<div dir="ltr"><div><br>Dear FIS Fellows,<br><br></div>I was also about writing some concluding remarks, since our time for math in bio is about to end this week, but realized that Lou was fast with an excellent final comment and list of references for postprocessing. I am happy that after some initial hesitation on the forum the key messages came accross and we were able to cover within short time the broad span of views within short time. You are very welcome to continue the discussion also privately and of course, within the scope of the next themes to come: bio/cybersemiotics with Soeren Brier and physics with Alex Hankey, which were nicely introduced by some earlier comments and associations like Bob's triad from his inspiring book "The Third Window" which I see related to C.S. Pierce's initiations in math, philosophy and semiotics. It became clear that such important issues as circularity and recursion/repetition in biology are closely related to distiction, (autocatalytic re)action, memory, (negative) feedback, automation, self-organization, autocells on the one side and (prime) numbers, fractional calculus, triangular/quadrangular/polihedral structures, (Riemann) wave function (analysis), QM and fractal geometry on the other, with opening room for covering even more phenomenology and creating ideas along the multiple lines of causation up to the limits of thought and imagination, nicely reflected by the participants in the discussion. So I have no other chance but to say: that's real life in a nutshell of exchanged messages! The most astonishing characteristic of this communication which comes to end, but just began in my eyes, is that we succeed to build together something that is capabloe to not only link remote and sometimes obscure and absurd ideas and question, but also attribute, enfold and evolve them with what we call a trace of information, an ontology of a creative development process we are participating, as if life becomes that what we really discover, revolve and impress just in time: in Alex's words "a living from that e can interact with, and (which) we are". And this is recursively wraped again within Francesco's phrase: "la conoscenca ha fondamenti biologici ... e viceversa, la biologia ha fondamenti quantistici". How could I say this in Latin? Thank you all for this precious present! And welcome to the next/this discussion topic again.<br><br><div class="gmail_extra"><div><div class="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div><br></div><div>Plamen<br><br></div><div><div>____________________________________________________________</div></div><div><br></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div>
<br><div class="gmail_quote">On Thu, Mar 31, 2016 at 9:49 AM, Louis H Kauffman <span dir="ltr"><<a href="mailto:loukau@gmail.com" target="_blank">loukau@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div style="word-wrap:break-word">Dear Folks,<div>I will close with some comments about the relationship between recursive distinctioning and replication in biology.</div><div>This will be another example of the sort of modeling excursion that one can make by looking at patterns and analogies.</div><div>See</div><div><a href="http://homepages.math.uic.edu/~kauffman/RD.html" target="_blank">homepages.math.uic.edu/~kauffman/RD.html</a></div><div><br></div><div><b style="font-family:Times"><p>RECURSIVE DISTINCTIONING </p><b><p>This folder contains links to papers related to Recursive Distinctioning. Recursive Distinctioning means just what it says. A pattern of distinctions is given in a space based on a graphical structure (such as a line of print or a planar lattice or given graph). Each node of the graph is occupied by a letter from some arbitrary alphabet. A specialized alphabet is given that can indicate distinctions about neighbors of a given node. The neighbors of a node are all nodes that are connected to the given node by edges in the graph. The letters in the specialized alphabet (call it SA) are used to describe the states of the letters in the given graph and at each stage in the recursion, letters in SA are written at all nodes in the graph, describing its previous state. The recursive structure that results from the iteration of descriptions is called Recursive Distinctioning. Here is an example. We use a line graph and represent it just as a finite row of letters. The Special Alphabet is SA = { =, [, ], O} where "=" means that the letters to the left and to the right are equal to the letter in the middle. Thus if we had AAA in the line then the middle A would be replaced by =. The symbol "[" means that the letter to the LEFT is different. Thus in ABB the middle letter would be replaced by [. The symbol "]" means that the letter to the right is different. And finally the symbol "O" means that the letters both to the left and to the right are different. SA is a tiny language of elementary letter-distinctions. Here is an example of this RD in operation where we use the proverbial three dots to indicate a long string of letters in the same pattern. For example,</p><pre>... AAAAAAAAAABAAAAAAAAAA ... is replaced by
... =========]O[========= ... is replaced by
... ========]OOO[======== ... is replaced by 
... =======]O[=]O[======= ... .
