onsdag 23 maj 2012

The “metabolic mystery.”

Dana foundation has a blogpost  The Brain’s Metabolic Mysteries where she talks of  the odd featre that 'less is more' regarding nutrients, what Charles Mobbs calls the “metabolic mystery”. He studies  the basic mechanisms by which hypothalamic neurons sense and regulate metabolic state (including body weight and food intake), and how these mechanisms are impaired in metabolic diseases and during aging. A driving question of our laboratory is what may be called the metabolic mystery. This refers to the fascinating phenomenon that obesity is a risk factor for most age-related diseases and indeed for mortality, and conversely dietary restriction appears to slow down the aging process and extend maximum lifespan.  
This has been shown so many times, also for plants, and is linked to immunity and health.
More restrictive diets result in a complicated (and counterintuitive) cascade of protective effects, preventing aging-related diseases and ultimately prolonging life. Fasting (intermittent, one day on, one day off, or even one day a week off food) and regular exercise may help promote optimal brain health in aging adults.

So food is not such a limiting factor for living, but quite the opposite? Mobb: 
almost all major pathologies are influenced by caloric intake, the mechanisms underlying the metabolic mystery may be considered among the most compelling in biomedical science. Why would caloric intake should lead to diseases?
We have thus begun to define a "nutritional field" of neurons which contain overlapping domains sensitive to different nutrients and which regulate different aspects of metabolism. Of particular interest is that the maximum overlap of these nutritional stimulation (e.g., glucose and leptin) may occur within the POMC neurons, which we now believe play a critical role in regulating metabolism. This is particularly interesting because the POMC neurons are among the most sensitive to decline during aging.

Mark Mattson.  “And what we’re thinking, from the standpoint of evolution, is that animals living in the wild, including our ancestors, often had to go extended time periods without food.  If you haven’t had food for a while, your mind becomes more active—it has to become very active, to help you figure out how to find food.
Normal ageing is accompanied by alterations in neuronal calcium handling and changes in lipid peroxidation, leading to increased generation of reactive oxygen species (ROS) and damage to mitochondria. These changes are permissive or instructive for the suppression of adult neurogenesis beginning in middle age. Successful ageing is characterized by the implementation of alternative plasticity mechanisms to compensate for changes in the local microenvironment. Age-related pathologies such as Alzheimer's disease, Parkinson's disease and Huntington's disease arise from a combination of genetic and environmental factors, but each disease shares a common feature in that age is a risk factor for disease onset. In this respect, ageing sets the stage for the onset of pathology.
"Give bread and theatre to the masses", said the Roman Emperors. The full stomach made people easier to handle. It is certainly valid today too. Never before has so many people been so overweighted. And we struggle to pay the health care bill. But very little money are directed to this research about the foundations of health.

Stress is good?
Fasting is a challenge, a stress, so we get focus on the stress-proteins, the chaperones, enzyme-like proteins that assist in folding or unfolding and the assembly or disassembly of other macromolecular structures. That is energy-transfer, neutralizing energy by relaxation/compression? Many chaperones are heat shock proteins, that is, proteins expressed in response to elevated temperatures or other cellular stresses. Stress makes more heat? Chaperones are membrane bound (ER) usually.

Why is stress good? So many times we have heard it is only bad. But stress is about everything that makes us living, the homeostasis is governed by stress. Without stress we would be dead. The body also handles challenges by producing more stress, in the allostasis. So...

That activity manifests itself in neuroplasticity, says Mattson. Plasticity is flexibility due to more stress? More swing in the system?
The manner in which experience can influence the synaptic organization of the brain is also the basis for a number of theories of brain function including the general theory of mind and epistemology referred to as Neural Darwinism and developed by immunologist Nobel laureate Gerald Edelman. The concept of neuroplasticity is also central to theories of memory and learning that are associated with experience-driven alteration of synaptic structure and function in studies of classical conditioning in invertebrate animal models such as Aplysia. This latter program of neuroscience research has emanated from the ground-breaking work of another Nobel laureate, Eric Kandel.
 Thinking (the talk cure) can change the brain, as meditation too. Stress copying is the essential tool in handling stress. It sits between the ears, not in what you actually have to do, I often say.

"Perhaps we eat to get information, negentropic entanglement. This explains why the metabolic energy must come from biomatter and we cannot get it by putting plug in the wall!", says Matti Pitkänen. Folding and molecule sort and size, as instance? Eating as a 'sampling' of our environment?

Linked to oxidative stress, says Mattson.  "Those protective effects result in the upregulation of brain-derived neurotrophic factor (BDNF) as well as anti-oxidants, DNA-repair enzymes, and other gene products that help promote plasticity and survival of neurons over time." BDNF is made on ER.
Exercise and caffeine imroves the levels too.  In 2009, variants close to the BDNF gene were found to be associated with obesity. Caffeine is  linked to diabetics too (diminish the stress). And linked to many other (stressinduced?) diseases.

