Dear FISers,

Tomorrow we will start the new session on Infobiosemiotics, by Soeren Brier. 
Before so, let me pen some comments.

First, to join Plamen and others in thanking Louis. Particularly interesting 
for me was his last text on recursive distinctioning. Quite curiously, an old 
work of mine I mentioned weeks ago was about a sort of algebra for distinctions 
(to be applied to a putative "language of cells" via signaling systems) that 
contains remarkable similarities. Our elimination of items in the letter 
strings was based on three principles: symmetry, economy, and parsimony... we 
used "0" and inverse elements, and after the arrival of some new letters-signs 
the whole set/node was collapsing and "emitting", etc. etc. Anyhow, I will 
re-read with high interest, looking for further connections & ideas.

About some of the biological points raised in the discussion a few days ago 
(unfortunately I was caught in administrative compromises), I would reiterate 
that the present day biomolecular panorama of the simplest cells suggests a 
more cogent relationship between self-production and communication. I already 
gave some arguments: direct communication with the world is a prerequisite for 
organizing a metabolically efficient cellular system. Such direct communication 
via "one component systems" outnumbers any other signaling tools; this is well 
known in signaling science more than 10 years ago but has had no general impact 
yet.  The prokaryote is not really so autopoietic, it could be something else 
(maybe "infopoietic", but is the label needed??)... What the theme strongly 
suggests is a reconceptualization on how the cell "is in the world," only 
viable through unending communication tricks with the environment. 
Communication for "eking out" a life runs densely across the whole evolutionary 
process. Even more, it runs very deeply in the innards of our social life, in a 
curious trans-kingdom evolutionary twist. As I remarked in the previous session 
with Maxine, the origins of our own human communication via language are 
closely related to our wild "microbiome experiment". Given that we count with 
50% less microbiota in our gut and we have to produce an extra 20% of metabolic 
output, the social knitting via language for group feeding (cooking, 
fermentation, etc.) made the miracle. The big, communicative "social brain" 
(Allman, Dunbar) was essentially born for achieving group nutritional survival. 
Group communion... as is symbolically reminded in some religious rites. (Well, 
as an aside, my own mini-group is cooperating in some microbiome research on a 
very essential nutrient, with very curious results that we will publicize quite 
soon. I cannot help but having the theme in mind!). Anyhow, the final point 
from this ignored vital dependence and from similar ones is that we live 
crisscrossed by multitude of information flows that we are unaware of. That 
some disciplines could have deciphered faster some of them has had a tremendous 
influence on how we have approached during last two generations the whole 
information phenomena. Witness the terrible conceptual problems we have in 
whatever aggregate scales (often, already navigated elegantly by nervous 

The gist of the above tangents, is that some sort of premature closure in the 
the relationship between life and formal/philosophical arenas has introduced an 
unnecessary, cumbersome complexity. New forms of thought and of expression may 
be at hand to clarify the biological/social roots of information/communication 
phenomena, also for better capturing the personal meanings of life in these 
strange times of information and complexity overload. McLuhan revisited... And 
finally, a hint addressed to the quantum oriented colleagues: "When we look at 
a biological system we are looking at the face of the underlying physics of the 
universe." (Michael Conrad, First FIS Conference, Madrid 1994).

It will be quite interesting continuing the present discussion under the new 
themes proposed by Soeren.

Best regards

El 31/03/2016 a las 9:49, Louis H Kauffman escribió:
Dear Folks,
I will close with some comments about the relationship between recursive 
distinctioning and replication in biology.
This will be another example of the sort of modeling excursion that one can 
make by looking at patterns and analogies.


This folder contains links to papers related to Recursive Distinctioning. 
Recursive Distinctioning means just what it says. A pattern of distinctions is 
given in a space based on a graphical structure (such as a line of print or a 
planar lattice or given graph). Each node of the graph is occupied by a letter 
from some arbitrary alphabet. A specialized alphabet is given that can indicate 
distinctions about neighbors of a given node. The neighbors of a node are all 
nodes that are connected to the given node by edges in the graph. The letters 
in the specialized alphabet (call it SA) are used to describe the states of the 
letters in the given graph and at each stage in the recursion, letters in SA 
are written at all nodes in the graph, describing its previous state. The 
recursive structure that results from the iteration of descriptions is called 
Recursive Distinctioning. Here is an example. We use a line graph and represent 
it just as a finite row of letters. The Special Alphabet is SA = { =, [, ], O} 
where "=" means that the letters to the left and to the right are equal to the 
letter in the middle. Thus if we had AAA in the line then the middle A would be 
replaced by =. The symbol "[" means that the letter to the LEFT is different. 
Thus in ABB the middle letter would be replaced by [. The symbol "]" means that 
the letter to the right is different. And finally the symbol "O" means that the 
letters both to the left and to the right are different. SA is a tiny language 
of elementary letter-distinctions. Here is an example of this RD in operation 
where we use the proverbial three dots to indicate a long string of letters in 
the same pattern. For example,

... AAAAAAAAAABAAAAAAAAAA ... is replaced by
... =========]O[========= ... is replaced by
... ========]OOO[======== ... is replaced by
... =======]O[=]O[======= ... .

Note that the element ]O[ appears and it has replicated itself in a kind of 
mitosis. To see this in more detail, here is a link to a page from a 
mathematica program written by LK that uses a 'blank' or 'unmarked state' 
instead of the '=" sign. Program and 
Output<>. Elementary RD patterns are 
fundamental and will be found in many structures at all levels. To see an 
cellular automaton example of this phenomenon, look at the next link. Here we 
see a replicator in 'HighLife' a modification of John Horton Conway's automaton 
'Life'. The Highlife Replicator follows the same pattern as our RD Replicator! 
We can begin to understand how the RD Replicator works. This gives a foundation 
for understanding how the more complex HighLife Replicator behaves in its 
context. HighLife 
Finally, here is an excerpt from a paper by LK about replication in biology and 
the role of RD. Excerpt.<>

See RDLetter.<> This is 
the Isaacson-Kauffman report on RD, summarized in a letter-to-the-editor of 
JSP, Vol. 4, No. 1, Spring 2015, directly accessed on this server.

See Patent. <> 
This is Joel Isaacson's patent document for RD.

See Biological 
Replication.<> This is a 
related paper by Kauffman.

You see above a very simple distinction making/using automaton that produces a 
‘cell’  ]O[ from an elementary distinction (of B from the background of equal 
and that this cell then undergoes mitosis. Then as an observer you must look 
again and note that the nothing that happens in this automaton is local. The 
cell happens
because of the global structure of the one-dimensional automata space. The 
apparent splitting from the inside of the cell is actually a consequence of the 
condition of the cell in the whole space. The entire evolution of the process 
is a repeated articulation of the distinctions that are present in the process. 
This is
a new holistic modeling paradigm and we are exploring with simple examples the 
extent to which it will apply to more complex phenomena.

A more extended paper by myself and Joel Isaacson will be available soon.
Lou Kauffman

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)<>

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