<html><head><meta http-equiv="Content-Type" content="text/html charset=windows-1252"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Dear Folks,<div class="">I will close with some comments about the relationship between recursive distinctioning and replication in biology.</div><div class="">This will be another example of the sort of modeling excursion that one can make by looking at patterns and analogies.</div><div class="">See</div><div class=""><a href="http://homepages.math.uic.edu/~kauffman/RD.html" class="">homepages.math.uic.edu/~kauffman/RD.html</a></div><div class=""><br class=""></div><div class=""><b style="font-family: Times;" class=""><p class="">RECURSIVE DISTINCTIONING </p><b class=""><p class="">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 class="">... 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" class="">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)" class="">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" class="">Excerpt.</a></b></b></div><div class=""><b style="font-family: Times;" class=""><b class=""><p style="display: inline !important;" class="">See <a href="http://homepages.math.uic.edu/~kauffman/RDLetter.pdf" class="">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;" class=""><b class=""><p style="display: inline !important;" class="">See <a href="https://dl.dropbox.com/u/11067256/JoelIsaacsonPatentDocument.pdf" class="">Patent. </a>This is Joel Isaacson's patent document for RD.</p></b></b></div><div class=""><b class=""><b class=""><div style="font-family: Times;" class=""><b class="">See <a href="https://dl.dropbox.com/u/11067256/KauffmanJPBM1033.pdf" class="">Biological Replication.</a> This is a related paper by Kauffman.</b></div><div style="font-family: Times;" class=""><b class=""><br class=""></b></div><div class=""><b class=""><font face="Times" class="">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 class=""><b class=""><font face="Times" class="">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 class=""><b class=""><font face="Times" class="">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 class=""><b class=""><font face="Times" class="">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 class=""><b class=""><font face="Times" class="">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 class=""><b class=""><font face="Times" class=""><br class=""></font></b></div><div class=""><b class=""><font face="Times" class="">A more extended paper by myself and Joel Isaacson will be available soon.</font></b></div><div class=""><b class=""><font face="Times" class="">Best,</font></b></div><div class=""><font face="Times" class="">Lou Kauffman</font></div></b></b></div><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On Mar 30, 2016, at 7:18 AM, Pedro C. Marijuan <<a href="mailto:pcmarijuan.iacs@aragon.es" class="">pcmarijuan.iacs@aragon.es</a>> wrote:</div><br class="Apple-interchange-newline"><div class="">
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<div class="moz-cite-prefix">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 class="">
best--Pedro<br class="">
<br class="">
<br class="">
El 30/03/2016 a las 1:06, Dr. Plamen L. Simeonov escribió:<br class="">
</div>
<blockquote cite="mid:CAMBikj4SJLgD6HEpMZFkoDZejOCRWBu5L2Jrb=-NDuvcsh1K9A@mail.gmail.com" type="cite" class="">
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<div dir="ltr" class="">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 class=""><br class="">
</div>
<div class="">Best,</div>
<div class=""><br class="">
</div>
<div class="">Plamen<br class="">
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<br class="">
<div class="gmail_quote">On Wed, Mar 30, 2016 at 12:33 AM,
Louis H Kauffman <span dir="ltr" class=""><<a moz-do-not-send="true" href="mailto:kauffman@uic.edu" target="_blank" class=""></a><a class="moz-txt-link-abbreviated" href="mailto:kauffman@uic.edu">kauffman@uic.edu</a>></span> wrote:<br class="">
<blockquote class="gmail_quote" style="margin:0 0 0
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<div style="word-wrap:break-word" class="">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 class="">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>
