Fis Digest Vol 24, Issue 20. RE: Lou Kauffman's, "If we can make hypotheses on how topological geometric forms should develop in a way that is resonant with biology, then we can explore these in a systematic way."
ME: In my upcoming section of the discussion, I shall present a new kind of information supported by organism regulatory systems, which is based on instabilities. At the heart of an instability is a catastrophe of the kind demonstrated by Rene Thom in his work of catastrophe theory (La Theorie des Catastrophes) developed in his famous book, 'Structural Stability and Morphogenesis'. Organism loci of control in complexity biology are centred on critical instabilities, either due to feedback instabilities, or to critical points in switching processes regarded as phase transitions - though there may be an equivalence between these two. The catastrophes in the differential topology of switching processes permit regulatory cytokines to exert symmetry breaking in specific ways supported by the catastrophe in question. Embryogenesis exhibits a number of such symmetry breaking, morphogenetic processes, all of which can be modelled by appropriate catastrophes. The place to look for such catastrophes is in the epigenetic networks controlling gene expression. Simple gene expression cannot give rise to structure, as any topologist will tell you. It is only through Thomian catastrophes within epigenetic networks that morphogenesis becomes possible, and (to quote Lou) "topological geometric forms develop." Denis Noble of 'Music of Life' fame, has clearly stated as one of his 'Principles of Systems Biology', "There is no Genetic Program". The response from complexity biology is that, "It is an Epigenetic Program". What controls the genesis of form is completely different from the genesis of proteins and their folding, fascinating as that topic surely is (as we have heard). On 25 March 2016 at 00:01, <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: SYMMETRY & _ On BioLogic (Louis H Kauffman) > 2. Re: SYMMETRY & _ On BioLogic (Louis H Kauffman) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 24 Mar 2016 11:42:08 -0500 > From: Louis H Kauffman <lou...@gmail.com> > To: fis <fis@listas.unizar.es> > Subject: Re: [Fis] SYMMETRY & _ On BioLogic > Message-ID: <d198b218-e2f1-430c-9a75-0ce110033...@gmail.com> > Content-Type: text/plain; charset="utf-8" > > Sorry Louis, but try again, please, for your address was wrong in the > list!!!! --Pedro > (I have just discovered, in a trip pause) > BlackBerry de movistar, all? donde est?s est? tu oficin@ > From: Louis H Kauffman <lou...@gmail.com> > Date: Tue, 22 Mar 2016 17:56:06 -0500 > To: fis<fis@listas.unizar.es> > Cc: Pedro C. Marijuan<pcmarijuan.i...@aragon.es> > Subject: Re: [Fis] SYMMETRY & _ On BioLogic > > Dear Plamen, > It is possible. We are looking here at Pivar and his colleagues working > with the possibilities of materials. It is similar to how people in origami > have explored the possibilities of producing forms by folding paper. > If we can make hypotheses on how topological geometric forms should > develop in a way that is resonant with biology, then we can explore these > in a systematic way. An example is indeed the use of knot theory to study > DNA recombination. We have a partial model of the topological aspect of > recombination, and we can explore this by using rope models and the > abstract apparatus of corresponding topological models. Something similar > might be possible for developmental biology. > > On Mar 17, 2016, at 2:45 AM, Dr. Plamen L. Simeonov < > plamen.l.simeo...@gmail.com <mailto:plamen.l.simeo...@gmail.com>> wrote: > > > > Dear Lou and Colleagues, > > > > yes, I agree: an artistic approach can be very fruitful. This is like > what Stuart Kauffman says about speaking with metaphors. At some point our > mathematical descriptive tools do not have sufficient expressional power to > grasp more global general insights and we reach out to the domains of > narration, music and visualisation for help. And this is the point where > this effort of reflection upon a subject begins to generate and develop new > expressional forms of mathematics (logics, algebras, geometries). I think > that you and Ralph Abraham noted this in your contributions about the > mystic of mathematics in the 2015 JPBMB special issue. Therefore I ask > here, if we all feel that there is some