Researchers may have discovered how memories are encoded in the brain.

While it’s generally accepted that memories are stored somewhere, somehow in our brains, the exact process has never been entirely understood. Strengthened synaptic connections between neurons definitely have something to do with it, although the synaptic membranes involved are constantly degrading and being replaced – this seems to be somewhat at odds with the fact that some memories can last for a person’s lifetime. Now, a team of scientists believe that they may have figured out what’s going on. Their findings could have huge implications for the treatment of diseases such as Alzheimer's.
Leading the study is Prof. Jack Tuszynski, a physicist from the University of Alberta. Also taking part are his graduate student Travis Craddock, and the University of Arizona’s Prof. Stuart Hameroff.
The project was inspired by an outside research paper, that described experiments in which memories were successfully erased from animals’ brains. That study concluded that a specific protein (calcium-calmodulin dependent kinase complex II, or CaMKII) played a large role in the encoding and erasing of memories, by strengthening or eliminating neural connections. [a growing and reducing of flux tubes?]

Tuszynski and his colleagues noted that the geometry of the CaMKII molecule was very similar to that of tubulin protein compounds. These tubulins are contained within microtubule protein structures, which in turn occupy the interiors of the brain’s neurons. They are particularly concentrated in the neurons’ axons and dendrites, which are active in the memory process.
The scientists wanted to understand the interaction between CaMKII, tubulin and microtubules, so based on 3D atomic-resolution structural data for all three protein molecules, they developed highly-accurate computer models. What they discovered was that the spatial dimensions and geometry of the CaMKII and microtubule molecules allow them to fit together. Furthermore, according to the models, the microtubules and CaMKII molecules are capable of electrostatically attracting one another, so that a binding process can occur between them.
This process takes place within the neurons, after they have been synaptically connected, to (in some cases) permanently store memories.
“This could open up amazing new possibilities of dealing with memory loss problems, interfacing our brains with hybrid devices to augment and 'refresh' our memories,” said Tuszynski. “More importantly, it could lead to new therapeutic and preventive ways of dealing with neurological diseases such as Alzheimer's and dementia, whose incidence is growing very rapidly these days.”

A paper on the research was recently published in the journal PLoS Computational Biology. Cytoskeletal Signaling: Is Memory Encoded in Microtubule Lattices by CaMKII Phosphorylation? Travis J. A. Craddock, Jack A. Tuszynski, Stuart Hameroff, mars 2012. Abstract: ...In long-term potentiation (LTP), a cellular and molecular model for memory, post-synaptic calcium ion (Ca²⁺) flux activates the hexagonal Ca²⁺-calmodulin dependent kinase II (CaMKII), a dodacameric holoenzyme containing 2 hexagonal sets of 6 kinase domains. Each kinase domain can either phosphorylate substrate proteins, or not (i.e. encoding one bit). Thus each set of extended CaMKII kinases can potentially encode synaptic Ca²⁺ information via phosphorylation as ordered arrays of binary ‘bits’. Candidate sites for CaMKII phosphorylation-encoded molecular memory include microtubules (MTs), cylindrical organelles whose surfaces represent a regular lattice with a pattern of hexagonal polymers of the protein tubulin. Using molecular mechanics modeling and electrostatic profiling, we find that spatial dimensions and geometry of the extended CaMKII kinase domains precisely match those of MT hexagonal lattices. This suggests sets of six CaMKII kinase domains phosphorylate hexagonal MT lattice neighborhoods collectively, e.g. conveying synaptic information as ordered arrays of six “bits”, and thus “bytes”, with 64 to 5,281 possible bit states per CaMKII-MT byte. Signaling and encoding in MTs and other cytoskeletal structures offer rapid, robust solid-state information processing which may reflect a general code for MT-based memory and information processing within neurons and other eukaryotic cells.

LTP is supported experimentally in vitro [2], [3], and may occur over many brain regions [4] as a common feature of excitatory synapses [5].

