måndag 31 maj 2010

The secret behind acupuncture is adenosine?

Today an interesting report is reviewed in Science Daily. Adenosine A1 receptors mediate local anti-nociceptive effects of acupuncture by Nanna Goldman and collaborators.

In the central nervous system, acupuncture creates signals that cause the brain to churn out natural pain-killing endorphins. This effect has been known for along time. This research focuses on adenosine, a natural compound known for its role in regulating sleep, for its effects on the heart, and for its anti-inflammatory properties. But adenosine also acts as a natural painkiller, becoming active in the skin after an injury to inhibit nerve signals and ease pain in a way similar to lidocaine. It is also possible to triple the beneficial effects of acupuncture in mice by adding a medication approved to treat leukemia in people.

What are the messages of all these chemicals? Endorphins gives also a stress-reaction. What tells adenosine? The study is cited by 64 articles.

In the current study, scientists found that the chemical is also very active in deeper tissues affected by acupuncture.

The team made a number of observations regarding adenosine:

- In mice with normal functioning levels of adenosine, acupuncture reduced discomfort by two-thirds.
- In special "adenosine receptor knock-out mice" not equipped with the adenosine receptor, acupuncture had no effect.
- When adenosine was turned on in the tissues, discomfort was reduced even without acupuncture.
- During and immediately after an acupuncture treatment, the level of adenosine in the tissues near the needles was 24 times greater than before the treatment.

Once scientists recognized adenosine's role, the team explored the effects of a cancer drug called deoxycoformycin*, which makes it harder for the tissue to remove adenosine. The compound boosted the effects of acupuncture treatment dramatically, nearly tripling the accumulation of adenosine in the muscles and more than tripling the length of time the treatment was effective.

*inhibition of deaminase activity enhances increases in adenosine and prolongs anti-nociception actions of acupuncture. Two major pathways involved in extracellular enzymatic degradation of AMP. The nucleoside analog deoxycoformycin inhibits both AMP deaminase (AMPD) and adenosine deaminase (ADA).

Acupuncture triggers an increase in the extracellular concentration of ATP, ADP, AMP and adenosine. 
Acupuncture triggers an increase in the extracellular concentration of ATP, ADP, AMP and adenosine. From Nature.

"Acupuncture has been a mainstay of medical treatment in certain parts of the world for 4,000 years, but because it has not been understood completely, many people have remained skeptical," said  Maiken Nedergaard, who led the research.

In fact acupuncture is a very fast developing discipline today, in spite of its old age.

This is just one way acupuncture could work.

A centrally acting agent cannot explain why acupuncture is conventionally applied in close proximity to the locus of pain and why the analgesic effects of acupuncture are restricted to the ipsilateral side.

Acupuncture triggers adenosine and ATP metabolites release
ATP is released in response to either mechanical and electrical stimulation or heat. Once released, ATP acts as a transmitter that binds to purinergic receptors, but ATP cannot be transported back into the cell but is rapidly degraded to adenosine. Thus, adenosine acts as an analgesic agent that suppresses pain through Gi-coupled A1-adenosine receptors.

Injury-signal: Damage is associated with an increase in extracellular nucleotides and adenosine. 'Similar to other types of tissue injury, accumulation of nucleotides in the interstitial space during acupuncture is probably a consequence of unspecific membrane damage or opening of stress-activated channels', says the study. This also Helene Langevin said, and it is true for many therapies, and also used by Nature herself.

Robert Becker in 'The Body Electric' showed a 'current of injury', a very small DC-current.

The relatively high extracellular concentration of ATP metabolites compared with ATP likely reflects the rapid enzymatic degradation of ATP. ATP is about 100-fold higher than AMP and adenosine in cytosol, and that only a fraction of AMP is dephosphorylated to adenosine. Although acupuncture has been practiced for over 4,000 years, it has been difficult to establish its biological basis. Our findings indicate that adenosine is central to the mechanistic actions of acupuncture. We found that insertion and manual rotation of acupuncture needles triggered a general increase in the extracellular concentration of purines, including the transmitter adenosine.

Deqi deactivates areas within the brain that are associated with the processing of pain. "The results are fascinating. Whether such brain deactivations constitute a mechanism which underlies or contributes to the therapeutic effect of acupuncture is an intriguing possibility which requires further research."
Because ATP is released during acupuncture the pinching sensation may be mediated by nociceptive P2X3 receptors, which are expressed by small-diameter, primary afferent neurons, some of which are sensitive to capsaicin, says the new study, concentrating on peripheral nerves.

Why is this a big piece of the puzzle?
Adenosine is shown to be important for the quantum biology in photosynthesis, where the enzyme ATPase has electrons quantum tunnelling. Also in biology the quantal aspect is very important, for the coherence and synergy, and hence for the regulation of biological molecular machines. The degrees of freedom responsible for the entropic Yin/Yang cycle is also dependent on the quantum biology.

Quantum tunnelling is important for our perceptions, which are electromagnetic and quantal.

The ratio of purines/pyrimidines also tells something about the functional states, not only in genes.

Receptors was shown to be crucial (GCPRs), and receptors need ATP, and are often using hexamer and pentamer rings. Water is hexameric. The hexamers change the magnetic moment very fast.

One may speculate that other non-allopathic treatments of chronic pain, such as chiropractic manipulations and massage, modalities that involve the mechanical manipulation of joints and muscles, might also be associated with an efflux of cytosolic ATP that is sufficient to elevate extracellular adenosine. As in acupuncture, adenosine may accumulate during these treatments and dampen pain, says the discussion.

The acupuncture and other therapies are often called 'Energy medicine', something that mainstream dislike strongly. Any hint at diffuse energy is non-scientific, according to them. Well, they are wrong.

Asghar et al. Acupuncture needling sensation: The neural correlates of deqi using fMRI. Brain Research, 2010; 1315111 DOI: 10.1016/j.brainres.2009.12.019
Science Daily in febr Study Maps Effects of Acupuncture On the Brain
and in may Acupuncture's Molecular Effects Pinned Down: New Insights Spur Effort to Boost Treatment's Impact Significantly.
Radiological Society of North America. Nina Theysohn "Acupuncture changes brain's perception and processing of pain, researchers find." /ScienceDaily, 30 Nov. 2010. Web. 25 Aug. 2011.
University of York York study maps the effects of acupuncture on the brain,
Nature article  Adenosine A1 receptors mediate local anti-nociceptive effects of acupuncture, Nanna Goldman et al., Nature Neuroscience 13, 883–888 (2010)

fredag 21 maj 2010

What is Life?

J. Craig Venter Institute Creation of a bacterial cell controlled by a chemically synthesized genome. Science, Published online May 20 2010.

The News told us this morning the scientists at the Venter Institute had created Life. That's a big News.

Next years Nobelist?
J. Craig Venter, Ph.D., founder, president and chairman of the J. Craig Venter Institute (JCVI), has been named a recipient of this year’s National Medal of Science. Dr. Venter was awarded the Medal from President Obama on October 7 at a White House ceremony.

Lubos say: The era of synthetic life has begun. Although Venter is technically not God, my opinion is that the future artificially created and engineered humans, if their inner working is qualitatively similar to the natural people, deserve human rights! But if they behave too badly, they have to be punished, too. Guess Lubos would be the Master then telling what is bad?

Alla Katsnelson: Scientists have built a bacterial genome from scratch and used it to 'reboot' a cell from a different species of bacterium The genome of Mycoplasma mycoides consisting of about 1.1 million base pairs. Having assembled the genome inside a yeast cell, they transplanted it into a cell from a closely related species, Mycoplasma capricolum. After the newly made cell had divided, the cells of the bacterial colony that it formed contained only proteins characteristic of M. mycoides.

The cell was ready from the beginning. They did it by putting together a series of previously developed steps. What is so different from cloning? That the species is a close relative? Would it hinder the talk of immune system? Bacteria recognize foreign invaders by the lack of chemical marks called methyl groups on their DNA.
The new thing is that the genome was manmade, with added methyl groups. But the instructions from a real microbe was used, so it was basically copied, just a few nonessential genes removed and a small number of sequence errors that don't affect the organism's function + four special 'watermark sequences' to distinguish it from the original. Encoded in the watermarks is a new DNA code for writing words, sentences and numbers. The two species' genomes are only about 75% identical.

"It is a technical advance, not a conceptual one. Chimeric organisms have long been created through breeding and, more recently, through the transfer of native genomes into denucleated target cells" says Martin Fussenegger .

We now have the ability to start with a DNA sequence and design organisms exactly like we want," says Gibson. A release was given already 13.5 by the funding organization with couplings to Exxon, Oil Palm and Jatropha.

A statement to get more fundings? Synthetic cells? Not at all.

How does he treat the regulation problem? The intrones that nobody yet knows how they function? Only that they increase with the phylogeneteic ladder. Maybe ancient forms of life can be created again? Multiple personal genomes await?

An unprecedented ability to make many changes to a genome at once, and to add segments of DNA that aren't found in nature but might be designed to perform useful functions, he continues. Of course, the 'engineering' can be useful. Innumerous different ways can easily be thought of, as free energy, medicines for free, genetic 'chirurgy', etc. But also wast risks. The problem is basically the same as for GMO-crops. The manmade portion is not the main problem, but the dispersation of foreign genetic material in Nature.

"This is the first time any synthetic DNA has been in complete control of a cell", says Gibson. A coarse overstatement. "To produce a synthetic cell, our group had to learn how to sequence, synthesize, and transplant genomes. Many hurdles had to be overcome, but we are now able to combine all of these steps to produce synthetic cells in the laboratory."

The way to Lubos dream is very long. Fortunately.
"He isn't God! he's actually being very human; trying to get money invested in his technology and avoid regulation that would restrict its use", Helen Wallace says. Also here. With a video.

"There needs to be a lot of work in understanding how to go about designing a genetic system at the scale of the genome," Christopher Voigt says. "We don't really have a framework to think at that level." And Jim Collins: Scientists don't know enough about biology to create life. Although the Human Genome Project has expanded the parts list for cells, there is no instruction manual for putting them together to produce a living cell.

