Re: [Fis] Fis Digest, Vol 24, Issue 32

[Alex Hankey]

proofs? yet, because
> the proofs also emerge as subjective (or perhaps ?suggested?! ? ask the
> psychologists for that aspect) thoughts in the minds of the mathematicians.
> I am really glad that we began such a phenomenological discussion on this
> aspect such as Hipolito?s paper (
> http://www.sciencedirect.com/science/article/pii/S0079610715000899) that
> was widely commented in the reviewer?s circle. In many cases when we have a
> ?fuzzy? intuition about a certain relationship or analogy we miss the
> correct definitions and concepts, and so in a creative act to hold down the
> flying thought we move to using examples, metaphors, pictures. Pedro
> correctly addressed the explanatory problem of science which presupposes a
> certain causative and predicative ?workflow? to derive a conclusion from
> the facts, and this is the way in which also proofs are (selectively) made.
> As a young scholar I often wondered how artificially people like Gauss,
> Cauchy and Weierstrass  design their proofs, but then I got used to that
> style. It was a question of overall convention. I am thankful to Lou for
> his response on my question about using adequate ?resonant? methods to
> model developmental biology, because this is also an important aspect of
> the biology (and physics as well) including the
> phenomenological/first-person view of an ?observer-participant? (to use
> Vrobel?s term) which is crucial for understanding the process of
> self-reflection/recursion/cycle in science, which is usually led by what?:
> the intuition, also well recognized by such giants like Poincare and
> Einstein. Isn?t not ?resonance? in the core of detecting such vibration
> between the observer and the observed? Because logic, backtracing and proof
> come later.
>
>
> And finally, when looking at the clear simple mathematical abstractions of
> numbers, vectors, directions, sets, algebras, geometries, etc. used by many
> without scrutinizing when developing system (biological) models of yet
> another kind of mechanics/automation/machinery of the physical reality, I
> am asking myself which are the premises for using such tools to describe a
> model: the parameters, or the idea behind? It is probably not a commonly
> known fact (even for those who are engaged with such exciting disciplines
> as algebraic geometry and geometrical algebra, now considered to be very
> close to what we wish to express in biology) that William Hamilton, the
> inventor of the quaternions did not simply use the already known concept of
> ?vector? in his method. Instead he used ?step? with ?direction? to express
> a duration of time (or ?duree? as Husserl called it from the other side of
> the phenomenological divide) and action (to move from A to B): two very
> biology-related concepts at that time (although they may be considered as
> physical or computational today). He actually stated that if there is
> geometry as a pure science of space, then algebra must be the pure science
> of time [1]. What did we actually gain for biology from merging space and
> time in physics? And if we apply a specific mathematical-computational
> technique what is the key idea/intuition behind it?. Because, as a
> colleague pathologist told me this morning about the model correctness when
> predicting the development of tumors: the model can be assumed for being
> correct based on the interpretation of some (limited) set of data, but
> Ptolemy's system was also considered to be correct in its rather complex
> way of predicting the movement of the celestial bodies. Where is the
> difference? I am curious about your opinion.
>
>
> *Reference:*
>
> [1] W. R. Hamilton, 1835. Theory of Conjugate Functions, or Algebraic
> Couples; with a Preliminary or Elementary Essay on Algebra as the Science
> of Pure Time. *Trans. Royal Irish Acad*., Vol. XVII, Part II. 292-422.
>
>
>
> Best,
>
>
>
> Plamen
> __
>
> 2015 JPBMB Special Issue on Integral Biomathics: Life Sciences, Mathematics
> and Phenomenological Philosophy
> <http://www.sciencedirect.com/science/journal/00796107/119/3>
> (note: free access to all articles until July 19th, 2016)
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> ***
>



-- 
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


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and Phenomenological Philosophy
<http://www.sciencedirect.com/science/journal/00796107/119/3>
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[Fis] _ Re: _ Re: _ Re: _ Re: On mathematical theories and models in biology

[Dr. Plamen L. Simeonov]

I think you are right, Lou, with respect to Deutsch who actually met
Everett III with the multiple universe hypothesis. The sole name
“constructor theory” invoked associations beyond the quantum frame in me,
but he did not went that far. As for Josephson, I am not quite sure about
his notion. Brian remains firmly on the quantum level in the papers I
referred earlier, but he often returns to Ilexa Yarley”s “circular theory”
which offers a much broader interpretation in my opinion. I expected your
mentioning of (the vibrations of) “thought forms”, which are supposed to
invoke the emergence of word and action. I welcome your understanding for
the necessity of a deeper QM to make the links between actuality and the
bounded potentiality more comprehensive.

