[Fis] Biologic - at the interface between biology, topology, logic and cybernetics (by Lou Kauffman)
Eric Werner
eric.werner at oarf.org
Sat Jan 4 16:36:42 CET 2025
Dear Louis and All,
Sorry there is a '1' missing in the genome semantics link. This should work:
https://urldefense.com/v3/__https://febs.onlinelibrary.wiley.com/doi/10.1016/j.febslet.2005.02.011__;!!D9dNQwwGXtA!WEnKRZnHsI3XpOQozGc_5rQy_1S9OrE-jwJLZ0b7TZGpsr2ErXttoMCW8MalIFQE53UbsDxNNV2nTU6ZkdK6T7c$
Eric
On 1/4/25 4:26 PM, Eric Werner wrote:
>
> 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!WEnKRZnHsI3XpOQozGc_5rQy_1S9OrE-jwJLZ0b7TZGpsr2ErXttoMCW8MalIFQE53UbsDxNNV2nTU6ZkHazhMQ$
>
> (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!WEnKRZnHsI3XpOQozGc_5rQy_1S9OrE-jwJLZ0b7TZGpsr2ErXttoMCW8MalIFQE53UbsDxNNV2nTU6Z-ZQnTUY$
>
> 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!WEnKRZnHsI3XpOQozGc_5rQy_1S9OrE-jwJLZ0b7TZGpsr2ErXttoMCW8MalIFQE53UbsDxNNV2nTU6ZEMrgtEo$
>>
>>
>>
>> *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!WEnKRZnHsI3XpOQozGc_5rQy_1S9OrE-jwJLZ0b7TZGpsr2ErXttoMCW8MalIFQE53UbsDxNNV2nTU6ZtxiPxhY$
>> Here are other papers included in this email:
>>
>>
>> Click to Download
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>> VirtualLogic.pdf
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>> 4 MB
>> Click to Download
>> <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$>
>>
>> Autopoiesis and Eigenform -computation-11-00247-v3.pdf
>> 4.8 MB
>>
>> Very best,
>> Louis H Kauffman
>> Dept Mathematics
>> University of Illinois at Chicago
>>
>>
>>
>>
>>
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> --
> /Dr. Eric Werner, FLS
> Oxford Advanced Research Foundation
> https://urldefense.com/v3/__https://oarf.org__;!!D9dNQwwGXtA!WEnKRZnHsI3XpOQozGc_5rQy_1S9OrE-jwJLZ0b7TZGpsr2ErXttoMCW8MalIFQE53UbsDxNNV2nTU6Z5NOk_fY$
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>
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> ----------
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>
> Ud. recibe este correo por pertenecer a una lista de correo gestionada por la Universidad de Zaragoza.
> Puede encontrar toda la información sobre como tratamos sus datos en el siguiente enlace:https://sicuz.unizar.es/informacion-sobre-proteccion-de-datos-de-caracter-personal-en-listas
> Recuerde que si está suscrito a una lista voluntaria Ud. puede darse de baja desde la propia aplicación en el momento en que lo desee.
> http://listas.unizar.es
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/Dr. Eric Werner, FLS
Oxford Advanced Research Foundation
https://urldefense.com/v3/__https://oarf.org__;!!D9dNQwwGXtA!WEnKRZnHsI3XpOQozGc_5rQy_1S9OrE-jwJLZ0b7TZGpsr2ErXttoMCW8MalIFQE53UbsDxNNV2nTU6Z5NOk_fY$
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