The group also plans to use the approach to continue work on its project to create a 'minimal' cell that contains only the genes necessary for a cell's most basic survival. "We finally have an assay for determining the functionality of a genome," says Gibson, "So we want to try to determine the smallest number of genes needed to sustain life. This minimal cell will be a platform for analyzing the function of every essential gene in a cell. This will help us better understand how cells work."

But is Life starting from a cell at all? The minimal thing is not a cell? Look at a virus. Usually viruses are not considered 'Life', but their functional aspects tell another story. It's about self-assembly. Also DNA shows self-assembly. It is not inherent in the DNA? Also tensions from outside is needed?

David Deamer: "Using the tools of synthetic biology, perhaps DNA and proteins can be discarded — RNA itself can act both as a genetic molecule and as a catalyst. If a synthetic RNA can be designed to catalyse its own reproduction within an artificial membrane, we really will have created life in the laboratory, perhaps resembling the first forms of life on Earth nearly four billion years ago."

"They bring to an end a debate about the nature of life that has lasted thousands of years", says Arthur Caplan. Really? May be not. Life is not that simple.

'Bottom-up' researchers, like myself, aim to assemble life — including the hardware and the program — as simply as possible, even if the result is different from what we think of as life. Constructing life using different materials and blueprints will teach us more about the nature of life than will reproducing life as we know it." Steen Rasmussen.

The synthetic biology and its ethics, very good in Nature.

American Biotechnologist:
Gibson et. al. from the Venter Institute have just published a report in Science Express (online only) that sounds very cool, but whose implications don’t seem to be well understood yet from experts in the field. Essentially the group synthesized the genome of one bacterial species and transplanted it into another bacterial species. What resulted was a new bacterial colony that only contained the proteins of the first species.

Gibson, D.A. et al., Science advance online publication doi:10.1126/science.1190719 (2010)
We report the design, synthesis, and assembly of the 1.08-Mbp Mycoplasma mycoides JCVI-syn1.0 genome starting from digitized genome sequence information and its transplantation into a Mycoplasma capricolum recipient cell to create new Mycoplasma mycoides cells that are controlled only by the synthetic chromosome. The only DNA in the cells is the designed synthetic DNA sequence, including "watermark" sequences and other designed gene deletions and polymorphisms, and mutations acquired during the building process. The new cells have expected phenotypic properties and are capable of continuous self-replication.

Lartigue, C., Vashee, S., Algire, M., Chuang, R., Benders, G., Ma, L., Noskov, V., Denisova, E., Gibson, D., Assad-Garcia, N., Alperovich, N., Thomas, D., Merryman, C., Hutchison, C., Smith, H., Venter, J., & Glass, J. (2009). Creating Bacterial Strains from Genomes That Have Been Cloned and Engineered in Yeast Science, 325 (5948), 1693-1696 DOI: 10.1126/science.1173759

We recently reported the chemical synthesis, assembly, and cloning of a bacterial genome in yeast. To produce a synthetic cell, the genome must be transferred from yeast to a receptive cytoplasm. Here we describe methods to accomplish this. We cloned a Mycoplasma mycoides genome as a yeast centromeric plasmid and then transplanted it into Mycoplasma capricolum to produce a viable M. mycoides cell. While in yeast, the genome was altered by using yeast genetic systems and then transplanted to produce a new strain of M. mycoides. These methods allow the construction of strains that could not be produced with genetic tools available for this bacterium.

Lartigue, C., Glass, J., Alperovich, N., Pieper, R., Parmar, P., Hutchison, C., Smith, H., & Venter, J. (2007). Genome Transplantation in Bacteria: Changing One Species to Another Science, 317 (5838), 632-638 DOI: 10.1126/science.1144622

As a step toward propagation of synthetic genomes, we completely replaced the genome of a bacterial cell with one from another species by transplanting a whole genome as naked DNA. Intact genomic DNA from Mycoplasma mycoides large colony (LC), virtually free of protein, was transplanted into Mycoplasma capricolum cells by polyethylene glycol–mediated transformation. Cells selected for tetracycline resistance, carried by the M. mycoides LC chromosome, contain the complete donor genome and are free of detectable recipient genomic sequences. These cells that result from genome transplantation are phenotypically identical to the M. mycoides LC donor strain as judged by several criteria.

fredag 7 maj 2010

Emergent Mind?

There are so many models of consciousness. A way to get the essence of it is to scale down the question to its essentials to see what it is about. Popp is very good at that.

He uses the same picture as Rakovic and Pitkänen, and based on thinkings of Henry Stapp. Also Wilhelm Tiller is on the same line with his simulator hypothesis.

Zurek 2002:
Quantum mechanics works exceedingly well in all practical applications. No example of conflict between its predictions and experiment is known.

Without quantum physics, we could not explain the behavior of the solids, the structure and function of DNA, the color of the stars, the action of lasers, or the properties of superfluids. Yet nearly a century after its inception, the debate about the relation of quantum physics to the familiar physical world continues. Why is a theory that seems to account with precision for everything we can measure still deemed lacking?
The only “failure” of quantum theory is its inability to provide a natural framework for our prejudices about the workings of the Universe. States of quantum systems evolve according to the deterministic, linear Schrödinger equation and there is no indication of a border between quantum and classical - The measurement tools (numbers?) are classic usually - so the results are classic? Our perceptions are often difficult to reconcile with the predictions of quantum mechanics, with many alternatives.

And he adds: While the ultimate evidence for the choice of one alternative resides in our elusive “consciousness,” there is every indication that the choice occurs much before consciousness ever gets involved and that, once made, the choice is irrevocable.
Zurek has the opposite sight on the problem. Quantal states origin in classical, and the consciousness arise before the quantum state origin. But it is a very difficult statement to do.

Bohr emphasized that the border between quantum and classical world must be mobile so that even the "ultimate apparatus"— the human nervous system — could in principle be measured and analyzed as a quantum object. But he also said that the measurements was classic.

Example of a macroscopic superposition state from Hamerhoff. Schematic of quantum computation of three tubulins which begin (left) in initial classical states, then enter isolated quantum superposition in which all possible states coexist. After reduction, one particular classical outcome state is chosen (right).

Stapp says: ...according to the new conception, the physically described world is built not out of bits of matter, as matter was understood in the nineteenth century, but out of objective tendencies – potentialities and the potential degrees of freedom. That is both psychology and physical at the same time = knowledge and an action that change the potentailities.

and 2010 recently in 'Quantum Mechanical Approach to the Relationship Between Mind and Brain', -
According to those (reductionistic) principles, the mind-brain connection is fundamentally bottom-up: mental events are imagined to be determined by physical activities in the brain, and to have no capacity to influence brain activities in ways not traceable to prior physical activities. The possibility of genuine top-down causation originating in the mental realm is excluded. Puzzlements arising from this bottom-up approach are well known. Why do the mental aspects exist at all if every physical event is causally traceable to prior physical events?

Yes, why do we have a mental side? What is it good for?

...it is worth noting that the essential change wrought in science early in the twentieth century by the switch from classical mechanics to quantum mechanics is not the introduction of probabilities. It is the introduction of mental aspects of reality into the basic causal structure of our fundamental physical theory... a concomitant reversal of ideas. Newton must be replaced by von Neumann.

That is of course true. The change is mental mostly, as an awareness of the possibilities.That awareness can then be realized, but only if we first see the possibilities. So the observer and the consciousness are very important. Then the decoherence problem face us. Is consciousness required for the wave collapse? Is the moon there when we don't look? How are far away galaxies born, when we didn't were there to look? Who's consciousness was then acting? Some Universal consciousness?

Common sense say this is rubbish. Of course Moon is there, The anthropic principle is Medevial thinking, and the cat is either dead or alive, without our participation.

But then are other results telling exactly the opposite to common sense. PSI-research, Tiller's results, quantum computating results etc. Something 'spooky' is there? Our world relies on quantum mechanics. We are just blind, not to see it.

In 'Rhytms of the brain', of Buzsáki 2006, he points out:
The basic circuitry is the hierarchy of multiple parallell loops. Sensory information is not required for movement, but sensors are developed to guide movements in an effective way. During evolution the basic circuit isn't fundamentally modified, but instead multiple parallell circuits consisting of intermediate and longer chains of neurons, are superimposed on the exisisting wiring. No matter what fraction of the brain, neuronal loops are the principal organization at nearly every level. A physist would call this multilevel, self-similar organization a fractal of loops. Moreover links between lower and higher levels are formed, generating a hierarchial form of organization. The problem is in expanding this construction. New brains are modified versions of older brains; the most recently developed structure is laid on the top of the hierarchy level. The new hierarchy can suppress, reroute or amplify the circuits. The main difference between 'simple and complex brains' are the number of loops that link outputs (actions) with inputs (sensations). The loops are not closed by brain wiring, but there is a 'gap' between the neuronal connections controlling the outputs and inputs that transmit information. The 'gap' may be closed by 'calibrating' actions of the circuits to the metric of the physical world, and allows the brain to learn to sense. The actions are teaching the sensors. The ultimate outcome is that from past experience the brain can calculate the potential outcomes and convey this prediction to the effectors (as muscles).
So our nervous system is a number of superimposed network hierarchies. Evolution is to lay a new layer upon the old ones. Mathemathically this is exponentiality. The quantal world is exponential.

The number of variable ways (potentials) grows exponentially with complexity? This is a kind of 'superposition'. The biological aim is to do as efficient calculations as possible of the potentialities, kind of risk management. This is parallell computing, especially well developed in the right hemisphere. The important thing is not the known facts, but the predictions. The emotions are very fast and represented at every hierarchial level by links and modulations. These emotions are constructed also into the body as reactionpatterns in a predictive behavior (memory). The most effective way is to react on the thoughts and emotions directly. This is the mental state.

In that 'gap' the extracellular matrix is very important.

The border between quantum and classic.
In the absence of a crisp criterion to distinguish between quantum and classical, an identification of the classical with the macroscopic has often been tentatively accepted. The inadequacy of this approach has become apparent as a result of relatively recent developments, says Zurek 2002, and he gives many ex., as; Quantum states associated with the currents of superconducting Josephson junctions involve macroscopic numbers of electrons, but still they can tunnel between the minima of the effective potential corresponding to the opposite sense of rotation. The nerve pulse use a Josephson current and is superconductive in that sense. Biological systems becomes quantal using synchronization, polarization, oscillation? - If macroscopic systems cannot be always safely placed on the classical side of the boundary, then might there be no boundary at all, asks Zurek?

