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--></style></head><body><div><div id="x96d20ad0b684413ba2eb74a35ff8baa7"><a href="https://urldefense.com/v3/__https://leydesdorff.net/hertzberger/hetty/25dec22.pdf__;!!D9dNQwwGXtA!TwhH4Dtpds5jfSZ8XLpZ8dKzmgVaEUXzLLBoWnn8-_z68rVMr66jPqob3e6veMx6v1MTVxllUYaPGu2f5oE$" style="">https://leydesdorff.net/hertzberger/hetty/25dec22.pdf</a><div><br /></div><div>Dear colleagues, family, and frineds</div><div><br /></div><div>Pleiase, find a pdf ile at the webpage above. </div><div>This file is in DUtch. </div><div><br /></div><div>The reference is::</div><div>
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<span style="font-family:Arial;font-size:12pt;">Leydesorff, L. (2022). „Herr Obersturmbahnführer, gestatten Sie daß Ich rede?</span>
<span style="font-family:Arial;font-size:12pt;">. (<a href="https://urldefense.com/v3/__https://leydesdorff.net/hertzberger/hetty/25dec22.pdf__;!!D9dNQwwGXtA!TwhH4Dtpds5jfSZ8XLpZ8dKzmgVaEUXzLLBoWnn8-_z68rVMr66jPqob3e6veMx6v1MTVxllUYaPGu2f5oE$">https://leydesdorff.net/hertzberger/hetty/25dec22.pdf</a>), 39 pp. </span>
</div></div><div>Comments are most welcome in this stage: </div><div><br /></div><div>Best, Loet</div><div></div></div></div>
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<p class="MsoNormal" style="line-height:normal;" xmlns="http://www.w3.org/TR/REC-html40"><font face="Times New Roman"><span style="font-size: 12px;">PS. Given a health condition, I am no longer able to read and write emails without mistakes. </span></font><span style="font-size: 12px; font-family: "Times New Roman";">Please, consider using the telephone or skype. </span><span style="font-size: 12px; font-family: "Times New Roman";">Best, Loet</span></p><p class="MsoNormal" style="line-height:normal;" xmlns="http://www.w3.org/TR/REC-html40"><span style="font-size: 12px; font-family: "Times New Roman";"><br /></span></p><p class="MsoNormal" style="line-height:normal;" xmlns="http://www.w3.org/TR/REC-html40"><b><font face="Times New Roman" style="font-size: 9pt;" size="1">---------------------------------------------------------------------------------------------</font></b></p><p class="MsoNormal" style="line-height:normal;" xmlns="http://www.w3.org/TR/REC-html40"><b style=""><font style="font-size: 9pt;" face="Times New Roman" size="1"><a href="https://urldefense.com/v3/__https://link.springer.com/book/10.1007/978-3-030-59951-5__;!!D9dNQwwGXtA!TwhH4Dtpds5jfSZ8XLpZ8dKzmgVaEUXzLLBoWnn8-_z68rVMr66jPqob3e6veMx6v1MTVxllUYaPmgC-yRI$" style="">"The Evolutionary Dynamics of Discusive Knowledge"</a>(Open Access)</font></b></p><div id="x37dfff32a36b4410ad8e891fea6bb1b8"></div><p class="MsoNormal" style="line-height: normal;" xmlns="http://www.w3.org/TR/REC-html40"><font face="Times New Roman" style="font-size: 9pt;" size="1">Professor emeritus, University of Amsterdam </font></p><p class="MsoNormal" style="line-height: normal; font-size: 9pt;" xmlns="http://www.w3.org/TR/REC-html40"><br /></p></div><div id="x37dfff32a36b4410ad8e891fea6bb1b8"><span>
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<div>------ Original Message ------</div>
<div>From "<a href="mailto:joe.brenner@bluewin.ch">joe.brenner@bluewin.ch</a>" <<a href="mailto:joe.brenner@bluewin.ch">joe.brenner@bluewin.ch</a>></div>
<div>To <a href="mailto:pedroc.marijuan@gmail.com">pedroc.marijuan@gmail.com</a></div>
<div>Cc <a href="mailto:fis@listas.unizar.es">fis@listas.unizar.es</a></div>
<div>Date 12/25/2022 10:05:10 PM</div>
<div>Subject Re: [Fis] Fwd: A new discussion session; Self-Other in Biology</div></div><div><br /></div>
<div id="x727f69efe519490"><blockquote cite="426941038.10772.1672002310405@bluewin.ch" type="cite" class="cite2">
Dear Pedro, Dear All,<div><br /></div><div>Christmas is not even over and already a fascinating disagreement! In my system, Gödel is closer to reality because incompleteness is a feature of reality. Fixed points look pretty inert to me, and in biology??</div><div><br /></div><div>I believe since I don't have all the skills needed to be sure that fixed points eliminate the need for recursive functions but you have just gotten rid of another, probably real mental process. Recursion and anticipation, using dynamic forms of information, are what mind is about. </div><div><br /></div><div>I don't claim that mine is the "right" handle. I just plead for it to humbly accompany the story from computer science.</div><div><br /></div><div>Thank you and Happy New Year!<br /><blockquote style="margin-right: 0px; margin-left:15px;">----Original Message----<br />From : <a href="mailto:pedroc.marijuan@gmail.com">pedroc.marijuan@gmail.com</a><br />Date : 25/12/2022 - 21:42 (E)<br />To : <a href="mailto:fis@listas.unizar.es">fis@listas.unizar.es</a><br />Subject : [Fis] Fwd: A new discussion session; Self-Other in Biology<br /><br /><div class="moz-forward-container">
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<th valign="BASELINE" nowrap="" align="RIGHT">Asunto: </th>
<td>Re: [Fis] A new discussion session; Self-Other in Biology</td>
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<th valign="BASELINE" nowrap="" align="RIGHT">Fecha: </th>
<td>Fri, 23 Dec 2022 09:31:53 +0100</td>
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<th valign="BASELINE" nowrap="" align="RIGHT">De: </th>
<td>guillaume.bonfante <a class="moz-txt-link-rfc2396E" style="text-decoration: underline; color: blue;"><guillaume.bonfante@loria.fr></a></td>
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<th valign="BASELINE" nowrap="" align="RIGHT">Para: </th>
<td>Louis Kauffman <a class="moz-txt-link-rfc2396E" style="text-decoration: underline; color: blue;"><loukau@gmail.com></a>, Markose, Sheri <a class="moz-txt-link-rfc2396E" style="text-decoration: underline; color: blue;"><scher@essex.ac.uk></a></td>
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<th valign="BASELINE" nowrap="" align="RIGHT">CC: </th>
<td>Pedro C. Marijuán <a class="moz-txt-link-rfc2396E" style="text-decoration: underline; color: blue;"><pedroc.marijuan@gmail.com></a>, fis <a class="moz-txt-link-rfc2396E" style="text-decoration: underline; color: blue;"><fis@listas.unizar.es></a>, <a class="moz-txt-link-abbreviated" style="text-decoration: underline; color: blue;">guillaume.bonfante@mines-nancy.univ-lorraine.fr</a><a class="moz-txt-link-rfc2396E" style="text-decoration: underline; color: blue;"><guillaume.bonfante@mines-nancy.univ-lorraine.fr></a>, <a class="moz-txt-link-abbreviated" style="text-decoration: underline; color: blue;">mikhail.prokopenko@sydney.edu.au</a><a class="moz-txt-link-rfc2396E" style="text-decoration: underline; color: blue;"><mikhail.prokopenko@sydney.edu.au></a>, Neil Gershenfeld <a class="moz-txt-link-rfc2396E" style="text-decoration: underline; color: blue;"><neil.gershenfeld@cba.mit.edu></a>, Koonin, Eugene (NIH/NLM/NCBI) [E] <a class="moz-txt-link-rfc2396E" style="text-decoration: underline; color: blue;"><koonin@ncbi.nlm.nih.gov></a>, Oron Shagrir <a class="moz-txt-link-rfc2396E" style="text-decoration: underline; color: blue;"><oron.shagrir@gmail.com></a>, <a class="moz-txt-link-abbreviated" style="text-decoration: underline; color: blue;">Noson@sci.brooklyn.cuny.edu</a><a class="moz-txt-link-rfc2396E" style="text-decoration: underline; color: blue;"><Noson@sci.brooklyn.cuny.edu></a>, Friston, Karl <a class="moz-txt-link-rfc2396E" style="text-decoration: underline; color: blue;"><k.friston@ucl.ac.uk></a>, John Mattick <a class="moz-txt-link-rfc2396E" style="text-decoration: underline; color: blue;"><j.mattick@unsw.edu.au></a></td>