Neurotrophin is also linked to regeneration (stem cells) and the DC-fields in our tissues, as explained by Robert Becker in his NEJ (neural epidermic junction) as a result of a 'signal of injury' and necessary for the healing process. Neurotrophins may be the chemical analog? They belong to a class of growth factors, secreted proteins that are capable of signaling particular cells to survive, differentiate, or grow. They act on Trk-receptors, a family of tyrosine kinases that regulates synaptic strength and plasticity. The common ligands of trk receptors are neurotrophins which are growth factors. Another receptor is p75, which affects the binding affinity and specificity of Trk receptor activation by neurotrophins.

Mechanism of action.
BDNF binds at least two receptors on the surface of cells that are capable of responding to this growth factor, TrkB (pronounced "Track B") and the LNGFR (for low-affinity nerve growth factor receptor, also known as p75). It may also modulate the activity of various neurotransmitter receptors, including the Alpha-7 nicotinic receptor.
TrkB is a receptor tyrosine kinase (meaning it mediates its actions by causing the addition of phosphate molecules on certain tyrosines in the cell, activating cellular signaling). There are other related Trk receptors, TrkA and TrkC. Also, there are other neurotrophic factors structurally related to BDNF: NGF (for Nerve Growth Factor), NT-3 (for Neurotrophin-3) and NT-4 (for Neurotrophin-4). While TrkB is the primary receptor for BDNF and NT-4, TrkA is the receptor for NGF, and TrkC is the primary receptor for NT-3. NT-3 binds to TrkA and TrkB as well, but with less affinity (thus the caveat "primary receptor").
The other BDNF receptor, the p75, plays a somewhat less clear role. Some researchers have shown that the p75NTR binds and serves as a "sink" for neurotrophins. Cells that express both the p75NTR and the Trk receptors might, therefore, have a greater activity, since they have a higher "microconcentration" of the neurotrophin. It has also been shown, however, that the p75NTR may signal a cell to die via apoptosis; so, therefore, cells expressing the p75NTR in the absence of Trk receptors may die rather than live in the presence of a neurotrophin.
Neurotrophin and Trk receptors are linked to stochastic resonance, which can be used as a therapeutics in treatment of neuropsychiatric diseases.

Then I read about chaperones:
The common perception that chaperones are concerned primarily with protein folding is incorrect. The first protein to be called a chaperone assists the assembly of nucleosomes from folded histones and DNA and such assembly chaperones, especially in the nucleus, are concerned with the assembly of folded subunits into oligomeric structures.
And is also linked to phantom limbs, which is strangely common, occurring in 60-80% of amputees. Treatment approaches have included drugs such as antidepressants, Spinal cord stimulation, Vibration therapy, acupuncture, hypnosis, and biofeedback. Typical stochastic resonance theraphy? Phantom limb pain (rather than referred sensations) is the perceptual correlate of cortical reorganization.

Maps are topological and hierarchial microsystems of the body.

Well, now this gets interesting!

Stress used as medicine? WOW. And stochastic resonance is linked to tryptophan and serotonine. Pain relief is linked to breakdown of serotonin. Tryptophan is outside the nerves, serotonine inside. Like a polarization, also linked to stochastic resonance.

In fact acupuncture too works by inducing a strain on the tissue, we must achive damage or injury before we can get some emergency actions. Acupuncture effect is linked to adenosine Adenosine A1 receptors mediate local anti-nociceptive effects of acupuncture by Nanna Goldman and collaborators.  
We found that adenosine, a neuromodulator with anti-nociceptive properties, was released during acupuncture in mice and that its anti-nociceptive actions required adenosine A1 receptor expression. Direct injection of an adenosine A1 receptor agonist replicated the analgesic effect of acupuncture. Inhibition of enzymes involved in adenosine degradation potentiated the acupuncture-elicited increase in adenosine, as well as its anti-nociceptive effect. These observations indicate that adenosine mediates the effects of acupuncture and that interfering with adenosine metabolism may prolong the clinical benefit of acupuncture. 
This works against stress created by stochastic resonance. Acupuncture is balancing the homeostasis, as said by therapists. Is there a difference between outer and inner stress?

Also, CNS and perifer nerves does not work in the same way, shown by Alexander Presman with  “Electromagnetic Fields and Life” long ago (1970). From this scientific angle Presman found that the seemingly contradictory results started to make sense, and that the empirical data made up a rational whole. The information content of electromagnetic radiation is determined by its frequency, frequency range, coherence, pulse form, polarization and modulation. The biological effects of such kinds of electromagnetic fields will, according to Presman, affect three different levels of biological organisation:
1.      Effects on the physiological regulation of vital functions.
2.      Effects on the transmission of biological information within the organism and its internal regulation and co-ordination.
3.      Effects on the interaction between living beings and in the social interplay between them.
  (I have the book, here a link from Norwegian dr, Wilhelm Schelderup).