Stapp: The physical descriptions specify ‘potentialities’ for psychophysical events to occur. These events are the only actual things represented in the conceptual structure. Each such event is supposed to have both a psychologically described aspect, and a physically described aspect. The latter is expressed as a ‘reduction’ of the prior set of potentialities in "Quantum Interactive Dualism"

Popp: Reality and consciousness are different things. What is the quantity of consciousness? There are also the 'consciousness about consciousness' problem (qualia). Consciousness is not a strange property of matter, and it is not quantal only. Quantum theory is a product of our consciousness instead. The boundaries are 'virtual' particles, a 'real' quantum vacuum state. These particles cannot be identical to the real ones, because then nothing would happen. This 'exchange' is also time-dependent and dependent of the Planck's constant energetically, and coupled to a 'real' event. The chemistry serves as example, seen in different strengths on binding forces responsible for stable configurations. Exchange forces are 'virtual' forces of the vacuum field, resulting in van der Waals forces, Casimir forces, London forces etc.

A virtual, antagonistic world, or a world of our imagination? But what is imagination? I would say as - if loops, or some kind of prediction about the future (memory of the future?).
Popp: The essential point is the dialogue between the "actual" world and the "virtual" world, this is a permanent and active transformation from the "world of events" into the "world of imagination", from actual into potential information, and vice versa. Up to a point (where it has possibly to get corrected) I suggest to define consciousness then as an active process where actual and potential information are mutually transformed into each other. Consciousness is required to register the measure so it get a meaning. A gap between actual and potential information is a measure of consciousness.

Higher stability depends on the spin. The 'tightness' of the package will change. The density will oscillate. Also the weight will change a little. The exclusion principle, depending on repellation of the same kinds of spin, is the border, that holds the atom configurations fixed.

Zurek: Superpositions evolve forever according to the Schrödinger equation. Each time a suitable interaction takes place between any two quantum systems, the wave function of the universe splits, developing ever more “branches.” There is nothing more macroscopic than the Universe. It can have no a priori classical subsystems. There can be no observer “on the outside.” In this universal setting, classicality must be an emergent property of the selected observables or systems. But which is these 'observables'? In the 2003 text he says; the ability of quantum environment to rapidly decohere systems to which they are coupled. So it is the quantum world that do the decoherence?

The Copenhagen Interpretation demands an a priori “classical domain” with a border that enforces a classical “embargo” by letting through just one potential outcome. The 'Many Worlds' aims to abolish the need for the border altogether, pushing it to the boundary between the physical Universe and consciousness.
“Why do I, the observer, perceive only one of the outcomes?” The key fact has been known almost since the inception of quantum theory, but its significance for the transition from quantum to classical is being recognized only now: Macroscopic systems are never isolated from their environments. Macroscopic systems are open, quantal are closed. There is also the link to the enthropy. The natural loss of quantum coherence, which “leaks out” into the environment, resulting in “decoherence” even in quantal reduced waves/states. Decoherence imposes, in effect, the required “embargo” on the potential outcomes by allowing the observer to maintain records of alternatives but to be aware of only one of the branches—one of the “decoherent histories”.

So it is the awareness that is selective. No wave collapse at all. Many 'histories' are recorded but they are 'implicit', not allowed to talk. This is the same as Freud said. The energy content is the factor making the choise? Perception studies have conformed this picture that we percieve much more than we are aware of.

Reduction of the initial pure state vector decreases the information available to the observer about the resulting reduced, mixed, complex system. The information loss is needed if the outcomes are to become classical and thereby available as initial conditions to predict the future. The effect of this loss is to increase the entropy. Information gain—the objective of the measurement—is accomplished only when the observer interacts and becomes correlated with the detector in the already precollapsed state. In particular, the entanglement between the system and the detector is obviously quantum, because classical systems cannot be entangled. For macroscopic objects, the decoherence time is typically much less than the relaxation time.

Zurek 2002: p 20. Classical reality can be defined purely in terms of classical states obeying classical laws.
In the past few sections, we have seen how this reality emerges from the substrate of quantum physics: Open quantum systems are forced into states described by localized wave packets. They obey classical equations of motion, although with damping terms and fluctuations that have a quantum origin. What else is there to explain?
Controversies regarding the interpretation of quantum physics originate in the clash between the predictions of the Schrödinger equation and our perceptions. I will therefore conclude this paper by revisiting the source of the problem—our awareness of definite outcomes. If these mental processes were essentially unphysical, there would be no hope of formulating and addressing the ultimate question—why do we perceive just one of the quantum alternatives?—within the context of physics. Indeed, one might be tempted to follow Eugene Wigner (1961) and give consciousness the last word in collapsing the state vector. I shall assume the opposite. That is, I shall examine the idea that the higher mental processes all correspond to well-defined, but at present, poorly understood information-processing functions that are being carried out by physical systems, our brains.

In particular, the process of decoherence we have described above is bound to affect the states of the brain: Relevant observables of individual neurons, including chemical concentrations and electrical potentials, are macroscopic. They obey classical, dissipative equations of motion. Thus, any quantum superposition of the states of neurons will be destroyed far too quickly for us to become conscious of the quantum “goings on.” Decoherence, or more to the point, environment-induced superselection, applies to our own 'state of mind'.

There is, however, another reason for this focus on the classical that must have played a decisive role: Our senses did not evolve for the purpose of verifying quantum mechanics. Rather, they have developed in the process in which survival of the fittest played a central role. There is no evolutionary reason for perception when nothing can be gained from prediction. And, as the predictability sieve illustrates, only quantum states that are robust in spite of decoherence, and hence, effectively classical, have predictable consequences. Indeed, classical reality can be regarded as nearly synonymous with predictability.

Decoherence destroys superpositions. The environment induces, in effect, a superselection rule that prevents certain superpositions from being observed. Only states that survive this process can become classical.

I must emphazise that Zurek talks of open quantum systems.

Creativity and relaxation.
Consciousness is associated with the capacity of becoming aware of something. To get some 'degree of awareness', but the difficulty is in the roles and interferences of the outer world and the observer. Consciousness cannot be objectified, the role of the observer can't be removed. Stapp identified the consciousness as the collapse of the wave function, or the condensation of external events onto the observers detector system (sensors) into reality. This is the decoherence. Pitkänen say it is the jump between histories (of whom = the observer), Rakovic say we ought to eliminate the quantal 'memory attractors' (of whom = the observer) to get the decoherenced, healthy stage.

In this process it is the potential information that is important. This can be measured in Shannon's approach, and the probabilities are measured in an open system.

Consciousness gives evolutionary significans, because the knowledge of the potentials gives better predictions of the 'virtual' world (as - if loops), that is, the most important survival information is in the probability field. Intuition and the sixth sense are very important. PSI research has also shown that most of us can use this sense. We experience via the senses, but according to consciousness we can also change the conditions in our outer world by consciousness. Tiller has done good science on this. He writes:
We have discovered that there are actually two levels of physical reality and not just one. It is this “new” level of physical reality that can be significantly influenced by human intention! How? There are two basic kinds of unique substances found in these two levels of physical reality. They appear to interpenetrate each other but, normally, they do not interact with each other. We call this the uncoupled state of physical reality. In the uncoupled state we are able detect our normal physical environment with our five physical senses. But the substance in this normal state of physical reality is not influenced by human intention. The substance in the “new” level of physical reality, appears to function in the empty space between the fundamental electric particles that make up our normal electric atoms and molecules. As such, it is currently invisible to us and to our traditional measurement instruments. But the substance in this “new” level is influenced by human intention.
Why would this be so important? Because it gives creativity, and it invokes on health. Not too much creativity, but in suitable amounts. Creativity gives a survival benefit. Brain can in fact be seen as a sense organ too (for creativity?). It doesn't only recieve sensory inputs, it will also make them to some extent.

It also gives an evolutionary advantage to draw out the highest amount of 'possibilities' from real events (calculation?), and to store them. This is a maximation of possibilities, or negentropy, as Pitkänen puts it? Popp talks of optimizing the negentropy.
Or it might be better to discover highest amounts of realizations in a few possibilities (resolution). We must also remember that negative information is important, a lack of (good) information. Also the consciousness storage gives a relaxation, and a life-time of coherent time, because stored electromagnetic waves do not loose their phase information during this time. And if the stored potential information is exponential the fields become coherent (superfluidy) and give relations of the wave (every point is connected to every other point= holism) by phase correlation. A maximation of relaxation gives a better flexibility, a wider action potential for work. A coherent field can keep the initial state permanently in mind too. In fact, this is a requirement for the developement of consciousness. It optimizes the capacity for differentation, communication, a realization of space and time, and health.

Humor and laghter are excellent relaxtants, and very healthy too.

Popp writes: In order to develop 'consciousness' Nature seems to use the possibility of a strict maximization of the entropy as a time average, in order to arrive at highest stability and of coupling the informational carriers (coherent photons of different modes) to one degree of freedom, in order to arrive at highest sensitivity and holistic information of the body. There are some models based on exciplex (excited complex) systems of DNA.
Li & Popp:
...exciplex systems of biological systems to be the molecular base of life altogether. Exciplexes (excited complexes) are metastable states of always two similar molecules physically bound in such a way that the (ideal) groundstate is formed by the separated molecules and the (ideal) excited state corresponds to the strongly bound molecule, forming, for instance, a dimer. Between these states there are the many possible steps of excited complexes of both partners. They are linked by a manifold of different binding forces, e.g. H-bridging, van-der-Waals binding forces, partially also charge transfer, ionic or exchange forces. Exciplexes are formed by all base pairs of the DNA, in a perpendicular as well as in a parallel direction to the DNA strand axis. The fundamental biological importance of the exciplex formation concerns their extraordinary capacity in establishing powerful photon traps. According to our proposals the network of photon traps in the biological system is at the same time the basic source of the communication system of the living system. By mutual absorption and emission (annihilation and creation) of photons within this network, intracellular as well as intercellular communication takes place where the "sucking potentials" of the traps and the available light intensities are the decisive regulatory quantities of the three-dimensional channel system of the cells communication base. We now have some evidence of the existence and of some rather interesting properties of this system. Therefore we use this occasion to explain the most decisive properties of exciplex states in terms of their photon sucking potential.