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<br />
<br /> Dear all,
<br />
<br /> End of the year, and now some spare time. As a computer scientist, in my opinion, Goedel's Incompleteness Theorem is touchy but not the right handle. As some of you mentioned below, I think that fix-points are much more promising.
<br />
<br /> They have various forms. They exist at every layer of the arithmetical hierarchy (you don't need to implement recursive functions). So, a very flexible tool.
<br />
<br /> All the best,
<br />
<br /> Guillaume
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<br />
<br />
<div class="moz-cite-prefix">
Le 05/12/2022 à 00:25, Louis Kauffman a écrit :
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Dear Sheri,
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It would indeed be very helpful to have a zoom conversation about these themes.
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Please let me know when you would be available to have it.
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We could start with an hour meeting and discussion and then perhaps extend to a second meeting with some presentations.
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Included below is a slide show of mine that is a bit cryptic but does summarize some points of view.
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I have downloaded the papers you indicated in your email and will read them now.
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Very best,
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Lou
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On Dec 5, 2022, at 2:53 PM, Markose, Sheri <
<a style="text-decoration: underline; color: blue;" class="moz-txt-link-freetext" moz-do-not-send="true">scher@essex.ac.uk</a>> wrote:
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<span style="font-size: 12.0pt;font-family: Arial , sans-serif;color: rgb(31,73,125);" class="">Dear Louis, Pedro and All –
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<span style="font-size: 12.0pt;font-family: Arial , sans-serif;" class="">I apologize again for not attending to the comments as soon as they appear. Autumn term is my very busy teaching term. Also, one of the reasons why I got waylaid is that I had to urgently send in my external examiner review of a Thesis of Adam Svahn (University of Sydney) on 25 Nov. I was free to invite folk who I have had some convos with on this topic and may be interested in the Foundations of Information Systems online forum as participants and potential leads on topics… I do this somewhat belatedly, my apologies again.
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<span style="font-size: 12.0pt;font-family: Arial , sans-serif;" class=""><span class="">(i)<span style="font-style: normal;font-variant: normal;font-weight: normal;font-size: 7.0pt;line-height: normal;font-family: "Times New Roman";" class=""> <span class="Apple-converted-space"> </span></span></span></span>
<span style="font-size: 12.0pt;font-family: Arial , sans-serif;" class="">The bulk of Adam Svahn’s work co-authored with Mikhail Prokopenko (S & P) is already published and can be found here
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<span style="font-size: 12.0pt;font-family: Arial , sans-serif;border: 1.0pt none windowtext;padding: 0.0cm;background-color: white;" class=""><a href="https://urldefense.com/v3/__https://doi.org/10.1162/artl_a_00370__;!!D9dNQwwGXtA!R8lchYgfzUtRK_UvjczZjG4odrY4nCT90ap2vplSNdF7nmHYAjY30NMIkzAIZPRsIn5AxYjgQKn_X6p4BTG0vMTREdnb$" style="color: blue;text-decoration: underline;" class="" moz-do-not-send="true"><span class="">https://doi.org/10.1162/artl_a_00370</span></a> and is relevant to our discussion. While we are still in the dark about<span class="Apple-converted-space"> </span></span>
<span style="font-family: Arial , sans-serif;" class="">how the near universal genomic (ACGT/U) alphabets emerged, the genome clearly manifests an unbroken chain of life with programs encoded in these alphabets and their execution via gene expression produce the somatic and phenotype identity of organisms.</span>
<span style="font-size: 12.0pt;font-family: Arial , sans-serif;border: 1.0pt none windowtext;padding: 0.0cm;background-color: white;" class=""><span class="Apple-converted-space"> </span>S & P share objectives as those that I have given<span class="Apple-converted-space"> </span></span>
<span style="font-family: Arial , sans-serif;" class="">specifically re how self-reference and negator operations known from Gödel (1931) incompleteness theorems and undecidability thereof arise so the software based genomic system is capable of endogenous novelty production and evolvability.</span>
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<span style="font-size: 12.0pt;font-family: Arial , sans-serif;border: 1.0pt none windowtext;padding: 0.0cm;background-color: white;" class="">S& R give an interesting and plausible account of how RNA-push down automata<span class="Apple-converted-space"> </span></span>
<span style="font-family: Arial , sans-serif;" class="">with their push and pop rules can produce limit cycle dynamics or the extensively found repetitive motifs sometimes called biological palindromes in the genome. They argue that a 2-stack RNA-push down automata is necessary to produce reflexive structures where the automata in addition to simply executing a program can use the 2<sup class="">nd</sup>stack to reflect on codes and make changes to them.</span>
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<span style="font-size: 12.0pt;font-family: Arial , sans-serif;color: rgb(31,73,125);" class=""><span class="">(ii)<span style="font-style: normal;font-variant: normal;font-weight: normal;font-size: 7.0pt;line-height: normal;" class=""> <span class="Apple-converted-space"> </span></span></span></span>
<span style="font-size: 12.0pt;font-family: Arial , sans-serif;color: rgb(31,73,125);" class="">Section 5 of S&P relates to undecidability as fixed points of negation functions<span class="Apple-converted-space"> </span><span style="background-color: yellow;background-position: initial initial;background-repeat: initial initial;" class="">and has much in common Louis’s 15 Nov email point 5 below ( I have scissored and pasted this in the email trail below) on the ease with which self-negating Gödel sentences can be created by logicians.</span> However, biology unlike Gödel (and other logicians) is not directly concerned about undecidability, incompleteness, or whether a program halts. I have stuck my neck out and said that Gödel machinery used by biology and the formidable genomic self-referential general intelligence is to establish a hack free agenda for the genome geared toward autonomous life.
