Re: [Fis] SYMMETRY & _ On BioLogic
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 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> 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. Marijuán > Grupo de Bioinformación / Bioinformation Group > Instituto Aragonés de Ciencias de la Salud > Centro de Investigación Biomédica de Aragón (CIBA) > Avda. San Juan Bosco, 13, planta X > 50009 Zaragoza, Spain > Tfno. +34 976 71 3526 (& 6818) > pcmarijuan.i...@aragon.es > http://sites.google.com/site/pedrocmarijuan/ > - > > ___ > Fis mailing list > Fis@listas.unizar.es > http://listas.unizar.es/cgi-bin/mailman/listinfo/fis > ___ Fis mailing list Fis@listas.unizar.es http://listas.unizar.es/cgi-bin/mailman/listinfo/fis
Re: [Fis] SYMMETRY & _ On BioLogic
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. What do you think? Best, Plamen On Thu, Mar 17, 2016 at 8:09 AM, Louis H Kauffman 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> 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 > > 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> 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. Marijuán >> Grupo de Bioinformación / Bioinformation Group >> Instituto Aragonés de Ciencias de la Salud >> Centro de Investigación Biomédica de Aragón (CIBA) >> Avda. San Juan Bosco, 13, planta X >> 50009 Zaragoza, Spain >> Tfno. +34 976 71 3526 (& 6818) >> pcmarijuan.i...@aragon.es >> http://sites.google.com/site/pedrocmarijuan/ >> - >> >>
Re: [Fis] SYMMETRY & _ On BioLogic
Dear Lou and All, I am sorry. The FIS server has returned my email as undelivered, most probably because of the PDF attachment. This is actually a paper authored by Bob Root-Bernstein and his daughter, Meredith. It is on researchegate.net and can be requested from them. The title is: “The ribosome as missing link in the prebiotic evolution II: Robosomes encode ribosomal proteins that bind to common regions of their own mRNAs and mRNAs”. Journal of Theoretical Biology. 2016(?). You can look for it on Elsevier’s ScienceDirect too. These are actually 2 papers parts I (2015) and II (in print) Best, Plamen On Thu, Mar 17, 2016 at 6:15 PM, Dr. Plamen L. Simeonov < plamen.l.simeo...@gmail.com> wrote: > Dear Lou, > > This sounds really motivating! Thank you for your positive response. So, > this approach can be actually used to prove biological hypotheses like this > one in the attachment. Have a look at the pictures. You may be able to > derive transformations based on your knot logic and prove that this way is > at least logically consistent and possible. It is another question to claim > that this actually did happen. > > What do you think? > > Best, > > Plamen > > > > On Thu, Mar 17, 2016 at 9:00 AM, Louis H Kauffman > wrote: > >> 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. >> Best, >> Lou >> >> On Mar 17, 2016, at 2:45 AM, Dr. Plamen L. Simeonov < >> 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. What do you think? >> >> Best, >> >> Plamen >> >> >> >> >> On Thu, Mar 17, 2016 at 8:09 AM, Louis H Kauffman >> 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,
fis@listas.unizar.es
Pedro -- You are right to look dubiously at the achievement of neoDarwinism as the sole theory of biology. What is missing (and it was realized already in the 1950’s with Schmalgausen and Waddington) is development. All dissipative structures develop -- immaturity followed by a short maturity followed by senescence -- and this was not escaped when the genetic system was incorporated, creating living dissipative structures. Development is a material law of nature, to be added to the underlying physical laws in the case of dissipative structures. Evo-Devo is a currently burgeoning part of biology discourse aimed at replacing ‘random mutation’ as the source of new directions with material divergences occurring during ontogeny. These reflect material tendencies that can not always be suppressed by genetic information guidance. They might also in some way reflect choices made by a developing system. This approach will result in bringing in a major fact of biological evolution long ignored by neoDarwinians because their explanatory tool kit could simply bot explain it -- convergent evolution. STAN ___ Fis mailing list Fis@listas.unizar.es http://listas.unizar.es/cgi-bin/mailman/listinfo/fis
Re: [Fis] Fis Digest, Vol 24, Issue 14
Dear Plamen, Pedro and colleques, I have no experience with the medium of this forum so hopefully my suggestion will arrive at the right spot. Plamen, I like to link to your suggestion below. It is interesting to see that you view the theory that the first cells have emerged without genetics as VERY controversial. It may perhaps be inspiring to associate such a viewpoint with a different perspective that also exists. In recent decades the work of e.g. Martin and Müller 1998, or more recently the work of Michael Russell seems to indicate that autocatalytic chemistry in a vesicle (while also producing the components of the vesicle) may well be a serious option for the first simple organism. When last year I visited the conference "Reconceptualizing the origin of life" in Washington the idea of abiogenesis in the precipitation material of undersee vents was discussed as a very serious option. And it is an interesting question whether simple catalytic molecules -as a set- can have been capable of producing all the molecules in the set? To perform this, they would have to transforming chemical sources obtained from outside and turn them into molecules of the catalytic set, and/or membrane material. Maybe that the first catalytic molecules have been so simple in their structure that one could not already speak about them as representing 'genes', or 'genetic material'. Possibly the emergence of long, coding, 'genetic' molecules could have occurred in a later phase, when -over a range of generations of variation and selection of autocatalytic vesicles- the catalytic molecules of the autocatalytic set became more complex? How is your feeling about such viewpoints? Kind regards, Gerard Dr. dr. Gerard Jagers op Akkerhuis Animal Ecology Alterra P.O.Box 47 6700 AA Wageningen The Netherlands Droevendaalsesteeg 3 (building 100) 6708 PB Wageningen +31 (0) 317 486561 ee gerard.jag...@wur.nl -Oorspronkelijk bericht- Van: Fis [mailto:fis-boun...@listas.unizar.es] Namens fis-requ...@listas.unizar.es Verzonden: donderdag 17 maart 2016 12:00 Aan: fis@listas.unizar.es Onderwerp: Fis Digest, Vol 24, Issue 14 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 (Dr. Plamen L. Simeonov) 2. Re: SYMMETRY & _ On BioLogic (Dr. Plamen L. Simeonov) -- Message: 1 Date: Wed, 16 Mar 2016 15:43:11 +0100 From: "Dr. Plamen L. Simeonov" < > To: "Pedro C. Marijuan" < > Cc: "fis >> 'fis'" Subject: Re: [Fis] SYMMETRY & _ On BioLogic Message-ID: Content-Type: text/plain; charset="utf-8" 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 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> 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, 1
