<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Dear Rukhsan,<div class="">I agree that we have not plumbed the depths of quantum theory in its present formulations.</div><div class="">What needs to be done and is being done is the long process of taking to its limits the applications and foundational understanding of quantum theory.</div><div class="">From my point of view, the most mysterious part of standard quantum theory is that its measurement postulate seems to work! I think that there is a clue there to </div><div class="">how quantum theory may be part of a deeper or more general structure. The analogy one can follow is that an eigenvector (for a non-zero eigenvalue Lambda) is</div><div class="">a fixed point of (1/Lamba)T where Tv = Lambda v. There is a beautiful theory of fixed points in great generality (beyond linear transformations) called Lambda Calculus (no pun intended) where any transformation F has a fixed point via Gx = F(xx) whence GG = F(GG). These fixed points can be correlated with ‘objects’ at</div><div class="">all levels including the imaginary. I won’t preach here!</div><div class="">Best,</div><div class="">Lou</div><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On Mar 31, 2016, at 8:58 AM, Rukhsanulhaq <<a href="mailto:rukhsanulhaq@gmail.com" class="">rukhsanulhaq@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class=""><div class=""><div class=""><div class=""><div class=""><div class=""><div class=""><div class=""><div class=""><div class=""><div class=""><div class=""><div class=""><div class=""><div class="">Dear all,thank you very much for very interesting and insightful discussions.<br class=""></div>I have been following them very keenly. Though the discussions have come<br class=""></div>to "new beginning" rather than to an end as Dr Plamen has rightly put it.,I want to<br class=""></div>add here couple of comments about quantum mechanics and biology.<br class=""></div>Prof Kauffman has expressed the need for the deeper quantum mechanics which<br class=""></div>surely must be due to the limited scope which present formulations and interpretations<br class=""></div>provide. However I would say that quantum theory is full fledged paradigm which<br class=""></div>has yet to be understood fully even after more than century after its inception by Planck.<br class=""></div>Quantum theory keeps on throwing surprises as we delve deeper into it. However the fact<br class=""></div>that quantum theory will provide a framework to understand biological phenomena was realized<br class=""></div>early on by one of the pioneers of the theory,Erwin Schroedinger and he went on to write a famous book<br class=""></div>about it where concepts like "quantum jump" were used to understand discrete and probabilistic nature<br class=""></div>of genetic phenomena. In recent times many authors have tried to look deeper into the relation between<br class=""></div>quantum theory and biology and have dubbed this subject as "quantum biology".<br class=""></div><div class=""> There is a lot of work that needs to be done to understand various aspects of quantum theory<br class=""></div><div class="">in more mathematically and philosophically transparent way. My approach to the foundations is based<br class=""></div><div class="">on Clifford algebras which are also central theme of other approaches like those of Bohm and Hiley,Penrose<br class=""></div><div class="">via twistors,Kauffman's via iterants, Finkelestein via quantum sets and quantum logic,Hesten's via geometric algebra.<br class=""></div><div class="">I am very hopeful that this approach will uncover the depths of quantum theory and will give us a very transport<br class=""></div><div class="">formulation and interpretation of this "jewel of physics".<br class=""></div><div class="">Rukhsan<br class=""></div><div class="">Thank you very much<br class=""></div></div><div class="gmail_extra"><br class=""><div class="gmail_quote">On Thu, Mar 31, 2016 at 4:45 PM, <span dir="ltr" class=""><<a href="mailto:fis-request@listas.unizar.es" target="_blank" class="">fis-request@listas.unizar.es</a>></span> wrote:<br class=""><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 class="">
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1. Re: concluding by beginning (Dr. Plamen L. Simeonov)<br class="">
<br class="">
<br class="">
----------------------------------------------------------------------<br class="">
<br class="">
Message: 1<br class="">
Date: Thu, 31 Mar 2016 13:14:45 +0200<br class="">
From: "Dr. Plamen L. Simeonov" <<a href="mailto:plamen.l.simeonov@gmail.com" class="">plamen.l.simeonov@gmail.com</a>><br class="">
To: Louis H Kauffman <<a href="mailto:loukau@gmail.com" class="">loukau@gmail.com</a>><br class="">
Cc: fis <<a href="mailto:fis@listas.unizar.es" class="">fis@listas.unizar.es</a>>, Joel Isaacson <<a href="mailto:isaacsonj@hotmail.com" class="">isaacsonj@hotmail.com</a>><br class="">
Subject: Re: [Fis] concluding by beginning<br class="">
Message-ID:<br class="">
<<a href="mailto:CAMBikj5o_c1otwJKXYtvdi_q1WKS_%2BfJz4-fFEq5Ba22iNe1qw@mail.gmail.com" class="">CAMBikj5o_c1otwJKXYtvdi_q1WKS_+fJz4-fFEq5Ba22iNe1qw@mail.gmail.com</a>><br class="">
Content-Type: text/plain; charset="utf-8"<br class="">
<br class="">
Dear FIS Fellows,<br class="">
<br class="">
