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    <p>Dear Louis,<br>
    </p>
    <p>Fascinating approach and tremendous effort. Thank you for all
      your work! </p>
    <p>But a lot to read!  But from an initial skimming, we have some
      commonalities of interest and concepts. </p>
    <p>Since your work is a bit overwhelming, hence my first response is
      with a "Back at ya!"   Have a look at: <br>
    </p>
    <p>(1.) A formalization of embryogenesis of cancer  which contains
      many of the ideas and forms you talk about:</p>
    <p>    'Cybernetics' of Cancer:  <a class="moz-txt-link-freetext" href="https:arxiv.org/abs/1110.5865">https:arxiv.org/abs/1110.5865</a></p>
    <p>(2.) And a wider view of inter-genome interactions versus your
      intra-genome copy-cat interactions that may be related to your
      'knotty' ideas:</p>
    <p>    Genome Interactions in Development and Evolution:   
      <a class="moz-txt-link-freetext" href="https://urldefense.com/v3/__https://arxiv.org/abs/1212.5439__;!!D9dNQwwGXtA!UYK3U5uPm8X_-PYmhQ2uxvCO7o6Hj3NY7b7EsSRPKK1hbtjJyZOJ8284ZeGmKVdcAgnY0XUyshx3NQQh2Bw_zvM$">https://arxiv.org/abs/1212.5439</a></p>
    <p>(3.) And a philosophical - semantic view of genomes:<br>
    </p>
    <p>    Genome semantics:
      <a class="moz-txt-link-freetext" href="https://urldefense.com/v3/__https://febs.onlinelibrary.wiley.com/doi/10.1016/j.febslet.2005.02.01__;!!D9dNQwwGXtA!UYK3U5uPm8X_-PYmhQ2uxvCO7o6Hj3NY7b7EsSRPKK1hbtjJyZOJ8284ZeGmKVdcAgnY0XUyshx3NQQhD9ODzN8$">https://febs.onlinelibrary.wiley.com/doi/10.1016/j.febslet.2005.02.01</a></p>
    <p>There is more of course, but we don't want to get too wordy. 😉</p>
    <p>Kind regards,</p>
    <p>Eric <br>
    </p>
    <div class="moz-cite-prefix">On 1/4/25 1:42 PM, Pedro C. Marijuán
      wrote:<br>
    </div>
    <blockquote type="cite"
      cite="mid:9075dcab-cdfc-4484-be40-e77dca0f868e@gmail.com">
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      <title>Biologic - at the interface between biology, topology,
        logic and cybernetics.</title>
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              <th valign="BASELINE" align="RIGHT" nowrap="nowrap">Asunto:
              </th>
              <td>Re: Biologic - at the interface between biology,
                topology, logic and cybernetics.</td>
            </tr>
            <tr>
              <th valign="BASELINE" align="RIGHT" nowrap="nowrap">Fecha:
              </th>
              <td>Fri, 3 Jan 2025 12:38:13 -0600</td>
            </tr>
            <tr>
              <th valign="BASELINE" align="RIGHT" nowrap="nowrap">De: </th>
              <td>Louis Kauffman <a class="moz-txt-link-rfc2396E"
                  href="mailto:loukau@gmail.com" moz-do-not-send="true"><loukau@gmail.com></a></td>
            </tr>
            <tr>
              <th valign="BASELINE" align="RIGHT" nowrap="nowrap">Para:
              </th>
              <td>"Pedro C. Marijuán" <a class="moz-txt-link-rfc2396E"
                  href="mailto:pedroc.marijuan@gmail.com"
                  moz-do-not-send="true"><pedroc.marijuan@gmail.com></a></td>
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              <div class="" align="center"><font size="4"><b>Biologic -
                    at the interface between biology, topology, logic
                    and cybernetics.</b></font></div>
              <div class="" align="center"><font size="4"><b><br>
                  </b></font></div>
              <div class="" align="center"><b>Louis H Kauffman, UIC</b></div>
              <div class=""><br class="">
              </div>
              <div class="" align="center">“What can be shown, cannot be
                said.”</div>
              <div class="" align="center">“Was gezeigt werden kann,
                kann nicht gesagt werden.”</div>
              <div class="" align="center">(Wittgenstein, Tractatus,
                4.1212)</div>
              <div class="" align="center"><br class="">
              </div>
              <div class="" align="center">“We take the form of
                distinction for the form.”</div>
              <div class="" align="center">(Spencer-Brown, Laws of Form,
                Chapter 1)</div>
              <div class=""><br class="">
              </div>
              <div class="">What is the form of biology?</div>
              <div class="">Is there a biology of form?</div>
              <div class=""><br>
              </div>
              <div class="">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?</div>
              <div class=""> </div>
              <div class="">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?</div>
              <div class=""><br class="">
              </div>
