Sunday, February 21, 2010

Could high energy phosphate bond be negentropic bond with negative binding energy?

Most people assign the word "love" to the word "life" as their first association. There is a notable exception to this: scientists including biologists. Un-educated layman might however wonder whether one can understand life without identifying any physical counterpart for this notion (, which could be replaced with that of compassion, sex, or ability to act synergetically or just X if some of these notions sounds less un-scientific). Certainly the word "love" stimulates a deep feeling of disgust in a reductionistically conditioned scientist. But isn't the duty of scientist to win this kind of feelings and try to see whether this identification might be possible after all? The prize could be high: the understanding of what distinguishes between living and dead matter could change the entire culture. Who knows, maybe it could be possible to identify some poorly understood fundamental biological process allowing a quantitative model using a guess for what this physical correlate could be. The basic step of metabolism is at the core of life and indeed poorly understood, and I shall argue that the identification of the negentropic entanglement as the counterpart for the notion of love could allow to model quantititatively what happens in this process.

Before continuing general motivating comments about implications of negentropic entanglement are in order.

  1. Ordinary bound states are stable because they have positive binding energy. One can visualize this kind of binding as a jail: the second particle resides near the bottom of a potential well. Organized marriage is a social analogy for this situation. Negentropic entanglement makes possible bound states for which binding energy can have and perhaps even has always a wrong sign. The state is not prevented from decaying to free particles in state function reduction by energy conservation: Negentropy Maximization Principle (NMP) takes care that they remain correlated. The social analogy would be a voluntary marriage based on love. Partners are competely free to leave but want to stay together.

    One implication could be explanation for the stability of highly charged basic molecules of life such as DNA and ATP.

  2. The presence of the negentropic entanglement implies the directedness of the biological processes since the outcome of the state function reduction would be far from random since the behavior of negentropic bonds could be almost deterministic. In the case of time-like entanglement this would select only particular initial final state pairs so that determinism would emerge also in this sense and could lead to almost deterministic irreversible cellular automaton behavior characteristic for the living matter very different from the reversible determinism of classical physics and very difficult to understand in quantum context.

  3. The determinism would of course be only partial and would allow volition not spoiled by randomness of quantum jump. This would provide a general explanation for the ability of the living matter to overcome the second law basically implied by quantum randomness predicted by the standard quantum theory. This would happen in time scales shorter than the time scale of the appropriate causal diamond (CD) only but one would have hierarchy of CD meaning that in arbitrary long time scales there are levels of hierarchy at which second law is broken. The hierarchy of Planck constants would be also crucial since it would allow zooming up to arbitrarily long time scale. Non-equilibrium thermodynamics and cellular automaton models could be seen as phenomenological descriptions for the actual breaking of second law in the intersection of real and p-adic worlds.

I do not bother to do the painful transformation of the the tex file to html so that the reader interested in details can just click the six page article Could high energy phosphate bond be negentropic bond with negative binding energy?.


Ulla said...

:) :) :)
A very special text from a very special person :) Why would biologists be included? I know they are generally very reductionistic, but there are some special cases :) When I first talked of this you did not understand it :)

I remember C. Pert talked of cellular 'sex' when she talked of the receptors. They were 'singing of joy' usually. Certainly that plasma-like joy that I felt sometimes. Pert got an almost religious experience from her insights.

In an atom this comparision can also be used. The 'jail' is the stable ground state, and excitation let the atom sing and vibrate. It lifts the energy level higher and then entangle with some other atom happen. Chirality is also this? In a metal this is achieved by taking away an electron, so that every electron would be free.

Living matter is always excitated, vibrating, with an higher energy level, that make the interactions possible. The emotions are the interacting agents, some kind of entanglement for shorter or longer time. A very longlasting entanglement would be the personality and maybe the hierarchial self. That personal Big Book :).

In this way life must be quantum physical, I cannot understand it otherwise. I think also the biological interactions must be quantum physical. They all depend on the Gaussian probabilities.

There must also be another, smaller hierarchy than p-adic. Perhaps the Golden Mean in some way? It is a fact that many of the living structures is divided or split by Golden Mean, which in fact is emergent, meaning non-existent?. The symmetry is broken? Not continuous any more? But it is broken somewhat assymmetrically. Rings and spheres are very biological structures.

Also the Platonic solides are very interesting in this context.

"The social analogy would be a voluntary marriage based on love. Partners are competely free to leave but want to stay together."
You have experience of this kind. It is the energy, the entanglement must give more free energy, or a higher energy level. If it takes energy, then you want to leave. It is the correlation and synergy that gives the energy? Then you want to chose it again, and again, and again. But don't look in the wrong direction!

This is the overseen part in evolution.

I like this very, very much. Thank you, Matti.

Ulla said...

I remembered Mae wan Ho had something about this. In Living with oxygen, she say: To appreciate the momentous importance of getting oxygen from water, one has to realise that life is energized by nothing more than the intricately orchestrated flows of electrons and protons carrying negative and positive electricity respectively. In the process, life creates itself and transforms the entire earth.

Could this be the Chi-concept, the life-force? Oxygen makes more energy available and at greater efficiency; at the same time, it increases the complexity of metabolic networks.