Best,

Plamen




On Wed, Mar 30, 2016 at 12:33 AM, Louis H Kauffman  wrote:

> Josephson and Deutsh are not ‘deeper than QM’. Deutsch for example is a
> very literal interpretation of QM that says that all the trajectories in
> the Feynman path sum are real, and they occur in parallel universes. This
> is a nice mathematical way to think, but it is not deeper than present QM!
> Energy is conserved, but ‘particles’ and indeed universes can be created
> from vacuum. If we want to go to discussion of ‘holy spirit’ then one
> should look at the structure of thought itself. For it is at the level of
> thought that every concept has a life behind it. Every idea is real and
> alive. Platonism asserts this directly in the belief in the existence of
> form and this form is a living form that we interact with and we are. How
> these notions are related to QM probably does await the emergence of a
> deeper QM.
>
> On Mar 29, 2016, at 4:43 PM, Dr. Plamen L. Simeonov <
> plamen.l.simeo...@gmail.com> wrote:
>
>
>
> Thank you for your responses, Lou and Stan. I am aware about the details
> of the autopoietic model. What I was actually addressing by the transition
> from abiotic to biotic structures and the later emergence of RNA and DNA
> was  this elusive aspect of “mass action” which Stan mentioned, that in my
> opinion must have emerged out of the field of “triggered  (by resonance)
> potentialities  which deeper theories than QM are trying to develop (cf.
> Josephson and Deutsch mentioned earlier). This enigmatic emergence of
> action out of nothing (vacuum or pure potentiality) naturally allows  the
> (co-)existence of such  heretic ideas as the immaterial “Holy Spirit” or
> Hans Driesch”s vitalism, Jean Sharon’s eternal electron, or “The Matrix of
> Matter and Life”at the sub-Planckian scale. How about this possible link to
> Platonism, theology, logic and algebra?
>
> All the best,
>
> Plamen
>
> PS. I do not know why my notes appear twice on this list.
>
>
>
> On Tue, Mar 29, 2016 at 10:55 PM, Louis H Kauffman 
> wrote:
>
>> This is a reply to Plamen’s comment about autopoeisis. In their paper
>> Maturana,Uribe and Varela give a working model (computer model) for
>> autopoeisis.
>> It is very simple, consisting of a subtrate of nodal elements that tend
>> to bond when in proximity, and a collection of catalytic nodal elements
>> that promote bonding in their vicinity. The result of this dynamics is that
>> carapaces of linked nodal elements form around the catalytic elements and
>> these photo-cells tend to keep surviving the perturbations built into the
>> system. This model shows that cells can arise from a very simple dynmamic
>> geometric/topological substrate long before anything as sophisticated as
>> DNA has happened.
>>
>> On Mar 29, 2016, at 2:54 PM, Stanley N Salthe 
>> wrote:
>>
>> Plamen wrote:
>>
>>  I begin to believe that the transition from abiotic to biotic
>> structures, incl. Maturana-Varela.-Uribe’s autopoiesis may, really have
>> some underlying matrix/”skeleton”/”programme” which has nothing in common
>> with the nature of DNA, and that DNA and RNA as we know them today may
>> have emerged as secondary or even tertiary “memory” of something underlying
>> deeper below the microbiological surface. It is at least worth thinking in
>> this direction. I do not mean necessarily the role of the number concept
>> and Platonic origin of the universe, but something probably much more
>> “physical”
>>
>>
>>
>> S: An interesting recently published effort along these lines is:
>>
>> Alvaro Moreno and Matteo Mossio: Biological Autonomy: A Philosophical and
>> Theoretical Enquiry (History, Philosophy and Theory of the Life Sciences
>> 12) Springer
>>
>> They seek a materialist understanding of biology as a system, attempting
>> to refer to the genetic system as little as possible.
>>
>> I have until very recently attempted to evade/avoid mechanistic thinking
>> in regard to biology, but, on considering the origin of life generally
>> while keeping Howard Pattee's thinking in mind, I have been struck by the
>> notion that the origin of life (that is: WITH the genetic system) was the
>> origin of mechanism in the universe.  Before that coding system, everythi

Re: [Fis] _ Re: _ Re: _ Re: On mathematical theories and models in biology

[Guy A Hoelzer]

Hi Robert,

I haven’t read your book yet, but thanks for the link.  You have certainly 
thought through these issues much more deeply than I have and I appreciate your 
perspective.  I am trying to parse the meanings of your three fundamentals, so 
please let me know if I am getting the main ideas right.  

“Aleatoricism” seems to reflect the creativity associated with dynamics at ‘the 
edge of chaos’, or inherent to self-organization.  I would strongly agree with 
this as an essential fundamental that was not explicit in my formulation.  I 
would argue that aleatoricism and feedback are implicit in the notion of 
metabolism, but I like that you pull them out.

I’m not sure what you are suggesting with the term “centripetality’.  Is this 
meant to reference the functional and dynamical coherence of self-organizing 
systems?

