[Fis] [External Email] Re: Biological computation session - Kickoff Text. Comment

Sat Jun 18 16:28:38 CEST 2022

Dear Stan, dear Gordana,

I completely agree with your statement. The QM interpretation can be validated as the concept substantiating, e.g., the criteria of the system's optimization and efficiency in prevailing against disturbances, etc. The question here is whether metamathematics can be validated and be efficient as mathematics itself, as the foundations of theoretical biology are relevant to metamathematical challenges of formulation of the basic principles of reasoning relevant to those that we have in the foundations of mathematics. The concept of univalent foundations of mathematics developed by Voevodsky, which we discussed in the special issue of Biosystems last year, assumes that metamathematical statements can be validated also on computer. Here is the link to the editorial and to the papers of the special issue on the foundations of mathematics and theoretical biology:

https://www.sciencedirect.com/journal/biosystems/special-issue/10PPLLRFK11

When we analyze the transitions between the potential and the actual and apply QM approaches to biological systems, the practical goal is to validate evolutionary efficiency of biological systems, their optimality and organizational invariance.

Thank you Gordana for definitive formulation in your post the ideas, concepts and chalenges related to natural computation.  In particular, it is important that memory that appears in living systems having loop causality enables them to anticipate external changes, memorize and react on them. This provides the link to the semiotic aspect of living systems, as memory appears as a sign-creating activity which underlies operation and evolution of living systems. Overcoming of the limits of computation itself is non-computable as novelty is the event of zero probability but we need to have an approach to analyze this and thus to comprehend the basis of the evolutionary process.

All the best,
Andrei

________________________________
From: Stanley N Salthe <ssalthe en binghamton.edu>
Sent: June 17, 2022 7:35 PM
To: Andrei Igamberdiev <a_igamberdiev en hotmail.com>; fis <fis en listas.unizar.es>
Subject: Re: [External Email] Re: [Fis] Biological computation session - Kickoff Text. Comment

Andrei --

So then, a QM interpretation would be validated as being ¡®about¡¯ something real in an aspect of actual nature (here a living cell) by way of constructing compatibility with a microscopic perspective derived from conventional microscopic science?

STAN

On Fri, Jun 17, 2022 at 1:59 PM Andrei Igamberdiev <a_igamberdiev en hotmail.com<mailto:a_igamberdiev en hotmail.com>> wrote:
Stan,
I don't see another way of explaining how a system holds coherent state for a prolonged time, without applying a theory that deals with the transition between the potential and the actual. If the quantum idea is removed, then we remove any possible explanations of internal determination of biological activity and the problem of self.
Andrei

________________________________
From: Stanley N Salthe <ssalthe en binghamton.edu<mailto:ssalthe en binghamton.edu>>
Sent: June 17, 2022 1:17 PM
To: Andrei Igamberdiev <a_igamberdiev en hotmail.com<mailto:a_igamberdiev en hotmail.com>>; fis <fis en listas.unizar.es<mailto:fis en listas.unizar.es>>
Subject: Re: [External Email] Re: [Fis] Biological computation session - Kickoff Text. Comment

Andrei -- What happens to your statement if the quantum idea is removed?
STAN

On Thu, Jun 16, 2022 at 4:28 PM Andrei Igamberdiev <a_igamberdiev en hotmail.com<mailto:a_igamberdiev en hotmail.com>> wrote:
Dear Joseph, Marcus, Gordana, Koichiro, Jorge and All,

The basic function of rational activity that includes computation is to move and arrange external objects, i.e. an anticipatory operation on and with externality. Biological organisms perceive the world because they actively move and arrange external bodies. From this point of view, although the physical world is computable, the computational activity itself appears with life in its ability to anticipate and predict the outcome from the potential reality. Mathematics is thus a reflection of the real world that can be transformed into a computable principle of its actualizations and potentializations. Computation is a powerful tool for anticipating some actualizations themselves, and it assumes that the cognitive mathematical entities are separable from the actual reality (abstracting capacity).

