[Fis] Biologic - at the interface between biology, topology, logic and cybernetics (by Lou Kauffman)

Tue Jan 7 18:52:53 CET 2025

Dear Eric,
The curious thing about mathematics is that, while we do work with highly simplified and concise models, the details of our “prison” then become highly relevant.
For example, once we have the abstract concept of a triangle and the background of the rules for parallels in Euclidean geometry, then we can deduce the Pythagorean theorem.
without the concise abstraction, the Theorem cannot appear! And then the Theorem is seen to be approximated in multitudes of actual instances in the more complicated worlds 
That partake of the abstraction.

This is probably why I am fascinated by the abstraction of distinction and form in Spencer-Brown. It has its own “details” and it applies to everything/nothing.
The other example, I am using in this discussion is that topology as formulated for knots at our scale appears to apply to molecules at a microscale. 
And one can speculate about topology in relation to quantum level structures as well. Patterns go across boundaries in ways that can be quite surprising.
Best,
Lou

> On Jan 7, 2025, at 2:26 AM, Eric Werner <eric.werner at oarf.org> wrote:
> 
> Dear Lou and All,
> 
> I second your points Lou and Francesco. Abstraction and logic is the answer to the confused and overly complicating mind. 
> 
> The Devil is in the detail but God is in the abstract. 
> 
> Best,
> 
> Eric
> 
> On 1/7/25 8:19 AM, Louis Kauffman wrote:
>> Dear Francesco,
>> "Precisely because reality is more complex and larger than theory, a useful economy of thought, like mathematics, is essential to avoid unnecessary thoughts.”
>> 
>> Your sentence admirably sums up one of the advantages of a mathematical approach.
>> Note that when one speaks of an “economy of thought” it means that some thoughts are economical enough to encompass a very wide reference and meaningfully as well.
>> This is the practical value of abstraction.
>> 
>> Best,
>> Lou
>> 
>> 
>>> On Jan 6, 2025, at 2:41 AM, Francesco Rizzo <13francesco.rizzo at gmail.com <mailto:13francesco.rizzo at gmail.com>> wrote:
>>> 
>>> Cari tutti,
>>> la problematica che stiamo affrontando è fondata, come sostengo da mezzo secolo, sui valori normali dal punto di vista soggettivo e sui processi di tras-infomazione, più o meno retro-attivi, evocanti prigogineane infra-strutture che creano ordine (neg-entropico) dal disordine (entropico) mediante fluttuazioni.
>>> La mia nuova teoria economica è basata sul triangolo dei tre surplus neg-entropici: termodinamici, eco-biologici e semiotico-ermeneutici, più o meno matematici.
>>> Proprio, qualche settimana fa, ha visto la luce la “Teo-umano-logia economica o economia teo-umano-logica” (Aracne, Roma).
>>> Tuttavia, sono felicemente aperto e pronto ad apprendere cose nuove.
>>> Grazie,
>>> Francesco Rizzo, 23.10.2024, ore10.04.
>>> 
>>> Dear Pedro and Dear All,
>>> Precisely because reality is more complex and larger than theory, a useful economy of thought, like mathematics, is essential to avoid unnecessary thoughts.
>>> «We need to resize the very concept of method, finishing building "cathedrals" for it. Writing about evaluation does not mean being an evaluator. Estimation is theorized by practicing and professing it. A manual cannot be a "service briefcase" containing all the tools to center a specific reality" (Rizzo F., Economics of happiness or unhappiness. Critical analysis of the theory of evaluations, University of Catania, 1977 1st ed. pp . 131-132 and 2nd ed., Arachne, Rome, 2011).
>>> Everything can take on topologically different forms in time and space, therefore the philosophy of concrete reality is unavoidable, as Joe Brenner authoritatively maintains.
>>> Francis
>>>  
>>> Caro Pedro e Cari Tutti,
>>> proprio perché la realtà è più complessa e grande della teoria è indispensabile un’economia del pensiero utile, come la matematica, ad evitare i pensieri non necessari.