grain of imaginative truth in the > works of Pivar and team, what piece of mathematics does it needs to become > a serious theory. Spencer-Brown did also have similar flashy insights in > the beginning, but he needed 20+ years to abstract them into a substantial > book and theory. This is what also ! > other mathematicians do. They are providing complete works. Modern > artists and futurists are shooting fast and then moving to the next > ?inspiration?, often without ?marketing? the earlier idea. And then they > are often disappointed that they were not understood by their > contemporaries. The lack of They are often arrogant and do not care about > the opinion of others like we do in our FIS forum. But they often have some > ?oracle? messages. So, my question to you and the others here is: Is there > a way that we, scientists, can build a solid theory on the base of others' > artistic insights? Do you think you can help here as an expert in topology > and logic to fill the formalisation gaps in Pivar?s approach and develop > something foundational. All this would take time and I am not sure if such > artists like Pivar would be ready to participate a scientific-humanitarian > discourse, because we know that most of these talents as extremely > egocentric and ignorant and we cannot change this. Wh! > at do you think? > > > > Best, > > > > Plamen > > > > > > > > > > On Thu, Mar 17, 2016 at 8:09 AM, Louis H Kauffman <lou...@gmail.com > <mailto:lou...@gmail.com>> wrote: > > Dear Plamen, > > I do not know why Gel-Mann supported this. It is interesting to me > anyway. It is primarily an artistic endeavor but is based on some ideas of > visual development of complex forms from simpler forms. > > Some of these stories may have a grain of truth. The sort of thing I do > and others do is much more conservative (even what D?Arcy Thompson did is > much more conservative). We look for simple patterns that definitely seem > to occur in complex situations and we abstract them and work with them on > their own grounds, and with regard to how these patterns work in a complex > system. An artistic approach can be very fruitful. > > Best, > > Lou > > > >> On Mar 16, 2016, at 9:43 AM, Dr. Plamen L. Simeonov < > plamen.l.simeo...@gmail.com <mailto:plamen.l.simeo...@gmail.com>> wrote: > >> > >> Dear Lou, Pedro and Colleagues, > >> > >> I have another somewhat provoking question about the "constructive" > role of topology in morphogenesis. What do you think about the somewhat > artistic, but scientifically VERY controversial theory about the origin and > development of life forms based on physical forces from classical mechanics > and topology only, thus ignoring all of genetics, Darwinism and Creationism: > >> > >> http://www.ilasol.org.il/ILASOL/uploads/files/Pivar_ILASOL-2010.pdf < > http://www.ilasol.org.il/ILASOL/uploads/files/Pivar_ILASOL-2010.pdf> > >> > >> What part of this can be regarded as science at all, and If there is > something missing what is it? Why did a person like Murray Gel-Mann support > this? > >> > >> > >> Best > >> > >> Plamen > >> > >> ____________________________________________________________ > >> > >> > >> On Tue, Mar 15, 2016 at 12:00 PM, Pedro C. Marijuan < > pcmarijuan.i...@aragon.es <mailto:pcmarijuan.i...@aragon.es>> wrote: > >> Louis, a very simple question: in your model of self-replication, when > you enter the environment, could it mean something else than just providing > the raw stuff for reproduction? It would be great if related to successive > cycles one could include emergent topological (say geometrical-mechanical) > properties. For instance, once you have divided three times the initial > egg-cell, you would encounter three symmetry axes that would co-define the > future axes of animal development--dorsal/ventral, anterior/posterior, > lateral/medial. Another matter would be about the timing of complexity, > whether mere repetition of cycles could generate or not sufficient > functional diversity such as Plamen was inquiring in the case of molecular > clocks (nope in my opinion). best--Pedro > >> > >> > >> -- > >> ------------------------------------------------- > >> Pedro C. Mariju?n > >> Grupo de Bioinformaci?n / Bioinformation Group > >> Instituto Aragon?s de Ciencias de la Salud > >> Centro de Investigaci?n Biom?dica de Arag?n (CIBA) > >> Avda. San Juan Bosco, 13, planta X > >> 50009 Zaragoza, Spain > >> Tfno. +34 976 71 3526 <tel:%2B34%20976%2071%203526> (& 6818) > >> pcmarijuan.i...