fredag 3 september 2010

Quantum biology - DNA

The Relevance Of Continuous Variable Entanglement In DNA June 28, 2010. ArXive blog.

Quantum entanglement helps prevent the molecules of life from breaking apart? Earlier I wrote of quantum photosynthesis, now the DNA-bondings. I quote:

There was a time, not so long ago, when biologists swore black and blue that quantum mechanics could play no role in the hot, wet systems of life. Since then, the discipline of quantum biology has emerged as one of the most exciting new fields in science. It's beginning to look as if quantum effects are crucial in a number of biological processes, such as photosynthesis and avian navigation which we've looked at here and here.

Now a group of physicists say that the weird laws of quantum mechanics may be more important for life than biologists could ever have imagined. Their new idea is that DNA is held together by quantum entanglement.

Entanglement is the weird quantum process in which a single wavefunction describes two separate objects. When this happens, these objects effectively share the same existence, no matter how far apart they might be.

The question that Elisabeth Rieper at the National University of Singapore and a couple of buddies have asked is what role might entanglement play in DNA. To find out, they've constructed a simplified theoretical model of DNA in which each nucleotide consists of a cloud of electrons around a central positive nucleus. This negative cloud can move relative to the nucleus, creating a dipole. And the movement of the cloud back and forth is a harmonic oscillator.

When the nucleotides bond to form a base, these clouds must oscillate in opposite directions to ensure the stability of the structure.

Rieper and co ask what happens to these oscillations, or phonons as physicists call them, when the base pairs are stacked in a double helix. Phonons are quantum objects, meaning they can exist in a superposition of states and become entangled.

To start with, Rieper and co imagine the helix without any effect from outside heat. "Clearly the chain of coupled harmonic oscillators is entangled at zero temperature," they say (T=0K). They then go on to show that the entanglement can also exist at room temperature.

That's possible because phonons have a wavelength which is similar in size to a DNA helix and this allows standing waves to form, a phenomenon known as phonon trapping. When this happens, the phonons cannot easily escape. A similar kind of phonon trapping is known to cause problems in silicon structures of the same size.

That would be of little significance if it had no overall effect on the helix. But the model developed by Rieper and co suggests that the effect is profound.

Although each nucleotide in a base pair is oscillating in opposite directions, this occurs as a superposition of states, so that the overall movement of the helix is zero. In a purely classical model, however, this cannot happen, in which case the helix would vibrate and shake itself apart.

So in this sense, these quantum effects are responsible for holding DNA together.

The question of course is how to prove this. They say that one line of evidence is that a purely classical analysis of the energy required to hold DNA together does not add up. However, their quantum model plugs the gap. That's interesting but they'll need to come up with something experimentally convincing to persuade biologists of these ideas.

One tantalising suggestion at the end of their paper is that the entanglement may have an influence on the way that information is read off a strand of DNA and that it may be possible to exploit this experimentally.

Speculative but potentially explosive work. Maybe the experimental proofs comes from things discussed at Gibbs and Keas bloggs? Keas hexagons are also interesting as a minute synapse model and receptor model in biology. I have long looked for something like that. Also TGD has much on DNA and quantum biology.

9 kommentarer:

  1. :-) and quantum coherence between the bases seems to help stabilize the DNA helix I read somewhere in New Scientist I think.

  2. But what sort of entanglement? How much information is the minimum bits? Yes quantum theory is deep into the mechanisms of biology but it is not deep enough- and the information there itself is only meaningful if the bases are not the same yet not random- it is a question of bell's inequality too as far as probability as local or non-local goes also. And in what direction in the maze of quantum information is it easy to find paths out of?

  3. I think the answer is in the entangled wave and its size, with superpositions it is 'trapped'. It is as big as the helix itself. Maybe this wave has scaled-up variants? The whole man would be one scalar result?

    In fact this wave can go long outside the DNA - helix, as Peter Gariaev showed. The chromosome act as some kind of sense-organ, a memory-trap.

    And the chromosome is a fractal construction, holding a topological map of a whole organism. In TGD you find more of this kind of stuff.

    Another kind of 'trap' happens from outside in form of methyl-groups holding the DNA in a firm grip. This is the mechanism behind epigenetics. In fact, it is said that 'some kind of wave from outside is the first signal that opens up the chromosome so the replication can start'. This are things unknown so far.

    To get the minimum bits of information you must look at the degrees of freedom in particle physics. They are entangled to qubits.

    The probabilities are constrained by the genetic alphabet.
    I think I have read somewhere too that the information in DNA isn't definitive, that it can be overrun by forces from the wave. Guess that is free will :)

    I'm very sceptic to the fancyness of genetic science. It is a path going into blindness?

  4. One good link more, from a popular.

    Decoherence is not a problem in living things, in fact, entanglement is a basic condition for Life.

    The simple fact that we can communicate depends on superpositions between individuals. Also thoughts and psychology have quantum biological facetts.

  5. Ulla,

    I like that you are sensitive to how organically this may relate to what some see as the less scientific aspects of consciousness.

    Let us recall Rowlands pointing out that decoherence is entropy. I think some things we imagine as extrasensory will be shown to have such links of sensitivity between people as if we can read directly the DNA.

    Again, where the memory is stored in physics that cannot really pin down causality does seem to be stored in the DNA potentially- but if you think about it, as if our uniqueness of soul- it does not vanish or has been known to return in awareness despite the loss because things on this level are deeper than that defined by nerve connections or chemicals or electric fields and the like. That is in such ultimate (beyond chemistry this beyond quantum ideas) structures the overriding of these structures is not the last word nor that we cannot learn and adapt to them like language.

    Free will? well that is after all the acid test of philosophy. You have great insights!

    The PeSla

  6. You have a difficult language.

    Life is negentropy, and this story tells that the entanglement is important, not decoherence. One of the big obstacles lies here. High temperature superconductivity is hinted at at high temperatures too, means that Life has means to overcome decoherence. This can only be realized in non-locality, as a phase in-between quantum and classic physic?

    I say nothing about if we can read directly the DNA. Virus has a memory that is magnetic, and maybe also humans? In some way I think more of nerves in relation to memory, but chromosomes are a little topological and fractal man :) Also cells must have some kind of memory.

    Memory doesn't die. It can be transferred between humans/organisms, as emotions can be. This is also culture.

  7. Look at this as instance:

  8. try to tell this to a biologist! in the best case they would tell you an irritated 'so what??'. or say a dignified hmmm, but this happens only on special occasions, cos mostly they just protestingly remain silent. a recent favourite excuse of mine is 'I don't have time now for almost a year'.
    they are obsessed with their tiny little articles, cos it is so important, but dont read others' articles, cos it is not important, or even more, if they dont like an article, they decide that the author must be an imbecille, whose stupidity might even be infectious, so keep your distance.

  9. Hi Donkerhead, nice to hear from you,

    I know, the attitude - don't come and disturb my little tidy cicles. This is understandable if you are a specialist.

    But if you try to model reality you cannot have this small picture, you are forced to take in all possible pictures and make them fit. This is what I have tried to do.

    Much of the honour belongs to Matti, of course. I would not have been able to look so profoundly with new eyes without him. But I also brought new visions for him. The surprice was that our pictures fit so well together.

    I surely belongs to dangerous imbecilles :)