### Re: [Fis] If always n>0 why we need log

Hi Krassimir,

I think the main reason that we express 'information'  as a logarithmic
function of the number of choices available, n, may be because the human brain
finds it easier to remember (and communicate and reason with)  10 than
100, or 100 than 10. . . . 0, etc.

All the best.

Sung

From: Krassimir Markov
Sent: Sunday, June 3, 2018 12:06 PM
To: Foundation of Information Science
Cc: Sungchul Ji
Subject: If always n>0 why we need log

Dear Sung,

A simple question:

I = -log_2(m/n) = - log_2 (m) + log_2(n)   (1)

Friendly greetings

Krassimir

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### Re: [Fis] If always n>0 why we need log

Hi Krassimir,

I think the main reason that we express 'information'  as a logarithmic
function of the number of choices, n, may be because the human brain finds it
easier to remember (and communicate and reason with)  10 than  100, or
100 than 10. . . . 0, etc.

All the best.

Sung

From: Krassimir Markov
Sent: Sunday, June 3, 2018 12:06:54 PM
To: Foundation of Information Science
Cc: Sungchul Ji
Subject: If always n>0 why we need log

Dear Sung,

A simple question:

I = -log_2(m/n) = - log_2 (m) + log_2(n)   (1)

Friendly greetings

Krassimir

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### Re: [Fis] The information-entropy relation clarified: The New Jerseyator

Hi FISers,

I found a typo in the legend to Figure 1 in my last post:  ".. . .  without
energy dissipation, no energy, . . ." shoud read

"Without energy dissipation, no information."
(4).

In fact, Statement (4) may be fundamental to informatics in general so that it
may be referred to as the "First Principle of Informatics" (FPI).

If this conjecture is correct, FPI may apply to the controversioal
interpretations of the wavefunction of a material system (WFMS), since WFMS is
supposed to encode all the information we have about the material system under
consideration and hence implicates "information".  It thus seems to me that the
complete interpretation of a wavefucntion, according to FPI, must specify the
selection process as well, i.e., the free energy-dissipating step, which I am
tempted to identified with "measurement" , "quantum jump", or "wavefunction
collapse".

I am not a quantum mechanician, so it is possible that I have committed some
logical errors somewhere in my arguemnt above.  If you diectect any, please let
me know.

With All the best.

Sung

From: Fis  on behalf of Sungchul Ji

Sent: Sunday, June 3, 2018 12:13:11 AM
To: 'fis'
Subject: [Fis] The information-entropy relation clarified: The New Jerseyator

Hi  FISers,

One simple (and may be too simple) way to distinguish between information and
entropy may be as follows:

(i)  Define  information (I) as in Eq. (1)

I = -log_2(m/n) = - log_2 (m) + log_2(n)
(1)

where n is the number of all possible choices (also called variety) and m is
the actual choices made or selected.

(ii) Define the negative binary logarithm of n, i.e., -log_2 (n), as the
'variety' of all possible choices  and hence identical with Shannon entropy H,
as suggested by Wicken [1].  Then Eq. (1) can be re-writtens as Eq. (2):

I = - log_2(m) - H
(2)

(iii) It is evident that when m = 1 (i.e., when only one is chosen out of all
the variety of choices available) , Eq. (2) reduces to Eq. (3):

I = - H
(3)

(iv) As is well known, Eq. (3) is the basis for the so-called the "negentropy
priniciple of Information" frist advocated by Shroedinger followed by
Brillouin,and others.  But Eq. (3) is clearly not a principle but a special
case of Eq. (2)  with m = 1.

(v)  In conlcusion, I claim that information and negative entropry are not the
same qualitatively nor quantiatively (except when m = 1 in Eq. (2)) and
represent two opposite nodes of a fundamental triad [2]:

Selection

H
>  I
(uncertainty before selection)
(Uncertainty after selection)

Figure 1.  The New Jerseyator model of information (NMI) [3].  Since selection
requires free energy dissipation, NMI implicates both information and energy.
That is, without energy dissipation, no energy, and hence NMI may be viewed as
a self-organizing process (also called dissipative structure) or an ‘-ator’.
Also NMI is consistent with “uncertainty reduction model of information.”

With all the best.

Sung

P.s.  There are experimetnal evidences that informattion and entropy are
orthogonal, thus giving rise to the Planck-Shannon plane that has been shown to
distiguish between cancer and healthy cell mRNA levels.  I will discus this in
n a later post.

References:

[1]  Wicken, J. S. (1987).  Entropy and information: suggestions for common
language. Phil. Sci. 54: 176=193.
[2] Burgin, M (2010).  Theory of Information: Funadamentality, Diversity,
and Unification.  World Scientific Publishing, New Jersey,

[3] Ji, S. (2018).  The Cell Langauge theory: Connecting Mind and Matter.
World Scientific Publishing, New Jersey.  Figure 10.24.
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### [Fis] The information-entropy relation clarified: The New Jerseyator

Hi  FISers,

One simple (and may be too simple) way to distinguish between information and
entropy may be as follows:

(i)  Define  information (I) as in Eq. (1)

I = -log_2(m/n) = - log_2 (m) + log_2(n)
(1)

where n is the number of all possible choices (also called variety) and m is
the actual choices made or selected.

(ii) Define the negative binary logarithm of n, i.e., -log_2 (n), as the
'variety' of all possible choices  and hence identical with Shannon entropy H,
as suggested by Wicken [1].  Then Eq. (1) can be re-writtens as Eq. (2):

I = - log_2(m) - H
(2)

(iii) It is evident that when m = 1 (i.e., when only one is chosen out of all
the variety of choices available) , Eq. (2) reduces to Eq. (3):

I = - H
(3)

(iv) As is well known, Eq. (3) is the basis for the so-called the "negentropy
priniciple of Information" frist advocated by Shroedinger followed by
Brillouin,and others.  But Eq. (3) is clearly not a principle but a special
case of Eq. (2)  with m = 1.

(v)  In conlcusion, I claim that information and negative entropry are not the
same qualitatively nor quantiatively (except when m = 1 in Eq. (2)) and
represent two opposite nodes of a fundamental triad [2]:

Selection

H
>  I
(uncertainty before selection)
(Uncertainty after selection)

Figure 1.  The New Jerseyator model of information (NMI) [3].  Since selection
requires free energy dissipation, NMI implicates both information and energy.
That is, without energy dissipation, no energy, and hence NMI may be viewed as
a self-organizing process (also called dissipative structure) or an ‘-ator’.
Also NMI is consistent with “uncertainty reduction model of information.”

With all the best.

Sung

P.s.  There are experimetnal evidences that informattion and entropy are
orthogonal, thus giving rise to the Planck-Shannon plane that has been shown to
distiguish between cancer and healthy cell mRNA levels.  I will discus this in
n a later post.

References:

[1]  Wicken, J. S. (1987).  Entropy and information: suggestions for common
language. Phil. Sci. 54: 176=193.
[2] Burgin, M (2010).  Theory of Information: Funadamentality, Diversity,
and Unification.  World Scientific Publishing, New Jersey,

[3] Ji, S. (2018).  The Cell Langauge theory: Connecting Mind and Matter.
World Scientific Publishing, New Jersey.  Figure 10.24.
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### [Fis] Sound-induced Faraday waves in water droplets: The Effects of System Sizes

Hi FISers,

About 6 months ago, John Stuart Reid [1] of the Sonic Age Lab in Cumbria,
England, published on-line a fascinating video strip showing the sound
vibration-induced formation of standing waves in individual water droplets of
50 to 100 microns in size [1], almost comparable to living cells, which is
reproduced below (click the picture to activate the video).

https://youtu.be/Z0St42jfgMU
[https://i.ytimg.com/vi/Z0St42jfgMU/hqdefault.jpg]<https://youtu.be/Z0St42jfgMU>

Sessile drop experiment<https://youtu.be/Z0St42jfgMU>
youtu.be
In this short video we see a field of sessile drops, many of them in the 50 to
100 micron range, mimicking the mass of many types of human cell. The sound
us...

The standing waves formed within these small water droplets are the examples of
the Faraday waves first reported in 1831 [2]. In the following explanation,
John invokes the resonance mechanism to account for the differential effects of
the same sound input on the wave patterns exhibited by differently sized sessle
droplets, which I think is valid:
"In this short video we see a field of sessile drops, many of them in the 50 to
100 micron range, mimicking the mass of many types of human cell. The sound
used to excite the drops is code 133 of Cyma Technologies AMI 1000 sound
therapy device. The entire field is around 4 mm in width yet the uptake of
acoustic energy is significantly different between the various sizes of
microscopic sessile drops, and at the point of Faraday Instability only two
droplets reach full expression, while in others there is a very reduced
acoustic uptake. This suggests that resonance may play a major role in the
ability of cells to absorb acoustic energy."
The reason I am interested in the Faraday waves in sessile droplets is because
I saw the link between these waves and the waves that I postulated to be
induced by energy input in all the material systems in the Universe, from atoms
to enzymes, cells, brains, human societies, and to the Universe Itself,
depending on the pattern of which the functions of a given system is thought to
be determined [3, 4].  This idea is schematically represented in Figure 1
reproduced from [3, 4]:

[cid:3ba4a188-c858-4818-ab73-4e0a020409e5]
Figure 1.  One possibility to account for the universality of the Planckian
distribution in nature is to postulate that the wave-particle duality first
discovered in atomic physics operates at all scales of material systems, from
atoms to the Universe. Reproduced from [2, 3].

water droplets captured by the CymaScope simply by adding a 10^th arrow
directed to "10. Faraday waves in sessile droplets".

According to this interpretation, the sound-induced Faraday waves formed in
sessile water droplets as visualized  the CymaScope obey and embody the
principle of wave-particle duality (PWPD) and hence I predict that the digital
CymaScopic images of these droplets should fit PDE, the Planckian Distribution
Equation, y = (A/(x + B)^5/(Exp (C/(x + B)) - 1), where x is the signal
intensity of the CymaScopic image pixels, and y is their frequency.  If this
prediction proves to be validated, the phenomenon of the sound-induced Faraday
waves in sessile water droplets visualized by the CymaScope may be considered
as one of the simplest mesoscopic material system in which PWPD is proven to
operate, thus opening up the possibility that PWPD may also operate in living
cells and their component biopolymers as I suggested in the abstract to the
2017 Biophysical Society Annual Meeting [6] which is reproduced below:

"261-Pos Board B26
Protein Folding as a Resonance Phenomenon, with Folding Free Energies
Determined by Protein-Hydration Shell Interactions   Sungchul Ji. Pharmacology
and Toxicology, Rutgers University, Kendall Park, NJ, USA.

The single-molecule enzyme-turnover-time histogram of cholesterol oxidase [1]
resembles the blackbody radiation spectrum at 4000 K. This observation
motivated the author to generalize the Planck radiation equation (PRE), Sl =
(8phc/l5 )/(ehc/lkT 1), by replacing the universal constants and temperature by
free parameters, resulting in the Planckian Distribution Equation (PDE), y =
(A/(x þ B)5 )/(eC/(x þ B) 1) [2]. Since the first factor in PRE reflects the
number of standing waves generated in the blackbody and the second factor the
average energy of the standing waves [3], it was postulated that any material
system that generates data fitting PDE can be interpreted as implicating
standing waves with associated average energies [2]. PDE has been found to fit
the long-tailed histogram of the folding free-energy changes measured from
4,300 proteins isolated from E. coli [4]. One possible interpretation of this
finding is (i) that proteins (P) and their hydration shells (HS) are organized
systems of oscillators with unique sets o

### Re: [Fis] Are there 3 kinds of motions in physics and biology?

Hi Michel,

post (which I happened to have deleted by accident).  In any case I have a copy

(1)  I am defining the Planckian information, I_P, as the information required
to transform a symmetric, Gaussian-like equation (GLE), into the Planckian
distribution.  which is the Gaussian distribution with the pre-exponential
factor replaced with a free parameter, A,   i.e., y = A*exp(-(\m - x)^2/2\s^2),
which was found to overlap with PDE (Planckian Distribution Equation) in the
rising phase.  So far we have two different ways of quantifying I_P: (i) the
Plamck informaiton of the fist kind, i_PF = log_2 [AUC(PDE)/AUC(GLE)], where
AUC is the area under the curve, and (ii) the Planckian information of the
second kind, I_PS = -log_2[(\m -mode)/ \s], which applies to right-skewed
long-tailed histograms only.  To make it apply also to the left-skewed
long-tailed histograms, it would be necessary to replace (\m - mode) with its
absolute value, i.e., |\m - mode|.

(2)  There can be more than two kinds of Planckian information, including what
may be called the Planckian information of the third kind, i.e., I_PT = -
long_2 (\chi), as you suggest.  (By the way, how do you define \chi ?).

(3)  The definition of Planckian information given in (1) implies that  I_P is
associated with asymmetric distribution generated by distorting the symmetric
Gaussian-like distribution by transforming the x coordinate non-linearly while
keeping the y-coordinate of the Gaussian distribution invariant [1].

GP
definition
Gaussian-like Distribution -> PDE
> IP

Figure 1.  The definitions of the Gaussian process (GP) and the Planckian
information (IP) based on PDE, Planckian Distribution Equation.  GP is the
physicochemical process generating a long-tailed histogram fitting PDE.

(4)  I am assuming that the PDE-fitting asymmetric histograms will always have
non-zero measures of asymetry.

(5)  I have shown in [1] that the human decision-making process is an example
of the Planckian process that can be derived from a Gaussian distribution based
on the drift-diffusion model well-known in the field of decision-making
psychophysics.

Reference:
[1] Ji, S. (2018).  The Cell Language theory: Connecting Mind and Matter.
World Scientific Publishing, New Jersey.   Figure 8.7, p. 357.

All the best.

Sung

From: Fis  on behalf of Michel Petitjean

Sent: Monday, May 7, 2018 2:05 PM
To: fis
Subject: Re: [Fis] Are there 3 kinds of motions in physics and biology?

Dear Karl,
In my reply to Sung I was dealing with the asymmetry of probability
distributions.
Then, the skewness is explained on an other wiki page:
Possibly the content of these two pages is unclear for you.
In order to avoid a huge of long and non necessary explanations, you
what was unclear from my post, then I can explain more efficiently.
However, I let Sung explain about his own post :)
Best regards,
Michel.

2018-05-07 19:55 GMT+02:00 Michel Petitjean :
> Dear Karl,
> Yes I can hear you.
> About symmetry, I shall soon send you an explaining email, privately, because
> I do not want to bother the FISers with long explanations (unless I am
> required to do it).
> However, I confess that many posts that I receive from the FIS list are very
> hard to read, and often I do not understand their deep content :)
> In fact, that should not be shocking: few people are able to read texts from
> very diverse fields (as it occurs in the FIS forum), and I am not one of them.
> Even the post of Sung was unclear for me, and it is exactly why I asked him
> questions, but only on the points that I may have a chance to understand (may
> be).
> Best regards,
> Michel.
>
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### [Fis] Are there 3 kinds of motions in physics and biology?

Hi FISers,

I think information and energy are inseparable in reality.  Hence to understand
what information is, it may be helpful to understand what energy (and the
associated concept of motion) is.  In this spirit, I am forwarding the
following email that I wrote motivated by the lecture given by Dr. Grossberg
this afternoon at the 119th Statistical Mechanics Conference.  In Table 1 in
the email, I divided particle motions studied in physics and biology into three
classes -- (i) random, (ii) passive, and (iii) active, and identified the field
of specialization wherein these motions are studied as (i) statistical
mechanics, (ii) stochastic mechanics, and (iii) info-statistical mechanics.
The last term was coined by me in 2012  in [1].  I will be presenting a short
talk (5 minutes) on Info-statistical mechanics on Wednesday, May 9, at the
above meeting.   The abstract of the short talk is given below:

Short talk to be presented at the 119th Statistical Mechanics Conference,
Rutgers University, Piscataway, N.J., May 6-9, 2018).

