Re: [Fis] TR: some notes

[Sungchul Ji]

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
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."


(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 
Chladini plate shown below:


https://www.youtube.com/watch?v=wvJAgrUBF4w

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

Amazing Resonance Experiment!
www.youtube.com
Add me on Facebook - (click LIKE on Facebook to add me) 
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] Math, math, math!

[tozziarturo]

Dear FISers,

My so called pseudoscience has been published in not dispisable journals, for a 
simple reason: I provide what is required by truly scientific reviewers, i.e., 
testable mathematical predictions.  


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[Fis] TR: some notes

[Christophe Menant]

Thanks for that Pedro,
Just a few comments.

All the best,

Christophe


De : Fis  de la part de Pedro C. Marijuan 

Envoyé : lundi 13 novembre 2017 14:30
À : 'fis'
Objet : [Fis] some notes

Dear All,

Herewith some notes on the exchanges of past weeks (sorry, I was away in
bureaucratic tasks).

1. Agents & Information. There were very good insights exchanged;
probably both terms make a fertile marriage. Actually I have been
writing about "informational entities" or "subjects" as
receivers/builders of information but taking into account the other
disciplines around, "agents" look as the most natural companion of
information. The only thing I don't quite like is that they usually
appear as abstract, disembodied communicative entities that do not need
self-producing. Their communication is free from whatever life
maintenance...

Yes, agents naturally go with information as they are the source of meaning
generation, of sense making. Agents can be organic, human and artificial.
(I look at agents as  identifyable entities submitted to internal
constraints and capable of actions for the satisfaction of the constraints).
Artificial agents can be looked at as disembodied but their  being is
derived from our human ones. So their self (if any) is part of the
human designer's self.

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?


Perhaps it could be interesting here to highlight  that physics/chemistry
and biology/psychology cannot address information the same way.
Physics and chemistry use tools with precise definitions allowing to
model our environment in a deterministic and predictable way
(QM and Chaos deserving more investigations).
Biology/psychology do not benefit of such rigorous mathematical
support. We do not even know how to define life or consciousness,
and our models are incomplete.
So what about separating the two domains and looking at their relations
as a third domain?
1) Thermodynamics, entropy, quantity of information, channel capacity,
data transmission.
2) Meaning generation, biology and self-consciousness
3) Emergence and locality of constraints, emergence of meanings
This puts again the focus on meaning generation, a key evolutionary
step without which we would not be here.
Also, let's not forget that data transmission and quantification of
information are about meaningful information.
So why not consider internal constraint satisfaction, the source of
meaning generation,  as an essential direction of communication?

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
http://sites.google.com/site/pedrocmarijuan/
[https://sites.google.com/site/pedrocmarijuan/_/rsrc/1468865628625/home/DSC00254-1.JPG?height=420=346]

Pedro.C.Marijuan
sites.google.com
Personal Webpage of Pedro C. Marijuán



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Re: [Fis] some notes

[Stanley N Salthe]

Pedro -- Regarding:

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?

S: It is interesting on this point to note the studied avoidance of serious
discourses to include the "life cycle itself" (i.e.: immaturity
->maturity-> senescence) in any scientific study other than some areas of
biology (gerontology).  One can conclude that we have such a fear of aging
that it has blinded our discourses to this basic fact.

STAN

On Mon, Nov 13, 2017 at 8:30 AM, Pedro C. Marijuan <
pcmarijuan.i...@aragon.es> wrote:

> Dear All,
>
> Herewith some notes on the exchanges of past weeks (sorry, I was away in
> bureaucratic tasks).
>
> 1. Agents & Information. There were very good insights exchanged; probably
> both terms make a fertile marriage. Actually I have been writing about
> "informational entities" or "subjects" as receivers/builders of information
> but taking into account the other disciplines around, "agents" look as the
> most natural companion of information. The only thing I don't quite like is
> that they usually appear as abstract, disembodied communicative entities
> that do not need self-producing. Their communication is free from whatever
> life maintenance...
>
> 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?
>
> 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
> http://sites.google.com/site/pedrocmarijuan/
> -
>
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[Fis] some notes

[Pedro C. Marijuan]

Dear All,

Herewith some notes on the exchanges of past weeks (sorry, I was away in 
bureaucratic tasks).


1. Agents & Information. There were very good insights exchanged; 
probably both terms make a fertile marriage. Actually I have been 
writing about "informational entities" or "subjects" as 
receivers/builders of information but taking into account the other 
disciplines around, "agents" look as the most natural companion of 
information. The only thing I don't quite like is that they usually 
appear as abstract, disembodied communicative entities that do not need 
self-producing. Their communication is free from whatever life 
maintenance...


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?


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
http://sites.google.com/site/pedrocmarijuan/
-

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