@aragon.es <mailto:pcmarijuan.i...@aragon.es> > >> http://sites.google.com/site/pedrocmarijuan/ < > http://sites.google.com/site/pedrocmarijuan/> > >> ------------------------------------------------- > >> > >> _______________________________________________ > >> Fis mailing list > >> Fis@listas.unizar.es <mailto:Fis@listas.unizar.es> > >> http://listas.unizar.es/cgi-bin/mailman/listinfo/fis < > http://listas.unizar.es/cgi-bin/mailman/listinfo/fis> > >> > > > > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://listas.unizar.es/pipermail/fis/attachments/20160324/0329c64f/attachment-0001.html > > > > ------------------------------ > > Message: 2 > Date: Thu, 24 Mar 2016 13:31:01 -0500 > From: Louis H Kauffman <kauff...@uic.edu> > To: fis <fis@listas.unizar.es> > Subject: Re: [Fis] SYMMETRY & _ On BioLogic > Message-ID: <506a70a7-25f2-476d-ac4b-e4efec97e...@uic.edu> > Content-Type: text/plain; charset="utf-8" > > Sorry Louis, but try again, please, for your address was wrong in the > list!!!! --Pedro > (I have just discovered, in a trip pause) > BlackBerry de movistar, all? donde est?s est? tu oficin@ > From: Louis H Kauffman <lou...@gmail.com <mailto:lou...@gmail.com>> > Date: Tue, 22 Mar 2016 17:56:06 -0500 > To: fis<fis@listas.unizar.es <mailto:fis@listas.unizar.es>> > Cc: Pedro C. Marijuan<pcmarijuan.i...@aragon.es <mailto: > pcmarijuan.i...@aragon.es>> > Subject: Re: [Fis] SYMMETRY & _ On BioLogic > > Dear Plamen, > It is possible. We are looking here at Pivar and his colleagues working > with the possibilities of materials. It is similar to how people in origami > have explored the possibilities of producing forms by folding paper. > If we can make hypotheses on how topological geometric forms should > develop in a way that is resonant with biology, then we can explore these > in a systematic way. An example is indeed the use of knot theory to study > DNA recombination. We have a partial model of the topological aspect of > recombination, and we can explore this by using rope models and the > abstract apparatus of corresponding topological models. Something similar > might be possible for developmental biology. > > On Mar 17, 2016, at 2:45 AM, Dr. Plamen L. Simeonov < > plamen.l.simeo...@gmail.com <mailto:plamen.l.simeo...@gmail.com>> wrote: > > > > Dear Lou and Colleagues, > > > > yes, I agree: an artistic approach can be very fruitful. This is like > what Stuart Kauffman says about speaking with metaphors. At some point our > mathematical descriptive tools do not have sufficient expressional power to > grasp more global general insights and we reach out to the domains of > narration, music and visualisation for help. And this is the point where > this effort of reflection upon a subject begins to generate and develop new > expressional forms of mathematics (logics, algebras, geometries). I think > that you and Ralph Abraham noted this in your contributions about the > mystic of mathematics in the 2015 JPBMB special issue. Therefore I ask > here, if we all feel that there is some grain of imaginative truth in the > works of Pivar and team, what piece of mathematics does it needs to become > a serious theory. Spencer-Brown did also have similar flashy insights in > the beginning, but he needed 20+ years to abstract them into a substantial > book and theory. This is what also ! > other mathematicians do. They are providing complete works. Modern > artists and futurists are shooting fast and then moving to the next > ?inspiration?, often without ?marketing? the earlier idea. And then they > are often disappointed that they were not understood by their > contemporaries. The lack of They are often arrogant and do not care about > the opinion of others like we do in our FIS forum. But they often have some > ?oracle? messages. So, my question to you and the others here is: Is there > a way that we, scientists, can build a solid theory on the base of others' > artistic insights? Do you think you can help here as an expert in topology > and logic to fill the formalisation gaps in Pivar?s approach and develop > something foundational. All this would take time and I am not sure if such > artists like Pivar would be ready to participate a scientific-humanitarian > discourse, because we know that most of these talents as extremely > egocentric and ignorant and we cannot change this. Wh! > at do you think? > > > > Best, > > > > Plamen > > > > > > > > > > On Thu, Mar 17, 2016 at 8:09 AM, Louis H Kauffman <lou...