Re: [Fis] SYMMETRY & _ On BioLogic

2016-03-19 Thread Dr. Plamen L. Simeonov
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

2016-03-19 Thread Dr. Plamen L. Simeonov
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

2016-03-19 Thread Dr. Plamen L. Simeonov
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

2016-03-19 Thread Stanley N Salthe
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

2016-03-19 Thread Jagers op Akkerhuis, Gerard
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