[Fis] Biologic - at the interface between biology, topology, logic and cybernetics--PCM

Pedro C. Marijuán pedroc.marijuan at gmail.com
Sun Jan 5 21:39:53 CET 2025 

Dear Lou,

Thanks a lot for the work done in this New Year Lecture!

You have made an interesting mixing of ideas, as the title was offering. 
Let me make a few critical comments, just to stimulate discussion:

-- Do you think the phenomenological stance provides a useful thinking 
basis in biology (in most fields of)?
I remember a quotation from AN Whitehead: "Civilization advances by 
extending the number of important operations which we can perform 
without thinking of them." Thus, well crafted 'indirect perception' 
becomes a must in most bio fields. And the discussion on the 
observed/observed interrelationship has so rarely provided any 
interesting outcome. It directly goes against the principle of "economy 
of thought" inherent in ANW, or in Occam's. In my opinion, putting it 
together with Autopoiesis, it is quite dubious they have contributed to 
fundamental matters in the biosciences and neurosciences. That they 
militate against reductionism may be a good point, but quite insufficient.

-- Regarding DNA, it is subject to so many happenstances along the life 
course of the living. Natural "biotechnology" looks endless. Some of 
these operations may be enticing for mathematicians, while the biggest 
conundrums appear, say, on the enzymatic side.  Another quotation, from 
Kornberg: " DNA and genes captured the spotligt from enzymes; but in my 
theater enzymes kept the leading role... they do the acting." I say this 
because the intense focus on DNA has created an unproductive avenue for 
biological information (& biosemiotics). Simplest cells (bacteria and 
archea) do manage environmental information flows by means of their 
signaling systems, channels, transporters, etc. But this is 
rudimentarily conceptualized yet. I think this is a serious challenge to 
mathematicians too, as almost everything of physiological/developmental 
relevance passes through the "hands" of a prokaryotic or eukaryotic 
signaling systems.

-- And finally, I find your final paragraph on the limits of logic of 
high interest and fertility. And will look for it in your other 
publications. Almost by definition I would put that "reality --and 
life-- are always larger than our formal approaches".

Don't take me too seriously... and let me wish a Happy New Year to you 
and all FISers.

Best--Pedro

>> 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!S8XZiIC8EM5g0mFtdbtdtm3SSvVrsBTMi46kFnAiEPyB2LjlPmM_YGDIsGHAnd-A_cutwrXF-o-9whNAe2rMs67R-xpf$ 
>>
>>
>>
>> *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!S8XZiIC8EM5g0mFtdbtdtm3SSvVrsBTMi46kFnAiEPyB2LjlPmM_YGDIsGHAnd-A_cutwrXF-o-9whNAe2rMs5j8IjR3$ 
>> Here are other papers included in this email:
>>
>>
>> Click to Download 
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>>
>> 1512.04325v1.pdf
>> 717 KB
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>> CyberneticsMeaningCircularityForm.pdf
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>> SelfRefRecurForm.pdf
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>> BioLogic.key.pdf
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>> VirtualLogic.pdf
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>> RecursiveForms.pdf
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>> 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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