I was also about writing some concluding remarks, since our time for math<br class="">
in bio is about to end this week, but realized that Lou was fast with an<br class="">
excellent final comment and list of references for postprocessing. I am<br class="">
happy that after some initial hesitation on the forum the key messages came<br class="">
accross and we were able to cover within short time the broad span of views<br class="">
within short time. You are very welcome to continue the discussion also<br class="">
privately and of course, within the scope of the next themes to come:<br class="">
bio/cybersemiotics with Soeren Brier and physics with Alex Hankey, which<br class="">
were nicely introduced by some earlier comments and associations like Bob's<br class="">
triad from his inspiring book "The Third Window" which I see related to<br class="">
C.S. Pierce's initiations in math, philosophy and semiotics. It became<br class="">
clear that such important issues as circularity and recursion/repetition in<br class="">
biology are closely related to distiction, (autocatalytic re)action,<br class="">
memory, (negative) feedback, automation, self-organization, autocells on<br class="">
the one side and (prime) numbers, fractional calculus,<br class="">
triangular/quadrangular/polihedral structures, (Riemann) wave function<br class="">
(analysis), QM and fractal geometry on the other, with opening room for<br class="">
covering even more phenomenology and creating ideas along the multiple<br class="">
lines of causation up to the limits of thought and imagination, nicely<br class="">
reflected by the participants in the discussion. So I have no other chance<br class="">
but to say: that's real life in a nutshell of exchanged messages! The most<br class="">
astonishing characteristic of this communication which comes to end, but<br class="">
just began in my eyes, is that we succeed to build together something that<br class="">
is capabloe to not only link remote and sometimes obscure and absurd ideas<br class="">
and question, but also attribute, enfold and evolve them with what we call<br class="">
a trace of information, an ontology of a creative development process we<br class="">
are participating, as if life becomes that what we really discover, revolve<br class="">
and impress just in time: in Alex's words "a living from that e can<br class="">
interact with, and (which) we are". And this is recursively wraped again<br class="">
within Francesco's phrase: "la conoscenca ha fondamenti biologici ... e<br class="">
viceversa, la biologia ha fondamenti quantistici". How could I say this in<br class="">
Latin? Thank you all for this precious present! And welcome to the<br class="">
next/this discussion topic again.<br class="">
<br class="">
<br class="">
Plamen<br class="">
<br class="">
____________________________________________________________<br class="">
<br class="">
<br class="">
On Thu, Mar 31, 2016 at 9:49 AM, Louis H Kauffman <<a href="mailto:loukau@gmail.com" class="">loukau@gmail.com</a>> wrote:<br class="">
<br class="">
> Dear Folks,<br class="">
> I will close with some comments about the relationship between recursive<br class="">
> distinctioning and replication in biology.<br class="">
> This will be another example of the sort of modeling excursion that one<br class="">
> can make by looking at patterns and analogies.<br class="">
> See<br class="">
> <a href="http://homepages.math.uic.edu/~kauffman/RD.html" rel="noreferrer" target="_blank" class="">homepages.math.uic.edu/~kauffman/RD.html</a><br class="">
><br class="">
> *RECURSIVE DISTINCTIONING This folder contains links to papers related to<br class="">
> Recursive Distinctioning. Recursive Distinctioning means just what it says.<br class="">
> A pattern of distinctions is given in a space based on a graphical<br class="">
> structure (such as a line of print or a planar lattice or given graph).<br class="">
> Each node of the graph is occupied by a letter from some arbitrary<br class="">
> alphabet. A specialized alphabet is given that can indicate distinctions<br class="">
> about neighbors of a given node. The neighbors of a node are all nodes that<br class="">
> are connected to the given node by edges in the graph. The letters in the<br class="">
> specialized alphabet (call it SA) are used to describe the states of the<br class="">
> letters in the given graph and at each stage in the recursion, letters in<br class="">
> SA are written at all nodes in the graph, describing its previous state.<br class="">
> The recursive structure that results from the iteration of descriptions is<br class="">
> called Recursive Distinctioning. Here is an example. We use a line graph<br class="">
> and represent it just as a finite row of letters. The Special Alphabet is<br class="">
> SA = { =, [, ], O} where "=" means that the letters to the left and to the<br class="">
> right are equal to the letter in the middle. Thus if we had AAA in the line<br class="">
> then the middle A would be replaced by =. The symbol "[" means that the<br class="">
> letter to the LEFT is different. Thus in ABB the middle letter would be<br class="">
> replaced by [. The symbol "]" means that the letter to the right is<br class="">
> different. And finally the symbol "O" means that the letters both to the<br class="">