The exciplex states form photon traps (E<0).This mechanism provides the very basis of life since it opens an infinite play of competition for light with infinite possibilities of modulations in all frequency ranges lower than ionizing UV. This mechanism is universal in all living systems.

Amico et al. shows the properties of the entanglement in many-body systems, and how entanglement is tightly connected to the characteristics of the phase diagram. The entanglement can have different hierarchies too, as bipartite, tripartite etc. (compare with the qubit/quantum dot research with different energy levels proceeding at the same time, entanglement - the spooky, distance-defying link that can form between objects such as atoms even when they are completely shielded.) The success of quantum computation and communication relied on the longevity of entanglement in multi-particle quantum states. The presence of decoherence in communication channels and computing devices, degrades the entanglement when the particles propagate or the computation evolves. Decoherence leads to both local dynamics, associated with single-particle dissipation, diffusion, and decay, and to global dynamics, which may provoke the eventual disappearance of entanglement, known as “entanglement sudden death”.

One important cause of decoherence is the interaction of a quantum system with its environment, which ’entangles’ the two and distributes the quantum coherence over so many degrees of freedom as to render it unobservable. Large molecules are particularly suitable for the investigation of the quantumclassical transition because they can store much energy in numerous internal degrees of freedom; the internal energy can be converted into thermal radiation and thus induce decoherence.

Free will.

Stapp: Quantum mechanics explains voluntary control of bodily actions. At its essential core quantum mechanics is a theory of the mind-brain connection in which acquisition of knowledge is achieved without any direct action of the physical upon the mental. "the ‘free will’ problem is to explain the connection between ‘willed’ physical actions and the conscious efforts that seem to be causing them. How, in the classical approach, does one explain how the conscious thoughts come into being at all, and in just the way that makes them appear to be doing just what, according to quantum mechanics, they actually are doing? And how can they, during the evolution of our species, evolve in just the right way as to be always in accord with what the brain is causing the body to do if there could be no adverse physical consequences of the thoughts themselves going completely haywire?

Neuroscience and philosophy have struggled for years with the mystery of how a physical motion can create (or be) a mental reality. By identifying that puzzle as a misleading relic of known-to-be-false early science we take a major step toward achieving a rationally coherent understanding of the mind-brain connection that is fully in accord with our deepest contemporary science. Stripping away the classical blinders allows us to see how the sophisticated quantum measurement process itself resolves the long-standing puzzles. It does so by doing exactly what that process is designed to do: enlighten the enquiring mind with the knowledge of physical properties that it actively seeks.

Von Neumann’s development of the theory of measurement allows the mental/psychological aspects of the agent to be cleanly separated from his bodily/physical aspects, and then explains how the agent acquires knowledge about the physical properties of his brain.

The basic idea of understanding all these phenomena is the superposition of electromagnetic fields, in particular biophotons, in a way that during biologically relevant time intervals within biologically relevant structures, interference patterns of destructive and constructive interference are built up that "organize" the movement and activity of the biomolecules within and between the cell populations, destructive interference of incoming and reflected wave at a non-linearly polarizable double layer. As a consequence, in the inside constructive interference takes place.

This sounds a lot like the magnetic flux tube model in Pitkänens theory. Consciousness arise in the quantum jumps.

Matjaž Perc, 2005: we show that the introduction of long-range couplings induces decoherence of otherwise coherent noise-induced spatial patterns - Importantly, already a small fraction of long-range couplings is sufficient to destroy coherent pattern formation. We argue that the small-world network topology destroys spatial order due to the lack of a precise internal spatial scale, which by regular connectivity is given by the coupling constant and the noise robust excursion time that is characteristic for the local dynamics.

Tiller also points out the two different pathways to knowledge in ancient times, called Mythos and Logos the inner and the outer path of knowledge. The inner path was seen as more sacred, and gave true knowledge, Gnosis. This is nothing more than the potential informational well, pointing to a storage of memories in the virtual world, experienced in form of collective consciousness and archetypes. Jung talked of these too, and of other 'virtual figures' like Anima, Animus, The shadow etc. This form of matter is highly intelligent? Pitkänen links it to dark matter.

The possibility of macroscopic quantum states in biological systems seems unlikely. Everything depends on coherent states. And as in technological proposals, perfect isolation of the quantum state from the environment (and/or quantum error correction codes) would be required while the system must also somehow communicate with the external world. Living cells including the brain's neurons seem unsuitably warm and wet for delicate quantum states which would seem susceptible to thermal noise and environmental decoherence. However specific conditions supporting quantum states - in microtubules, meridians, nerves etc. may have evolved. As Rakovic say: Nature has solved the noise problem. The coherent superpositional states are created by shielding and isolation, polarization, etc. The wave and the surfer.

Environmental decoherence (noise) collapse the quantum state in classical systems, but in living systems noise is creating coherence up to a limit. The coherence give entangled, temporal, isolated quantum systems (subselves). Superimposed on one degree of freedom = the whole body, or a subfractal system of the body? The holographic principle states that the part acts as the whole, the part is a mirror of the whole, or contrarily.

Quantum computation with objective reduction may be somehow involved in consciousness.

Quantum consciousness.
Stuart Hameroff, the highest function of life—consciousness—is likely a quantum phenomenon too. This is illustrated, he says, through anesthetics. The brain of a patient under anesthesia continues to operate actively, but without a conscious mind at work.
One can ask how this is possible? It must mean that consciousness is not created in the brain, only that it is switched off with anesthetics. The brain acts like a lens for the light, and consciousness is the light?

What enables anesthetics such as xenon or isoflurane gas to switch off the conscious mind? Hameroff speculates that anesthetics “interrupt a delicate quantum process” within the neurons of the brain. Anesthetics, Hameroff says, dissolve inside tiny oily regions of the microtubules, affecting how some electrons inside these regions behave.

The action unfolds like this:
When certain key electrons are in one "place," call it to the "left," part of the microtubule is squashed; when the electrons fall to the "right", the section is elongated. But the laws of quantum mechanics allow for electrons to be both “left” and "right" at the same time, and thus for the micro­tubules to be both elongated and squashed at once. Each section of the constantly shifting system has an impact on other sections, potentially via quantum entanglement, leading to a dynamic quantum-mechanical dance.

It is in this faster-than-light subatomic communication, Hameroff says, that consciousness is born. Anesthetics get in the way of the dancing electrons and stop the gyration at its quantum-mechanical core; that is how they are able to switch consciousness off.

Consciousness and brain.
Can consciousness be created as Hamerhoff say? His model has meet a lot of critique.

Chris Carter, the man inventing the X-files, writes: In his book 1891, Ferdinand Schiller proposes that ‘matter is admirably calculated machinery for regulating, limiting and restraining the consciousness which it encases.’ He argues that the simpler physical structure of ‘lower beings’ depresses their consciousness to a lower point, and that the higher organizational complexity of man allows a higher level of consciousness.
This consciousness should be awareness. In other words, consciousness and awareness are like night and day. Awareness is constraining the consciousness.

Matter is not what produces consciousness but what limits it and confines its intensity within certain limits … This explanation admits the connection of Matter and Consciousness, but contends that the course of interpretation must proceed in the contrary direction. Thus it will fit the facts which Materialism rejected as ‘supernatural’ and thereby attains to an explanation which is ultimately tenable instead of one which is ultimately absurd. And it is an explanation the possibility of which no evidence in favour of Materialism can possibly affect.

As for the effects of brain injury, Schiller argues that an equally good explanation is to say that the manifestation of consciousness has been prevented by the injury, rather than extinguished by it. With regard to memory, he thinks that it is forgetfulness rather than memory that is in need of a physical explanation: pointing out the total recall experienced under hypnosis and ‘the extraordinary memories of the drowning and dying generally’, he argues that we never really forget anything, but rather are prevented from recalling it by the limitations of the brain.

This article is also here, with links.

That's it. It is our left brainhalf that make us human, by compressing our consciousness and making our awareness emerge. The same thing is happening when we concentrate on something. Our attention becomes very narrow. Or when we remember something, think at something... The logic thinking is a critical action, constraining us very much. This is the entropic brain, entropy is creativity, negentropy is the constrainment. All matter is negentropic. Life is negentropic. Or is it?
The brain is therefore both ‘the organ of attention to life’ and an obstacle to wider awareness. He speculates that if the brain is a limiting obstacle, filtering out forms of consciousness not necessary for the organism’s biological needs, then freedom from the body may well result in a more extended form of consciousness, which continues along its path of creative evolution.

The brain is not an organ that generates consciousness, but rather an instrument evolved to transmit and limit the processes of consciousness and of conscious attention so as to restrict them to those aspects of the material environment which at any moment are crucial for the terrestrial success of the individual. In that case such phenomena as telepathy and clairvoyance would be merely instances in which some of the limitations were removed.
Something is wrong with our entropic model of the Universe? It is like two circles eating each other. The Ouroborus.

The French philosopher Henri Bergson (living too at 1800) held similar ideas to those of Schiller. Bergson attempted to reconcile physical determinism with the apparent freedom of human behavior by proposing a theory of evolution whereby matter is crossed by creative consciousness: matter and consciousness interact, with both being elemental components of the universe, neither reducible to the other.

The wave never collapse? It is our perception that creates only one possibility in the quantum tunnelling? The collapse is in our perception? In reality there are also the wave all the time. The Schrödinger cat is both dead and living. It is we that see only one possibility. Our modern science is leading us astray? We don't see the forest for all trees.

Tiller has looked at this aspect very closely and has arrived at odd results.

-Henry Stapp's online papers and book
-Matti Pitkänens online papers and books.
-Dejan Rakovic online papers and books.
-Fritz-Albert Popp online papers.
- Wilhelm Tiller online papers and books.

