<div dir="ltr">RE: Volume 24, Issue 32<div>Plamen Simeonov: <span style="font-size:12.8px">What did we actually gain for biology from merging space and </span><span style="font-size:12.8px">time in physics? </span></div><div><span style="font-size:12.8px"><br></span></div><div><span style="font-size:12.8px">ME: Of course it is a little absurd in this context to observe that time and space were merged (1) </span><span style="font-size:12.8px">by</span><span style="font-size:12.8px"> </span><span style="font-size:12.8px">H.A. Lorentz in his explanation of the 'Lorentz Group' of symmetries of Maxwell's equations, and (2) by the young Albert Einstein, to explain the anomalous results of the Michelson-Morley experiment. Both without a thought for biology. </span></div><div><span style="font-size:12.8px"><br></span></div><div><span style="font-size:12.8px">But what seems important to me is that the structure of information at loci of control in all organisms appears to have the non-digital information structure, <======<b>O</b>, where the arrow, <======, represents a non-separable, irreducible vector mixture, which seems to be able to encode three dimensions of space, while the attached loop, <b>O</b>, encodes the sense of 'self' together with its 'internal sense of time passing'; at any rate, both can be attributed to it. </span></div><div><span style="font-size:12.8px"><br></span></div><div><span style="font-size:12.8px">Thus, the double aspect structure presented by arrow plus loop, foreshadowed in the work of David Chalmers, represents Space-Time. Though why it should be a Lorentz-Einstein space-time rather than a Galilean space-time is not obvious. </span></div><div><span style="font-size:12.8px"><br></span></div><div><span style="font-size:12.8px">It is possible that that question can only be answered from the perspective of enlightenment when the realisation of the 'wholeness-of-all-things' comes to be realised as something essentially within the realisation of the unbounded awareness identified as the real 'Self'. </span></div><div><span style="font-size:12.8px"><br></span></div></div><div class="gmail_extra"><br><div class="gmail_quote">On 29 March 2016 at 17:11, <span dir="ltr"><<a href="mailto:fis-request@listas.unizar.es" target="_blank">fis-request@listas.unizar.es</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Send Fis mailing list submissions to<br>
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Today's Topics:<br>
<br>
1. On mathematical theories and models in biology<br>
(Dr. Plamen L. Simeonov)<br>
<br>
<br>
----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Tue, 29 Mar 2016 13:40:54 +0200<br>
From: "Dr. Plamen L. Simeonov" <<a href="mailto:plamen.l.simeonov@gmail.com">plamen.l.simeonov@gmail.com</a>><br>
To: fis <<a href="mailto:fis@listas.unizar.es">fis@listas.unizar.es</a>><br>
Subject: [Fis] On mathematical theories and models in biology<br>
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<br>
Dear Lou, Pedro and All,<br>
<br>
<br>
<br>
I am going to present a few opportunistic ideas related to what was said<br>
before in this session. Coming back to Pivar?s speculative<br>
mechano-topological model of life excluding genetics I wish to turn your<br>
attention to another author with a similar idea but on a sound mathematical<br>
base, Davide Ambrosi with his resume at<br>
<a href="https://www.uni-muenster.de/imperia/md/content/cim/events/cim-mathmod-workshop-2015_abstracts.pdf" rel="noreferrer" target="_blank">https://www.uni-muenster.de/imperia/md/content/cim/events/cim-mathmod-workshop-2015_abstracts.pdf</a><br>
:<br>
<br>
?Davide Ambrosi:<br>
<br>
A role for mechanics in the growth, remodelling and morphogenesis of living<br>
systems In the XX Century the interactions between mechanics in biology<br>
were much biased by a bioengineering attitude: people were mainly<br>
interested in evaluating the state of stress that bones and tissues<br>
undergo in order to properly design prosthesis and devices. However in the<br>
last decades a new vision is emerging. "Mechano-biology" is changing the<br>
point of view, with respect to "Bio-mechanics", emphasizing the biological<br>
feedback. Cells, tissues and organs do not only deform when loaded: they<br>
reorganize, they duplicate, they actively produce dynamic patterns that<br>
apparently have multiple biological aims.<br>
<br>
In this talk I will concentrate on two paradigmatic systems where the<br>