</pre>Note that the element ]O[ appears and it has replicated itself in a kind of mitosis. To see this in more detail, here is a link to a page from a mathematica program written by LK that uses a 'blank' or 'unmarked state' instead of the '=" sign. <a href="https://dl.dropbox.com/u/11067256/RDL.pdf" target="_blank">Program and Output</a>. Elementary RD patterns are fundamental and will be found in many structures at all levels. To see an cellular automaton example of this phenomenon, look at the next link. Here we see a replicator in 'HighLife' a modification of John Horton Conway's automaton 'Life'. The Highlife Replicator follows the same pattern as our RD Replicator! We can begin to understand how the RD Replicator works. This gives a foundation for understanding how the more complex HighLife Replicator behaves in its context. <a href="https://en.m.wikipedia.org/wiki/Highlife_(cellular_automaton)" target="_blank">HighLife Replicator.</a> Finally, here is an excerpt from a paper by LK about replication in biology and the role of RD. <a href="https://dl.dropbox.com/u/11067256/KauffmanExcerpt.pdf" target="_blank">Excerpt.</a></b></b></div><div><b style="font-family:Times"><b><p style="display:inline!important">See <a href="http://homepages.math.uic.edu/~kauffman/RDLetter.pdf" target="_blank">RDLetter.</a> This is the Isaacson-Kauffman report on RD, summarized in a letter-to-the-editor of JSP, Vol. 4, No. 1, Spring 2015, directly accessed on this server.</p></b></b><b style="font-family:Times"><b><p style="display:inline!important">See <a href="https://dl.dropbox.com/u/11067256/JoelIsaacsonPatentDocument.pdf" target="_blank">Patent. </a>This is Joel Isaacson's patent document for RD.</p></b></b></div><div><b><b><div style="font-family:Times"><b>See <a href="https://dl.dropbox.com/u/11067256/KauffmanJPBM1033.pdf" target="_blank">Biological Replication.</a> This is a related paper by Kauffman.</b></div><div style="font-family:Times"><b><br></b></div><div><b><font face="Times">You see above a very simple distinction making/using automaton that produces a ‘cell’  ]O[ from an elementary distinction (of B from the background of equal A’s),</font></b></div><div><b><font face="Times">and that this cell then undergoes mitosis. Then as an observer you must look again and note that the nothing that happens in this automaton is local. The cell happens</font></b></div><div><b><font face="Times">because of the global structure of the one-dimensional automata space. The apparent splitting from the inside of the cell is actually a consequence of the global </font></b></div><div><b><font face="Times">condition of the cell in the whole space. The entire evolution of the process is a repeated articulation of the distinctions that are present in the process. This is</font></b></div><div><b><font face="Times">a new holistic modeling paradigm and we are exploring with simple examples the extent to which it will apply to more complex phenomena.</font></b></div><div><b><font face="Times"><br></font></b></div><div><b><font face="Times">A more extended paper by myself and Joel Isaacson will be available soon.</font></b></div><div><b><font face="Times">Best,</font></b></div><div><font face="Times">Lou Kauffman</font></div></b></b></div><div><br><div><blockquote type="cite"><div>On Mar 30, 2016, at 7:18 AM, Pedro C. Marijuan <<a href="mailto:pcmarijuan.iacs@aragon.es" target="_blank">pcmarijuan.iacs@aragon.es</a>> wrote:</div><br><div>
  
    
  
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    <div>Sorry but the dancing time is over...
      maybe tomorrow or on Friday Lou could send some concluding
      comment, and next Monday Soeren would start the new part. The
      present Q. discussion can surface again during the coming
      session...<br>
      best--Pedro<br>
      <br>
      <br>
      El 30/03/2016 a las 1:06, Dr. Plamen L. Simeonov escribió:<br>
    </div>
    <blockquote type="cite">
      
      <div dir="ltr">I think you are right, Lou, with respect to Deutsch
        who actually met Everett III with the multiple universe
        hypothesis. The sole name “constructor theory” invoked
        associations beyond the quantum frame in me, but he did not went
        that far. As for Josephson, I am not quite sure about his
        notion. Brian remains firmly on the quantum level in the papers
        I referred earlier, but he often returns to Ilexa Yarley”s
        “circular theory” which offers a much broader interpretation in
        my opinion. I expected your mentioning of (the vibrations of)
        “thought forms”, which are supposed to invoke the emergence of
        word and action. I welcome your understanding for the necessity
        of a deeper QM to make the links between actuality and the
        bounded potentiality more comprehensive.
        <div><br>
        </div>
        <div>Best,</div>
        <div><br>
        </div>
        <div>Plamen<br>
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            <div class="gmail_quote">On Wed, Mar 30, 2016 at 12:33 AM,
              Louis H Kauffman <span dir="ltr"><<a href="mailto:kauffman@uic.edu" target="_blank"></a><a href="mailto:kauffman@uic.edu" target="_blank">kauffman@uic.edu</a>></span> wrote:<br>
              <blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
                <div style="word-wrap:break-word">Josephson and Deutsh
                  are not ‘deeper than QM’. Deutsch for example is a
                  very literal interpretation of QM that says that all
                  the trajectories in the Feynman path sum are real, and
                  they occur in parallel universes. This is a nice
                  mathematical way to think, but it is not deeper than
                  present QM!
                  <div>Energy is conserved, but ‘particles’ and indeed
                    universes can be created from vacuum. If we want to
                    go to discussion of ‘holy spirit’ then one should
                    look at the structure of thought itself. For it is
                    at the level of thought that every concept has a
                    life behind it. Every idea is real and alive.
                    Platonism asserts this directly in the belief in the
                    existence of form and this form is a living form
                    that we interact with and we are. How these notions
                    are related to QM probably does await the emergence
                    of a deeper QM.</div>
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                      <div><br>
                        <div>
                          <blockquote type="cite">
                            <div>On Mar 29, 2016, at 4:43 PM, Dr. Plamen
                              L. Simeonov <<a href="mailto:plamen.l.simeonov@gmail.com" target="_blank">plamen.l.simeonov@gmail.com</a>>
                              wrote:</div>
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                                                          <div><font face="georgia,
                                                          serif">Thank
                                                          you for your
                                                          responses, Lou
                                                          and Stan. I am
                                                          aware about
                                                          the details of
                                                          the
                                                          autopoietic
                                                          model. What I
                                                          was actually
                                                          addressing by
                                                          the transition
                                                          from abiotic
                                                          to biotic
                                                          structures and
                                                          the later
                                                          emergence of
                                                          RNA and DNA
                                                          was  this
                                                          elusive aspect
                                                          of “mass
                                                          action” which
                                                          Stan
                                                          mentioned,
                                                          that in my
                                                          opinion must
                                                          have emerged
                                                          out of the
                                                          field
                                                          of “triggered
                                                           (by
                                                          resonance)
                                                          potentialities
                                                           which deeper
                                                          theories than
                                                          QM are trying
                                                          to develop
                                                          (cf. 