Regards,

Guy


> On Mar 29, 2016, at 3:39 PM, Robert E. Ulanowicz  wrote:
> 
> Dear Guy,
> 
> Please allow me to respond to your invitation to Terry with my two cents.
> 
> My triad for supporting the dynamics of life is a bit different. I see the
> three essential fundamentals as:
> 
> 1. Aleatoricism
> 
> 2. Feedback
> 
> 3. Memory
> 
> Just to briefly elaborate on each:
> 
> 1. I use aleatoricism to avoid the baggage associated with the term
> "chance", which most immediately associate with "blind" chance. The
> aleatoric spans the spectrum from unique events to blind chance to
> conditional chance to propensities to just short of determinism.
> 
> 2. More specifically (and in parallel with autopoesis) I focus on
> autocatalytic feedback, which exhibits the property of "centripetality".
> Centripetality appears on almost no one's list of properties of life,
> despite its ubiquity in association with living systems.
> 
> 3. Memory (and information) likely inhered in stable configurations of
> processes (metabolism) well before the advent of molecular encoding. Terry
> speaks to this point in Biological Theory 1(2):136-49.
> 
> My fundamentals do not include reproduction, because I see reproduction as
> corollary to 2 & 3.
> 
> I propose a full metaphysics for life predicated on these three
> assumptions.
> 
> 
> Looking forward to what others see as fundamental.
> 
> Peace,
> Bob
> 
> 
>> I personally consider metabolism to be at the core of what constitutes
>> â?~lifeâ?T, so the notion of autopoeisis is very attractive to me.  It is
>> also possible that the richness of life as we know it depends on having
>> metabolisms (activity), genomes (memory), and reproduction combined.  The
>> reductionistic approach to singling out one of these three pillars of life
>> as its essence may be futile.  However, I want to point out that the most
>> reduced version of â?~lifeâ?T I have seen was proposed by Terry Deacon in
>> the concept he calls â?oautocellsâ?.  Terry has made great contributions
>> to FIS dealing with related topics, and I hope he will chime in here to
>> describe his minimalist form of life, which is not cellular, does not have
>> any metabolism or genetically encoded memory.  Autocells do, however,
>> reproduce.
>> 
>> Regards,
>> 
>> Guy
> 
> 


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[Fis] _ Re: _ Re: _ Re: _ Re: On mathematical theories and models in biology

[Robert E. Ulanowicz]

Dear Guy,

Please allow me to respond to your invitation to Terry with my two cents.

My triad for supporting the dynamics of life is a bit different. I see the
three essential fundamentals as:

1. Aleatoricism

2. Feedback

3. Memory

Just to briefly elaborate on each:

1. I use aleatoricism to avoid the baggage associated with the term
"chance", which most immediately associate with "blind" chance. The
aleatoric spans the spectrum from unique events to blind chance to
conditional chance to propensities to just short of determinism.

2. More specifically (and in parallel with autopoesis) I focus on
autocatalytic feedback, which exhibits the property of "centripetality".
Centripetality appears on almost no one's list of properties of life,
despite its ubiquity in association with living systems.

3. Memory (and information) likely inhered in stable configurations of
processes (metabolism) well before the advent of molecular encoding. Terry
speaks to this point in Biological Theory 1(2):136-49.

My fundamentals do not include reproduction, because I see reproduction as
corollary to 2 & 3.

I propose a full metaphysics for life predicated on these three
assumptions.


Looking forward to what others see as fundamental.

Peace,
Bob


> I personally consider metabolism to be at the core of what constitutes
> ‘life’, so the notion of autopoeisis is very attractive to me.  It is
> also possible that the richness of life as we know it depends on having
> metabolisms (activity), genomes (memory), and reproduction combined.  The
> reductionistic approach to singling out one of these three pillars of life
> as its essence may be futile.  However, I want to point out that the most
> reduced version of ‘life’ I have seen was proposed by Terry Deacon in
> the concept he calls “autocells”.  Terry has made great contributions
> to FIS dealing with related topics, and I hope he will chime in here to
> describe his minimalist form of life, which is not cellular, does not have
> any metabolism or genetically encoded memory.  Autocells do, however,
> reproduce.
>
> Regards,
>
> Guy


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[Fis] _ Re: _ Re: _ Re: _ Re: On mathematical theories and models in biology

[Louis H Kauffman]

Josephson and Deutsh are not ‘deeper than QM’. Deutsch for example is a very 
literal interpretation of QM that says that all the trajectories in the Feynman 
path sum are real, and they occur in parallel universes. This is a nice 
mathematical way to think, but it is not deeper than present QM!
Energy is conserved, but ‘particles’ and indeed universes can be created from 
vacuum. If we want to go to discussion of ‘holy spirit’ then one should look at 
the structure of thought itself. For it is at the level of thought that every 
concept has a life behind it. Every idea is real and alive. Platonism asserts 
this directly in the belief in the existence of form and this form is a living 
form that we interact with and we are. How these notions are related to QM 
probably does await the emergence of a deeper QM.