interplay between mechanics and biology is, in my opinion, particularly<br>
challenging: the homeostatic stress as a driver for remodeling of soft<br>
tissue and the tension as a mechanism to transmit information about the<br>
size of organs during morphogenesis. In both cases it seems that mechanics<br>
plays a role which at least accompanies and enforces the biochemical<br>
signaling.?<br>
<br>
<br>
<br>
<br>
<br>
Some more details about this approach can be found here:<br>
<br>
<a href="http://rsta.royalsocietypublishing.org/content/367/1902/3335" rel="noreferrer" target="_blank">http://rsta.royalsocietypublishing.org/content/367/1902/3335</a><br>
<br>
<a href="http://biomechanics.stanford.edu/paper/MFOreport.pdf" rel="noreferrer" target="_blank">http://biomechanics.stanford.edu/paper/MFOreport.pdf</a><br>
<br>
In other words, for the core information theorists in FIS, the question is:<br>
is there really only (epi)genetic evolution communication in living<br>
organisms. Stan Salthe and Lou Kauffman already provided some answers. I<br>
begin to believe that the transition from abiotic to biotic structures,<br>
incl. Maturana-Varela.-Uribe?s autopoiesis may, really have some underlying<br>
matrix/?skeleton?/?programme? which has nothing in common with the nature<br>
of DNA, and that DNA and RNA as we know them today<br>
<br>
<a href="http://www.sciencedirect.com/science/article/pii/S0022519314006778" rel="noreferrer" target="_blank">http://www.sciencedirect.com/science/article/pii/S0022519314006778</a><br>
<br>
<a href="http://www.sciencedirect.com/science/article/pii/S0022519316001260" rel="noreferrer" target="_blank">http://www.sciencedirect.com/science/article/pii/S0022519316001260</a><br>
<br>
<a href="https://www.sciencedaily.com/releases/2015/01/150107101405.htm" rel="noreferrer" target="_blank">https://www.sciencedaily.com/releases/2015/01/150107101405.htm</a><br>
<br>
may have emerged as secondary or even tertiary ?memory? of something<br>
underlying deeper below the microbiological surface. It is at least worth<br>
thinking in this direction. I do not mean necessarily the role of the<br>
number concept and Platonic origin of the universe, but something probably<br>
much more ?physical? or at least staying at the edge between<br>
physical/material and immaterial such as David Deutsch?s constructor theory<br>
(<a href="http://constructortheory.org/" rel="noreferrer" target="_blank">http://constructortheory.org/</a>) and Brian Josephson?s ?structural/circular<br>
theory? (<a href="http://arxiv.org/ftp/arxiv/papers/1502/1502.02429.pdf" rel="noreferrer" target="_blank">http://arxiv.org/ftp/arxiv/papers/1502/1502.02429.pdf</a>;<br>
<a href="http://arxiv.org/ftp/arxiv/papers/1506/1506.06774.pdf" rel="noreferrer" target="_blank">http://arxiv.org/ftp/arxiv/papers/1506/1506.06774.pdf</a>;<br>
<a href="http://arxiv.org/pdf/1108.4860.pdf" rel="noreferrer" target="_blank">http://arxiv.org/pdf/1108.4860.pdf</a>) searching for the theories underpinning<br>
the foundations of the physical laws (and following Wheeler?s definition<br>
for a ?Law without Law?.<br>
<br>
Some of you may say that QT and Gravitation Theory are responsible for such<br>
kind of strange effects, but I would rather leave the brackets open,<br>
because the recent discussion about potentialities and actualities in QM<br>
brings up the idea that there are still different ways of looking at those<br>
concepts (although they are strictly defined in their core domains). This<br>
was actually also the lesson from the last special issue on integral<br>
biomathics (2015) dedicated to phenomenology, with the different opinions<br>
of scientists and philosophers on obviously clear matters in their domains.<br>
This is why also the question of what we define as science needs to be<br>
probably revised in future to include also such issues that are ?felt?<br>
rather than ?reasoned?, even if we do not have the ?proofs? yet, because<br>
the proofs also emerge as subjective (or perhaps ?suggested?! ? ask the<br>
psychologists for that aspect) thoughts in the minds of the mathematicians.<br>
I am really glad that we began such a phenomenological discussion on this<br>
aspect such as Hipolito?s paper (<br>
<a href="http://www.sciencedirect.com/science/article/pii/S0079610715000899" rel="noreferrer" target="_blank">http://www.sciencedirect.com/science/article/pii/S0079610715000899</a>) that<br>
was widely commented in the reviewer?s circle. In many cases when we have a<br>