Stuart Hamerhoff. Quantum computation in brain microtubules? The Penrose-Hameroff "Orch OR" model of consciousness. http://www.quantumconsciousness.org/penrose-hameroff/quantumcomputation.html

William A. Tiller, 2003: CONSCIOUS ACTS OF CREATION: THE EMERGENCE OF A NEW PHYSICS*. http://www.wholistichealingresearch.com/user_files/documents/doublebonusdownload.pdf

Matjaž Perc 2005: Spatial decoherence induced by small-world connectivity in excitable media. New J. Phys. 7 252. http://iopscience.iop.org/1367-2630/7/1/252/fulltext

Wojciech H. Zurek, 2002: Decoherence and the Transition from Quantum to Classical—Revisited. Los Alamos Science Number 27. http://arxiv.org/ftp/quant-ph/papers/0306/0306072.pdf

Wojciech Hubert Zurek, 2003: DECOHERENCE, EINSELECTION, AND THE QUANTUM ORIGINS OF THE CLASSICAL. http://arxiv.org/PS_cache/quant-ph/pdf/0105/0105127v3.pdf

Luigi Amico, 2008: Entanglement in Many-Body Systems. http://arxiv.org/PS_cache/quant-ph/pdf/0703/0703044v3.pdf

söndag 2 maj 2010

TGD and D.Rakovic. The quantum field body, a comprision.

The problem of superpositions and quantum field body. A comparision between two models.

Both TGD and the Rakovic model are based on p-V pair corresponding to the geometric, classic existence and is replaced with generalized force-generalized coordinate pairs in quantum fluctuating degrees of freedom, the same as in Popps model. Quark - N pair corresponds to 'objective existence' defined by quantum histories and N is generalized to a number of particle like excitations in the photon number state resulting in the state preparation. Rakovic talks of biomolecules where Pitkänen talks of particles and dark matter. The difference between the models is in the consciousness mechanism, mainly. In TGD cognition and intention are linked to p-adic primes; Rakovic see no need to talk of dark matter and primes, only complex valued quantum field holography. How that holography arise remain unclear to me.

"I suggest you to read my attached paper on integrative medicine to see my viewpoint on the origin of quantum-coherent states in acupuncture system/consciousness", said Dejan Rakovic in a mail, regarding the superconduction in biology. Quantum-informational medicine and quantum-holographic informatics, with special reference to numerous psychosomatic-cognitive implications, is the approach 'in developed countries', he says.
"Psychosomatic diseases indicates the necessity of application of holistic methods, implying their macroscopic quantum origin. The most intelligent way is the treatment of man as a whole and not diseases as symptoms of disorders of this wholeness. The focus of these quantum-holistic methods are the body’s acupuncture system and consciousness, incl. quantum-informational medicine with quantum-holographic informatics - with surprisingly significant psychosomatic and cognitive implications." Rakovic call his model the biophysical quantum-holographic/quantum-relativistic model of consciousness.

TGD involves a quite far-reaching generalization of the space-time concept and, apart from the notion of quantum jump, reduces quantum theory to in finite-dimensional geometry, which is highly unique from the mere requirement that it exists. Quantum TGD requires the introduction of several new mathematical tools and concepts. Dark matter hierarchy with p-adic primes in a scaled up topological way.
TGD is also a classic physical theory based on 'the wholy trinity' from the elemental particle physics. The emergence of the notions of zero energy ontology and hierarchy of Planck constants together with the increased understanding of the special features of number theoretical universality have led to a considerable deepening of the understanding during last half decade.

Can this new physics give the answer? What are the similarities between TGD and Rakovic model?

Non-locality (infiniteness) in both space and time is given in quantum TGD. It is the interaction between non-locality and locality that make up the interactions in the (quantal) magnetic body. This means also that the time concept will change, which is behind the consciousness.

Quantum information and holography.
Rakovic says: "The quantum-informational structure with memory attractors as a possible quantum-holographic informational basis of psychosomatic diseases." Then what is these structures with attractors? To get an answer on that we need to look at quantum non-material memory (from quantum computer science).

Quantum memory.
The first Bose-Einstein condensates were generated in 1995. A Bose–Einstein condensate represents the most 'classical' form of a matter wave, just as an optical laser emits the most classical form of an electromagnetic wave. Optical lattices are interference patterns comprised of laser beams, which are shone onto the atomic cloud and force their periodic structure onto it, with the creation of crystal-like formations, as results. Atoms and molecules move completely freely and randomly in gases unlike they do in solids. All vectors are free? The interesting aspect is that the movement of the atoms in an optical lattice within a quantum gas is similar to the behavior of electrons in solid bodies. Quantum gases are thus able to simulate the physical properties of solid bodies.

After ultracold atoms are maneuvered into superpositions they are released to allow interference (noise-production) of each atom's two 'selves' (wave and matter). They are then illuminated with light, which casts a shadow, revealing a characteristic interference pattern, with red representing higher atom density. The variations in density are caused by the alternating constructive and destructive interference between the two 'parts' of each atom, magnified by thousands of atoms acting in unison. Each site is split into two wells, about 400 nanometers apart. Under the rules of the quantum world, the atom doesn't choose between the two sites but rather assumes a "superposition," located in both places simultaneously. From National Institute of Standards and Technology, NIST

So, in quantum world are no choises (no 'environment' because of the non-locality?). The free will, the intention, where does these things emerge? This is true for matter, but certainly also for living matter.

Quantum computing relies on the transmission of entangled qubits, or 'quantum bits', over distance in the form of photons. As photons travel along the lines they degrade steadily. Therefore, a device that can read and retransmit the signal would allow for the transmission of quantum data over any distance. This is what happens in the meridians in Popps model. The photons functions as solitons. The same function as in the nerve pulse of TGD and the Heimburg group.

An optical lattice uses laser beams of different frequencies, shining in the same area, to create energy 'buckets' that hold atoms in place. The lattice can be tuned to place atoms where they are desired, and it can be used to extend the lifetime of quantum memory. The Georgia Tech team.

The red spheres are atoms sitting in the energy 'buckets' created by interfering laser beams. Wikipedia.

To encode information onto the atoms, a laser beam carrying a signal is shined on the array of atoms confined to the lattice. Each atom stores a portion of the quantum information, which is sensitive to the relative locations of the atoms. The lattice, therefore, allows the information to be stored longer by preserving the locations of the atoms more effectively.

This memory is physical (atomic)? The quantum memory is degrees of freedom on an atom. These energy 'buckets' are the same looking as the cells cytoskeleton tensions inducing 'buckets' on the environment in the extracellular matrix (Ingber 1998). So memory can be physical, stored in tensions in the tissues? Physical + quantal memory.

Cleland group do research on quantum integrated circuits, based on the Josephson phase qubit, a superconducting device whose operation relies on the physics of the Josephson junction (low electrical impedance and relatively large capacitance). Other groups have used spin etc. The qubit is coupled = entangled groups of degrees of freedoms.

This was an extension, but I think it was necessary to understand the quantum memory, at least for me.

Rakovic: "Peruš’s theoretical investigations show that any quantum system has formal mathematical structure of quantum-holographic Hopfield-like neural network . Then memory attractors of the acupuncture network can be treated as psychosomatic disorders representing EM MW/ULF-modulated (quantum)holistic records = gives a biophysical basis of (quantum)holistic local psychosomatics? (removed only holistically + extreme efficiency of the quantum-informational therapies, that consequently erase the very information of the psychosomatic disorders). And according to the Tibetan traditional medicine, an acupuncture procedure must be repeated every several months – presumably as a consequence of restituted patient’s mental loads from his mental-transpersonal-environment of closely related relatives/enemies/deceased, that remained non-reprogrammed on the level of quantum-holographic collective consciousness."

So, if one changed, then also the other, but in an iniert way, as life itself is iniert. The memory is iniert. The mental aspect is most important. It is (quantum)holistic. Is memory an EM-system or even quantal? And a memory can be a collective/individual stress trapped in the tissue network.

Pitkänen: "The identification of quantum jump between quantum histories as moment of consciousness defines microscopic theory of consciousness whereas the notions of self and self hierarchy allow to understand macroscopic aspects of consciousness absolutely essential for brain consciousness. Self is identified as a sub-system effectively behaving like its own subuniverse quantum mechanically, and physically self is a sub-system able to not generate bound state entanglement with environment during subsequent quantum jumps. Also self measurements are possible leading to a completely unentangled state."

History requres memory and memory requires a self. And we have two self, one quantal and one physical. The quantal self has the memories? Also two consciousnesses.

Rakovic: "For modeling most cognitive and especially psychosomatic functions the subtle biophysical acupuncture neural networks (modulated by UNF EM fields of brainwaves) are necessary as well, combined with quantum decoherence theory. It appeared, within the Feynman propagator version of the Schrödinger equation, that the quantum level is described by analogous mathematical formalism as Hopfield-like quantum-holographic associative neural network. How the quantum parallel processing level gives rise to classical parallel processing level, which is a general problem of the relationship between quantum and classical levels within the quantum decoherence theory.

They demonstrate existence of two cognitive modes of consciousness (direct religious/creative one, characteristic of quantum-coherent transitional and altered states of consciousness, and indirect perceptively/rationally mediated one characteristic of classically-reduced normal states of consciousness) – together with conditions for their mutual transformations."

Might this correspond to the different brain halfs?

Pitkänen: The reduction of the standard quantum measurement theory to fundamental quantum physics is a triumph of TGD approach. Each quantum jump involves localization in the so called zero modes having interpretation as classical variables characterizing the observable geometric properties of the space-time surface, and thus of external macroscopic observer (magnetic body), together with an additional condition guaranteing that the density matrix characterizing the entanglement between quantum fluctuating degrees of freedom and zero modes is diagonal, implies standard quantum measurement theory.

Rakovic: "Quantum neural holography combined with quantum decoherence might be very significant element of the feedback bioinformatics, from the level of cell to the level of organism. Whole psychosomatics is quantum hologram, both on the level of individual and collective consciousness, and that quantum-holographic hierarchical parts carry information on wholeness, enabling quantum-holographic fractal coupling of various hierarchical levels. Acupuncture-based-quantum-informational (un)intentional control of ontogenesis and morphogenesis; quantum-holographic language-influence on the genes expression, with implications of great psychosomatic significance of thought-emotional contents; and global fractal information coupling of various hierarchical levels in Nature with fundamental holistic implications on the origin of miraculous deep creativities and determinism of the History through the coupling with the existing evolving state of collective consciousness. This forecasts a great synthesis of two cognitive/consciousness modes. The personal role becomes indispensable due to the influence and care for collective mental environment, which is fundamental question of both mental health and civil decency, i.e. of both spiritual and civil morality. Some manifestations of consciousness must have deeper quantum origin – with significant psychosomatic and transpersonal implications."

