Dear Dr Plamen I find many common themes in your work and my approach to the foundational questions of physics mathematics and biology. I find integral biomaths approach very appealing and it fits very well with my understanding from quantum field theory approach to quantum matter. I would like to know about the biologists who use Grassmann algebra. As regards your criticism about the quantum approach to biology my reply is that quantum theory shares the categorical structure with biology. In other words to see how quantum theory is related to biology we must realize that both quantum theory and biology have category theoretical formulations and hence both share the similar algebraic structures and hence the underlying philosophy is Whiteheadean process philosophy which has been discussed by authors like Henry Stapp. I emphasize that one fundamental difference between classical mechanics and quantum mechanics is that the latter has scope of accommodating life and mind which is because of the reason that logical foundations of quantum theory are entirely different. I resonate here with Robert Rosen who has worked out the logic of biology and I find striking similarities between his work and quantum theory. So it opens up a field of research where we need to use category theory to bring biology under the umbrella of quantum theory. I invite all those interested in this endeavor to join the hands!
PLease refer me to the works about Grassmann algebra in biology. Rukhsan On Fri, Apr 1, 2016 at 7:41 PM, <fis-requ...@listas.unizar.es> wrote: > Send Fis mailing list submissions to > fis@listas.unizar.es > > To subscribe or unsubscribe via the World Wide Web, visit > http://listas.unizar.es/cgi-bin/mailman/listinfo/fis > or, via email, send a message with subject or body 'help' to > fis-requ...@listas.unizar.es > > You can reach the person managing the list at > fis-ow...@listas.unizar.es > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Fis digest..." > > > Today's Topics: > > 1. _ Re: Postface on math: Fis Digest, Vol 24, Issue 46 > (Dr. Plamen L. Simeonov) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 1 Apr 2016 16:11:03 +0200 > From: "Dr. Plamen L. Simeonov" <plamen.l.simeo...@gmail.com> > To: Rukhsanulhaq <rukhsanul...@gmail.com> > Cc: fis <fis@listas.unizar.es>, Louis H Kauffman <lou...@gmail.com> > Subject: [Fis] _ Re: Postface on math: Fis Digest, Vol 24, Issue 46 > Message-ID: > < > cambikj76uvslwukykgjkemljc1kbm-+aq50_lvnmoo7k5zi...@mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Dear All, > > I was about to close this chapter on math following Pedro's announcement of > Soeren's theme to start this weekend, when I discovered these two messages > by Rukhsan Ulhaq on QM. > > Relating this to recursion and what Pedro said in his final note on Lou's > exposition, I'd like to refer to an older book by S. C. Kleene and R. S. > Vesley entitled: "The Foundations of Intuitionistic Mathematics: Especially > in Relation to Recursive Functions". It has impressed me once with its rich > and powerful way of relating *Brouwer's inuitionistic theory of > mathematics* > (known for rejecting classical Aristotelian logic) to *recursive > functions*. > This is just as an idea where the way in modern constructive biomathematics > could go again. An exciting survey on this aspect of developing mathematics > was given by Fernando Zalamea (who also contributed to the 2015 special > issue) in his 2012 book ?Synthetic Philosophy of Contemporary > Mathematics?, commented > by Longo > < > http://www.di.ens.fr/users/longo/files/PhilosophyAndCognition/Review-Zalamea-Grothendieck.pdf > >. > I liked Rukhsan's reference to Grassman's algebra in QM, which was already > suggested for use in biology by some colleagues (perhaps with the same > motivation). And I relate this again in the associative way that Robert > Rosen would do to my earlier comment on Hamilton's distinction between > algebra and geometry as the abstractions for the space and time continuums > with the note by Gebser I used in my contribution to the special issue, > that from the phenomenological perspective time is not a di-mention but an > a-mension, i.e. it cannot be measurable in the way we do with the 3 spatial > dimensions. And this is where the major conflict between modern natural > scientists represented by Einstein and phenomenological philosophers, > represented by Bergson, begins. We still do not have a solution of these > two viewpoints and only began understanding each other after multiple > recursive revisions of the 500+ pages contributions. > > > Therefore, when picking up QM as a challenging paradoxal continuum which > demands adequate mathematical formalisms, in particular in the context of > biology, a few questions arise in my mind. > > Do we necessarily need a known mathematical technique for addressing some > problem it was not developed for? We know that physicists are very skilled > in developing their theories as pure new mathematics; take M-theory for > instance. Why should biologists follow them? Do we need "classical" QM to > answer biological questions? > > I think that we are mixing some very important aspects of living (incl. > time's passing) by considering them measurable and computable in the usual > sense. Rukhsan's question wether the quantum prioperties of matter do > emerge from geometry needs a better formulation, because in its present > version it is close to the contradicting and mistaken relation between > potentiality and actuality discussed earlier by Lou and Bruno. > > In the course of this discussion we realised that we do not necessarily > need genetics (a later developed memorization mechanism in evolution) to > understad the emergence of biological forms. Why should be QM (as we know > it today) the common denominator to understanding life, aside form the fact > that Schr?dinger and others who followed him felt attracted to its unsolved > puzzles? I believe that there is more in perpetuating life that has not > been captured by QM yet. To capture this, it needs to be developed further. > > I do agree with both Lou and Rukhsan that geometry and algebra will be > crucial in understanding the phenomena of life, but we also need to develop > new mathematical thinking with respect to biology, just as Grassman, > Brouwer and Grothendieck did for their domains. > We may be able to use their approaches. But we will be strongly advised to > always strive going beyond what we know at present. > That Lou is using recursive functions and Spencer-Brown's "Laws" > http://homepages.math.uic.edu/~kauffman/Laws.pdf > is a fairly enlightening. > > All the best. > > Plamen > > ____________________________________________________________ > > > On Thu, Mar 31, 2016 at 8:04 PM, Rukhsanulhaq <rukhsanul...@gmail.com> > wrote: > > > Dear All > > As Prof Kauffman has pointed out that there are many mysteries in quantum > > theory which need to be decoded. The measurement problem being the > central > > one. And I agree with Prof Kauffman that taking the eigenvalue aspect of > > quantum theory seriously and relating to Lambda calculus can help us to > > understand its deeper aspects. > > However I would like to point to yet another related aspect. Spin is > > called essentially quantum mechanical property which has no classical > > analogue. Yet when one does construct the formalism to treat spin we just > > use SU(2) group which provides the double cover for SO((3) group and all > of > > it was known before quantum theory as well. Similarly fermions are also > > very quantum objects but their algebra was once again developed by > > Grassmann in an entirely different context. It begs the question how does > > the Grassmann algebra which was developed to understand geometry is > exactly > > the same for building blocks of matter. Is somehow quantum > > properties of matter coming from geometry. You will be surprised that in > > recent developments in quantum theory(Berry phases) it has been found > that > > important physical properties of matter are related to geometry and > > topology of space of quantum states. > > So all of it suggests that we have a long way to go before we resolve the > > paradoxes of quantum theory. Geometry and topology are going to be beacon > > lights in this endeavor. I am not forgetting algebra and logic which are > > already there in the quantum theory itself,Heisenberg commutation > relations > > are algebraic and logical expressions of underlying quantum world. > > > > Rukhsan > > > > On Thu, Mar 31, 2016 at 6:28 PM, <fis-requ...