Monday, January 20, 2014

Are microtubules macroscopic quantum systems?

There has been a lot of buzz about the claimed discovery of quantum vibrations in microtubules: see this. I have been working for two days trying to understand the work of Anirban Bandyopadhyay. Certainly, the experimental finding- if true - would be a breakthrough for quantum consciousness but certainly not for Orch-OR. Therefore I was surprised for the heavy hyping of Penrose-Hameroff theory. The result only tells that microtubules are macroscopic quantums systems, it says nothing about Orch-OR.

I did not find any article about experiment. I found and listened the earlier talk (2111) of Anirban Bandyopadhyay whose group might discovered the quantum vibrations. The talk was also was about experiments done with microtubules and looked very interesting. See this .

I got the impression that he is excellent sharply thinking experimentalist and had identified the signatures for what he interpreted in terms of Froehlich B-E condensation, topological qubit, superconductivity like state of electrons inside microtubules, and so on. One can interpret the findings differently and I have been working with TGD interpretation assuming that basic findings are correct.

What was frustrating was the fuzzy terminology: for instance, he talked about conduction pathways at micro tubular surface as topological qubits and did not explain when asked about this issue. Excellent experimentalist need not be a theorist: was this the reason? Or was the unclarity purposeful?

Also the interpretation of experiments seems to be internally inconsistent and I got the impression that it reflects his own theories. It might rely on the earlier proposal of Penrose and Hameroff, which I did not find as freely available article. The only article mentioning conduction pathways that I found from web did not help: I have the feeling that they have no detailed model but want to give the impression that they have.

The wrong interpretation need not mean catastrophe: as a good experimentalist he is looking for signatures of these phenomena, and if he has found them, there are all reasons to take the findings under serious discussion.

I also looked for the Penrose Hameroff theory. As a professional I known that the Penrose's contribution relating to speculations about gravitation does not tolerate daylight and the only calculations are just dimensional analysis involving Uncertainty Principle. I had thought that Hameroff's microtubule contribution is on less shaky grounds. I learned within few hours that this is not the case. For instance, the assumption that microtubules in brain are of type A, is simply wrong: all microtubules in living matter seem to be of type B, in particular in brain this is the case. See this .

Therefore the proposal of Penrose and Hameroff for microtubules as topological quantum computers relying on Fibonacci conduction paths (with periodicity 3,5,8, or 13) possible only for A-type microtubules is simply wrong. The same is true about Hameroff's and indian theorists Gupta's later proposal suggesting that MAPs act as quantum gates. As a matter of fact, the abstract of the article contained horrible terminological errors: I tried to explain this by language but why Hameroff did not check the language? See this .

Now Penrose and Hameroff propose explanation for the origin of EEG based on beat phenomenon for MHz frequencies: it seems that they are trying to mimic what I have done in TGD and get the honour for discovering quantum theory of consciousness;-).

I must say that I am confused. Certainly the discovery that microtubules are macroscopic quantum systems would be wonderful if true, and the claimed earlier findings of Indian experimentalist support the TGD based picture based on the identification of braids as magnetic flux tubes. But can I trust to experimentalist without name when I cannot trust on namy theorists?

To sum up, these are my first impressions after two day's listening and reading. I might have misinterpreted and misunderstood. I am writing a summary about TGD based interpretation of the earlier experiments of the group of Bandyopadhyay -assuming that experimental findings are correct (I do not believe that the interpretation is correct) - and give a link to the article later.

Addition: I wrote a short analysis of the talk of Bandyopadhyay.

24 Comments:

At 1:20 PM, Blogger Ulla said...

http://gravitationalandspacebiology.org/index.php/journal/article/view/179

and a search on Ingber D.E., Integrins, tensegrity, and mechanotransduction.

Stick and string may be replaced by flux tubes?

 
At 6:02 PM, Anonymous Matti Pitkanen said...


To Ulla:

Flux tubes and string worlds sheets accompany each other in TGD framework.

 
At 6:25 PM, Anonymous Matti Pitkanen said...


My own proposal for DNA as topological quantum computer that I suggested around 2003 or so;-) relies on braids connecting lipids and DNA nucleotids or codons. See the chapter

http://www.tgdtheory.fi/public_html/genememe/genememe.html#dnatqc .

The 2-D flow of lipids would induce braiding of magnetic flux tubes attached to them and connecting them to DNA nuclelotides or codons - perhaps intronic ones. DNA is stationary. This results in two braidings. Dynamical time like braiding in time direction corresponding to a running tqc program and generation of space-like braiding storing it to memory. This could be responsible for passive memory representations about what happens near the cellular surface. This would not be yet active computation as simulation but might define some aspect of experience at neuronal level.