Pitkänen: The dynamics of self measurement is governed by Negentropy Maximization Principle (NMP), which speci es which subsystems are subject to quantum measurement in a given quantum jump. NMP can be regarded as a basic law for the dynamics of quantum jumps and states that the information content of the conscious experience is maximized. In p-adic context NMP dictates the dynamics of cognition.

It is the quantal self that is repaired (by max. information, magnetic body, observer), and it direct our physical self which is hierarchial. The last stage is 'arousal' or awareness, attention etc. The energy grows with computation/entanglement. This is usually called the 'self' in biology. The archetypes in Jung, that is information from the past, but today is also told of an influence from the future (Holger Nielsen among others).

There are a big confuseness on the terminology. I usually prefer Damasios terminology.

Pitkänen: "TGD predicts two kinds of super-conformal symmetries, super-Kac Moody symmetries assignable to partonic 2-surfaces identi able as time = constant sections of light-like causal determinants (diamonds) of 4-surfaces correspond to the gauge symmetries of fundamental interactions. Super-symplectic symmetries act at imbedding space level, with some future/past light-cone of space. There is a fractal hierarchy of quantum holograms inside quantum holograms. Super-symplectic representations correspond to genuine quantum gravitational e effcts since wave functionals in the space of threesurfaces are involved: space-time ceases to be a passive arena of quantum dynamics. Super-symplectic degrees of freedom makes massless extremals ideal candidates for the correlates of higher level consciousness."

The models shortly.

Rakovic considers information processing within the central nervous system as occurring through hierarchically organized and interconnected neural networks.

Hierarchical models of brain’s neural networks can be divided into:
- Kohonen’s selforganized mapping feature mapping unidirectionally oriented multilayer neural networks
- Hopfield’s associative or attractor , massively and bidirectionally connected neural networks,
- Haken’s synergetic classical and
- Peruš’s neuro-quantum multilayer neural networks.

"It is firstly noted that models of brain’s hierarchical neural networks demonstrate encouraging advances in modeling cognitive functions – which is not surprising bearing in mind that information processing on the level of central nervous system is going via hierarchically organized and interconnected neural networks. It seems that this hierarchy of biological neural networks is going down to sub-cellular cytoskeleton mesoscopic level, being a kind of interface between neural and quantum levels."

This sounds like the reductionistic emergent kind of consciousness, as a consequence of network complexity. But also Pitkänens self-entanglement is of the same kind. No essential difference.

Pitkänen: "Self measurements are governed by Negentropy Maximization Principle, and give rise to quantum level self repair mechanism. In p-adic context NMP is the basic variational principle of cognition. The quantum jump at a given level of hierarchy corresponds to a sequence of quantum jumps at lower levels, which also contributes to the experience of the higher level self. The last stage gets the highest energy level (because these sub-selves entangle and give energy) and is the 'wake-up' self."

"The proposal is that the dynamics of consciousness is governed by Negentropy Maximization Principle, which states the information content of conscious experience is maximal."

"Negentropy Maximization Principle (NMP) codes for the dynamics of standard state function reduction and states that the state function reduction process following U-process gives rise to a maximal reduction of entanglement entropy at each step. In the generic case this implies at each step a decomposition of the system to unique unentangled subsystems and the process repeats itself for these subsystems. The process stops when the resulting subsystem cannot be decomposed to a pair of free systems since energy conservation makes the reduction of entanglement kinematically impossible in the case of bound states. The natural assumption is that self loses consciousness when it entangles via bound state entanglement."

Arousal-stage where dopamine is important?

In the model of Hopfield’s classical neural network, emergent collective computation is either regulated by global (variational) minimization of the Hamiltonian energy function or by local (interactional) network learning in discrete or continuous forms (incorporating spatio-temporal description of neuronal and synaptic activities). Haken has shown that introduction of biologically more plausible neuronal oscillatory activities gives richer dynamics of the neural network, with Hopfield’s classical neural net real-valued variables replaced by the complex-valued ones (similarly to quantum variables, although in contrast to thus conveniently modified classical formalism, the complex-valued quantum formalism is essential). A step further was done with quantum generalization of Hopfield’s classical neural network: Sutherland’s holographic neural network and, equivalent to it, Peruš’s model of Hopfield-like quantum associative neural network.

Again, not so big difference. P-adics versus complex-valued quantum formalism are used.

Kohonen maps:"Kohonen - a system model that is composed of at least two interacting subsystems of different nature. One of these subsystems is a competitive neural network that implements the winner-take-all function (digital), but there is also another subsystem that is controlled by the neural network and which modifies (modifying neurotransmitters) the local synaptic plasticity of the neurons in learning (LTP). The learning is restricted spatially to the local neighborhood of the most active neurons. The plasticity-control subsystem could be based on nonspecific neural interactions, but more probably it is a chemical control effect. Only by means of the separation of the neural signal transfer and the plasticity control has it become possible to implement an effective and robust self-organizing system. The SOM principle can also be expressed mathematically in a pure abstract form, without reference to any underlying neural or other components. The first application area of the SOM was speech recognition."

The SOM is one of the most realistic models of the biological brain function, acc. to his latest book. Dynamic modeling using nonlinear state-space models, on his web page, with simulations. Also relational models, with many real-world sequences such as protein secondary structures or shell logs exhibit rich internal structures, logical hidden Markov models, etc.

We combine two of these methods, relational Markov networks and hierarchical nonlinear factor analysis (HNFA), resulting in using nonlinear models in a structure determined by the relations in the data. This model is a structure and a field oscillating on the structure.

Gao et al 2008: "Inference of latent chemical species in biochemical interaction networks is a key problem in estimation of the structure and parameters of the genetic, metabolic and protein interaction networks that underpin all biological processes. We present a framework for Bayesian marginalization of these latent chemical species through Gaussian process priors.

A challenging problem for parameter estimation in ODE models occurs where one or more chemical species influencing the dynamics are controlled outside of the sub-system being modelled. For example, a signalling pathway can be triggered by a signal external to the pathway itself. In a regulatory sub-system, one or more transcription factors (TFs) may influence the expression of a set of target genes, but these TFs may not be regulated at the transcriptional level, instead being activated by another sub-system such as a signalling pathway. Similarly, in a metabolic pathway external metabolites and enzymes will influence the dynamics of the pathway. If these external chemical species have a constant influence, e.g. as in the case of steady state behaviour of a metabolic pathway, then they can simply be treated as additional parameters of the model and their effect can be estimated along with the other model parameters. However, more often these external factors are time-varying quantities."

Hopfield-like neural network have certain shortcomings as descibed by Joya et al, 2002. They are widely used in neural computings. The complex neural fields can change both the amplitude and the phase, and their dynamics has a close analogy with the dynamics of self-oscillation generated in a phase-conjugate resonator.

Torres et al.2003 in 'Influence of topology on the performance of a neural network': "the capacity to store and retrieve binary patterns is higher for attractor neural network with scale–free topology than for highly random–diluted Hopfield networks with the same number of synapses."
Topology is better?

Pitkänen: In standard physics context the existence of the required macroscopic quantum phases is not at all obvious whereas the new physics implied by TGD predicts their existence. The point is that the Universe according to TGD is a quantum critical system. Quantum criticality is mathematically very similar to thermodynamical criticality and implies long range quantum correlations in all length scales. This in turn implies the existence of macroscopic quantum phases. TGD Universe is also quantum spin glass with state degeneracy broken only by the classical gravitational energy of the space-time sheets having same induced Kähler fi eld. This degeneracy makes it possible to have quantum coherence over time periods longer than CP2 time of order 10^-39 seconds characterizing the duration of single quantum jump so that biosystems can act as quantum computers in macroscopic time scales.

Mitja Perus, 2000. NEURAL NETWORKS AS A BASIS FOR QUANTUM ASSOCIATIVE NETWORKS. "We have got a lot of experience with computer simulations of Hopfield’s and holographic neural net models. Starting with these models, an analogous quantum information processing system, called quantum associative network, is presented in this article. It was obtained by translating an associative neural net model into the mathematical formalism of quantum theory in order to enable microphysical implementation of associative memory and pattern recognition. In a case of successful quantum implementation of the model, expected benefits would be significant increase in speed, in miniaturization, in efficiency of performance, and in memory capacity, mainly because of additionally exploiting quantum-phase encoding. We have earlier presented in detail how and where the mathematical formalism of associative neural network models by Hopfield and Haken is analogous to the mathematical formalism of quantum theory. By saying Hopfield-like we mean a system that is based on the Hopfield model of neural networks or spin glass systems (i.e., amorphous assemblies of spins or small 'magnets'), respectively. The results depend very much on the correlation structure of a specific set of input patterns. In other words, beside the 'hardware' (implementation) and the 'software' ('algorithm'), also the 'virtual software' (i.e., the input-data correlation structure) is essential."

Small magnets are used also in the creation of the magnetic boby (magnetic flux tubes).
Baez says it in another way in What's the energy density of the vacuum?: You need to know not just the answer, but also the assumptions and reasonings that went into the answer.

Silent knowledge is important. This is the quantal self.

Pitkänen: "For algebraic entanglement p-adic Shannon entropies obtained by replacing logarithms of probabilities with the logarithms of their p-adic norms are well-defined, and there is a prime p for which Shannon entropy is negative and minimum and identifiable as negentropy. The vision about dark matter hierarchy leads to a more refi ned view about self hierarchy and hierarchy of moments of consciousness."

Perus: "If we try to implement Shannon-type information processing in quantum networks, some essential quantum features, manifested in the complex-valued formalism, are unavoidably partly eliminated. However, nature has obviously always performed a sort of non-Shannon-type implicit-information processing (Bohm uses term 'active information') where the 'users of information' are not human observers, but natural systems (e.g., immune systems) themselves.
Neuro-quantum (classical-quantum) cooperation, as manifested in the collapse-readout, is thus essential for the brain which combines Shannon-type cognitive information and non-Shannon-type consciousness phenomenalism."