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<span style="font-size: 12.0pt;font-family: Arial , sans-serif;" class="">Thus, some further thought needs to be expended as to how the negator operation naturally occurs in biology. I have stated it is the bio malware or the viral software that Eugene Koonin et al have said has been coextensive with life having provided the copy/replicate program possibly in what the computer literature calls Quines. The latter are distinct from online self-assembly of somatic self which requires gene expression or machine execution as in the ribosomal machines. To make out gene-codes that self-assemble the organism have been changed/tampered with by software of non-self other appears to be a pressing matter for homeostasis which is clearly a bio-cybersecurity problem.<span class="Apple-converted-space"> </span>
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<span style="font-size: 12.0pt;font-family: Arial , sans-serif;color: rgb(31,73,125);" class=""><span class="">(iii)<span style="font-style: normal;font-variant: normal;font-weight: normal;font-size: 7.0pt;line-height: normal;" class=""> <span class="Apple-converted-space"> </span></span></span></span>
<span style="font-size: 12.0pt;font-family: Arial , sans-serif;" class="">The over 85% offline recording in the Thymic MHC receptors of expressed genes in humans for example brings us to the points made by Pedro in his 1 December email on<span class="Apple-converted-space"> </span><span style="color: rgb(31,73,125);" class="">Self and non-self antigen recognition in Adaptive Immune System. Thank you Pedro for the nugget of information of how the MHC receptors has two strips of <span class="Apple-converted-space"> </span></span></span>
<span style="font-size: 12.0pt;font-family: Arial , sans-serif;" class="">8-10 amino acids residues for Class 1, mostly "self", and 13-18 amino acids residues for Class 2 for non-self. I did not know this. I will read "Sensing the world and its dangers: An evolutionary perspective in<br class="" /> neuroimmunology." By Aurora Krauset al. In, eLife 2021;10:e66706. DOI:<span class="Apple-converted-space"> </span></span>
<span style="font-size: 12.0pt;font-family: Arial , sans-serif;" class=""><a href="https://urldefense.com/v3/__https://linkprotect.cudasvc.com/url?a=https*3a*2f*2fdoi.org*2f10.7554*2feLife.66706&c=E,1,mnuJARbiz5DP5j0H1X0ciBwcFLUNxlmdaZCNXX6tuWJ7oLj-36Vg9-Wauvxar1tDnTFYRaRF0eqlIxd2zzkL3LoskpUW1kBa2CHZaMqYUapU2iEi&typo=1__;JSUlJSU!!D9dNQwwGXtA!R8lchYgfzUtRK_UvjczZjG4odrY4nCT90ap2vplSNdF7nmHYAjY30NMIkzAIZPRsIn5AxYjgQKn_X6p4BTG0vN18TkB3$" style="color: blue;text-decoration: underline;" class="" moz-do-not-send="true">https://doi.org/10.7554/eLife.66706</a></span>
<span style="font-size: 12.0pt;font-family: Arial , sans-serif;" class="">.<br class="" /><br class="" /></span>
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<span style="font-size: 12.0pt;font-family: Arial , sans-serif;color: rgb(31,73,125);" class=""> If you recall how the Recursive Fixed Point Theorem which starts with a mirror mapping between online self-assembly program execution,<span class="Apple-converted-space"> </span></span>
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<span style="font-size: 12.0pt;font-family: Arial , sans-serif;color: rgb(31,73,125);" class=""> that have halted and create somatic identity and the<span class="Apple-converted-space"> </span><i class="">offline</i><span class="Apple-converted-space"> </span>record of the<span class="Apple-converted-space"> </span><br class="" /> same in a<span class="Apple-converted-space"> </span><span style="background-color: yellow;background-position: initial initial;background-repeat: initial initial;" class="">2-<span class="Apple-converted-space"> </span></span> <span style="background-color: yellow;background-position: initial initial;background-repeat: initial initial;" class="">place</span> function <span class="Apple-converted-space"> </span></span>
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<span style="font-size: 12.0pt;font-family: Arial , sans-serif;color: rgb(31,73,125);" class=""><span class="Apple-converted-space"> </span>(g, g) in the MHC receptors creating the Thymic self. I say the first g from the left in<span class="Apple-converted-space"> </span></span>
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<span style="font-size: 12.0pt;font-family: Arial , sans-serif;color: rgb(31,73,125);" class=""><span class="Apple-converted-space"> </span>(g, g) and changes thereof relate to what happens to self and the second is self’s record of what<span class="Apple-converted-space"> </span><br class="" /> the other has done to self. So if the 2<sup class="">nd</sup><span class="Apple-converted-space"> </span>entry is different from the first entry in<span class="Apple-converted-space"> </span></span>
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<span style="font-size: 12.0pt;font-family: Arial , sans-serif;color: rgb(31,73,125);" class=""><span class="Apple-converted-space"> </span>(g, g) it is off diagonal etc. The non-self hostile other is a projection of self g ‘gene codes’ and those <span class="Apple-converted-space"> </span><i class="">f ¬ !</i> which are reactive to the self g-<br class="" /> codes denoted as g¬. As we know an astronomic number of potential indexes g¬ are generated by the RAG genes.