<div class="">
<div class="h5">
<div class=""><br class="">
<div class="">
<blockquote type="cite" class="">
<div class="">On Mar 29, 2016, at 4:43 PM, Dr. Plamen
L. Simeonov <<a moz-do-not-send="true" href="mailto:plamen.l.simeonov@gmail.com" target="_blank" class="">plamen.l.simeonov@gmail.com</a>>
wrote:</div>
<br class="">
<div class="">
<div dir="ltr" class=""><br class="">
<div class="gmail_extra"><br clear="all" class="">
<div class="">
<div class="">
<div dir="ltr" class="">
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<div class="">
<div dir="ltr" class="">
<div class="">
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<div dir="ltr" class="">
<div class=""><font face="georgia,
serif" class="">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 class=""><font face="georgia,
serif" class=""><br class="">
</font></div>
<div class=""><font face="georgia,
serif" class="">All the
best,</font></div>
<div class=""><font face="georgia,
serif" class=""><br class="">
</font></div>
<div class=""><font face="georgia,
serif" class="">Plamen</font></div>
<div class=""><font face="georgia,
serif" class=""><br class="">
</font></div>
<div class=""><font face="georgia,
serif" class="">PS. I
do not know
why my notes
appear twice
on this list.</font></div>
<div class=""><font face="georgia,
serif" class=""><br class="">
</font></div>
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<br class="">
<div class="gmail_quote">On Tue, Mar
29, 2016 at 10:55 PM, Louis H
Kauffman <span dir="ltr" class=""><<a moz-do-not-send="true" href="mailto:kauffman@uic.edu" target="_blank" class=""></a><a class="moz-txt-link-abbreviated" href="mailto:kauffman@uic.edu">kauffman@uic.edu</a>></span>
wrote:<br class="">
<blockquote class="gmail_quote" style="margin:0 0 0
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solid;padding-left:1ex">
<div style="word-wrap:break-word" class="">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 class="">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 class=""><br class="">
<div class="">
<blockquote type="cite" class="">
<div class="">On Mar 29, 2016, at
2:54 PM, Stanley N
Salthe <<a moz-do-not-send="true" href="mailto:ssalthe@binghamton.edu" target="_blank" class=""></a><a class="moz-txt-link-abbreviated" href="mailto:ssalthe@binghamton.edu">ssalthe@binghamton.edu</a>>
wrote:</div>
<br class="">
<div class="">
<div dir="ltr" class="">Plamen
wrote:
<div class=""><br class="">
</div>
<div class=""><p class="MsoNormal" style="font-size:12.8px"><span style="font-family:'Arial
Narrow',sans-serif" lang="EN-US" class=""> 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 style="font-family:'Arial
Narrow',sans-serif;font-size:12.8px" class="">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 style="font-family:'Arial
Narrow',sans-serif;font-size:12.8px" class=""><br class="">
</span></p><p class="MsoNormal"><span style="font-family:'Arial
Narrow',sans-serif" class=""><br class="">
</span></p><p class="MsoNormal"><span style="font-family:'Arial
Narrow',sans-serif" class="">S: An interesting recently published effort along
these lines is: </span></p><p class="">Alvaro Moreno and
Matteo Mossio:
Biological
Autonomy: A
Philosophical and
Theoretical
Enquiry (History,
Philosophy and
Theory of the Life
Sciences 12)
Springer</p><p class="">They seek a
materialist
understanding of
biology as a
system, attempting
to refer to the
genetic system as
little as
possible.</p><p class="">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 class="">STAN</p>
</div>
</div>
<div class="gmail_extra"><br class="">
<div class="gmail_quote">On
Tue, Mar 29, 2016 at
7:40 AM, Dr. Plamen
L. Simeonov <span dir="ltr" class=""><<a moz-do-not-send="true" href="mailto:plamen.l.simeonov@gmail.com" target="_blank" class=""></a><a class="moz-txt-link-abbreviated" href="mailto:plamen.l.simeonov@gmail.com">plamen.l.simeonov@gmail.com</a>></span>
wrote:<br class="">
<blockquote class="gmail_quote" style="margin:0 0
0
.8ex;border-left:1px
#ccc
solid;padding-left:1ex">
<div dir="ltr" class="">
<div class=""><br class="">
</div>
Dear Lou, Pedro