Active computing by microtubules could be based on a 2-D coordinate line grid formed by two kinds of parallel flux tubes along the micro tubular surface. The crossing points are points at which swap (braiding) could occur and this would be dictated by the state of tubulin, may its conformation (two of them) could the bit telling whether swar occurs. Microtubular surface would be a bit map -classical computer program - defining braiding structure defining in turn topological quantum-computer program.

The proposal of the indian experimenter about *groups* of parallel conduction pathtways is not consistent with HP proposal but is consistent with a families of coordinate grids at micro tubular defined by this kind of braidings. They would be parametrized by the gap between two subsequet braid strands defining the analog of coordinate resolution. One set of strands would go parallel to flux tube and other strands wind around it. This is possible for microtubules of type B, which are experimentally the only possible one. Tubules of type A considered by Penrose and Hameroff are not possible at all - neither in living matter nor in vitro.

One can consider also a generalisation. For instance, one can slice brain by 2-D systems of this kind to get 3-D tqc as pile of 2-D tqc:s. This in neuron scale with each neuron telling whether swap occurs of not at crossing point flux tubes along 2-D surface. For year or two ago the first evidence for a 3-D coordinate grid structure of brain emerged and possible interpretation would be in terms of TQC constructed by layering 2-D TQCs. Brain would be doing what mathematicians do all the time: constructing coordinate charts!

Matti

 
At 4:16 AM, Blogger Ulla said...

This is very interesting for me :)

Better articles are here:
www.fasebj.org/content/20/7/811.long

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2570054/

http://www.mechanobio.info/Home/topics/nuclear-mechanotransduction

This links with carbon too.

Also mitochondrias are found to be transported between cells in order to maintain selfhealing. This request must be communicated somehow, and these two, tension as flux tubes and density points as sheets may meet each others?

http://emboj.embopress.org/content/early/2014/01/15/embj.201386030
http://zone-reflex.blogspot.fi/2010/09/walking-molecules_18.html

 
At 6:16 AM, Blogger Ulla said...

http://www.anirbanlab.co.nr/ go tp publications
works of Aniban.

 
At 7:35 AM, Anonymous Matti Pitkanen said...


Thank you. I hoped to find something about the talk
about microtubules but failed.

 
At 1:55 PM, Blogger Ulla said...

Can these help?
http://dx.doi.org/10.1016/j.plrev.2013.11.003
http://www.sciencedirect.com/science/article/pii/S1571064513001917


E. Nogales, S.G. Wolf, K.H. Downing

Structure of the alpha beta tubulin dimer by electron crystallography

Nature, 91 (6663) (1998), pp. 199–203

 
At 2:00 PM, Blogger Ulla said...

C. Jumper, G. Scholes

Life—Warm, wet and noisy? Comment on “Consciousness in the universe: A review of the ‘Orch OR’ theory” by Hameroff and Penrose

Phys Life Rev (2013) http://dx.doi.org/10.1016/j.plrev.2013.10.008

 
At 6:20 PM, Anonymous Matti Pitkanen said...


I have been puzzled why Orch-OR is taken so seriously. Probably the reason is the same as always nowadays: name cult. As a quantitative theory Orch-OR reduces to some order of magnitude estimates based on Uncertainty Principle. The first link in the first post tells about the weakness of Orch-OR at the biological side.

There is no convincing identification of qubit (cannot be without introduction of large h_eff), Froehlich condensation does not seem to happen (something happens but it is not this condensation ), macroscopic quantum coherence is not possible at physiological temperatures in standard physics. The gravitational part of the theory speaking about superposition of microtubule conformations is handweaving. I read the article about conduction pathways as TQC: also it contained only loose statements not consistent with the claimed experimental finding (helical Fibonacci paths are not claimed in experiments).

The basic vision that macroscopic quantum coherence is involved, is correct. I might bet also for the possibility of A-type microtubules. They would be generated in h_eff increasing phase transitions at certain resonance frequencies: this would explain why they have not been seen experimentally. This Indian experimenter would have seen these phase transitions if his experiments are OK.

New physics is needed: magnetic flux tubes as conduction paths and large h_eff implying macroscopic quantum coherence, cyclotron B-E condensates, negentropic entanglement: to mention the most important pieces of the picture.

It this Indian experimenter is right, his experiments are of nobel caliber. But how many decades it takes before theoretical physicists - badly needed in quantum biology - are mature to understand their implications? Communications would be needed but from my own experience I know that it is very difficult to establish intelligent communications with the members of this academic upper class.


 
At 2:21 AM, Blogger Ulla said...

The art to make perceptions would be of exactly this sort. The observer-effect contracts what is measured. This means that the 'sensings' themselves are in form of flux tubes? This is directly linked to cytoskeleton and nuclear membrane-chromosome, but to the shield of methyl around the chromosome? Not DNA itself directly? DNA is the output part only?

see also this http://phys.org/news/2014-01-theory-teleport-energy-distances.html

 
At 3:16 AM, Blogger Ulla said...

http://scitation.aip.org/content/aip/journal/apl/102/12/10.1063/1.4793995

Look for Satyajit Sahu microtubule

 
At 9:17 PM, Anonymous Anonymous said...

