[Fis] Biologic - at the interface between biology, topology, logic and cybernetics (by Lou Kauffman)
Eric Werner
eric.werner at oarf.org
Sat Jan 4 16:26:27 CET 2025
Dear Louis,
Fascinating approach and tremendous effort. Thank you for all your work!
But a lot to read! But from an initial skimming, we have some
commonalities of interest and concepts.
Since your work is a bit overwhelming, hence my first response is with a
"Back at ya!" Have a look at:
(1.) A formalization of embryogenesis of cancer which contains many of
the ideas and forms you talk about:
'Cybernetics' of Cancer: https:arxiv.org/abs/1110.5865
(2.) And a wider view of inter-genome interactions versus your
intra-genome copy-cat interactions that may be related to your 'knotty'
ideas:
Genome Interactions in Development and Evolution:
https://urldefense.com/v3/__https://arxiv.org/abs/1212.5439__;!!D9dNQwwGXtA!UYK3U5uPm8X_-PYmhQ2uxvCO7o6Hj3NY7b7EsSRPKK1hbtjJyZOJ8284ZeGmKVdcAgnY0XUyshx3NQQh2Bw_zvM$
(3.) And a philosophical - semantic view of genomes:
Genome semantics:
https://urldefense.com/v3/__https://febs.onlinelibrary.wiley.com/doi/10.1016/j.febslet.2005.02.01__;!!D9dNQwwGXtA!UYK3U5uPm8X_-PYmhQ2uxvCO7o6Hj3NY7b7EsSRPKK1hbtjJyZOJ8284ZeGmKVdcAgnY0XUyshx3NQQhD9ODzN8$
There is more of course, but we don't want to get too wordy. 😉
Kind regards,
Eric
On 1/4/25 1:42 PM, Pedro C. Marijuán wrote:
> Biologic - at the interface between biology, topology, logic and
> cybernetics.
> Asunto: Re: Biologic - at the interface between biology, topology,
> logic and cybernetics.
> Fecha: Fri, 3 Jan 2025 12:38:13 -0600
> De: Louis Kauffman <loukau at gmail.com>
> Para: "Pedro C. Marijuán" <pedroc.marijuan at gmail.com>
>
>
> Download of below articles available until Feb 2, 2025
> 'Slides Festival' available at: https://urldefense.com/v3/__https://fis.sciforum.net/resources/__;!!D9dNQwwGXtA!UYK3U5uPm8X_-PYmhQ2uxvCO7o6Hj3NY7b7EsSRPKK1hbtjJyZOJ8284ZeGmKVdcAgnY0XUyshx3NQQh0pM7nOg$
>
>
>
> *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.
> #############################
>
> Here is a related paper:
> https://urldefense.com/v3/__https://arxiv.org/abs/1512.04325__;!!D9dNQwwGXtA!UYK3U5uPm8X_-PYmhQ2uxvCO7o6Hj3NY7b7EsSRPKK1hbtjJyZOJ8284ZeGmKVdcAgnY0XUyshx3NQQhHkpaNbU$
> Here are other papers included in this email:
>
>
> Click to Download
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> RecursiveForms.pdf
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> 4 MB
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> <https://urldefense.com/v3/__https://www.icloud.com/attachment/?u=https*3A*2F*2Fcvws.icloud-content.com*2FB*2FAa3ViSw9Q_ZsqJl2l7FQHhO6epqSAfHL1V0LsPHFyNnoJStJkVWsxdYS*2F*24*7Bf*7D*3Fo*3DAugz17HcsnNDKFXL38CRQCgUvn1fxuuJkvhIXjgguEV1*26v*3D1*26x*3D3*26a*3DCAogSlvExVpOkZwaxdZ9XVrUdNHGv-rexsttbomoaEpbrWASdhDC7NfrwjIYwvzSv8wyIgEAKgkC6AMA_zjCwvBSBLp6mpJaBKzF1hJqJTN95Qck513tFY_f9NVc-No2KXkbN4_sp7zr0rPW3AdDmgXuroJyJSNa52bS8up0ObB_HQiiRyim6yuo2ZJ226NrbZVqIp4kgafFTxo*26e*3D1738521493*26fl*3D*26r*3D7E4C9DD2-1CC1-4351-908F-A396F925C240-1*26k*3D*24*7Buk*7D*26ckc*3Dcom.apple.largeattachment*26ckz*3D07A918FF-8BDC-4700-9934-3E1E502E4652*26p*3D173*26s*3DFqbhY6e0T0QNTugXqHWqfQNvwp8&uk=Jmg5S3MdA-dOmalq2ArhIg&f=Autopoiesis*20and*20Eigenform*20-computation-11-00247-v3.pdf&sz=4840405__;JSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUl!!D9dNQwwGXtA!Xuz20L8dnuTZYF9WFBHOLyZrvHTyVKqbCy4P55woe-bSQswWK6oGtDnIfdh8ErbhHvbI71N24gtkTUTyEMIjVsCS-fWW$>
>
> Autopoiesis and Eigenform -computation-11-00247-v3.pdf
> 4.8 MB
>
> Very best,
> Louis H Kauffman
> Dept Mathematics
> University of Illinois at Chicago
>
>
>
>
>
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--
/Dr. Eric Werner, FLS
Oxford Advanced Research Foundation
https://urldefense.com/v3/__https://oarf.org__;!!D9dNQwwGXtA!UYK3U5uPm8X_-PYmhQ2uxvCO7o6Hj3NY7b7EsSRPKK1hbtjJyZOJ8284ZeGmKVdcAgnY0XUyshx3NQQhyu4v2Mw$
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