<html><head></head><body><div class="ydp59a3b195yahoo-style-wrap" style="font-size: 24px; font-family: Verdana, Arial, Helvetica, sans-serif;"><div style="font-family: Verdana, Arial, Helvetica, sans-serif;"></div>
<div dir="ltr" data-setdir="false" style="font-family: Verdana, Arial, Helvetica, sans-serif;">pedro--</div><div dir="ltr" data-setdir="false" style="font-family: Verdana, Arial, Helvetica, sans-serif;"><br></div><div dir="ltr" data-setdir="false" style="font-family: Verdana, Arial, Helvetica, sans-serif;">wonderful quote<span><span style="font-family: Helvetica Neue, Helvetica, Arial, sans-serif; letter-spacing: -0.32px;"> from AN Whitehead: "Civilization advances by extending the number of important operations which we can perform without thinking of them." </span></span></div><div dir="ltr" data-setdir="false" style="font-family: Verdana, Arial, Helvetica, sans-serif;"><span><span style="font-family: Helvetica Neue, Helvetica, Arial, sans-serif; letter-spacing: -0.32px;"><br></span></span></div><div dir="ltr" data-setdir="false" style=""><font face="Helvetica Neue, Helvetica, Arial, sans-serif">in my work "the <span><span style="color: rgb(0, 0, 0); font-family: Helvetica Neue, Helvetica, Arial, sans-serif; font-size: 24px; letter-spacing: -0.32px;">operations which we can perform without thinking of them" are called "the infrastructure of habit."</span></span></font></div><div dir="ltr" data-setdir="false" style=""><font face="Helvetica Neue, Helvetica, Arial, sans-serif"><span><span style="color: rgb(0, 0, 0); font-family: Helvetica Neue, Helvetica, Arial, sans-serif; font-size: 24px; letter-spacing: -0.32px;"><br></span></span></font></div><div dir="ltr" data-setdir="false" style=""><font face="Helvetica Neue, Helvetica, Arial, sans-serif"><span><span style="color: rgb(0, 0, 0); font-family: Helvetica Neue, Helvetica, Arial, sans-serif; font-size: 24px; letter-spacing: -0.32px;">habit works hand in hand with "the infrastructure of fantasy". </span></span></font></div><div dir="ltr" data-setdir="false" style=""><font face="Helvetica Neue, Helvetica, Arial, sans-serif"><span><span style="color: rgb(0, 0, 0); font-family: Helvetica Neue, Helvetica, Arial, sans-serif; font-size: 24px; letter-spacing: -0.32px;"><br></span></span></font></div><div dir="ltr" data-setdir="false" style=""><font face="Helvetica Neue, Helvetica, Arial, sans-serif"><span><span style="color: rgb(0, 0, 0); font-family: Helvetica Neue, Helvetica, Arial, sans-serif; font-size: 24px; letter-spacing: -0.32px;">which in turn works with something i haven't been able to squeeze into my published work yet, "expectancy theory." your expectations rule your life.</span></span></font></div><div style="font-family: Verdana, Arial, Helvetica, sans-serif;"><br></div><div style="font-family: Verdana, Arial, Helvetica, sans-serif;" dir="ltr" data-setdir="false">may your 2025 be wonderful. and may your highest expectations be fulfilled.</div><div style="font-family: Verdana, Arial, Helvetica, sans-serif;" dir="ltr" data-setdir="false"><br></div><div style="font-family: Verdana, Arial, Helvetica, sans-serif;" dir="ltr" data-setdir="false"><span>with warmth and oomph--howard</span><br></div><div style="font-family: Verdana, Arial, Helvetica, sans-serif;"><br></div>
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On Sunday, January 5, 2025 at 03:40:20 PM EST, Pedro C. Marijuán <pedroc.marijuan@gmail.com> wrote:
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<p>Dear Lou,</p>
<p>Thanks a lot for the work done in this New Year Lecture! <br clear="none">
</p>
<p>You have made an interesting mixing of ideas, as the title was
offering. Let me make a few critical comments, just to stimulate
discussion:</p>
-- Do you think the phenomenological stance provides a useful
thinking basis in biology (in most fields of)?<br clear="none">
I remember a quotation from AN Whitehead: "Civilization advances by
extending the number of important operations which we can perform
without thinking of them." Thus, well crafted 'indirect perception'
becomes a must in most bio fields. And the discussion on the
observed/observed interrelationship has so rarely provided any
interesting outcome. It directly goes against the principle of
"economy of thought" inherent in ANW, or in Occam's. In my opinion,
putting it together with Autopoiesis, it is quite dubious they have
contributed to fundamental matters in the biosciences and
neurosciences. That they militate against reductionism may be a good