Planckian Information may be to Info-Statistical Mechanics what Boltzmann
Entropy is to Statistical Mechanics.
Sungchul Ji, Department of Pharmacology and Toxicology, Ernest Mario School of
Pharmacy, Rutgers University, Piscataway, N.J. 08854
Traditionally, the dynamics of any N-particle systems in statistical mechanics
is completely described in terms of the 6-dimensional phase space consisting of
the 3N positional coordinates and 3N momenta, where N is the number of
particles in the system [1]. Unlike the particles dealt with in statistical
mechanics which are featureless and shapeless, the particles in biology have
characteristic shapes and internal structures that determine their biological
properties.  The particles in physics are completely described in terms of
energy and matter in the phase space but the description of the particles in
living systems require not only the energy and matter of the particle but also
their genetic information, consistent with the information-energy
complementarity (or gnergy) postulate discussed in [2, Section 2.3.2].  Thus,
it seems necessary to expand the dimensionality of the traditional phase space
to accommodate the information dimension, which includes the three coordinates
encoding the amount (in bits), meaning (e.g., recognizability), and value
(e.g., practical effects) of information [2, Section 4.3]. Similar views were
expressed by Bellomo et al. [3] and Mamontov et al. [4].  The expanded “phase
space” would comprise the 6N phase space of traditional statistical mechanics
plus the 3N information space entailed by molecular biology.  The new space (to
be called the “gnergy space”) composed of these two subspaces would have 9N
dimensions as indicated in Eq. (1).  This equation also makes contact with the
concepts of  synchronic and diachronic informations discussed in [2, Section
4.5].  It was suggested therein that the traditional 6N-dimensional phase space
deals with  the synchronic information and hence was referred to as the
Synchronic Space while the 3N-dimensional information space is concerned with
the consequences of history and evolution encoded in each particle and thus was
referred to as the Diachronic Space.  The resulting space was called the gnergy
space (since it encodes not only energy but also information).

Gnergy Space =  6N-D Phase Space  +  3N-D  Information Space
(1)
(Synchronic Space)
(Diachronic Space)

The study of both energy and information was defined as “info-statistical
mechanics” in 2012 [2, pp. 102-106, 297-301].  The Planckian information of the
second kind, IPS, [5] was defined as the negative of the binary logarithm of
the skewness of the long-tailed histogram that fits the Planckian Distribution
Equation (PDE) [6].   In Table 1, the Planckian information is compared to the
Boltzmann entropy in the context of the complexity theory of Weaver [8]. The
inseparable relation between energy and information that underlies
“info-statistical mechanics” may be expressed by the following aphorism:
“Information without energy is useless;
Energy without information is valueless.”

Table 1.  A comparison between Planckian Information (of the second kind) and
Boltzmann entropy.  Adopted from [6, Table 8.3].

Order

Disorder

IPS = - log2 [(µ - mode)/σ]

(2008-2018)

S = k log W

(1872-75)

Planckian Information

Boltzmann entropy [7]

Organized Complexity [8]

Disorganized Complexity [8]

Info-Statistical Mechanics [2, pp. 102-106]

Statistical Mechanics [1]

References:
[1] Tolman, R. C. (1979). The Principles of Statistical Mechanics,  Dover
Publications, Inc.,
New York, pp. 42-46.
[2] Ji, S. (2012) Molecular Theory of the Living Cell: Concepts, Molecular
Mechanisms, and
Biomedical Applications.  Springer, New York.
[3] Bellomo, N., Bellouquid, A. and Harrero, M. A. (2007).  From

### Re: [Fis] Fw: The 'Shirasawa phenomenon' or the 'Shirasawa effect"

Hi Karl,

According to N. Bohr, there are two kinds of opposites, A and B -- (i)
supplementarity wherein A and B adds up to make the whole (e.g., the
forest-tree pair), and  (ii) complementarity wherein A or B is the whole,
depending on how the whole is observed (e.g., light as either wave or particle
depending on how it is measured).  I can send you the reference if needed.

Sung

From: karl javorszky <umok.vede...@gmail.com>
Sent: Friday, May 4, 2018 2:50:50 PM
To: Sungchul Ji
Cc: Stanley N. Salthe; fis
Subject: Re: [Fis] Fw: The 'Shirasawa phenomenon' or the 'Shirasawa effect"

Dear Sung,

Very encouraging the discussion of the difficulties human perception poses
while trying to consolidate opposites.

The existence of the mental image is built on contrasts, so no wonder we find
it hard to get a good grip on the mechanisms at work consolidating

To the opposites we work on :

tree vs. forest,
top vs. bottom,
little vs. big,

background vs. foreground,
across the flow vs. along the flow of time,
commutative vs. sequenced?

If so, there appear some encouraging hints, that a rational methodology has
been found to consolidate opposites.

Karl

Sungchul Ji <s...@pharmacy.rutgers.edu<mailto:s...@pharmacy.rutgers.edu>>
schrieb am Do., 3. Mai 2018 18:01:

Hi Stan,

True.  Our brain seems to have many limitations, one of which is our inability
to see the forest and the trees simultaneously.

It is interesting to note that we cannot measure (or at least not easy to
measure) particles and waves of quons  (or quantum objects) simultaneously
either,  although there are occasional claims asserting otherwise. Here we have
two entities, A and B, that are not compositionally related (i.e., A is not a
part of B) as are trees and the forest, but "complementarily" related (i.e.,
A^B, read A or B, depending on measurement) and hence does not involve any
hierarchy.

All the best.

Sung

From: Fis <fis-boun...@listas.unizar.es<mailto:fis-boun...@listas.unizar.es>>
on behalf of Stanley N Salthe
<ssal...@binghamton.edu<mailto:ssal...@binghamton.edu>>
Sent: Sunday, April 29, 2018 9:49 AM
To: fis
Subject: Re: [Fis] Fw: The 'Shirasawa phenomenon' or the 'Shirasawa effect"

Sung -- regarding:

The reason epigenetics (defined here as the process of inheritance without
imlplicating any changes in the nucleotide sequences of DNA)  was not mentioned
in my previous post is because I was mainly interested in the bottom-up (from
micro to macro) mechanism of genetics, not the top-down (from macro to micro)
mechanism.  It is interesting to note that our brain seems unable to handle
both bottom-up and top-down mechanisms simultaneously, perhaps it may have
something to do with the fact that we have two brain hemispheres (Yin and Yang)
but only one vocal cord (the Dao).

It is interesting that I early realized the difficulty many folks have with
visualizing at one time both the top-down AND bottom-up aspects of the
compositional hierarchy:
[large scale constraints -> [activity in focus <- [small scale
affordances]]]

Perhaps your suggestion is involved here as well!

STAN

On Sat, Apr 28, 2018 at 5:17 PM, Sungchul Ji
<s...@pharmacy.rutgers.edu<mailto:s...@pharmacy.rutgers.edu>> wrote:

Hi Arthur and  FISers,

Thank you for asking an important question. The reason epigenetics (defined
here as the process of inheritance without imlplicating any changes in the
nucleotide sequences of DNA)  was not mentioned in my previous post is because
I was mainly interested in the bottom-up (from micro to macro) mechanism of
genetics, not the top-down (from macro to micro) mechanism.  It is interesting
to note that our brain seems unable to handle both bottom-up and top-down
mechanisms simultaneously, perhaps it may have something to do with the fact
that we have two brain hemispheres (Yin and Yang) but only one vocal cord (the
Dao).

One way to integrate the bottom-up and top-down mechanisms underlying genetic
phenomenon may be to invoke the principle of vibrational resonance -- to view
both the micro-scale DNA and  the macro-scale environment of organisms as
vibrational systems or systems of oscillators that can exchange information and
energy through the well-known mechanisms of resonance (e.g., the resonance
between the oscillatory motions of the swing and the arms of the mother; both
motions must have same frequencies. otherwise the child will not swing).
According to the Fourier theorem, any oscillatory motions of DNA including very
low frequencies can be generated by linear combinations of  very fast covalent
bond vibrations in  DNA and  hence can be coupled to slow oscillatory motions
of the environment, e.g., musical sounds. If this view is correct, music can
affect,

### Re: [Fis] Fw: The 'Shirasawa phenomenon' or the 'Shirasawa effect"

Hi Stan,

True.  Our brain seems to have many limitations, one of which is our inability
to see the forest and the trees simultaneously.

It is interesting to note that we cannot measure (or at least not easy to
measure) particles and waves of quons  (or quantum objects) simultaneously
either,  although there are occasional claims asserting otherwise. Here we have
two entities, A and B, that are not compositionally related (i.e., A is not a
part of B) as are trees and the forest, but "complementarily" related (i.e.,
A^B, read A or B, depending on measurement) and hence does not involve any
hierarchy.

All the best.

Sung

From: Fis <fis-boun...@listas.unizar.es> on behalf of Stanley N Salthe
<ssal...@binghamton.edu>
Sent: Sunday, April 29, 2018 9:49 AM
To: fis
Subject: Re: [Fis] Fw: The 'Shirasawa phenomenon' or the 'Shirasawa effect"

Sung -- regarding:

The reason epigenetics (defined here as the process of inheritance without
imlplicating any changes in the nucleotide sequences of DNA)  was not mentioned
in my previous post is because I was mainly interested in the bottom-up (from
micro to macro) mechanism of genetics, not the top-down (from macro to micro)
mechanism.  It is interesting to note that our brain seems unable to handle
both bottom-up and top-down mechanisms simultaneously, perhaps it may have
something to do with the fact that we have two brain hemispheres (Yin and Yang)
but only one vocal cord (the Dao).

It is interesting that I early realized the difficulty many folks have with
visualizing at one time both the top-down AND bottom-up aspects of the
compositional hierarchy:
[large scale constraints -> [activity in focus <- [small scale
affordances]]]

Perhaps your suggestion is involved here as well!

STAN

On Sat, Apr 28, 2018 at 5:17 PM, Sungchul Ji
<s...@pharmacy.rutgers.edu<mailto:s...@pharmacy.rutgers.edu>> wrote:

Hi Arthur and  FISers,

Thank you for asking an important question. The reason epigenetics (defined
here as the process of inheritance without imlplicating any changes in the
nucleotide sequences of DNA)  was not mentioned in my previous post is because
I was mainly interested in the bottom-up (from micro to macro) mechanism of
genetics, not the top-down (from macro to micro) mechanism.  It is interesting
to note that our brain seems unable to handle both bottom-up and top-down
mechanisms simultaneously, perhaps it may have something to do with the fact
that we have two brain hemispheres (Yin and Yang) but only one vocal cord (the
Dao).

One way to integrate the bottom-up and top-down mechanisms underlying genetic
phenomenon may be to invoke the principle of vibrational resonance -- to view
both the micro-scale DNA and  the macro-scale environment of organisms as
vibrational systems or systems of oscillators that can exchange information and
energy through the well-known mechanisms of resonance (e.g., the resonance
between the oscillatory motions of the swing and the arms of the mother; both
motions must have same frequencies. otherwise the child will not swing).
According to the Fourier theorem, any oscillatory motions of DNA including very
low frequencies can be generated by linear combinations of  very fast covalent
bond vibrations in  DNA and  hence can be coupled to slow oscillatory motions
of the environment, e.g., musical sounds. If this view is correct, music can
affect, DIRECTLY (i.e., unmediated by the auditory system of the brain), the
molecular motions of DNA in every cell in our body.  In other words, we can
hear music not only through our ears but also through our whole body including
blood.  Because of the patent  issue, I cannot reveal the experimental evidence
supporting this claim, but, indue course, I hope to share with you the
scientific evidence we obtained recently.

In conclusion, it may be that  the yin-yang doctrine of the Daoist philosophy
(or any other equivalent principles) applies here, since molecular genetics and
epigenetics may constitute  the irreconcilable opposites:

"Genetics has two complementary aspects -- molecular genetics and epigenetics."

"Molecular genetics and epigenetics are the complementary aspects of genetics."

"Genetic phenomena can be accounted for in two irreconcilably opposite manner
with equal validity -- through the bottom-up (or reductionistic) or the
top-down  (or holistic) approaches."

The last statement would help avoid many wasteful debates in the field of
genetics.

If you have any questions or corrections, please let me know.

Sung

From: Arthur Wist <arthur.w...@gmail.com<mailto:arthur.w...@gmail.com>>
Sent: Friday, April 27, 2018 6:48 PM
To: Sungchul Ji; FIS FIS
Cc: sbur...@proteomics.rutgers.edu<mailto:sbur...@proteomics.rutgers.edu>;
Sergey Petoukhov; ole20

### [Fis] Fw: The 'Shirasawa phenomenon' or the 'Shirasawa effect"

Hi,

I am forwarding a slightly modified version of my previous post with the same
title which was rejected by the FIS list due to the heavy attachments. The most
significant addition is written in green.  The removed attachments are now
charge.

Best.

Sung

From: Sungchul Ji
Sent: Thursday, April 19, 2018 11:02 AM
To: FIS FIS
Cc: Sergey Petoukhov; dani...@shirasawa-acl.net; John Stuart Reid; sayer ji;
sji.confor...@gmail.com; x...@chemistry.harvard.edu;
sbur...@proteomics.rutgers.edu; n...@princeton.edu
Subject: The 'Shirasawa phenomenon' or the 'Shirasawa effect"

Hi FISers,

In 2003, Takuji Shirasawa and his coworkers [1] found that mutating certain
amino acids in the hemoglobin molecule (Hb) in mice produced the following
effects:

(1) increase O_2 consumption and CO_2 production,

(2) the conversion of the muscle histology from a fast glycolytic to a fast
oxidative type,

(3) a mild anemia, and

(4) faster running speed.

In other words, Shirasawa et al provided a concrete example of molecular
changes (e.g., amino acid mutations in Hb)  leading to (or associated with)
macroscopic physiological changes in whole animals (e.g., anemia,  running
behavior, etc.).  For the convenience of discussions, I am taking the liberty
of referring to this finding as the "Shirasawa et al. phenomenon/effect" or,
more briefly, the "Shirasawa phenomenon/effect" which may be viewed as the
macroscopic version of the Bohr effect [2].

The 'Shirasawa phenomenon/effect' is not limited to hemoglobin.  There are now
many similar phenomena found in the fields of voltage-gated ion channels, i.e.,
molecular changes in the amino acid sequences of ion channel proteins leading
to (or associated with) macroscopic effects on the human body called diseases
[3].

Although the current tendency among practicing molecular biologists and
biophysicists would be to explain away what is here called the Shirasawa
phenomenon in terms of the microscopic changes "causing" the macroscopic
phenomenon in a 1:1 basis, another possibility is that the microscopic changes
"cause" a set of other microscopic changes at the DNA molecular level which in
turn cause a set of macroscopic changes", in a many-to-many fashion.

Current trend:  Microscopic change (Hb mutation) ->  Macroscopic change
1 (Oxygen affinity change of blood) -> Macroscopic change 2 (O_2
anemia, running behavior)

Althernative mechanism:  Microscopic change 1 (Hb mutation) --->
Microscopic change 2 (Changes in the standing waves in DNA) ---> Multiple
macroscopic changes (O_2 metabolism, anemia, muscle cell histological changes).

The alternative mechanism proposed here seems to me to be more consistent with
the newly emerging models of molecular genetics [4] and single-molecule
enzymology [5, 6].

Since the 'Shirasawa phenomenon/effect' evidently implicates information
transfer from the microscale to the macroscale, it may be of interest to many
information theoreticians in this group.   If you have any questions, comments,
or suggestions, please let me know.

All the best.

Sung

References:

[1] Shirasawa, T., et al. (2003).  Oxygen Affinity of Hemoglboin Regulaters
O_2 Comsumtion, Metabolism, and Physical Activity.  J. Biol. Chem. 278(7):
5035-5043.  PDF at http://www.jbc.org/content/278/7/5035.full.pdf

[2] The Bohr effect.  https://en.wikipedia.org/wiki/Bohr_effect
[3] Huang W, Liu M, S Yan F, Yan N. (2017).  Structure-based assessment of
disease-related mutations in human voltage-gated sodium
channels.<https://molbio.princeton.edu/publications/structure-based-assessment-disease-related-mutations-human-voltage-gated-sodium>
Protein Cell. 8(6):401-438. PDF at https://www.ncbi.nlm.nih.gov/pubmed/28150151

[4] Petoukhov, S. V. (2016).  The system-resonance approach in modeling
genetic structures. BioSystems 139: 1–11. PDF at
https://www.sciencedirect.com/science/article/pii/S0303264715001732

[5] Lu, H. P., Xun, L. and Xie, X. S. (1998) Single-Molecule Enzymatic
Dynamics. Science 282:1877-1882.  PDF at
http://www.jbc.org/content/274/23/15967.short
[6] Ji, S. (2017). RASER Model of Single-Molecule Enzyme Catalysis and Its
Application to the Ribosome Structure and Function. Arch Mol. Med & Gen 1:104.
PDF at http://hendun.org/journals/AMMG/PDF/AMMG-18-1-104.pdf

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Hi FISers,

I am not sure whether I am a Procrustes (bed) or a Peirce (triadomaniac), but I
cannot help but seeing an ITR (irreducible Triadic Relation) among Text,
Context and Meaning, as depicted in Figure 1.

f
g

Context  >  Text
->  Meaning

|
^

|
|
|
|

|_|

h

“The meaning of a text is irreducibly dependent on its context.”