Hello Matti! I particularly like the statement in your PDF, "Personally I find it difficult to believe in the reduction of consciousness to the microtubular level, but see microtubules as one particular layer in the hierarchy of conscious entities. I prefer fractality over the naive length scale reductionism." Prior to this microtubular development I was thinking of the fractal-like hierarchy of conscious entities (sub-selves) supporting "the self we identify with" as all being members of the same "level" (although of course in a fractal like hierarchy of sizes). But perhaps now we will do better to consider the entire hierarchy of nature as participants in consciousness at some time/space-scale?
with renewed regard, MW (Martha)

 
At 6:36 PM, Anonymous Matti Pitkanen said...


Hi Martha,

nice to hear about you.

The hierarchy - not of course stable and unchangeable - means conceptual economy. Mental images are subselves and we are mental images of higher level selves. The problem of One Mind theories is obvious: there are many minds who tend to disagree almost everything! It is very
difficult to explain this plurality if it is not real.


 
At 9:25 PM, Anonymous Anonymous said...

Your response seems to convey a vein of humor! Of course we disagree about everything (even though when I read your essays they always seem very logical to me.) "Free Will" seems a fact -- which is also seen through a microscope when monitoring the activity of microorganisms. My assumption would be that at even smaller scales (molecular, atomic...etc) we simply can't distinguish individual behavior and so the term "mechanical" serves to describe the behavior distribution of a group at that scale.
BTW - while reading your message I translate "mental image" to "CD" and feel that this concept should not require strict hierarchical nesting, but, as in the case of multiple personalities, underlying CD's can be shared. I think you have read about WJ Freeman's EEG experiments, and he reports a lot of chaos surrounds the formation of CDs (he doesn't call them that, of course). But to have a unified functioning organism it does seem the entangled CDs all would be in a strict hierarchy at any given instant of time.
with friendly regards, MW

 
At 11:08 AM, Anonymous Anonymous said...

Hi! Very interesting post!
Please take a look at the following new:
http://phys.org/news/2014-02-team-limits-famous-quantum-principle.html

Does it have any consequence on the quantum mind theories?

D.

 
At 4:40 AM, Blogger Christopher Heck said...

Hi Matti, Do you agree that MTs are without doubt, superconductive at the ground state, and if so, would a single MT have a macroscopic wavefunction ?

 
At 4:53 AM, Anonymous Matti Pitkänen said...


One possibility is that MTs become superconducting when AC voltage is applied at certain quantum critical frequencies: h_eff increasing phase transition. The configuration in which MT has no helical symmetry and the basic unit is 13 tubulins would make a phase transition to configuration in which the current carrying unit becomes much longer and current runs along conduction pathways. This would be analogous to the transition to high Tc super-conductivity from the gap phase in which super-conductivity is possible in short length scales( 13 tubules). Conduction pathways could be flux tubes carrying electronic Cooper pairs.

 
At 4:57 PM, Blogger Christopher Heck said...

Do you have any experimental examples to support Cooper pairs in MTs ? Aside from quantum mind theories, I am hoping at least Superconductivity can be proven or supported.

 
At 8:23 PM, Anonymous Matti Pitkänen said...


Bandynophyal talks about currents which are ballistic - resistance is at the ends of the pathways. This is indication for the presence of supracurrents but not a proof of course. Here the problem from TGD viewpoint is that Cooper pairs would be pair of h_eff=n*h electrons at parallel flux tubes. At this moment very few experimentalist is even aware about this idea requiring new experimental approach. Situation would be however similar to high Tc superconductivity. Quantum criticality would be essential element. Below gap temperature Cooper pairs with smaller Planck constant and supracurrents in much smaller length scale would flow. At Tc transition to larger h_eff and
superconductivity in long scales. Now tubules of type A without helical symmetry and pathways consisting of 13 tubulin units would correspond to gap. Helical phase to superconduction and extremal AC with critical frquencies would induce the transition. Experimentalist should start from this picture in the attempts to identify Cooper pairs and I think that high Tc superconducitivity would be of great help. Few days ago I saw a claim about superconductivity above room temperature: http://www.nextbigfuture.com/2016/12/researchers-at-japan-tokai-university.html .