@listas.unizar.es> wrote: > > > >> Send Fis mailing list submissions to > >> fis@listas.unizar.es > >> > >> To subscribe or unsubscribe via the World Wide Web, visit > >> http://listas.unizar.es/cgi-bin/mailman/listinfo/fis > >> or, via email, send a message with subject or body 'help' to > >> fis-requ...@listas.unizar.es > >> > >> You can reach the person managing the list at > >> fis-ow...@listas.unizar.es > >> > >> When replying, please edit your Subject line so it is more specific > >> than "Re: Contents of Fis digest..." > >> > >> > >> Today's Topics: > >> > >> 1. _ Re: Fis Digest, Vol 24, Issue 45 (Rukhsanulhaq) > >> > >> > >> ---------------------------------------------------------------------- > >> > >> Message: 1 > >> Date: Thu, 31 Mar 2016 18:28:28 +0530 > >> From: Rukhsanulhaq <rukhsanul...@gmail.com> > >> To: fis@listas.unizar.es > >> Subject: [Fis] _ Re: Fis Digest, Vol 24, Issue 45 > >> Message-ID: > >> <CAA-SiodrpjfDfijOLcg7pG_TX6pBg= > >> ytdthu3qchyef2lw1...@mail.gmail.com> > >> Content-Type: text/plain; charset="utf-8" > >> > >> Dear all,thank you very much for very interesting and insightful > >> discussions. > >> I have been following them very keenly. Though the discussions have come > >> to "new beginning" rather than to an end as Dr Plamen has rightly put > >> it.,I > >> want to > >> add here couple of comments about quantum mechanics and biology. > >> Prof Kauffman has expressed the need for the deeper quantum mechanics > >> which > >> surely must be due to the limited scope which present formulations and > >> interpretations > >> provide. However I would say that quantum theory is full fledged > paradigm > >> which > >> has yet to be understood fully even after more than century after its > >> inception by Planck. > >> Quantum theory keeps on throwing surprises as we delve deeper into it. > >> However the fact > >> that quantum theory will provide a framework to understand biological > >> phenomena was realized > >> early on by one of the pioneers of the theory,Erwin Schroedinger and he > >> went on to write a famous book > >> about it where concepts like "quantum jump" were used to understand > >> discrete and probabilistic nature > >> of genetic phenomena. In recent times many authors have tried to look > >> deeper into the relation between > >> quantum theory and biology and have dubbed this subject as "quantum > >> biology". > >> There is a lot of work that needs to be done to understand various > >> aspects of quantum theory > >> in more mathematically and philosophically transparent way. My approach > to > >> the foundations is based > >> on Clifford algebras which are also central theme of other approaches > like > >> those of Bohm and Hiley,Penrose > >> via twistors,Kauffman's via iterants, Finkelestein via quantum sets and > >> quantum logic,Hesten's via geometric algebra. > >> I am very hopeful that this approach will uncover the depths of quantum > >> theory and will give us a very transport > >> formulation and interpretation of this "jewel of physics". > >> Rukhsan > >> Thank you very much > >> > >> On Thu, Mar 31, 2016 at 4:45 PM, <fis-requ...@listas.unizar.es> wrote: > >> > >> > Send Fis mailing list submissions to > >> > fis@listas.unizar.es > >> > > >> > To subscribe or unsubscribe via the World Wide Web, visit > >> > http://listas.unizar.es/cgi-bin/mailman/listinfo/fis > >> > or, via email, send a message with subject or body 'help' to > >> > fis-requ...