In CNS endorphins are produced by acupuncture-stress-injury. Endorphins deactivates the brains pain-processing. Note that pain and pleasure centers are side by side in brain. So there needs to be just a shift? "Activation of brain areas involved in pain perception was significantly reduced or modulated under acupuncture," Dr. Nina Theysohn said in “Acupuncture Changes Brain's Perception and Processing of Pain”. During the fMRI sessions, scientists captured pictures of the brain while patients were exposed to an external pain stimulus. The interesting part? The obtained data revealed that significantly reduced was not only the pain perception, but the patient's expectation of pain, too.

Functional magnetic resonance (fMR) images showing brain activity during electrical pain stimulation at the left ankle. Parts of the so-called "pain matrix" are activated: (a) primary somatosensory cortex (S1), (b) right insula, (c) precuneus, (d) left insula. (Credit: Image courtesy of Radiological Society of North America). 

fMRI was shown by Jie Tian to make "a dynamic reconfiguration of  complex neural networks." in "Acupuncture Effects measured by fMRI" p 8.  Earlier the focus in research was on acute effects, but the effects may peak long after the treatment is finished. So then the mechanism was missed? And the responses are functional, not spatial. Acupoints can have converging effects, as instance, that spatially overlap the posterior cingulate cortex/precuneus or encoding center. The delayed correspondence between visual acupoints (GB37, BL60) - but not the non-visual acupoints (KI8) - and the intrinsic visual networks via the encoding center indicated a temporal-spatial encoding mechanism underlying the sustained effects of acupuncture, he said. Different resource distribution in spatial and temporal domains. Mars 2011.

Pain relief as a superposition or 'negative negentropy' (not entropy)? By growing fields that lay the pain-field in the 'shadow'?

But DC-currents are not 'generated', Langevin showed the energy came from the connective tissue that acts as a storage of energy in its helical structure, just as DNA do.

The energy link is ATP/AMP/adenosine receptors, linked to stochastic noise. Maybe the needles create noise by relaxing (=unwinding the helix) the tissue, the 'signal of injury', and that starts ther process? So Becker and biochemists measure the same thing with different tools? The energy is simply transferred to ATP from connective tissue? And ATP is quantal?

Note also that pain and pleasure areas are side by side in brain, modulated by N. trigeminus, as Antonio Damasio showed. It has a very strong 'field'. Mortons headache is the worst possible.
The link to adaptation by stressproteins makes the mechanism delayed, and incorporates the time-aspect.

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.

Wikipedia: In humans, there are four types of adenosine receptors. Each is encoded by a separate gene and has different functions, although with some overlap. For instance, both A1 receptors and A2A play roles in the heart, regulating myocardial oxygen consumption and coronary blood flow, while the A2A receptor also has broader anti-inflammatory effects throughout the body. These two receptors also have important roles in the brain, regulating the release of other neurotransmitters such as dopamine and glutamate while the A2B and A3 receptors are located mainly peripherally and are involved in processes such as inflammation and immune responses.
Most older compounds acting on adenosine receptors are nonselective, with the endogenous agonist adenosine being used in hospitals as treatment for severe tachycardia (rapid heart beat), and acting directly to slow the heart through action on all four adenosine receptors in heart tissue, as well as producing a sedative effect through action on A1 and A2A receptors in the brain. Xanthine derivatives such as caffeine and theophylline act as non-selective antagonists at A1 and A2A receptors in both heart and brain and so have the opposite effect to adenosine, producing a stimulant effect and rapid heart rate. These compounds also act as phosphodiesterase inhibitors, which produces additional anti-inflammatory effects, and makes them medically useful for the treatment of conditions such as asthma, but less suitable for use in scientific research.
Newer adenosine receptor agonists and antagonists are much more potent and subtype-selective, and have allowed extensive research into the effects of blocking or stimulating the individual adenosine receptor subtypes, which is now resulting in a new generation of more selective drugs with many potential medical uses. Some of these compounds are still derived from adenosine or from the xanthine family, but researchers in this area have also discovered many selective adenosine receptor ligands that are entirely structurally distinct, giving a wide range of possible directions for future research.
On Mattis blog:

And I wonder if the nerve loop take a turn outside the body too? It must get the information through communication. How would a model look like where there is no definite boundary? I don't think of the magnetic body now.

Stochastic resonance (from outer world) must be important. Take a locked-in patient with no dopamine and no communication with outer world, nor her inner self.

This can be a big piece in the puzzle. Thanks for bringing my attention here once again. Now the real happenings begins to be seen. Endorphin acts by deactivating brain areas and modulating, through intervention with the energy transport. But are the fields made bigger (=erasing?), so they create superposition, and that's the mechanism of modulation? Dopamine is the 'arousing' media (SR), creating oscillations of energy and coherence or decoherence giving actions (connects to outgoing loop?)? This is seen in the CREATION of disease?  Serotonin is the pain-producing media (inner SR?)?
See 'Quantum Model for the DC of Becker'.