> On Mar 29, 2016, at 4:43 PM, Dr. Plamen L. Simeonov 
>  wrote:
> 
> 
> 
> Thank you for your responses, Lou and Stan. I am aware about the details of 
> the autopoietic model. What I was actually addressing by the transition from 
> abiotic to biotic structures and the later emergence of RNA and DNA was  this 
> elusive aspect of “mass action” which Stan mentioned, that in my opinion must 
> have emerged out of the field of “triggered  (by resonance) potentialities  
> which deeper theories than QM are trying to develop (cf.  Josephson and 
> Deutsch mentioned earlier). This enigmatic emergence of action out of nothing 
> (vacuum or pure potentiality) naturally allows  the (co-)existence of such  
> heretic ideas as the immaterial “Holy Spirit” or Hans Driesch”s vitalism, 
> Jean Sharon’s eternal electron, or “The Matrix of Matter and Life”at the 
> sub-Planckian scale. How about this possible link to Platonism, theology, 
> logic and algebra? 
> 
> All the best,
> 
> Plamen
> 
> PS. I do not know why my notes appear twice on this list.
> 
> 
> 
> On Tue, Mar 29, 2016 at 10:55 PM, Louis H Kauffman  > wrote:
> This is a reply to Plamen’s comment about autopoeisis. In their paper 
> Maturana,Uribe and Varela give a working model (computer model) for 
> autopoeisis.
> It is very simple, consisting of a subtrate of nodal elements that tend to 
> bond when in proximity, and a collection of catalytic nodal elements that 
> promote bonding in their vicinity. The result of this dynamics is that 
> carapaces of linked nodal elements form around the catalytic elements and 
> these photo-cells tend to keep surviving the perturbations built into the 
> system. This model shows that cells can arise from a very simple dynmamic 
> geometric/topological substrate long before anything as sophisticated as DNA 
> has happened. 
> 
>> On Mar 29, 2016, at 2:54 PM, Stanley N Salthe > > wrote:
>> 
>> Plamen wrote:
>> 
>>  I begin to believe that the transition from abiotic to biotic structures, 
>> incl. Maturana-Varela.-Uribe’s autopoiesis may, really have some underlying 
>> matrix/”skeleton”/”programme” which has nothing in common with the nature of 
>> DNA, and that DNA and RNA as we know them today may have emerged as 
>> secondary or even tertiary “memory” of something underlying deeper below the 
>> microbiological surface. It is at least worth thinking in this direction. I 
>> do not mean necessarily the role of the number concept and Platonic origin 
>> of the universe, but something probably much more “physical”
>> 
>> 
>> 
>> 
>> 
>> S: An interesting recently published effort along these lines is: 
>> 
>> Alvaro Moreno and Matteo Mossio: Biological Autonomy: A Philosophical and 
>> Theoretical Enquiry (History, Philosophy and Theory of the Life Sciences 12) 
>> Springer
>> 
>> They seek a materialist understanding of biology as a system, attempting to 
>> refer to the genetic system as little as possible.
>> 
>> I have until very recently attempted to evade/avoid mechanistic thinking in 
>> regard to biology, but, on considering the origin of life generally while 
>> keeping Howard Pattee's thinking in mind, I have been struck by the notion 
>> that the origin of life (that is: WITH the genetic system) was the origin of 
>> mechanism in the universe.  Before that coding system, everything was mass 
>> action.  I think we still do not understand how this mechanism evolved.
>> 
>> STAN
>> 
>> 
>> On Tue, Mar 29, 2016 at 7:40 AM, Dr. Plamen L. Simeonov 
>> mailto:plamen.l.simeo...@gmail.com>> wrote:
>> 
>> Dear Lou, Pedro and All,
>> 
>>  
>> I am going to present a few opportunistic ideas related to what was said 
>> before in this session. Coming back to Pivar’s speculative 
>> mechano-topological model of life excluding genetics I wish to turn your 
>> attention to another author with a similar idea but on a sound mathematical 
>> base, Davide Ambrosi with his resume at 
>> https://www.uni-muenster.de/imperia/md/content/cim/events/cim-mathmod-workshop-2015_abstracts.pdf
>>  
>> 

[Fis] _ Re: _ Re: _ Re: On mathematical theories and models in biology

[Guy A Hoelzer]

I personally consider metabolism to be at the core of what constitutes ‘life’, 
so the notion of autopoeisis is very attractive to me.  It is also possible 
that the richness of life as we know it depends on having metabolisms 
(activity), genomes (memory), and reproduction combined.  The reductionistic 
approach to singling out one of these three pillars of life as its essence may 
be futile.  However, I want to point out that the most reduced version of 
‘life’ I have seen was proposed by Terry Deacon in the concept he calls 
“autocells”.  Terry has made great contributions to FIS dealing with related 
topics, and I hope he will chime in here to describe his minimalist form of 
life, which is not cellular, does not have any metabolism or genetically 
encoded memory.  Autocells do, however, reproduce.

Regards,

Guy

On Mar 29, 2016, at 1:55 PM, Louis H Kauffman 
mailto:kauff...@uic.edu>> wrote:

This is a reply to Plamen’s comment about autopoeisis. In their paper 
Maturana,Uribe and Varela give a working model (computer model) for autopoeisis.
It is very simple, consisting of a subtrate of nodal elements that tend to bond 
when in proximity, and a collection of catalytic nodal elements that promote 
bonding in their vicinity. The result of this dynamics is that carapaces of 
linked nodal elements form around the catalytic elements and these photo-cells 
tend to keep surviving the perturbations built into the system. This model 
shows that cells can arise from a very simple dynmamic geometric/topological 
substrate long before anything as sophisticated as DNA has happened.

On Mar 29, 2016, at 2:54 PM, Stanley N Salthe 
mailto:ssal...@binghamton.edu>> wrote:

Plamen wrote:

 I begin to believe that the transition from abiotic to biotic structures, 
incl. Maturana-Varela.-Uribe’s autopoiesis may, really have some underlying 
matrix/”skeleton”/”programme” which has nothing in common with the nature of 
DNA, and that DNA and RNA as we know them today may have emerged as secondary 
or even tertiary “memory” of something underlying deeper below the 
microbiological surface. It is at least worth thinking in this direction. I do 
not mean necessarily the role of the number concept and Platonic origin of the 
universe, but something probably much more “physical”


S: An interesting recently published effort along these lines is:

Alvaro Moreno and Matteo Mossio: Biological Autonomy: A Philosophical and 
Theoretical Enquiry (History, Philosophy and Theory of the Life Sciences 12) 
Springer

They seek a materialist understanding of biology as a system, attempting to 
refer to the genetic system as little as possible.