> left and to the right are different. SA is a tiny language of elementary<br class="">
> letter-distinctions. Here is an example of this RD in operation where we<br class="">
> use the proverbial three dots to indicate a long string of letters in the<br class="">
> same pattern. For example,... AAAAAAAAAABAAAAAAAAAA ... is replaced by ...<br class="">
> =========]O[========= ... is replaced by ... ========]OOO[======== ... is<br class="">
> replaced by ... =======]O[=]O[======= ... . Note that the element ]O[<br class="">
> appears and it has replicated itself in a kind of mitosis. To see this in<br class="">
> more detail, here is a link to a page from a mathematica program written by<br class="">
> LK that uses a 'blank' or 'unmarked state' instead of the '=" sign. Program<br class="">
> and Output <<a href="https://dl.dropbox.com/u/11067256/RDL.pdf" rel="noreferrer" target="_blank" class="">https://dl.dropbox.com/u/11067256/RDL.pdf</a>>. Elementary RD<br class="">
> patterns are fundamental and will be found in many structures at all<br class="">
> levels. To see an cellular automaton example of this phenomenon, look at<br class="">
> the next link. Here we see a replicator in 'HighLife' a modification of<br class="">
> John Horton Conway's automaton 'Life'. The Highlife Replicator follows the<br class="">
> same pattern as our RD Replicator! We can begin to understand how the RD<br class="">
> Replicator works. This gives a foundation for understanding how the more<br class="">
> complex HighLife Replicator behaves in its context. HighLife Replicator.<br class="">
> <<a href="https://en.m.wikipedia.org/wiki/Highlife_(cellular_automaton)" rel="noreferrer" target="_blank" class="">https://en.m.wikipedia.org/wiki/Highlife_(cellular_automaton)</a>> Finally,<br class="">
> here is an excerpt from a paper by LK about replication in biology and the<br class="">
> role of RD. Excerpt.<br class="">
> <<a href="https://dl.dropbox.com/u/11067256/KauffmanExcerpt.pdf" rel="noreferrer" target="_blank" class="">https://dl.dropbox.com/u/11067256/KauffmanExcerpt.pdf</a>>*<br class="">
><br class="">
> *See RDLetter. <<a href="http://homepages.math.uic.edu/~kauffman/RDLetter.pdf" rel="noreferrer" target="_blank" class="">http://homepages.math.uic.edu/~kauffman/RDLetter.pdf</a>> This<br class="">
> is the Isaacson-Kauffman report on RD, summarized in a letter-to-the-editor<br class="">
> of JSP, Vol. 4, No. 1, Spring 2015, directly accessed on this server.*<br class="">
><br class="">
> *See Patent.<br class="">
> <<a href="https://dl.dropbox.com/u/11067256/JoelIsaacsonPatentDocument.pdf" rel="noreferrer" target="_blank" class="">https://dl.dropbox.com/u/11067256/JoelIsaacsonPatentDocument.pdf</a>>This is<br class="">
> Joel Isaacson's patent document for RD.*<br class="">
><br class="">
><br class="">
> *See Biological Replication.<br class="">
> <<a href="https://dl.dropbox.com/u/11067256/KauffmanJPBM1033.pdf" rel="noreferrer" target="_blank" class="">https://dl.dropbox.com/u/11067256/KauffmanJPBM1033.pdf</a>> This is a related<br class="">
> paper by Kauffman.You see above a very simple distinction making/using<br class="">
> automaton that produces a ?cell? ]O[ from an elementary distinction (of<br class="">
> B from the background of equal A?s),and that this cell then undergoes<br class="">
> mitosis. Then as an observer you must look again and note that the nothing<br class="">
> that happens in this automaton is local. The cell happensbecause of the<br class="">
> global structure of the one-dimensional automata space. The apparent<br class="">
> splitting from the inside of the cell is actually a consequence of the<br class="">
> global condition of the cell in the whole space. The entire evolution of<br class="">
> the process is a repeated articulation of the distinctions that are present<br class="">
> in the process. This isa new holistic modeling paradigm and we are<br class="">
> exploring with simple examples the extent to which it will apply to more<br class="">
> complex phenomena.A more extended paper by myself and Joel Isaacson will be<br class="">
> available soon.Best,Lou Kauffman*<br class="">
><br 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>><br class="">
> wrote:<br class="">
><br class="">
> Sorry but the dancing time is over... maybe tomorrow or on Friday Lou<br class="">
> could send some concluding comment, and next Monday Soeren would start the<br class="">
> new part. The present Q. discussion can surface again during the coming<br class="">
> session...<br class="">
> best--Pedro<br class="">
><br class="">
><br class="">
> El 30/03/2016 a las 1:06, Dr. Plamen L. Simeonov escribi?:<br class="">
><br class="">
> I think you are right, Lou, with respect to Deutsch who actually met<br class="">
> Everett III with the multiple universe hypothesis. The sole name<br class="">
> ?constructor theory? invoked associations beyond the quantum frame in me,<br class="">
> but he did not went that far. As for Josephson, I am not quite sure about<br class="">
> his notion. Brian remains firmly on the quantum level in the papers I<br class="">
> referred earlier, but he often returns to Ilexa Yarley?s ?circular theory?<br class="">
> which offers a much broader interpretation in my opinion. I expected your<br class="">
