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 systems). 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 --Pedro 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. See homepages.math.uic.edu/~kauffman/RD.html<http://homepages.math.uic.edu/%7Ekauffman/RD.html> RECURSIVE DISTINCTIONING 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<https://dl.dropbox.com/u/11067256/RDL.pdf>. 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 Replicator.<https://en.m.wikipedia.org/wiki/Highlife_%28cellular_automaton%29> Finally, here is an excerpt from a paper by LK about replication in biology and the role of RD. Excerpt.<https://dl.dropbox.com/u/11067256/KauffmanExcerpt.pdf> See RDLetter.<http://homepages.math.uic.edu/%7Ekauffman/RDLetter.pdf> 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. <https://dl.dropbox.com/u/11067256/JoelIsaacsonPatentDocument.pdf> This is Joel Isaacson's patent document for RD. See Biological Replication.<https://dl.dropbox.com/u/11067256/KauffmanJPBM1033.pdf> 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 A’s), 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 global 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. Best, 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) pcmarijuan.i...@aragon.es<mailto:pcmarijuan.i...@aragon.es> http://sites.google.com/site/pedrocmarijuan/ -------------------------------------------------
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