“Text, context, and meaning are irreducibly triadic.”   The “TCM principle” (?)

Figure 1.  The Procrustean bed, the Peircean triadomaniac, or both ?

f =  Sign production;  g =  Sign interpretation;  h = Correlation or
information flow.

According to this 'Peircean/Procrustesian' diagram, both what Terry said and
what Xueshan said may be valid.  Although their thinking must have been
irreducibly triadic (if Peirce is right), Terry may have focused on (or
prescinded) Steps f and h, while Xueshan prescinded Steps g and h, although he
did indicate that his discussion was limited to the context of human
information and human meaning (i.e., Step  f).  Or maybe there are many other
interpretations possible, depending on the interpreter of the posts under
discussion and the ITR diagram.

There are an infinite number of examples of algebraic operations: 2+3 = 5, 3 -
1 = 2, 20 x 45 = 900, etc., etc.
If I say "2 + 3 = 5", someone may say, but you missed "20 x 45 = 900".  In
other words, no matter what specific algebraic operation I may come up with, my
opponent can always succeed in coming up with an example I missed.   The only
solution to such an end-less debate would be to discover the axioms of algebra,
at which level, there cannot be any debate.  When I took an abstract algebra
course as an undergraduate at the University of Minnesota, Duluth, in 1962-5, I
could not believe that underlying all the complicated algebraic calculations
possible, there are only 5 axioms
(https://www.quora.com/What-is-the-difference-between-the-5-basic-axioms-of-algebra).

So can it be that there are the axioms (either symbolic,  diagrammatic, or
both) of information science waiting to be discovered, which will end all the
heated debates on information, meaning, data, etc. ?

All the best.

Sung

From: Fis  on behalf of Terrence W. DEACON

Sent: Monday, February 26, 2018 1:13 PM
To: Xueshan Yan
Cc: FIS Group

It is so easy to get into a muddle mixing technical uses of a term with
colloquial uses, and add a dash of philosophy and discipline-specific
terminology and it becomes mental quicksand. Terms like 'information' and
'meaning" easily lead us into these sorts of confusions because they have so
many context-sensitive and pardigm-specific uses. This is well exhibited in
these FIS discusions, and is a common problem in many interdisciplinary
discussions. I have regularly requested that contributors to FIS try to label
which paradigm they are using to define their use of the term "information' in
these posts, but sometimes, like fish unaware that they are in water, one
forgets that there can be alternative paradigms (such as the one Søren
suggests).

So to try and avoid overly technical usage can you be specific about what you
intend to denote with these terms.
E.g. for the term "information" are you referring to statisitica features
intrinsic to the character string with respect to possible alternatives, or
what an interpreter might infer that this English sentence refers to, or
whether this reference carries use value or special significance for such an
interpreter?
And e.g. for the term 'meaning' are you referring to what a semantician would
consider its underlying lexical structure, or whether the sentence makes any
sense, or refers to anything in the world, or how it might impact some reader?
dissolve.

— Terry

On Mon, Feb 26, 2018 at 1:47 AM, Xueshan Yan
> wrote:

Dear colleagues,

In my teaching career of Information Science, I was often puzzled by the
following inference, I call it Paradox of Meaning and Information or Armenia
Paradox. In order not to produce unnecessary ambiguity, I state it below and
strictly limit our discussion within the human context.

Suppose an earthquake occurred in 

### [Fis] ITR (Irreducible Triadic Relation) in Plato's Cave Allegory (PCA)

Hi FISers,

(1) Perhaps this has been discussed already either on this lsit or elsewhere,
i.e, the possible connection between the Irreducible Triadic Relation (ITR) and
Plato's Allegory of the Cave (PAC).  Regardless, I would like to propose below
my own version of the relation between ITR and PAC.

[cid:5ffda82e-0661-4afd-8e02-6119cbe799d2]

https://philosophyzer.wordpress.com/2012/09/21/the-allegory-of-the-cave-by-plato-summary-and-meaning/

(2) We can represent ITR diagrammatically as shown in the legend to Table 1
which is also known as the commutative triangle in category theory. As I
summarized in the main body of Table 1, the 3 nodes (A, B, & C) and 3 edges (f,
g, & h) of the ITR diagram have specific examples in three different systems --
(i) Plato's cave, (ii) natural science, and (iii) semiotics.

Table 1.  The Irreducible Triadic Relation (ITR) in Plato’s cave, science , and
semiotics.

f   g

A  > B  > C

| ^
|  |

|_|

h

Agent

A

B

C

f

g

h

Plato’s cavemen

Form
(or Real world)

on the wall

Thought

Physical laws

Perception

Universal causality

Scientists

4-D structure of enzymes

3-D structure of enzymes

Scientific model

measurement

Interpretation

Correlation

semioticians

Object

Sign

Interpretant

Sign production

Grounding Correlation

(3) I am assuming that Plato’s cavemen divide into two groups -- (i) the common
cavemen who think (and believe) that the shadows are real, and (ii) the
enlightened cavemen whose intellect distinghishes between shadows and the real
objects casting them.  It may be justified to describe the difference between
the way the common cavemen think and the way the enlightened cavemen think as
the ‘dyadic thinking’ (i.e, Step f reversed, or  A <- B only) and ‘the
triadic thinking’ (i.e., the entire commutative triangle), respectively.

(4) I liken to the common cavemen defined above the many briliant and
hardworking scientists who believe that studying the static 3-dimensional
structures of all the enzymes and proteins in the mitochondrion will eventually
solve the mystery of how the organell works in living cells. In this sense, I
believe that Plato's allegory of the cave applies to contemproary science.

(5) If it can be validated that there are indeed two types of Plato's cavemen
and in modern science, it may also apply to information science, leading to the
prediction that there will be two kinds of information scientists -- (i) dyadic
thinking information scientis and (ii) and triadic thinking information
scientis.

(6) Finally, One interesting spinoff of Table 1 may be that its Column A sheds
new light on what Plato might have meant by his Form or Idea, thus contributing
to solving the Plato-Aristotle debate on the Form-Matter dualtiy.

Any questions or commens are welcome as always.

Sung

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### Re: [Fis] The unification of the theories of information based on the cateogry theory

Hi Terry,  and FISers,

Can it be that "language metaphor" is akin to a (theoretical) knife that, in
the hands of a surgeon, can save lives but, in a wrong hand, can kill?

All the best.

Sung

From: Francesco Rizzo <13francesco.ri...@gmail.com>
Sent: Thursday, February 8, 2018 2:56:11 AM
To: Terrence W. DEACON
Cc: Fis,; Sungchul Ji
Subject: Re: [Fis] The unification of the theories of information based on the
cateogry theory

Caro Terry estensibile a tutti,
è sempre un piacere leggerTi e capirTi. La  general theory of information è
preceduta da un sistema (o semiotica) di significazione e seguita da un sistema
(o semiotica ) di comunicazione. Tranne che quando si ha un processo
comunicativo come il passaggio di un Segnale (che non significa necessariamente
'un segno') da una Fonte, attraverso un  Trasmettitore, lungo un Canale, a un
Destinatario. In un processo tra macchina e macchina il segnale non ha alcun
potere 'significante'. In tal caso non si ha significazione anche se si può
dire che si ha passaggio di informazione. Quando il destinatario è un essere
umano (e non è necessario che la fonte sia anch'essa un essere umano) si è in
presenza di un processo di significazione. Un sistema di significazione è una
costruzione semiotica autonoma, indipendente da ogni possibile atto di
comunicazione che l'attualizzi. Invece ogni processo di comunicazione tra
esseri umani -- o tra ogni tipo di apparato o struttura 'intelligente, sia
meccanico che biologico, -- presuppone un sistema di significazione come
propria o specifica condizione. In conclusione, è possibile avere una semiotica
della significazione indipendente da una semiotica della comunicazione; ma è
impossibile stabilire una semiotica della comunicazione indipendente da una
semiotica della significazione.
Ho appreso molto da Umberto Eco a cui ho dedicato il capitolo 10. Umberto Eco e
il processo di re-interpretazione e re-incantamento della scienza economica
(pp. 175-217) di "Valore e valutazioni. La scienza dell'economia o l'economia
della scienza" (FrancoAngeli, Milano, 1997). Nello mio stesso libro si trovano:
- il capitolo 15. Semiotica economico-estimativa (pp. 327-361) che si colloca
nel quadro di una teoria globale di tutti i sistemi di significazione e i
processi di comunicazione;
- il sottoparagrafo 5.3.3 La psicologia genetica di Jean Piaget e la
neurobiologia di Humberto Maturana e Francesco Varela. una nuova epistemologia
sperimentale della qualità e dell'unicità (pp. 120-130).
Chiedo scusa a Tutti se Vi ho stancati o se ancora una volta il mio scrivere in
lingua italiana Vi crea qualche problema. Penso che il dono che mi fate è, a
proposito della QUALITA' e dell'UNICITA',  molto più grande del (per)dono che
Vi chiedo. Grazie.
Un saluto affettuoso.
Francecso

2018-02-07 23:02 GMT+01:00 Terrence W. DEACON
<dea...@berkeley.edu<mailto:dea...@berkeley.edu>>:
Dear FISers,

In previous posts I have disparaged using language as the base model for
building a general theory of information.
Though I realize that this may seem almost heretical, it is not a claim that
all those who use linguistic analogies are wrong, only that it can be causally
I came to this view decades back in my research into the neurology and
evolution of the human language capacity.
And it became an orgnizing theme in my 1997 book The Symbolic Species.
Early in the book I describe what I (and now other evolutionary biologists)
have come to refer to as a "porcupine fallacy" in evolutionary thinking.
Though I use it to critique a misleading evolutionary taxonomizing tendency, I
think it also applies to biosemiotic and information theoretic thinking as well.
So to exemplify my reasoning (with apologies for quoting myself) I append the
following excerpt from the book.

"But there is a serious problem with using language as the model for analyzing
other

species’ communication in hindsight. It leads us to treat every other form of
communication as

exceptions to a rule based on the one most exceptional and divergent case. No
analytic method

could be more perverse. Social communication has been around for as long as
animals have

interacted and reproduced sexually. Vocal communication has been around at
least as long as frogs

have croaked out their mating calls in the night air. Linguistic communication
was an afterthought,

so to speak, a very recent and very idiosyncratic deviation from an ancient and
well-established

mode of communicating. It cannot possibly provide an appropriate model against
which to assess

other forms of communication. It is the rare exception, not the rule, and a
quite anomalous

exception at that. It is a bit like categorizing birds’ wings with respect to
the extent they possess or

lack the characteristics of penguins’ wings, or like analyzing the types of
hair on different mammals

with respe

### [Fis] The unification of the theories of information based on the cateogry theory

Hi  FISers,

On 10/8/2017, Terry wrote:

" So basically, I am advocating an effort to broaden our discussions and
recognize that the term information applies in diverse ways to many different
contexts. And because of this it is important to indicate the framing, whether
physical, formal, biological, phenomenological, linguistic, etc.

. . . . . . The classic syntax-semantics-pragmatics distinction introduced by
Charles Morris has often been cited in this respect, though it too is in my
opinion too limited to the linguistic paradigm, and may be misleading when
applied more broadly. I have suggested a parallel, less linguistic (and nested
in Stan's subsumption sense) way of making the division: i.e. into intrinsic,
referential, and normative analyses/properties of information."

I agree with Terry's concern about the often overused linguistic metaphor in
defining "information".  Although the linguistic metaphor has its limitations
(as all metaphors do), it nevertheless offers a unique advantage as well, for
example, its well-established categories of functions (see the last column in
Table 1.)

The main purpose of this post is to suggest that all the varied theories of
information discussed on this list may be viewed as belonging to the same
category of ITR (Irreducible Triadic Relation) diagrammatically represented as
the 3-node closed network in the first column of Table 1.

Table 1.  The postulated universality of ITR (Irreducible Triadic Relation) as
manifested in information theory, semiotics, cell language theory, and
linguistics.

Category Theory

fg
A -> B --> C
|   ^
||
|__|
h

Deacon’s theory of information

Shannon’s
Theory of
information

Peirce’s theory of signs

Cell language theory

Human language
(Function)

A

Intrinsic information

Source

Object

Nucleotides*/
Amion acids

Letters
(Building blocks)

B

Referential information

Message

Sign

Proteins

Words
(Denotation)

C

Normative information

Interpretant

Metabolomes
(Totality of cell metabolism)

Systems of words
(Decision making & Reasoning)

f

?

Encoding

Sign production

Physical laws

Second articulation

g

?

Decoding

Evoutionary selection

First and Third articulation

h

?

Information flow

Information flow

Inheritance

Grounding/
Habit

Scale   Micro-Macro?Macro   Macro   Micro   Macro

*There may be more than one genetic alphabet of 4 nucleotides.  According to
the "multiple genetic alphabet hypothesis', there are n genetic alphabets, each
consisting of 4^n letters, each of which in turn consisting of n nucleotides.
In this view, the classical genetic alphabet is just one example of the n
alphabets, i.e., the one with n = 1.  When n = 3, for example, we have the
so-called 3rd-order genetic alphabet with 4^3 = 64 letters each consisting of 3
nucleotides, resulting in the familiar codon table.  Thus, the 64 genetic
codons are not words as widely thought (including myself until recently) but
letters!  It then follows that proteins are words and  metabolic pathways are
sentences.  Finally, the transient network of metbolic pathways (referred to as
"hyperstructures" by V. Norris in 1999 and as "hypermetabolic pathways" by me
more recently) correspond to texts essential to represent
arguement/reasoning/computing.  What is most exciting is the recent discovery
in my lab at Rutgers that the so-called "Planck-Shannon plots" of mRNA levels
in living cells can identify function-dependent "hypermetabolic pathways"
underlying breast cancer before and after drug treatment (manuscript under
review).

Any comments, questions, or suggestions would be welcome.

Sung

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### Re: [Fis] Summing up: New Year Lecture

Hi John, Pedro, and FISers

(1) I agree with John that there must exist a set of the principles, laws or
concepts that apply universally, from molecules to cells to human brains to the
cosmos.  But the millions dollar question is what are these  principles, laws
and concepts?

(2)  I disagree that "chemiosmosis" of P. Mitchell is one of the principles
underlying life's physiology.  I will delineate the reasons for my objecting
the concept of chemiosmosis being a fundamental mechanism of energy
transduction in living cells in a later post.  I recently discussed this topic
in Section 3.3.3 in [1] entitled "Deconstructing the Chemiosmotic Model"

(3) I disagree that "negentropy", also called "negative entropy", is a
fundamental concept in biology or physics.  I critiqued this concept in Section
3.3.3 in [2].  To make a long story sort,  there are two meanings to the term
"negentropy", one violating the Third Law of thermodynamics and the other not
(see Table 1 below).

Table 1.  The dual meanings of the term “negentropy”

Negentropy

Negative Entropy
(-S)

Negative Entropy Change
(- ΔS)

Third Law of thermodynamics

is violated

is not violated

(4)  The Second Law of thermodynamics when applied to an isolated system (i.e.,
a system that does not exchange energy nor matter with its environment) states
that the entropy of the system increases with time or that the thermodynamic
driving force of an isolated system is the increase in entropy:

ΔS = S_final - S_initial > 0.
(I)

But many scientists do not realize that Inequality (I) holds only for isolated
systems and not for non-isolated systems such as living organisms (which are
open systems, i.e., systems that exchange both energy and matter with their
environment) or physical systems, e.g., refrigerators that are closed (i.e.,
exchange energy but not matter with their environment).

