Re: [Fis] (Sending again)

2016-03-24 Thread Louis H Kauffman
Dear Pedro,
I think that we should assess the role of formal tools that are already in 
place.

1. We use the accepted (graph-theoretical + geometry) models of molecules. 
These models are very powerful and fundamentally simple, but the complexities 
of their application in molecular biology is very great, requiring 
computational handling of the data and geometry. Some molecular biologists add 
features related to physics such as electromagnetic fields and quantum 
mechanics to these models, and it should be expected that the quantum level 
will eventually be very important to the structure of molecular biology. 

1(a).  This is a further comment on 1. In protein-folding we use the basics of 
model 1, plus elementary modeling of energy and probability of bonding. These 
models are insufficient to do what Nature does naturally.
The models are combinatorial and graph theoretic in nature but they do not 
address the right issues (what are they?) to impinge on the actualities of 
protein folding as it happens. The same is probably true about the topological 
side of protein folding — one can easily construct topological invariants at 
the combinatorial level (I have written about this) but their use by biologists 
has not happened yet. At least one researcher (Anti Niemi) suggests a different 
and more field theoretic approach to protein folding. See 
https://www.researchgate.net/profile/Antti_Niemi/publications 


1(b). There has been a nice success in applying topology via the embedded-graph 
paradigm for molecules. See
DNA Topology 

DNA Topology Kauffman and Lambropoulou] 

It is in this domain, that I became interested in looking at the 
self-reproduction of DNA as an instance of an abstract self-replication schema. 
There is much more to be done here in linking this abstraction back
to the topology and to the actualities of the biology. The investigation led to 
a number of analogies with structure of quantum mechanics and this will in turn 
related to quantum topology. This is in development.

2. Further topological/geometric work is very possible. The sort of thing seen 
in Pivar could be examined for mathematical problems to be articulated. We are 
aware that biological forms must arise via self-assembly  and this is in itself 
a possibly new field of geometry! The simplest example of self-assembly as a 
model is the model of autopoesis of Maturana, Uribe and Varela from long ago. 
Their model shows how a two dimensional cell boundary can arise naturally from 
an abstract ‘chemical soup’.

3. While I do not agree with Max Tegmark that Mathematics is identical to 
Reality, I do believe that the key to actuality is in the essence of 
relationships. The essence of relationships is often accompanied by a 
mathematical essence or simple fundamental pattern. This is so striking in the 
case of DNA reproduction (e.g.) that I cannot help but feel that some real 
progress can occur in looking at that whole story from the abstract and 
recursive self-replication to how it is instantiated in the biology. The 
question in general is: What can we see about the way mathematical models are 
instantiated in actuality?!

I will stop here in the interest of bevity.
Best,
Lou


> On Mar 20, 2016, at 2:04 PM, PEDRO CLEMENTE MARIJUAN FERNANDEZ 
> > wrote:
> 
> May I suggest that Louis make some further comment on the formal tools for 
> develop., answering Stan? Then, I think we should derive towards generalizing 
> on the bio problem and arguing about the existing philosophical gap(s) that a 
> tentative new phenom of life could fill in... it may be a good opportunity to 
> focus the entire discussion sessions. Plamen and me could attempt that, of 
> course Louis in his response to Stan too, irrespective that other parties may 
> finally plunge into the discussion or not. At least we will have done our 
> part.
> best --Pedro

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Re: [Fis] SYMMETRY & _ On BioLogic

2016-03-24 Thread Louis H Kauffman

From: Louis H Kauffman >
Date: Tue, 22 Mar 2016 17:56:06 -0500
To: fis>
Cc: Pedro C. Marijuan>
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 
> > 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,
> Lou
> 
>> On Mar 16, 2016, at 9:43 AM, Dr. Plamen L. Simeonov 
>> > 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
>> 
>> 

Re: [Fis] SYMMETRY & _ On BioLogic

2016-03-24 Thread Louis H Kauffman
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, allí donde estés está tu oficin@
From: Louis H Kauffman 
Date: Tue, 22 Mar 2016 17:56:06 -0500
To: fis
Cc: Pedro C. Marijuan
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 
> > 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,
> Lou
> 
>> On Mar 16, 2016, at 9:43 AM, Dr. Plamen L. Simeonov 
>> > 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