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

[Francesco Rizzo]

Caro Plamen Simeonov e Cari Tutti,
secondo U. Maturana e F. Varela la conoscenza ha fondamenti biologici.
Tutta la conoscenza, anche quella fisica, soprattutto quella quantistica,
ha fondamenti biologici. E viceversa, la biologia ha fondamenti
quantistici. Quel che scrivo qui sinteticamente può sembrare apodittico e
dogmatico, ma nei miei libri questo è analizzato, approfondito e sistemato
in modo organico: beninteso, secondo l'ottica della mia "Nuova economia".
Quindi vi sono elementi fondati per condividere l'accostamento tra
"platonismo, teologia, logica e algebra". Così come, a me pare ben fondato
il rapporto quadrangolare che passa tra: i numeri primi, la funzione d'onda
di Riemann, la meccanica quantistica e la geometria frattale (dei mercati)
(cfr. fra gli altri,  Rizzo R., "Una vita. Il figlio del garzone", Aracne
editrice, Roma, 2015, pp. 305-306.)
Un augurio, ancora, pasquale.
Francessco

2016-03-30 1:00 GMT+02:00 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: 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 
> 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 
> 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 

[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