[Fis] Summarising this weeks discussion

Thu Jun 30 03:21:18 CEST 2022

Dear Plamen, Koichiro and All,
Thank you Plamen for your important messages. I think, the Heisenberg uncertainty ratio "energy-time" can be named, in relation to the internal measurement and following Liberman's principle of "minimum price of action", as the principle of "precision of action". It can be considered as a sub-principle of the first principle and in biological computation it determines the balance between the precision of action and its duration. It can be the basis of optimality in biosystems that determines the choice between the fast and less precise reaction and slow and highly precise. All this is controlled through the achievement of maximum efficiency of the system in concrete conditions (environment, etc.). Long conformational relaxation of macromolecules corresponds to holding coherent state and providing the precision of the output. This is the model of quantum non-demolition (QND) measurement, which corresponds to the internal measurement with a high precision. The sensitivity of detector is determined by its relaxation properties. The QND measurements are characterized by low energy dissipation and provide the basis for quantum computation in biosystems. Actual energy dissipation in the course of measurement proceeds by emitting quanta carrying energy E at the time interval t. Calculation of this energy was done, e.g., in the paper of Matsuno and Paton (2000). Thus, these ideas can be experimentally verified.

All the best,
Andrei

________________________________
From: Plamen <plamen.l.simeonov en gmail.com>
Sent: June 26, 2022 10:12 AM
To: Koichiro Matsuno <CXQ02365 en nifty.com>
Cc: Andrei Igamberdiev <a_igamberdiev en hotmail.com>; Gordana Dodig Crnkovic <gordana.dodig-crnkovic en chalmers.se>; Nikita Shklovsky <nikitashk en gmail.com>; joe.brenner en bluewin.ch <joe.brenner en bluewin.ch>; fis en listas.unizar.es <fis en listas.unizar.es>
Subject: Re: [Fis] Summarising this weeks discussion

This is an interesting idea I like, Koichiro and Andrei.
Are there any other (anticipated) forms of biocomputation languages beyond the symbolical and indexing ones that can get mixed up at a later point in time? I think we should keep in mind Gödel‘s inheritance avoid repeating Hilbert‘s mistake, which is a biological one at its core.

Best,

Plamen

On Jun 26, 2022, at 11:07 AM, Koichiro Matsuno <CXQ02365 en nifty.com> wrote:

Saturday, June 25, 2022 3:54 AM, Andrei Igamberdiev a_igamberdiev en hotmail.com<mailto:a_igamberdiev en 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 en hotmail.com<mailto:a_igamberdiev en hotmail.com>>
Sent: Saturday, June 25, 2022 3:54 AM
To: Gordana Dodig Crnkovic <gordana.dodig-crnkovic en chalmers.se<mailto:gordana.dodig-crnkovic en chalmers.se>>; Nikita Shklovsky <nikitashk en gmail.com<mailto:nikitashk en gmail.com>>; Koichiro Matsuno <cxq02365 en nifty.com<mailto:cxq02365 en nifty.com>>; joe.brenner en bluewin.ch<mailto:joe.brenner en bluewin.ch>; fis en listas.unizar.es<mailto:fis en 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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________________________________
From: Plamen <plamen.l.simeonov en gmail.com>
Sent: June 26, 2022 10:12 AM
To: Koichiro Matsuno <CXQ02365 en nifty.com>
Cc: Andrei Igamberdiev <a_igamberdiev en hotmail.com>; Gordana Dodig Crnkovic <gordana.dodig-crnkovic en chalmers.se>; Nikita Shklovsky <nikitashk en gmail.com>; joe.brenner en bluewin.ch <joe.brenner en bluewin.ch>; fis en listas.unizar.es <fis en listas.unizar.es>
Subject: Re: [Fis] Summarising this weeks discussion

This is an interesting idea I like, Koichiro and Andrei.
Are there any other (anticipated) forms of biocomputation languages beyond the symbolical and indexing ones that can get mixed up at a later point in time? I think we should keep in mind Gödel‘s inheritance avoid repeating Hilbert‘s mistake, which is a biological one at its core.

Best,

Plamen

On Jun 26, 2022, at 11:07 AM, Koichiro Matsuno <CXQ02365 en nifty.com> wrote:

Saturday, June 25, 2022 3:54 AM, Andrei Igamberdiev a_igamberdiev en hotmail.com<mailto:a_igamberdiev en 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 en hotmail.com<mailto:a_igamberdiev en hotmail.com>>
Sent: Saturday, June 25, 2022 3:54 AM
To: Gordana Dodig Crnkovic <gordana.dodig-crnkovic en chalmers.se<mailto:gordana.dodig-crnkovic en chalmers.se>>; Nikita Shklovsky <nikitashk en gmail.com<mailto:nikitashk en gmail.com>>; Koichiro Matsuno <cxq02365 en nifty.com<mailto:cxq02365 en nifty.com>>; joe.brenner en bluewin.ch<mailto:joe.brenner en bluewin.ch>; fis en listas.unizar.es<mailto:fis en 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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