(5) For biological systems under constant pressure (P) and temperature (T), the
driving force behind all spontaneous physicochemical changes occurring in them
(e.g., respiration, morphogenesis) is a decrease in Gibbs free energy (ΔG) ,
which is a function of both energy and entropy:

ΔG = ΔE + PΔV - TΔS
(II)

As you can see here,  ΔG can be negative (thus driving all spontaneous living
processes) without any negative entropy change (or negentropy), since ΔG <0 as
long as (ΔE + PΔV) < - TΔS, regardless of whether ΔS is negative or positive.
This demonstrates that negentropy cannot serve as a fundamental focces for
life's physiology.

(6)

References:

[1] Ji, S. (2018).  "The Cell Language Theory: Connecting Mind and Matter",
World Scientific Publishing, New Jersey.

[2] Ji, S. (2012). The Third Law of Thermodynamics and “Schroedinger’s
the Living Cell: Concepts, Molecular Mechanisms, and Biomedical Applications.
Springer, New York.  pp. 12-15.  PDF at

From: Fis  on behalf of JOHN TORDAY

Sent: Wednesday, January 24, 2018 9:33 AM
To: fis@listas.unizar.es
Subject: Re: [Fis] Summing up: New Year Lecture

Dear FIS colleagues, Pedro has pointed out some rookie errors in my post. You
can find my paper "From cholesterol to consciousness" at
https://www.ncbi.nlm.nih.gov/pubmed/28830682.
email
me at jtor...@ucla.edu and i will send you a copy. As
for addressing consciousness at the cellular/molecular level, I understand that
the mental
health
professionals have a problem with consciousness beyond the brain/mind. But I
consider that 

### Re: [Fis] Response to Sungchul. Generative Logic

Hi Soren,

Which comment is for me?

Also, I want to clarify the following:

(1) 'Semiotics' is the name given to the study of signs generally and existed
since long before Peirce's time (1839-1914).

(2) If we represent 'semiotics' as a large circle, it will contain many small
sub-circles representing various theories about sign processes, including
Peirce's own, yours, mine, and many others', each sub-circles contributing to
the complete description of the large circle.

(3) In this Venn diagrammatic sense, 'neo-semiotics' is a sub-circle belonging
to the large circle of Semiotics that should have some overlap with the
Peircean semiotics since it is an extension of the latter.  Further,
neo-semiotics has many new features not contained in the Peircean semiotics
(e.g., molecular signs and their mechanisms of action driven by free energy
dissipation, the essential thermodynamic requirement for semiosis, and the
relation between micro- and macrosemiotics, etc.) and hence cannot be
completely contained within the sub-circle of the Peircean semiotics.

All the best.

Sung

From: Søren Brier <sbr@cbs.dk>
Sent: Sunday, January 14, 2018 10:32 AM
To: Loet Leydesdorff; Joseph Brenner; Terrence W. DEACON; Alex Hankey; Fis,
Cc: Emanuel Diamant; Sungchul Ji
Subject: RE: [Fis] Response to Sungchul. Generative Logic

Dear Pedro

Their seems to be some malfunction in the system. Three comments – the last one
to Sung – have not appeared on the list. Could you investigate?

Best

Søren Brier
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### Re: [Fis] I salute to Sungchul

guages: molecualr
biological, bioinformatic and linguistic implications.
BioSystems 44:17-39.  PDF at

[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]

(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, l

### Re: [Fis] I salute to Sungchul

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]

(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 

### Re: [Fis] New Year Lecture

Hi Pedro, John and other FISers,

(1)  Thank you John for the succinct summary of your cell-based evolutionary
theory.  As I indicated offline, I too proposed a cell-based evolutionary
theory in 2012 [1] and compared it with the gene-centered evolutionary theory
of Zeldovich and Shankhnovich (see Table 14.10 in [1]).

(2) I agree with Pedro that

". . . ..  essential informational ideas are missing too, and this absence of
the informational perspective in the ongoing evo discussions is not a good
thing. . . . "

I often wonder if this situation has arisen in biology because biologists
blindly apply to their problems the information theory as introduced by Shannon
almost 7 decades ago in the context of communication engineering without due
attention paid to the fact that  the Shannon-type information theory is not
designed to handle the "meaning" or semantics of messages but only the AMOUNT
of the information they carry.  If we agree that there are three essential
aspects to information, i.e., amount (e.g., my USB stores 3 Megabytes of
information), meaning (e.g., the nucleotide triplet, ACG, encodes threonine),
and value (e.g., the same message, 'Yes', can have different monetary values,
depending on the context), we can readily see that the kind of information
theory most useful for biologists is not (only) the Shannon-type but (also)
whatever type that can handle the semantics and pragmatics of information.

(3) One way to avoid the potential confusions in applying information theory to
biology may be 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(+), and what Pedro regarded as the
missing "essential informational ideas" above may be identified with I(+) (?)

(4)  There may be many forms of the I(+) theories to emerge in the field of
"new informatics" in the coming decades.  Based on my research results obtained
over the past two decades, I am emboldened to suggest that "linguistics" can be
viewed as an example of the I(+) theory. The term "linguistics" was once
fashionable in Western philosophy and humanities
(https://en.wikipedia.org/wiki/Linguistic_turn) in the form of "linguistic
turn" but apparently became outmoded (for some unknown reason to me, a
non-philosopher), but I am one of the many (including Chargaff who discovered
his two parity rules of DNA sequences;
https://en.wikipedia.org/wiki/Chargaff%27s_rules) who believes that linguistics
provide a valuable tool for elucidating the workings of living structures and
processes [2, 3].  In fact we may refer to the emerging trend in the early 21st
century that explore the basic relations between linguistics and biology as the
"Linguistic Return", in analogy to the "Linguistic Turn" referring to the
"major development in Western philosophy during the early 20th century, the
most important characteristic of which is the focusing of philosophy and the
other humanities primarily on the relationship between philosophy and
language." ((https://en.wikipedia.org/wiki/Linguistic_turn)

(5)  So, linguistics played an important role in philosophy in the early 20th
century and may play a similarly important role in biology in the coming
linguistics to solve their basic problems ?   If not linguistics, perhaps
semiotics, the study of signs?  The latter possibility was suggested by Brian
Josephson in his lecture

"Biological Organization as the True Foundation of Reality"

given at the 66th Lindau Nobel Laureate Meeting held in Lindau, Germany,
stating that

“Semiotics will eventually overtake quantum mechanics in the same way as
quantum mechanics overtook classical physics.”

I referred to this statement as the "Josephson conjecture" in [3].  When I
visited him in Cambridge last summer to discuss this statement, he did not
object to his name being used in this manner.

(6)  If the concepts of the "Linguistic Return" in biology and the Josephson
conjecture  in physics prove to be correct in the coming decades and centuries,
it may be possible to conclude that philosophy, biology, and physics are
finally united/integrated in the framework of semiotics viewed as a generalized
linguistics.

All the best.

Sung

[1] Ji, S. (2012).  The Zeldovich-Shakhnovich and MTLC Models of
Evolution: From Sequences to
Species.  In: Molecular Theory of the Living Cell: concepts, Molecular
Mechanisms, and Biomedical Applications.  Sprinter, New York.  Pp. 509-519. PDF
at http://www.conformon.net/model-of-evolution/
[2] Ji, S. (2012).  The Isomorphism between Cell and Human Languages: The
Cell Language Theory. In:
Molecular Theory of the Living Cell: Concepts, Molecular Mechanisms, and
Biomedical Applications.  

### Re: [Fis] Social information, Sociotype

Hi Emanuel, Pedro & Fishers,

Emanuel is rasing an important point.  It is clear that the duality of genetic
and epigenetic informations is fundamental.  But I think the triadicity of
genotype, phenotype, and sociotype is as important and fundametnal, if we
interpret the triadicity to mean that three cannot be reduced to two or one
just as the duality means that two cannot be reduced to one.  The two
not be mutually exclusive or contradictory (as they may appear on the surface)
but reflect different aspects of the information of livign systems -- one
aspect is irreducibly dyadic and the other is irreducibly triadic, depending on
how the phenomonon of life is viewed.   We may represent this idea
diagrammatically as infigure 1 below, which is an elaboration and extension of
the ITR (Irreducible Triadic Relation) diagram that I used in my previous post:

__

|___|

| k   | i
|   |Epigenetic Information flows

|  |
|   |||

V  f  V g
|   |   i, j, & k

Genotype  >  Phenotype  -> Sociotype

|  ^  |
^

|  |  j |
|

|  |__|  |
||Genetic
Information flows

h
||

f, g, & h

Figure 1.  The duality of the genetic and epigenetic information flows in the

Let me know if you have any questions or suggestions.

Sung

From: Fis  on behalf of Emanuel Diamant

Sent: Tuesday, December 19, 2017 3:25 PM
To: 'Pedro C. Marijuan'
Cc: fis@listas.unizar.es
Subject: [Fis] Social information, Sociotype

Dear Pedro, Dear Fises,

I apologize, as usual, for intervening in your respected discussion. But in my
humble understanding, the genotype-phenotype-sociotype triad is simply a list
of behavioral forms (or types). Evidently, they all are endorsed and inspired
by the information that is in the disposal of every living being. But from
information point of view (and we are busy with information essence quest) only
two types of information are involved in a living being behavior production:
genetic information and epigenetic information. That is: vertically exchanged
inheritance information and horizontally exchanged experience information.
These two types of information are responsible for the behavior of living
beings at every known to us level of biological organization: single cell -
genotype, cell assembly or organism - phenotype, groups of organisms or
societies - sociotype.

Again, I apologize for invading your discussion, but we are busy with
information, aren’t we?

Best regards, Emanuel.

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### Re: [Fis] Comes the Revolution. The Real

Hi Joseph,

Sorry for my mis-spelling your first name in my previous email.

Sung

From: Fis  on behalf of Joseph Brenner

Sent: Saturday, December 16, 2017 11:56 AM
To: 'Søren Brier'; 'fis'
Subject: Re: [Fis] Comes the Revolution. The Real

Dear Søren,

Thank you for a positive and constructive note and question. Although I
maintain my critique of Peirce’s tychism and synechism and his concepts of and
manipulations of signs and diagrams, I have always seen value in many of his
intuitions. I would be glad to consider him a ‘humanist with a semiotic
worldview’. It takes all kinds . . .

I think for participants in this list to say what they mean by reality, exactly
for, as you put it, a discussion of the ontology and science behind various
informational paradigms, would be very useful. Pedro, what do you think? For me
reality is change and stability, being and becoming, appearance and,
contradictorially, the reality behind appearance. This is why standard logic
doesn’t work.

Best Season’s Greetings,

Joseph

P.S. Perhaps a typo, but what is the sense of ‘treading’ in ‘treading
processual concept’?

From: Søren Brier [mailto:sbr@cbs.dk]
Sent: samedi, 16 décembre 2017 13:28
To: Joseph Brenner; fis
Subject: RE: [Fis] Comes the Revolution

Dear Joseph

This very Peircean of you as “The challenge is to reconcile our roles as
informational organisms and agents within nature and as stewards of nature.” is
at the centre of Peirce’s thinking instead that he uses the treading processual
call Peirce an objective idealist, although it is a form of realism I am not
sure that this concept covers his combination of Tychism and synechism with a
semiotic worldview. I think Peirce’s view is unique. But your mail does put the
focus on the importance of discussion the ontology behind the various

What do we mean when we use the term real for instance about Lupasco’s physical
– biological – contradictorial information? As I understand the term has been

Best

Søren

From: Fis [mailto:fis-boun...@listas.unizar.es] On Behalf Of Joseph Brenner
Sent: 16. december 2017 10:15
To: fis
Subject: [Fis] Comes the Revolution

Dear Pedro, Dear FISers,

I regret that I have difficulty in relating to the current FIS discussion, but
that is my problem. I see little progress since the appearance of  Lupasco’s
physical – biological – contradictorial information; Kauffman, Logan’s biotic
and Ulanowicz’ apophatic information; Deacon’s Shannon – Boltzmann – Darwin
information; and Wu’s revolution. Sungchul’s intuition of an “irreversible
discussion is blocked by his use of the word ‘irreversible’, required by the
underlying idealist Peircean structure of his argument.

What I would like to see is the foundations of information being discussed in
relation to the real problems of society, beyond questionnaires. Some of these
led yesterday to a prohibition of the use of seven words including foetus,
diversity and science-based from certain U. S. Government documents. I think we
need to have in the forefront of our minds the statement made by Floridi in his
2010 book, Information. A Very Short Introduction (which all of you have read,
of course): “The challenge is to reconcile our roles as informational organisms
and agents within nature and as stewards of nature.”

I believe that such a perspective, placed as a criterion for selection of
pertinent concepts, would make our discussions a lot deeper and more relevant.

Thank you and best wishes,

Joesph

[https://ipmcdn.avast.com/images/icons/icon-envelope-tick-round-orange-animated-no-repeat-v1.gif]

Garanti sans virus.
www.avast.com

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### Re: [Fis] Comes the Revolution. The Real

Hi Joeph,

You wrote on December 16 as follows:

" Sungchul’s intuition of an “irreversible triadic relation” reflects the power
of triads as cognitive attractors, but discussion is blocked by his use of the
word ‘irreversible’, required by the underlying idealist Peircean structure of
his argument."

Please correct "irreversible" to "irreducible".  This may have caused some
confusions in your understanding of my argument and Peirce's.  The former is
primarily a thermodynamic concept whereas the latter is a logical one, in my
opinion.

Sung

From: Fis  on behalf of Joseph Brenner

Sent: Saturday, December 16, 2017 11:56 AM
To: 'Søren Brier'; 'fis'
Subject: Re: [Fis] Comes the Revolution. The Real

Dear Søren,

Thank you for a positive and constructive note and question. Although I
maintain my critique of Peirce’s tychism and synechism and his concepts of and
manipulations of signs and diagrams, I have always seen value in many of his
intuitions. I would be glad to consider him a ‘humanist with a semiotic
worldview’. It takes all kinds . . .

I think for participants in this list to say what they mean by reality, exactly
for, as you put it, a discussion of the ontology and science behind various
informational paradigms, would be very useful. Pedro, what do you think? For me
reality is change and stability, being and becoming, appearance and,
contradictorially, the reality behind appearance. This is why standard logic
doesn’t work.

Best Season’s Greetings,

Joseph

P.S. Perhaps a typo, but what is the sense of ‘treading’ in ‘treading
processual concept’?

From: Søren Brier [mailto:sbr@cbs.dk]
Sent: samedi, 16 décembre 2017 13:28
To: Joseph Brenner; fis
Subject: RE: [Fis] Comes the Revolution

Dear Joseph

This very Peircean of you as “The challenge is to reconcile our roles as
informational organisms and agents within nature and as stewards of nature.” is
at the centre of Peirce’s thinking instead that he uses the treading processual
call Peirce an objective idealist, although it is a form of realism I am not
sure that this concept covers his combination of Tychism and synechism with a
semiotic worldview. I think Peirce’s view is unique. But your mail does put the
focus on the importance of discussion the ontology behind the various

What do we mean when we use the term real for instance about Lupasco’s physical
– biological – contradictorial information? As I understand the term has been

Best

Søren

From: Fis [mailto:fis-boun...@listas.unizar.es] On Behalf Of Joseph Brenner
Sent: 16. december 2017 10:15
To: fis
Subject: [Fis] Comes the Revolution

Dear Pedro, Dear FISers,

I regret that I have difficulty in relating to the current FIS discussion, but
that is my problem. I see little progress since the appearance of  Lupasco’s
physical – biological – contradictorial information; Kauffman, Logan’s biotic
and Ulanowicz’ apophatic information; Deacon’s Shannon – Boltzmann – Darwin
information; and Wu’s revolution. Sungchul’s intuition of an “irreversible
discussion is blocked by his use of the word ‘irreversible’, required by the
underlying idealist Peircean structure of his argument.

What I would like to see is the foundations of information being discussed in
relation to the real problems of society, beyond questionnaires. Some of these
led yesterday to a prohibition of the use of seven words including foetus,
diversity and science-based from certain U. S. Government documents. I think we
need to have in the forefront of our minds the statement made by Floridi in his
2010 book, Information. A Very Short Introduction (which all of you have read,
of course): “The challenge is to reconcile our roles as informational organisms
and agents within nature and as stewards of nature.”

I believe that such a perspective, placed as a criterion for selection of
pertinent concepts, would make our discussions a lot deeper and more relevant.

Thank you and best wishes,

Joesph

[https://ipmcdn.avast.com/images/icons/icon-envelope-tick-round-orange-animated-no-repeat-v1.gif]

Garanti sans virus.