Mathematics also contains many formulations that are not actualized in the real world. Also, mathematics itself cannot establish the basis of the values of the fundamental constants in physics. However, these constants determine the process in which the contradictory statements (dynamic oppositions) are separated in time and consequently appear in the process of development.  The potential field of the internal quantum state implies the simultaneous existence of contradictory statements. The actualization of this potential state ends up that this self-contradiction realizes one possibility from many. The basic fundamental idea of Liberman is that computation has its physical limits expressed in fundamental constants, and, actually, these limits shape our world and shape the agents (in the biological world - organisms, but generally can be called ontolons as suggested by Joseph in our book "Philosophy in Reality") that perform computation. Liberman attempted to describe the naturally existing form for such idea in his model of neuron. The model may have some shortcomings in detail but the intention was to find how these basic principles work in the real world.

Thus, the presupposition of computation is the ability to hold the potential state in a kind of physical structure for a prolonged time to generate certain output in the end. That is why the models appear that consider microtubules, hypersound effects, etc. There should be some structure that can hold the potential state. In my opinion, Joseph¡¯s approach and the statements that he provided are fully correct, but their realization, if taken not only philosophically but also from the point of view of natural science, require certain structures that can hold potentiality, the idea arising to Aristotle. Returning to Liberman, we are entering into the search how the complex interplay between actuality and potentiality, continuity and discontinuity, presence and absence, meaning and non-meaning are realized in biological reality, and this relates to the question of macroscopic quantum phenomena that presumably underlie this interplay.

All the best,

Andrei

________________________________
From: joe.brenner en bluewin.ch<mailto:joe.brenner en bluewin.ch> <joe.brenner en bluewin.ch<mailto:joe.brenner en bluewin.ch>>
Sent: June 16, 2022 9:24 AM
To: 'Andrei Igamberdiev' <a_igamberdiev en hotmail.com<mailto:a_igamberdiev en hotmail.com>>; 'Jorge Navarro L¨®pez' <jnavarrol en unizar.es<mailto:jnavarrol en unizar.es>>; fis en listas.unizar.es<mailto:fis en listas.unizar.es> <fis en listas.unizar.es<mailto:fis en listas.unizar.es>>
Subject: RE: [Fis] Biological computation session - Kickoff Text. Comment

Dear Andrei, Dear Nikita and Dear Gordana,

This is to express my gratitude for the expert and felt way in which you have made available to us the work of Efim Liberman and its consequences. There is much I need to ponder about in it, but I make the following interim comment as a possible contribution to its understanding.

As I see it, Liberman developed his concepts of quantum phenomena in life and human consciousness because he felt that standard physics was insufficient to describe their complexity.

I feel however, and have tried to show elsewhere, that the inclusion of the co-existence and co-evolution of potential as well as actual states does permit a dialectic description of the antagonistic aspects of reality including consciousness and life. I note that potentiality is referred to in the documents you have provided, but I argue that its potential (sic!) has not been adequately explored.

My approach, which is due to Stephane Lupasco (Bucharest, 1900-Paris, 1989), is a ¡°logic¡± of interaction, the alternation of the dualities found in real phenomena. Thus, in additional to actuality and potentiality, the same considerations should apply to continuity and discontinuity, presence and absence, meaning and non-meaning and so on. In ascribing quantum characteristics to consciousness for example, implies the existence of quantum levels, hence of discontinuity. But some phenomena clearly instantiate continuity (frequency), and its source needs to be specified.

Note that in principle, my approach is more parsimonious since it does not require the existence of additional physical structures (microtubules, long-lived states) for the functions of interest.

At this time, all I would wish and hope for is that there might be some indication in Liberman or elsewhere that what I have just summarized superficially is not total nonsense.

Thank you and best wishes,

Joseph

From: Fis <fis-bounces en listas.unizar.es<mailto:fis-bounces en listas.unizar.es>> On Behalf Of Andrei Igamberdiev
Sent: Thursday, June 16, 2022 12:33 AM
To: Jorge Navarro L¨®pez <jnavarrol en unizar.es<mailto:jnavarrol en unizar.es>>; fis en listas.unizar.es<mailto:fis en listas.unizar.es>
Subject: Re: [Fis] Biological computation session - kickoff text

Dear Jorge and All,

The concept of Hameroff and Penrose probably catches the main peculiarities of natural computing in nervous system but it has no development for many years, so it is ¡°frozen¡± being in the state of anesthesia. First, it should be expanded from microtubules to long-range coherent event in all macromolecules, e.g., to explain enzymatic catalysis. Second, it should be complemented by concrete molecular mechanisms associated with the postulated quantum phenomena. From this point of view, the model of neuron suggested by Liberman has certain advantages and has a better perspective for development and experimental verification. According to this model, membrane ionic channels can be used for coding and decoding as a molecular computer of neuron operating by implementation of Markov algorithms.  The crucial in operation of this molecular computer is the transmission of signal through cytoskeleton. The views of Liberman probably do not contradict the postulated mechanism of Hameroff and Penrose but emphasize its particular concrete aspects.