@listas.unizar.es > >> > > >> > You can reach the person managing the list at > >> > fis-ow...@listas.unizar.es > >> > > >> > When replying, please edit your Subject line so it is more specific > >> > than "Re: Contents of Fis digest..." > >> > > >> > > >> > Today's Topics: > >> > > >> > 1. Re: concluding by beginning (Dr. Plamen L. Simeonov) > >> > > >> > > >> > ---------------------------------------------------------------------- > >> > > >> > Message: 1 > >> > Date: Thu, 31 Mar 2016 13:14:45 +0200 > >> > From: "Dr. Plamen L. Simeonov" <plamen.l.simeo...@gmail.com> > >> > To: Louis H Kauffman <lou...@gmail.com> > >> > Cc: fis <fis@listas.unizar.es>, Joel Isaacson <isaacs...@hotmail.com> > >> > Subject: Re: [Fis] concluding by beginning > >> > Message-ID: > >> > < > >> > cambikj5o_c1otwjkxytvdi_q1wks_+fjz4-ffeq5ba22ine...@mail.gmail.com> > >> > Content-Type: text/plain; charset="utf-8" > >> > > >> > Dear FIS Fellows, > >> > > >> > I was also about writing some concluding remarks, since our time for > >> math > >> > in bio is about to end this week, but realized that Lou was fast with > an > >> > excellent final comment and list of references for postprocessing. I > am > >> > happy that after some initial hesitation on the forum the key messages > >> came > >> > accross and we were able to cover within short time the broad span of > >> views > >> > within short time. You are very welcome to continue the discussion > also > >> > privately and of course, within the scope of the next themes to come: > >> > bio/cybersemiotics with Soeren Brier and physics with Alex Hankey, > which > >> > were nicely introduced by some earlier comments and associations like > >> Bob's > >> > triad from his inspiring book "The Third Window" which I see related > to > >> > C.S. Pierce's initiations in math, philosophy and semiotics. It became > >> > clear that such important issues as circularity and > >> recursion/repetition in > >> > biology are closely related to distiction, (autocatalytic re)action, > >> > memory, (negative) feedback, automation, self-organization, autocells > on > >> > the one side and (prime) numbers, fractional calculus, > >> > triangular/quadrangular/polihedral structures, (Riemann) wave function > >> > (analysis), QM and fractal geometry on the other, with opening room > for > >> > covering even more phenomenology and creating ideas along the multiple > >> > lines of causation up to the limits of thought and imagination, nicely > >> > reflected by the participants in the discussion. So I have no other > >> chance > >> > but to say: that's real life in a nutshell of exchanged messages! The > >> most > >> > astonishing characteristic of this communication which comes to end, > but > >> > just began in my eyes, is that we succeed to build together something > >> that > >> > is capabloe to not only link remote and sometimes obscure and absurd > >> ideas > >> > and question, but also attribute, enfold and evolve them with what we > >> call > >> > a trace of information, an ontology of a creative development process > we > >> > are participating, as if life becomes that what we really discover, > >> revolve > >> > and impress just in time: in Alex's words "a living from that e can > >> > interact with, and (which) we are". And this is recursively wraped > again > >> > within Francesco's phrase: "la conoscenca ha fondamenti biologici ... > e > >> > viceversa, la biologia ha fondamenti quantistici". How could I say > this > >> in > >> > Latin? Thank you all for this precious present! And welcome to the > >> > next/this discussion topic again. > >> > > >> > > >> > Plamen > >> > > >> > ____________________________________________________________ > >> > > >> > > >> > On Thu, Mar 31, 2016 at 9:49 AM, Louis H Kauffman <lou...