?fuzzy? intuition about a certain relationship or analogy we miss the<br>
correct definitions and concepts, and so in a creative act to hold down the<br>
flying thought we move to using examples, metaphors, pictures. Pedro<br>
correctly addressed the explanatory problem of science which presupposes a<br>
certain causative and predicative ?workflow? to derive a conclusion from<br>
the facts, and this is the way in which also proofs are (selectively) made.<br>
As a young scholar I often wondered how artificially people like Gauss,<br>
Cauchy and Weierstrass design their proofs, but then I got used to that<br>
style. I am thankful to Lou for his response on my question about using<br>
adequate ?resonant? methods to model developmental biology, because this is<br>
also an important aspect of the biology (and physics as well) including the<br>
phenomenological/first-person view of an ?observer-participant? (to use<br>
Vrobel?s term) which is crucial for understanding the process of<br>
self-reflection/recursion/cycle in science, which is usually led by what?:<br>
the intuition, also well recognized by such giants like Poincare and<br>
Einstein. Isn?t not ?resonance? in the core of detecting such vibration<br>
between the observer and the observed? Because logic, back trace, prove<br>
come later.<br>
<br>
And finally, when looking at the clear simple mathematical abstractions of<br>
numbers, vectors, directions, sets, algebras, geometries, etc. used by many<br>
without scrutinizing when developing system (biological) models of yet<br>
another kind of mechanics/automation/machinery of the physical reality, I<br>
am asking myself which are the premises for using such tools to describe a<br>
model: the parameters, or the idea behind? It is probably not a commonly<br>
known fact (even for those who are engaged with such exciting disciplines<br>
as algebraic geometry and geometrical algebra, now considered to be very<br>
close to what we wish to express in biology) that William Hamilton, the<br>
inventor of the quaternions did not simply use the already known concept of<br>
?vector? in his method. Instead he used ?step? with ?direction? to express<br>
a duration of time (or ?duree? as Husserl called it from the other side of<br>
the phenomenological divide) and action (to move from A to B): two very<br>
biology-related concepts at that time (although they may be considered as<br>
physical or computational today). He actually stated that if there is<br>
geometry as a pure science of space, then algebra must be the pure science<br>
of time [1]. What did we actually gain for biology from merging space and<br>
time in physics?<br>
<br>
Reference:<br>
<br>
[1] W. R. Hamilton, 1835. Theory of Conjugate Functions, or Algebraic<br>
Couples; with a Preliminary or Elementary Essay on Algebra as the Science<br>
of Pure Time. *Trans. Royal Irish Acad*., Vol. XVII, Part II. 292-422.<br>
<br>
<br>
<br>
Best,<br>
<br>
<br>
<br>
Plamen<br>
<br>
<br>
<br>
I have a few provoking notes related to what was said before in this<br>
session. Coming back to Pivar?s speculative mechano-topological model of<br>
life excluding genetics I wish to turn your attention to another author<br>
with a similar idea but on a sound mathematical base, Davide Ambrosi with<br>
his resume at<br>
<a href="https://www.uni-muenster.de/imperia/md/content/cim/events/cim-mathmod-workshop-2015_abstracts.pdf" rel="noreferrer" target="_blank">https://www.uni-muenster.de/imperia/md/content/cim/events/cim-mathmod-workshop-2015_abstracts.pdf</a><br>
:<br>
<br>
?Davide Ambrosi:<br>
<br>
A role for mechanics in the growth, remodelling and morphogenesis of living<br>
systems In the XX Century the interactions between mechanics in biology<br>
were much biased by a bioengineering attitude: people were mainly<br>
interested in evaluating the state of stress that bones and tissues<br>
undergo in order to properly design prosthesis and devices. However in the<br>
last decades a new vision is emerging. "Mechano-biology" is changing the<br>
point of view, with respect to "Bio-mechanics", emphasizing the biological<br>
feedback. Cells, tissues and organs do not only deform when loaded: they<br>
reorganize, they duplicate, they actively produce dynamic patterns that<br>
apparently have multiple biological aims.<br>
<br>
In this talk I will concentrate on two paradigmatic systems where the<br>
