Re: [Fis] [Fwd: Information And Locality, Addendum's]--Steven

[Francesco Rizzo]

Cari Tutti,
leggendo i messaggi di Steven e quello di Pedro desidero precisare che la
triade sintattica (relazione tra segni), semantica (relazione tra segni e
significato) e pragmatica (relazione tra uomo e segni) -- dal sottoscritto
approfondita e applicata alla mia "Nuova economia"-- non esclude l'uso
della teoria matematica (relazione tra simboli) della comunicazione, ma va
oltre per comprendere anche ciò che nessuna formula matematica potrà
esaurire tutte le variabili eventuali e intervenienti relative alla
bellezza e alla bruttezza della realtà poetica dell'esistenza e della
conoscenza. Inoltre, non so quante volte ho ribadito che è necessaria
un'armonia del disaccordo tra le diverse categorie di informazione usate
dalle persone di questo mondo per descrivere e comunicare qualunque
disciplina scientifica e qualsiasi prassi esistenziale. Ma ho l'impressione
che quel che scrivo io per alcuni, non so quanti, non conta niente.
Pazienza o resistenza.
Saluti, senza polemica o risentimento che non mi appartengono.
Francesco Rizzo.

2015-10-02 14:00 GMT+02:00 Pedro C. Marijuan :

> Dear Steven and FIS colleagues,
>
> Sorry about the problems with the server. Next messages, please, send them
> directly to me and I will re-enter.
>
> The approach to locality you have explained is interesting. In general it
> looks right, as biological information can be widely delocalized,
> relatively delocalized, but also strictly localized. Apart from your
> examples on allosterism and receptor synergistic action, the gradients of
> second messengers and the transmembrane transmission of signaling effects
> in other receptors may be instances of the relative class, and the base
> pairing of nucleotides would correspond to the localized class. If I am not
> wrong, it is quite difficult to shoehorn into a single category the bioinfo
> architectures of the cell. Therefore in general I use the "info flow"
> parlance, for the result of the cell's communication with the environment
> is quite often a Brownian flow or an "influence" (mostly of the delocalized
> class) that travels towards the action centers of the cell --the
> transcription factors that guide gene expression.
>
> Then, arriving at that instance, I have some disagreement in the way
> Guenther speaks about the syntactic-semantic-pragmatic rules applying to
> any sign-system of natural biocommunication language. Imagine, following
> with the previous paragraph, that we have just received (E. coli) a puff of
> cAMP signal from the environment. It has been trapped by some receptors of
> a two component system and some activated transcription factors  CRP type
> travel to express around 400 different genes. Of course, it previously
> depends on the dominant sigma factors (if sigma 70 dominates, it is OK,
> otherwise there might be problems with the previous sequence). Well, most
> of this narrative is fictitious, but the problem is how do you express in
> "rule-mediated" statements this type of half-known tremendous complexity?
> How do you handle the very different signaling capabilities/properties of
> one component systems, two components, three components, and above all, the
> sigma factors --that in my view are most of them essential for connecting
> with the life cycle; they represent the equivalent to our "moods" and
> "emotions". Otherwise I think he is quite right in the conflation of signs
> and sign-users at the sub-viral level. I consider it, potentially, a
> breakthrough complementing the symbiotic theory of Lynn Margulis with a new
> viral (sub-viral) branch, plus the well-known archeal and eubacterial ones.
>
> Unfortunately, the neglect of the life cycle is almost universal. Neither
> neuroscientists nor psychologists nor social scientists are sufficiently
> aware of this invisible "water" that permeates all living stuff. Echoing
> some old evolutionary statement, everything should made sense in relation
> with the advancement of the corresponding life cycle. Just the superficial
> observation of human exchanges in our societies, or in whatever historical
> epoch, the conversational small-talk topics, the way people greet each
> other, the gossip media... the condensates of the individuals' info cycles
> are everywhere. A new conceptualization of information as accompanying the
> development of human action for the sake of life cycles and subtending the
> cooperation structures of economic life could have wide multidisciplinary
> interest--I think. (Unfortunately, these adventures are discouraged: Mark
> is terribly right about the sorrow state of our collective brain
> reservoirs--poor universities! kingdoms of conventionalism and tunnel
> vision).
>
> To conclude, the emphasis on the generative also allows some connection
> with Howard's and Bob's  criticisms on the "dead"  approach to
> cosmological matters.  I do not venture to expose my own naive views,
> rather will repeat a wonderful sentence from Michael Conrad (1996): 

Re: [Fis] [Fwd: Information And Locality, Addendum's]--Steven

[Jerry LR Chandler]

Steven, Pedro, List:

Steven:  Your posts are a breath of fresh air.  

I have long wondered about how you were associating information theory with 
biophysics and the Peirce philosophic notions of information and symbols.  This 
is now partially clarified.