I have until very recently attempted to evade/avoid mechanistic thinking in 
regard to biology, but, on considering the origin of life generally while 
keeping Howard Pattee's thinking in mind, I have been struck by the notion that 
the origin of life (that is: WITH the genetic system) was the origin of 
mechanism in the universe.  Before that coding system, everything was mass 
action.  I think we still do not understand how this mechanism evolved.

STAN

On Tue, Mar 29, 2016 at 7:40 AM, Dr. Plamen L. Simeonov 
mailto:plamen.l.simeo...@gmail.com>> wrote:

Dear Lou, Pedro and All,


I am going to present a few opportunistic ideas related to what was said before 
in this session. Coming back to Pivar’s speculative mechano-topological model 
of life excluding genetics I wish to turn your attention to another author with 
a similar idea but on a sound mathematical base, Davide Ambrosi with his resume 
at 
https://www.uni-muenster.de/imperia/md/content/cim/events/cim-mathmod-workshop-2015_abstracts.pdf[uni-muenster.de]:
“Davide Ambrosi:
A role for mechanics in the growth, remodelling and morphogenesis of living 
systems  In the XX Century the interactions between mechanics in biology were 
much  biased by a bioengineering attitude: people were mainly interested in  
evaluating the state of stress that bones and tissues undergo in order to  
properly design prosthesis and devices. However in the last decades a new 
vision is emerging. "Mechano-biology" is changing the point of view, with 
respect to "Bio-mechanics", emphasizing the biological feedback. Cells, tissues 
and organs do not only deform when loaded: they reorganize, they duplicate, 
they actively produce dynamic patterns that apparently have multiple biological 
aims.
In this talk I will concentrate on two paradigmatic systems where the interplay 
between mechanics and biology is, in my opinion, particularly challenging: the 
homeostatic stress as a driver for remodeling of soft tissue and the tension as 
a mechanism to t

[Fis] _ Re: _ Re: _ Re: On mathematical theories and models in biology

[Dr. Plamen L. Simeonov]

Thank you for your responses, Lou and Stan. I am aware about the details of
the autopoietic model. What I was actually addressing by the transition
from abiotic to biotic structures and the later emergence of RNA and DNA
was  this elusive aspect of “mass action” which Stan mentioned, that in my
opinion must have emerged out of the field of “triggered  (by resonance)
potentialities  which deeper theories than QM are trying to develop (cf.
Josephson and Deutsch mentioned earlier). This enigmatic emergence of
action out of nothing (vacuum or pure potentiality) naturally allows  the
(co-)existence of such  heretic ideas as the immaterial “Holy Spirit” or
Hans Driesch”s vitalism, Jean Sharon’s eternal electron, or “The Matrix of
Matter and Life”at the sub-Planckian scale. How about this possible link to
Platonism, theology, logic and algebra?

All the best,

Plamen

PS. I do not know why my notes appear twice on this list.



On Tue, Mar 29, 2016 at 10:55 PM, Louis H Kauffman  wrote:

> This is a reply to Plamen’s comment about autopoeisis. In their paper
> Maturana,Uribe and Varela give a working model (computer model) for
> autopoeisis.
> It is very simple, consisting of a subtrate of nodal elements that tend to
> bond when in proximity, and a collection of catalytic nodal elements that
> promote bonding in their vicinity. The result of this dynamics is that
> carapaces of linked nodal elements form around the catalytic elements and
> these photo-cells tend to keep surviving the perturbations built into the
> system. This model shows that cells can arise from a very simple dynmamic
> geometric/topological substrate long before anything as sophisticated as
> DNA has happened.
>
> On Mar 29, 2016, at 2:54 PM, Stanley N Salthe 
> wrote:
>
> Plamen wrote:
>
>  I begin to believe that the transition from abiotic to biotic structures,
> incl. Maturana-Varela.-Uribe’s autopoiesis may, really have some underlying
> matrix/”skeleton”/”programme” which has nothing in common with the nature
> of DNA, and that DNA and RNA as we know them today may have emerged as
> secondary or even tertiary “memory” of something underlying deeper below
> the microbiological surface. It is at least worth thinking in this
> direction. I do not mean necessarily the role of the number concept and
> Platonic origin of the universe, but something probably much more “physical”
>
>
>
> S: An interesting recently published effort along these lines is:
>
> Alvaro Moreno and Matteo Mossio: Biological Autonomy: A Philosophical and
> Theoretical Enquiry (History, Philosophy and Theory of the Life Sciences
> 12) Springer
>
> They seek a materialist understanding of biology as a system, attempting
> to refer to the genetic system as little as possible.
>
> I have until very recently attempted to evade/avoid mechanistic thinking
> in regard to biology, but, on considering the origin of life generally
> while keeping Howard Pattee's thinking in mind, I have been struck by the
> notion that the origin of life (that is: WITH the genetic system) was the
> origin of mechanism in the universe.  Before that coding system, everything
> was mass action.  I think we still do not understand how this mechanism
> evolved.
>
> STAN
>
> On Tue, Mar 29, 2016 at 7:40 AM, Dr. Plamen L. Simeonov <
> plamen.l.simeo...@gmail.com> wrote:
>
>>
>> Dear Lou, Pedro and All,
>>
>>
>>
>> I am going to present a few opportunistic ideas related to what was said
>> before in this session. Coming back to Pivar’s speculative
>> mechano-topological model of life excluding genetics I wish to turn your
>> attention to another author with a similar idea but on a sound mathematical
>> base, Davide Ambrosi with his resume at
>> https://www.uni-muenster.de/imperia/md/content/cim/events/cim-mathmod-workshop-2015_abstracts.pdf
>> :
>>
>> “Davide Ambrosi:
>>
>> A role for mechanics in the growth, remodelling and morphogenesis of
>> living systems  In the XX Century the interactions between mechanics in
>> biology were much  biased by a bioengineering attitude: people were
>> mainly interested in  evaluating the state of stress that bones and
>> tissues undergo in order to  properly design prosthesis and devices.
>> However in the last decades a new vision is emerging. "Mechano-biology" is
>> changing the point of view, with respect to "Bio-mechanics", emphasizing
>> the biological feedback. Cells, tissues and organs do not only deform when
>> loaded: they reorganize, they duplicate, they actively produce dynamic
>> patterns that apparently have multiple biological aims.
>>
>> In this talk I will concentrate on two paradigmatic systems where the
>> interplay between mechanics and biology is, in my opinion, particularly
>> challenging: the homeostatic stress as a driver for remodeling of soft
>> tissue and the tension as a mechanism to transmit information about the
>> size of organs during morphogenesis. In both cases it seems that mechanics
>> plays a role which at least accompanies and enforce