> mentioning of (the vibrations of) ?thought forms?, which are supposed to<br class="">
> invoke the emergence of word and action. I welcome your understanding for<br class="">
> the necessity of a deeper QM to make the links between actuality and the<br class="">
> bounded potentiality more comprehensive.<br class="">
><br class="">
> Best,<br class="">
><br class="">
> Plamen<br class="">
><br class="">
><br class="">
><br class="">
><br class="">
> On Wed, Mar 30, 2016 at 12:33 AM, Louis H Kauffman < <<a href="mailto:kauffman@uic.edu" class="">kauffman@uic.edu</a>><br class="">
> <a href="mailto:kauffman@uic.edu" class="">kauffman@uic.edu</a>> wrote:<br class="">
><br class="">
>> Josephson and Deutsh are not ?deeper than QM?. Deutsch for example is a<br class="">
>> very literal interpretation of QM that says that all the trajectories in<br class="">
>> the Feynman path sum are real, and they occur in parallel universes. This<br class="">
>> is a nice mathematical way to think, but it is not deeper than present QM!<br class="">
>> Energy is conserved, but ?particles? and indeed universes can be created<br class="">
>> from vacuum. If we want to go to discussion of ?holy spirit? then one<br class="">
>> should look at the structure of thought itself. For it is at the level of<br class="">
>> thought that every concept has a life behind it. Every idea is real and<br class="">
>> alive. Platonism asserts this directly in the belief in the existence of<br class="">
>> form and this form is a living form that we interact with and we are. How<br class="">
>> these notions are related to QM probably does await the emergence of a<br class="">
>> deeper QM.<br class="">
>><br class="">
>> On Mar 29, 2016, at 4:43 PM, Dr. Plamen L. Simeonov <<br class="">
>> <a href="mailto:plamen.l.simeonov@gmail.com" class="">plamen.l.simeonov@gmail.com</a>> wrote:<br class="">
>><br class="">
>><br class="">
>><br class="">
>> Thank you for your responses, Lou and Stan. I am aware about the details<br class="">
>> of the autopoietic model. What I was actually addressing by the transition<br class="">
>> from abiotic to biotic structures and the later emergence of RNA and DNA<br class="">
>> was this elusive aspect of ?mass action? which Stan mentioned, that in my<br class="">
>> opinion must have emerged out of the field of ?triggered (by resonance)<br class="">
>> potentialities which deeper theories than QM are trying to develop (cf.<br class="">
>> Josephson and Deutsch mentioned earlier). This enigmatic emergence of<br class="">
>> action out of nothing (vacuum or pure potentiality) naturally allows the<br class="">
>> (co-)existence of such heretic ideas as the immaterial ?Holy Spirit? or<br class="">
>> Hans Driesch?s vitalism, Jean Sharon?s eternal electron, or ?The Matrix of<br class="">
>> Matter and Life?at the sub-Planckian scale. How about this possible link to<br class="">
>> Platonism, theology, logic and algebra?<br class="">
>><br class="">
>> All the best,<br class="">
>><br class="">
>> Plamen<br class="">
>><br class="">
>> PS. I do not know why my notes appear twice on this list.<br class="">
>><br class="">
>><br class="">
>><br class="">
>> On Tue, Mar 29, 2016 at 10:55 PM, Louis H Kauffman < <<a href="mailto:kauffman@uic.edu" class="">kauffman@uic.edu</a>><br class="">
>> <a href="mailto:kauffman@uic.edu" class="">kauffman@uic.edu</a>> wrote:<br class="">
>><br class="">
>>> This is a reply to Plamen?s comment about autopoeisis. In their paper<br class="">
>>> Maturana,Uribe and Varela give a working model (computer model) for<br class="">
>>> autopoeisis.<br class="">
>>> It is very simple, consisting of a subtrate of nodal elements that tend<br class="">
>>> to bond when in proximity, and a collection of catalytic nodal elements<br class="">
>>> that promote bonding in their vicinity. The result of this dynamics is that<br class="">
>>> carapaces of linked nodal elements form around the catalytic elements and<br class="">
>>> these photo-cells tend to keep surviving the perturbations built into the<br class="">
>>> system. This model shows that cells can arise from a very simple dynmamic<br class="">
>>> geometric/topological substrate long before anything as sophisticated as<br class="">
>>> DNA has happened.<br class="">
>>><br class="">
>>> On Mar 29, 2016, at 2:54 PM, Stanley N Salthe < <<a href="mailto:ssalthe@binghamton.edu" class="">ssalthe@binghamton.edu</a>><br class="">
>>> <a href="mailto:ssalthe@binghamton.edu" class="">ssalthe@binghamton.edu</a>> wrote:<br class="">
>>><br class="">
>>> Plamen wrote:<br class="">
>>><br class="">
>>> I begin to believe that the transition from abiotic to biotic<br class="">
>>> structures, incl. Maturana-Varela.-Uribe?s autopoiesis may, really have<br class="">
>>> some underlying matrix/?skeleton?/?programme? which has nothing in common<br class="">
>>> with the nature of DNA, and that DNA and RNA as we know them today may<br class="">
>>> have emerged as secondary or even tertiary ?memory? of something underlying<br class="">
>>> deeper below the microbiological surface. It is at least worth thinking in<br class="">
>>> this direction. I do not mean necessarily the role of the number concept<br class="">
>>> and Platonic origin of the universe, but something probably much more<br class="">