Liberman suggested that the transfer of information through neuron includes molecular (DNA, RNA, protein operators with complementary addresses), holographic (quick changeable lattice ¨C cytoskeleton), quantum (each phonon examines whole lattice), and hypersound (with wavelengths 10-1000 nm that do not destroy molecules) constituents. Processing in the cytoskeleton may include phonon interference, absorption and generation, in the result of which sound signals control sodium and potassium output ionic channels. In particular, Liberman suggested that cytoskeleton operates as an extreme quantum molecular hypersonic regulator with the price of action equal to the Planck's constant.

According to this hypothesis, the input ionic channels generate hypersonic signals, which propagate through the cytoskeleton and generate an output in the form of digital code. The latter is realized by opening or closing ionic channels on the other side of neuron. Thus, neuron sends a code that is the message what the next neuron (or muscle) should do. This code can be represented by the duration of interval or by the distance between the impulses but it is not related to different channels of transmission, as it was demonstrated in his initial experiments that the transmission of perception of blue and red colors occurs through the same filament.

The cellular computing device of neuron receives the information when receptors located on the outer membrane interact with certain effectors. As a result, the device ¡°calculates¡± how to react on this signal. This can be achieved via cutting and gluing together the parts of nucleic acids. In this regard, it is important to mention here that E.A. Liberman predicted splicing before its discovery. As a result, protein molecules are synthesized which initiate the subsequent response reaction. In the case of neuron, it may be a rearrangement of the cytoskeleton. In line with these assumptions, it was claimed that the cells of human brain act similarly as a big telephonic station operated according to the principles of the analog computer. It is not possible to analyze its work with perfect precision because of the uncontrolled influence on the internally operating system, according to the nature of quantum measurement.

The cytoskeleton, to serve as a ¡°calculating medium¡±, supports a long-distance coherence and may represent a 3D diffraction pattern for the hypersound, which distribution results in slow conformational movements. Hameroff also suggested that in living systems, protein conformational states represent fundamental informational units utilized in quantum computation. Long-living coherent states in the cytoskeleton can explain non-local effects in biological function, including operation of consciousness.

Indeed, the electromagnetic waves with a length of about the molecular size, as Liberman mentioned, destroy molecular structures and that is why they cannot be effectively used for control inside of the living cell. At the same time, mechanical and hypersound vibrations spread with much less speed and in the proposed ranges they do not destroy these extremely small calculating elements. Microtubule-associated proteins can ¡°tune¡± the quantum oscillations of the coherent superposed states. In Liberman's words, cytoskeleton forms a calculating medium for the molecular computer of neuron.

It seems to me that the model of Liberman has a good potential for development but its specific details need further investigation.

Regards,

Andrei

________________________________

From: Fis <fis-bounces en listas.unizar.es<mailto:fis-bounces en listas.unizar.es>> on behalf of Jorge Navarro L¨®pez <jnavarrol en unizar.es<mailto:jnavarrol en unizar.es>>
Sent: June 15, 2022 10:49 AM
To: fis en listas.unizar.es<mailto:fis en listas.unizar.es> <fis en listas.unizar.es<mailto:fis en listas.unizar.es>>
Subject: Re: [Fis] Biological computation session - kickoff text

Thanks, Nikita and Andrei, for your text and the very intriguing special issue. The personal figure of Efim Liberman is fascinating.

Currently I am working in AI, in the field of sentiment analysis (using big data from social networks). In this field we have a bottleneck in the way data are processed and stored, for the classical von Neumann architecture keeps them separately and processors have to spend most of their time and energy moving data back and forth. There are some partial achievements and special processors have been developed, but clearly it is not enough for the current needs of AI and IoT. So, the interest, or at least the need, for exploring bio-inspired and brain-inspired computing is growing substantially.

In this sense, I have two questions. Those theoretical schemes of MCC and QMR from Liberman have they been explored in the sense of suggesting alternative architectures of data processing? And further, I have curiosity on what relationship could be established between QMR and Hameroff and Penrose's quantum computation in the microtubules? I have not heard that the "tubulin qubit" had any feasibility within the cellular environment... Could the hypothesis of hypersound quasiparticles be more feasible cellularly?