This negentropic bonds must depend much on oxidation and reduction, as seen in phosphorylation as instance. My thought is that this oxidation directly would mean a p-adic transformation to a higher hbar. reduction would mean a lower spacetime sheat. Also the same mechanism with magnetic flux tubes?

Mae: Oxygen meant a step towards multicellular organisms, and an electron-source. Oxygen was also important for the 'Cambrian explosion' and the emergence of gigantic insects. Photosynthesis is 'the Great Oxidation Event' creating larger clusters of cells and more different types of cells. Oxygen is an electon-acceptor in 'burning'.

Oxygen is mostly 'in jail' in a stable triplet-molecule, but get freedom by oxidation. Reactive radicals is also very energetic and important for the defense. It is no accident the nerves contain so much of it.

Mae writes: most metabolites have one or a few connections, and the number of nodes with many connections drops off rapidly. Significantly, the most highly connected metabolites were those associated directly with energy transfer, with water at the top of the list! This ‘scale-free’ or fractal network has been found to describe biological structures and living processes in general, also social networks.

Four discrete groups of networks of increasing complexity was separated, with transitions between groups contingent on the presence of the key metabolites: NAD+, S-adenosyl methionine, coenzyme A, ATP O2, CO2, NH3, pyruvate or 2-oxoglutarate. The most complex group IV reactions were associated almost exclusively with the presence of O2, and had as many as 1 000 reactions more than those of the largest networks achieved without O2.

Matti Pitkänen said...

If I had to find correlate for chi or subtle energies or various other analogous notions, it would be magnetic flux tubes with negentropic entanglement between their ends and no binding energy between their ends.

DNA is highly charged and its stability is a well-known puzzle. If I remember correctly, two units of negative charge per nucleotide, and the phosphates extending the system by bringing in negentropic flux tubes and negentropic entanglement could stabilize DNA. DNA as topological quantum computer model assumes that flux tubes connect DNA and nuclear and cell membrane.

It is also known that DNA is stable against dehydration only inside cell nucleus: negentropic entanglement need not but could relate to this. An alternative explanation is that water inducing polymerization by hydration is in ordered ice like state.

Large hbar for flux tubes increases the time period during which negentropic entanglement prevails: recall that in zero energy ontology basic structure is causal diamond, chronon, or event. The larger the bar the longer the duration of this event. Breakdown of second law is always below some time scale.

This comment of Mae about networks fits very nicely with the proposed mechanism of metabolism. The strong prediction is that ADP and P_i remain connected by long flux tube and find each other in the next event. Also ADP remains connected with the system for which provided metabolic energy. These predictions should be testable by radioactively marking ADP and P_i of ATP with same "color" and finding whether the colors remains the same during the subsequent cycles or whether they mix immediately. Mixing of colours is of course possible by the reconnection of flux tubes in which two ADPs exchange their P_is.

Opening the meaning of the last paragraph would require some work: I am not a professional!

Matti Pitkänen said...

One must be careful with the meaning of "life is quantum physical". Standard wave mechanics or quantum field theory is certainly not enough. p-Adic physics brings in negentropic entanglement; hierarchy of Planck scales brings in macroscopic and even astroscopic quantum coherence besides dark matter; new view about space-time brings in the notion of magnetic body among other things; zero energy ontology brings in the new view about time, thermodynamics, and self-organization.

Ulla said...

And about that redox-reaction? It would perhaps mean the difference between hydrogen and oxygen or generally between diamagnetic and paramagnetic molecules? Also reactive molecules belongs here.

Ulla said...

Look at this article from Holger Nielsen.

The second law of thermodynamics concerns the initial state conditions — or better the actual solution among the various possible solutions to the equations of motion — rather than the time development. an attempt to unify the second law of thermodynamics with the other laws, the time development laws

a more microscopic formulation of this second law of thermodynamics in terms of a postulated “fundamental” probability density P(“path”) defined for all possible
solutions of the equations of motion “path”. A priori we would like to formulate all the
laws in the language of microscopic degrees of freedom - these be fields or particles - rather than in terms of the only macroscopically understandable concept of entropy.

In the beginning of the present article we shall keep the discussion so abstract that we
do not even explicitly write down that we are concerned with a (classical) field theory with
three space dimensions and one time dimension,

In the following section 2 we shall put forward how to get an idea for searching for the most likely the highest log(hpi es) — classes of path and see how such considerations lead quite naturally to an effective second law of thermodynamics. At first we only make crude suggestions. But then in section 3 we deliver a very general limitation on how much entropy can go first up and then down and a formal derivation of the second law of thermodynamics follows under the same reasonable approximation. But a further clean up is still needed to apply the second law of thermodynamics even for subsystems. In section 4 we rather shortly put a more concrete cosmological picture on our so far very abstract model. In section 5 we review shortly the various outcomes of the model behind the second law of thermodynamics in addition to the practical outcome of this law itself. In section 7 we conclude and present outlook especially by taking the lack of perfect derivation of the second law of thermodynamics as an extremely interesting suggestion for seeming effects of a foresight.

Sorry for the long excerpt, but links are so easily overseen. :)