>>> ?physical?<br class="">
>>><br class="">
>>><br class="">
>>><br class="">
>>> S: An interesting recently published effort along these lines is:<br class="">
>>><br class="">
>>> Alvaro Moreno and Matteo Mossio: Biological Autonomy: A Philosophical<br class="">
>>> and Theoretical Enquiry (History, Philosophy and Theory of the Life<br class="">
>>> Sciences 12) Springer<br class="">
>>><br class="">
>>> They seek a materialist understanding of biology as a system, attempting<br class="">
>>> to refer to the genetic system as little as possible.<br class="">
>>><br class="">
>>> I have until very recently attempted to evade/avoid mechanistic thinking<br class="">
>>> in regard to biology, but, on considering the origin of life generally<br class="">
>>> while keeping Howard Pattee's thinking in mind, I have been struck by the<br class="">
>>> notion that the origin of life (that is: WITH the genetic system) was the<br class="">
>>> origin of mechanism in the universe. Before that coding system, everything<br class="">
>>> was mass action. I think we still do not understand how this mechanism<br class="">
>>> evolved.<br class="">
>>><br class="">
>>> STAN<br class="">
>>><br class="">
>>> On Tue, Mar 29, 2016 at 7:40 AM, Dr. Plamen L. Simeonov <<br class="">
>>> <<a href="mailto:plamen.l.simeonov@gmail.com" class="">plamen.l.simeonov@gmail.com</a>><a href="mailto:plamen.l.simeonov@gmail.com" class="">plamen.l.simeonov@gmail.com</a>> wrote:<br class="">
>>><br class="">
>>>><br class="">
>>>> Dear Lou, Pedro and All,<br class="">
>>>><br class="">
>>>><br class="">
>>>><br class="">
>>>> I am going to present a few opportunistic ideas related to what was<br class="">
>>>> said before in this session. Coming back to Pivar?s speculative<br class="">
>>>> mechano-topological model of life excluding genetics I wish to turn your<br class="">
>>>> attention to another author with a similar idea but on a sound mathematical<br class="">
>>>> base, Davide Ambrosi with his resume at<br class="">
>>>> <a href="https://www.uni-muenster.de/imperia/md/content/cim/events/cim-mathmod-workshop-2015_abstracts.pdf" rel="noreferrer" target="_blank" class="">https://www.uni-muenster.de/imperia/md/content/cim/events/cim-mathmod-workshop-2015_abstracts.pdf</a><br class="">
>>>> :<br class="">
>>>><br class="">
>>>> ?Davide Ambrosi:<br class="">
>>>><br class="">
>>>> A role for mechanics in the growth, remodelling and morphogenesis of<br class="">
>>>> living systems In the XX Century the interactions between mechanics<br class="">
>>>> in biology were much biased by a bioengineering attitude: people were<br class="">
>>>> mainly interested in evaluating the state of stress that bones and<br class="">
>>>> tissues undergo in order to properly design prosthesis and devices.<br class="">
>>>> However in the last decades a new vision is emerging. "Mechano-biology" is<br class="">
>>>> changing the point of view, with respect to "Bio-mechanics", emphasizing<br class="">
>>>> the biological feedback. Cells, tissues and organs do not only deform when<br class="">
>>>> loaded: they reorganize, they duplicate, they actively produce dynamic<br class="">
>>>> patterns that apparently have multiple biological aims.<br class="">
>>>><br class="">
>>>> In this talk I will concentrate on two paradigmatic systems where the<br class="">
>>>> interplay between mechanics and biology is, in my opinion, particularly<br class="">
>>>> challenging: the homeostatic stress as a driver for remodeling of soft<br class="">
>>>> tissue and the tension as a mechanism to transmit information about the<br class="">
>>>> size of organs during morphogenesis. In both cases it seems that mechanics<br class="">
>>>> plays a role which at least accompanies and enforces the biochemical<br class="">
>>>> signaling.?<br class="">
>>>><br class="">
>>>><br class="">
>>>><br class="">
>>>> Some more details about this approach can be found here:<br class="">
>>>><br class="">
>>>> <a href="http://rsta.royalsocietypublishing.org/content/367/1902/3335" rel="noreferrer" target="_blank" class="">http://rsta.royalsocietypublishing.org/content/367/1902/3335</a><br class="">
>>>><br class="">
>>>> <a href="http://biomechanics.stanford.edu/paper/MFOreport.pdf" rel="noreferrer" target="_blank" class="">http://biomechanics.stanford.edu/paper/MFOreport.pdf</a><br class="">
>>>><br class="">
>>>> In other words, for the core information theorists in FIS, the question<br class="">
>>>> is: is there really only (epi)genetic evolution communication in living<br class="">
>>>> organisms. Stan Salthe and Lou Kauffman already provided some answers. I<br class="">
>>>> begin to believe that the transition from abiotic to biotic structures,<br class="">
>>>> incl. Maturana-Varela.-Uribe?s autopoiesis may, really have some underlying<br class="">
>>>> matrix/?skeleton?/?programme? which has nothing in common with the nature<br class="">
>>>> of DNA, and that DNA and RNA as we know them today<br class="">
>>>><br class="">
>>>> <<a href="http://www.sciencedirect.com/science/article/pii/S0022519314006778" rel="noreferrer" target="_blank" class="">http://www.sciencedirect.com/science/article/pii/S0022519314006778</a>><br class="">
>>>> <a href="http://www.sciencedirect.com/science/article/pii/S0022519314006778" rel="noreferrer" target="_blank" class="">http://www.sciencedirect.com/science/article/pii/S0022519314006778</a><br class="">
