[Fis] Biologic - at the interface between biology, topology, logic and cybernetics (by Lou Kauffman)
Louis Kauffman
loukau at gmail.com
Sat Jan 4 23:54:29 CET 2025
Dear Eric,
Thank you for these references. I will read them.
As for my collection of references, there is no need to read a lot before responding.
I would be most interested in responses to the email message itself.
Very best,
Lou
> On Jan 4, 2025, at 9:36 AM, Eric Werner <eric.werner at oarf.org> wrote:
>
> 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!UskeAq_gqNp_mnjJ21aNnSAjs56e9rN_aYeDEsiEKEbEYyHhb53bnPfT7dBZvNBjtKsSo-29sfJwbRm3$ <https://urldefense.com/v3/__https://febs.onlinelibrary.wiley.com/doi/10.1016/j.febslet.2005.02.011__;!!D9dNQwwGXtA!WEnKRZnHsI3XpOQozGc_5rQy_1S9OrE-jwJLZ0b7TZGpsr2ErXttoMCW8MalIFQE53UbsDxNNV2nTU6ZkdK6T7c$>
> Eric
>
> On 1/4/25 4:26 PM, Eric Werner wrote:
>> Dear Louis,
>>
>> Fascinating approach and tremendous effort. Thank you for all your work!
>>
>> But a lot to read! But from an initial skimming, we have some commonalities of interest and concepts.
>>
>> Since your work is a bit overwhelming, hence my first response is with a "Back at ya!" Have a look at:
>>
>> (1.) A formalization of embryogenesis of cancer which contains many of the ideas and forms you talk about:
>>
>> 'Cybernetics' of Cancer: https:arxiv.org/abs/1110.5865 <https://urldefense.com/v3/__https://arxiv.org/abs/1110.5865__;!!D9dNQwwGXtA!UskeAq_gqNp_mnjJ21aNnSAjs56e9rN_aYeDEsiEKEbEYyHhb53bnPfT7dBZvNBjtKsSo-29sRusMPcF$ >
>> (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!UskeAq_gqNp_mnjJ21aNnSAjs56e9rN_aYeDEsiEKEbEYyHhb53bnPfT7dBZvNBjtKsSo-29sZlMKWMs$ <https://urldefense.com/v3/__https://arxiv.org/abs/1212.5439__;!!D9dNQwwGXtA!UYK3U5uPm8X_-PYmhQ2uxvCO7o6Hj3NY7b7EsSRPKK1hbtjJyZOJ8284ZeGmKVdcAgnY0XUyshx3NQQh2Bw_zvM$>
>> (3.) And a philosophical - semantic view of genomes:
>>
>> Genome semantics: https://urldefense.com/v3/__https://febs.onlinelibrary.wiley.com/doi/10.1016/j.febslet.2005.02.01__;!!D9dNQwwGXtA!UskeAq_gqNp_mnjJ21aNnSAjs56e9rN_aYeDEsiEKEbEYyHhb53bnPfT7dBZvNBjtKsSo-29sSFQ2kFh$ <https://urldefense.com/v3/__https://febs.onlinelibrary.wiley.com/doi/10.1016/j.febslet.2005.02.01__;!!D9dNQwwGXtA!UYK3U5uPm8X_-PYmhQ2uxvCO7o6Hj3NY7b7EsSRPKK1hbtjJyZOJ8284ZeGmKVdcAgnY0XUyshx3NQQhD9ODzN8$>
>> There is more of course, but we don't want to get too wordy. 😉
>>
>> Kind regards,
>>
>> Eric
>>
>> On 1/4/25 1:42 PM, Pedro C. Marijuán wrote:
>>>
>>> Asunto: Re: Biologic - at the interface between biology, topology, logic and cybernetics.
>>> Fecha: Fri, 3 Jan 2025 12:38:13 -0600
>>> De: Louis Kauffman <loukau at gmail.com> <mailto:loukau at gmail.com>
>>> Para: "Pedro C. Marijuán" <pedroc.marijuan at gmail.com> <mailto:pedroc.marijuan at gmail.com>
>>> Download of below articles available until Feb 2, 2025
>>> 'Slides Festival' available at: https://urldefense.com/v3/__https://fis.sciforum.net/resources/__;!!D9dNQwwGXtA!UskeAq_gqNp_mnjJ21aNnSAjs56e9rN_aYeDEsiEKEbEYyHhb53bnPfT7dBZvNBjtKsSo-29sakpL9sk$ <https://urldefense.com/v3/__https://fis.sciforum.net/resources/__;!!D9dNQwwGXtA!Xuz20L8dnuTZYF9WFBHOLyZrvHTyVKqbCy4P55woe-bSQswWK6oGtDnIfdh8ErbhHvbI71N24gtkTUTyEMIjVuWJIXes$>
>>>
>>>
>>>
>>> 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.