and All,<br class="">
<br class="">
<div class=""><span style="font-family:"Arial
Narrow",sans-serif" class=""> </span><br class="">
</div><p class="MsoNormal"><span style="font-family:"Arial
Narrow",sans-serif" lang="EN-US" class="">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 style="font-family:"Arial
Narrow",sans-serif" lang="EN-US" class=""><a moz-do-not-send="true" href="https://www.uni-muenster.de/imperia/md/content/cim/events/cim-mathmod-workshop-2015_abstracts.pdf" target="_blank" class="">https://www.uni-muenster.de/imperia/md/content/cim/events/cim-mathmod-workshop-2015_abstracts.pdf</a></span><span style="font-family:"Arial
Narrow",sans-serif" lang="EN-US" class="">:</span></p><p class="MsoNormal"><span style="font-family:"Arial
Narrow",sans-serif" lang="EN-US" class="">“</span><span style="font-family:"Arial
Narrow",sans-serif" lang="EN-US" class="">Davide Ambrosi:</span></p><p class="MsoNormal" style="margin-bottom:0.0001pt;line-height:normal"><span style="font-family:"Arial
Narrow",sans-serif" lang="EN-US" class="">A role for mechanics in the
growth,
remodelling
and
morphogenesis
of living
systems <span class=""> </span>In
the XX Century
the
interactions
between
mechanics in
biology were
much <span class=""> </span>biased
by
a
bioengineering
attitude:
people were
mainly
interested in
<span class=""> </span>evaluating
the state of
stress that
bones and
tissues
undergo in
order to <span class=""> </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 style="font-family:"Arial
Narrow",sans-serif" lang="EN-US" class="">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" class=""><span style="font-family:"Arial
Narrow",sans-serif" lang="EN-US" class=""> </span><br class="">
</div>
<div style="margin-bottom:0.0001pt;line-height:normal" class=""><span style="font-family:"Arial
Narrow",sans-serif" lang="EN-US" class=""> </span><br class="">
</div><p class="MsoNormal" style="margin-bottom:0.0001pt;line-height:normal"><span style="font-family:"Arial
Narrow",sans-serif" lang="EN-US" class="">Some more details about this
approach can
be found here:</span></p><p class="MsoNormal"><span style="font-family:"Arial
Narrow",sans-serif" lang="EN-US" class=""><a moz-do-not-send="true" href="http://rsta.royalsocietypublishing.org/content/367/1902/3335" target="_blank" class="">http://rsta.royalsocietypublishing.org/content/367/1902/3335</a>
</span></p><p class="MsoNormal"><span style="font-family:"Arial
Narrow",sans-serif" lang="EN-US" class=""><a moz-do-not-send="true" href="http://biomechanics.stanford.edu/paper/MFOreport.pdf" target="_blank" class="">http://biomechanics.stanford.edu/paper/MFOreport.pdf</a></span></p><p class="MsoNormal"><span style="font-family:"Arial
Narrow",sans-serif" lang="EN-US" class="">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" class=""><a moz-do-not-send="true" href="http://www.sciencedirect.com/science/article/pii/S0022519314006778" target="_blank" class=""></a><a class="moz-txt-link-freetext" href="http://www.sciencedirect.com/science/article/pii/S0022519314006778">http://www.sciencedirect.com/science/article/pii/S0022519314006778</a></span></p><p class="MsoNormal"><span lang="EN-US" class=""><a moz-do-not-send="true" href="http://www.sciencedirect.com/science/article/pii/S0022519316001260" target="_blank" class=""></a><a class="moz-txt-link-freetext" href="http://www.sciencedirect.com/science/article/pii/S0022519316001260">http://www.sciencedirect.com/science/article/pii/S0022519316001260</a>
</span></p><p class="MsoNormal"><span lang="EN-US" class=""><a moz-do-not-send="true" href="https://www.sciencedaily.com/releases/2015/01/150107101405.htm" target="_blank" class=""></a><a class="moz-txt-link-freetext" href="https://www.sciencedaily.com/releases/2015/01/150107101405.htm">https://www.sciencedaily.com/releases/2015/01/150107101405.htm</a></span></p><p class="MsoNormal"><span style="font-family:"Arial
Narrow",sans-serif" lang="EN-US" class="">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 moz-do-not-send="true" href="http://constructortheory.org/" target="_blank" class=""></a><a class="moz-txt-link-freetext" href="http://constructortheory.org/">http://constructortheory.org/</a>)