The quantal self is also the dark matter self, as a mirror-self of 'antimatter'? It is achieved by "The hierarchy of dark matter levels and is labelled by the values of Planck constant having quantized but arbitrarily large values." This is the spooky action of quantum mechanics in a nutshell.

Pitkänen: "Dark matter hierarchy leads to a quantitative model for high Tc superconductivity as quantum critical phenomenon predicting the basic length scales L(149) and L(151) associated with lipid layers of cell membrane and cell membrane itself. Also cell size emerges naturally. At higher levels of dark matter hierarchy scaled up versions of this basic structure appear. Cyclotron states at magnetic flux tubes are carriers of Bose-Einstein condensates of Cooper pairs and of bosonic ions. For instance, neurons correspond to k(em) = 3 level of dark matter hierarchy whereas ordinary EEG correspond to k(em) = 4, with Josephson junctions as the (superconductive) mediating tool."

Rakovic: "An additional support that the acupuncture system is really related to consciousness is provided by meridian (psycho)therapies (with very fast removing of traumas, phobias, allergies, posttraumatic stress, and other psychosomatic disorders – with simultaneous effects of visualization and tapping/touching of acupuncture points."

This I have personal experiencies of. Sometimes you can just wonder what a miracle is happening also to very severe, lifelong traumas, seen in many of my patients.
- "A ’smearing’ and associative integration of memory attractors of the psychosomatic disorders, through successive imposing new boundary conditions in the acupuncture energy-state space during visualizations of the psychosomatic problems."

Pitkänen: "The connection between thermodynamics and qualia was the real breakthrough in the development of ideas. In some sense this finding is not a news: the close connection between pressure sense and temperature sense and thermodynamics is basic facts of psychophysics (also neural nets, my comm.). In TGD framework the contents of consciousness is determined as some kind of average over a sequence of very large number of quantum jump. Thus non-geometric qualia should allow a statistical description generalizing ordinary thermodynamical ensemble to the ensemble formed by the prepared states in the sequence of quantum jumps occurred after the last 'wake-up' of self. For instance, this picture allows to see the ageing of self with respect to subjective time as an approach to thermal equilibrium."

The world of conscious experience is classical, means standard quantum measurement theory follows."

Pitkänen: "There are two basic mechanisms generating sensory qualia.
1. Quantum phase transition in which single particle transition occurs coherently for some macroscopic quantum phase produces qualia de fined by the increments of quantum numbers in the transition. The magnetic quantum phase transitions at super-conducting magnetic flux tubes provide a basic example of this mechanism, and the quantum model of hearing relies on Z0 magnetic quantum phase transitions.

2. The flow of particles with fixed quantum numbers between "electrodes" of what might be called a quantum capacitor induces qualia defined by the quantum numbers of the particles involved. The "electrodes" carry opposite net quantum numbers. Second electrode corresponds to the sub-self defining the quale mental image. Obviously cell interior and exterior are excellent candidates for the electrodes of the quantum capacitor. Also neuron and postsynaptic neuron. In fact, living matter is full of electrets defining capacitor like structures. The capacitor model applies to various chemical qualia and also to color vision and predicts that also cells should have senses. The ensuing general model of how cell membrane acts as a sensory receptor has unexpected implications for the entire TGD inspired view about biology."

The 'Islands of Life'?
Pitkänen: "The observation that Shannon entropy allows an infinite number of number theoretic variants for which the entropy can be negative in the case that probabilities are algebraic numbers leads to the idea that living matter in a well-defined sense corresponds to the intersection of real and p-adic worlds. This would mean that the mathematical expressions for the space-time surfaces (or at least 3-surfaces or partonic 2-surfaces and their 4-D tangent planes) make sense in both real and p-adic sense for some primes p. Same would apply to the expressions defining quantum states. In particular, entanglement probabilities would be rationals or algebraic numbers so that entanglement can be negentropic and the formation of bound states in the intersection of real and p-adic worlds generates information and is thus favored by NMP.
For n=2 it contains all rational multiples of integer valued points defining Pythagorean triangles, for n=3,4,... only origin is as rational point .

The mappings of the real geometric structures to their p-adic counterparts interpreted as cognitive mappings plays also key role in TGD inspired theory of consciousness."

At center of the interception lies factors like protein transcription and folding mechanism, DNA memory and coding, phase transitions, phosphorylation etc. these are mechanisms that in fact are coding for life itself.

That border between classical and quantum physics are nets like the nervenets and acupuncture meridian nets? They are doing the 'dance' in a sensitive, collecting way? What is special is that the nerves can be seen as skin, invoked in the body, as 'skin channels'. Skin and nerves belongs to the same embryological tissue. Skin is extremely sensitive.

Cognition and consciousness are hierarchic.
Pitkänen: Cognition are of two types. "Quantum TGD requires the introduction of several new mathematical tools and concepts, in particular p-adic numbers. p-Adic number fields Rp (one number field for each prime p = 2; 3; 5; :::) are analogous to real numbers but differ from them in that p-adic numbers are not well-ordered. p-Adic physics describes the physics of cognitive representations and matter-mind decomposition at space-time level corresponds to the decomposition of space-time surface to real and p-adic regions. The higher the value of p, the better the resolution of cognitive experience is, so that p serves as kind of intelligence quotient. p-Adic length scale hypothesis provides quantitative realization for the hierarchy of space-time sheets and is in key role in TGD inspired theory of consciousness.

The spin flipping transitions associated with the fermionic generators of super-symplectic algebra might give rise to Boolean consciousness with intrinsic meaning ('This is true'). Quantum numbers at opposite light-like elementary particle horizons of a wormhole contact could correspond to Boolean cognition in which the presence/absence of fermion representing to 1/0. Boolean statements might be just bit sequences without consciously experienced intrinsic meaning (1/0 instead of true/false)."

Of some reason I think of left, versus right brain half. And 'enlightment'.

Rakovic: "It should be especially pointed out that quantum decoherence might play fundamental role in biological quantum-holographic neural networks, through adaptation of the energystate hypersurface of acupuncture system/consciousness (in contrast to low-temperature artificial qubit quantum processors where it must be avoided until the very read-out act of quantum computation! = the 'virus model' presented earlier) – which implies that Nature presumably has chosen elegant room-temperature solution for biological quantum-holographic information processing, permanently fluctuating between quantum-coherent states and classically-reduced states of acupuncture system/consciousness, through non-stationary interactions with out-of-body farther environment and through decoherence by bodily closer environment."

Pitkänen: "Everything is conscious and consciousness can be only lost" with the additional statement "This happens when non-algebraic bound state entanglement is generated and the system does not remain in the intersection of real and p-adic worlds anymore".

This is the reason the Schrödinger cat hasn't been recognized? It is 'out-of body experiencies'; not dead or alive, although death is one form of this quantum state. It is dead and alive. Life itself is a paranormal phenomen. Life is a critical phenomenon. The body is no border for our 'self'. There is a 'magnetic body' too. What is the purpose of this magnetic body, this oscillating wave-function? Is it the collection of qualias; the use of our classical, decoherenced body as a sensor and motor organ for our magnetic body, as Pitkänen suggests?

He writes in General Theory of Qualia: "The idea is that EEG (or ZEG, WEG, or GEG) massless extremals can be assigned with entanglement of a subself of magnetic body with sub-self of biological representing various mental images. That sub-selves can entangle with selves remaining themselves unentangled is one aspect of the generalized notion of sub-system and inspired by the hierarchy of space-time sheets allowing to identify the space-time correlate for this kind of entanglement as join along boundaries bonds connecting space-time sheets representing the sub-systems of disjoint space-time sheets. The entanglement in question could be in cyclotron degrees of freedom, charge entanglement, or color entanglement.

Although EEG and its generalizations seem to serve communication and control purposes rather than representing qualia directly, the notion of spectroscopy of consciousness makes still sense. Furthermore, the identification of the fractal hierarchy of EWEGs and GEGs means a dramatic generalization of this notion making precise quantitative predictions in a huge range of frequency scales resulting by simple scaling from EEG. Cyclotron frequency and Josephson frequency, can be assigned with the communications of sensory data to magnetic body and the n frequencies from both types with the quantum control performed by the magnetic body. For ordinary EEG the harmonics of cyclotron frequencies of bosonic ions correspond to alpha band and its harmonics assignable to quantum control. Beta and theta bands and their analogs for the harmonics of alpha band correspond to the communication of sensory and cognitive data to the magnetic body.

The rough correlations of EEG with the state of consciousness can be understood."

The hierarchies.
Rakovic: "Lower hierarchical quantum-holographic macroscopic open quantum cellular enzyme-gene level, which might be also functioning on the level of permanent quantum-conformational quantum-holographic like biomolecular recognition – so that quantum neural holography combined with quantum decoherence might be very significant element of the feedback bioinformatics, from the level of cell to the level of organism. This presumably represents a natural framework for explanation of psychosomatic diseases related to somatization of environmentally-generated memory attractor’s states of the open macroscopic quantum acupuncture system/consciousness – quantum-holographically projected upon lower hierarchical cellular level, thus changing the expression of genes (so called macroscopic 'downward causation', as biofeedback control of microscopic 'upward causation' in ontogenesis and morphogenesis, starting from the first fertilised cell division which initialises differentiation of the acupuncture system of (electrical synaptic) 'gap-junctions'."

This means that the lower levels get the conscious inputs from the surroundings and modify them. Eventually the genes can also be incorporated in this change (epigenetics), if necessary. The conscious part is reflected also to the genes, analogy to the sensory input into the nerves are reflected to the brain?

And in fact the conscious part is diminished/computated and transformed/made negentropic in the process. The consciousness is computated in the networks in an upwards regulation, and the motoric output is a result of that computation, seen in the readiness potential by Libet.

Perus: "It seems that, in the brain, neural networks trigger the collapse of quantum wave-function and thus transform the quantum complex-valued, probabilistic dynamics into the neural(classical) real-valued, deterministic dynamics. So, neural nets serve as an interface between classical environment of the organism and its quantum basis."

