[Fis] LOF Friday the generation of form and the geometry of the cell

[Eric Werner]

Dear Lou and All, //failed to fis because of message size so sending it 
to FIS alone

The replication and biology of form is also influenced the geometry of 
the cell, in particular its chirality. Thus the growing embryo is a 
complex interaction between the two parental genomes, their 
interpretation by the cell, cell and multicellular physics, cell 
signaling and the chirality of the cell.

See for example: https://urldefense.com/v3/__https://arxiv.org/abs/1207.3289__;!!D9dNQwwGXtA!SQqzCRSo2Z_EUFA3NXfjwOydbgsFMYrESlCYu0O3dZZFpc54gnclyYoJESWT31k0kgn9JHr2jtMpR9PUC_ATNW0$  for how bilateral 
symmetry develops

and https://urldefense.com/v3/__https://arxiv.org/abs/1212.5439__;!!D9dNQwwGXtA!SQqzCRSo2Z_EUFA3NXfjwOydbgsFMYrESlCYu0O3dZZFpc54gnclyYoJESWT31k0kgn9JHr2jtMpR9PUjRiFR0M$  for how parental genomes interact in 
development.

Best,

Eric

On 1/17/25 7:54 AM, Louis H Kauffman wrote:
> We shall next meet:
>  Friday, January 17, 2024 at noon CDT Chicago time:
>
> We’ll continue the discussion.
> Along with the points of view as outlined below there were many 
> contributions from participants.
> Some of these points are:
> 1. LK talked about the meaning of “=“ in terms of “Identity” A = B.
> Jerry Swatez pointed out that
> A = B can be seen to mean that A and B represent the same value or 
> that there is a series of steps that can be taken from A to B.
> 3. Karl Javorszky began to talk about natural numbers in his original way.
> 4. Many other threads of discussion appeared, including a number of 
> thoughts related to Rudolf Steiner.
> 5. I shall discuss further the role of topology in biology and in 
> fundamental epistemology, at the meeting of percept and concept.
>
>
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>
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>
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> ################################
>
> Biologic - at the interface between biology, topology, logic and 
> cybernetics.
> Louis H Kauffman, UIC
>
> “What can be shown, cannot be said.”
> “Was gezeigt werden kann, kann nicht gesagt werden.”
> (Wittgenstein, Tractatus, 4.1212)
>
> “We take the form of distinction for the form.”
> (Spencer-Brown, Laws of Form, Chapter 1)
>
> What is the form of biology?
> Is there a biology of form?
> In particular, this is a study of different forms and formalisms for 
> replication. We concentrate on diagrammatic formal systems not only 
> for the sake of showing how there may be fundamental mathematical 
> structure in biology, but also to consider philosophical and 
> phenomenological points of view in relation to natural science and 
> mathematics. 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. Our original point of departure was the idea of distinction and 
> cybernetic epistemology. Cybernetic epistemology has much to say about 
> the relation of the self to structures that may harbor a self. What is 
> the interlacement of selves and organisms?
>
> Our point of view is structural. There is a distinct difference 
> between building up structures in terms of principles and imagining 
> that models of the world are constructed from some sort of 
> building-bricks. I want  to make this point as early as possible 
> because in mathematics one naturally generates hierarchies, but that 
> does not make the mathematician a reductionist. We think of geometry 
> as the consequences of certain axioms for the purpose of organizing 
> our knowledge, not to insist that these axioms are in any way other 
> than logically prior to the theorems of the system. Just so, we look 
> for fundamental patterns from which certain complexes of phenomena and 
> ideas can be organized. This does not entail any assumption about 
> ``the world'' or how the world may be built from parts. What is a part 
> that a world might be built from it?
>
> We examine the schema behind the reproduction of DNA. The pattern of 
> the DNA reproduction is very simple. The DNA molecule consists of two 
> interwound strands, the Watson Strand (W)  and the Crick Strand (C). 
> The two strands are bonded to each other via a backbone of 
> base-pairings and these bonds can be broken by certain enzymes present 
> in the cell. In reproduction of DNA the bonds between the two strands 
> are broken and the two strands then acquire the needed complementary 
> base molecules from the cellular environment to reconstitute each a 
> separate copy of the DNA. At this level the situation can be described 
> by a symbolism like this.
