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

Fri Jun 17 15:17:47 CEST 2022

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> 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 <joe.brenner en bluewin.ch>
> *Sent:* June 16, 2022 9:24 AM
> *To:* 'Andrei Igamberdiev' <a_igamberdiev en hotmail.com>; 'Jorge Navarro
> López' <jnavarrol en unizar.es>; fis en listas.unizar.es <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> *On Behalf Of *Andrei
> Igamberdiev
> *Sent:* Thursday, June 16, 2022 12:33 AM
> *To:* Jorge Navarro López <jnavarrol en unizar.es>; 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 – 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> on behalf of Jorge Navarro
> López <jnavarrol en unizar.es>
> *Sent:* June 15, 2022 10:49 AM
> *To:* fis en listas.unizar.es <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 escribió:
>
> 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—it 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 MСС 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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