Source: University of Alberta, 
http://www.gizmag.com/memory-storage-theory/21900/


Note how well it suits TGD and its flux tubes. The encoding is magnetic (spin) using negative/metabolic energy? See also Intelligent neurons. The fundamental sensory qualia reside at the level of sensory receptors.The sensation of color involves quantum entanglement of magnetic body, brain, and retina. [and quantum measurements as qualia?]  Brain builds up symbolic representations by decomposing the sensory input to objects and giving them names. [categories, epigenetic tags that can be both intrinsic and extrinsic?] Neuronal lipid layer serves as the analog of computer monitor screen [stochastic resonance makes the screen play?] Neurons are conscious creatures able to co-operate because they have a collective magnetic body controlling the neuron population, and can therefore rapidly adapt in changing environment.

ZEO; the notion of magnetic body, braiding and reconnection; hierarchy of Planck constants; etc..- explain the basic mechanisms of biology and neuroscience extended to theory of consciousness.

One can apply these concepts directly to build models for various phenomena to which we assign words like water memory, remote mental interactions, paranormal phenomena. Standard biology and neuroscience are about remote mental interactions between biological body and magnetic body. There is no need for separate hypothesis. This is the point. The essential point is the interaction of magnetic bodies of operator and water. The basic mechanism is reconnection of flux tube loops from operator and water to a pair of flux tubes connecting these objects so that cyclotron radiation propagating along them and causing effects can propagate along this bridge and induce further interactions.

Reconnection is fundamental also in molecular scales and equally crucial for understanding of bio-catalysis, the generation of qualia, the basic mechanism of homeopathy, water memory, immune reaction, and evolution of immune system at gene level. The notion of fractality becomes more than a mere buzz word.

The deep irony is that reconnection represents the basic vertex of closed string model! String like objects are key structures in TGD. String world sheets also emerge in finite measurement resolution. And all is tightly connected with physics
A concrete model for the interaction would be in terms of the reconnections of closed flux tubes emerging from the biological body of subject person with the flux tubes of the magnetic body of water creating direct flux tube contacts between the two bodies. The presence of magnetic flux tube connections between water sample and operator's magnetic and biological body would induce the effects on crystallization of water. Water memory should be stable in human time scales. This requires that these flux tube patterns are rather stable modification of the magnetic body of water. Large values of Planck constant assignable to the magnetic body of human agent would be needed. What is required is that the crystallization patterns and therefore structures of water clusters correlate with the structure of the magnetic body of the water sample.

My comment: One more stupid question, is a lightlike spacetime always entangled or continuous? It should be (it is holistic?), but it must also be descreate with different fields meeting, maybe with 'massgaps'? So it both have symmetry and break the symmetry. This is made visible by Feynmans diagrams and loops? Loops for creativity (the 3 body problem?)?

About different kinds of memory, note the different kinds of consciousness too.
Mattis answer:  You cannot perceive a state which is superposition of states in which Schrodinger's cat is dead and bottle of poison is open and Schrodinger's cat is alive and bottle of poison closed. Mathematically this kind of state makes complete sense but not at the level of sensory experience.

The basic property of sensory perception indeed is that it makes state classical by state function reduction.

Automatic consciousness is in TGD Universe a non-sensical notion. And also in the real universe: when a performance requiring learning becomes automatic it is not anymore a conscious performance. If there is still consciousness, it is at lower levels of the hierarchy, not ours, where things need not be automatic.

This is a good example of how prevailing theories of consciousness - in this case computationalism - neglect even the most elementary facts about consciousness.
 My comment: What you say only is that measurements in sensing are classic measurements. This was the problem I talked of earlier. Entanglement is coming into the pic much earlier and are independent of measurements. This is why they 'collapse' in the measurement. Or can we say the sampling is only from a certain field that oscillate? Wrong 'sampling' are sorted out.

You also talk of the Big Book and Josephsons currents as the back of the Book. Then Josephsons currents must be interfering with the entangled fields (via Yang Mills and twistors, knots?), Knots and Feynman diagrams, loops are very much the same as the 3 body problem, but in microscale?

