Pedro wrote:
"3. About logics in the pre-science, Joseph is quite right demanding that discussion to accompany principles or basic problems. Actually principles, rules, theories, etc. are interconnected or should be by a logic (or several logics?) in order to give validity and coherence to the different combinations of elements. For instance, in the biomolecular realm there is a fascinating interplay of activation and inhibition among the participating molecular partners (enzymes and proteins) as active elements. I am not aware that classical ideas from Jacob (La Logique du vivant) have been sufficiently continued; it is not about Crick's Central Dogma but about the logic of pathways, circuits, modules, etc. Probably both Torday and Ji have their own ideas about that-- I would be curious to hear from them." (1) Enzymes, like all molecular and sub-molecular species (generally called microscopic entities, quantum objects, quons [1], or wavicles) exhibit the wave-particle duality (as evidenced by the fact that they obey the Planckian Distribution Equation (PDE) [2-4]). And yet most of the descriptions of enzyme mechanisms given in the current literature are based on the particle aspect of enzymes including all the efforts directed to understanding enzyme activities in terns of the causal role of the static 1-dimensional sequences of amino acids or their 3-dimensional folds as revealed by the X-ray crystallography. Alternatively, we can describe enzyme structure and function based on their wave attributes, in which case enzymes are viewed as systems of oscillators and their functions are determined by the collective vibrational motions of amino acid residues called "standing waves" (see Figure 8 in [3]). (2) Like electrons (see (4) below)), enzymes (and biopolymers in general, including DNA; see Table 1 below) may possesses two complementary attributes -- static and dynamic. Just as the position and momentum of the electron cannot be accounted for by their static attributes alone, so perhaps the static attributes of enzymes (e.g., amino acid sequences) alone may not be sufficient to account for their dynamic attributes, i.e., their catalytic activities. The missing link may be sought in their wave attributes which have collective organizing power. Traveling waves generated within a volume can interact to form "standing waves", also called "resonant waves", as exemplified by the Chladini plate shown below: https://www.youtube.com/watch?v=wvJAgrUBF4w<https://www.youtube.com/watch?v=wvJAgrUBF4w> [https://www.bing.com/th?id=OVP.0CuEeLYreRH1jrVSaq2sMwEsDh&pid=Api]<https://www.youtube.com/watch?v=wvJAgrUBF4w> Amazing Resonance Experiment!<https://www.youtube.com/watch?v=wvJAgrUBF4w> www.youtube.com Add me on Facebook - (click LIKE on Facebook to add me) http://www.facebook.com/brusspup The song in the video is my latest song. You can find it on iTunes o... (3) There is accumulating evidence (references available upon request) to support the following mechanism of enzyme action: E <-----------> E' (1) E' + S <-----------> [E.S <===> E.P] (2) [E.S <===> E.P] <-----------> E + P (3) ________________________________________ E + S <-----------> E + P (4) Figure 1. The pre-fit mechanism (in contrast to the better-known "induced-fit mechanism of Koshland) of enzyme catalysis [1]. Symbols are defined as follows: E = ground-state enzyme; E' = conformationally excited enzyme through thermal fluctuations; S = substrate; E.S = Enzyme-substrate complex in the transition state; E.P = the enzyme-product complex in the transition state; <-----> = thermally equilibrium; <===> = the resonance hybrid between the enzyme-substrate and enzyme-product complexes. Step (1) indicates that an enzyme molecule is a collection of oscillators that interact with one another to form higher-order structures, either local or global, known as resonances or standing waves. In the Chladni plate, what causes the 'visible' standing waves of particles on it is the 'invisible' vibrational motions of the plate itself and the particles are forced to form standing waves through resonance energy transfer from the plate to individual particles. In enzymes, what causes the formation of the standing waves or resonant waves of the enzyme molecule are the component amino acid residues acting as elementary oscillators whose periodic motions can combine, obeying the Fourier theorem, to form almost infinite number of standing waves, some of which are 