point, but quite insufficient.<br clear="none">
<p>-- Regarding DNA, it is subject to so many happenstances along
the life course of the living. Natural "biotechnology" looks
endless. Some of these operations may be enticing for
mathematicians, while the biggest conundrums appear, say, on the
enzymatic side. Another quotation, from Kornberg: " DNA and genes
captured the spotligt from enzymes; but in my theater enzymes kept
the leading role... they do the acting." I say this because the
intense focus on DNA has created an unproductive avenue for
biological information (& biosemiotics). Simplest cells
(bacteria and archea) do manage environmental information flows by
means of their signaling systems, channels, transporters, etc. But
this is rudimentarily conceptualized yet. I think this is a
serious challenge to mathematicians too, as almost everything of
physiological/developmental relevance passes through the "hands"
of a prokaryotic or eukaryotic signaling systems.</p>
<p>-- And finally, I find your final paragraph on the limits of
logic of high interest and fertility. And will look for it in your
other publications. Almost by definition I would put that "reality
--and life-- are always larger than our formal approaches".<br clear="none">
</p>
<p>Don't take me too seriously... and let me wish a Happy New Year
to you and all FISers.</p>
<p>Best--Pedro</p><div id="ydpc955e2c1yiv4163135744yqtfd27347" class="ydpc955e2c1yiv4163135744yqt6136348163"><br clear="none">
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<table cellpadding="0" cellspacing="0" border="0" class="ydpc955e2c1yiv4163135744moz-email-headers-table"><tbody><tr><th align="RIGHT" colspan="1" nowrap="" rowspan="1" valign="BASELINE">Asunto:
</th><td colspan="1" rowspan="1">Re: Biologic - at the interface between biology,
topology, logic and cybernetics.</td></tr><tr><th align="RIGHT" colspan="1" nowrap="" rowspan="1" valign="BASELINE">Fecha:
</th><td colspan="1" rowspan="1">Fri, 3 Jan 2025 12:38:13 -0600</td></tr><tr><th align="RIGHT" colspan="1" nowrap="" rowspan="1" valign="BASELINE">De:
</th><td colspan="1" rowspan="1">Louis Kauffman <a shape="rect" href="mailto:loukau@gmail.com" class="ydpc955e2c1yiv4163135744moz-txt-link-rfc2396E" rel="nofollow" target="_blank"><loukau@gmail.com></a></td></tr><tr><th align="RIGHT" colspan="1" nowrap="" rowspan="1" valign="BASELINE">Para:
</th><td colspan="1" rowspan="1">"Pedro C. Marijuán" <a shape="rect" href="mailto:pedroc.marijuan@gmail.com" class="ydpc955e2c1yiv4163135744moz-txt-link-rfc2396E" rel="nofollow" target="_blank"><pedroc.marijuan@gmail.com></a></td></tr></tbody></table>
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of below articles available until Feb 2, 2025</div>
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</div></div><div><div class="ydpc955e2c1yiv4163135744">'Slides Festival' available at: <a shape="rect" href="https://urldefense.com/v3/__https://fis.sciforum.net/resources/__;!!D9dNQwwGXtA!Xuz20L8dnuTZYF9WFBHOLyZrvHTyVKqbCy4P55woe-bSQswWK6oGtDnIfdh8ErbhHvbI71N24gtkTUTyEMIjVuWJIXes$" class="ydpc955e2c1yiv4163135744moz-txt-link-freetext" rel="nofollow" target="_blank">https://fis.sciforum.net/resources/</a><br clear="none">
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<div align="center" class="ydpc955e2c1yiv4163135744"><font size="4"><b>Biologic
- at the interface between biology, topology,
logic and cybernetics.</b></font></div>
<div align="center" class="ydpc955e2c1yiv4163135744"><font size="4"><b><br clear="none">
</b></font></div>
<div align="center" class="ydpc955e2c1yiv4163135744"><b>Louis H Kauffman, UIC</b></div>
<div class="ydpc955e2c1yiv4163135744"><br clear="none" class="ydpc955e2c1yiv4163135744">
</div>
<div align="center" class="ydpc955e2c1yiv4163135744">“What can be shown,
cannot be said.”</div>
<div align="center" class="ydpc955e2c1yiv4163135744">“Was gezeigt werden kann,
kann nicht gesagt werden.”</div>
<div align="center" class="ydpc955e2c1yiv4163135744">(Wittgenstein, Tractatus,
4.1212)</div>
<div align="center" class="ydpc955e2c1yiv4163135744"><br clear="none" class="ydpc955e2c1yiv4163135744">
</div>
<div align="center" class="ydpc955e2c1yiv4163135744">“We take the form of
distinction for the form.”</div>
<div align="center" class="ydpc955e2c1yiv4163135744">(Spencer-Brown, Laws of
Form, Chapter 1)</div>
<div class="ydpc955e2c1yiv4163135744"><br clear="none" class="ydpc955e2c1yiv4163135744">
</div>
<div class="ydpc955e2c1yiv4163135744">What is the form of biology?</div>