A stress-pill?
Some studies suggested that caloric restriction promoted good health - and researchers have seen improved outcomes in animal models of Alzheimer’s disease, Parkinson’s disease, stroke and Huntington’s disease, but the intermittent fasting increases neurogenesis while limited daily reduction in calories has very little effect, say Mattson. Ye, increasing the swung?
we have now shown that transgenic enhancement of neuronal POMC will completely correct the diabetes and other impairments in genetically obese mice. These studies have led to discovery of a new class of anti-obesity drugs that we are now studying.
Ketogenic diet low.carb diet also reverse effects of high caloric diets? "We assessed if prolonged maintenance on a ketogenic diet would reverse nephropathy produced by diabetes" .So much that medicines act exactly as ketogenic diet. And doctors that almost forbid the patients to eat ketogenic. "Whether reduced glucose metabolism mediates the protective effects of the ketogenic diet remains to be determined." What is so special with carbohydrates and carbon as a foundation of life, is the automatic question? How can avoiding carbon give health? What about vegetarians, they are seldom fat? Mobb:  
We have discovered over 20 novel genes that regulate obesity in C. elegans and a transcriptional complex that mediates the protective effects of dietary restriction to increase lifespan and protect against age-related diseases, including Alzheimer-type pathology and diabetic complications. Pharmacological activation of this pathway increases lifespan and protects against neurodegenerative diseases, and the same complex predicts lifespan and obesity in mice. We have now also developed novel high-throughput methods to discover novel anti-obesity and anti-diabetes drugs, and have discovered over 20 drugs in each class so far.
  •  Mizuno TM, Bergen H, Funabashi T, Kleopoulos SP, Zhong YG, Bauman WA, Mobbs CV. Obese gene expression: reduction by fasting and stimulation by insulin and glucose in lean mice, and persistent elevation in acquired (diet- induced) and genetic (yellow agouti) obesity. Proc Natl Acad Sci U S A 1996; 93(8): 3434-3438.
  • Poplawski MM, Mastaitis JW, Isoda F, Grosjean F, Zheng F, et al. (2011) Reversal of Diabetic Nephropathy by a Ketogenic Diet. PLoS ONE 6(4): e18604. doi:10.1371/journal.pone.0018604
Medicalisation of something completely natural? So the health care bill can grow! Why do we have to go this way? Physicians and scientists on the faculty of Mount Sinai School of Medicine often interact with pharmaceutical, device and biotechnology companies...

Endorphins gives also a stress-reaction. In Acupuncture and Endorphins, by Han JS. 2004:
Studies on the mechanisms of action have revealed that endogenous opioid peptides in the central nervous system play an essential role in mediating the analgesic effect of EA[electroacupuncture]. Further studies have shown that different kinds of neuropeptides are released by EA with different frequencies. For example, EA of 2 Hz accelerates the release of enkephalin, beta-endorphin and endomorphin, while that of 100 Hz selectively increases the release of dynorphin. A combination of the two frequencies produces a simultaneous release of all four opioid peptides, resulting in a maximal therapeutic effect.
Local activation of adenosine A1 receptors by acupuncture needles in mice contributes to the anti-nociceptive effects of acupuncture.

Can different neuromodulators act as a cascade of frequencies, modulating our 'consciousness' through creation of flux tubes, in different ways (bigger/smaller). This we so often mix with our awareness of things and our intelligence. Intuition is also a form of intelligence?

"The efficiency of somatic energy metabolism is correlated with cognitive change over the lifespan. This relationship is bidirectional", says Alexis Stranahan and Mark Mattson in Bidirectional metabolic regulation of neurocognitive function. Cognition and metabolism are intertwined and interdependent.  Exercise and dietary energy restriction enhance cognition and improve metabolism.  Diabetes induces memory deficits and impairs metabolism.  Changes in immune function occur in metabolically enhanced or compromised states. The metabolic spectrum regulates the onset and extent of neuropathology.

Memory in the Body is a reality? It is seen in so many therapies, and is a basic prediction of TGD. Note also that caffeine diminish stress, so memory is a form of stress-energy? Metabolism is important. Note also that the main purpose of the blood-brain barrier in the brain is to create different metabolism for the brain, AND different polarizations, as shown by Becker. This is the basis for our 'consciousness'?