'selected' by the substrate via complementary binding. I am not a quantum mechanician, but I think (please correct me if I am in error) the enzyme catalytic mechanism depicted in Figure 1 can be represented in terms of the matrix algebra used in quantum mechanics thus: A*S =λ*S (5) where A is the matrix consisting of all the possible conformational states of an enzyme, S is the substrate, and λ is the conformational state of the enzyme that is selected by S binding because it transforms S to P. In physics, A is called the operator, S is the eigenvector, and λ is the eigenvalue. From the infomation-theoretic point of view, an enzyme molecule can be viewed as the information source containing all the conformaitonal states accessible through thermal fluctuations or Brownian motions, and substrate binding selects a subset of those conformational states that are conducive to catalytic actions. If the number of all possible conformational state of an enzyme is N and substrate S selects n of these to be transformed into P, then the the amount of information generated by the catalytic reaction would be log_2(N/n) bits, (6) assuming for simplicity that all the conformations accessible to the enzyme have equal probabilities of being exposed to the substrate. (4) Physicists recognize two complementary attributes of quantum entities, also called quons or wavicles -- (i) static and (ii) dynamic attributes. For example, the electron has the static attributes of mass, charge and spin magnitude and the dynamic attributes of position, momentum, and spin direction. Herbert [6. p. 99] writes: "Each quon possesses two kinds of attributes static and dynamic. A static attribute always has the same size each time it is measured, and thus serves to distinguish one type of quon from another. . . . " . Similarly, I think it is reasonable to assume that DNA (and other biopolymers, including enzymes, see (3) above) has two kinds of attributes -- (i) static (e.g., nucleotide sequences of genes) and (ii) dynamic (e.g., vibrational patterns of DNA as a whole which are predictable in principle, based on the Fourier theorem, from the elementary vibrational motions of the molecules constituting the genetic alphabet, A, C, G and T). (5) The dynamic attributes of DNA may be compared to the audio music and its static attributes with sheet music (see Rows 4 and 5 in Table 1). Table 1 contains other interesting comparisons between a piano and the DNA molecule viewed as a self-organizing or self-playing molecular piano, in agreement with the recent conclusions drawn by S. Petohukhov who developed the novel system-resonance approach to studying the genetic codes [7, 8]. According to my crude estimation, the maximum information capacity of DNA is about 200 bits (see the 2nd Row, Table 1). Table 1. The Postulate that DNA is a self-organizing molecular piano keyboard (SOMPK) DNA Piano 1. Units of oscillations ~ 1010 nucleotides 88 keys 2. Number of possible resonant oscillations 410^10 ~ almost infinite Maximum Shannon information content of DNA = log_2(4)^(10^10) =200 bits, if each oscillation can act as a potential message almost infinite (?) 3. Agent Living cell Pianist 4. Dynamic structures (including standing waves) Time-dependent folding patterns of DNA, chromatins and chromosomes which are thought to determine its biological functions (see Figure 8 in [3]) Musical melodies (also called Audio music) 5. Static structures Nucleotide sequences of individual cells, not of species Sheet music 6. Scale Microscopic Macroscopic 7. Thermal Fluctuations Essential for Function Detrimental to Function 8. Obeys Matter-Energy Conservation Law Wave-Particle Duality Principle [2-4] Fourier Theorem Minimum Energy Requirement for Information Transmission Matter-Energy Conservation Law Wave-Particle Duality Principle [2-4] Fourier Theorem Minimum Energy Requirement for Information Transmission Any questions, corrections, or suggestions are welcome. All the best. Sung References: [1] Ji, S. (2012). The Kinetics of Ligand-Protein Interactions: The“Pre-fit” Mechanism <http://www.conformon.net/?attachment_id=983> Based on the Generalized Franck-Condon Principle. In: Molecular Theory of the Living Cell: Concepts, Molecular Mechanisms, and Biomeduical Applicaitons. Springer, New Y0ork. Pp. 209-214. http://www.conformon.net/wp-content/uploads/2014/01/Pre_fit_hypothesis_p209_p213.pdf<http://www.conformon.net/wp-content/uploads/2014/01/Pre_fit_hypothesis_p209_p213.pdf><http://www.conformon.net/wp-content/uploads/2014/01/Pre_fit_hypothesis_p209_p213.pdf> [2] Ji, S. (2016). WAVE-PARTICLE DUALITY IN PHYSICS AND BIOMEDICAL SCIENCES.