### [Fis] Decoding the Cell Language: The role of PDE and its derivative, the Planck-Shannon plot, in identifying MOLECULAR TEXTS

Hi FISers,

(1)  In 1997 [9], I defined the cell language as follows:

"Cell language is a self-organizing system of molecules, some of which

encode, act as signs for, or trigger, gene-directed cell processes."

So defined the cell language shares many qualitative similarities or principles
with the human language as summarized in Tables 2 and 6-3 in my 11/27/2017 post
to this list.  In contrast, Table 3 in the same post provides quantitative
similarities between the two languages, since

(i) PDE, y = (A/(x + B)^5)/(Exp (C/(x + B)) -1) derived from physics and MAL, y
= (Ax^-B)/Exp (Cx), derived from linguistics [15] have a similar mathematical
form in that they are both the products of a power function and an exponential
function, and

(ii) PDE and MAL are equivalent as far as their ability to fit long-tailed
histograms regardless of whether they came from physics or linguistics.

These findings strongly indicate that there are structural features of cell and
human languages that are similar in terms of their functions as inferred in
Table 4.  Please note that the first two terms in the following are well
established in linguistics and the third term was introduced in the cell
language theory in 2012 [6]:

1st articulation = words forming sentences

2nd articulation = letters forming words
3rd articulation = sentences forming texts.

Table 4.  Isomorphism between cell and human languages deduced from a
qualitative comparison between linguistics and cell biology [1, 2, 3, 4].

Cell Language

Human Language

Function

Alphabet

A, C, G, T/U

Elementary signs [5]

Words

Gene/mRNA/protein

Denotation

Sentences

Metabolic pathways

Decision making

Texts

Functionally related sets of metabolic pathways (FRMPs)

Logical reasoning or computing

(2)  What is the Planckian-Shannon plot (PSP) or the Planckian-Shannon space
(PSS) ?

E hAs pointed out earlier on this list, PDE has been found to fit almost all
long-tailed histograms we have analyzed so far that have been reported in the
fields of atomic physics, molecular biology, cell biology, neurophysiology,
psychology, glottometrics (also called quantitative linguistics), econometrics,
cosmology [7-9], and most recently social network science [10].  The deviation
of the asymmetric PDE from a symmetric curve such as the Gaussian distribution
function [4, Figure 8.7] can be used as a measure of non-randomness, order, or
information encoded in PDE [11].  There are two ways of quantifying the
information content of PDE:

Plankian information of the first kind:   IPF = log2 [AUC (PDE)/AUC (GLE)]
(1)

Plankian information of the second kind: IPS = - log2 [(\mu – mode)/(\sigma)]
(2)

where AUC = Area Under the Curve; GLE = Gaussian-Like Equation whose rising
portion approximate closely the rising portion of PDE, and \mu and \sigma are,
respectively, the mean and the standard deviation of the data set that can be
represented as a long-tailed histogram fitting PDE.  In addition PDE allows us
to calculate the associated Shannon entropy as

H = - \Sigma (pi log2 pi)
(3)

wh  where \Sigma is the sum over i from 1 to n, the number of data points, and
pi is the probability of the occurrence of the ith data point.
We have analyzed the mRNA level data of the arbitrarily selected 10
metabolic pathways measured from human breast tissues using microarrays by
Perou et al. [12]. These data sets all produced long-tailed histograms that
fitted PDE, thus generating 10 pairs of the I_PS and H values. (We found that
I_PS values are more reproducible than I_PF.)  When these 10 pairs of numbers
were plotted in the so-called “Plank-Shannon space”, a linear correlation
(called the Planck-Shannon plot) was found with the R^2 value of 0.686(see the
upper panel of Figure 1).  Interestingly, when similarly sized 10 sets of the
mRNA levels were selected from the the human transcriptome that have no known
metabolic functions and plotted in the PSS, no correlation was found, the R^2
value being 0.213, far less than 0.7, the minimum threshold for a significant
correlation (see the lower panel of Figure 1).

[cid:a3e6c6be-7963-4aff-860c-4f025c88cd7b]

(3)  Until just recently (fall, 2017), there has been no method to identify
FRMPs although they were predicted to exist by the cell language theory.  It
now seems that we have such a method in the form of the Planck-Shannon plots as
exemplified in Figure 1.  In other words, when two sets of metabolic pathways
are chosen that have 30 or more mRNA molecules in each pathway (so that a
decent histogram can be obtained), one set encoding functions while  the other
set having no metabolic functions, we see the difference in the correlation
coefficients between their Planck-Shannon plots, indicating that the
Planck-Shannon space (or the IPS vs. H plot) is capable of 

### Re: [Fis] Is there a boundary between genetic informatics and genetics?

Hi Xueshan and FISers,

(1)  You are probably right that  "Genetics is an information science, the
first and most fully developed information science." It seems to be more real.

(2)  In Sung’s statement, imitating human linguistics of letters, words,
sentences, texts, he divided the substrate or the media that carry genetic
information into the following categories:

1   2
3
A. C, G, T or U → genes/mRNA/proteins → metabolic pathways → functional
networks of metabolic pathways

^
|
|
|
|
|

||
4

. . .  Our bewilderment is: Is there a boundary between genetic informatics and
genetics?

This is a million dollar question, as they say.  There can be more than one
answers to this fundamental question depending on the perspective of the
answerer.  My answer, based on the above  scheme or network (modified from the
original one by adding the backward U-shaped arrow and four numbers, all in
black) would be as follows:

(i) The network is the complementary union of two aspects -- the formal and
the material.  The study of the formal aspect of the network may be identified
as an example of "informatics" and the study of the material aspect as
"genetics" (which can be divided into molecular or microscopic genetics and
macroscopic or classical genetics).

(ii) The network has 4 nodes and 4 arrows, each of these 8 items or any
combinations of them  can be studied as a specialized discipline, including the
study of all of the items simultaneously, as I attempted to do in my 11/27/2017
post to this list. I regard such a comprehensive (and ambitious) discipline as
a part of what I came to refer to as "gnergetics", or the study ("-tics") of
information ("gn-") and energy ("erg-") around 1985 [1].   In contrast,  the
work of Petoukhov is primarily concerned with the mathematical underpinning of
the molecular genetic structures which he has identified with tensor products
of matrices [2].
(iii) Based on the above considerations, my answer to the above question
would two fold:

(a) There is no clear boundary in principle between genetic informatics and
genetics.

(b) It may be convenient to distinguish between molecular genetics and
classical genetics, the former being more closely related to informatics and
the latter to genetics.

All the best.

Sung

References:
[1] Ji, S. (2012).
Complementarity.
In: Molecular Theory of the Living Cell: Concepts, Molecular Mechanisms, and
Biomedical Applications.  Springer, New York.  Section 2.3, pp. 24-50.  PDF at
[2]  See Ref. [12] in my 11/27/2017 post.

From: Fis  on behalf of Xueshan Yan

Sent: Wednesday, December 6, 2017 10:28 AM
To: FIS Group
Subject: [Fis] Is there a boundary between genetic informatics and genetics?

Dear FIS Colleagues:

Last week, Sung and I discussed the problem of information in cell language and
human language. Pedro gave his opinion too. I think the Sung’s work is very
important to our information science study.

Biology is an informational science, this is the view of Leroy E. Hood of the
Nobel
prize
winner of 2002. As to this argument, he didn't give a complete biological
argument — only a genomics one. Review the history of those disciplines that
claimed to be the member of information science in the past years, although we
cannot wholly agree with them, for example, Bradley Efron — the former
president of the American Statistical Association — thought: "Statistics is an
information science, the first and most fully developed information science."
But I believe, imitating the Efron's statement: "Genetics is an information
science, the first and most fully 

### Re: [Fis] some notes

Hi FISers,

I find it convenient to define communication as an irreducibly triadic process
(physical, chemical, biological, physiological, or mental).  I identify such a
triadic process with the Peircean semiosis (or the sign process) often
represented as the following diagram which is isomorphic with the commutative
triangle of the category theory.  Thus, to me, communication is a category:

fg

A -->  B  ---> C
|   ^
|   |
|__|
h

Figure 1.  A diagrammatic representation of semiosis, sign process, or
communication.  The names of the nodes and edges can vary depending on the
communication system under consideration, which can be chemical reaction
systems, gene expression mechanisms, human communication using symbols,
computer systems using electrical signals.  If applied to the Shannon
communication system, A = source, B = signals, C = receiver, f = encoding, g =
decoding, and h = information transfer/flow.  When applied to human symbolic
communicatioin, A = object, B = sign, C = interpretant, f = sign production, g
= interpretation, and h = information flow.

One usefulness of Figure 1 is its ability to distinguish between "interactions"
(see Steps f and g) and "communication" (see Steps f, g and h); the former is

All the best.

Sung

From: Fis  on behalf of Loet Leydesdorff

Sent: Friday, November 17, 2017 8:06 AM
To: Pedro C. Marijuan; fis
Subject: Re: [Fis] some notes

Dear Pedro and colleagues,

2. Eigenvectors of communication. Taking the motif from Loet, and continuing
with the above, could we say that the life cycle itself establishes the
eigenvectors of communication? It is intriguing that maintenance, persistence,
self-propagation are the essential motives of communication for whatever life
entities (from bacteria to ourselves). With the complexity increase there
appear new, more sophisticated directions, but the basic ones probably remain
intact. What could be these essential directions of communication?
I am not so convinced that there is an a priori relation between life and
communication. Communication is not alive. Non-living systems (e.g., computers,
robots) also communicate. Perhaps, it matters for the communication whether the
communicators are living systems; but this needs to be specified.

Communication studies is not biology. Perhaps, there is a specific biological
communication as Maturana claims: when molecules are exchanged, one can expect
life. Can one have life without communication? It seems to me that one can have
communication without life. Communication would then be the broader category
and life a special case.

Best,
Loet

3. About logics in the pre-science, Joseph is quite right demanding that
discussion to accompany principles or basic problems. Actually principles,
rules, theories, etc. are interconnected or should be by a logic (or several
logics?) in order to give validity and coherence to the different combinations
of elements. For instance, in the biomolecular realm there is a fascinating
interplay of activation and inhibition among the participating molecular
partners (enzymes and proteins) as active elements.  I am not aware that
classical ideas from Jacob (La Logique du vivant) have been sufficiently
continued; it is not about Crick's Central Dogma but about the logic of
pathways, circuits, modules, etc. Probably both Torday and Ji have their own
ideas about that-- I would be curious to hear from them.

4. I loved Michel's response to Arturo's challenge. I think that the two
"zeros" I mentioned days ago (the unsolved themes around the cycle and around
the observer) imply both multidisciplinary thinking and philosophical
speculation...

Best wishes--Pedro

-
Pedro C. Marijuán
Grupo de Bioinformación / Bioinformation Group
Instituto Aragonés de Ciencias de la Salud
Centro de Investigación Biomédica de Aragón (CIBA)
Avda. San Juan Bosco, 13, planta 0
50009 Zaragoza, Spain
Tfno. +34 976 71 3526 (& 6818)
pcmarijuan.i...@aragon.es
-

___
Fis mailing list
Fis@listas.unizar.es


### Re: [Fis] TR: some notes

Pedro wrote:

"3. About logics in the pre-science, Joseph is quite right demanding that
discussion to accompany principles or basic problems. Actually
principles, rules, theories, etc. are interconnected or should be by a
logic (or several logics?) in order to give validity and coherence to
the different combinations of elements. For instance, in the
biomolecular realm there is a fascinating interplay of activation and
inhibition among the participating molecular partners (enzymes and
proteins) as active elements.  I am not aware that classical ideas from
Jacob (La Logique du vivant) have been sufficiently continued; it is not
modules, etc. Probably both Torday and Ji have their own ideas about
that-- I would be curious to hear from them."

(1)  Enzymes, like all molecular and sub-molecular species (generally called
microscopic entities, quantum objects, quons  [1], or wavicles) exhibit the
wave-particle duality (as evidenced by the fact that they obey the Planckian
Distribution Equation (PDE) [2-4]).  And yet most of the descriptions of enzyme
mechanisms  given in the current literature are based on the particle aspect of
enzymes including all the efforts directed to understanding enzyme activities
in terns of the causal role of the static 1-dimensional sequences of amino
acids or their 3-dimensional folds as revealed by the X-ray crystallography.
Alternatively, we can describe enzyme  structure and function based on their
wave attributes, in which case enzymes are viewed as systems of oscillators and
their functions are determined by the collective vibrational motions of amino
acid residues called "standing waves" (see Figure 8 in [3]).

(2)  Like electrons (see (4) below)), enzymes (and biopolymers in general,
including DNA; see Table 1 below) may possesses  two complementary attributes
-- static and dynamic.  Just as the position and momentum of the electron
cannot be accounted for by their static attributes alone, so perhaps the static
attributes of enzymes (e.g., amino acid sequences) alone may not be sufficient
to account for their dynamic attributes, i.e., their catalytic activities.  The
missing link may be sought in their wave attributes which have collective
organizing power.  Traveling waves generated within a volume can interact to
form "standing waves", also called "resonant waves", as exemplified by the

[https://www.bing.com/th?id=OVP.0CuEeLYreRH1jrVSaq2sMwEsDh=Api]

Amazing Resonance Experiment!
http://www.facebook.com/brusspup The song in the video is my latest song. You
can find it on iTunes o...

(3)  There is accumulating evidence (references available upon request) to
support the following mechanism of enzyme action:

E   <--->  E'
(1)

E'  +  S   <--->   [E.S
<===> E.P]   (2)

[E.S <===> E.P]   <--->   E + P
(3)

E  +  S<--->   E  + P
(4)

Figure 1.  The pre-fit mechanism (in contrast to the better-known "induced-fit
mechanism of Koshland) of enzyme catalysis [1].  Symbols are defined as
follows: E = ground-state enzyme; E' = conformationally excited enzyme through
thermal fluctuations; S = substrate; E.S = Enzyme-substrate complex in the
transition state; E.P = the enzyme-product complex in the transition state;
<-> = thermally equilibrium; <===> = the resonance hybrid between the
enzyme-substrate and enzyme-product complexes.

Step (1) indicates that an enzyme molecule is a collection of  oscillators that
interact with one another to form higher-order structures, either local or
global, known as resonances or standing waves.  In the Chladni plate, what
causes the 'visible' standing waves of particles  on it is the 'invisible'
vibrational motions of the plate itself and the particles are forced to form
standing waves through resonance energy transfer from the plate to individual
particles.  In enzymes, what causes the formation of the standing waves or
resonant waves of the enzyme molecule  are the component amino acid residues
acting as elementary oscillators whose periodic motions can combine, obeying
the Fourier theorem, to form almost infinite number of standing waves, some of


### [Fis] Two kinds of the Planckian Information -- the First (I_PF)and the Second Kind (I_PS)

Hi FISers,

(I)  In the post dated March 21, 2017, I attached a file entitled "What is the
Planckian information ?".   The Planckian information (symbolized by I_P) is
defined as the binary logarithm of the ratio between the area under the curve
(AUC) of PDE (Planckian Distribution Equation; see Eqn (1) in the file) and
that of GLE(Gaussian-like Equation; see Eqn (2) in the file):

I_P = log_2 (AUC(PDE)/AUC(GLE))
(1)

PDE is the function for long-tailed histograms (both right and left long
tailed) and GLE is the bell-shaped curve whose rising portion overlaps with the
rising portion of the right-long tailed PDE as exemplifed by Figures 1g, 1i,
1k, 1o, 1r and 1t in the above file and in Figures 15, 16, 20, 22, and 23 in
[1].  It is clear that the greater the deviation of PDE from GLE, the greater
is the I_P value, since GLE represents randomness and the deviation of PDE from
GLE represents non-randomness, order, or information.

(2) There may be many physical, chemical, or mental processes  that can give
rise to I_P by producing PDE from GLE.  One such mechanism is the so-called
"drift-diffusion" mechanism well-known in the field of decision-making
pyschophysics (see Figure 6 in [2]).

