RE: Dr Jagers comment 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'.
ME: As I understand it, the variety of random molecules with 30 or 40 atoms in them is so vast that an autocatalytic process is essential for the sets to achieve substantial fractions of any one kind of molecule. Second, the purines and pyrimidines are full of polar side groups using O and N atoms / moieties, and so are ideal for participating as key members of autocatalytic sets. Also, they conveniently form in interstellar space, and were present in the earliest environments on earth. Linking them to sugars, and so overcoming their basic hydrophobic nature was a next vital step in their concentration, and linking them into coordinated activity with phosphate linkages was another key step. Non-linear processes are therefore vital in the development of proto-life. Please note also that, before the encapsulation of a self-sustaining organism in a membrane, *all of the encapsulated processes must have been going on in the proto-biotic soup*. Was the biosphere itself at that time, in some sense, a 'living organism'? On 17 March 2016 at 23:05, <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 14 (Jagers op Akkerhuis, Gerard) > 2. Re: SYMMETRY & _ On BioLogic (Dr. Plamen L. Simeonov) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 17 Mar 2016 11:35:48 +0000 > From: "Jagers op Akkerhuis, Gerard" <gerard.jag...@wur.nl> > To: "'plamen.l.simeo...@gmail.com'" <plamen.l.simeo...@gmail.com>, > "'pcmarijuan.i...@aragon.es'" <pcmarijuan.i...@aragon.es> > Cc: "'fis@listas.unizar.es'" <fis@listas.unizar.es> > Subject: Re: [Fis] Fis Digest, Vol 24, Issue 14 > Message-ID: <7be7e7653df145f99d32a676cf056...@scomp5294.wurnet.nl> > Content-Type: text/plain; charset="utf-8" > > 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 M?ller 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'" <fis@listas.unizar.es> > Subject: Re: [Fis] SYMMETRY & _ On BioLogic > Message-ID: > < > cambikj4ea5qq6latssewwgmlt+ukolvo1k605r9akn5wro3...@mail.gmail.com> > 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, 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 > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://listas.unizar.es/pipermail/fis/attachments/20160316/4f503a41/attachment-0001.html > > > > ------------------------------ > > Message: 2 > Date: Thu, 17 Mar 2016 08:45:31 +0100 > From: "Dr. Plamen L. Simeonov" <plamen.l.simeo...@gmail.com> > To: Louis H Kauffman <lou...@gmail.com> > Cc: "fis >> 'fis'" <fis@listas.unizar.es> > Subject: Re: [Fis] SYMMETRY & _ On BioLogic > Message-ID: > <CAMBikj5qjNkBEybZq-_0yZn+mXK4HnT= > tkp9p0ca5psexyp...@mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > 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 ot! > her 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 <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> 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. 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 (& 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 > >> > > > > > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://listas.unizar.es/pipermail/fis/attachments/20160317/1946d8bf/attachment-0001.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 14 > *********************************** > > > > ------------------------------ > > Message: 2 > Date: Thu, 17 Mar 2016 18:34:43 +0100 > From: "Dr. Plamen L. Simeonov" <plamen.l.simeo...@gmail.com> > To: Louis H Kauffman <lou...@gmail.com> > Cc: "fis >> 'fis'" <fis@listas.unizar.es> > Subject: Re: [Fis] SYMMETRY & _ On BioLogic > Message-ID: > < > cambikj5uvhkf3br809qgoxy8sgmbbeb+n2d5_dfjoz0us2t...@mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > 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 <lou...@gmail.com> > > 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 <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> 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. 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 (& 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 > >>>> > >>> > >>> > >>> > >> > >> > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://listas.unizar.es/pipermail/fis/attachments/20160317/e791d268/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 15 > *********************************** > -- 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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