                                                          Josephson and
                                                          Deutsch
                                                          mentioned
                                                          earlier). This
                                                          enigmatic
                                                          emergence of
                                                          action out of
                                                          nothing
                                                          (vacuum or
                                                          pure
                                                          potentiality)
                                                          naturally
                                                          allows  the
                                                          (co-)existence
                                                          of such
                                                           heretic ideas
                                                          as the
                                                          immaterial
                                                          “Holy Spirit”
                                                          or Hans
                                                          Driesch”s
                                                          vitalism, Jean
                                                          Sharon’s
                                                          eternal
                                                          electron, or
                                                          “The Matrix of
                                                          Matter and
                                                          Life”at the
                                                          sub-Planckian
                                                          scale. How
                                                          about this
                                                          possible link
                                                          to Platonism,
                                                          theology,
                                                          logic and
                                                          algebra? </font></div>
                                                          <div><font face="georgia,
                                                          serif"><br>
                                                          </font></div>
                                                          <div><font face="georgia,
                                                          serif">All the
                                                          best,</font></div>
                                                          <div><font face="georgia,
                                                          serif"><br>
                                                          </font></div>
                                                          <div><font face="georgia,
                                                          serif">Plamen</font></div>
                                                          <div><font face="georgia,
                                                          serif"><br>
                                                          </font></div>
                                                          <div><font face="georgia,
                                                          serif">PS. I
                                                          do not know
                                                          why my notes
                                                          appear twice
                                                          on this list.</font></div>
                                                          <div><font face="georgia,
                                                          serif"><br>
                                                          </font></div>
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                                                          serif"><br>
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                                  <br>
                                  <div class="gmail_quote">On Tue, Mar
                                    29, 2016 at 10:55 PM, Louis H
                                    Kauffman <span dir="ltr"><<a href="mailto:kauffman@uic.edu" target="_blank"></a><a href="mailto:kauffman@uic.edu" target="_blank">kauffman@uic.edu</a>></span>
                                    wrote:<br>
                                    <blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
                                      <div style="word-wrap:break-word">This
                                        is a reply to Plamen’s comment
                                        about autopoeisis. In their
                                        paper Maturana,Uribe and Varela
                                        give a working model (computer
                                        model) for autopoeisis.
                                        <div>It is very simple,
                                          consisting of a subtrate of
                                          nodal elements that tend to
                                          bond when in proximity, and a
                                          collection of catalytic nodal
                                          elements that promote bonding
                                          in their vicinity. The result
                                          of this dynamics is that
                                          carapaces of linked nodal
                                          elements form around the
                                          catalytic elements and these
                                          photo-cells tend to keep
                                          surviving the perturbations
                                          built into the system. This
                                          model shows that cells can
                                          arise from a very simple
                                          dynmamic geometric/topological
                                          substrate long before anything
                                          as sophisticated as DNA has
                                          happened. </div>
                                        <div><br>
                                          <div>
                                            <blockquote type="cite">
                                              <div>On Mar 29, 2016, at
                                                2:54 PM, Stanley N
                                                Salthe <<a href="mailto:ssalthe@binghamton.edu" target="_blank"></a><a href="mailto:ssalthe@binghamton.edu" target="_blank">ssalthe@binghamton.edu</a>>
                                                wrote:</div>
                                              <br>
                                              <div>
                                                <div dir="ltr">Plamen
                                                  wrote:
                                                  <div><br>
                                                  </div>
                                                  <div><p class="MsoNormal" style="font-size:12.8px"><span lang="EN-US"> I
                                                        begin to believe
                                                        that the
                                                        transition from
                                                        abiotic to
                                                        biotic
                                                        structures,
                                                        incl.
                                                        Maturana-Varela.-Uribe’s
                                                        autopoiesis may,
                                                        really have some
                                                        underlying
                                                        matrix/”skeleton”/”programme”
                                                        which has
                                                        nothing in
                                                        common with the
                                                        nature of DNA,
                                                        and that DNA and
                                                        RNA as we know
                                                        them today </span><span>may have emerged as secondary or
                                                        even tertiary
                                                        “memory” of
                                                        something
                                                        underlying
                                                        deeper below the
                                                        microbiological
                                                        surface. It is
                                                        at least worth
                                                        thinking in this
                                                        direction. I do
                                                        not mean
                                                        necessarily the
                                                        role of the
                                                        number concept
                                                        and Platonic
                                                        origin of the
                                                        universe, but
                                                        something
                                                        probably much
                                                        more “physical”</span></p><p class="MsoNormal" style="font-size:12.8px"><span><br>
                                                      </span></p><p class="MsoNormal"><span><br>
                                                      </span></p><p class="MsoNormal"><span>S: An interesting recently published effort along
                                                        these lines is: </span></p><p>Alvaro Moreno and
                                                      Matteo Mossio:
                                                      Biological
                                                      Autonomy: A
                                                      Philosophical and
                                                      Theoretical
                                                      Enquiry (History,
                                                      Philosophy and
                                                      Theory of the Life
                                                      Sciences 12)
                                                      Springer</p><p>They seek a
                                                      materialist
                                                      understanding of
                                                      biology as a
                                                      system, attempting
                                                      to refer to the
                                                      genetic system as
                                                      little as
                                                      possible.</p><p>I have until very
                                                      recently attempted
                                                      to evade/avoid
                                                      mechanistic
                                                      thinking in regard
                                                      to biology, but,
                                                      on considering the
                                                      origin of life
                                                      generally while
                                                      keeping Howard
                                                      Pattee's thinking
                                                      in mind, I have
                                                      been struck by the
                                                      notion that the
                                                      origin of life
                                                      (that is: WITH the
                                                      genetic system)
                                                      was the origin of
                                                      mechanism in the
                                                      universe.  Before
                                                      that coding
                                                      system, everything
                                                      was mass action. 