interplay between mechanics and biology is, in my opinion, particularly<br>
challenging: the homeostatic stress as a driver for remodeling of soft<br>
tissue and the tension as a mechanism to transmit information about the<br>
size of organs during morphogenesis. In both cases it seems that mechanics<br>
plays a role which at least accompanies and enforces the biochemical<br>
signaling.?<br>
<br>
<br>
<br>
<br>
<br>
Some more details about this approach can be found here:<br>
<br>
<a href="http://rsta.royalsocietypublishing.org/content/367/1902/3335" rel="noreferrer" target="_blank">http://rsta.royalsocietypublishing.org/content/367/1902/3335</a><br>
<br>
<a href="http://biomechanics.stanford.edu/paper/MFOreport.pdf" rel="noreferrer" target="_blank">http://biomechanics.stanford.edu/paper/MFOreport.pdf</a><br>
<br>
In other words, for the core information theorists in FIS, the question is:<br>
is there really only (epi)genetic evolution communication in living<br>
organisms. Stan Salthe and Lou Kauffman already provided some answers. I<br>
begin to believe that the transition from abiotic to biotic structures,<br>
incl. Maturana-Varela.-Uribe?s autopoiesis may, really have some underlying<br>
matrix/?skeleton?/?programme? which has nothing in common with the nature<br>
of DNA, and that DNA and RNA as we know them today<br>
<br>
<a href="http://www.sciencedirect.com/science/article/pii/S0022519314006778" rel="noreferrer" target="_blank">http://www.sciencedirect.com/science/article/pii/S0022519314006778</a><br>
<br>
<a href="http://www.sciencedirect.com/science/article/pii/S0022519316001260" rel="noreferrer" target="_blank">http://www.sciencedirect.com/science/article/pii/S0022519316001260</a><br>
<br>
<a href="https://www.sciencedaily.com/releases/2015/01/150107101405.htm" rel="noreferrer" target="_blank">https://www.sciencedaily.com/releases/2015/01/150107101405.htm</a><br>
<br>
may have emerged as secondary or even tertiary ?memory? of something<br>
underlying deeper below the microbiological surface. It is at least worth<br>
thinking in this direction. I do not mean necessarily the role of the<br>
number concept and Platonic origin of the universe, but something probably<br>
much more ?physical? or at least staying at the edge between<br>
physical/material and immaterial such as David Deutsch?s constructor theory<br>
(<a href="http://constructortheory.org/" rel="noreferrer" target="_blank">http://constructortheory.org/</a>) and Brian Josephson?s ?structural/circular<br>
theory? (<a href="http://arxiv.org/ftp/arxiv/papers/1502/1502.02429.pdf" rel="noreferrer" target="_blank">http://arxiv.org/ftp/arxiv/papers/1502/1502.02429.pdf</a>;<br>
<a href="http://arxiv.org/ftp/arxiv/papers/1506/1506.06774.pdf" rel="noreferrer" target="_blank">http://arxiv.org/ftp/arxiv/papers/1506/1506.06774.pdf</a>;<br>
<a href="http://arxiv.org/pdf/1108.4860.pdf" rel="noreferrer" target="_blank">http://arxiv.org/pdf/1108.4860.pdf</a>) searching for the theories underpinning<br>
the foundations of the physical laws (and following Wheeler?s definition<br>
for a ?Law without Law?.<br>
<br>
Some of you may say that QT and Gravitation Theory are responsible for such<br>
kind of strange effects, but I would rather leave the brackets open,<br>
because the recent discussion about potentialities and actualities in QM<br>
brings up the idea that there are still different ways of looking at those<br>
concepts (although they are strictly defined in their core domains). This<br>
was actually also the lesson from the last special issue on integral<br>
biomathics (2015) dedicated to phenomenology, with the different opinions<br>
of scientists and philosophers on obviously clear matters in their domains.<br>
This is why also the question of what we define as science needs to be<br>
probably revised in future to include also such issues that are ?felt?<br>
rather than ?reasoned?, even if we do not have the ?proofs? yet, because<br>
the proofs also emerge as subjective (or perhaps ?suggested?! ? ask the<br>
psychologists for that aspect) thoughts in the minds of the mathematicians.<br>
I am really glad that we began such a phenomenological discussion on this<br>
aspect such as Hipolito?s paper (<br>
<a href="http://www.sciencedirect.com/science/article/pii/S0079610715000899" rel="noreferrer" target="_blank">http://www.sciencedirect.com/science/article/pii/S0079610715000899</a>) that<br>
was widely commented in the reviewer?s circle. In many cases when we have a<br>