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<span style="font-size: 12.0pt;font-family: Arial , sans-serif;color: rgb(31,73,125);" class=""> How the immune system identifies a yet to happen attack by a novel non-self antigen requires the first part of the fix point of the latter generated in the Thymic T-cell receptors to sync with those generated in the<span class="Apple-converted-space"> </span><br class="" /> the peripheral MHC receptors when the said expressed genes are attacked (like the lung tissue etc) in real time. The latter is experientially generated and while the former is a spectacular case of predictive coding. So<span class="Apple-converted-space"> </span><br class="" /> unless the T-cell receptor has cloned the index of the novel bio-malware in advance via V(D) J, the AIS will not be recognize the biomalware should it attack. I have said fixed point for the software/algorithm<span class="Apple-converted-space"> </span><i class="">f ¬ !</i> requires<span class="Apple-converted-space"> </span><br class="" /> the full use of say Rogers Second Recursion Theorem and the Gödel Sentence thereof, viz. far more machinery self-referential structures than in the original Gödel (1931) formats. <br class="" /><br class="" />
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<span style="font-size: 12.0pt;font-family: Arial , sans-serif;color: rgb(31,73,125);" class=""><span class="">(iv)<span style="font-style: normal;font-variant: normal;font-weight: normal;font-size: 7.0pt;line-height: normal;" class=""> <span class="Apple-converted-space"> </span></span></span></span>
<span style="font-size: 12.0pt;font-family: Arial , sans-serif;color: rgb(31,73,125);" class="">Finally, there is the problem that the information processing for advanced code based systems is one akin to Formal Systems of Theorems and non-Theorems. For this Raymond Smullyan’s book of the same name is what gave me the idea that a tight grip will be exerted with all inference based recursive reductions and Gödel Sentences when some potential negations to theorems viz. the halting self-assembly gene codes that generate the organism, are in the offing. This self-referential genomic blockchain distributed ledger of the unbroken chain of life has similarities with manmade BCDL, but latter are not self-referential with individual nodes being able to self-report attacks.
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<span style="font-size: 12.0pt;font-family: Arial , sans-serif;color: rgb(31,73,125);" class="">Louis, I would love to have a zoom chat with you as it will be great to sound you out more. You are right about the mindboggling variants of self-reference ….
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<span style="font-size: 12.0pt;font-family: Arial , sans-serif;color: rgb(31,73,125);" class="">Ditto for many others who I hope to be in touch with soon.
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<span style="font-size: 12.0pt;font-family: Arial , sans-serif;color: rgb(31,73,125);" class="">Many thanks again for the great comments.
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<b class=""><span class="" lang="EN-US">From:</span></b>
<span class="" lang="EN-US"><span class="Apple-converted-space"> </span>Pedro C. Marijuán <<a style="text-decoration: underline; color: blue;" class="moz-txt-link-freetext" moz-do-not-send="true">pedroc.marijuan@gmail.com</a>><span class="Apple-converted-space"> </span><br class="" /><b class="">Sent:</b><span class="Apple-converted-space"> </span>01 December 2022 13:03<br class="" /><b class="">To:</b><span class="Apple-converted-space"> </span>Markose, Sheri <<a style="text-decoration: underline; color: blue;" class="moz-txt-link-freetext" moz-do-not-send="true">scher@essex.ac.uk</a>>; Louis Kauffman <<a style="text-decoration: underline; color: blue;" class="moz-txt-link-freetext" moz-do-not-send="true">loukau@gmail.com</a>><br class="" /><b class="">Cc:</b><span class="Apple-converted-space"> </span>fis <<a style="text-decoration: underline; color: blue;" class="moz-txt-link-freetext" moz-do-not-send="true">fis@listas.unizar.es</a>>;<span class="Apple-converted-space"> </span><a style="text-decoration: underline; color: blue;" class="moz-txt-link-freetext" moz-do-not-send="true">guillaume.bonfante@mines-nancy.univ-lorraine.fr</a><br class="" /><b class="">Subject:</b><span class="Apple-converted-space"> </span>Re: [Fis] A new discussion session
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Dear Sheri, Lou, and all discussants,
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It is a pity that this excellent discussion has taken place in complicated academic weeks, as it has been caught in a sort of "punctuated equilibrium" of longer stasis than activities in our evolutionary list. Well, I have a couple of very brief comments:
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First, emphasizing that one of the references in Youri's last messages should be obligated reading for biologically interested parties: "Sensing the world and its dangers: An evolutionary perspective in
<br class="" /> neuroimmunology." By Aurora Krauset al. In, eLife 2021;10:e66706. DOI:
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<a href="https://urldefense.com/v3/__https://linkprotect.cudasvc.com/url?a=https*3a*2f*2fdoi.org*2f10.7554*2feLife.66706&c=E,1,mnuJARbiz5DP5j0H1X0ciBwcFLUNxlmdaZCNXX6tuWJ7oLj-36Vg9-Wauvxar1tDnTFYRaRF0eqlIxd2zzkL3LoskpUW1kBa2CHZaMqYUapU2iEi&typo=1__;JSUlJSU!!D9dNQwwGXtA!R8lchYgfzUtRK_UvjczZjG4odrY4nCT90ap2vplSNdF7nmHYAjY30NMIkzAIZPRsIn5AxYjgQKn_X6p4BTG0vN18TkB3$" style="color: blue;text-decoration: underline;" class="" moz-do-not-send="true">https://doi.org/10.7554/eLife.66706</a>
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<span class="Apple-converted-space"> </span>In this vein, I will follow with the argument that the multicellular self is a composite, an association with a microbial consortium that probably was the big evolutionary cause to create a defense system of such a great complexity. The innate immune system would represent the evolutionary learning about those dangers, with scores of different components and pattern recognition strategies...