@gmail.com> > >> > wrote: > >> > > >> > > Dear Folks, > >> > > I will close with some comments about the relationship between > >> recursive > >> > > distinctioning and replication in biology. > >> > > This will be another example of the sort of modeling excursion that > >> one > >> > > can make by looking at patterns and analogies. > >> > > See > >> > > homepages.math.uic.edu/~kauffman/RD.html > >> > > > >> > > *RECURSIVE DISTINCTIONING 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,... AAAAAAAAAABAAAAAAAAAA ... is replaced > by > >> > ... > >> > > =========]O[========= ... is replaced by ... ========]OOO[======== > >> ... is > >> > > replaced by ... =======]O[=]O[======= ... . 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. > >> > Program > >> > > and Output <https://dl.dropbox.com/u/11067256/RDL.pdf>. 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. HighLife > >> Replicator. > >> > > <https://en.m.wikipedia.org/wiki/Highlife_(cellular_automaton)> > >> Finally, > >> > > here is an excerpt from a paper by LK about replication in biology > and > >> > the > >> > > role of RD. Excerpt. > >> > > <https://dl.dropbox.com/u/11067256/KauffmanExcerpt.pdf>* > >> > > > >> > > *See RDLetter. < > http://homepages.math.uic.edu/~kauffman/RDLetter.pdf> > >> > 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.* > >> > > > >> > > *See Patent. > >> > > <https://dl.dropbox.com/u/11067256/JoelIsaacsonPatentDocument.pdf > >> >This > >> > is > >> > > Joel Isaacson's patent document for RD.* > >> > > > >> > > > >> > > *See Biological Replication. > >> > > <https://dl.dropbox.com/u/11067256/KauffmanJPBM1033.pdf> This is a > >> > related > >> > > paper by Kauffman.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),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 happensbecause 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 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 isa new holistic modeling paradigm and we are > >> > > exploring with simple examples the extent to which it will apply to > >> more > >> > > complex phenomena.A more extended paper by myself and Joel Isaacson > >> will > >> > be > >> > > available soon.Best,Lou Kauffman* > >> > > > >> > > On Mar 30, 2016, at 7:18 AM, Pedro C. Marijuan < > >> > pcmarijuan.i...@aragon.es> > >> > > wrote: > >> > > > >> > > 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... > >> > > best--Pedro > >> > > > >> > > > >> > > El 30/03/2016 a las 1:06, Dr. Plamen L. Simeonov escribi?: > >> > > > >> > > 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. > >> > > > >> > > Best, > >> > > > >> > > Plamen > >> > > > >> > > > >> > > > >> > > > >> > > On Wed, Mar 30, 2016 at 12:33 AM, Louis H Kauffman < < > >> kauff...@uic.edu> > >> > > kauff...@uic.edu> wrote: > >> > > > >> > >> 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! > >> > >> 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. > >> > >> > >> > >> On Mar 29, 2016, at 4:43 PM, Dr. Plamen L. Simeonov < > >> > >> plamen.l.simeo...@gmail.com> wrote: > >> > >> > >> > >> > >> > >> > >> > >> 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? > >> > >> > >> > >> All the best, > >> > >> > >> > >> Plamen > >> > >> > >> > >> PS. I do not know why my notes appear twice on this list. > >> > >> > >> > >> > >> > >> > >> > >> On Tue, Mar 29, 2016 at 10:55 PM, Louis H Kauffman < < > >> kauff...@uic.edu> > >> > >> kauff...@uic.edu> wrote: > >> > >> > >> > >>> 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. > >> > >>> 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. > >> > >>> > >> > >>> On Mar 29, 2016, at 2:54 PM, Stanley N Salthe < < > >> > ssal...@binghamton.edu> > >> > >>> ssal...@binghamton.edu> wrote: > >> > >>> > >> > >>> Plamen wrote: > >> > >>> > >> > >>> 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 > >> 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? > >> > >>> > >> > >>> > >> > >>> > >> > >>> S: An interesting recently published effort along these lines is: > >> > >>> > >> > >>> Alvaro Moreno and Matteo Mossio: Biological Autonomy: A > >> Philosophical > >> > >>> and Theoretical Enquiry (History, Philosophy and Theory of the > Life > >> > >>> Sciences 12) Springer > >> > >>> > >> > >>> They seek a materialist understanding of biology as a system, > >> > attempting > >> > >>> to refer to the genetic system as little as possible. > >> > >>> > >> > >>> 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. > >> > >>> > >> > >>> STAN > >> > >>> > >> > >>> On Tue, Mar 29, 2016 at 7:40 AM, Dr. Plamen L. Simeonov < > >> > >>> <plamen.l.simeo...