<http://www.conformon.net/wp-content/uploads/2016/09/PDE_SymmetryFestival_2016.pdf> Symmetry: Science and Culture 27 (2): 99-127 (2016). http://www.conformon.net/wp-content/uploads/2016/09/PDE_SymmetryFestival_2016.pdf [3] Ji, S. (2015). Planckian distributions in molecular machines, living cells, and brains: The wave-particle duality in biomedical sciences.<http://www.conformon.net/wp-content/uploads/2016/09/PDE_Vienna_2015.pdf> In: Proceedings of the International Conference on Biology and Biomedical Engineering, Vienna, March 15-17, 2015. Pp. 115-137. http://www.conformon.net/wp-content/uploads/2016/09/PDE_Vienna_2015.pdf [4] Ji, S. (2015). PLANCKIAN INFORMATION (IP): A NEW MEASURE OF ORDER IN ATOMS, ENZYMES, CELLS, BRAINS, HUMAN SOCIETIES, AND THE COSMOS. <http://www.conformon.net/wp-content/uploads/2016/09/PDE_Vigier9.pdf> In: Unified Field Mechanics: Natural Science beyond the Veil of Spacetime (Amoroso, R., Rowlands, P., and Kauffman, L. eds.), World Scientific, New Jersey, 2015, pp. 579-589). http://www.conformon.net/wp-content/uploads/2016/09/PDE_Vigier9.pdf <http://www.conformon.net/wp-content/uploads/2016/09/PDE_Vigier9.pdf><http://www.conformon.net/wp-content/uploads/2016/09/PDE_Vigier9.pdf> [5] Ji, S. (2017). The Cell Language Theory: Connecting Mind and Matter. World Scientific Publications, New Jersey. Section 4.12. [6] Herbert, N. (1987). Quantum Reality: Beyond the New Physics, an Excursion into Metaphysics . . . Anchor Books, New York. [7] Petoukhov, S. V. (2016). The system-resonance approach in modeling genetic structures. BioSystems 139:1-11. http://www.sciencedirect.com/science/article/pii/S0303264715001732 [8] Petoukihov, S. V. (2017). The rules of long DNA-sequences and tetra-groups of oligonucleotides. https://arxiv.org/ftp/arxiv/papers/1709/1709.04943.pdf ________________________________ From: Fis <fis-boun...@listas.unizar.es> on behalf of Christophe Menant <christophe.men...@hotmail.fr> Sent: Monday, November 13, 2017 11:27 AM To: pcmarijuan.i...@aragon.es Cc: fis@listas.unizar.es >> fis@listas.unizar.es Subject: [Fis] TR: some notes Thanks for that Pedro, Just a few comments. All the best, Christophe ________________________________ De : Fis <fis-boun...@listas.unizar.es> de la part de Pedro C. Marijuan <pcmarijuan.i...@aragon.es> Envoyé : lundi 13 novembre 2017 14:30 À : 'fis' Objet : [Fis] some notes Dear All, Herewith some notes on the exchanges of past weeks (sorry, I was away in bureaucratic tasks). 1. Agents & Information. There were very good insights exchanged; probably both terms make a fertile marriage. Actually I have been writing about "informational entities" or "subjects" as receivers/builders of information but taking into account the other disciplines around, "agents" look as the most natural companion of information. The only thing I don't quite like is that they usually appear as abstract, disembodied communicative entities that do not need self-producing. Their communication is free from whatever life maintenance... Yes, agents naturally go with information as they are the source of meaning generation, of sense making. Agents can be organic, human and artificial. (I look at agents as identifyable entities submitted to internal constraints and capable of actions for the satisfaction of the constraints). Artificial agents can be looked at as disembodied but their being is derived from our human ones. So their self (if any) is part of the human designer's self. 2. Eigenvectors of communication. Taking the motif from Loet, and continuing with the above, could we say that the life cycle itself establishes the eigenvectors of communication? It is intriguing that maintenance, persistence, self-propagation are the essential motives of communication for whatever life entities (from bacteria to ourselves). With the complexity increase there appear new, more sophisticated directions, but the basic ones probably remain intact. What could be these essential directions of communication? Perhaps it could be interesting here to highlight that physics/chemistry and biology/psychology cannot address information the same way. Physics and chemistry use tools with precise definitions allowing to model our environment in a deterministic and predictable way (QM and Chaos deserving more investigations). Biology/psychology do not benefit of such rigorous mathematical support. We do not even know how to define life or consciousness, and our models are incomplete. So what about separating the two domains and looking at their relations as a third domain? 