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 this notion of locality.  In the organism structure, 
> no localized action is entirely isolated.  Even "... the very different 
> signaling capabilities/properties of one component, two components, three 
> components, and above all, the sigma factors ..." are unified by it, and this 
> is manifest in our own refined and coordinated capacity to see, taste, hear, 
> touch, smell the roses, feel pain, pleasure, and move simultaneously.  
> 
> We cannot apply the strict locality notions of computer engineering. There is 
> no isolated point-to-point signal.
> 
> So I do expect that the same hyperfunctor mathematics of closed structure 
> that I have described for cells applies across all (closed) membrane 
> structures and within. 
> 
> Despite this, we, as an example of this messy complexity, are still able to 
> refine the action of habit to amazing precision and refine thought to 
> stunning exactitude.
> 
> This is clearly an article of faith on my part in Wigner's "unreasonable 
> effectiveness" of mathematics and the simplicity advocated by Einstein. Who 
> could have imagined a century ago that the apparent complexity of  celestial 
> mechanics would be tractable to a single theory such as Einstein's?
> 
> So because of this I am confident in my very simple approach and you will see 
> shortly, in a subsequent post, how the mathematics is simplified and extends 
> to the forces of physical science generally to produce a holistic 
> mathematical physics, including the effects of gravitation, electromagnetism 
> (chemistry), and sense.
> 
> I suspect that Darwinian evolution is itself messy, leaving behind it both 
> redundant and useless artifacts. 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. And, 
> of course, I return to those in large-scale computation and to my 
> grand-challenge to place life where it would not otherwise occur.
> 
> Regards,
> Steven
> 
> 
> 
> 
> 
> On Fri, Oct 2, 2015 at 5:00 AM, Pedro C. Marijuan <pcmarijuan.i...@aragon.es> 
> wrote:
> 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): "When we look at a biological 
> system we are looking at the face of the underlying physics of the universe."
> 
> best--Pedro
> 
> 
> 
> Pedro C. Marijuan wrote:
> (From Steven)
> 
> -------- Original Message --------
> Subject:     Information And Locality, Addendum's
> Date:     Mon, 28 Sep 2015 16:46:41 -0700
> From:     Steven Ericsson-Zenith <ste...@iase.us>
> To:     Foundations of Information Science Information Science 
> <fis@listas.unizar.es>
> CC:     Pedro Marijuan <pcmarijuan.i...@aragon.es>
> 
> 
> 
> 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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> 
> 
> 
> -- 
> -------------------------------------------------
> 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 X
> 50009 Zaragoza, Spain
> Tfno. +34 976 71 3526 (& 6818)
> pcmarijuan.i...@aragon.es
> http://sites.google.com/site/pedrocmarijuan/
> -------------------------------------------------
> 
> 
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