>>> «Bisogna ridimensionare lo stesso concetto di metodo, finendo di erigergli “cattedrali”. Scrivere di valutazione non significa essere valutatori. L’estimo si teorizza praticandolo e professandolo. Un manuale non può essere una “valigetta di servizio” contenente tutti gli attrezzi per centrare una realtà specifica» (Rizzo F., Economia della felicità o dell’infelicità. Analisi critica della teoria delle valutazioni, Università di Catania, 1977 1ᵃ ed. pp. 131-132 e 2ᵃ ed., Aracne, Roma, 2011).
>>> Ogni cosa può assumere nel tempo e nello spazio forme topologicamente diverse, quindi è ineludibile la filosofia della realtà concreta, come anche Joe Brenner autorevolmente sostiene.
>>> Francesco
>>>  
>>>  
>>>  
>>> 
>>> Il giorno lun 6 gen 2025 alle ore 07:57 Karl Javorszky <karl.javorszky at gmail.com <mailto:karl.javorszky at gmail.com>> ha scritto:
>>> (DNA in its logical habitat 2025 01 06)
>>> 
>>>  
>>> Dear Lou,
>>> 
>>> Your excellent opening statement about how the strands of the DNA are arranged and how some physiological relations are relevant while it duplicates, and more, are an enlightening recapitulation of what applied science has so far discovered.
>>> 
>>> Due to limits of space, it is impractical to insert your whole essay here. To cut it short, all your assertions are welcomed as true statements. Specifically, thank you for the concise formulation:
>>> 
>>> Mathematical biology is concerned with … structures leading to recursive generation of structures from themselves and from their environments.
>>>  
>>> Your questions:
>>> 
>>> What is the form of biology? Is there a biology of form?
>>> 
>>> Your  own definition above shows biology as a subject of logic to be a collection of sentences describing circular procedures (that are themselves subject to periodic processes) determining positions of a limited number of diverse elements in several dimensions in such a fashion that both longitudinal and transversal additions add up to such an extent of an expression of order which is within limits, thus one kind of reading being a feedback and restriction set of parameters for the other reading. The concept ‘Order’ denotes sentences that are statements concurrently true about the properties of an element and its position among its peers.  
>>> 
>>> The relationship with phenomenology comes about in the questions that arise about the nature of the observer in relation to the observed that arise in philosophy, but also in science in the very act of determining the context and models upon which it shall be based.
>>> 
>>> New in the 21st century is that we have now access to tabulating machines that show us every possible way of combining and recombining the relatively few diverse elements that are the logical building blocks of our picture of biology. If we understand the nature of the structural bias* that separates a human observer from a mechanical observer, and manage to eliminate the effects of the artefact, there is no need to complicate the observation of the self-referencing interdependence by investigating whether the observer is a human, an alien or a machine. (* Cortex imagines using one, Sumerian N, the underlying neurology uses Nsimilarities, Ndiversities which is the correct way within the habitat.)
>>> 
>>> What is a part that a world might be built from it?
>>> 
>>> Why don’t we try to use the symbols a, b to depict two otherwise unknown entities that through their interactions create structures that can be read horizontally, vertically, etc.?
>>> 
>>> The comparison made, what questions do you ask? … What are the physical/biological roots of the DNA replication?
>>> 
>>> This here group of learned friends has no access to and no knowledge to operate the apparats applied science uses. Our task is to understand the data processing procedures that make a linear pointer fragment into an array of search criteria.
>>> 
>>> One wants to know how far a world-view can be extended before it disintegrates.
>>> 
>>> There is a very prosaic answer to that. Once one starts investigating how more than 137.03 idealized distinct elements interact, one has left reality as we refer to it in the context of biology. Nature has caught a very small little opportunity where the number of elements, how these elements are similar among each other and how these elements are diverse among each other shows a slight discongruence-based variability. Nature has delineated a number theoretical habitat (a Nirvana for logical primitives /© M. Abundis/). Let us name it the Eddington habitat. Within it, objects can be referenced both sequentially and categorically.