Note, homeostasis is always negentropic in a low level. The lower the better. Allostasis is equilibrium at higher negentropic levels and always indicate disturbed balance. The Josephson junctions are also always at slight negentropic state (groundstate of living matter). If they are allowed to relax furter death (of self?) is a consequence. At lower entropic level are the sheets wider, thus hbar grows?

Also between sensing and entanglements are a field of computations or braidings making all those geometric figures, matrices and numbers? Matrices don't come by themselves, they are possibilities. Those are sensed and analyzed further, most are sorted out, then the perception first comes, and the consciousness, which also contains much learned things. Intention and Self is essential, yes, but only for things allowed to enter the 'flame' in working memory. p-adics fields are linked here, making the 'flame' in form of flux tubes, fusing the sheets?. My point is that there are so much consciousness 'left over' in the body, not used to anything else but memories. Hypnosis etc. can take these memories into consideration. They are also seen in split brain patients.

This must mean there are different hierarchies of consciousness, beginning from almost nothing, in kind of 'automatic consciousness' and built up into awareness in working 'flame' where the cognition also is extracted. But there must also be hierarchies in cognitions as there are hierarchies of selves? Some sort? Consciousness is more like 'saved memories of consciousness in the body/sense organs. The phospholylation-link is very interesting here, as I have seen them as saved frequencies of some kinds, or topological islands. Thoughts and emotions are 'rasing up from the body' many times, say in walking. They need some energy to get into awareness, either from your intention, meaning, emotional status, or from the body itself. This is very much the meaning of pain.

Also the enzyme is interesting, linked to the same form in carbon and water. What this means is a metabolic question? Oxygen and Nitrogen also need to be there. Then you have the molecules of Life (and negentropy?).
Mattis answer:  I am not saying that sensory perceptions are classical measurements. I am saying that fundamental character of quantum measurements is that they make the world to look classical. When you measure whether Schroedingers cat is dead ore alive, you find that it is dead or alive but not both.

Interference is possible for similar field components: for instance, wave components representing electric field propagating in same direction. Therefore
It does not make sense to speak about interference of em fields and Josephson currents: it would be like summing temperature and pressure. All this is difficult to understand without appropriate mathematics but become totally trivial when one has it.

The basic problem is lack of common language. Mathematics is extremely abstract, technical, and powerful language but writing everything using formulas is not practical. Hence words like interference, entanglement, coherence, etc.... These words provide a loose higher level language. Unfortunately, this language is misleading without the understanding of the lower level language based on precise mathematical notions.
My comment:  Schrödinger cat is one particle only, but for the biological effects you need the many-body state, and there you can have the dead and alive state in total. After all humans are more dead than alive, usually.

Krennikov (K) use the many minds approach. What are your thoughts about him? He don't use p-adics as cognition medium, but he use p-adics in his theory. I feel it is quite good, except the cognition. Quantum waves are transmitting consciousness as superpositions, but how are they made commutative for linear transmission? I like the basic idea, though.
Mattis answer:  As a mathematician K has written a book about p-adic analysis. His approach in this books is different from mine. K sees the number theoretic constraints posed by p-adics as a hindrance and introduces maximal algebraic extension of p-adics analogous to algebraic numbers. For me these constraints are absolutely essential and evolution would be generation of extensions of rationals and p-adics with increasing dimension and algebraic complexity would correlate with evolutionary level. One could talk about number theoretical quantization in this framework.

K has proposed a 2-adic model for neural networks in brain. Tree like structures which branch again and again. Also some ideas involving 4-adicity (4-adic numbers are not a field but ring) in the case of DNA code. My own purely mathematical models of genetic code have not led to any big insights whereas the dark matter inspired view predicts all the basic numbers related to the code and even more. K has also proposed a brain model involving notions assigned to psychology. This is of course something out of question in Finland, where independent thinking has been criminalized in academic circles. In fact, I had the honor to serve as a referee of some articles of K;-) .