>>> <DNAknot-trefoil..jpeg>
>>>
>>> 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!UskeAq_gqNp_mnjJ21aNnSAjs56e9rN_aYeDEsiEKEbEYyHhb53bnPfT7dBZvNBjtKsSo-29sWMECFEl$ <https://urldefense.com/v3/__https://arxiv.org/abs/1512.04325__;!!D9dNQwwGXtA!Xuz20L8dnuTZYF9WFBHOLyZrvHTyVKqbCy4P55woe-bSQswWK6oGtDnIfdh8ErbhHvbI71N24gtkTUTyEMIjViUloF5d$>
>>> Here are other papers included in this email:
>>>
>>>
>>> Click to Download
>>> <https://urldefense.com/v3/__https://www.icloud.com/attachment/?u=https*3A*2F*2Fcvws.icloud-content.com*2FB*2FATn_nnxHcyh_SfWYzB1pkpVr9vdHAYr5N41_25ywwn3LTm0hVYULEOug*2F*24*7Bf*7D*3Fo*3DArD8ICzSw7Xg083yawjkpdvqeFEe-arHpPFPmN-RCbvN*26v*3D1*26x*3D3*26a*3DCAogm-JBZUe4rv4lM-GdROzhO0kNv5Gg2V5ev1BYaB-HurUSdhC139frwjIYte_Sv8wyIgEAKgkC6AMA_392U1dSBGv290daBAsQ66BqJZoxjHqilao5AqmOuPrt9birKtnnpMBCFSalgr9x7wI40ZT-FT5yJSvR6Pg64ur_Ydw6RZabrqmW_o0Ajr4iRmOhBxHxbS-BqcNk1lg*26e*3D1738521491*26fl*3D*26r*3DE63E95B3-6570-4D8F-B1C4-F48F4A3ED650-1*26k*3D*24*7Buk*7D*26ckc*3Dcom.apple.largeattachment*26ckz*3D07A918FF-8BDC-4700-9934-3E1E502E4652*26p*3D173*26s*3D7JO-tuvc3h6PicDvS_8nxF8hoRQ&uk=Oas0OTNPysoPpsuy008VhA&f=1512.04325v1.pdf&sz=717429__;JSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUl!!D9dNQwwGXtA!Xuz20L8dnuTZYF9WFBHOLyZrvHTyVKqbCy4P55woe-bSQswWK6oGtDnIfdh8ErbhHvbI71N24gtkTUTyEMIjVtxmU_jQ$>1512.04325v1.pdf
>>> 717 KB
>>> Click to Download
>>> <https://urldefense.com/v3/__https://www.icloud.com/attachment/?u=https*3A*2F*2Fcvws.icloud-content.com*2FB*2FAfWDD-xThY-6u3B_O4UcMuaxj7GaASDKi2Ll2EAIdvqQczfU6SxBrhUf*2F*24*7Bf*7D*3Fo*3DArHPLPr1dN99Ey7QnOcE1UdD15fTvkN441MMtCKW-r0I*26v*3D1*26x*3D3*26a*3DCAogUT9GgoPiAV4KHaYFXTAM4Iu_q2nXyt6Hznxr866BIVYSdhC43dfrwjIYuO3Sv8wyIgEAKgkC6AMA_yr1okBSBLGPsZpaBEGuFR9qJaOvQVc_KBdxw5fisfBOrx_VLhHWPd1wSJUsfmSOhYHIJnnDJbZyJcEpBm7iabDEWhM1D0EkwMqVfVDOQmlOWV-c5GCdgcVTONbG5zs*26e*3D1738521491*26fl*3D*26r*3DDB8C7A77-0863-40CE-B0A3-AF937EF6F979-1*26k*3D*24*7Buk*7D*26ckc*3Dcom.apple.largeattachment*26ckz*3D07A918FF-8BDC-4700-9934-3E1E502E4652*26p*3D173*26s*3Dq0PkhL6x6MMJH4B_Sw6GDRkSKw8&uk=KXpUaywKrBABaHF9ovz55Q&f=CyberneticsMeaningCircularityForm.pdf&sz=929333__;JSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUl!!D9dNQwwGXtA!Xuz20L8dnuTZYF9WFBHOLyZrvHTyVKqbCy4P55woe-bSQswWK6oGtDnIfdh8ErbhHvbI71N24gtkTUTyEMIjVvoKLyUs$>CyberneticsMeaningCircularityForm.pdf
>>> 929 KB
>>> Click to Download
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>>> 1.7 MB
>>> Click to Download
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>>> 865 KB
>>> Click to Download
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>>> 9.4 MB
>>> Click to Download
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>>> 2.2 MB
>>> Click to Download
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>>> 2 MB
>>> Click to Download