A typical glutamatergic neuron in the hippocampus is depicted receiving excitatory inputs (red) from neurons activated in response to exercise, cognitive challenges and dietary energy restriction. Examples of seven different adaptive stress response signalling pathways that protect neurons against degeneration and promote synaptic plasticity are shown. During exercise and cognitive challenges, postsynaptic receptors for glutamate (a,b), serotonin (c) and acetylcholine (d) are activated to engage intracellular signalling cascades and transcription factors that induce the expression of neuroprotective proteins including brain-derived neurotrophic factor (BDNF), mitochondrial uncoupling proteins (UCPs) and anti-apoptotic proteins (for example, BCL-2). BDNF promotes neuronal growth, in part, by activating mammalian target of rapamycin (mTOR). Mild cellular stress resulting from reduced energy substrates (e) and reactive oxygen species (ROS) (f) engages adaptive stress response pathways, including those that upregulate antioxidant enzymes (AOEs) and protein chaperones. Release of GABA from interneurons (g) in response to activity in excitatory circuits (as occurs during exercise and cognitive challenges) hyperpolarizes excitatory neurons protecting them from Ca2+ overload and excitotoxicity. CaMKII, calcium/calmodulin kinase II; CREB, cyclic AMP response element-binding protein; DAG, diacylglycerol; FOXO3, forkhead box protein O3; HO1, haem oxygenase 1; HSF1, heat shock factor 1; IP3 PKC, inositol-trisphosphate 3 protein kinase C; MnSOD, manganese superoxide dismutase; NF-κB, nuclear factor-κB; NQO1, NAD(P)H-quinone oxidoreductase 1; NRF2, nuclear regulatory factor 2; Ph2E, phase 2 enzyme; PMRS, plasma membrane redox system; SIRT, sirtuin.

But how many ways are there? We have five senses for input, or six, or seven, eight... if we also count the environmental input in stochastic resonance?
And how many for outputs?

PS. This text is still a bit premature, but I still want to publish it now. THIS IS GREAT NEWS.
I will come back and update the text. Also with references.

lördag 19 maj 2012

Forest full of white flowers.

It was a beautiful day in spring
the birds were singing
sun shining, warming the skin
a little wind in the hair

and I stood in the forest
full of white, small flowers
Oxalis acetosella, the little sour one,
and I remembered another forest
another time
full of white flowers, Anemones,
and my eyes were full of tears

Why is it
that when we have the chance
we are not brave enough
to jump on the wave?
Though we know
this security is an illusion
and we can jump and feel in the stomach
endless happiness, flying

And I turn my face away
and cry
this beautiful day in may
when the sun is shining
and the birds are singing
and the wind touches my face.

I am here, now
but my mind is somewhere else
thinking its why and how
old sorrows still not healed
the lonely child in me
the outsider

Will it help to heal the scars
to scream and shout
kick and hit
if there is no way
to ever not being alone?

Alone is an illusion
my therapist says
ye, I know that
but how tell the little child
it should not bother being left alone
to be chosen away, unwanted, unseen
like something disgusting and awful

There was never anyone
there will never be someone
so smile and be happy.

Never think of what could be
think of what is
with small adorable white flowers
the whole forest full
sun that shines
birds singing
and wind in the hair
warming you.

A depressed one sees only the darkness
a lonely one sees only the loneliness
a deprived one sees only what is missing
an unloved one seeks love only where there are no love
an abused one hits itself again and again and again
so without pardon, merciless

Oh poor humans...

I tried so very hard to forget
leave it behind
not gather those sour apples
but instead the beautiful pearls
of wisdom
light, the white and blessing one
in my loneliness
and it feels like I pretend.

I would want to tell someone
about the beauty and the light
and the sorrow
the forest full of white flowers
sharing makes the difference
healing the soul.

A Flirt with Models in Biology

In Biologists flirt with Models, says The Digital Biologist Gordon Webster, "little seems to have changed beyond the fact that the crisis in the pharmaceutical industry has deepened to the point that even the biggest companies in the sector are starting to question whether their current business model is sustainable."

Correlation has failed, which is no surprice sinse it is a faked one. It gives more questions than answers. Now biologists hope for the modeling!

Modeling can provide the kind of intellectual frameworks needed to transform data into knowledge, yet very few modeling methodologies currently exist that are applicable to the large, complex systems of interest to biologists.

The systems of interest to biologists tend to be far more refractory to modeling than the systems that are studied inphysics and chemistry. Living systems are more open, with feedbacks and feedforwards.
At the molecular level the fundamental processes that occur in living systems can also be described in terms of physics and chemistry. However, at the more macroscopic scales at which these systems can be studied as “biological” entities, the researcher is confronted with an enormous number of moving parts, a web of interactions of astronomical complexity, significant heterogeneity between the many “copies” of the system and a degree of stochasticity that challenges any intuitive notion of how living systems function, let alone survive and thrive in hostile environments. Biology is, in a word, messy.

Decoherent, says the physicists. Exactly what does this mean? Noncommutativity? Complexity is the problem, and how to create more coherent systems? Coherence and correlation are friends.

How master the complexity?
A tsunami of data in genetics due to HUGO? Linked to cure for cancer, which is a symptom of decoherence? No, kidding?