[Fis] _ Re: _ Re: On mathematical theories and models in biology

[Louis H Kauffman]

This is a reply to Plamen’s comment about autopoeisis. In their paper 
Maturana,Uribe and Varela give a working model (computer model) for autopoeisis.
It is very simple, consisting of a subtrate of nodal elements that tend to bond 
when in proximity, and a collection of catalytic nodal elements that promote 
bonding in their vicinity. The result of this dynamics is that carapaces of 
linked nodal elements form around the catalytic elements and these photo-cells 
tend to keep surviving the perturbations built into the system. This model 
shows that cells can arise from a very simple dynmamic geometric/topological 
substrate long before anything as sophisticated as DNA has happened. 

> On Mar 29, 2016, at 2:54 PM, Stanley N Salthe  wrote:
> 
> Plamen wrote:
> 
>  I begin to believe that the transition from abiotic to biotic structures, 
> incl. Maturana-Varela.-Uribe’s autopoiesis may, really have some underlying 
> matrix/”skeleton”/”programme” which has nothing in common with the nature of 
> DNA, and that DNA and RNA as we know them today may have emerged as secondary 
> or even tertiary “memory” of something underlying deeper below the 
> microbiological surface. It is at least worth thinking in this direction. I 
> do not mean necessarily the role of the number concept and Platonic origin of 
> the universe, but something probably much more “physical”
> 
> 
> 
> 
> 
> S: An interesting recently published effort along these lines is: 
> 
> Alvaro Moreno and Matteo Mossio: Biological Autonomy: A Philosophical and 
> Theoretical Enquiry (History, Philosophy and Theory of the Life Sciences 12) 
> Springer
> 
> They seek a materialist understanding of biology as a system, attempting to 
> refer to the genetic system as little as possible.
> 
> I have until very recently attempted to evade/avoid mechanistic thinking in 
> regard to biology, but, on considering the origin of life generally while 
> keeping Howard Pattee's thinking in mind, I have been struck by the notion 
> that the origin of life (that is: WITH the genetic system) was the origin of 
> mechanism in the universe.  Before that coding system, everything was mass 
> action.  I think we still do not understand how this mechanism evolved.
> 
> STAN
> 
> 
> On Tue, Mar 29, 2016 at 7:40 AM, Dr. Plamen L. Simeonov 
> mailto:plamen.l.simeo...@gmail.com>> wrote:
> 
> Dear Lou, Pedro and All,
> 
>  
> I am going to present a few opportunistic ideas related to what was said 
> before in this session. Coming back to Pivar’s speculative 
> mechano-topological model of life excluding genetics I wish to turn your 
> attention to another author with a similar idea but on a sound mathematical 
> base, Davide Ambrosi with his resume at 
> https://www.uni-muenster.de/imperia/md/content/cim/events/cim-mathmod-workshop-2015_abstracts.pdf
>  
> :
> 
> “Davide Ambrosi:
> 
> A role for mechanics in the growth, remodelling and morphogenesis of living 
> systems  In the XX Century the interactions between mechanics in biology were 
> much  biased by a bioengineering attitude: people were mainly interested in  
> evaluating the state of stress that bones and tissues undergo in order to  
> properly design prosthesis and devices. However in the last decades a new 
> vision is emerging. "Mechano-biology" is changing the point of view, with 
> respect to "Bio-mechanics", emphasizing the biological feedback. Cells, 
> tissues and organs do not only deform when loaded: they reorganize, they 
> duplicate, they actively produce dynamic patterns that apparently have 
> multiple biological aims.
> In this talk I will concentrate on two paradigmatic systems where the 
> interplay between mechanics and biology is, in my opinion, particularly 
> challenging: the homeostatic stress as a driver for remodeling of soft tissue 
> and the tension as a mechanism to transmit information about the size of 
> organs during morphogenesis. In both cases it seems that mechanics plays a 
> role which at least accompanies and enforces the biochemical signaling.”
>  
>  
> Some more details about this approach can be found here:
> http://rsta.royalsocietypublishing.org/content/367/1902/3335 
> 
> http://biomechanics.stanford.edu/paper/MFOreport.pdf 
> 
> In other words, for the core information theorists in FIS, the question is: 
> is there really only (epi)genetic evolution communication in living 
> organisms. Stan Salthe and Lou Kauffman already provided some answers. I 
> begin to believe that the transition from abiotic to biotic structures, incl. 
> Maturana-Varela.-Uribe’s autopoiesis may, really have some underlying 
> matrix/”skeleton”/”programme” which has nothing in common with the nature of 
> DNA, and that DNA and RNA as we know them today
> 
> http://www.sciencedirect.com