>>> <https://urldefense.com/v3/__https://www.icloud.com/attachment/?u=https*3A*2F*2Fcvws.icloud-content.com*2FB*2FAVF0MhWBm54WgbrzMnPJejEEICc6ATmj6R5dc6p3fYrhBDjhxtEx607Z*2F*24*7Bf*7D*3Fo*3DAuDpRbBE9VPLfPD587kAy3O6MGOYR-YgC77_57OBPWzY*26v*3D1*26x*3D3*26a*3DCAogYNQku6Eei7Bqym-BRSVGDIwRCSb7ReBc4w-PiL6RkNASdhDT6tfrwjIY0_rSv8wyIgEAKgkC6AMA_xqa92hSBAQgJzpaBDHrTtlqJfuDajJFDB-DIKOOOSECjgRNXoLe8bFtEjKFE5E6Z881ip7PMLdyJf_BWdAIlnZh3x59aC7rlceAHhmOJb-tIt9Priae0XuJ_zOjNSY*26e*3D1738521492*26fl*3D*26r*3DFD4D865D-F646-4B8D-9EBE-8CE1668E06E3-1*26k*3D*24*7Buk*7D*26ckc*3Dcom.apple.largeattachment*26ckz*3D07A918FF-8BDC-4700-9934-3E1E502E4652*26p*3D173*26s*3DEDS2z2N2LBnL3xctM-w88P6e2fw&uk=PcvMHeC8kiHJwYeU4osFRw&f=KnotLogic.pdf&sz=3984876__;JSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUl!!D9dNQwwGXtA!Xuz20L8dnuTZYF9WFBHOLyZrvHTyVKqbCy4P55woe-bSQswWK6oGtDnIfdh8ErbhHvbI71N24gtkTUTyEMIjVnzBDW2w$>KnotLogic.pdf
>>> 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$>Autopoiesis and Eigenform -computation-11-00247-v3.pdf
>>> 4.8 MB
>>>
>>> Very best,
>>> Louis H Kauffman
>>> Dept Mathematics
>>> University of Illinois at Chicago
>>>
>>>
>>>
>>>
>>>
>>>
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>> --
>> Dr. Eric Werner, FLS
>> Oxford Advanced Research Foundation
>> https://urldefense.com/v3/__https://oarf.org__;!!D9dNQwwGXtA!UskeAq_gqNp_mnjJ21aNnSAjs56e9rN_aYeDEsiEKEbEYyHhb53bnPfT7dBZvNBjtKsSo-29sRaTFax4$ <https://urldefense.com/v3/__https://oarf.org__;!!D9dNQwwGXtA!UYK3U5uPm8X_-PYmhQ2uxvCO7o6Hj3NY7b7EsSRPKK1hbtjJyZOJ8284ZeGmKVdcAgnY0XUyshx3NQQhyu4v2Mw$>
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>> ----------
>> INFORMACIÓN SOBRE PROTECCIÓN DE DATOS DE CARÁCTER PERSONAL
>>
>> Ud. recibe este correo por pertenecer a una lista de correo gestionada por la Universidad de Zaragoza.
>> Puede encontrar toda la información sobre como tratamos sus datos en el siguiente enlace: https://sicuz.unizar.es/informacion-sobre-proteccion-de-datos-de-caracter-personal-en-listas <https://sicuz.unizar.es/informacion-sobre-proteccion-de-datos-de-caracter-personal-en-listas>
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>> ----------
> --
> Dr. Eric Werner, FLS
> Oxford Advanced Research Foundation
> https://urldefense.com/v3/__https://oarf.org__;!!D9dNQwwGXtA!UskeAq_gqNp_mnjJ21aNnSAjs56e9rN_aYeDEsiEKEbEYyHhb53bnPfT7dBZvNBjtKsSo-29sRaTFax4$ <https://urldefense.com/v3/__https://oarf.org__;!!D9dNQwwGXtA!WEnKRZnHsI3XpOQozGc_5rQy_1S9OrE-jwJLZ0b7TZGpsr2ErXttoMCW8MalIFQE53UbsDxNNV2nTU6Z5NOk_fY$>
>
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> ----------
> INFORMACI�N SOBRE PROTECCI�N DE DATOS DE CAR�CTER PERSONAL
>
> Ud. recibe este correo por pertenecer a una lista de correo gestionada por la Universidad de Zaragoza.
> Puede encontrar toda la informaci�n sobre como tratamos sus datos en el siguiente enlace: https://sicuz.unizar.es/informacion-sobre-proteccion-de-datos-de-caracter-personal-en-listas <https://sicuz.unizar.es/informacion-sobre-proteccion-de-datos-de-caracter-personal-en-listas>
> Recuerde que si est� suscrito a una lista voluntaria Ud. puede darse de baja desde la propia aplicaci�n en el momento en que lo desee.
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