[Fis] Summarising this weeks discussion. Another oxymoron

[Dr. Plamen L. Simeonov]

Dear Koichiro, Joe, Andrei and All,

sorry for joining the discussion a bit late. I was observing it with
interest but other duties distracted me from earlier reactions.
Let's agree on one particular important aspect that needs attention at all
subsumptive hierarchy levels of biocomputation - to use Stan
Salthe's model,  -  related to the pair homeostasis-illness, - I refer to
earlier discussions with John Torday, partly in this forum, I think - which
declare two entirely different modes of biocomputation: correct,
regulated and incorrect, false or dysregulated, while accepting the fact
that there is no perfect health or illness, but usually some configuration
which is very distinct in each individual's "(self-)programming". What do
we mean exactly when referring to related issues of computation from the
quantum level, through macromolecules up to organs and systems in a living
organism? We refer to the logical validation of systemic processes that
needs to be balanced (with some degree of fault tolerance) in order to
compute and make transitions, deliver concentrations of substances,
fields interferences, enable signalling, etc. correctly between the diverse
levels. This is what makes comprehending biocomputing so difficult. It is
like a mixture of digital, analog, quantum and fuzzy processing all in one,
often unnoticeable, although available, at some levels and emphasized at
others.  We cannot reduce that kind of interactions in living systems just
to one or two or even 10 kinds of phenomena or (sub)-computations. They are
all available and interact with each other simultaneously. There is not a
single form of such biocomputing or "intelligence" of a cell, an organ or a
system that can be said as a major manifestation of this process, since
they all emerged and evolved with the purpose maintain homeostasis and
negentropy (negative entropy) in contradiction to purely physical systems,
and yet being a part of a complex with them. What I wish to say with all
this is that e.g. an infection with a novel virus from outside, introduces
a (computing) process of regulation, adaptation and inclusion of new modes
of computing into the organism. It happens permanently:  an unfinished and
infinite process. This is how eukaryotes emerged from prokaryotes and
mitochondria were adopted and integrated within the cell plasma to deliver
beneficial modulating forms of processing, usually at a different level
than the one of the adopter, and communicate with other peers inside and
inside the host system. RNAs and DNAs, as well as CNS and other tools,
engines and utilities emerged and/or were ready adopted at certain points
in evolution (spare time), which also means that a selective process was
undergoing. The different modi of biocomputing have different logics, but
they need to be made compatible with each other at the "joint"/ transition
points, since when homeostasis is disturbed, this ultimately leads to death
of the entire system.

Just as a comment.

Best,

plamen

On Sun, Jun 26, 2022 at 12:04 PM <joe.brenner at bluewin.ch> wrote:

> Dear Koichiro,
>
>
>
> This statement is certainly valid. What Andrei and I have been trying to
> say is that Heisenberg uncertainty is one of a larger group of process
> descriptions characterized by uncertainty, imprecision, ‘diversity’,
> *etc.* Their elements, however. are always dual, instantiating actuality
> and potentiality in a changing, reciprocal relation. “Integration”, e.g.,
> of symbolical and indexical is not necessary if this would mean that the
> terms lose their identity. The logic is a logic of dynamic coexistence.
>
>
>
> It is, at least for me, a measure of the validity of your approach that
> what others might consider an oxymoron applies: *uncertainty* at the
> origin of the *precision* of macromolecules as computing devices”. I
> think Lupasco would have appreciated this formulation.
>
>
>
> Best,
>
>
>
> Joseph
>
>
>
>
>
> *From:* Fis <fis-bounces at listas.unizar.es> *On Behalf Of *Koichiro Matsuno
> *Sent:* Sunday, June 26, 2022 10:06 AM
> *To:* 'Andrei Igamberdiev' <a_igamberdiev at hotmail.com>; 'Gordana Dodig
> Crnkovic' <gordana.dodig-crnkovic at chalmers.se>; 'Nikita Shklovsky' <
> nikitashk at gmail.com>; joe.brenner at bluewin.ch; fis at listas.unizar.es
> *Subject:* Re: [Fis] Summarising this weeks discussion
>
>
>
> Saturday, June 25, 2022 3:54 AM, Andrei Igamberdiev
> a_igamberdiev at hotmail.com wrote;
>
> I suggested the idea that the Heisenberg uncertainty ratio “energy-time”
> can explain the precision of operation of macromolecules as computing
> devices in living systems
>
>
>
> Quantum mechanics has been an attempt for preventing us from falling into
> a helpless abyss in case symbolical and indexical languages simply got
> mixed up. QM regulation integrating both the symbolical and indexical,
> e.g., conservation laws and measurements, as epitomized in the uncertainty
> relation, is an instance of quantum computation, and relevant to biology
> also.
>
>
>
>   Best,
>
>   Koichiro
>
>
>
>
>
>
>
> *From:* Andrei Igamberdiev <a_igamberdiev at hotmail.com>
> *Sent:* Saturday, June 25, 2022 3:54 AM
> *To:* Gordana Dodig Crnkovic <gordana.dodig-crnkovic at chalmers.se>; Nikita
> Shklovsky <nikitashk at gmail.com>; Koichiro Matsuno <cxq02365 at nifty.com>;
> joe.brenner at bluewin.ch; fis at listas.unizar.es
> *Subject:* Re: Summarising this weeks discussion
>
>
>
> Dear Gordana, Joseph, Koichiro and Nikita,
>
> In my opinion, the exchange between Joseph and Koichiro regarding the
> transitions between the potential and the actual is very important as this
> is the point where we can approach closer to the nature of macromolecular
> (and biological) computation. The whole process of computation is directly
> related to the aspects of “potentiality in reality”. The advanced systems
> that developed complex behavior are able to hold the potential for a
> prolonged time to make precise outputs based on the choice of particular
> result that help the system to navigate in the external world. This means
> that such holding the potential corresponds to the abstracting capacity,
> which was clarified in recent papers of Koichiro. This also corresponds to
> the duality of actual entity and of abstract entity in the philosophy of
> A.N. Whitehead.
>
> Many years ago, in my first paper of BioSystems (1993) I suggested the
> idea that the Heisenberg uncertainty ratio “energy-time” can explain the
> precision of operation of macromolecules as computing devices in living
> systems in a way that the prolonged time of quantum measurement corresponds
> to the minimum dissipation of energy in it, i.e. to the precise result and
> thus represents the basis of natural computation performed by
> macromolecular devices.  These devices operate as molecular automata of the
> extremal quantum computer, and their set maintains highly ordered robust
> coherent state, which precisely directs actualizations in the course of
> natural computational process. During this process, single events
> corresponding to realization of interacting individual programs form a
> percolating network, and this leads to concrete spatial patterns
> constructed using optimal coordinate scales.
>
> I am confident that this concept has a potential for development, and it
> is grounded in the ideas expressed by Efim Liberman in his conceptual
> approach to natural computation. Several concrete aspects of the quantum
> biological computation were outlined in the works of Koichiro Matsuno,
> including the estimation of actual energy dissipation in the course of
> measurement accompanied by emitting quanta, each carrying energy E at every
> time interval τ (Matsuno and Paton, 2000, BioSystems 55: 39-46). The works
> of Yukio Gunji, of Andrei Khrennikov, also earlier works of Howard Pattee
> and others, are particularly important in this development, although we are
> still at the beginning of this important paradigm of the “new science”.  In
> this development, the paradigm of the new science will incorporate the
> ideas of relational biology formulated by Robert Rosen, which will result
> in overcoming their too abstract original representation.  Summarizing, I
> would say that we have all prerequisites for the concept of natural
> computation that can be applied to the real world, and the logic of
> potentiality in reality is in the core of this paradigm. The real world is *tantot
> libre, tantot recherché *(Beethoven words), and this is a pledge of
> freedom, which is the basis of the existence of the world and its
> evolution.
>
> All the best,
>
> Andrei
>
>
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