<div class="ydpc955e2c1yiv4163135744">Is there a biology of form?</div>
<div class="ydpc955e2c1yiv4163135744"><br clear="none">
</div>
<div class="ydpc955e2c1yiv4163135744">In particular, this is a study of
different forms and formalisms for replication. We
concentrate on diagrammatic formal systems not only
for the sake of showing how there may be fundamental
mathematical structure in biology, but also to
consider philosophical and phenomenological points
of view in relation to natural science and
mathematics. The relationship with phenomenology
comes about in the questions that arise about the
nature of the observer in relation to the observed
that arise in philosophy, but also in science in the
very act of determining the context and models upon
which it shall be based. Our original point of
departure was the idea of distinction and cybernetic
epistemology. Cybernetic epistemology has much to
say about the relation of the self to structures
that may harbor a self. What is the interlacement of
selves and organisms?</div>
<div class="ydpc955e2c1yiv4163135744"> </div>
<div class="ydpc955e2c1yiv4163135744">Our point of view is structural. There
is a distinct difference between building up
structures in terms of principles and imagining that
models of the world are constructed from some sort
of building-bricks. I want to make this point as
early as possible because in mathematics one
naturally generates hierarchies, but that does not
make the mathematician a reductionist. We think of
geometry as the consequences of certain axioms for
the purpose of organizing our knowledge, not to
insist that these axioms are in any way other than
logically prior to the theorems of the system. Just
so, we look for fundamental patterns from which
certain complexes of phenomena and ideas can be
organized. This does not entail any assumption about
``the world'' or how the world may be built from
parts. What is a part that a world might be built
from it?</div>
<div class="ydpc955e2c1yiv4163135744"><br clear="none" class="ydpc955e2c1yiv4163135744">
</div>
<div class="ydpc955e2c1yiv4163135744">We examine the schema behind the
reproduction of DNA. The pattern of the DNA
reproduction is very simple. The DNA molecule
consists of two interwound strands, the Watson
Strand (W) and the Crick Strand (C). The two
strands are bonded to each other via a backbone of
base-pairings and these bonds can be broken by
certain enzymes present in the cell. In reproduction
of DNA the bonds between the two strands are broken
and the two strands then acquire the needed
complementary base molecules from the cellular
environment to reconstitute each a separate copy of
the DNA. At this level the situation can be
described by a symbolism like this.</div>
<div class="ydpc955e2c1yiv4163135744">DNA = <W|C> -----> <W| E
|C> -----> <W|C> <W|C> = DNA DNA.</div>
<div class="ydpc955e2c1yiv4163135744">Here E stands for the environment of the
cell. The first arrow denotes the separation of the
DNA into the two strands. The second arrow denotes
the action between the bare strands and the
environment (the creation of new base-pairings) that
leads to the production of the two DNA molecules.</div>
<div class="ydpc955e2c1yiv4163135744"><br clear="none" class="ydpc955e2c1yiv4163135744">
</div>
<div class="ydpc955e2c1yiv4163135744">Much is left out of this schema. Indeed
the DNA molecule is a tight spiral winding of its
two interlocked strands and so the new DNA's would
be linked around one another if it were not for the
work of toposomerase enzymes that manage to unlink
the new DNA's in time for cell division to occur.
Nevertheless, this is the large scale description of
the replication of DNA that is fundamental to the
division of cells and to the continuance of living
organisms.</div>
<div class="ydpc955e2c1yiv4163135744"><br clear="none" class="ydpc955e2c1yiv4163135744">
</div>
<div class="ydpc955e2c1yiv4163135744">This form of replication can be compared
with other forms. For example, John von Neumann
suggested a “building machine” B such that when B is
supplied with a “blueprint” x then </div>
<div class="ydpc955e2c1yiv4163135744">B, x —> B,x , X,x</div>
<div class="ydpc955e2c1yiv4163135744">This means that B and the blueprint x
will produce X the entity whose plan is x along with
a copy of the blueprint x. The first B,x is the
persistence of the original machine B.</div>
<div class="ydpc955e2c1yiv4163135744">Let b be the blueprint for B itself.
