.co
> m/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> 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.co
> m/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> on behalf of Emanuel Diamant <
> emanl....@gmail.com>
> *Sent:* Friday, January 12, 2018 11:20 AM
> *To:* 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
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> ____________________________________________________________
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