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And second, about the adaptive immune system, it is where the ongoing mostly formal discussion would apply (can we agree with that?). Then, it seems that the core of this adaptive immune branch is the Major Histocompatibility Complex molecule (MHC). This MHC molecules of two major classes are highly complex (polygenic and polymorphic) and they are in charge of presenting to lymphocyte T cells the protein fragments churned out from the proteosomes inside cells (fragments of variable lenght: 8-10 amino acids residues for Class 1, mostly "self", and 13-18 amino acids residues for Class 2, mostly "non self"). Then, the thymus is in charge of deactivating the T cells loaded with self stuff. My point is that the defense in front of the non-self is based on
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<u class="">indirect products of protein translation</u>. This causes me some uneasiness, as protein translation (see Youri's presentation months ago) introduces a layer of extra complexity, not to speak the processing via proteosomes. Further, with just 10 or 12 amino acids can we faithfully ascertain algorithmic non-self provenance??
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Well, Sheri is far more acknowledged with all this stuff. And perhaps Lou can say something about the formal distinguishability of 10-12 aa.
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Best--Pedro
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<b class=""><span class="" lang="EN-US">From:</span></b>
<span class="" lang="EN-US"><span class="Apple-converted-space"> </span>Louis Kauffman<span class="Apple-converted-space"> </span></span>
<a style="text-decoration: underline; color: blue;" class="" moz-do-not-send="true"><span class="" lang="EN-US">loukau@gmail.com</span></a>
<span class="" lang="EN-US"><span class="Apple-converted-space"> </span><br class="" /><b class="">Sent:</b><span class="Apple-converted-space"> </span>15 November 2022 23:02<br class="" /><b class="">To:</b><span class="Apple-converted-space"> </span>Markose, Sheri<span class="Apple-converted-space"> </span></span>
<a style="text-decoration: underline; color: blue;" class="" moz-do-not-send="true"><span class="" lang="EN-US">scher@essex.ac.uk</span></a>
<span class="" lang="EN-US"><br class="" /><b class="">Cc:</b><span class="Apple-converted-space"> </span>"Pedro C. Marijuán"<span class="Apple-converted-space"> </span></span>
<a style="text-decoration: underline; color: blue;" class="" moz-do-not-send="true"><span class="" lang="EN-US">pedroc.marijuan@gmail.com</span></a>
<span class="" lang="EN-US">; fis<span class="Apple-converted-space"> </span></span>
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<a style="text-decoration: underline; color: blue;" class="" moz-do-not-send="true"><span class="" lang="EN-US">guillaume.bonfante@mines-nancy.univ-lorraine.fr</span></a>
<span class="" lang="EN-US"><br class="" /><b class="">Subject:</b><span class="Apple-converted-space"> </span>Re: [Fis] A new discussion session
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I will try to respond to your letter about the post Goedel structures by first quoting the last part of my previous letter that discusses Goedelian ideas from the point of view of fixed points.
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My letter was quite long, and it is possible to not get to the second half.
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Note also that the first half is based on a referential situation g —> F where #g ——> Fg is what I call the Indicative Shift of g —> F. This is formal and does not assume anythng other than arrow structure.
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With g —> F# we have #g —> F#g making F#g refer to its own name. There is more to say herd and references that I cannot send to the list, so I will get a dropbox for it and further discussion later today.
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Best,
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Lou K.
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<span style="font-size: 10.0pt;font-family: Arial , sans-serif;" class="">It is a very interesting question whether such encoding or such multiple relationships to context occur in biology. Here are some remarks.
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<span style="font-size: 10.0pt;font-family: Arial , sans-serif;" class="">1. In biology is is NORMALLY the case that certain key structures have multiple interpretations and uses in various contexts.
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<span style="font-size: 10.0pt;font-family: Arial , sans-serif;" class="">The understanding of such multiple uses and the naming of them requires an observer of the biology. Thus we see the action of a cell membrane and we see the action of mitosis, and so on.
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<span style="font-size: 10.0pt;font-family: Arial , sans-serif;" class="">2. There are implicit encodings in biology such as the sequence codes in DNA and RNA and their unfoldment. To what extent do they partake of the properties of Goedel coding?
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<span style="font-size: 10.0pt;font-family: Arial , sans-serif;" class="">3. The use of the Goedel coding in the Incompleteness theorem depends crucially on the relationship of syntax and semantic in the formal system and in the mathematician’s interpretation of the workings of that system. The Goedel argument depends upon the formal system S being seen as a mathematical object that itself can be studied for its properties and behavior.
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<span style="font-size: 10.0pt;font-family: Arial , sans-serif;" class="">When we speak of the truth of G, we are speaking of our assessment of the possible behaviour of S, given its consistency. We are reasoning about S just as Euclid reasons about the structure of right triangle.
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<span style="font-size: 10.0pt;font-family: Arial , sans-serif;" class="">4. In examining biological structures we take a similar position and reason about what we know about them. Sufficiently complex biological structures can be seen as modeled by certain logical formal systems.
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<span style="font-size: 10.0pt;font-family: Arial , sans-serif;" class="">And then Goedelian reasoning can be applied to them. This can even be extended to ourselves. Suppose that I am modeled correctly in my mathematical reasoning by a SINGLE CONSISTENT FORMAL SYSTEM S.
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<span style="font-size: 10.0pt;font-family: Arial , sans-serif;" class="">Then “I” can apply the above proof of Goedel’s Therem to S and deduce that G cannot be proven by S. Thus “I” have exceeded the capabilities of S. Therefore it is erroneous to assume that my mathematical reasoning is encapsulated by a single formal system S. If I am a formal system, that system must be allowed to grow in time. Such reasoning as this is subtle, but the semantics of the relationship of mathematicians and the formal systems that they study is subtle and when biology is brought in the whole matter becomes exceedingly interesting.
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<span style="font-size: 10.0pt;font-family: Arial , sans-serif;" class="">5. We man not need numbers to have these kinds of relationships. And example is the Smullyan Machine that prints sequences of symbols from the alphabet {~,P,R} on a tape. Sequences that begin with P,~P,PR and ~PR are regarded as meaningful, with the meanings:
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<span style="font-size: 10.0pt;font-family: Arial , sans-serif;" class="">~PX: X cannot be printed.