>>>><br class="">
>>>> <<a href="http://www.sciencedirect.com/science/article/pii/S0022519316001260" rel="noreferrer" target="_blank" class="">http://www.sciencedirect.com/science/article/pii/S0022519316001260</a>><br class="">
>>>> <a href="http://www.sciencedirect.com/science/article/pii/S0022519316001260" rel="noreferrer" target="_blank" class="">http://www.sciencedirect.com/science/article/pii/S0022519316001260</a><br class="">
>>>><br class="">
>>>> <<a href="https://www.sciencedaily.com/releases/2015/01/150107101405.htm" rel="noreferrer" target="_blank" class="">https://www.sciencedaily.com/releases/2015/01/150107101405.htm</a>><br class="">
>>>> <a href="https://www.sciencedaily.com/releases/2015/01/150107101405.htm" rel="noreferrer" target="_blank" class="">https://www.sciencedaily.com/releases/2015/01/150107101405.htm</a><br class="">
>>>><br class="">
>>>> may have emerged as secondary or even tertiary ?memory? of something<br class="">
>>>> underlying deeper below the microbiological surface. It is at least worth<br class="">
>>>> thinking in this direction. I do not mean necessarily the role of the<br class="">
>>>> number concept and Platonic origin of the universe, but something probably<br class="">
>>>> much more ?physical? or at least staying at the edge between<br class="">
>>>> physical/material and immaterial such as David Deutsch?s constructor theory<br class="">
>>>> ( <<a href="http://constructortheory.org/" rel="noreferrer" target="_blank" class="">http://constructortheory.org/</a>><a href="http://constructortheory.org/" rel="noreferrer" target="_blank" class="">http://constructortheory.org/</a>) and<br class="">
>>>> Brian Josephson?s ?structural/circular theory? (<br class="">
>>>> <<a href="http://arxiv.org/ftp/arxiv/papers/1502/1502.02429.pdf" rel="noreferrer" target="_blank" class="">http://arxiv.org/ftp/arxiv/papers/1502/1502.02429.pdf</a>><br class="">
>>>> <a href="http://arxiv.org/ftp/arxiv/papers/1502/1502.02429.pdf" rel="noreferrer" target="_blank" class="">http://arxiv.org/ftp/arxiv/papers/1502/1502.02429.pdf</a>;<br class="">
>>>> <<a href="http://arxiv.org/ftp/arxiv/papers/1506/1506.06774.pdf" rel="noreferrer" target="_blank" class="">http://arxiv.org/ftp/arxiv/papers/1506/1506.06774.pdf</a>><br class="">
>>>> <a href="http://arxiv.org/ftp/arxiv/papers/1506/1506.06774.pdf" rel="noreferrer" target="_blank" class="">http://arxiv.org/ftp/arxiv/papers/1506/1506.06774.pdf</a>;<br class="">
>>>> <<a href="http://arxiv.org/pdf/1108.4860.pdf" rel="noreferrer" target="_blank" class="">http://arxiv.org/pdf/1108.4860.pdf</a>><a href="http://arxiv.org/pdf/1108.4860.pdf" rel="noreferrer" target="_blank" class="">http://arxiv.org/pdf/1108.4860.pdf</a>)<br class="">
>>>> searching for the theories underpinning the foundations of the physical<br class="">
>>>> laws (and following Wheeler?s definition for a ?Law without Law?.<br class="">
>>>><br class="">
>>>> Some of you may say that QT and Gravitation Theory are responsible for<br class="">
>>>> such kind of strange effects, but I would rather leave the brackets open,<br class="">
>>>> because the recent discussion about potentialities and actualities in QM<br class="">
>>>> brings up the idea that there are still different ways of looking at those<br class="">
>>>> concepts (although they are strictly defined in their core domains). This<br class="">
>>>> was actually also the lesson from the last special issue on integral<br class="">
>>>> biomathics (2015) dedicated to phenomenology, with the different opinions<br class="">
>>>> of scientists and philosophers on obviously clear matters in their domains.<br class="">
>>>> This is why also the question of what we define as science needs to be<br class="">
>>>> probably revised in future to include also such issues that are ?felt?<br class="">
>>>> rather than ?reasoned?, even if we do not have the ?proofs? yet, because<br class="">
>>>> the proofs also emerge as subjective (or perhaps ?suggested?! ? ask the<br class="">
>>>> psychologists for that aspect) thoughts in the minds of the mathematicians.<br class="">
>>>> I am really glad that we began such a phenomenological discussion on this<br class="">
>>>> aspect such as Hipolito?s paper (<br class="">
>>>> <<a href="http://www.sciencedirect.com/science/article/pii/S0079610715000899" rel="noreferrer" target="_blank" class="">http://www.sciencedirect.com/science/article/pii/S0079610715000899</a>><br class="">
>>>> <a href="http://www.sciencedirect.com/science/article/pii/S0079610715000899" rel="noreferrer" target="_blank" class="">http://www.sciencedirect.com/science/article/pii/S0079610715000899</a>)<br class="">
>>>> that was widely commented in the reviewer?s circle. In many cases when we<br class="">
>>>> have a ?fuzzy? intuition about a certain relationship or analogy we miss<br class="">
>>>> the correct definitions and concepts, and so in a creative act to hold down<br class="">
>>>> the flying thought we move to using examples, metaphors, pictures. Pedro<br class="">
>>>> correctly addressed the explanatory problem of science which presupposes a<br class="">
>>>> certain causative and predicative ?workflow? to derive a conclusion from<br class="">
