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. 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/
>>>> -------------------------------------------------
>>>>
>>>> _______________________________________________
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>>>>
>>>
>>>
>>>
>>
>>
>
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