and
Brian
Josephson’s
“structural/circular
theory” (<a moz-do-not-send="true" href="http://arxiv.org/ftp/arxiv/papers/1502/1502.02429.pdf" target="_blank" class=""></a><a class="moz-txt-link-freetext" href="http://arxiv.org/ftp/arxiv/papers/1502/1502.02429.pdf">http://arxiv.org/ftp/arxiv/papers/1502/1502.02429.pdf</a>;
<a moz-do-not-send="true" href="http://arxiv.org/ftp/arxiv/papers/1506/1506.06774.pdf" target="_blank" class=""></a><a class="moz-txt-link-freetext" href="http://arxiv.org/ftp/arxiv/papers/1506/1506.06774.pdf">http://arxiv.org/ftp/arxiv/papers/1506/1506.06774.pdf</a>;
<a moz-do-not-send="true" href="http://arxiv.org/pdf/1108.4860.pdf" target="_blank" class=""></a><a class="moz-txt-link-freetext" href="http://arxiv.org/pdf/1108.4860.pdf">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 class=""> </span></span></p><p class="MsoNormal"><span style="font-family:"Arial
Narrow",sans-serif" lang="EN-US" class="">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 moz-do-not-send="true" href="http://www.sciencedirect.com/science/article/pii/S0079610715000899" target="_blank" class=""></a><a class="moz-txt-link-freetext" href="http://www.sciencedirect.com/science/article/pii/S0079610715000899">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 class=""> </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 class=""> </span><span class=""> </span></span></p><p class="MsoNormal"><span style="font-family:"Arial
Narrow",sans-serif" lang="EN-US" class="">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 style="font-family:"Arial
Narrow",sans-serif" lang="EN-US" class="">Reference:</span></p><p class="MsoNormal"><span lang="EN-US" class="">[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 class="">Trans.
Royal Irish
Acad</i>.,
Vol. XVII,
Part II.
292-422.</p>
<div class=""><span style="font-family:"Arial
Narrow",sans-serif" class=""><span class=""> </span><span class=""> </span><span lang="EN-US" class=""></span></span><br class="">
</div><p class="MsoNormal"><span style="font-family:"Arial
Narrow",sans-serif" lang="EN-US" class="">Best,</span></p>
<div class=""><span style="font-family:"Arial
Narrow",sans-serif" lang="EN-US" class=""> </span><br class="">
</div><p class="MsoNormal"><span style="font-family:"Arial
Narrow",sans-serif" lang="EN-US" class="">Plamen</span></p>
<div class=""><span style="font-family:"Arial
Narrow",sans-serif" class=""> </span><br class="">
</div><p class="MsoNormal"><span style="font-family:"Arial
Narrow",sans-serif" lang="EN-US" class="">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 style="font-family:"Arial
Narrow",sans-serif" lang="EN-US" class=""><a moz-do-not-send="true" href="https://www.uni-muenster.de/imperia/md/content/cim/events/cim-mathmod-workshop-2015_abstracts.pdf" target="_blank" class="">https://www.uni-muenster.de/imperia/md/content/cim/events/cim-mathmod-workshop-2015_abstracts.pdf</a></span><span style="font-family:"Arial
Narrow",sans-serif" lang="EN-US" class="">:</span></p><p class="MsoNormal"><span style="font-family:"Arial
Narrow",sans-serif" lang="EN-US" class="">“</span><span style="font-family:"Arial
Narrow",sans-serif" lang="EN-US" class="">Davide Ambrosi:</span></p><p class="MsoNormal" style="margin-bottom:0.0001pt;line-height:normal"><span style="font-family:"Arial
Narrow",sans-serif" lang="EN-US" class="">A role for mechanics in the
growth,
remodelling
and
morphogenesis
of living
systems <span class=""> </span>In
the XX Century
the
interactions
between
mechanics in
biology were
much <span class=""> </span>biased
by
a
bioengineering
attitude:
people were
mainly
interested in
<span class=""> </span>evaluating
the state of
stress that
bones and
tissues
undergo in
order to <span class=""> </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 style="font-family:"Arial
Narrow",sans-serif" lang="EN-US" class="">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" class=""><span style="font-family:"Arial
Narrow",sans-serif" lang="EN-US" class=""> </span><br class="">
</div>
<div style="margin-bottom:0.0001pt;line-height:normal" class=""><span style="font-family:"Arial