(3)  Another mechanism of generating PDE from Gaussian distribution is what I
call the "Rutgers University Admissions Mechanism" (RUAM).  That is, if RAUM
does not take into account the students' heights in their admissions process,
the hieght distribution of the RU students would be most likely Gaussian.
However, if RUAM favors short students over tall ones, the RU students' height
distribution  will be skewed from the normal curve thus producing PDE.  The
degree of skewness of PDE from its Gaussian counterpart (with an equal area
under the curve) can be used as a measure of the information used by RAUM in
selecting RU students.   The information derived from PDE based on its skewness
will be referred to as the Planckian information of the second kind, I_PS, to
distinguish it from the Planckian information defined previously (see Eqn (1))
which is now called the Planckian information of the first kind, I_PF:

I_PS = - log_2 (mean - mode/standard deviation)
(2)

(4)  We have  found that some experimetnal data (e.g., digitized water wave
patterns produced by the sonified Raman spectral bands measured from single
cells) that fit PDE are better modeled with I_PF and some others (e.g., the
mRNA levels measured from yeast cell ensembles) are better modeled with I_PS.

(5)  If these considerations are substantiated further in the future, the
following conclusions may be drawn:

(a) There can be more than one kind of information that can be defined based
on the same empirically derived mathematical euqation, depending on supporting
physical mechanisms (or formal algorithms ?).
(b) The reasoning in (1) suggests that the mathematically defined
"information" is arbitrary in the sense of Saussure.
(c)  The mathematically defined "information" can be viewed as a sign in the
Peircean sense and hence is irreducibly triadic as depicted in Figure 1:

f
g

Reality  -> Quantitative Information
->  Mechanism

|
^
|
|
|
|
|___|
h

Figure 1.  The irreducibly triadic nature of the "quantitative information" or
the "mathematical information".
f = measurement;  g = mental process; h = correspondence,
grounding.

(6)  Finally, it may be that PDE (or the skewed Gaussian distribution) provides
a more general model for defining what "information" is than Shannon's
communication system.

All the best.

Sung

References:

[1] Ji, S. (2016).  PLANCKIAN INFORMATION (IP): A NEW MEASURE OF ORDER IN
ATOMS, ENZYMES, CELLS, BRAINS, HUMAN SOCIETIES, AND THE COSMOS  In: Unified
Field Mechanics: Natural Science beyond the Veil of Spacetime (Amoroso, R.,
Rowlands, P., and Kauffman, L. eds.), World Scientific, New Jersey, 2015, pp.
579-589).  PDF at
[2] Ji, S. (2015). Planckian distributions in molecular machines, living
cells, and brains: The wave-particle duality in biomedical


### Re: [Fis] Data - Reflection - Information

Hi FISers,

Reading the recent posts on "information" and related issues by Terry, Joseph,
Pedro, Mark,  Krassimir, Loet, and others suggested to me the following
possible definition of information (see Table 1) that may be consistent with
those proposed by Terry, Shannon, Volkenstein,  Saussure, and Peirce (as I
understand him), to varying degrees.

Table 1.  A unified definition of information based on the  Mechanism of

“Information is something that is transferred from A (e.g., the sender) to C
(e.g., the receiver) mediated by B (e.g., sound signal) in such a manner that A
and C become coupled, correlated, or coordinated.”

f  g
A ---> B ---> C
|
^
|
|
||
h

Terry

Shannon

Volkenstein

Peirce

Saussure

A

Object

Sender

-

Object

Object

B

Sign

Message

-

Sign

Sign

C

Interpretant

-

Interpretant

-

f

Intrinsic

Coding

Amount

Natural process

Differentiation (?)

g

Referential

Decoding

Meaning

Mental process

Arbitrariness

h

Normative

Communication

Value

Correspondence/
Communication

-

I have the feeling that that number of columns in Table 1 can be increased to
the right significantly, as we extend the MITR-based definition of information
to various fields of inquires in natural and human sciences.

Any suggestions, comments or corrections would be welcome.

Sung

From: Terrence W. DEACON <dea...@berkeley.edu>
Sent: Sunday, October 8, 2017 8:30 PM
To: Sungchul Ji
Cc: KrassimirMarkov; foundationofinformationscience; 钟义信
Subject: Re: [Fis] Data - Reflection - Information

Against "meaning"

I think that there is a danger of allowing our anthropocentrism to bias the
discussion. I worry that the term 'meaning' carries too much of a linguistic
bias.
By this I mean that it is too attractive to use language as our archtypical
model when we talk about information.
Language is rather the special case, the most unusual communicative adaptation
to ever have evolved, and one that grows out of and depends on
informationa/semiotic capacities shared with other species and with biology in
general.
So I am happy to see efforts to bring in topics like music or natural signs
like thunderstorms and would also want to cast the net well beyond humans to
include animal calls, scent trails, and molecular signaling by hormones. And it
is why I am more attracted to Peirce and worried about the use of Saussurean
concepts.
Words and sentences can indeed provide meanings (as in Frege's Sinn - "sense" -
"intension") and may also provide reference (Frege's Bedeutung - "reference" -
"extension"), but I think that it is important to recognize that not all signs
fit this model. Moreover,

A sneeze is often interpreted as evidence about someone's state of health, and
a clap of thunder may indicate an approaching storm.
These can also be interpreted differently by my dog, but it is still
information about something, even though I would not say that they mean
something to that interpreter. Both of these phenomena can be said to provide
reference to something other than that sound itself, but when we use such
phrases as "it means you have a cold" or "that means that a storm is
approaching" we are using the term "means" somewhat metaphorically (most often
in place of the more accurate term "indicates").

And it is even more of a stretch to use this term with respect to pictures or
diagrams.
So no one would say the a specific feature like the ears in a caricatured face
mean something.
Though if the drawing is employed in a political cartoon e.g. with exaggerated
ears and the whole cartoon is assigned a meaning then perhaps the exaggeration
of this feature may become meaningful. And yet we would probably agree that
every line of the drawing provides information contributing to that meaning.

So basically, I am advocating an effort to broaden our discussions and
recognize that the term information applies in diverse ways to many different
contexts. And because of this it is important to indicate the framing, whether
physical, formal, biological, phenomenological, linguistic, etc.
For this reason, as I have suggested before, I would love to have a
conversation in which we try to agree about which different uses of the
information concept are appropriate for which contexts. The classic
syntax-semantics-pragmatics distinction introduced by Cha

### Re: [Fis] A PROPOSAL ABOUT THE DEFINITION OF INFORMATION

Hi Arturo,

I agree.  Engtropy can be negative MATHEMATICALLY, as Shroedinger assumed.

But what I am claiming is that that may be a mathematical artifact, since,
according to the Third Law of Thermodynamics, therer is no negative entropy.

All the best.

Sung

From: tozziart...@libero.it <tozziart...@libero.it>
Sent: Friday, October 13, 2017 6:02 PM
To: Sungchul Ji
Cc: fis@listas.unizar.es
Subject: Re[2]: Re: [Fis] A PROPOSAL ABOUT THE DEFINITION OF INFORMATION

Dear Sung,
I'm sorry, but the "Unreasonable Effectiveness of Mathematics" still holds true.
Forget philosophical concepts like Yin and Yang, because, in some cases and
contexts , entropy is negative.
Just to make an example,
"Since the entropy H(S|O) can now become negative, erasing a system can result
in a net gain of work (and a corresponding cooling of the environment)."

https://www.nature.com/nature/journal/v474/n7349/full/nature10123.html

--
Inviato da Libero Mail per Android

venerdì, 13 ottobre 2017, 10:11PM +02:00 da Sungchul Ji
s...@pharmacy.rutgers.edu<mailto:s...@pharmacy.rutgers.edu>:

Hi Arturo,

(1)  I don't understand where you got (or how you can justify) S = 1 J/K in

"With the same probability mass function, you can see that H = S/(ln(2)*kB), so
setting S = 1J/K gives a Shannon entropy of 1.045×1023 bits."

(2) I can see how one can get H = S/(ln(2)*k_B mathematically, but what does
this equality mean physically ?

(3) This reminds me of what Schroedinger did when he came up with the
conclusion that "negative entropy" is equivalent to "order", which led to
Brillouin's so-called the "negentropy Principle of Information (NPI)" [1, 2].

Simply by multiplying the both sides of the Boltzmann equation with negative
one, Schroedinger obtained the following formula:

- S = - k lnW = k ln (1/W)

and then equating W with disorder, D, led him to

- S = k ln (1/D).

Since (1/D) can be interpreted as the opposite of "disorder", namely, "order",
he concluded that

"negative entropy = order".

As you can see, the above derivation is mathematically sound but the result
violates the Third Law of Thermodynamics, according to which thermodynamic
entropy cannot be less than zero.

Thus, in 2012 I was led to formulate what I called the "Schroedinger paradox"
as follows [3]

"Schroedinger's paradox refers to the mathematical equations, concepts, or
general statements that are formally true but physically meaningless."

(4) If my argument in (3) is valid, this may provide an example of what may be
called

the "Unreasonable Ineffectiveness of Mathematics"

which, together with Wigner's "Unreasonable Effectiveness of Mathematics", may
constitute an Yin-Yang pair of mathematics.

All the best.

Sung

References:
[1]  Brillouin, L. (1953).  Negentropy Principle of Information, J. Applied
Phys. 24(9), 1152-1163.

[2]  Brillouin, L. (1956). Science and Information Theory, Academic Press,
Inc., New York, pp. 152-156.

[3] Ji, S. (2012).  The Third Law of
In:Molecular Theory of the Living Cell: Concepts, Molecular Mechanisms, and
Biomedical Applications.  Springer, New York.  pp. 12-15.  PDF at

From: tozziart...@libero.it<mailto:tozziart...@libero.it>
<tozziart...@libero.it<mailto:tozziart...@libero.it>>
Sent: Friday, October 13, 2017 4:43 AM
To: Sungchul Ji; fis@listas.unizar.es<mailto:fis@listas.unizar.es>
Subject: R: Re: [Fis] A PROPOSAL ABOUT THE DEFINITION OF INFORMATION

Dear Sung,
One J/K corresponds to 1.045×1023 bits.

Indeed,
The Gibbs entropy formula states that thermodynamic entropy S equals
kB*sum[pi*ln(1/pi)], with units of J/K, where kB is the Boltzmann constant and
pi is the probability of microstate i. On the other hand, the Shannon entropy
is defined as H = sum[pi*log2(1/pi)], with units of bits. With the same
probability mass function, you can see that H = S/(ln(2)*kB), so setting S =
1J/K gives a Shannon entropy of 1.045×1023 bits.

On the other side, The
energy<http://7769domain.com/Ad/GoIEx2/?token=SVpHR1pPRjQ5cjMwK1E1b3NhUVdYZWNCcGxiZlJjUGhlbEFPemROVE1xYU1VTHJoZWF5T2p0d0Z5YXNDWmt2NDBGdk1jb3Eybm5JNDRoTytMVEUxUE9WaUV0bC9qMTdaZWI3UUJhQSt4S2xjaHlhcFdTUi8rWm52WVMvdndnaTZIakl3Y2JyejFqazFGM1hpb2RxWjY4UmtzQ3FuTWtlQzAzQ0FrNDFQS2Z3PQ2&g

### Re: [Fis] A PROPOSAL ABOUT THE DEFINITION OF INFORMATION

Hi Arturo,

(1)  I don't understand where you got (or how you can justify) S = 1 J/K in

"With the same probability mass function, you can see that H = S/(ln(2)*kB), so
setting S = 1J/K gives a Shannon entropy of 1.045×1023 bits."

(2) I can see how one can get H = S/(ln(2)*k_B mathematically, but what does
this equality mean physically ?

(3) This reminds me of what Schroedinger did when he came up with the
conclusion that "negative entropy" is equivalent to "order", which led to
Brillouin's so-called the "negentropy Principle of Information (NPI)" [1, 2].

Simply by multiplying the both sides of the Boltzmann equation with negative
one, Schroedinger obtained the following formula:

- S = - k lnW = k ln (1/W)

and then equating W with disorder, D, led him to

- S = k ln (1/D).

Since (1/D) can be interpreted as the opposite of "disorder", namely, "order",
he concluded that

"negative entropy = order".

As you can see, the above derivation is mathematically sound but the result
violates the Third Law of Thermodynamics, according to which thermodynamic
entropy cannot be less than zero.

Thus, in 2012 I was led to formulate what I called the "Schroedinger paradox"
as follows [3]

"Schroedinger's paradox refers to the mathematical equations, concepts, or
general statements that are formally true but physically meaningless."

(4) If my argument in (3) is valid, this may provide an example of what may be
called

the "Unreasonable Ineffectiveness of Mathematics"

which, together with Wigner's "Unreasonable Effectiveness of Mathematics", may
constitute an Yin-Yang pair of mathematics.

All the best.

Sung

References:
[1]  Brillouin, L. (1953).  Negentropy Principle of Information, J. Applied
Phys. 24(9), 1152-1163.
[2]  Brillouin, L. (1956). Science and Information Theory, Academic Press,
Inc., New York, pp. 152-156.

[3] Ji, S. (2012).  The Third Law of
Thermodynamics<http://www.conformon.net/publications/book-chapters/#> and
In:Molecular Theory of the Living Cell: Concepts, Molecular Mechanisms, and
Biomedical Applications.  Springer, New York.  pp. 12-15.  PDF at

________
From: tozziart...@libero.it <tozziart...@libero.it>
Sent: Friday, October 13, 2017 4:43 AM
To: Sungchul Ji; fis@listas.unizar.es
Subject: R: Re: [Fis] A PROPOSAL ABOUT THE DEFINITION OF INFORMATION

Dear Sung,
One J/K corresponds to 1.045×1023 bits.

Indeed,
The Gibbs entropy formula states that thermodynamic entropy S equals
kB*sum[pi*ln(1/pi)], with units of J/K, where kB is the Boltzmann constant and
pi is the probability of microstate i. On the other hand, the Shannon entropy
is defined as H = sum[pi*log2(1/pi)], with units of bits. With the same
probability mass function, you can see that H = S/(ln(2)*kB), so setting S =
1J/K gives a Shannon entropy of 1.045×1023 bits.

On the other side, The
consumption per bit of data on the Internet is around 75 μJ at low access
rates and decreases to around 2-4 μJ at an access rate of 100 Mb/s.
see:

Futher, according to Landauer's theory, a minimum amount of heat – roughly
10–21 J per erased bit – must be dissipated when information is destroyed.
http://physicsworld.com/cws/article/news/2012/mar/12/wiping-data-will-cost-you-energy

In other words, summarizing, if you use the free energy to assess the
information, it works the same, giving a quantifiable value.

Arturo Tozzi

AA Professor Physics, University North Texas

Pediatrician ASL Na2Nord, Italy

Comput Intell Lab, University Manitoba

Messaggio originale
Da: "Sungchul Ji" <s...@pharmacy.rutgers.edu>
Data: 12/10/2017 22.08
A: "Francesco Rizz

### Re: [Fis] A PROPOSAL ABOUT THE DEFINITION OF INFORMATION

ety of environmental signals and component pathways (which have been
called 1–2-3 Component Systems), including the role of a few second messengers
which have been pointed out in bacteria too. And in the other side, the gene
transcription system as depending not only on signaling inputs but also on a
diversity of factors. Amidst the continuum of energy, matter, and information
flows, there seems to be evidence for signaling codes, mostly established
around the arrangement of life-cycle stages, in large metabolic changes, or in
the relationships with conspecifics (quorum sensing) and within microbial
ecosystems. Additionally, and considering the complexity growth of signaling
systems from prokaryotes to eukaryotes, four avenues or “roots” for the
advancement of such complexity would come out. A comparative will be
established in between the signaling strategies and organization of both kinds
of cellular systems. Finally, a new characterization of “informational
architectures” will be proposed in order to explain the coding spectrum of both
prokaryotic and eukaryotic signaling systems. Among other evolutionary aspects,
cellular strategies for the construction of novel functional codes via the
intermixing of informational architectures could be related to the persistence
of retro-elements with obvious viral ancestry.
---

El 10/10/2017 a las 11:14, tozziart...@libero.it<mailto:tozziart...@libero.it>
escribió:
Dear FISers,

Indeed, we know that, for an engine:
enthalpy = free energy + entropy x temperature.

At a fixed temperature,
enthalpy = free energy +entropy

The information detected (from an environmental object) by an observer is not
the total possible one (the enthalpy encompassed in the object), but just a
part, i.e., the part that it is not uncertain for him (the free energy).
Hence, every observer, depending on his peculiar features, detects a different
amont of free energy and does not detect the uncertain part (the entropy).