                                                      I think we still
                                                      do not understand
                                                      how this mechanism
                                                      evolved.</p><p>STAN</p>
                                                  </div>
                                                </div>
                                                <div class="gmail_extra"><br>
                                                  <div class="gmail_quote">On
                                                    Tue, Mar 29, 2016 at
                                                    7:40 AM, Dr. Plamen
                                                    L. Simeonov <span dir="ltr"><<a href="mailto:plamen.l.simeonov@gmail.com" target="_blank"></a><a href="mailto:plamen.l.simeonov@gmail.com" target="_blank">plamen.l.simeonov@gmail.com</a>></span>
                                                    wrote:<br>
                                                    <blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
                                                      <div dir="ltr">
                                                        <div><br>
                                                        </div>
                                                        Dear Lou, Pedro
                                                        and All,<br>
                                                        <br>
                                                        <div><span> </span><br>
                                                        </div><p class="MsoNormal"><span lang="EN-US">I am going to present a few
                                                          opportunistic
                                                          ideas related
                                                          to
                                                          what was said
                                                          before in this
                                                          session.
                                                          Coming back to
                                                          Pivar’s
                                                          speculative
                                                          mechano-topological
                                                          model of life
                                                          excluding
                                                          genetics I
                                                          wish to turn
                                                          your attention
                                                          to another
                                                          author with a
                                                          similar idea
                                                          but on a sound
                                                          mathematical
                                                          base, Davide
                                                          Ambrosi
                                                          with his
                                                          resume at </span><span lang="EN-US"><a href="https://www.uni-muenster.de/imperia/md/content/cim/events/cim-mathmod-workshop-2015_abstracts.pdf" target="_blank">https://www.uni-muenster.de/imperia/md/content/cim/events/cim-mathmod-workshop-2015_abstracts.pdf</a></span><span lang="EN-US">:</span></p><p class="MsoNormal"><span lang="EN-US">“</span><span lang="EN-US">Davide Ambrosi:</span></p><p class="MsoNormal" style="margin-bottom:0.0001pt;line-height:normal"><span lang="EN-US">A role for mechanics in the
                                                          growth,
                                                          remodelling
                                                          and
                                                          morphogenesis
                                                          of living
                                                          systems <span> </span>In
                                                          the XX Century
                                                          the
                                                          interactions
                                                          between
                                                          mechanics in
                                                          biology were
                                                          much <span> </span>biased
                                                          by
                                                          a
                                                          bioengineering
                                                          attitude:
                                                          people were
                                                          mainly
                                                          interested in
                                                          <span> </span>evaluating
                                                          the state of
                                                          stress that
                                                          bones and
                                                          tissues
                                                          undergo in
                                                          order to <span> </span>properly
design
                                                          prosthesis and
                                                          devices.
                                                          However in the
                                                          last decades a
                                                          new vision is
                                                          emerging.
                                                          "Mechano-biology"
                                                          is changing
                                                          the point of
                                                          view, with
                                                          respect
                                                          to
                                                          "Bio-mechanics",
                                                          emphasizing
                                                          the biological
                                                          feedback.
                                                          Cells, tissues
                                                          and organs do
                                                          not only
                                                          deform when
                                                          loaded: they
                                                          reorganize,
                                                          they
                                                          duplicate,
                                                          they actively
                                                          produce
                                                          dynamic
                                                          patterns that
                                                          apparently
                                                          have multiple
                                                          biological
                                                          aims. </span></p><p class="MsoNormal" style="margin-bottom:0.0001pt;line-height:normal"><span lang="EN-US">In this talk I will
                                                          concentrate on
                                                          two
                                                          paradigmatic
                                                          systems where
                                                          the interplay
                                                          between
                                                          mechanics
                                                          and biology
                                                          is, in my
                                                          opinion,
                                                          particularly
                                                          challenging:
                                                          the
                                                          homeostatic
                                                          stress
                                                          as a driver
                                                          for remodeling
                                                          of soft tissue
                                                          and the
                                                          tension as a
                                                          mechanism to
                                                          transmit
                                                          information
                                                          about the size
                                                          of organs
                                                          during
                                                          morphogenesis.
                                                          In both
                                                          cases it seems
                                                          that mechanics
                                                          plays a role
                                                          which at least
                                                          accompanies
                                                          and
                                                          enforces the
                                                          biochemical
                                                          signaling.”</span></p>
                                                        <div style="margin-bottom:0.0001pt;line-height:normal"><span lang="EN-US"> </span><br>
                                                        </div>
                                                        <div style="margin-bottom:0.0001pt;line-height:normal"><span lang="EN-US"> </span><br>
                                                        </div><p class="MsoNormal" style="margin-bottom:0.0001pt;line-height:normal"><span lang="EN-US">Some more details about this
                                                          approach can
                                                          be found here:</span></p><p class="MsoNormal"><span lang="EN-US"><a href="http://rsta.royalsocietypublishing.org/content/367/1902/3335" target="_blank">http://rsta.royalsocietypublishing.org/content/367/1902/3335</a>
                                                          </span></p><p class="MsoNormal"><span lang="EN-US"><a href="http://biomechanics.stanford.edu/paper/MFOreport.pdf" target="_blank">http://biomechanics.stanford.edu/paper/MFOreport.pdf</a></span></p><p class="MsoNormal"><span lang="EN-US">In other words, for the core
                                                          information
                                                          theorists in
                                                          FIS, the
                                                          question is:
                                                          is there
                                                          really only
                                                          (epi)genetic
                                                          evolution
                                                          communication
                                                          in living
                                                          organisms.