Narrow",sans-serif" lang="EN-US" class=""> </span><br class="">
</div><p class="MsoNormal" style="margin-bottom:0.0001pt;line-height:normal"><span style="font-family:"Arial
Narrow",sans-serif" lang="EN-US" class="">Some more details about this
approach can
be found here:</span></p><p class="MsoNormal"><span style="font-family:"Arial
Narrow",sans-serif" lang="EN-US" class=""><a moz-do-not-send="true" href="http://rsta.royalsocietypublishing.org/content/367/1902/3335" target="_blank" class="">http://rsta.royalsocietypublishing.org/content/367/1902/3335</a>
</span></p><p class="MsoNormal"><span style="font-family:"Arial
Narrow",sans-serif" lang="EN-US" class=""><a moz-do-not-send="true" href="http://biomechanics.stanford.edu/paper/MFOreport.pdf" target="_blank" class="">http://biomechanics.stanford.edu/paper/MFOreport.pdf</a></span></p><p class="MsoNormal"><span style="font-family:"Arial
Narrow",sans-serif" lang="EN-US" class="">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" class=""><a moz-do-not-send="true" href="http://www.sciencedirect.com/science/article/pii/S0022519314006778" target="_blank" class=""></a><a class="moz-txt-link-freetext" href="http://www.sciencedirect.com/science/article/pii/S0022519314006778">http://www.sciencedirect.com/science/article/pii/S0022519314006778</a></span></p><p class="MsoNormal"><span lang="EN-US" class=""><a moz-do-not-send="true" href="http://www.sciencedirect.com/science/article/pii/S0022519316001260" target="_blank" class=""></a><a class="moz-txt-link-freetext" href="http://www.sciencedirect.com/science/article/pii/S0022519316001260">http://www.sciencedirect.com/science/article/pii/S0022519316001260</a>
</span></p><p class="MsoNormal"><span lang="EN-US" class=""><a moz-do-not-send="true" href="https://www.sciencedaily.com/releases/2015/01/150107101405.htm" target="_blank" class=""></a><a class="moz-txt-link-freetext" href="https://www.sciencedaily.com/releases/2015/01/150107101405.htm">https://www.sciencedaily.com/releases/2015/01/150107101405.htm</a></span></p><p class="MsoNormal"><span style="font-family:"Arial
Narrow",sans-serif" lang="EN-US" class="">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 moz-do-not-send="true" href="http://constructortheory.org/" target="_blank" class=""></a><a class="moz-txt-link-freetext" href="http://constructortheory.org/">http://constructortheory.org/</a>)
and
Brian
Josephson’s
“structural/circular
theory” (<a moz-do-not-send="true" href="http://arxiv.org/ftp/arxiv/papers/1502/1502.02429.pdf" target="_blank" class=""></a><a class="moz-txt-link-freetext" href="http://arxiv.org/ftp/arxiv/papers/1502/1502.02429.pdf">http://arxiv.org/ftp/arxiv/papers/1502/1502.02429.pdf</a>;
<a moz-do-not-send="true" href="http://arxiv.org/ftp/arxiv/papers/1506/1506.06774.pdf" target="_blank" class=""></a><a class="moz-txt-link-freetext" href="http://arxiv.org/ftp/arxiv/papers/1506/1506.06774.pdf">http://arxiv.org/ftp/arxiv/papers/1506/1506.06774.pdf</a>;
<a moz-do-not-send="true" href="http://arxiv.org/pdf/1108.4860.pdf" target="_blank" class=""></a><a class="moz-txt-link-freetext" href="http://arxiv.org/pdf/1108.4860.pdf">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 class=""> </span></span></p><p class="MsoNormal"><span style="font-family:"Arial
Narrow",sans-serif" lang="EN-US" class="">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 moz-do-not-send="true" href="http://www.sciencedirect.com/science/article/pii/S0079610715000899" target="_blank" class=""></a><a class="moz-txt-link-freetext" href="http://www.sciencedirect.com/science/article/pii/S0079610715000899">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 class=""> </span>design
their proofs,
but then I got
used to
that style. It
was a question
of overall
convention. 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,
backtracing
and proof come
later. <span class=""> </span><span class="">
<br class="">
</span></span></p><p class="MsoNormal"><span style="font-family:"Arial
Narrow",sans-serif" lang="EN-US" class=""><br class="">
</span></p><p class="MsoNormal"><span style="font-family:"Arial
Narrow",sans-serif" lang="EN-US" class="">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?