Arturo Tozzi

AA Professor Physics, University North Texas

Pediatrician ASL Na2Nord, Italy

Comput Intell Lab, University Manitoba

Messaggio originale
Da: "Christophe Menant"
<christophe.men...@hotmail.fr><mailto:christophe.men...@hotmail.fr>
Data: 10/10/2017 11.01
A:
"dea...@berkeley.edu"<mailto:dea...@berkeley.edu><dea...@berkeley.edu><mailto:dea...@berkeley.edu>
Cc:
"fis@listas.unizar.es"<mailto:fis@listas.unizar.es><fis@listas.unizar.es><mailto:fis@listas.unizar.es>
Ogg: [Fis] TR: Data - Reflection - Information

We should indeed be careful not to focus too much on language because 'meaning'
is not limited to human communication. And also because starting at basic life
level allows to address 'meaning' without the burden of complex performances
like self-consciousness or free will. (The existing bias on language may come
from analytic philosophy initially dealing with human performances).
Interestingly, a quite similar comment may apply to continental philosophy
where the 'aboutness' of a mental state was invented for human consciousness.
And this is of some importance for us because 'intentionality' is close to
'meaning'. Happily enough 'bio-intentionality' is slowly becoming an acceptable
entity
Regarding Peirce,  I'm a bit careful about using the triadic approach in FIS
because non human life was not a key subject for him and also because the
Interpreter which creates the meaning of the sign (the Interpretant) does not
seem that much explicited or detailed.
The divisions you propose look interesting  (intrinsic, referential,
normative). Would it be possible to read more on that (sorry if I have missed
Best
Christophe

De : Fis <fis-boun...@listas.unizar.es><mailto:fis-boun...@listas.unizar.es> de
la part de Terrence W. DEACON <dea...@berkeley.edu><mailto:dea...@berkeley.edu>
Envoyé : lundi 9 octobre 2017 02:30
À : Sungchul Ji
Cc : foundationofinformationscience
Objet : Re: [Fis] Data - Reflection - Information

Against "meaning"

I think that there is a danger of allowing our ant

### Re: [Fis] I agree with your considerations.

Hi Krassimir,

You have my permission.

Good luck.

Sung

From: Fis  on behalf of Krassimir Markov

Sent: Monday, October 9, 2017 5:32:59 AM
To: Foundation of Information Science
Subject: [Fis] I agree with your considerations.

Dear Yixin, Sung, Terry, Mark, and FIS Colleagues,

Let me remark that the General Information Theory is much more than a
single concept. You have seen that I have some answers in advance due to

What is important now is to finish this step and after that to continue
with the next. It may be just the idea about meaning.

What we have till now is the understanding that the information is some
more than data. In other words:

d = r
i = r + e

where:

d => data;
i => information;
r = > reflection;
e => something Else, internal for the subject (interpreter, etc.).

I need a week to finish our common with you current publication and to
send it to co-authors for final editing and after that for reviewing.

Dear Sung, Terry, and Mark, if you agree and give me the permissions, I
shall include your considerations in the end of the paper in the point
"Future work" and shall include you in the co-authors of the paper.

My next (second) post will be at the end of week.

Thank you very much for your great effort!

Friendly greetings
Krassimir

___
Fis mailing list
Fis@listas.unizar.es
___
Fis mailing list
Fis@listas.unizar.es
http://listas.unizar.es/cgi-bin/mailman/listinfo/fis



### Re: [Fis] Data - Reflection - Information

Hi FISers,

Recent discussions on information on this list reminds me of one of the main
principles of signs advanced by Ferdinand de Saussure (1859-1913)  -- the
arbitrariness of linguistic signs.  In contrast, Peirce (1839-1914), a
chemist-turned-logician-philosopher,  seems to have succeeded in capturing the
universal features of all signs, however fleeting, both linguistic and
otherwise.

The power and utility of the Peircean definition of signs can be illustrated by
applying his  triadic definition of signs to the term, 'information', veiwed as
a sign (having an arbitrariy meaning, according to Saussure).  My impression is
that all the varied defintions of information discussed on this list (which
supports the Saussre's principle of the arbitrariness of signs) can be
organized using the ITR (Irreducible Triadic Relation) diagram embodying the
Peircean principle of semiotics.   This is done in Figure 1 below, using the
definition of 'information' that Professor Zhong  recently provided as an
example.  As you can see, the ITR template has 6 place-holders, 3 nodes and 3
arrows, which can be populatedf by more than one set of concepts or terms, as
long as the terms or concepts are consistent with one another and obeys
well-established laws of physics and logic.

f g
Object -->   Sign -->
Interpretant
(Object Information) (Data)   (Perceived
Information)
|
^
|
|
|
|
|__|
h

f = natural process (or information production)
g = mental process or computing (or information interpretation)
h = correspondence (or information flow)

Object = Something referred to by a sign

Sign = Something that stands to someone for something other than itself in
some context.  Also called ‘representamen’
Interpretant = The effect a sign has  on the mind (or state) of the interpreter
(human or non-human)

Figure 1.  A suggested definition of ‘information’ based on the triadic
definition of the sign proposed by Peirce (1839-1914).  The symbol, A --- > B,
reads as "A determines B', 'A leads to B', ' A is presupposed by B', 'B is
supervened on A' (http://www.iep.utm.edu/superven), etc.

With all the best.

Sung

From: Fis  on behalf of 钟义信
Sent: Sunday, October 8, 2017 4:07:53 AM
To: KrassimirMarkov; foundationofinformationscience
Subject: Re: [Fis] Data - Reflection - Information

Dear Krassiir,

The formulars you proposed in your summary is good. May I mention that the
following formulas will be more precise:

Object Info = External info = Syntactic info = Data
Perceived info = Internal info = Syntactic info + Semantic info + Pragmatic info

In other words, data is also a kind of information - called syntactic
information, the information without meaning and utility associated. And
therefore we have a uniform concept of information.

So, the discussions we have last week is very much helpful!

Thank you!

--

Prof. Y. X. Zhong （钟义信）

Center for Intelligence Science Research

University of Posts & Telecommunications

Beijing 100876, China

- 回复邮件 -

Dear FIS Colleagues,

It is time for my second post this week.

Many thanks to Christophe Menant (for the profound question) and to all
colleagues (for the very nice and useful comments)!

**

“However, I'm not sure that “meaning” is enough to separate information
from data. A basic flow of bits can be considered as meaningless data.
But the same flow can give a meaningful sentence once correctly
demodulated.
I would say that:
1) The meaning of a signal does not exist per se. It is agent dependent.
- A signal can be meaningful information created by an agent (human
voice, ant pheromone).
- A signal can be meaningless (thunderstorm noise).
- A meaning can be generated by an agent receiving the signal
(interpretation/meaning generation).
2) A given signal can generate different meanings when received by
different agents (a thunderstorm noise generates different meanings for
someone walking on the beach or for a person in a house).
3) The domain of efficiency of the meaning should be taken into account
(human beings, 

### Re: [Fis] Heretic

Hi FISers,

If the "information periodic table" approach  to  Information Science is right,
which was described on this list a few days ago, the following  predictions may

(1)  Just as there are a finite number of elements in the chemical periodic
table that account for all the meteral objects in the Universe, so there may be
a finite number(~ 10^2 ?)  of  token informations in the information periodic
table that serve as the ontological basis for all the informations in the
mental Universe.

(2) Again, just as quantum physicists recognize two kinds of attributes of
quantum objects (also called quons or wavicles), i.e., 'static' attributes and
'dynamic' attributes, the former being constant in time and
observer-independent, while  the latter being time- and observer-dependent [1],
so perhaps  information scientists  may find it necessary to recognize  two
aspects of information -- (i) 'static' information, and (ii) 'dynamic'
information, the former being absolute and observer-independent (also called
'objective information' ?), while the latter is relative and observer-dependent
(also called 'subjective information' ?).

(3)  The famous 'complementarity' principle of Bohr, the Heisenberg principle,
and the quantum wave functions do not apply to  the static attributes of quons
but only to their dynamic attributes [1].

(4)  There are many dual aspects of information frequently discussed in the
field of information science, e.g., "it from bit", "static vs. dynamic",
"objective vs. subjective:, "medium vs. message", and "signifier vs. signified"
(see Table 1).  According to the  triadic metaphysics of Peirce [2] (as I
understand it),  all these dualities are just the prescinded (i.e., to detach
for the convenience of thought) aspect of the ultimate reality which is

(5)  As you may recall, the periodic table of information was based on the
three nodes, A, B and C, of the ITR (Irreducible Triadic Relation) network.  It
is interesting to note that the three categories appearing in the first row of
Table 1 below are related to these nodes and in fact can be viewed as their
tokens:

f
g

Firstness  --->  Secondness  ---> Thirdness

|
^
|
|
|
|
|___|

h

Figure 1. The isomorphism between the Peircean categoris and the ITR

f = manifestation/reification; g = habit formation; h =
correspondence/information flow

(6)  In conclusion, it may turn out that all these discussions on the concept
of information that we are having on this list and elsewhere may turn out to be
mere tips of enormous iceberg we call "information".

All the best.

Sung

Table 1.  The postulate that Peirce’s metaphysics [2] is a theory of
everything.  Red = Type;  Green = Tokens

Peirce’s metaphysics

Firstness

Secondness

Thirdness

1.  Quantum mechanics

Static information

Measurement/Data

Dynamic information
(Quantum mechanical information ?)

2.  Wheeler’s theory

Ultimate Reality (?)

It

Bit

3.  Cognitive science

Objective information (?)

Sign (?)

Subjective information (?)

4.  McLuhan

Ontology

Medium/Sign

Message

5.  Saussure’ semiology

Signified

Signfier

?

6.  Peirce’s semiotics

Object

Sign

Interpretant

7.  Periodic  table theory of information

Time-invariant information

Data/Sign (?)

Time-dependent  information

References:

[1] Herbert, N. (1987). Quantum Reality: Beyond the New Physics and
Excursion into  Metaphysics . . . . Anchor Books, New York.  pp. 46, 99-100,
102, 168, 193.
[2]  Categories (Peirce).  https://en.wikipedia.org/wiki/Categories_(Peirce)
[3] Ji, S. (2017).  The Cell Language  Theory: Connecting Mind and Matter.
World Scientific, New Jersey.  Section 10.20.

From: Fis  on behalf of Bob Logan

Sent: Thursday, October 5, 2017 12:39 PM
To: Arturo Tozzi
Cc: fis
Subject: Re: [Fis] Heretic

Dear Arturo - I enjoyed your expression of your opinion  because of its
directness and honesty even though I do not quite agree with everything you
said. I enjoyed it because it provoked the following thoughts.

Yes you are right there seems to be a variety of opinions as to just what
information is. All of them are correct and all of them are wrong including
mine which I will share with you in a moment. They are 

### [Fis] Information Periodic Table (IPT) or the Periodic Table of Information Science (PTIS)

 Euclidean geometry and politics, biology,
etc. I think Ortega makes right an interpretation about that. When
Aristotle makes the first classification of the sciences, he is continuing
with that very idea. Theoretical sciences, experimental or productive
sciences, and applied or practical sciences--with an emphasis on the
explanatory theoretical power of both physics and mathematics (ehm, Arturo
will agree fully with him). I have revisited my old reading notes and I
think that the Aristotelian confrontation with the Platonic approach to
the unity of knowledge that Ortega comments is extremely interesting for
our current debate on information principles.

There is another important aspect related to the first three principles in
my original message (see at the bottom). It would be rather strategic to
achieve a consensus on the futility of struggling for a universal
information definition. Then, the tautology of the first principle ("info
is info") is a way to sidestep that definitional aspect. Nevertheless, it
is clear that interesting notions of information may be provided relative
to some particular domains or endeavors. For instance, "propagating
influence" by our colleague Bob Logan, Stuart Kauffman and others, and
many other notions or partial definitions as well--I include my own
"distinction on the adjacent" as valuable for the informational approach
in biology. Is this "indefinability" an undesirable aspect? To put an
example from physics, time appears as the most undefinable of the terms,
but it shows up in almost all equations and theories of physics...
Principle three means that one can do a lot of things with info without
the need of defining it.

As for the subject that is usually coupled to the info term, as our
discussion advances further, entering the "information flows" will tend to
clarify things. The open-ended relationship with the environment that the
"informational entities" maintain via the channeling of those info
flows--it is a very special coupling indeed--allows these entities the
further channeling of the "energy flows" for self-maintenance. Think on
the living cells and their signaling systems, or think on our "info"
societies. Harold Morowitz's "energy flow in biology" has not been
paralleled yet by a similar "information flow in biology". One is
optimistic that the recent incorporation of John Torday, plus Shungchul Ji
and others, may lead to a thought-collective capable of illuminating the
panorama of biological information.

(shouldn't we make an effort to incorporate other relevant parties, also
interested in biological information, to this discussion?)

Best wishes--Pedro

El 23/09/2017 a las 21:27, Sungchul Ji escribió:

Hi Fisers,

I agree.

Communication may be the key concept in developing a theory of informaton.

Just as it is impossible to define what energy is without defining the
thermodynamic system under consideration (e.g., energy is conserved only
in an isolated system and not in closed or open systems; the Gibbs free
energy content decreases only when a spontaneous process  occurs in
non-isolsted systems with a constant temperature and pressure, etc), so it
may be that 'information' cannot be defined rigorously without  first
defining the "communication system" under consideration.   If this analogy
is true, we can anticipate that, just as there are many different kinds of
energies depending on the characteristics of the thermodynamic systems
involved, so there may be many different kinds of 'informations' depending
on the nature of the communication systems under consideration.

The properties or behaviors of all thermodynamic systems depend on their
environment, and there are three  system-environment relations -- (i)
isolated (e.g., the Universe, or the thermos bottle), (ii) closed (e.g.,
refriegerator), and (iii) open (e.g., the biosphere, living cells).

It is interesting to note that, all communication systems (e.g., cell,
organs, animals, humans) may embody ITR (Irreducible Triadic Relation)
which I  found it convenient to represent diagramamatically using a 3-node
network arrows as shown below:

f   g

A -->  B ->  C
|
^
|
|
|__|
h

Figure 1.  The Irreducible Triadic Relation (ITR) of C. S. Peirce
(1839-21914) represented as a 3-node,  closed and directed network.  The
arrows  form the commutative triangle of category theory, i.e., operations
f followed by g leads to the same result as operation h, here denoted as
fxg = h.

f = information production; g = information interpretation; h =
correspondence or information flow.   Pl

### Re: [Fis] Principles of IS

Hi Fisers,

I agree.

Communication may be the key concept in developing a theory of informaton.

Just as it is impossible to define what energy is without defining the
thermodynamic system under consideration (e.g., energy is conserved only in an
isolated system and not in closed or open systems; the Gibbs free energy
content decreases only when a spontaneous process  occurs in non-isolsted
systems with a constant temperature and pressure, etc), so it may be that
'information' cannot be defined rigorously without  first defining the
"communication system" under consideration.   If this analogy is true, we can
anticipate that, just as there are many different kinds of energies depending
on the characteristics of the thermodynamic systems involved, so there may be
many different kinds of 'informations' depending on the nature of the
communication systems under consideration.

The properties or behaviors of all thermodynamic systems depend on their
environment, and there are three  system-environment relations -- (i) isolated
(e.g., the Universe, or the thermos bottle), (ii) closed (e.g., refriegerator),
and (iii) open (e.g., the biosphere, living cells).

It is interesting to note that, all communication systems (e.g., cell, organs,
animals, humans) may embody ITR (Irreducible Triadic Relation) which I  found
it convenient to represent diagramamatically using a 3-node network arrows as
shown below:

f   g

A -->  B ->  C
|   ^
|   |
|__|
h

Figure 1.  The Irreducible Triadic Relation (ITR) of C. S. Peirce (1839-21914)
represented as a 3-node,  closed and directed network.  The arrows  form the
commutative triangle of category theory, i.e., operations f followed by g leads
to the same result as operation h, here denoted as fxg = h.

f = information production; g = information interpretation; h = correspondence
or information flow.   Please note that Processes f and g are driven by
exergonic physicochemical processes, and h requires a pre-existing code or
language that acts as the rule of mapping A and C.

Again, just as generations of thermodynamicists in the 19-20th centuries have
defined various kinds of "energies" (enthalpy, Helmholtz free energy, Gibbs
free energy) applicable to different kinds of thermodynamic systems, so
'information scientists' of the 21st century  may have the golden opportunity
to define as many kinds of 'informations' as needed for the different kinds of
"communcation systems" of their interest, some examples of which being
presented in Table 1.