                                                          Stan Salthe
                                                          and Lou
                                                          Kauffman
                                                          already
                                                          provided some
                                                          answers.
                                                          I begin to
                                                          believe that
                                                          the transition
                                                          from abiotic
                                                          to biotic
                                                          structures,
                                                          incl.
                                                          Maturana-Varela.-Uribe’s
                                                          autopoiesis
                                                          may, really
                                                          have some
                                                          underlying
                                                          matrix/”skeleton”/”programme”
                                                          which has
                                                          nothing in
                                                          common with
                                                          the nature of
                                                          DNA, and that
                                                          DNA and RNA as
                                                          we
                                                          know them
                                                          today</span></p><p class="MsoNormal"><span lang="EN-US"><a href="http://www.sciencedirect.com/science/article/pii/S0022519314006778" target="_blank"></a><a href="http://www.sciencedirect.com/science/article/pii/S0022519314006778" target="_blank">http://www.sciencedirect.com/science/article/pii/S0022519314006778</a></span></p><p class="MsoNormal"><span lang="EN-US"><a href="http://www.sciencedirect.com/science/article/pii/S0022519316001260" target="_blank"></a><a href="http://www.sciencedirect.com/science/article/pii/S0022519316001260" target="_blank">http://www.sciencedirect.com/science/article/pii/S0022519316001260</a>
                                                          </span></p><p class="MsoNormal"><span lang="EN-US"><a href="https://www.sciencedaily.com/releases/2015/01/150107101405.htm" target="_blank"></a><a href="https://www.sciencedaily.com/releases/2015/01/150107101405.htm" target="_blank">https://www.sciencedaily.com/releases/2015/01/150107101405.htm</a></span></p><p class="MsoNormal"><span lang="EN-US">may have emerged as secondary or
                                                          even tertiary
                                                          “memory”
                                                          of something
                                                          underlying
                                                          deeper below
                                                          the
                                                          microbiological
                                                          surface. It is
                                                          at
                                                          least worth
                                                          thinking in
                                                          this
                                                          direction. I
                                                          do not mean
                                                          necessarily
                                                          the role of
                                                          the number
                                                          concept and
                                                          Platonic
                                                          origin of the
                                                          universe, but
                                                          something
                                                          probably
                                                          much more
                                                          “physical” or
                                                          at least
                                                          staying at the
                                                          edge between
                                                          physical/material
                                                          and immaterial
                                                          such as David
                                                          Deutsch’s
                                                          constructor
                                                          theory (<a href="http://constructortheory.org/" target="_blank"></a><a href="http://constructortheory.org/" target="_blank">http://constructortheory.org/</a>)
                                                          and
                                                          Brian
                                                          Josephson’s
                                                          “structural/circular
                                                          theory” (<a href="http://arxiv.org/ftp/arxiv/papers/1502/1502.02429.pdf" target="_blank"></a><a href="http://arxiv.org/ftp/arxiv/papers/1502/1502.02429.pdf" target="_blank">http://arxiv.org/ftp/arxiv/papers/1502/1502.02429.pdf</a>;
                                                          <a href="http://arxiv.org/ftp/arxiv/papers/1506/1506.06774.pdf" target="_blank"></a><a href="http://arxiv.org/ftp/arxiv/papers/1506/1506.06774.pdf" target="_blank">http://arxiv.org/ftp/arxiv/papers/1506/1506.06774.pdf</a>;
                                                          <a href="http://arxiv.org/pdf/1108.4860.pdf" target="_blank"></a><a href="http://arxiv.org/pdf/1108.4860.pdf" target="_blank">http://arxiv.org/pdf/1108.4860.pdf</a>)
                                                          searching for
                                                          the theories
                                                          underpinning
                                                          the
                                                          foundations of
                                                          the physical
                                                          laws (and
                                                          following
                                                          Wheeler’s
                                                          definition for
                                                          a “Law without
                                                          Law”. <span> </span></span></p><p class="MsoNormal"><span lang="EN-US">Some of you may say that QT and
                                                          Gravitation
                                                          Theory are
                                                          responsible
                                                          for such kind
                                                          of strange
                                                          effects, but I
                                                          would rather
                                                          leave the
                                                          brackets
                                                          open, because
                                                          the recent
                                                          discussion
                                                          about
                                                          potentialities
                                                          and
                                                          actualities in
                                                          QM
                                                          brings up the
                                                          idea that
                                                          there are
                                                          still
                                                          different ways
                                                          of looking at
                                                          those
                                                          concepts
                                                          (although they
                                                          are strictly
                                                          defined in
                                                          their core
                                                          domains). This
                                                          was
                                                          actually also
                                                          the lesson
                                                          from the last
                                                          special issue
                                                          on integral
                                                          biomathics
                                                          (2015)
                                                          dedicated to
                                                          phenomenology,
                                                          with the
                                                          different
                                                          opinions of
                                                          scientists
                                                          and
                                                          philosophers
                                                          on obviously
                                                          clear matters
                                                          in their
                                                          domains. This
                                                          is why also
                                                          the question
                                                          of what we
                                                          define as
                                                          science needs
                                                          to be probably
                                                          revised in
                                                          future to
                                                          include also
                                                          such issues
                                                          that are
                                                          “felt” rather
                                                          than
                                                          “reasoned”,
                                                          even
                                                          if we do not
                                                          have the
                                                          “proofs” yet,
                                                          because the
                                                          proofs also
                                                          emerge as
                                                          subjective
                                                          (or perhaps
                                                          “suggested”! –
                                                          ask the
                                                          psychologists
                                                          for that
                                                          aspect)
                                                          thoughts in
                                                          the minds of
                                                          the
                                                          mathematicians.