Looking back over almost a decade since the first working draft of the human genome was completed - while there have certainly been some medical benefits from this work, I think it is fair to say that the impact has not been on anything like the scale that was initially anticipated, largely as a result of having underestimated how difficult it is to translate such a large and complex body of data into real knowledge. Even today, our understanding of the human genome remains far from complete and the research to fill the gaps in our knowledge continues apace. The as yet unfulfilled promise of genomics is also reflected in the fact that many of the biotechnology companies that were founded with the aim of commercializing its medical applications, have disappeared almost as rapidly as they arose. This is not to say that the Human Genome Project was in any way a failure - quite the opposite.

 Ye, to learn how little we know? That we really need a theory of biology, but how get a start? The complexity must be mastered?

The crucial lesson for biology however, is that as our capacity to make scientific observations and measurements grows, the need to deal with the complexity of the studied systems becomes more not less of an issue, requiring the concomitant development of the means by which to synthesize knowledge from the data. Real knowledge is much more than just data - it does not come solely from our ability to make measurements, but rather from the intellectual frameworks that we create to organize the data and to reason with them.

So much, just to learn that? How much knowledge can we not gain by reinterpreting old results, but today we think the only way is by measuring and collecting more data. Piuh! Maybe we instead need fewer data? I cannot but admire old thinkers that came up with brilliant ideas formed out of fewer datas. The difficulty is how to solve out unnecessary measurements.

Scientists of all persuasions are (and always have been) modelers, whether or not they recognize this fact or would actually apply the label to themselves. All scientific concepts are essentially implicit models since they are a description of things and not the things themselves. The advancement of science has been largely founded upon the relentless testing and improvement of these models, and their rejection in the case where they fail as consistent descriptions of the world that we observe through experimentation. As in other fields, implicit models are in fact already prevalent in biology and are applied in the daily research of even the most empirical of biologists.

One such implicit model is the genome. We take it for real. Usually we forget that the clue is the phenotype, as a result of Nature and Nurture, a blend of Self and Environment? And the soul? Life is a trinity, to make possible evolution and unknowns?

The successes that explicit modeling approaches have enjoyed in biology tend to be confined to a rather limited set of circumstances in which already established modeling methodologies are applicable. One example is at the molecular level where the quantitative methods of physics and chemistry can be successfully applied to objects of relatively low complexity. Or  applied to biological systems that exhibit behavior that can be captured by the language of classical mathematics. Many if not most of the big questions in biology today deal with large, complex systems that do not lend themselves readily to these kinds of modeling approaches.

No, because life is coherent and quantum-like? It is open systems, not classic ones. Environment is part of the organism.

How do cells make decisions based upon the information processed in cell signaling networks? How does phenotype arise? How do co-expressing networks of genes affect one another? These are the kinds of questions for which the considerable expenditure of time, effort and resources to collect the relevant data typically stands in stark contrast to the relative paucity of models with which to organize and understand these data."

Ye, exactly! The theory is wrong?

If the data are measured carefully enough and can be weighted and scaled meaningfully with respect to one another, parametric divergences that can be detected between similar biological systems under differing conditions may reveal important clues about the underlying biology as well as identify the critical components in the system.

But this is classic physics. Why do we get so different measures? Why do we have all these curves? The Gauss distribution? Because Life is fuzzy, shows uncertainty. It is more quantum-like?

Have given genomic and proteomic profiling, biomarker discovery and drug target identification, screening methods...
they do tend to compound the central problem alluded to earlier of generating data without knowledge. Moreover, their limitations are now starting to become apparent... drug companies has seen the approval rate of new drugs continue to fall as levels of R&D investment soar. The field of biomarkers has also seen a similar stagnation, despite years of significant investment in correlative approaches. Cancer biomarkers are a prime example of this stagnation. Since we don’t yet have a good handle on the subtle chains of cause and effect that divert a cell down the path

No, because we have no universal theory for illness either.

We are forced to wait until there are obvious alarm bells ringing, signaling that something has already gone horribly wrong. To use an analogy from the behavioral sciences, broken glass and blood on the streets are the "markers" of a riot already in progress but what you really need for successful intervention are the early signs of unrest in the crowd before any real damage is done.

So all our health industry is an emergency without plannings? And we just continue to pay the price?

The lack of new approaches has also created a situation in which many of the biomarkers in current use are years or even decades old and most of them have not been substantially improved upon since their discovery.

So we just live in an illusion of progress?

Given the general lack of useful mechanistic models or suitable intellectual frameworks for managing biological complexity, the tendency to fall back on phenomenology is easy to understand. Technology in the laboratory continues to advance, and the temptation to simply measure more data to try to get to where you need to be, grows ever stronger as the barriers to doing so get lower and lower.

So, we just close our eyes? Another just as important question is why do not the patients follow the advices they get? Why do they not bother about their own health? What can possibly be more important? Do we at all take the human in consideration in our health care? 