>>>> the facts, and this is the way in which also proofs are (selectively) made.<br class="">
>>>> As a young scholar I often wondered how artificially people like Gauss,<br class="">
>>>> Cauchy and Weierstrass design their proofs, but then I got used to<br class="">
>>>> that style. I am thankful to Lou for his response on my question about<br class="">
>>>> using adequate ?resonant? methods to model developmental biology, because<br class="">
>>>> this is also an important aspect of the biology (and physics as well)<br class="">
>>>> including the phenomenological/first-person view of an<br class="">
>>>> ?observer-participant? (to use Vrobel?s term) which is crucial for<br class="">
>>>> understanding the process of self-reflection/recursion/cycle in science,<br class="">
>>>> which is usually led by what?: the intuition, also well recognized by such<br class="">
>>>> giants like Poincare and Einstein. Isn?t not ?resonance? in the core of<br class="">
>>>> detecting such vibration between the observer and the observed? Because<br class="">
>>>> logic, back trace, prove come later.<br class="">
>>>><br class="">
>>>> And finally, when looking at the clear simple mathematical abstractions<br class="">
>>>> of numbers, vectors, directions, sets, algebras, geometries, etc. used by<br class="">
>>>> many without scrutinizing when developing system (biological) models of yet<br class="">
>>>> another kind of mechanics/automation/machinery of the physical reality, I<br class="">
>>>> am asking myself which are the premises for using such tools to describe a<br class="">
>>>> model: the parameters, or the idea behind? It is probably not a commonly<br class="">
>>>> known fact (even for those who are engaged with such exciting disciplines<br class="">
>>>> as algebraic geometry and geometrical algebra, now considered to be very<br class="">
>>>> close to what we wish to express in biology) that William Hamilton, the<br class="">
>>>> inventor of the quaternions did not simply use the already known concept of<br class="">
>>>> ?vector? in his method. Instead he used ?step? with ?direction? to express<br class="">
>>>> a duration of time (or ?duree? as Husserl called it from the other side of<br class="">
>>>> the phenomenological divide) and action (to move from A to B): two very<br class="">
>>>> biology-related concepts at that time (although they may be considered as<br class="">
>>>> physical or computational today). He actually stated that if there is<br class="">
>>>> geometry as a pure science of space, then algebra must be the pure science<br class="">
>>>> of time [1]. What did we actually gain for biology from merging space and<br class="">
>>>> time in physics?<br class="">
>>>><br class="">
>>>> Reference:<br class="">
>>>><br class="">
>>>> [1] W. R. Hamilton, 1835. Theory of Conjugate Functions, or Algebraic<br class="">
>>>> Couples; with a Preliminary or Elementary Essay on Algebra as the Science<br class="">
>>>> of Pure Time. *Trans. Royal Irish Acad*., Vol. XVII, Part II. 292-422.<br class="">
>>>><br class="">
>>>><br class="">
>>>> Best,<br class="">
>>>><br class="">
>>>><br class="">
>>>> Plamen<br class="">
>>>><br class="">
>>>><br class="">
>>>> I have a few provoking notes related to what was said before in this<br class="">
>>>> session. Coming back to Pivar?s speculative mechano-topological model of<br class="">
>>>> life excluding genetics I wish to turn your attention to another author<br class="">
>>>> with a similar idea but on a sound mathematical base, Davide Ambrosi with<br class="">
>>>> his resume at<br class="">
>>>> <a href="https://www.uni-muenster.de/imperia/md/content/cim/events/cim-mathmod-workshop-2015_abstracts.pdf" rel="noreferrer" target="_blank" class="">https://www.uni-muenster.de/imperia/md/content/cim/events/cim-mathmod-workshop-2015_abstracts.pdf</a><br class="">
>>>> :<br class="">
>>>><br class="">
>>>> ?Davide Ambrosi:<br class="">
>>>><br class="">
>>>> A role for mechanics in the growth, remodelling and morphogenesis of<br class="">
>>>> living systems In the XX Century the interactions between mechanics<br class="">
>>>> in biology were much biased by a bioengineering attitude: people were<br class="">
>>>> mainly interested in evaluating the state of stress that bones and<br class="">
>>>> tissues undergo in order to properly design prosthesis and devices.<br class="">
>>>> However in the last decades a new vision is emerging. "Mechano-biology" is<br class="">
>>>> changing the point of view, with respect to "Bio-mechanics", emphasizing<br class="">
>>>> the biological feedback. Cells, tissues and organs do not only deform when<br class="">
>>>> loaded: they reorganize, they duplicate, they actively produce dynamic<br class="">
>>>> patterns that apparently have multiple biological aims.<br class="">
>>>><br class="">
>>>> In this talk I will concentrate on two paradigmatic systems where the<br class="">
>>>> interplay between mechanics and biology is, in my opinion, particularly<br class="">
>>>> challenging: the homeostatic stress as a driver for remodeling of soft<br class="">
>>>> tissue and the tension as a mechanism to transmit information about the<br class="">
>>>> size of organs during morphogenesis. In both cases it seems that mechanics<br class="">
>>>> plays a role which at least accompanies and enforces the biochemical<br class="">