                                                          I am really
                                                          glad that we
                                                          began such a
                                                          phenomenological
                                                          discussion on
                                                          this aspect
                                                          such as
                                                          Hipolito’s
                                                          paper (<a href="http://www.sciencedirect.com/science/article/pii/S0079610715000899" target="_blank"></a><a href="http://www.sciencedirect.com/science/article/pii/S0079610715000899" target="_blank">http://www.sciencedirect.com/science/article/pii/S0079610715000899</a>)
                                                          that was
                                                          widely
                                                          commented in
                                                          the reviewer’s
                                                          circle. In
                                                          many cases
                                                          when we have
                                                          a “fuzzy”
                                                          intuition
                                                          about a
                                                          certain
                                                          relationship
                                                          or analogy we
                                                          miss the
                                                          correct
                                                          definitions
                                                          and concepts,
                                                          and so in a
                                                          creative act
                                                          to hold down
                                                          the flying
                                                          thought we
                                                          move to using
                                                          examples,
                                                          metaphors,
                                                          pictures.
                                                          Pedro
                                                          correctly
                                                          addressed the
                                                          explanatory
                                                          problem of
                                                          science which
                                                          presupposes a
                                                          certain
                                                          causative
                                                          and
                                                          predicative
                                                          “workflow” to
                                                          derive a
                                                          conclusion
                                                          from the
                                                          facts, and
                                                          this is
                                                          the way in
                                                          which also
                                                          proofs are
                                                          (selectively)
                                                          made. As a
                                                          young scholar
                                                          I often
                                                          wondered how
                                                          artificially
                                                          people like
                                                          Gauss, Cauchy
                                                          and
                                                          Weierstrass <span> </span>design
                                                          their proofs,
                                                          but then I got
                                                          used to
                                                          that style. I
                                                          am thankful to
                                                          Lou for his
                                                          response on my
                                                          question about
                                                          using
                                                          adequate
                                                          “resonant”
                                                          methods to
                                                          model
                                                          developmental
                                                          biology,
                                                          because this
                                                          is also
                                                          an important
                                                          aspect of the
                                                          biology (and
                                                          physics as
                                                          well)
                                                          including the
                                                          phenomenological/first-person
                                                          view of an
                                                          “observer-participant”
                                                          (to use
                                                          Vrobel’s
                                                          term) which is
                                                          crucial for
                                                          understanding
                                                          the process of
                                                          self-reflection/recursion/cycle
in
                                                          science, which
                                                          is usually led
                                                          by what?: the
                                                          intuition,
                                                          also well
                                                          recognized by
                                                          such giants
                                                          like Poincare
                                                          and Einstein.
                                                          Isn’t not
                                                          “resonance” in
                                                          the core of
                                                          detecting
                                                          such vibration
                                                          between the
                                                          observer and
                                                          the observed?
                                                          Because logic,
                                                          back
                                                          trace, prove
                                                          come later. <span> </span><span> </span></span></p><p class="MsoNormal"><span lang="EN-US">And finally, when looking at the
                                                          clear simple
                                                          mathematical
                                                          abstractions
                                                          of numbers,
                                                          vectors,
                                                          directions,
                                                          sets,
                                                          algebras,
                                                          geometries,
                                                          etc. used
                                                          by many
                                                          without
                                                          scrutinizing
                                                          when
                                                          developing
                                                          system
                                                          (biological)
                                                          models of yet
                                                          another kind
                                                          of
                                                          mechanics/automation/machinery
                                                          of the
                                                          physical
                                                          reality, I am
                                                          asking myself
                                                          which are the
                                                          premises for
                                                          using such
                                                          tools to
                                                          describe a
                                                          model:
                                                          the
                                                          parameters, or
                                                          the idea
                                                          behind? It is
                                                          probably not a
                                                          commonly known
                                                          fact (even
                                                          for those who
                                                          are engaged
                                                          with such
                                                          exciting
                                                          disciplines as
                                                          algebraic
                                                          geometry
                                                          and
                                                          geometrical
                                                          algebra, now
                                                          considered to
                                                          be very close
                                                          to what we
                                                          wish to
                                                          express in
                                                          biology) that
                                                          William
                                                          Hamilton, the
                                                          inventor of
                                                          the
                                                          quaternions
                                                          did
                                                          not simply use
                                                          the already
                                                          known concept
                                                          of “vector” in
                                                          his method.
                                                          Instead he
                                                          used “step”
                                                          with
                                                          “direction” to
                                                          express a
                                                          duration of
                                                          time (or
                                                          “duree” as
                                                          Husserl
                                                          called it from
                                                          the other side
                                                          of the
                                                          phenomenological
                                                          divide) and
                                                          action (to
                                                          move from A to
                                                          B): two very
                                                          biology-related
                                                          concepts at
                                                          that time
                                                          (although
                                                          they may be
                                                          considered as
                                                          physical or
                                                          computational
                                                          today). He
                                                          actually
                                                          stated
                                                          that if there
                                                          is geometry as
                                                          a pure science
                                                          of space, then
                                                          algebra must
                                                          be the
                                                          pure science
                                                          of time [1].