What is it to be a human?

In effect what we have witnessed in biology over the last decade or so is a secular movement away from approaches that deal with underlying causation, in favor of approaches that emphasize correlation. However, true to the famous universal law that there’s no such thing as a free lunch, the price to be paid for avoiding biological complexity in this way is a significant sacrifice with respect to knowledge about mechanism of action in the system being studied. Any disquieting feeling in the healthcare sector that it is probably a waste of time and money to simply invest more heavily in current approaches is perhaps the result of an uneasy acknowledgement that much of the low-hanging fruit has already been picked and that any significant future progress will depend upon a return to more mechanistic approaches to disease and medicine.

Have we lost the battle, just because we refuse to handle with theory?

Biological models.
Biological modeling has to date tended to be almost exclusively the realm of theoretical biology, but as platforms for generating and testing hypotheses, models can also be an invaluable adjunct to experimental work.

That is the simulation thechnique, and this should be obvious.

One misconception that is common amongst scientists who are relatively new to modeling is that models need to be complete to be useful. Many (arguably all) of the models that are currently accepted by the scientific community are incomplete to some degree or other, but even an incomplete model will often have great value as the best description that we have to date of the phenomena that it describes.

Scientists have also learned to accept the incomplete and transient nature of such models since it is recognized that they provide a foundation upon which more accurate or even radically new (and hopefully better) models can be arrived at through the diligent application of the scientific method. Models  can clearly have predictive value, even when they diverge from experimental observations and appear to be “wrong”.

It is essential that the chosen modeling system be transparent and flexible. Transparency here refers to the ease with which the model can be read and understood by the modeler (or a collaborator). Flexibility is a measure of how easily the model can be modified. A model that is hard to read and understand is also difficult to modify and, very importantly in this age of interconnectedness, difficult to share with others. The importance of this last point cannot be overstated since one of the most often ignored and underestimated benefits of models is their utility as vehicles for collaboration and communication. It is interesting to note that biological models based upon classical mathematical approaches generally fall far short of these ideals with respect to both transparency and flexibility.

 In fact “biology” is essentially the term that we apply to the complex, dynamic behavior that results from the combinatorial [synergetic and coherent] expression of their myriad components. For this reason, models that can truly capture the “biology” of these complex systems are also going to need to be dynamic representations.

Ye, so why do we not then research the synergy and coherence? Why use classic math that focus on borders and decoherence, creating static pathway maps. 

 ...the elements of causality and time are absent...

An ideal modeling platform would offer a “Play” button on such maps, allowing the biologist to set the system in motion and explore the its dynamic properties. 

But the biology community in large part are unlikely to adopt modeling approaches that require them to become either mathematicians or computer scientists...

A movie, ye?

Finally, let us not forget that thanks to the internet, we live in an era of connectivity that offers hitherto unimaginable possibilities for communication and collaboration. The monster of biological complexity is in all likelihood, too huge to ever be tamed by any single research group or laboratory working in isolation and it is for this reason that collaboration will be key. With knowledge and data distributed widely throughout the global scientific community, a constellation of tiny pieces of a colossal puzzle resides in the hands of many individual researchers who now have the possibility to connect and to work together as never before, and to assemble a richer and more complete picture of the machinery of life than we have ever seen.

Ye, but the CV? The Big Ego? Can it be overrun? Again, what is it to be HUMAN?
What happen the day we have 40 supercomputers, and the computers find out the humans are idiots?

söndag 6 maj 2012

The tunnel.

This tunnel they see in NDE must be a wormhole?

Seems the video has expired?

If we think it is, then humans must be a combination of two 'bodies', or a BEC? The love they talk of is an effect of the magnetic waves (I have experienced the wave, often, have seen the light :)). I have even been in the tunnel. I floated there on a wave. The wave is important. Usually we don't experience us as waves.

Testimonials in the video:
Life is an illusion, a game.
And they traveled at the speed of thought. Ye, so she says.
I was not in a body, I was in the hands of God.
She was taken even before the creation, before Big Bang..
I knew everything, I had no question, because I knew the answeres.
I was crying, because there was no longer the light.
I have a purpose to live.
The only thing that is here is love, the only purpose.
We are the heart of God.

I guess I needed this today, now. I will take the big jump. Light as a feather, as Plato says.

Assumption: There is a Life after death.
It cannot possibly be based on atoms and molecules of matter. So what distinguishes Life after death from Life before death? Only our illusions of matter?
Most all religions believe that the body is just a shell for the soul until it is released when the body dies. Through the wormhole, blogpost. Quantum Physics implies 3 states for the Universe. Mind, Space, and Time, and that neither of these can exist alone, but only together! If true, then there is a Universal Mind Set. Would this represent GOD?