Numerous, very numerous questions are raised by you posts and Pedro's 
translations into his views of molecular biology.

First, a general comment on the suggested background primer on Kahn which is 
laced with weak metaphors.
I particularly object to the notion (at about minute 2:45 of the first segment) 
that information is the answer to a single question, yes or no.

First objection to the Kahn video is that only an infinitesimal fraction of all 
scientific questions yield a "yes" or "no" answer.

Second objection is that, thus far, no one has constructed a general method for 
coding from the fundamental level of electrical particles to either chemical 
information or biological information.  For QM reasons, this coding problem 
appears to an intractable mathematical problem for any biological theory of 
information emerging from physical principles. 

In these cases, the rich physical behavior of relationships between polar 
opposites, positive and negatively charges apparently requires  the emergence 
of new codes  This is a critical fact that haunts any theoretical attempt to 
invoke Shannon information theory to either chemistry or biology.  

None-the-less, I strongly endorse the intimate linkage between communication 
and information.  This linkage appears necessary for a structural mathematics 
that can be used to exchange meanings.

But, lets ignore that issue for the moment. Let me start with the concepts that 
appears to me to motivate your notion of locality as information.  It is this 
notion that Pedro seeks to translate from a spatial concept, locality, to 
material concepts based on the physics of collections of atomic numbers 
arranged into biological patterns, such as DNA, RNA, and the usual list of 
acronyms that can not be literally (factually) translated into philosophical or 
rhetorical languages.

I am puzzled by the sentence:
It should be clear that the bit alone is local and that any organization of 
>> the bit what-so-ever, be it in the form of a word, a Turing machine tape, in 
>> some form on a disk drive or in a text book is, to some degree, lacking that 
>> locality.

In mathematical terms, what is locality?  
How would express this usage of "locality" in terms of topological spaces 
(another mathematical form of locality) and yet exclude QM theory?

In other words, how does "locality" know where it is at?

In mathematical terms, how is the concept of locality related to message 
content?
For a simple example, what happens to the notion of "locality" when a message 
is compressed 2 fold? 5 fold? 20 fold? Is this concept of locality consistent 
and complete under compression?

An alternative view could be that a bit has meaning only within the context of 
a bit string. In this case, the meaning of the bit string, as a combinatorial 
object, can be assigned a list of rules which change the order of the bit 
string with conservation of the meaning of the string as a whole. 

(As an aside, the preceding suggestion is a rough analogy with the 
"information" content of biological processes such as the flow of information 
from an inducer to a transport protein, as in the Lac operon.) 

On a more constructive avenue, 
> Engineering-wise I believe that a simplified genomics is both possible and 
> ultimately programmable. Enabling us to devise organisms with particular 
> behaviors able to serve our inevitable causes.


is a foundational conjecture seeking to link mathematics, physics, chemistry 
and biology.

First, I would note that molecular biologists, using well-understood chemical 
structural principles, can now
 
> "devise organisms with particular behaviors able to serve our inevitable 
> causes."
so that the second sentence is experimentally used now.

So, it appears that the principle (doctrine) of locality should work if a path 
from the conceptualization of "locality" to chemical structures can be 
constructed?

That is, the paths from quantitative "biophysical" symbolic representations to 
quantitative biochemical symbolic representations (and hence to subjective 
"biosemiotic representations) can be abstractly conceptualized and calculated.

Is this conjecture consistent with your conceptualization of biophysics?

Again, thanks for the highly original and stimulating posts. 

Cheers

Jerry






On Oct 2, 2015, at 3:50 PM, Steven Ericsson-Zenith wrote:

> 
> Dear Pedro,
> 
> I greet your response with thanks and a sigh of relief. At least someone is 
> paying attention. :-)
> 
> I understand your concern re. multiple parts and apparent complexity in the 
> full "life-cycle" as you speak of it.  I suspect that there underlie it all a 
> few very simple rules, and this is my premise.  
> 
> Central to this view is 

[Fis] [Fwd: Information And Locality, Addendum's]--Steven

[Pedro C. Marijuan]

(From Steven)

 Original Message 
Subject:Information And Locality, Addendum's
Date:   Mon, 28 Sep 2015 16:46:41 -0700
From:   Steven Ericsson-Zenith 
To: 	Foundations of Information Science Information Science 


CC: Pedro Marijuan 



Dear List,

Looking over my promises in this discussion I have two particular notes to 
provide. These got put aside as I became distracted by both the server issues 
and my health.

I promised to provide a historical statement (referencing Benjamin Peirce, 
Einstein and Turing) and a brief mathematical statement.  I will make these 
statements separately over the coming days.

Pedro, I note that server issues continue.  


Regards,
Steven


--
 Dr. Steven Ericsson-Zenith, Los Gatos, California. +1-650-308-8611
 http://iase.info
---

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