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<span style="font-size: 10.0pt;font-family: Arial , sans-serif;" class="">~PRX: XX cannot be printed.
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<span style="font-size: 10.0pt;font-family: Arial , sans-serif;" class="">Here X is any string of the symbols {~,P,R}.
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<span style="font-size: 10.0pt;font-family: Arial , sans-serif;" class="">Thus PR~~P means that XX can be printed where X = ~~P. Thus PR~~P means that ~~P~~P can be printed.
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<span style="font-size: 10.0pt;font-family: Arial , sans-serif;" class="">By printed we mean on one press of the button on the Machine, a string of characters is printed.
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<span style="font-size: 10.0pt;font-family: Arial , sans-serif;" class="">IT IS ASSUMED THAT THE SMULLYAN MACHINE ALWAYS TELLS THE TRUTH WHEN IT PRINTS A MEANINGFUL STATEMENT.
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<span style="font-size: 10.0pt;font-family: Arial , sans-serif;" class="">Then we have the
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<span style="font-size: 10.0pt;font-family: Arial , sans-serif;" class="">Theorem. There are meaningful true strings that the Smullyan Machine cannot print.
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<span style="font-size: 10.0pt;font-family: Arial , sans-serif;" class="">This is a non-numerical analog of the Goedel Theorem. And the string that cannot be printed is G = ~PR~PR.
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<span style="font-size: 10.0pt;font-family: Arial , sans-serif;" class="">For you see that G is meaningful and since G = ~PRX, G says that XX cannot be printed. But X = ~PR and XX = ~PR~PR = G. So G says that G cannot be printed.
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<span style="font-size: 10.0pt;font-family: Arial , sans-serif;" class="">If the machine were to print G, it would lie. And the machine does not lie.
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<span style="font-size: 10.0pt;font-family: Arial , sans-serif;" class="">Therefore G is unprintable.
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<span style="font-size: 10.0pt;font-family: Arial , sans-serif;" class="">But this is what G says.
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<span style="font-size: 10.0pt;font-family: Arial , sans-serif;" class="">So we have established the truth of G and proved the Theorem.
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<span style="font-size: 10.0pt;font-family: Arial , sans-serif;" class="">6. Examine this last paragraph 5. The Machine is like an organism with a limitation. This limitation goes through the semantics of reference. ~PRX refers to XX and so can refer to itself if we take X = ~PR. ~PX refers to X and cannot refer to itself since it is longer than X. In biological coding the DNA code is fundamentally smaller or equal to the structure to which it refers.
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<span style="font-size: 10.0pt;font-family: Arial , sans-serif;" class="">Thus the self-reproduction of the DNA is possible since DNA = W+C the convention of the Watson and Crick strand and each of W and C can by themselves engage in an action to encode, refer to, the other strand. W can produce a copy of C in the form W+C and C can produce a copy of W in the form W+C each by using the larger environment. Thus W+C refers to itself, reproduces itself by a method of encoding quite similar to the self reference of the Smullyan Machine.
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<span style="font-size: 10.0pt;font-family: Arial , sans-serif;" class="">7. Von Neuman devised a machine that can build itself. B is the von Neuman machine and B.x —> X,x where x is the plan or blueprint or code for and entity X. B builds X with given the blueprint x.
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<span style="font-size: 10.0pt;font-family: Arial , sans-serif;" class="">Then we have B,b —> B,b where b is the blueprint for B. B builds itself from its own blueprint. I hope you see the analogy with the Goedel code.
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<span style="font-size: 10.0pt;font-family: Arial , sans-serif;" class="">8. I will stop here. The relationships with biology are very worth discussing.
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<span style="font-size: 10.0pt;font-family: Arial , sans-serif;" class="">Before stopping it is worth remarking that the Maturana Uribe Varela autopoeisis is an example of a system arising into a form of self-reference that has a lifetime due to the probabilisitic dynamics of its process.
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<span style="font-size: 10.0pt;font-family: Arial , sans-serif;" class="">Lou Kauffman
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El 15/11/2022 a las 21:19, Markose, Sheri escribió:
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Dear Louis, dear Colleagues -
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Louis has given an excellent exposition of Gödel Numbering (g.n) (your point number 2 on coding and semantics is giving me food for thought) , giving example of prime factorization and also of Gödel Sentence as one that states its own unprovability. Unlike statements like "this is false", GS is not paradoxical and in a consistent system it is a theorem with a constructive g.n. The latter in terms of the prime factorization format, it is indeed a Hilbert 10 Diophantine equation with no integer solutions. A remarkable achievement in maths, considering Gödel was only 23 years of age .... But what has this got to do with Biology and novelty production, the objectives of the my FIS discussion ?
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In view of brevity and also urged by Pedro, I dropped a couple of paragraphs in my FIS kick off submission as to why we need to exceed Gödel (1931) and couch the Gödel Incompleteness Results and the Gödel Sentence with a fuller understanding of algorithms as encoded instructions and as machine executable codes, of the notion of recursive enumeration (re) and re sets that was developed in the Emil Post (1944). I hope Louis Kauffman can comment on the the application of the fuller Gödel-Turing -Post-Rogers framework mentioned in my FIS note and in my papers cited there.
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1. I have found the following statement by Joel Hamkins ( :
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<a href="https://urldefense.com/v3/__https://linkprotect.cudasvc.com/url?a=http*3a*2f*2fjdh.hamkins.org*2fwp-content*2fuploads*2fA-review-of-several-fixed-point-theorems-1.pdf&c=E,1,bKIlk9p4sIB5v1zLhbA_VCdX_aoMSPljj6KZdLjCesxOjPwYqUF5PkC4wqvoWq0qqGndGHjZ6ELzpZ8IhqbUDEGNINdm7Da4GNcSgCn3k0us&typo=1__;JSUlJSUl!!D9dNQwwGXtA!R8lchYgfzUtRK_UvjczZjG4odrY4nCT90ap2vplSNdF7nmHYAjY30NMIkzAIZPRsIn5AxYjgQKn_X6p4BTG0vHnETe5i$" style="color: blue;text-decoration: underline;" class="" moz-do-not-send="true"><span style="font-size: 11.0pt;font-family: Calibri , sans-serif;" class="">http://jdh.hamkins.org/wp-content/uploads/A-review-of-several-fixed-point-theorems-1.pdf</span></a>
<span class="Apple-converted-space"> </span>) useful as it makes an important observation that the original Gödel (1931) framework permits an encodable proposition to make statements about itself while Second Recursion Theorems (SRT) also called Fixed Point Theorems are needed “to construct programs/algorithms that refer to themselves”. The terms programs and algorithms will be used interchangeably.