K has proposed a p-adic approach to the Bell inequalities. The idea is that p-adic counterparts of classical probabilities might allow to describe state function events which do not allow description in terms of ordinary real probabilities. Experimentally these events are observed and this means death of hidden variable theories aiming to reduce quantum theory to classical physics. Interference effects due to the fact that quantum theory is in some sense (thermodynamic) square root of probability theory, prevent the reduction to classical physics. [This I cannot understand]. I am skeptic about the reduction to classical physics using p-adic probabilities: it is too tricky. I however hasten to admit that during first years of p-adics physics I also considered seriously some tricky ideas inspired by p-adic mathematics.

K has also discussed the idea that brain performs quantum like processing without being quantal. To me this looks quite too cautious and means losing the basic gift of quantum theory: the possibility to get grasp on what consciousness is . Using the phrase "quantum like" instead of "quantal" is probably wise since academic survival poses very strong constraints on what one can say. DNA as topological quantum computer is my own proposal for how brain processes informations and builds memory representations using braiding.

My comment:
In biology there is a lot of guiding 'strings'. They can be interpreted as environmental space/diamond and self-space/diamond meeting? The role of water in biology is a bit problematic. Usually it creates symmetry breakings.

Look, self-organized liquid chrystals, in experiments with data screen materials, showing both stability/continuity and change/discreateness. This example from classical world. Compare G.Pollack
Mattis answer: Magnetic flux tubes are indeed string like objects and they define the basic correlate for attention. Directing attention to an object of external world means formation of flux tubes connecting perceiver to the object.

Negentropic entanglement accompanies attention and qualia prevail as long as this attention continues. Note the resemblance with Orch Or and with active information of Bohm: attention is the activity.

The test would be finding whether (for instance) visual attention implies that "intentional imprinting" in the object of attention. This relates directly also to the proposed mechanism of remote mental interactions.

Question: is attention symmetric. Does external world attend us too? Answer: during attention there is no perceiver and perceived, only perception. As K says.

In the case of hearing our ability to tell whether the sound comes from external world or not is a mystery if one believes that qualia are product of neural activity. The flux tube model would assign also to hearing flux tubes which are attached to some object oscillating with the sound wave. Even molecules of air.

How it is possible to identify the sound source "correctly" if anything that oscillates with sound wave can serve as target of attention?

Answer: Both ears are needed to identify the target in direction in which intensity is maximal. I remember when my father lost hearing ability from his second ear. He had very grave difficulties to decide which was the direction where sound arrived.

"As you lower the temperature the liquid crystal starts to become organized and imprints that order into the surfactant itself, causing it to self assemble." What is this if not 'memory'?

Stereovision and stereohearing, ye. In my model serotonin is linked to attention too. This is maybe also why we need to discuss, to get some confirmation?

My thought is: What happen to the second law?
Mattis answer: One could argue that entropy is generated at ensemble level when the period of negentropic entanglement ends with ordinary state function reduction accompanied by the splitting of flux tubes between observer and observed and attention therefore ceases.

One can however argue that NMP requires maximization of negentropy gain in quantum jump and this requires compensating negentropy gain elsewhere so that pessimistic form of second law need not hold true. I am unable to decide whether I should be pessimist or optimist;-).

INTENTION is the reason? What does this make with the observer-effect? Intention is prior to the measurement. Can intention be seen as a morphic field? 

Add:
What is light? Classic or quantal? The 'particle' of light is a (holistic) photon. It interferes with an electron, that also isn't descreate? It doesn't interfere with protons? But something must dictate how the atom grows, and the interference between electrons, protons and neutrons. The outcome of lightlike space is particles?

Orwin said...
I think one must accept that attention is a focus within consciousness, so it appears at submanifold level. arXiv:hep-th/000109: non-linear analysis suited to organic oscillators (Winfree stc.).

Here's night vision, day vision & effort/error load: arXiv:0907.4882v1: Tolman's Luminosity-Distance, Poincare's Light-Distance and Cayley-Klein's Hyperbolic Distance, Yves Pierseaux

And a trig lead on the cone problem: arXiv:0806.2789 : Chromogeometry and relativistic conics, N. J. Wildberger

I think the quadric of general trig carries to the Kahler metric.

Will I ever learn this?