?fuzzy? intuition about a certain relationship or analogy we miss the<br>
correct definitions and concepts, and so in a creative act to hold down the<br>
flying thought we move to using examples, metaphors, pictures. Pedro<br>
correctly addressed the explanatory problem of science which presupposes a<br>
certain causative and predicative ?workflow? to derive a conclusion from<br>
the facts, and this is the way in which also proofs are (selectively) made.<br>
As a young scholar I often wondered how artificially people like Gauss,<br>
Cauchy and Weierstrass design their proofs, but then I got used to that<br>
style. It was a question of overall convention. I am thankful to Lou for<br>
his response on my question about using adequate ?resonant? methods to<br>
model developmental biology, because this is also an important aspect of<br>
the biology (and physics as well) including the<br>
phenomenological/first-person view of an ?observer-participant? (to use<br>
Vrobel?s term) which is crucial for understanding the process of<br>
self-reflection/recursion/cycle in science, which is usually led by what?:<br>
the intuition, also well recognized by such giants like Poincare and<br>
Einstein. Isn?t not ?resonance? in the core of detecting such vibration<br>
between the observer and the observed? Because logic, backtracing and proof<br>
come later.<br>
<br>
<br>
And finally, when looking at the clear simple mathematical abstractions of<br>
numbers, vectors, directions, sets, algebras, geometries, etc. used by many<br>
without scrutinizing when developing system (biological) models of yet<br>
another kind of mechanics/automation/machinery of the physical reality, I<br>
am asking myself which are the premises for using such tools to describe a<br>
model: the parameters, or the idea behind? It is probably not a commonly<br>
known fact (even for those who are engaged with such exciting disciplines<br>
as algebraic geometry and geometrical algebra, now considered to be very<br>
close to what we wish to express in biology) that William Hamilton, the<br>
inventor of the quaternions did not simply use the already known concept of<br>
?vector? in his method. Instead he used ?step? with ?direction? to express<br>
a duration of time (or ?duree? as Husserl called it from the other side of<br>
the phenomenological divide) and action (to move from A to B): two very<br>
biology-related concepts at that time (although they may be considered as<br>
physical or computational today). He actually stated that if there is<br>
geometry as a pure science of space, then algebra must be the pure science<br>
of time [1]. What did we actually gain for biology from merging space and<br>
time in physics? And if we apply a specific mathematical-computational<br>
technique what is the key idea/intuition behind it?. Because, as a<br>
colleague pathologist told me this morning about the model correctness when<br>
predicting the development of tumors: the model can be assumed for being<br>
correct based on the interpretation of some (limited) set of data, but<br>
Ptolemy's system was also considered to be correct in its rather complex<br>
way of predicting the movement of the celestial bodies. Where is the<br>
difference? I am curious about your opinion.<br>
<br>
<br>
*Reference:*<br>
<br>
[1] W. R. Hamilton, 1835. Theory of Conjugate Functions, or Algebraic<br>
Couples; with a Preliminary or Elementary Essay on Algebra as the Science<br>
of Pure Time. *Trans. Royal Irish Acad*., Vol. XVII, Part II. 292-422.<br>
<br>
<br>
<br>
Best,<br>
<br>
<br>
<br>
Plamen<br>
______________________<br>
<br>
2015 JPBMB Special Issue on Integral Biomathics: Life Sciences, Mathematics<br>
and Phenomenological Philosophy<br>
<<a href="http://www.sciencedirect.com/science/journal/00796107/119/3" rel="noreferrer" target="_blank">http://www.sciencedirect.com/science/journal/00796107/119/3</a>><br>
(note: free access to all articles until July 19th, 2016)<br>
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</blockquote></div><br><br clear="all"><div><br></div>-- <br><div class="gmail_signature"><div dir="ltr"><div><span style="font-family:arial,sans-serif;font-size:13px;border-collapse:collapse">Alex Hankey M.A. (Cantab.) PhD</span><span style="font-family:arial,sans-serif;font-size:13px;border-collapse:collapse"> (M.I.T.)<br>Distinguished Professor of Yoga and Physical Science,<br>
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