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I choose Rogers Fixed Point Theorem of (total) computable functions starting with the staple I have already indicated Diag (g) (RHS of (8) below) is what Neil Gerschenfeld calls ribosomal self-assembly machines in gene expression where the program
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<i class="">g builds the<span class="Apple-converted-space"> </span></i>machine that runs g.
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II. The first requirement of a system to identify Fixed Points viz. self-referential constructions of algorithms/programs is (8) viz to identify what function/algorithm has altered the Diag (g).
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When online gene expression takes place on RHS of (8), viz. these programs have halt commands and builds the somatic and phenotype identity of vertebrates online, the offline record of this is made in the Thymus that can not only represent the Thymic/immune self but also concatenate changes thereof.
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I have suggested that the Adaptive Immune System and the Mirror Neuron System have these structures in (8). And the domain of self-halting machines as in (8) are the Theorems of the system and a subset of Post (1944) Creative Set. The non-Theorems have codes say
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<span class="Apple-converted-space"> </span>which cannot halt in a formal system that is consistent. To my mind, the embodiment via the physical self being self-assembled and an offline record of this on LHS of (8) is what fuses syntax and semantics.
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II. Once, (8) is in place, the Adaptive immune system has to identify novel negation software function
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<i class="">f<sup class="">¬!<span class="Apple-converted-space"> </span></sup></i>
<sub class=""> </sub>of non-self antigens which is an uncountable infinite possibilities. Hence the close to astronomic search with V(D) J of 10
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<span class="Apple-converted-space"> </span>) of non-self antigens that can hijack the self- assembly machines as recorded on RHS of (8). Only from knowledge of self can the hostile other, in the case of the AIS, be identified.
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III. Roger Fixed Point assures us that the indexes of the fixed point for
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<sub class=""> </sub>be generated. I have cced Guillame Bonfante who I think was among the first (with coauthors, 2006) to suggest how SRT can be used to identify computer viruses. But they do not use the full force of Self-Ref and Self -Rep and only implicitly use Post Creative and Productive Sets. The index of the Godel Sentence for the fixed point will endogenously lie outside of Post listable or recusively enumerable set for Theorems and known non-Theorems.
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IV. From these Gödel Sentences produced in the immune-cognitive systems, the explicit use of Post (1944) Theorems indicates how novel antibodies cannot be produced in the absence of the Gödel Sentence which allows a biotic element to self-report it is under attack.
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V. In conclusion, while it has become fashionable for some like Jurgen Schmidhuber to claim that there can be endogenous self improving recursive novelty (he calls them Gödel machines) , the Gödel Logic says that the original theorems and self-codes are kept unchanged/hack free and novelty is produced only in response to adversarial attacks of self codes. So the AIS story is somatic hypermutation so that nothing in the genome changes. As to how the germline itself changes, needs more investigation, in Biosystems paper, I suggest something very briefly.
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So thankyou all again for your in depth comments and interest.
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Best Regards
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Sheri
<span class="Apple-converted-space"> </span>
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-----Original Message-----
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From: Fis <
<a style="text-decoration: underline; color: blue;" class="moz-txt-link-freetext" moz-do-not-send="true">fis-bounces@listas.unizar.es</a>> On Behalf Of Louis Kauffman
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Sent: 08 November 2022 00:13
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To: "Pedro C. Marijuán" <
<a style="text-decoration: underline; color: blue;" class="moz-txt-link-freetext" moz-do-not-send="true">pedroc.marijuan@gmail.com</a>>
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Cc: fis <
<a style="text-decoration: underline; color: blue;" class="moz-txt-link-freetext" moz-do-not-send="true">fis@listas.unizar.es</a>>
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Subject: Re: [Fis] A new discussion session
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CAUTION: This email was sent from outside the University of Essex. Please do not click any links or open any attachments unless you recognise and trust the sender. If you are unsure whether the content of the email is safe or have any other queries, please contact the IT Helpdesk.
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Dear Pedro,
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Here are some comments about Goedel numbering and coding.
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It is interesting to think about Goedel numbering in a biological context.
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Actually we are talking about how a given entity has semantics that can vary from context to context.
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It is not simply a matter of assigning a code number. If g —> F is the relation of a Goedel number g to a statement F, then we have two contexts for F.
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1. F as a well formed formula in a formal system S.
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2. g as a number in either a number system for an observer of S or g as a number in S, but g, as a representative for F can be regarded in the system S with the meanings so assigned.
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Thus we have produced by the assignment of Goedel numbers a way for a statement F to exist in the semantics of more than one context.
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This is the key to the references and self-references of the Goedelian situations.
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Lets look at this more carefully. Recall that there is a formal system S and that to every well formed formula in S, there is a code number g = g(S). The code number can be produced in many ways.
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For example, one can assign different index numbers n(X) to each distinct generating symbol in S. Then with an expression F regarded as an ordered string of symbols, one can assign to F the product of the prime numbers, in their standard order, with exponents the indices of the sequence of characters that compose F. For example, g(~ x^2 = 2) = 2^{n(~)} 3^{n(x)}5^{n(^)}7^{n(2)}11^{n(=)}13^{n(2)}. From such a code, one can retrieve the original formula in a unique way.
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The system S is a logical system that is assumed to be able to handle logic and basic number theory. Thus it is assumed that S can encode the function g: WFFS(S) —> N where N denotes the natural numbers.
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And S can decode a number to find the corresponding expression as well. It is assumed that S as a logical system, is consistent.
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With this backgound, let g —> F denote the condition that g = g(F). Thus I write a reference g —> F for a mathematical discussion of S, to indicate that g is the Goedel number of F.
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Now suppose that F(x) is a formula in S with a free variable x. Free variables refer to numbers. Thus if I write x^2 = 4 then this statement can be specialized to 2^2 = 4 with x =2 and the specialization is true.
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Or I can write 3^2 = 4 and this is a false statement. Given F(x) and some number n, I can make a new sentence F(n).