And if we
apply a
specific
mathematical-computational
technique what
is the key
idea/intuition
behind it?.
Because, as a
colleague
pathologist
told me this
morning about
the model
correctness
when
predicting the
development of
tumors: the
model can be
assumed for
being correct
based on the
interpretation
of some
(limited) set
of data, but
Ptolemy's
system was
also
considered to
be correct in
its rather
complex way of
predicting the
movement of
the celestial
bodies. </span><span style="font-family:"Arial
Narrow",sans-serif" lang="EN-US" class=""><span style="font-size:11pt;line-height:107%;font-family:"Arial
Narrow",sans-serif" lang="EN-US" class="">Where is the difference? </span>I
am curious
about your
opinion.<br class="">
</span></p><p class="MsoNormal"><b class=""><span style="font-family:"Arial
Narrow",sans-serif" lang="EN-US" class=""><br class="">
</span></b></p>
<b class="">
</b><p class="MsoNormal"><b class=""><span style="font-family:"Arial
Narrow",sans-serif" lang="EN-US" class="">Reference:</span></b></p><p class="MsoNormal"><span lang="EN-US" class="">[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 class="">Trans.
Royal Irish
Acad</i>.,
Vol. XVII,
Part II.
292-422.</p>
<div class=""><span style="font-family:"Arial
Narrow",sans-serif" class=""><span class=""> </span><span class=""> </span><span lang="EN-US" class=""></span></span><br class="">
</div><p class="MsoNormal"><span style="font-family:"Arial
Narrow",sans-serif" lang="EN-US" class="">Best,</span></p>
<div class=""><span style="font-family:"Arial
Narrow",sans-serif" lang="EN-US" class=""> </span><br class="">
</div><p class="MsoNormal"><span style="font-family:"Arial
Narrow",sans-serif" lang="EN-US" class="">Plamen</span></p>
<div class="">
<div class="">
<div class="">
<div dir="ltr" class="">
<div class="">
<div dir="ltr" class="">
<div class="">
<div dir="ltr" class="">
<div class="">
<div dir="ltr" class="">
<div class="">
<div dir="ltr" class="">
<div dir="ltr" class="">
<div dir="ltr" class="">
<div dir="ltr" class="">______________________<br class="">
<div dir="ltr" class="">
<div class=""><span style="font-family:georgia,serif" class=""><br class="">
</span></div>
<div class=""><span style="font-family:georgia,serif" class=""><a moz-do-not-send="true" href="http://www.sciencedirect.com/science/journal/00796107/119/3" target="_blank" class="">2015 JPBMB Special Issue on Integral Biomathics: Life
Sciences,
Mathematics
and
Phenomenological
Philosophy</a> </span></div>
<div class=""><span style="font-family:georgia,serif" class="">(note:
free access to
all articles
until July
19th, 2016)</span></div>
<br class="">
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
<br class="">
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<pre class="moz-signature" cols="72">--
-------------------------------------------------
Pedro C. Marijuán
Grupo de Bioinformación / Bioinformation Group
Instituto Aragonés de Ciencias de la Salud
Centro de Investigación Biomédica de Aragón (CIBA)
Avda. San Juan Bosco, 13, planta X
50009 Zaragoza, Spain
Tfno. +34 976 71 3526 (& 6818)
<a class="moz-txt-link-abbreviated" href="mailto:pcmarijuan.iacs@aragon.es">pcmarijuan.iacs@aragon.es</a>
<a class="moz-txt-link-freetext" href="http://sites.google.com/site/pedrocmarijuan/">http://sites.google.com/site/pedrocmarijuan/</a>
-------------------------------------------------
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