 
At 1:02 PM, Blogger Christopher Heck said...

well, we know for certain MTs are composed of electrons, so its my understanding, an electron-phonon interaction would then cause Cooper pairs to form.

http://physics.stackexchange.com/questions/67774/how-does-a-phonon-cause-two-electrons-to-attract-each-other-and-form-a-cooper-pa

"In condensed matter physics, a Cooper pair or BCS pair is two electrons (or other fermions) that are bound together at low temperatures in a certain manner first described in 1956 by American physicist Leon Cooper. Cooper showed that an arbitrarily small attraction between electrons in a metal can cause a paired state of electrons to have a lower energy than the Fermi energy, which implies that the pair is bound. In conventional superconductors, this attraction is due to the electron–phonon interaction. The Cooper pair state is responsible for superconductivity, as described in the BCS theory developed by John Bardeen, Leon Cooper, and John Schrieffer for which they shared the 1972 Nobel Prize.


Although Cooper pairing is a quantum effect, the reason for the pairing can be seen from a simplified classical explanation. An electron in a metal normally behaves as a free particle. The electron is repelled from other electrons due to their negative charge, but it also attracts the positive ions that make up the rigid lattice of the metal. This attraction distorts the ion lattice, moving the ions slightly toward the electron, increasing the positive charge density of the lattice in the vicinity. This positive charge can attract other electrons. At long distances this attraction between electrons due to the displaced ions can overcome the electrons' repulsion due to their negative charge, and cause them to pair up. The rigorous quantum mechanical explanation shows that the effect is due to electron–phonon interactions"

so under the right circumstances, an exposure to microwaves/phonons, should cause the electrons to become superconductive.. does this sound right ?

btw, this is awesome chatting with you Matti ! I've been a fan for a while.

 
At 7:19 PM, Anonymous Matti Pitkänen said...


What you gave is the explanation for the formation of Cooper pair in ordinary superconductivity. There is upper bound of about 30 K for the critical temperature. Two days ago I learned about high Tc superconductivity around 500 K for n-alkanes so that the mechanism for high Tc is certainly different. I repeat myself by explaining it again since this explaining is very useful: something new always emerges.

*In high Tc super conductors such as copper the anti-ferromagnetism is known to be essential as also 2-D sub-lattice structures.

*Antiferromagnetism suggests closed flux tubes form of squares with opposite directions of magnetic field at the opposite sides of square. The opposite sides of the square would carry the members of Cooper pair.

At quantum cirticality these squares would reconnect to long flattened squares by reconnection. The members of Cooper pairs would at parallel flux tubes. Gap energy would consists interaction energy with magnetic fields and the mutual interaction energy of magnetic moments. Large h_eff would make it large so that this mechanism does not work in standard QM.

*Second important distinction to BCS is that Cooper pairs would be there already below gap temperature. At quantum criticality the conduction pathways would become much longer by reconnection. This would be one example "topological" condensed matter physics.

*The analogs of phonons could be present as transversal oscillations of magnetic flux tubes: at criticality long wave length "magneto-phonons" would be present. The transverse oscillations of flux tube squares would give rise to reconnection and formation of conduction pathways.

 
At 7:23 PM, Anonymous Matti Pitkänen said...


Concerning your example is about BCS superconductivity.

If this mechanism or its generalization to high Tc works the energy of photon should be around gap energy BCS (microwave photon) and around energy difference per Cooper pair for the phases with long flux tubes pairs and short
square like flux tubes.

*To induce superconductivity one should induce formation of Cooper pairs. The system should radiate away the binding energy of Cooper pairs as Cooper pairs. When could this happen?

*One might think the analog of induced emission. Assume that Cooper pairs have two states: the genuine Cooper pair and the non-superconducting Cooper pair. This could be the case in high Tc superconductivity in some sense but in BCS not if the BCS theory is true. In BCS pair decays above critical temperature.

*Above Tc but below gap temperature one has the analog of inverted population: all pairs are in higher energy state. The irradiation with photon beam with energy corresponding to energy difference gives rise to stimulated emission and the system goes to lower energy state which corresponds to superconductivity.

This mechanism could explain the finding of Banydonophyay that incoming AC at certain critical frequencse gave rie to ballistic state (no dependence of the resistance on the length of the wire so that the resistance must be at its ends).

 
At 7:33 PM, Anonymous Matti Pitkänen said...


Still an important point. I remember that Bandyonophyay used photons with MHz, GHz, and TeraHz frequencies. Maybe also kHz. The corresponding photon energies are about 10^-8 eV 10^-5, 10^-2 eV. Below thermal energies.

In TGD classical radiation should have also large h_eff=n*h photonic counterparts with much larger energies E=h_eff*f to explain the quantal effects of ELF radiation at EEG frequency range on brain. The general proposal is that dark cyclotron photons have universal energy range and biophotons in visible and UV range (much above thermal energy (result in the transition tranforming dark photons with large h_eff to ordinary photons.

 
At 10:20 PM, Anonymous Matti Pitkänen said...

A polished form of the above answer containing several inaccuracies as blog posting: http://matpitka.blogspot.fi/2016/12/how-ac-voltage-at-critical-frequencies.html .

 

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