@gmail.com>plamen.l.simeo...@gmail.com> wrote: > >> > >>> > >> > >>>> > >> > >>>> Dear Lou, Pedro and All, > >> > >>>> > >> > >>>> > >> > >>>> > >> > >>>> 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 > >> > >>>> > >> > > >> > https://www.uni-muenster.de/imperia/md/content/cim/events/cim-mathmod-workshop-2015_abstracts.pdf > >> > >>>> : > >> > >>>> > >> > >>>> ?Davide Ambrosi: > >> > >>>> > >> > >>>> A role for mechanics in the growth, remodelling and morphogenesis > >> of > >> > >>>> living systems In the XX Century the interactions between > >> mechanics > >> > >>>> in biology were much biased by a bioengineering attitude: people > >> were > >> > >>>> mainly interested in evaluating the state of stress that bones > and > >> > >>>> tissues undergo in order to 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. > >> > >>>> > >> > >>>> 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.? > >> > >>>> > >> > >>>> > >> > >>>> > >> > >>>> Some more details about this approach can be found here: > >> > >>>> > >> > >>>> http://rsta.royalsocietypublishing.org/content/367/1902/3335 > >> > >>>> > >> > >>>> http://biomechanics.stanford.edu/paper/MFOreport.pdf > >> > >>>> > >> > >>>> 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 > >> > >>>> > >> > >>>> < > >> http://www.sciencedirect.com/science/article/pii/S0022519314006778> > >> > >>>> > http://www.sciencedirect.com/science/article/pii/S0022519314006778 > >> > >>>> > >> > >>>> < > >> http://www.sciencedirect.com/science/article/pii/S0022519316001260> > >> > >>>> > http://www.sciencedirect.com/science/article/pii/S0022519316001260 > >> > >>>> > >> > >>>> <https://www.sciencedaily.com/releases/2015/01/150107101405.htm> > >> > >>>> https://www.sciencedaily.com/releases/2015/01/150107101405.htm > >> > >>>> > >> > >>>> 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 > >> > >>>> ( <http://constructortheory.org/>http://constructortheory.org/) > >> and > >> > >>>> Brian Josephson?s ?structural/circular theory? ( > >> > >>>> <http://arxiv.org/ftp/arxiv/papers/1502/1502.02429.pdf> > >> > >>>> http://arxiv.org/ftp/arxiv/papers/1502/1502.02429.pdf; > >> > >>>> <http://arxiv.org/ftp/arxiv/papers/1506/1506.06774.pdf> > >> > >>>> http://arxiv.org/ftp/arxiv/papers/1506/1506.06774.pdf; > >> > >>>> <http://arxiv.org/pdf/1108.4860.pdf> > >> > http://arxiv.org/pdf/1108.4860.pdf) > >> > >>>> searching for the theories underpinning the foundations of the > >> > physical > >> > >>>> laws (and following Wheeler?s definition for a ?Law without Law?. > >> > >>>> > >> > >>>> 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 ( > >> > >>>> < > >> http://www.sciencedirect.com/science/article/pii/S0079610715000899> > >> > >>>> > http://www.sciencedirect.com/science/article/pii/S0079610715000899 > >> ) > >> > >>>> 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 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. > >> > >>>> > >> > >>>> 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? > >> > >>>> > >> > >>>> Reference: > >> > >>>> > >> > >>>> [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. *Trans. Royal Irish Acad*., Vol. XVII, Part II. > >> 292-422. > >> > >>>> > >> > >>>> > >> > >>>> Best, > >> > >>>> > >> > >>>> > >> > >>>> Plamen > >> > >>>> > >> > >>>> > >> > >>>> 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 > >> > >>>> > >> > > >> > https://www.uni-muenster.de/imperia/md/content/cim/events/cim-mathmod-workshop-2015_abstracts.pdf > >> > >>>> : > >> > >>>> > >> > >>>> ?Davide Ambrosi: > >> > >>>> > >> > >>>> A role for mechanics in the growth, remodelling and morphogenesis > >> of > >> > >>>> living systems In the XX Century the