              <div class="">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.</div>
              <div class="">DNA = <W|C> ----->  <W| E |C>
                ----->  <W|C> <W|C> = DNA DNA.</div>
              <div class="">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.</div>
              <div class=""><br class="">
              </div>
              <div class="">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.</div>
              <div class=""><br class="">
              </div>
              <div class="">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 </div>
              <div class="">B, x —> B,x , X,x</div>
              <div class="">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.</div>
              <div class="">Let b be the blueprint for B itself. Then</div>
              <div class="">B,b —> B,b , B,b.</div>
              <div class="">The Von Neumann Machine replicates itself. </div>
              <div class="">In the comparison, we see that The DNA
                contains (in its strands) the blueprint for its own
                replication.</div>
              <div class=""><br class="">
              </div>
              <div class="">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?</div>
              <div class=""><br class="">
              </div>
              <div class="">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.</div>
              <div class=""><img apple-inline="yes"
                  id="093308C2-C64C-41FE-8115-2651F174960D"
                  src="cid:part1.QTolAux4.sACJhX9d@oarf.org" class=""></div>
              <div class=""><br class="">
              </div>
              <div class="">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. </div>
              <div class="">One wants to know how far a world-view can
                be extended before it disintegrates.</div>
              <div class="">What we see in the electron micrograph is
                deeply shaped by the complex story of biological
                experiment that surrounds it.</div>
              <div class=""> </div>
              <div class="">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. </div>
              <div class="">Temporality may look like a tragedy for the
                classical mathematics, but it is exactly what interests
                us when studying biology. </div>
              <div class="">Mathematical biology is concerned with those
                structures leading to recursive generation of structures
                from themselves and from their environments. </div>
              <div class=""> </div>
              <div class="">#############################</div>
              <div class=""><br class="">
              </div>
            </div>
            <div class="">Here is a related paper:</div>
            <div class=""><a
href="https://urldefense.com/v3/__https://arxiv.org/abs/1512.04325__;!!D9dNQwwGXtA!Xuz20L8dnuTZYF9WFBHOLyZrvHTyVKqbCy4P55woe-bSQswWK6oGtDnIfdh8ErbhHvbI71N24gtkTUTyEMIjViUloF5d$"
                class="moz-txt-link-freetext" moz-do-not-send="true">https://arxiv.org/abs/1512.04325</a></div>
            <div class="">Here are other papers included in this email:</div>
            <div class=""><br class="">
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            <div class="">Very best,</div>
            <div class="">Louis H Kauffman</div>
            <div class="">Dept Mathematics</div>
            <div class="">University of Illinois at Chicago</div>
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      <pre wrap="" class="moz-quote-pre">_______________________________________________
Fis mailing list
<a class="moz-txt-link-abbreviated" href="mailto:Fis@listas.unizar.es">Fis@listas.unizar.es</a>
<a class="moz-txt-link-freetext" href="http://listas.unizar.es/cgi-bin/mailman/listinfo/fis">http://listas.unizar.es/cgi-bin/mailman/listinfo/fis</a>
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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: <a class="moz-txt-link-freetext" href="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</a>
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.
<a class="moz-txt-link-freetext" href="http://listas.unizar.es">http://listas.unizar.es</a>
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</pre>
    </blockquote>
    <div class="moz-signature">-- <br>
      <i>
        Dr. Eric Werner, FLS <br>
        Oxford Advanced Research Foundation <br>
        <a class="moz-txt-link-freetext" href="https://urldefense.com/v3/__https://oarf.org__;!!D9dNQwwGXtA!UYK3U5uPm8X_-PYmhQ2uxvCO7o6Hj3NY7b7EsSRPKK1hbtjJyZOJ8284ZeGmKVdcAgnY0XUyshx3NQQhyu4v2Mw$">https://oarf.org</a> <br>
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