1) Thermodynamics, entropy, quantity of information, channel capacity, data transmission. 2) Meaning generation, biology and self-consciousness 3) Emergence and locality of constraints, emergence of meanings This puts again the focus on meaning generation, a key evolutionary step without which we would not be here. Also, let's not forget that data transmission and quantification of information are about meaningful information. So why not consider internal constraint satisfaction, the source of meaning generation, as an essential direction of communication? 3. About logics in the pre-science, Joseph is quite right demanding that discussion to accompany principles or basic problems. Actually principles, rules, theories, etc. are interconnected or should be by a logic (or several logics?) in order to give validity and coherence to the different combinations of elements. For instance, in the biomolecular realm there is a fascinating interplay of activation and inhibition among the participating molecular partners (enzymes and proteins) as active elements. I am not aware that classical ideas from Jacob (La Logique du vivant) have been sufficiently continued; it is not about Crick's Central Dogma but about the logic of pathways, circuits, modules, etc. Probably both Torday and Ji have their own ideas about that-- I would be curious to hear from them. 4. I loved Michel's response to Arturo's challenge. I think that the two "zeros" I mentioned days ago (the unsolved themes around the cycle and around the observer) imply both multidisciplinary thinking and philosophical speculation... Best wishes--Pedro ------------------------------------------------- Pedro C. Marijuán Grupo de Bioinformación / Bioinformation Group Instituto Aragonés de Ciencias de la Salud Centro de Investigación Biomédica de Aragón (CIBA) Avda. San Juan Bosco, 13, planta 0 50009 Zaragoza, Spain Tfno. +34 976 71 3526 (& 6818) pcmarijuan.i...@aragon.es http://sites.google.com/site/pedrocmarijuan/<https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fsites.google.com%2Fsite%2Fpedrocmarijuan%2F&data=02%7C01%7Csji%40pharmacy.rutgers.edu%7C78f67b91e82e4c519b0f08d52ab3717a%7Cb92d2b234d35447093ff69aca6632ffe%7C1%7C0%7C636461872559064457&sdata=qGz8f8p2whictsWvX2ri56A6%2BsmU0JcI0EhxLdli3l8%3D&reserved=0> [https://sites.google.com/site/pedrocmarijuan/_/rsrc/1468865628625/home/DSC00254-1.JPG?height=420&width=346]<https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fsites.google.com%2Fsite%2Fpedrocmarijuan%2F&data=02%7C01%7Csji%40pharmacy.rutgers.edu%7C78f67b91e82e4c519b0f08d52ab3717a%7Cb92d2b234d35447093ff69aca6632ffe%7C1%7C0%7C636461872559064457&sdata=qGz8f8p2whictsWvX2ri56A6%2BsmU0JcI0EhxLdli3l8%3D&reserved=0> Pedro.C.Marijuan<https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fsites.google.com%2Fsite%2Fpedrocmarijuan%2F&data=02%7C01%7Csji%40pharmacy.rutgers.edu%7C78f67b91e82e4c519b0f08d52ab3717a%7Cb92d2b234d35447093ff69aca6632ffe%7C1%7C0%7C636461872559064457&sdata=qGz8f8p2whictsWvX2ri56A6%2BsmU0JcI0EhxLdli3l8%3D&reserved=0> sites.google.com Personal Webpage of Pedro C. Marijuán ------------------------------------------------- _______________________________________________ Fis mailing list Fis@listas.unizar.es http://listas.unizar.es/cgi-bin/mailman/listinfo/fis<https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Flistas.unizar.es%2Fcgi-bin%2Fmailman%2Flistinfo%2Ffis&data=02%7C01%7Csji%40pharmacy.rutgers.edu%7C78f67b91e82e4c519b0f08d52ab3717a%7Cb92d2b234d35447093ff69aca6632ffe%7C1%7C0%7C636461872559064457&sdata=sTP%2BgiNdkFgQTT6TDVnbHKnbQCCpSa1CnIEYqA%2FbP9A%3D&reserved=0> Fis Info Page - unizar.es<https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Flistas.unizar.es%2Fcgi-bin%2Fmailman%2Flistinfo%2Ffis&data=02%7C01%7Csji%40pharmacy.rutgers.edu%7C78f67b91e82e4c519b0f08d52ab3717a%7Cb92d2b234d35447093ff69aca6632ffe%7C1%7C0%7C636461872559064457&sdata=sTP%2BgiNdkFgQTT6TDVnbHKnbQCCpSa1CnIEYqA%2FbP9A%3D&reserved=0> listas.unizar.es The FIS initiative (Foundations of Information Science) started in 1994 with a first meeting in Madrid (organized by Michael Conrad and Pedro Marijuan), and was ...
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