[Fis] _ Re: On mathematical theories and models in biology

[Stanley N Salthe]

Plamen wrote:

 I begin to believe that the transition from abiotic to biotic structures,
incl. Maturana-Varela.-Uribe’s autopoiesis may, really have some underlying
matrix/”skeleton”/”programme” which has nothing in common with the nature
of DNA, and that DNA and RNA as we know them today may have emerged as
secondary or even tertiary “memory” of something underlying deeper below
the microbiological surface. It is at least worth thinking in this
direction. I do not mean necessarily the role of the number concept and
Platonic origin of the universe, but something probably much more “physical”



S: An interesting recently published effort along these lines is:

Alvaro Moreno and Matteo Mossio: Biological Autonomy: A Philosophical and
Theoretical Enquiry (History, Philosophy and Theory of the Life Sciences
12) Springer

They seek a materialist understanding of biology as a system, attempting to
refer to the genetic system as little as possible.

I have until very recently attempted to evade/avoid mechanistic thinking in
regard to biology, but, on considering the origin of life generally while
keeping Howard Pattee's thinking in mind, I have been struck by the notion
that the origin of life (that is: WITH the genetic system) was the origin
of mechanism in the universe.  Before that coding system, everything was
mass action.  I think we still do not understand how this mechanism evolved.

STAN

On Tue, Mar 29, 2016 at 7:40 AM, Dr. Plamen L. Simeonov <
plamen.l.simeo...@gmail.com> wrote:

>
> Dear Lou, Pedro and All,
>
>
>
> I am going to present a few opportunistic ideas related to what was said
> before in this session. Coming back to Pivar’s speculative
> mechano-topological model of life excluding genetics I wish to turn your
> attention to another author with a similar idea but on a sound mathematical
> base, Davide Ambrosi with his resume at
> https://www.uni-muenster.de/imperia/md/content/cim/events/cim-mathmod-workshop-2015_abstracts.pdf
> :
>
> “Davide Ambrosi:
>
> A role for mechanics in the growth, remodelling and morphogenesis of
> living systems  In the XX Century the interactions between mechanics in
> biology were much  biased by a bioengineering attitude: people were
> mainly interested in  evaluating the state of stress that bones and
> tissues undergo in order to  properly design prosthesis and devices.
> However in the last decades a new vision is emerging. "Mechano-biology" is
> changing the point of view, with respect to "Bio-mechanics", emphasizing
> the biological feedback. Cells, tissues and organs do not only deform when
> loaded: they reorganize, they duplicate, they actively produce dynamic
> patterns that apparently have multiple biological aims.
>
> In this talk I will concentrate on two paradigmatic systems where the
> interplay between mechanics and biology is, in my opinion, particularly
> challenging: the homeostatic stress as a driver for remodeling of soft
> tissue and the tension as a mechanism to transmit information about the
> size of organs during morphogenesis. In both cases it seems that mechanics
> plays a role which at least accompanies and enforces the biochemical
> signaling.”
>
>
>
>
>
> Some more details about this approach can be found here:
>
> http://rsta.royalsocietypublishing.org/content/367/1902/3335
>
> http://biomechanics.stanford.edu/paper/MFOreport.pdf
>
> In other words, for the core information theorists in FIS, the question
> is: is there really only (epi)genetic evolution communication in living
> organisms. Stan Salthe and Lou Kauffman already provided some answers. I
> begin to believe that the transition from abiotic to biotic structures,
> incl. Maturana-Varela.-Uribe’s autopoiesis may, really have some underlying
> matrix/”skeleton”/”programme” which has nothing in common with the nature
> of DNA, and that DNA and RNA as we know them today
>
> http://www.sciencedirect.com/science/article/pii/S0022519314006778
>
> http://www.sciencedirect.com/science/article/pii/S0022519316001260
>
> https://www.sciencedaily.com/releases/2015/01/150107101405.htm
>
> may have emerged as secondary or even tertiary “memory” of something
> underlying deeper below the microbiological surface. It is at least worth
> thinking in this direction. I do not mean necessarily the role of the
> number concept and Platonic origin of the universe, but something probably
> much more “physical” or at least staying at the edge between
> physical/material and immaterial such as David Deutsch’s constructor theory
> (http://constructortheory.org/) and Brian Josephson’s
> “structural/circular theory” (
> http://arxiv.org/ftp/arxiv/papers/1502/1502.02429.pdf;
> http://arxiv.org/ftp/arxiv/papers/1506/1506.06774.pdf;
> http://arxiv.org/pdf/1108.4860.pdf) searching for the theories
> underpinning the foundations of the physical laws (and following Wheeler’s
> definition for a “Law without Law”.
>
> Some of you may say that QT and Gravitation Theory are responsible for
> such kind of stran