Table 1.  A 'parametric' definition of information based on the values of the
three nodes
of the ITR, Figure 1.

Communication system   A  B
C
(Information)

Cells DNA/RNAProteins
Chemcal reactions
(Biological informations)
or chemical waves

_

HumansSenderMessage
(Linguistic informations)

_

Signs  Object
RepresentamenInterpretant
(Semiotic informations, or

'Universal informations' (?))
__

With all the best.

Sung

From: Fis  on behalf of JOHN TORDAY

Sent: Saturday, September 23, 2017 10:44:33 AM
To: fis@listas.unizar.es
Subject: [Fis] Principles of IS

Dear Fis, I am a newcomer to this discussion, but suffice it to say that I have
spent the last 20 years trying to understand how and why physiology has
evolved. I stumbled upon your website because Pedro Maijuan had reviewed a
paper of ours on 'ambiguity' that was recently published in Progr Biophys Mol
Biol July 22, 2017 fiy.
Cell-cell communication is the basis for molecular embryology/morphogenesis.
This may seem tangential at best to your discussion of Information Science, but
if you'll bear with me I will get to the point. In my (humble) opinion,
information is the 

### Re: [Fis] Causation is transfer of information

Hi Soeren and FISers,

(1) Tychism is intrinsic to the Planckian information, since it is defined as
the binary logarithm of the ratio of the area under the curve (AUC) of the
Planckian distribution (PDE)  over the AUC of the Gaussian-like Equation (GLE):

I_P  =  log (AUC(PDE)/AUC(GLE))

Tychism is implied in GLE.

(2)  The Planckian processes are defined as those physicochemical or formal
processes that generate long-tailed histograms (or their superpositions)
fitting PDE (or its suppositions).   The Planckian process seems irreducibly

f
g

Random processes --->   Long-tailed histograms
->  PDE

(Firstness)
(Secondness) (Thirdness)

|
^

|
|

|
|

|
|

||

h

Figure 2.  The Irreducible Triadic Relation (ITR) embodied in the Planckian
processes.  f = selection process either natural or artificial; g =
mathematical modeling; h = grounding, correspondence, or information flow.

(3)  (to be continued)

All the best.

Sung

From: Søren Brier <sbr@cbs.dk>
Sent: Wednesday, March 29, 2017 7:06 PM
To: Sungchul Ji; Terrence W. DEACON; John Collier
Cc: fis
Subject: RE: [Fis] Causation is transfer of information

Dear Sung

It is difficult for me to say as you do not make your metaphysical framework
explicit.  This was the great work Peirce did. I am pretty sure you do not have
a dynamic triadic process concept of semiosis based on a tychastic theory of
Firstness as potential qualia or forms of feeling of which information is only
an aspect.

Best

Søren

From: Sungchul Ji [mailto:s...@pharmacy.rutgers.edu]
Sent: 29. marts 2017 20:35
To: Søren Brier; Terrence W. DEACON; John Collier
Cc: fis
Subject: Re: [Fis] Causation is transfer of information

Hi Soeren,

Can  you be more specific about what aspect of my proposal described in my
previous emails you think are my own and has nothing to do with (or are even
based on my misinterpretation of) Peirce ?

Sung

From: Søren Brier <sbr@cbs.dk<mailto:sbr@cbs.dk>>
Sent: Wednesday, March 29, 2017 2:10 PM
To: Sungchul Ji; Terrence W. DEACON; John Collier
Cc: fis
Subject: RE: [Fis] Causation is transfer of information

Dear Sung

I suggest you call this your own theory and make your own definitions of terms,
because you confuse things by attempting to draw on Peirce, because there is a
whole process philosophy with synechism, tychism, agapism and Scholastic
realism plus a phenomenological and mathematically based  triadic metaphysics
as the basis of Peirce’s concepts, which is the fruit of his life’s work. I do
not think you are ready to carry that load. It takes many years to understand
fully. The ‘sign’ is a triadic process of representamen, object and
interpretant working in the realm of Firstness, Secondness and Thirdness in a
society at large or a society of researchers devoted to the search for truth
producing the meaning of signs, which when developed into propositional
arguments can be tested in the fallible scientific process  of generating more
rationality in culture as well as nature.

Best

Søren

From: Fis [mailto:fis-boun...@listas.unizar.es] On Behalf Of Sungchul Ji
Sent: 29. marts 2017 00:27
To: Terrence W. DEACON; John Collier
Cc: fis
Subject: Re: [Fis] Causation is transfer of information

Hi Fisers,

I agree with Terry that "information" has three irreducible aspects --- amount,
meaning, and value.  These somehow may be related to another triadic relation
called the ITR as depicted below, although I don't know the exact rule of
mapping between the two triads.  Perhaps, 'amount' = f, 'meaning' = g, and
'value' = h ? .

f   g

Object --->

### Re: [Fis] Causation is transfer of information

Hi Soeren,

Can  you be more specific about what aspect of my proposal described in my
previous emails you think are my own and has nothing to do with (or are even
based on my misinterpretation of) Peirce ?

Sung

From: Søren Brier <sbr@cbs.dk>
Sent: Wednesday, March 29, 2017 2:10 PM
To: Sungchul Ji; Terrence W. DEACON; John Collier
Cc: fis
Subject: RE: [Fis] Causation is transfer of information

Dear Sung

I suggest you call this your own theory and make your own definitions of terms,
because you confuse things by attempting to draw on Peirce, because there is a
whole process philosophy with synechism, tychism, agapism and Scholastic
realism plus a phenomenological and mathematically based  triadic metaphysics
as the basis of Peirce’s concepts, which is the fruit of his life’s work. I do
not think you are ready to carry that load. It takes many years to understand
fully. The ‘sign’ is a triadic process of representamen, object and
interpretant working in the realm of Firstness, Secondness and Thirdness in a
society at large or a society of researchers devoted to the search for truth
producing the meaning of signs, which when developed into propositional
arguments can be tested in the fallible scientific process  of generating more
rationality in culture as well as nature.

Best

Søren

From: Fis [mailto:fis-boun...@listas.unizar.es] On Behalf Of Sungchul Ji
Sent: 29. marts 2017 00:27
To: Terrence W. DEACON; John Collier
Cc: fis
Subject: Re: [Fis] Causation is transfer of information

Hi Fisers,

I agree with Terry that "information" has three irreducible aspects --- amount,
meaning, and value.  These somehow may be related to another triadic relation
called the ITR as depicted below, although I don't know the exact rule of
mapping between the two triads.  Perhaps, 'amount' = f, 'meaning' = g, and
'value' = h ? .

f   g

Object --->  Sign -->  Interpretant

|
^
|
|
|
|
|
|
|_|

h

Figure 1.  The Irreducible Triadic Relation (ITR) of seimosis (also called sign
process or communication) first clearly articulated by Peirce to the best of my
knowledge. Warning: Peirce often replaces Sign with Representamen and
represents the whole triad, i.e., Figure 1 itself (although he did not use such
a figure in his writings) as the Sign. Not distinguishing between these two
very different uses of the same word "Sign" can lead to semiotic confusions.
The three processes are defined as follows: f = sign production, g = sign
interpretation, h = information flow (other ways of labeling the arrows are not
by", etc., and the three arrows constitute a commutative triangle of category
theory, i.e., f x g = h, meaning f followed by g ledes to the same result as h.

I started using  the so-called  ITR template, Figure 1,  about 5 years ago, and
the main reason I am bringing it up here is to ask your critical opinion on my
suggestion published in 2012 (Molecular Theory of the Living  Cell: Concepts,
Molecular Mechanisms, and Biomedical Applications, Springer New York, p ~100 ?)
that there are two kinds of causality -- (i) the energy-dependent causality
(identified with Processes f and g in Figure 1) and (ii) the information (and
hence code)-dependent causality (identified with Process h).  For convenience,
I coined the term 'codality' to refer to the latter to contrast it with the

I wonder if we can  view John's idea of the relation between 'information' and
'cause' as being  an alternative way of expressing the same ideas as the
"energy-dependent causality" or the "codality" defined in Figure 1.

All the best.

Sung

From: Fis <fis-boun...@listas.unizar.es<mailto:fis-boun...@listas.unizar.es>>
on behalf of Terrence W. DEACON
<dea...@berkeley.edu<mailto:dea...@berkeley.edu>>
Sent: Tuesday, March 28, 2017 4:23:14 PM
To: John Collier
Cc: fis
Subject: Re: [Fis] Causation is transfer of information

Corrected typos (in case the intrinsic redundancy didn't compensate for these
minor corruptions of the text):

information-beqaring medium =  information-be

### Re: [Fis] Information: a metaphysical word

Hi FISers,

I wonder some of he controversies  surrounding information can be traced to
conflating  TYPE and TOKENS.  For example, apples and oranges (tokens) are not
the same but they are  all species of the fruit (type).  Likewise the
information exchanged among non-living systems like computers are not the same
as the information exchanged among humans or between humans and machines, but
they are species of the type called information which to me is characterized by
the Irreducible Triadic Relation (ITR) of C. S. Peirce.

If this line of reasoning is valid, it may be justified to coin a new term,
"informons", to refer to specific examples carrying Information.

All the best.

Sun

From: Fis  on behalf of Robert E. Ulanowicz

Sent: Monday, March 27, 2017 11:37:31 AM
To: tozziart...@libero.it
Cc: fis
Subject: Re: [Fis] Information: a metaphysical word

Dear Arturo,

I am less pessimistic than you about treating and measuring information.

First off, that information is always relative is the obverse of the third
law of thermodynamics. It cannot be otherwise.

Secondly, you are correct that there are important metaphysical aspects of
information. To my knowledge, it is the only discipline predicated on
*absence* -- the absence of constraint (popularly characterized as
"uncertainty"). We know from the third law that such entropic-like
measures are always relative to some assumed reference. Actual information
is calculated as a decrease in apophasis and shares that same relativity.

While you might feel that the metaphysical associations disqualify
information as an instrument of science, I would suggest that it rather
opens a new window onto our vision of reality.

Should you think information measures useless because of such metaphysical
associations, I would submit that measures of apophasis can be quite
useful in remediation of environmental problems (and problems in a host of
other realms as well). (See the example beginning on p51 of
.)

Let me end by saying that I understand fully your exasperation with
information theory (IT). For almost two decades I abjured IT, because I
considered it nonsensical that a TV screen with "snow" (no signal) should
have more information that a picture of a movie star. (My vexation was
based on similar reasons as yours.) Then it finally dawned on me that some
of the founders of IT had made serious pedagogical errors with their
definitions. I eventually sorted out my own perspective (See Chapter 5 of
), and went
on to build my entire career on concepts related to IT.

I would encourage you give it all another look. IT can be quite rewarding!

Peace,
Bob

>
> Dear FISers,
> The current debate about information has just a possible development, I
> think.
> Everybody defines information in the way he prefers: subjective, biotic,
> bit, and so on.
> Therefore, every study that talks about "information" is meaningless.
> In particular, subjective accounts of information are useless, because, in
> their framework, the information is not measurable, but just depends on
> the observer: if me, John and Mary see the same can, I think that the Coke
> is good, John thinks that he is thirsty and Mary that the aluminium is a
> malleable material.
> On the other side, I suggested in a previous post how the information
> entropy (such as Shannon's, or Bekenstein's, or Hawking's) may change
> according to the relativistic speed of the hypothetical observer.Â
> Therefore, I suggest to fully remove the term "information" from every
> scientific account.Â  The term "information" refers, in Popper's terms, to
> a not falsifiable theory, to pseudoscience: it is a metaphysical claim,
> like the concepts of Essence, Being, God and so on.Â
> Therefore, by now, the term "information" is definitely out of my
> scientificÂ  vocabulary.Â
> Â
> --
> Inviato da Libero Mail per
> Android___
> Fis mailing list
> Fis@listas.unizar.es
> http://listas.unizar.es/cgi-bin/mailman/listinfo/fis
>

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### Re: [Fis] PLANCKIAN INFORMATION: A NEW MEASURE OF ORDER (From S. Ji)

Hi Pedro,

Thanks for the excellent job done.

Sung

From: Fis <fis-boun...@listas.unizar.es> on behalf of Pedro C. Marijuan
<pcmarijuan.i...@aragon.es>
Sent: Thursday, March 23, 2017 6:25 AM
To: 'fis'
Subject: [Fis] PLANCKIAN INFORMATION: A NEW MEASURE OF ORDER (From S. Ji)

Note: what follows is an abbreviated text taken from the presentation.
The whole file, too big for our list, can be found at fis web pages:
A very recent article developing similar ideas:
http://www.mdpi.com/2078-2489/8/1/24
[http://www.mdpi.com/img/journals/information-logo-sq.png?a1aee442a5e8cd96]<http://www.mdpi.com/2078-2489/8/1/24>

Information | Free Full-Text | Waves as the Symmetry
...<http://www.mdpi.com/2078-2489/8/1/24>
www.mdpi.com
In 1997, the author concluded that living cells use a molecular language
(cellese) that is isomorphic with the human language (humanese) based on his
finding that the ...

Greetings to all--Pedro
---

What is the Planckian information ?

SUNGCHUL JI

Department of Pharmacology and Toxicology
Ernest Mario School of Pharmacy
Rutgers University
s...@pharmacy.rutgers.edu<mailto:s...@pharmacy.rutgers.edu>

The Planckian information (I_P) is defined as the information produced (or
used) by the so-called Planckian processes which are in turn defined as any
physicochemical or formal processes that generate long-tailed histograms
fitting the Planckian Distribution Equation (PDE),
y = (A/(x + B^5)/(Exp(C/(x + B)) – 1)
(1)
where A, B and C are free parameters, x is the class or the bin to which
objects or entities belong, and y is the frequency [1, 1a].  The PDE was
derived in 2008 [2] from the blackbody radiation equation discovered by M.
Planck (1858-1947) in 1900, by replacing the universal constants and
temperature with free parameters, A, B and C.  PDE has been found to fit not
only the blackbody radiation spectra (as it should) but also numerous other
long-tailed histograms [3, 4] (see Figure 1).
One possible explanation for the universality of PDE is that many long-tailed
histograms are generated by some selection mechanisms acting on
randomly/thermally accessible processes [3]. Since random processes obey the
Gaussian distribution, the ratio of the area under the curve (AUC) of PDE to
that of Gaussian-like symmetric curves can be used as a measure of
non-randomness or the order generated by the Planckian processes.

As can be seen in Figs. 1 (g), (i), (k), (o), (r) and (t), the curves labeled
‘Gaussian’ or ‘Gaussian-like’ overlap with the rising phase of the PDE curves.
The ‘Gaussian-like’ curves were generated by Eq. (2), which was derived from
the Gaussian equation by replacing its pre-exponential factor with free
parameter A:

y = Ae– (x – μ)^2/(2σ^2)
(2)

The degree of mis-match between the area under the curve (AUC) of PDE, Eq. (1),
and that of GLE, Eq. (2), is postulated to be a measure of non-randomness (and
hence order).  GLE is associated with random processes, since it is symmetric
with respect to the sign reversal of in its exponential term, (x - µ).  This
measure of order is referred to as the Planckian Information (IP) defined
quantitatively as shown in Eq. (3) or Eq. (4):

IP = log2 (AUC(PDE)/AUC(GLE))   bits
(3)
or

IP  = log2 [∫P(x)dx/∫G(x)dx] bits
(4)

where P(x) and G(x) are the Plackian Distribution Equation and the
Gaussian-Like Equation, respectively.

It is generally accepted that there are at least three basic aspects to
information – amount, meaning, and value.  Planckian information is primarily
concerned with the amount (and hence the quantitative aspect) of information.
There are numerous ways that have been suggested in the literature for
quantifying information bedside the well-known Hartley information, Shannon
entropy, algorithmic information, etc [5].  The Planckian information, given by
Equation (3), is a new measure of information that applies to the Planckian
process generally defined as in (5):

“Planckian processes are the physicochemical, neurophysiological,
(5)
biomedical, mental, linguistic, socioeconomic, cosmological, or any
other processes that generate long-tailed histograms obeying the
Planckian distribution equation (PDE).”

The Planckian information represents the degree of organization of physical (or
nonphysical) systems in contrast to the Boltzmann or the Boltzmann-Gibbs
entropy