interactions between > >> mechanics > >> > >>>> in biology were much biased by a bioengineering attitude: people > >> were > >> > >>>> mainly interested in evaluating the state of stress that bones > and > >> > >>>> tissues undergo in order to 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. > >> > >>>> > >> > >>>> 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.? > >> > >>>> > >> > >>>> > >> > >>>> > >> > >>>> Some more details about this approach can be found here: > >> > >>>> > >> > >>>> http://rsta.royalsocietypublishing.org/content/367/1902/3335 > >> > >>>> > >> > >>>> http://biomechanics.stanford.edu/paper/MFOreport.pdf > >> > >>>> > >> > >>>> 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 > >> > >>>> > >> > >>>> < > >> http://www.sciencedirect.com/science/article/pii/S0022519314006778> > >> > >>>> > http://www.sciencedirect.com/science/article/pii/S0022519314006778 > >> > >>>> > >> > >>>> < > >> http://www.sciencedirect.com/science/article/pii/S0022519316001260> > >> > >>>> > http://www.sciencedirect.com/science/article/pii/S0022519316001260 > >> > >>>> > >> > >>>> <https://www.sciencedaily.com/releases/2015/01/150107101405.htm> > >> > >>>> https://www.sciencedaily.com/releases/2015/01/150107101405.htm > >> > >>>> > >> > >>>> 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 > >> > >>>> ( <http://constructortheory.org/>http://constructortheory.org/) > >> and > >> > >>>> Brian Josephson?s ?structural/circular theory? ( > >> > >>>> <http://arxiv.org/ftp/arxiv/papers/1502/1502.02429.pdf> > >> > >>>> http://arxiv.org/ftp/arxiv/papers/1502/1502.02429.pdf; > >> > >>>> <http://arxiv.org/ftp/arxiv/papers/1506/1506.06774.pdf> > >> > >>>> http://arxiv.org/ftp/arxiv/papers/1506/1506.06774.pdf; > >> > >>>> <http://arxiv.org/pdf/1108.4860.pdf> > >> > http://arxiv.org/pdf/1108.4860.pdf) > >> > >>>> searching for the theories underpinning the foundations of the > >> > physical > >> > >>>> laws (and following Wheeler?s definition for a ?Law without Law?. > >> > >>>> > >> > >>>> 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, > >> > >>>> > >> > >>> ... > >> > > > >> > > [Message clipped] > >> > -------------- next part -------------- > >> > An HTML attachment was scrubbed... > >> > URL: < > >> > > >> > http://listas.unizar.es/pipermail/fis/attachments/20160331/cf3d6554/attachment.html > >> > > > >> > > >> > ------------------------------ > >> > > >> > Subject: Digest Footer > >> > > >> > _______________________________________________ > >> > Fis mailing list > >> > Fis@listas.unizar.es > >> > http://listas.unizar.es/cgi-bin/mailman/listinfo/fis > >> > > >> > > >> > ------------------------------ > >> > > >> > End of Fis Digest, Vol 24, Issue 45 > >> > *********************************** > >> > > >> -------------- next part -------------- > >> An HTML attachment was scrubbed... > >> URL: < > >> > http://listas.unizar.es/pipermail/fis/attachments/20160331/00f584ff/attachment.html > >> > > >> > >> ------------------------------ > >> > >> Subject: Digest Footer > >> > >> _______________________________________________ > >> Fis mailing list > >> Fis@listas.unizar.es > >> http://listas.unizar.es/cgi-bin/mailman/listinfo/fis > >> > >> > >> ------------------------------ > >> > >> End of Fis Digest, Vol 24, Issue 46 > >> *********************************** > >> > > > > > > _______________________________________________ > > Fis mailing list > > Fis@listas.unizar.es > > http://listas.unizar.es/cgi-bin/mailman/listinfo/fis > > > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://listas.unizar.es/pipermail/fis/attachments/20160401/fb7d97e0/attachment.html > > > > ------------------------------ > > Subject: Digest Footer > > _______________________________________________ > Fis mailing list > Fis@listas.unizar.es > http://listas.unizar.es/cgi-bin/mailman/listinfo/fis > > > ------------------------------ > > End of Fis Digest, Vol 25, Issue 3 > ********************************** >
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