Thanks again for the kickoff.

Regards,

Jorge Navarro

El 13/06/2022 a las 17:36, Andrei Igamberdiev escribi¨®:

Dear Colleagues,

here is the text to start the session on natural computation devoted to Efim Liberman (1925-2011).

We look forward for discussing this important topic. It became the basis of the special issue of the journal BioSystems:

https://www.sciencedirect.com/journal/biosystems/special-issue/107NLGRSL8M

With best regards,

Nikita Shklovskiy-Kordi and Andrei Igamberdiev

Natural computation (Biological computation)

Following the pioneering works of Efim A. Liberman (1972, 1979), Koichiro Matsuno (1995), and Michael Conrad (1999), it became apparent that computability is generated internally in evolving biological systems. While quantum computation in human technology is still in early stages and does not go beyond the simplest realizations, it develops in biological systems in a complex way starting from the origin of life to the sophistication of enzymes¡¯ work. A thorough search of the appropriate conceptual tools and mathematical language is needed, so that it will help theoretical biologists to provide new insights on the apparent goal-directedness, biological complexity, and human consciousness¡ªit is an important task for the future. The biological computation concept became a basis of the powerful scientific paradigm that is currently acquiring new important developments.

Professor Efim A. Liberman (1925-2011) pioneered the paradigm of biological computation and developed the concepts of the molecular cell computer and the computational operation of neuron. He published several important papers in BioSystems from 1979 to 1996, in close collaboration with the editor-in-chief Michael Conrad. His concept of biological cell as a molecular computer was published in 1972 (Liberman, 1972) followed by the series of papers where he developed this concept in more detail and made further advancement.

Efim Liberman suggested the existence of a quantum computing system of life based on an estimate of the proximity to the minimum possible of the energy spend by living organisms on the calculations necessary to control macroscopic bodies with many degrees of freedom in real time, as well as on the calculations that ensure the existence of our consciousness.

Liberman gave these quantum computing systems the names - "quantum molecular regulator" - QMR and - "extreme quantum regulator" - EQR.

Liberman proposed the available for experimental verification connection between the "molecular cell computer" - MCC and the quantum computer system of the cell, in the work of enzymes and ion channels of a living cell, functioning as input devices for transmitting information from the M§³§³ to quantum regulators, and the cytoskeleton as a computing environment for quantum calculations. The implementation of these experiments and the search for suitable conceptual tools and mathematical language are needed to help theoretical biologists take a fresh look at the apparent feasibility or teleonomic basis of living systems, the development of biological complexity, and the basis of human consciousness.

The virtual special issue of BioSystems ¡°Fundamental principles of biological computation: From molecular computing to biological complexity¡± commemorates the first publication of Efim Liberman on biological computation at its 50th anniversary. It was edited by Nikita Shklovskiy-Kordi, Koichiro Matsuno, Pedro Marijuan and Andrei Igamberdiev. The webpage of this special issue is:

https://www.sciencedirect.com/journal/biosystems/special-issue/107NLGRSL8M

Some papers of this issue have free access, and for other papers, you can send a request to the editors to receive a copy. The biographical essay of Efim Liberman ¡°On the way to a new science¡± (https://www.sciencedirect.com/science/article/pii/S0303264722000399) represents an autobiographic courageous creative story of life in science. Efim Liberman presented in this essay not only the story of his life but also his thoughts about the role of science and its future development and unification, with the ultimate goal to unite and harmonize our understanding of life and nature. Nikita Shklovskiy-Kordi and Andrei (Abir) igamberdiev review the contributions of Liberman in understanding the mechanisms of intracellular processing of information (https://www.sciencedirect.com/science/article/pii/S0303264722000454).  It can be considered as an overview of Liberman¡¯s efforts to create an integrative theory of natural computation that aims to unite biology, physics and mathematics, which he called Chaimatics.

In other papers of the issue, different aspects of biological computations are discussed including Physical foundations of biology; Quantum computation in biological organization; Molecular recognition; Cellular control; Neuromolecular computing; Molecular computing processes; Self-organizing and self-replicating systems; Computational principles in biological development; Origins and evolution of the genetic mechanism; Fundamental nature of biological information processing.

Nikita Sklovskiy-Kordi and Andrei Igamberdiev

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