Then</div>
<div class="ydpc955e2c1yiv4163135744">B,b —> B,b , B,b.</div>
<div class="ydpc955e2c1yiv4163135744">The Von Neumann Machine replicates
itself. </div>
<div class="ydpc955e2c1yiv4163135744">In the comparison, we see that The DNA
contains (in its strands) the blueprint for its own
replication.</div>
<div class="ydpc955e2c1yiv4163135744"><br clear="none" class="ydpc955e2c1yiv4163135744">
</div>
<div class="ydpc955e2c1yiv4163135744">The comparison made, what questions do
you ask? The mathematical roots of von Neumann’s
construction are very deep. What are the
physical/biological roots of the DNA replication?</div>
<div class="ydpc955e2c1yiv4163135744"><br clear="none" class="ydpc955e2c1yiv4163135744">
</div>
<div class="ydpc955e2c1yiv4163135744">We invite the reader to examine the form
of the science involved in this well-known
description. We speak of the DNA molecules as though
we could see them directly in the phenomenology of
our ordinary sight. Science does involve the direct
extension of sight as the experience of looking
through a telescope or a light microscope. But in
the case of the DNA one proceeds by logical
consistency and the indirect but vivid images via
the electron microscope and the patterns of gel
electrophoresis. In the case of electron microscope
images there is every reason to assume (it appears
consistent to assume) that the objects shown can be
taken to be analogous to the macroscopic objects of
our perception. This means that one has the
possibility of observing ``directly" that DNA
molecules can be knotted. I do not say that one can
observe directly the coiling of the Watson and the
Crick strands, but the DNA can be observed as though
it were a long rope. This rope can be seen to be
coiled and knotted in electron micrographs. Even
this ``showing'' requires a difficult technique
beyond the usual techniques of the electron
microscope. The DNA was coated with protein by the
experimenters so that it became a chain of larger
and more robust diameter. Then the electron
microscope revealed the patterns of knotting in an
apparent projection of the coated DNA from three
dimensional space to the two dimensional space of
the image.</div>
<div class="ydpc955e2c1yiv4163135744"><img id="ydpc955e2c1yiv4163135744093308C2-C64C-41FE-8115-2651F174960D" class="ydpc955e2c1yiv4163135744" data-inlineimagemanipulating="true" data-id="1736121443381" style="width: 50%; max-width: 0px;"></div>
<div class="ydpc955e2c1yiv4163135744"><br clear="none" class="ydpc955e2c1yiv4163135744">
</div>
<div class="ydpc955e2c1yiv4163135744">It is remarkable how consistent is the
hypothesis of indirect perception on which the work
is based. Most working biologists would not question
the basis of their biological perceptions direct or
indirect. For those who are philosophically inclined
there is a lesson to be learned about experimental
phenomenology. </div>
<div class="ydpc955e2c1yiv4163135744">One wants to know how far a world-view
can be extended before it disintegrates.</div>
<div class="ydpc955e2c1yiv4163135744">What we see in the electron micrograph
is deeply shaped by the complex story of biological
experiment that surrounds it.</div>
<div class="ydpc955e2c1yiv4163135744"> </div>
<div class="ydpc955e2c1yiv4163135744">Along with these forays into
experimentation, there are analogous forays into the
limits of logic. Here we meet the replication schema
again. Replication in logic is intimately related to
self-reference and to formalisms that can lead to
paradox. The reasons for this are, by now, apparent.
The usual mathematical formalisms for set theory
assume that there is no temporal evolution in the
structures. </div>
<div class="ydpc955e2c1yiv4163135744">Temporality may look like a tragedy for
the classical mathematics, but it is exactly what
interests us when studying biology. </div>
<div class="ydpc955e2c1yiv4163135744">Mathematical biology is concerned with
those structures leading to recursive generation of
structures from themselves and from their
environments. </div>
<div class="ydpc955e2c1yiv4163135744"> </div>
<div class="ydpc955e2c1yiv4163135744">#############################</div>
<div class="ydpc955e2c1yiv4163135744"><br clear="none" class="ydpc955e2c1yiv4163135744">
</div>
</div>
<div class="ydpc955e2c1yiv4163135744">Here is a related paper:</div>
<div class="ydpc955e2c1yiv4163135744"><a shape="rect" href="https://urldefense.com/v3/__https://arxiv.org/abs/1512.04325__;!!D9dNQwwGXtA!Xuz20L8dnuTZYF9WFBHOLyZrvHTyVKqbCy4P55woe-bSQswWK6oGtDnIfdh8ErbhHvbI71N24gtkTUTyEMIjViUloF5d$" class="ydpc955e2c1yiv4163135744moz-txt-link-freetext" rel="nofollow" target="_blank">https://arxiv.org/abs/1512.04325</a></div>
<div class="ydpc955e2c1yiv4163135744">Here are other papers included in this
email:</div>
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</div>
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<div class="ydpc955e2c1yiv4163135744">Very best,</div>
<div class="ydpc955e2c1yiv4163135744">Louis H Kauffman</div>
<div class="ydpc955e2c1yiv4163135744">Dept Mathematics</div>
<div class="ydpc955e2c1yiv4163135744">University of Illinois at Chicago</div>
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<div class="ydpc955e2c1yiv4163135744"><span>_______________________________</span></div>
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