[Fis] On mathematical theories and models in biology

[Dr. Plamen L. Simeonov]

Dear Lou, Pedro and All,



I am going to present a few opportunistic ideas related to what was said
before in this session. Coming back to Pivar’s speculative
mechano-topological model of life excluding genetics I wish to turn your
attention to another author with a similar idea but on a sound mathematical
base, Davide Ambrosi with his resume at
https://www.uni-muenster.de/imperia/md/content/cim/events/cim-mathmod-workshop-2015_abstracts.pdf
:

“Davide Ambrosi:

A role for mechanics in the growth, remodelling and morphogenesis of living
systems  In the XX Century the interactions between mechanics in biology
were much  biased by a bioengineering attitude: people were mainly
interested in  evaluating the state of stress that bones and tissues
undergo in order to  properly design prosthesis and devices. However in the
last decades a new vision is emerging. "Mechano-biology" is changing the
point of view, with respect to "Bio-mechanics", emphasizing the biological
feedback. Cells, tissues and organs do not only deform when loaded: they
reorganize, they duplicate, they actively produce dynamic patterns that
apparently have multiple biological aims.

In this talk I will concentrate on two paradigmatic systems where the
interplay between mechanics and biology is, in my opinion, particularly
challenging: the homeostatic stress as a driver for remodeling of soft
tissue and the tension as a mechanism to transmit information about the
size of organs during morphogenesis. In both cases it seems that mechanics
plays a role which at least accompanies and enforces the biochemical
signaling.”





Some more details about this approach can be found here:

http://rsta.royalsocietypublishing.org/content/367/1902/3335

http://biomechanics.stanford.edu/paper/MFOreport.pdf

In other words, for the core information theorists in FIS, the question is:
is there really only (epi)genetic evolution communication in living
organisms. Stan Salthe and Lou Kauffman already provided some answers. I
begin to believe that the transition from abiotic to biotic structures,
incl. Maturana-Varela.-Uribe’s autopoiesis may, really have some underlying
matrix/”skeleton”/”programme” which has nothing in common with the nature
of DNA, and that DNA and RNA as we know them today

http://www.sciencedirect.com/science/article/pii/S0022519314006778

http://www.sciencedirect.com/science/article/pii/S0022519316001260

https://www.sciencedaily.com/releases/2015/01/150107101405.htm

may have emerged as secondary or even tertiary “memory” of something
underlying deeper below the microbiological surface. It is at least worth
thinking in this direction. I do not mean necessarily the role of the
number concept and Platonic origin of the universe, but something probably
much more “physical” or at least staying at the edge between
physical/material and immaterial such as David Deutsch’s constructor theory
(http://constructortheory.org/) and Brian Josephson’s “structural/circular
theory” (http://arxiv.org/ftp/arxiv/papers/1502/1502.02429.pdf;
http://arxiv.org/ftp/arxiv/papers/1506/1506.06774.pdf;
http://arxiv.org/pdf/1108.4860.pdf) searching for the theories underpinning
the foundations of the physical laws (and following Wheeler’s definition
for a “Law without Law”.

Some of you may say that QT and Gravitation Theory are responsible for such
kind of strange effects, but I would rather leave the brackets open,
because the recent discussion about potentialities and actualities in QM
brings up the idea that there are still different ways of looking at those
concepts (although they are strictly defined in their core domains). This
was actually also the lesson from the last special issue on integral
biomathics (2015) dedicated to phenomenology, with the different opinions
of scientists and philosophers on obviously clear matters in their domains.
This is why also the question of what we define as science needs to be
probably revised in future to include also such issues that are “felt”
rather than “reasoned”, even if we do not have the “proofs” yet, because
the proofs also emerge as subjective (or perhaps “suggested”! – ask the
psychologists for that aspect) thoughts in the minds of the mathematicians.
I am really glad that we began such a phenomenological discussion on this
aspect such as Hipolito’s paper (
http://www.sciencedirect.com/science/article/pii/S0079610715000899) that
was widely commented in the reviewer’s circle. In many cases when we have a
“fuzzy” intuition about a certain relationship or analogy we miss the
correct definitions and concepts, and so in a creative act to hold down the
flying thought we move to using examples, metaphors, pictures. Pedro
correctly addressed the explanatory problem of science which presupposes a
certain causative and predicative “workflow” to derive a conclusion from
the facts, and this is the way in which also proofs are (selectively) made.
As a young scholar I often wondered how artificially people like Gauss,
Cauchy and W