                                                          What did we
                                                          actually gain
                                                          for biology
                                                          from merging
                                                          space and time
                                                          in physics?</span></p><p class="MsoNormal"><span lang="EN-US">Reference:</span></p><p class="MsoNormal"><span lang="EN-US">[1]
                                                          W. R.
                                                          Hamilton,
                                                          1835. Theory
                                                          of Conjugate
                                                          Functions, or
                                                          Algebraic
                                                          Couples; with
                                                          a Preliminary
                                                          or Elementary
                                                          Essay on
                                                          Algebra as the
                                                          Science of
                                                          Pure Time. </span><i>Trans.
                                                          Royal Irish
                                                          Acad</i>.,
                                                          Vol. XVII,
                                                          Part II.
                                                          292-422.</p>
                                                        <div><span><span> </span><span> </span><span lang="EN-US"></span></span><br>
                                                        </div><p class="MsoNormal"><span lang="EN-US">Best,</span></p>
                                                        <div><span lang="EN-US"> </span><br>
                                                        </div><p class="MsoNormal"><span lang="EN-US">Plamen</span></p>
                                                        <div><span> </span><br>
                                                        </div><p class="MsoNormal"><span lang="EN-US">I have a few provoking notes
                                                          related to
                                                          what was said
                                                          before in this
                                                          session.
                                                          Coming back to
                                                          Pivar’s
                                                          speculative
                                                          mechano-topological
                                                          model of life
                                                          excluding
                                                          genetics I
                                                          wish to turn
                                                          your attention
                                                          to another
                                                          author with a
                                                          similar idea
                                                          but on a sound
                                                          mathematical
                                                          base, Davide
                                                          Ambrosi
                                                          with his
                                                          resume at </span><span lang="EN-US"><a href="https://www.uni-muenster.de/imperia/md/content/cim/events/cim-mathmod-workshop-2015_abstracts.pdf" target="_blank">https://www.uni-muenster.de/imperia/md/content/cim/events/cim-mathmod-workshop-2015_abstracts.pdf</a></span><span lang="EN-US">:</span></p><p class="MsoNormal"><span lang="EN-US">“</span><span lang="EN-US">Davide Ambrosi:</span></p><p class="MsoNormal" style="margin-bottom:0.0001pt;line-height:normal"><span lang="EN-US">A role for mechanics in the
                                                          growth,
                                                          remodelling
                                                          and
                                                          morphogenesis
                                                          of living
                                                          systems <span> </span>In
                                                          the XX Century
                                                          the
                                                          interactions
                                                          between
                                                          mechanics in
                                                          biology were
                                                          much <span> </span>biased
                                                          by
                                                          a
                                                          bioengineering
                                                          attitude:
                                                          people were
                                                          mainly
                                                          interested in
                                                          <span> </span>evaluating
                                                          the state of
                                                          stress that
                                                          bones and
                                                          tissues
                                                          undergo in
                                                          order to <span> </span>properly
design
                                                          prosthesis and
                                                          devices.
                                                          However in the
                                                          last decades a
                                                          new vision is
                                                          emerging.
                                                          "Mechano-biology"
                                                          is changing
                                                          the point of
                                                          view, with
                                                          respect
                                                          to
                                                          "Bio-mechanics",
                                                          emphasizing
                                                          the biological
                                                          feedback.
                                                          Cells, tissues
                                                          and organs do
                                                          not only
                                                          deform when
                                                          loaded: they
                                                          reorganize,
                                                          they
                                                          duplicate,
                                                          they actively
                                                          produce
                                                          dynamic
                                                          patterns that
                                                          apparently
                                                          have multiple
                                                          biological
                                                          aims. </span></p><p class="MsoNormal" style="margin-bottom:0.0001pt;line-height:normal"><span lang="EN-US">In this talk I will
                                                          concentrate on
                                                          two
                                                          paradigmatic
                                                          systems where
                                                          the interplay
                                                          between
                                                          mechanics
                                                          and biology
                                                          is, in my
                                                          opinion,
                                                          particularly
                                                          challenging:
                                                          the
                                                          homeostatic
                                                          stress
                                                          as a driver
                                                          for remodeling
                                                          of soft tissue
                                                          and the
                                                          tension as a
                                                          mechanism to
                                                          transmit
                                                          information
                                                          about the size
                                                          of organs
                                                          during
                                                          morphogenesis.
                                                          In both
                                                          cases it seems
                                                          that mechanics
                                                          plays a role
                                                          which at least
                                                          accompanies
                                                          and
                                                          enforces the
                                                          biochemical
                                                          signaling.”</span></p>
                                                        <div style="margin-bottom:0.0001pt;line-height:normal"><span lang="EN-US"> </span><br>
                                                        </div>
                                                        <div style="margin-bottom:0.0001pt;line-height:normal"><span lang="EN-US"> </span><br>
                                                        </div><p class="MsoNormal" style="margin-bottom:0.0001pt;line-height:normal"><span lang="EN-US">Some more details about this
                                                          approach can
                                                          be found here:</span></p><p class="MsoNormal"><span lang="EN-US"><a href="http://rsta.royalsocietypublishing.org/content/367/1902/3335" target="_blank">http://rsta.royalsocietypublishing.org/content/367/1902/3335</a>
                                                          </span></p><p class="MsoNormal"><span lang="EN-US"><a href="http://biomechanics.stanford.edu/paper/MFOreport.pdf" target="_blank">http://biomechanics.stanford.edu/paper/MFOreport.pdf</a></span></p><p class="MsoNormal"><span lang="EN-US">In other words, for the core
                                                          information
                                                          theorists in
                                                          FIS, the
                                                          question is:
                                                          is there
                                                          really only
                                                          (epi)genetic
                                                          evolution
                                                          communication
                                                          in living
                                                          organisms.