Rakovic: "It seems that this hierarchy of biological neural networks is going down sub-cellular cytoskeleton mesoscopic level, being a kind of interface between neural and quantum levels. Quantum-holographic hierarchical parts carry information on wholeness, enabling quantum-holographic fractal coupling of various hierarchical levels."

Pitkänen: "Self hierarchy has as a geometric correlate, the hierarchy of space-time sheets. The scaling of hbar (ground state) by wavelength^k means also scaling for various basic quantum scales like Compton length and - time and de Broglie wave length. Compton length correspond to a size of space-time sheet associated with the particle. The energy of dark photons with frequency f is scaled up by wavelength^k. For instance, EEG photons at k(em) = 4 level of dark matter hierarchy have energy which is above thermal energy at room temperature: this is absolutely essential for understanding the role of EEG photons. The phase transition increasing k(em) by one unit means that the sizes of space-time sheets are scaled up by wavelength. If the density of particles is high enough, the overlap criterion for the formation of a macroscopic quantum phase is satisfied in the resulting dark phase and Bose-Einstein condensates become possible. Decoherence phase transition for dark matter particle means that the size of the space-time sheet is scaled down by 1/wavelength."

Rakovic: The whole psychosomatics is quantum hologram, both on the level of individual and collective consciousness, and that quantum-holographic hierarchical parts carry information on wholeness, enabling quantum-holographic fractal coupling of various hierarchical levels. Phenomenologically approved quantum-holographic (fractal) coupling of various hierarchical quantum levels – from-biological cell-to-acupuncture system/consciousness-to-collective consciousness (quantum-holographic feedback on cells’ conformational protein changes and genes’ expression (so called macroscopic ’downward causation’), and not only reversed (microscopic ’upward causation’), with mutual quantum-informational control of ontogenesis/embryogenesis and morphogenesis, starting from the first division of the fertilized cell when differentiation of the acupuncture system begins – with significant psychosomatic and cognitive bioinformational implications). With implications of great psychosomatic significance of thought-emotional contents; and global fractal information coupling of various hierarchical levels in Nature with fundamental holistic implications on the origin of miraculous deep creativities and determinism of the History through the coupling with the existing evolving state of collective consciousness.

Resonant Recognition Model
There is significant correlation between spectra of the numerical presentation of constitutive elements of primary sequences (amino acids, nucleotides) and their biological activity or interaction in corresponding biomolecules (proteins, DNAs). The presence of peak with significant signal-to-noise ratio in a multiple cross-spectral function of a group of sequences with the same biological function means that all of the analysed sequences within the group have this single-electron RRM frequency component in common, with the following general conclusions: (1) such a peak exists only for the group of biomolecules with the same function; (2) no significant peak exists for biologically unrelated biomolecules; (3) peak frequencies are different for different biological function; (4) ligand-proteins and their biomolecular target-receptors have the same characteristic frequency in common but almost opposite phase – providing also novel theoretical possibilities for protein de novo design with desired functions!

In the context of the RRM-model, the same characteristic single-electron RRM frequency, and almost opposite phase, presumably characterises not only biomolecular protein and target general function, but also their macroscopic quantum biomolecular recognition interaction on the level of biological cell – possibly by externally activated (compositionally/chemically, by averaged intermolecular approaching of proteins and targets necessary for non-vanishing overlap integrals of the corresponding electronic and vibrational wave functions, or thermally/optically, by supplying vibrational energy necessary for making conditions for electronic-vibrational nonradiative resonant transitions between two isomers, giving rise to dynamic modification of the many-electron hypersurface of the cell's protein macroscopic quantum system.

Pitkänen talks much of resonances, cyclotronic and other.

Psychosomatic implications.
Three front lines of psychosomatic medicine do exist:
1. spirituality; prayer for others mentally/emotionally involved erases for
good mutual memory attractors on the level of collective consciousness
2. traditional holistic Eastern medicine and deep psychotherapeutic techniques; temporary erase memory attractors on the level of acupuncture system/individual consciousness, and prevent or alleviate their somatization

3. modern symptomatic Western medicine, whose activities through immunology,
pharmacology, biomedical diagnostics, and surgery, hinder or soothe somatic consequences of the carelessness on the first two levels.

Pitkänen: The concept of many-sheeted space-time leads to fresh proposals for how biosystems manage to be macroscopic quantum systems. Examples of these mechanisms are so called wormhole superconductivity, electronic high Tc super-conductivity, neutrino super-conductivity, ionic and a mechanism for generating coherent light and gravitons.

Rakovic: I am ascribing consciousness to the macroscopic quantum (electromagnetic) field of the acupuncture system (which is then generalized to quantum (electromagnetic, and probably even unified) field of any quantum (sub)system, living or nonliving… including Universe…), and not to molecules themselves… and I don’t find it necessary to look at dark matter to understand consciousness…

And he wants to add, p. 89: So, our theoretical investigations imply real origin of religious and other transpersonal experiences of various traditions of East and West – and according to our elaborated theoretical relationship consciousness/acupuncture EM-ionic quantum-holographic Hopfield-like associative neural network, esoteric notions like astral body (manomaya, lingasarira, manovijnana, ka, psyche, subtle body, psychic body, soul...) and mental body (vijnanamaya, suksmasarira, manas, ba, thymos, noetic body, spiritual body, spirit...) might be biophysically related to out-of-body displaced part (connected with the body by miniature wormhole’ space-time tunnel) of the ionic acupuncture system, and with embedded EM component of ionic MW/ULF-modulated currents, respectively.”

Rakovic, with some very warm words:
So it seems that science is closing the circle, by re-discovering two cognitive modes of consciousness and at the same time by imposing its own epistemological limitations – as it was preserved for millennia in shamanistic tribal traditions, or as it was concisely described by Patanjali in Yoga Sutras, pointing out that mystical experience (samadhi) is ’filled with truth’ and that ’it goes beyond inference and scriptures’.

Pitkänen: This encourages to think the possibility of replacing the idea of a fixed axiomatic system with a living and dynamically evolving system becoming conscious of new axioms from which new theorems can grow. Mathematician would not be anymore an outsider but and active participator affecting the mathematical system he is studying. For instance, when paradoxal statement represented symbolically becomes conscious in quantum jump sequence, also the context in which it was originally stated changes.

The ancient time cease, the new magic time comes.

This is of course only a small part of the extensive litterature from both authors. The similarities are striking, although there of course also are big differences. I wanted to use citations not to distort the meanings too much, although this is like reading the Bible through small verses. To compare these models may though lead forward quite a lot. Next I will compare with Popps model.

As a rule TGD goes much deeper into the explanations and its strength is the coordination with theorethical physics, although the same features can be seen in Rakovic works at a higher hierarchial level.

Amit D.: Modeling Brain Functions (The World of Attractor Neural Nets). Cambridge Univ. Press, Cambridge, 1989. (the Hopfield model of neural networks)

P. Gao, A. Honkela, M. Rattray, N. D. Lawrence. (2008). Gaussian process modelling of latent chemical species: applications to inferring transcription factor activities. Bioinformatics 24(16), pp. i70-i75. In Proceedings of ECCB 2008. doi:10.1093/bioinformatics/btn278

Haken H.: Synergetic Computers and Cognition (A Top-Down Approach to Neural Nets). Springer, Berlin, 1991.

Mitja Perus, 2000: Neural networks as a basis for quantum associative networks. NEURAL NETWORK WORLD vol. 10 (2000) pp. 1001-1013.http://citeseerx.ist.psu.edu/viewdoc/download?doi= (computer simulations of Hopfield’s and holographic neural net models)

Matti Pitkänen, 2010: General Theory of Qualia (udated version). http://tgd.wippiespace.com/public_html/pdfpool/qualia.pdf
- Matter, Mind, Quantum, http://tgd.wippiespace.com/public_html/pdfpool/conscic.pdf
- Negentropy Maximization Principle, http://tgd.wippiespace.com/public_html/tgdconsc/tgdconsc.html#nmpc
- Self and Binding, http://tgd.wippiespace.com/public_html/tgdconsc/tgdconsc.html#selfbindc
- Quantum Model for Sensory Representations, http://tgd.wippiespace.com/public_html/tgdconsc/tgdconsc.html#expc
- Quantum Theory of Self-Organization, http://tgd.wippiespace.com/public_html/bioselforg/bioselforg.html#selforgac
- Quantum Control and Coordination in Bio-Systems: Part I, http://tgd.wippiespace.com/public_html/bioselforg/bioselforg.html#qcococI
- Worm-Hole Magnetic Fields, http://tgd.wippiespace.com/public_html/bioware/bioware.html#wormc
-Time, Space-time, and Consciousness, http://tgd.wippiespace.com/public_html/hologram/hologram.html#time
- Bio-Systems as Conscious Holograms, http://tgd.wippiespace.com/public_html/hologram/hologram.html#hologram
- TGD Inspired Model for Nerve Pulse, http://tgd.wippiespace.com/public_html/tgdeeg/tgdeeg.html#pulse

D. Raković, "Integrative Biophysics, Quantum Medicine, and Quantum-Holographic Informatics: Psychosomatic-Cognitive Implications", IASC & IEPSP, Belgrade, 2009, http://www.dejanrakovicfound.org/knjige/2009-Integ-Biophys-Quant-Medic.pdf

- "Quantum medicine: Phenomenology and quantum-holographic implications", Med Data Rev, Vol. 1, No. 2, pp. 71-73 (2009). http://www.dejanrakovicfound.org/papers/2009-MED-DATA-REV.pdf

- "Quantum-informational medicine and quantum-holographic informatics: Psychosomatic-cognitive implications", Speech and Language: Interdisciplinary Research III, S. Jovičić, M. Sovilj, eds., IEPSP, Belgrade (2009). http://www.dejanrakovicfound.org/papers/2009b-IEPSP.pdf

- "Thinking and language: EEG maturation and model of contextual language learning", Proc. "Speech and Language", Belgrade (2003). http://www.dejanrakovicfound.org/papers/2003-IEFPG.pdf


Donald E. Ingber, 1998: The Architecture of Life. A universal set of building rules seems to guidethe design of organic structures — from simple carbon compounds to complex cells and tissues. Scientific American January 1998, 48 - 57.