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

2016-03-29 Thread 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

Looking forward to what others see as fundamental.


> 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

2016-03-29 Thread 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.
>> 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