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Now suppose that
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g —> F(x).
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Then we can form F(g) and this new statement has a Goedel number. Let #g denote the Goedel number of F(g).
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#g —> F(g).
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This # is a new function on Goedel numbers and also can be encoded in the system S. I will abbreviate the encoding into S by writing #n for appropriate numbers n handled by S.
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Then we can consider
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F(#x) and it has a Goedel number
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h —> F(#x)
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And we can shift that to
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#h —> F(#h).
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This is the key point.
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Now we have constructed a number #h so that F(#h) discusses its own Goedel number.
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This construction allows the proof of the Goedel Incompleteness Theorem via the sentence B(x) that states
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B(x) = “The statement with Goedel number x is provable in S.” (This can also be encoded in S.)
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We then construct
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h—> ~B(#x)
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and
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#h —> ~B(#h)
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and obtain the statement
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G= ~B(#h).
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G states the unprovability of the Goedel decoding of #h.
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But the Goedel decoding of #h is the statement G itself.
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Thus G states its own unprovability.
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Therefore, S being consistent, cannot prove G.
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By making these arguments we have have proved that G cannot be proved by S.
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Thus we have shown that G is in fact true.
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We have shown that there are true statements in number theory unprovable by system S..
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##########################
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The above is a very concise summary of the proof of Goedel’s Incompleteness Theorem, using Goedel number encoding.
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It is a very interesting question whether such encoding or such multiple relationships to context occur in biology. Here are some remarks.
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1. In biology is is NORMALLY the case that certain key structures have multiple interpretations and uses in various contexts.
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The understanding of such multiple uses and the naming of them requires an observer of the biology. Thus we see the action of a cell membrane and we see the action of mitosis, and so on.
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2. There are implicit encodings in biology such as the sequence codes in DNA and RNA and their unfoldment. To what extent do they partake of the properties of Goedel coding?
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3. The use of the Goedel coding in the Incompleteness theorem depends crucially on the relationship of syntax and semantic in the formal system and in the mathematician’s interpretation of the workings of that system. The Goedel argument depends upon the formal system S being seen as a mathematical object that itself can be studied for its properties and behavior.
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When we speak of the truth of G, we are speaking of our assessment of the possible behaviour of S, given its consistency. We are reasoning about S just as Euclid reasons about the structure of right triangle.
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4. In examining biological structures we take a similar position and reason about what we know about them. Sufficiently complex biological structures can be seen as modeled by certain logical formal systems.
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And then Goedelian reasoning can be applied to them. This can even be extended to ourselves. Suppose that I am modeled correctly in my mathematical reasoning by a SINGLE CONSISTENT FORMAL SYSTEM S.
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Then “I” can apply the above proof of Goedel’s Therem to S and deduce that G cannot be proven by S. Thus “I” have exceeded the capabilities of S. Therefore it is erroneous to assume that my mathematical reasoning is encapsulated by a single formal system S. If I am a formal system, that system must be allowed to grow in time. Such reasoning as this is subtle, but the semantics of the relationship of mathematicians and the formal systems that they study is subtle and when biology is brought in the whole matter becomes exceedingly interesting.
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5. We man not need numbers to have these kinds of relationships. And example is the Smullyan Machine that prints sequences of symbols from the alphabet {~,P,R} on a tape. Sequences that begin with P,~P,PR and ~PR are regarded as meaningful, with the meanings:
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PX: X can be printed.
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~PX: X cannot be printed.
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PRX: XX can be printed.
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~PRX: XX cannot be printed.
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Here X is any string of the symbols {~,P,R}.
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Thus PR~~P means that XX can be printed where X = ~~P. Thus PR~~P means that ~~P~~P can be printed.
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By printed we mean on one press of the button on the Machine, a string of characters is printed.
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IT IS ASSUMED THAT THE SMULLYAN MACHINE ALWAYS TELLS THE TRUTH WHEN IT PRINTS A MEANINGFUL STATEMENT.
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Then we have the
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Theorem. There are meaningful true strings that the Smullyan Machine cannot print.
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This is a non-numerical analog of the Goedel Theorem. And the string that cannot be printed is G = ~PR~PR.
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For you see that G is meaningful and since G = ~PRX, G says that XX cannot be printed. But X = ~PR and XX = ~PR~PR = G. So G says that G cannot be printed.
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If the machine were to print G, it would lie. And the machine does not lie.
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Therefore G is unprintable.
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But this is what G says.
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So we have established the truth of G and proved the Theorem.
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6. Examine this last paragraph 5. The Machine is like an organism with a limitation. This limitation goes through the semantics of reference. ~PRX refers to XX and so can refer to itself if we take X = ~PR. ~PX refers to X and cannot refer to itself since it is longer than X. In biological coding the DNA code is fundamentally smaller or equal to the structure to which it refers.
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Thus the self-reproduction of the DNA is possible since DNA = W+C the convention of the Watson and Crick strand and each of W and C can by themselves engage in an action to encode, refer to, the other strand. W can produce a copy of C in the form W+C and C can produce a copy of W in the form W+C each by using the larger environment. Thus W+C refers to itself, reproduces itself by a method of encoding quite similar to the self reference of the Smullyan Machine.
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7. Von Neuman devised a machine that can build itself. B is the von Neuman machine and B.x —> X,x where x is the plan or blueprint or code for and entity X. B builds X with given the blueprint x.
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Then we have B,b —> B,b where b is the blueprint for B. B builds itself from its own blueprint. I hope you see the analogy with the Goedel code.
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8. I will stop here. The relationships with biology are very worth discussing.
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Before stopping it is worth remarking that the Maturana Uribe Varela autopoeisis is an example of a system arising into a form of self-reference that has a lifetime due to the probabilisitic dynamics of its process.
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Very best,
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Lou Kauffman
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_______________________________________________
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Fis mailing list
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INFORMACIN SOBRE PROTECCIN DE DATOS DE CARCTER PERSONAL
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Ud. recibe este correo por pertenecer a una lista de correo gestionada por la Universidad de Zaragoza.
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Puede encontrar toda la informacin sobre como tratamos sus datos en el siguiente enlace:
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Recuerde que si est suscrito a una lista voluntaria Ud. puede darse de baja desde la propia aplicacin en el momento en que lo desee.
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