> DNA = <W|C> ----->  <W| E |C> ----->  <W|C> <W|C> = DNA DNA.
> Here E stands for the environment of the cell. The first arrow denotes 
> the separation of the DNA into the two strands. The second arrow 
> denotes the action between the bare strands and the environment (the 
> creation of new base-pairings) that leads to the production of the two 
> DNA molecules.
>
> Much is left out of this schema. Indeed the DNA molecule is a tight 
> spiral winding of its two interlocked strands and so the new DNA's 
> would be linked around one another if it were not for the work of 
> toposomerase enzymes that manage to unlink the new DNA's in time for 
> cell division to occur. Nevertheless, this is the large scale 
> description of the replication of DNA that is fundamental to the 
> division of cells and to the continuance of living organisms.
>
> This form of replication can be compared with other forms. For 
> example, John von Neumann suggested a “building machine” B such that 
> when B is supplied with a “blueprint” x then
> B, x —> B,x , X,x
> This means that B and the blueprint x will produce X the entity whose 
> plan is x along with a copy of the blueprint x. The first B,x is the 
> persistence of the original machine B.
> Let b be the blueprint for B itself. Then
> B,b —> B,b , B,b.
> The Von Neumann Machine replicates itself.
> In the comparison, we see that The DNA contains (in its strands) the 
> blueprint for its own replication.
>
> The comparison made, what questions do you ask? The mathematical roots 
> of von Neumann’s construction are very deep. What are the 
> physical/biological roots of the DNA replication?
>
> We invite the reader to examine the form of the science involved in 
> this well-known description. We speak of the DNA molecules as though 
> we could see them directly in the phenomenology of our ordinary sight. 
> Science does involve the direct extension of sight as the experience 
> of looking through a telescope or a light microscope. But in the case 
> of the DNA one proceeds by logical consistency and the indirect but 
> vivid images via the electron microscope and the patterns of gel 
> electrophoresis. In the case of electron microscope images there is 
> every reason to assume (it appears consistent to assume) that the 
> objects shown can be taken to be analogous to the macroscopic objects 
> of our perception. This means that one has the possibility of 
> observing ``directly" that DNA molecules can be knotted. I do not say 
> that one can observe directly the coiling of the Watson and the Crick 
> strands, but the DNA can be observed as though it were a long rope. 
> This rope can be seen to be coiled and knotted in electron 
> micrographs. Even this ``showing'' requires a difficult technique 
> beyond the usual techniques of the electron microscope. The DNA was 
> coated with protein by the experimenters so that it became a chain of 
> larger and more robust diameter. Then the electron microscope revealed 
> the patterns of knotting in an apparent projection of the coated DNA 
> from three dimensional space to the two dimensional space of the image.
>
>
> It is remarkable how consistent is the hypothesis of indirect 
> perception on which the work is based. Most working biologists would 
> not question the basis of their biological perceptions direct or 
> indirect. For those who are philosophically inclined there is a lesson 
> to be learned about experimental phenomenology.
> One wants to know how far a world-view can be extended before it 
> disintegrates.
> What we see in the electron micrograph is deeply shaped by the complex 
> story of biological experiment that surrounds it.
>
> Along with these forays into experimentation, there are analogous 
> forays into the limits of logic. Here we meet the replication schema 
> again. Replication in logic is intimately related to self-reference 
> and to formalisms that can lead to paradox. The reasons for this are, 
> by now, apparent. The usual mathematical formalisms for set theory 
> assume that there is no temporal evolution in the structures.
> Temporality may look like a tragedy for the classical mathematics, but 
> it is exactly what interests us when studying biology.
> Mathematical biology is concerned with those structures leading to 
> recursive generation of structures from themselves and from their 
> environments.
>
>
-- 
/Dr. Eric Werner, FLS
Oxford Advanced Research Foundation
https://urldefense.com/v3/__https://oarf.org__;!!D9dNQwwGXtA!SQqzCRSo2Z_EUFA3NXfjwOydbgsFMYrESlCYu0O3dZZFpc54gnclyYoJESWT31k0kgn9JHr2jtMpR9PU1bBOXVE$ 


/
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