>>>> signaling.?<br class="">
>>>><br class="">
>>>><br class="">
>>>><br class="">
>>>> Some more details about this approach can be found here:<br class="">
>>>><br class="">
>>>> <a href="http://rsta.royalsocietypublishing.org/content/367/1902/3335" rel="noreferrer" target="_blank" class="">http://rsta.royalsocietypublishing.org/content/367/1902/3335</a><br class="">
>>>><br class="">
>>>> <a href="http://biomechanics.stanford.edu/paper/MFOreport.pdf" rel="noreferrer" target="_blank" class="">http://biomechanics.stanford.edu/paper/MFOreport.pdf</a><br class="">
>>>><br class="">
>>>> In other words, for the core information theorists in FIS, the question<br class="">
>>>> is: is there really only (epi)genetic evolution communication in living<br class="">
>>>> organisms. Stan Salthe and Lou Kauffman already provided some answers. I<br class="">
>>>> begin to believe that the transition from abiotic to biotic structures,<br class="">
>>>> incl. Maturana-Varela.-Uribe?s autopoiesis may, really have some underlying<br class="">
>>>> matrix/?skeleton?/?programme? which has nothing in common with the nature<br class="">
>>>> of DNA, and that DNA and RNA as we know them today<br class="">
>>>><br class="">
>>>> <<a href="http://www.sciencedirect.com/science/article/pii/S0022519314006778" rel="noreferrer" target="_blank" class="">http://www.sciencedirect.com/science/article/pii/S0022519314006778</a>><br class="">
>>>> <a href="http://www.sciencedirect.com/science/article/pii/S0022519314006778" rel="noreferrer" target="_blank" class="">http://www.sciencedirect.com/science/article/pii/S0022519314006778</a><br class="">
>>>><br class="">
>>>> <<a href="http://www.sciencedirect.com/science/article/pii/S0022519316001260" rel="noreferrer" target="_blank" class="">http://www.sciencedirect.com/science/article/pii/S0022519316001260</a>><br class="">
>>>> <a href="http://www.sciencedirect.com/science/article/pii/S0022519316001260" rel="noreferrer" target="_blank" class="">http://www.sciencedirect.com/science/article/pii/S0022519316001260</a><br class="">
>>>><br class="">
>>>> <<a href="https://www.sciencedaily.com/releases/2015/01/150107101405.htm" rel="noreferrer" target="_blank" class="">https://www.sciencedaily.com/releases/2015/01/150107101405.htm</a>><br class="">
>>>> <a href="https://www.sciencedaily.com/releases/2015/01/150107101405.htm" rel="noreferrer" target="_blank" class="">https://www.sciencedaily.com/releases/2015/01/150107101405.htm</a><br class="">
>>>><br class="">
>>>> may have emerged as secondary or even tertiary ?memory? of something<br class="">
>>>> underlying deeper below the microbiological surface. It is at least worth<br class="">
>>>> thinking in this direction. I do not mean necessarily the role of the<br class="">
>>>> number concept and Platonic origin of the universe, but something probably<br class="">
>>>> much more ?physical? or at least staying at the edge between<br class="">
>>>> physical/material and immaterial such as David Deutsch?s constructor theory<br class="">
>>>> ( <<a href="http://constructortheory.org/" rel="noreferrer" target="_blank" class="">http://constructortheory.org/</a>><a href="http://constructortheory.org/" rel="noreferrer" target="_blank" class="">http://constructortheory.org/</a>) and<br class="">
>>>> Brian Josephson?s ?structural/circular theory? (<br class="">
>>>> <<a href="http://arxiv.org/ftp/arxiv/papers/1502/1502.02429.pdf" rel="noreferrer" target="_blank" class="">http://arxiv.org/ftp/arxiv/papers/1502/1502.02429.pdf</a>><br class="">
>>>> <a href="http://arxiv.org/ftp/arxiv/papers/1502/1502.02429.pdf" rel="noreferrer" target="_blank" class="">http://arxiv.org/ftp/arxiv/papers/1502/1502.02429.pdf</a>;<br class="">
>>>> <<a href="http://arxiv.org/ftp/arxiv/papers/1506/1506.06774.pdf" rel="noreferrer" target="_blank" class="">http://arxiv.org/ftp/arxiv/papers/1506/1506.06774.pdf</a>><br class="">
>>>> <a href="http://arxiv.org/ftp/arxiv/papers/1506/1506.06774.pdf" rel="noreferrer" target="_blank" class="">http://arxiv.org/ftp/arxiv/papers/1506/1506.06774.pdf</a>;<br class="">
>>>> <<a href="http://arxiv.org/pdf/1108.4860.pdf" rel="noreferrer" target="_blank" class="">http://arxiv.org/pdf/1108.4860.pdf</a>><a href="http://arxiv.org/pdf/1108.4860.pdf" rel="noreferrer" target="_blank" class="">http://arxiv.org/pdf/1108.4860.pdf</a>)<br class="">
>>>> searching for the theories underpinning the foundations of the physical<br class="">
>>>> laws (and following Wheeler?s definition for a ?Law without Law?.<br class="">
>>>><br class="">
>>>> Some of you may say that QT and Gravitation Theory are responsible for<br class="">
>>>> such kind of strange effects, but I would rather leave the brackets open,<br class="">
>>>> because the recent discussion about potentialities and actualities in QM<br class="">
>>>> brings up the idea that there are still different ways of looking at those<br class="">
>>>> concepts (although they are strictly defined in their core domains). This<br class="">
>>>> was actually also the lesson from the last special issue on integral<br class="">
>>>> biomathics (2015) dedicated to phenomenology,<br class="">
>>>><br class="">
>>> ...<br class="">
><br class="">
> [Message clipped]<br class="">
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