>>> 
>>> Temporality may look like a tragedy for the classical mathematics, but it is exactly what interests us when studying biology.
>>> 
>>> Exactly. There are several clocks running within each living animal, these are coordinated and synchronized (if all goes well) by the Metronome of that individual organism. The metronomes of the organisms should better be aligned, being subject to a pressure of evolution, with the periodicity that blesses and torments the habitat (like the periodicities of Moon, Earth, Sun affect our real existing Nirvana).
>>> 
>>> The temporal aspect is useful in establishing the metronome that is valid within the habitat. In whichever way we rotate a + b = c the longest cycle we find is 129 long. This is practical, because in the grand context of things, both that is true for either 32 or 97 (two of the Zaragoza constants, where n? ~ n!), needs to be true also if both are the case. The metronome cycle is a half-twin of the folding cycle which is 128 elements long. There are only 122 elements that are included in both. There exists – in a logical-objective reality – an individuating tick along a counting of recurrent states of the metronome that refers to both temporal and spatial coordinates of an occurrence. Iterations are unavoidable. There exist structural and interlude cycles that maintain the overall tact locally congruent during iteration.
>>> 
>>>  
>>> To close, let me add a parable about an old man coming back from fishing and a young fashion influencer at the imperial court. They both miss something that has not survived contact with reality: the old man the flesh of his merlin, and the young girl the clothes of the emperor.
>>> 
>>> They both agree that the learned and respected tailors of the emperor have problems stitching clothes together out of pieces that are serrated differently. 
>>> The young girl says: had the right honorable learned tailors not used the big scissors first to cut out units that can be stitched together, but had used the appropriate small scissors to prepare parts that will fit together into a suit, they would have incurred the opportunity costs of not producing economically with identical units and pay the running costs of maintaining a complicated catalogue of which cuts fit together with which cuts, but would gain the benefits of having a variant of suits that really adapt to the Emperor’s everchanging body. 
>>> To which the old man says, yes there are costs to generalizing. As they use the big scissors to establish a + b = c they disregard the snippets that fall off as both of a, b suffers being robbed of their individuality as a resp. b. These are distances that get unaccounted for in the intuitive, generalized, practical Sumerian way of cutting the cloth of continuity. The Accadians, may they rest in peace, collected these different snippets and had built their own ideology based on them. The present day learned tailors point to various part-entities that they give different names to and would never want to look under the carpet of generalization into c where they had swept the snippets of the particularities of a, b. The snippets are arrays of distances that accumulate over the history of the elements involved and in the grand ledger. You cannot make particularities disappear just by not wanting to see them, concentrating on the general forms of particularities. It will blow up in your face if you manipulate the accounting to make  arrays of distances go away, for reasons of ease and practicability of accounting. 
>>> The young girl says: One should alert the tailors that they are horsing around with snippets they themselves have generated.
>>> 
>>> The old man says: Do that and see what happens to your social reputation. Tales will be written about you.
>>> 
>>>  
>>> Thank you again for bringing us up to the present state of knowledge in the wet sciences and for posing the right questions on the solvable riddle, what such an assembly would look like, in which coincidences and occurrences were indexed in several aspects concurrently.
>>> 
>>>  
>>> Karl
>>> 
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>> 
>> 
>> 
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> -- 
> Dr. Eric Werner, FLS 
> Oxford Advanced Research Foundation 
> https://urldefense.com/v3/__https://oarf.org__;!!D9dNQwwGXtA!TZZAwSlnc1HRfqh43y9P_0oNBfbtKa7CdZ5gwj0LLSClCfd4E5NUzb_8AcCe9c90S4lae4seCA8vhQtj$  <https://urldefense.com/v3/__https://oarf.org/__;!!D9dNQwwGXtA!TZZAwSlnc1HRfqh43y9P_0oNBfbtKa7CdZ5gwj0LLSClCfd4E5NUzb_8AcCe9c90S4lae4seCNlLpenk$ > 
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