@gmail.com > <mailto:lou...@gmail.com>> wrote: > > Dear Plamen, > > I do not know why Gel-Mann supported this. It is interesting to me > anyway. It is primarily an artistic endeavor but is based on some ideas of > visual development of complex forms from simpler forms. > > Some of these stories may have a grain of truth. The sort of thing I do > and others do is much more conservative (even what D?Arcy Thompson did is > much more conservative). We look for simple patterns that definitely seem > to occur in complex situations and we abstract them and work with them on > their own grounds, and with regard to how these patterns work in a complex > system. An artistic approach can be very fruitful. > > Best, > > Lou > > > >> On Mar 16, 2016, at 9:43 AM, Dr. Plamen L. Simeonov < > plamen.l.simeo...@gmail.com <mailto:plamen.l.simeo...@gmail.com>> wrote: > >> > >> Dear Lou, Pedro and Colleagues, > >> > >> I have another somewhat provoking question about the "constructive" > role of topology in morphogenesis. What do you think about the somewhat > artistic, but scientifically VERY controversial theory about the origin and > development of life forms based on physical forces from classical mechanics > and topology only, thus ignoring all of genetics, Darwinism and Creationism: > >> > >> http://www.ilasol.org.il/ILASOL/uploads/files/Pivar_ILASOL-2010.pdf < > http://www.ilasol.org.il/ILASOL/uploads/files/Pivar_ILASOL-2010.pdf> > >> > >> What part of this can be regarded as science at all, and If there is > something missing what is it? Why did a person like Murray Gel-Mann support > this? > >> > >> > >> Best > >> > >> Plamen > >> > >> ____________________________________________________________ > >> > >> > >> On Tue, Mar 15, 2016 at 12:00 PM, Pedro C. Marijuan < > pcmarijuan.i...@aragon.es <mailto:pcmarijuan.i...@aragon.es>> wrote: > >> Louis, a very simple question: in your model of self-replication, when > you enter the environment, could it mean something else than just providing > the raw stuff for reproduction? It would be great if related to successive > cycles one could include emergent topological (say geometrical-mechanical) > properties. For instance, once you have divided three times the initial > egg-cell, you would encounter three symmetry axes that would co-define the > future axes of animal development--dorsal/ventral, anterior/posterior, > lateral/medial. Another matter would be about the timing of complexity, > whether mere repetition of cycles could generate or not sufficient > functional diversity such as Plamen was inquiring in the case of molecular > clocks (nope in my opinion). best--Pedro > >> > >> > >> -- > >> ------------------------------------------------- > >> Pedro C. Mariju?n > >> Grupo de Bioinformaci?n / Bioinformation Group > >> Instituto Aragon?s de Ciencias de la Salud > >> Centro de Investigaci?n Biom?dica de Arag?n (CIBA) > >> Avda. San Juan Bosco, 13, planta X > >> 50009 Zaragoza, Spain > >> Tfno. +34 976 71 3526 <tel:%2B34%20976%2071%203526> (& 6818) > >> pcmarijuan.i...@aragon.es <mailto:pcmarijuan.i...@aragon.es> > >> http://sites.google.com/site/pedrocmarijuan/ < > http://sites.google.com/site/pedrocmarijuan/> > >> ------------------------------------------------- > >> > >> _______________________________________________ > >> Fis mailing list > >> Fis@listas.unizar.es <mailto:Fis@listas.unizar.es> > >> http://listas.unizar.es/cgi-bin/mailman/listinfo/fis < > http://listas.unizar.es/cgi-bin/mailman/listinfo/fis> > >> > > > > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://listas.unizar.es/pipermail/fis/attachments/20160324/50242f07/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 20 > *********************************** > -- Alex Hankey M.A. (Cantab.) PhD (M.I.T.) Distinguished Professor of Yoga and Physical Science, SVYASA, Eknath Bhavan, 19 Gavipuram Circle Bangalore 560019, Karnataka, India Mobile (Intn'l): +44 7710 534195 Mobile (India) +91 900 800 8789 ____________________________________________________________ 2015 JPBMB Special Issue on Integral Biomathics: Life Sciences, Mathematics and Phenomenological Philosophy <http://www.sciencedirect.com/science/journal/00796107/119/3>
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