                                                          Stan Salthe
                                                          and Lou
                                                          Kauffman
                                                          already
                                                          provided some
                                                          answers.
                                                          I begin to
                                                          believe that
                                                          the transition
                                                          from abiotic
                                                          to biotic
                                                          structures,
                                                          incl.
                                                          Maturana-Varela.-Uribe’s
                                                          autopoiesis
                                                          may, really
                                                          have some
                                                          underlying
                                                          matrix/”skeleton”/”programme”
                                                          which has
                                                          nothing in
                                                          common with
                                                          the nature of
                                                          DNA, and that
                                                          DNA and RNA as
                                                          we
                                                          know them
                                                          today</span></p><p class="MsoNormal"><span lang="EN-US"><a href="http://www.sciencedirect.com/science/article/pii/S0022519314006778" target="_blank"></a><a href="http://www.sciencedirect.com/science/article/pii/S0022519314006778" target="_blank">http://www.sciencedirect.com/science/article/pii/S0022519314006778</a></span></p><p class="MsoNormal"><span lang="EN-US"><a href="http://www.sciencedirect.com/science/article/pii/S0022519316001260" target="_blank"></a><a href="http://www.sciencedirect.com/science/article/pii/S0022519316001260" target="_blank">http://www.sciencedirect.com/science/article/pii/S0022519316001260</a>
                                                          </span></p><p class="MsoNormal"><span lang="EN-US"><a href="https://www.sciencedaily.com/releases/2015/01/150107101405.htm" target="_blank"></a><a href="https://www.sciencedaily.com/releases/2015/01/150107101405.htm" target="_blank">https://www.sciencedaily.com/releases/2015/01/150107101405.htm</a></span></p><p class="MsoNormal"><span lang="EN-US">may have emerged as secondary or
                                                          even tertiary
                                                          “memory”
                                                          of something
                                                          underlying
                                                          deeper below
                                                          the
                                                          microbiological
                                                          surface. It is
                                                          at
                                                          least worth
                                                          thinking in
                                                          this
                                                          direction. I
                                                          do not mean
                                                          necessarily
                                                          the role of
                                                          the number
                                                          concept and
                                                          Platonic
                                                          origin of the
                                                          universe, but
                                                          something
                                                          probably
                                                          much more
                                                          “physical” or
                                                          at least
                                                          staying at the
                                                          edge between
                                                          physical/material
                                                          and immaterial
                                                          such as David
                                                          Deutsch’s
                                                          constructor
                                                          theory (<a href="http://constructortheory.org/" target="_blank"></a><a href="http://constructortheory.org/" target="_blank">http://constructortheory.org/</a>)
                                                          and
                                                          Brian
                                                          Josephson’s
                                                          “structural/circular
                                                          theory” (<a href="http://arxiv.org/ftp/arxiv/papers/1502/1502.02429.pdf" target="_blank"></a><a href="http://arxiv.org/ftp/arxiv/papers/1502/1502.02429.pdf" target="_blank">http://arxiv.org/ftp/arxiv/papers/1502/1502.02429.pdf</a>;
                                                          <a href="http://arxiv.org/ftp/arxiv/papers/1506/1506.06774.pdf" target="_blank"></a><a href="http://arxiv.org/ftp/arxiv/papers/1506/1506.06774.pdf" target="_blank">http://arxiv.org/ftp/arxiv/papers/1506/1506.06774.pdf</a>;
                                                          <a href="http://arxiv.org/pdf/1108.4860.pdf" target="_blank"></a><a href="http://arxiv.org/pdf/1108.4860.pdf" target="_blank">http://arxiv.org/pdf/1108.4860.pdf</a>)
                                                          searching for
                                                          the theories
                                                          underpinning
                                                          the
                                                          foundations of
                                                          the physical
                                                          laws (and
                                                          following
                                                          Wheeler’s
                                                          definition for
                                                          a “Law without
                                                          Law”. <span> </span></span></p><p class="MsoNormal"><span lang="EN-US">Some of you may say that QT and
                                                          Gravitation
                                                          Theory are
                                                          responsible
                                                          for such kind
                                                          of strange
                                                          effects, but I
                                                          would rather
                                                          leave the
                                                          brackets
                                                          open, because
                                                          the recent
                                                          discussion
                                                          about
                                                          potentialities
                                                          and
                                                          actualities in
                                                          QM
                                                          brings up the
                                                          idea that
                                                          there are
                                                          still
                                                          different ways
                                                          of looking at
                                                          those
                                                          concepts
                                                          (although they
                                                          are strictly
                                                          defined in
                                                          their core
                                                          domains). This
                                                          was
                                                          actually also
                                                          the lesson
                                                          from the last
                                                          special issue
                                                          on integral
                                                          biomathics
                                                          (2015)
                                                          dedicated to
                                                          phenomenology,
                                               </span></p></div></blockquote></div></div></div></blockquote></div></div></div></blockquote></div></div></div></div></blockquote></div></div></div></div></div></blockquote></div></div></div></div></blockquote></div></div></blockquote></div></div></div>...<br><br>[Message clipped]  </blockquote></div><br></div></div>