Stephen Hawking: ‘There is no heaven; it’s a fairy story’ | Science | The Guardian

Dr. Eben Alexander’s Website

Interview with Skeptikko.
Dr. Eben Alexander: What I think is going to happen is that science and spirituality, which will be mainly be an acknowledgement of the profound nature of our consciousness, will grow closer and closer together.

One thing that we will have to let go of is this kind of addiction to simplistic, primitive reductive materialism because there’s really no way that I can see a reductive materialist model coming remotely in the right ballpark to explain what we really know about consciousness now.

Coming from a neurosurgeon who, before my coma, thought I was quite certain how the brain and the mind interacted and it was clear to me that there were many things I could do or see done on my patients and it would eliminate consciousness. It was very clear in that realm that the brain gives you consciousness and everything else and when the brain dies there goes consciousness, soul, mind—it’s all gone. And it was clear.
Now, having been through my coma, I can tell you that’s exactly wrong and that in fact the mind and consciousness are independent of the brain. It’s very hard to explain that, certainly if you’re limiting yourself to that reductive materialist view.

A video  of Dr Alexander's presentation on his near-death experience at the BPTC Bioethics meeting in Madison, WI April 26, 2012. And here another. His book will be published this summer.

Quantum Mind of the NDE, lots of links.

It is all about time and light?
 “Take comfort!  The Spirit and Heaven, like God, are timeless and have no beginning and no end.  Your father has not gone to the present Heaven, but to the future Heaven!   You and your descendants, as well as your ancestors, are all there to greet him!”

Update: It's all about Love, is a common tale. Love is the highest negentropic bond/entanglement, usually experienced as light? And light is holographic, allknowing. Two molecules cannot interact or communicate without Love as entanglement?  Can consciousness be separated from knowledge and cognition?

So, how is it that we sim in a ocean of Love, and still feel such shortage of it that we are ready to kill? How terrible wrong and dictated by fear (shortage of Love) isn't our society?

See Linus Paulings short text.
F. Jordan: The quantum-mechanical resonance would lead tp attraction between  molecules containing identical groups and autocatalytic reproduction of molecules.
If both molecules are in their lowest states the interaction is normal, but if one is excited we get a resonance phenomenon, The wavefunction is either the symmetric or antisymmetric combination of two functions, one representing molecule A normal and the other molecule B excited and the other the reverse. For one of these symmetry  types there is a  resonance stabilization and attraction between molecules, and for the other a repulsion. This is what Jordan said would induce a synthesis of a molecule similar to a molecule present in a cell (autocatalysis). This require a slight excitation, as instance thermal excitation, that raises the resonance.

This is realized by homeostasis?

A resonance between molecules can also be between different molecules, creating resonance integrals (waves). A water environment actually stops this kind of resonance interaction, he thought.
Attractive forces vary inversely with the power of distance and maximum stability of a complex (as protein is) is achieved by bridging the molecules as close together as possible. The minimum distances are approached by the repulsive potentials, where complementarity is important. Also the stability of the complex of two molecules  would be due to complementarity rather than identity. And we should model both these types of integrals.

lördag 5 maj 2012

Artificial synapses and brain?

It's probably still going to be a while before autonomous, self-aware androids are wandering amongst us. That scenario has come a little closer to reality, however, with researchers from the University of Southern California having created a functioning synapse circuit using carbon nanotubes. An artificial version of the connections that allow electrical impulses to pass between neurons in our brains, the circuit could someday be one component of a synthetic brain.
The USC Viterbi School of Engineering team was led by Professors Alice Parker and Chongwu Zhou. Parker has been looking into the feasibility of creating a synthetic brain for the past five years, as part of the BioRC Biomimetic Real-Time Cortex project.
The circuit itself consists of highly-aligned carbon nanotubes that are grown on a quartz wafer, then transferred to a silicon substrate. It mimics an actual synapse insofar as the waveforms that are sent to it, and then successfully output from it, resemble biological waveforms in shape, relative amplitudes and durations. In other words, it can take in the type of impulses generated by real neurons, and send them on in a form that could be further processed by other neurons - it can even vary the strength of those impulses, much as real synapses do in a biological process that is thought to facilitate learning.
"This is a necessary first step in the process," said Parker. "We wanted to answer the question: Can you build a circuit that would act like a neuron? The next step is even more complex. How can we build structures out of these circuits that mimic the neuron, and eventually the function of the brain?"
While Parker stated that synthetic brains are probably still decades away, she believes that the technology could ultimately be used in prosthetic nanotechnology for treating traumatic brain injuries, or for designing intelligent systems that could be used to make cars safer, among other applications.
These nanotubes are a billionth of a meter in diameter, so the transistors are quite small. The chance for lower power operation than conventional electronics is certainly possible. This simple synapse is only a single transistor but it would take more transistors to have variability in neurotransmitter release and reuptake, and receptor concentration, like our conventional synapses. And while we implement mechanisms as fast as the neuroscientists report their understanding, there are so many open questions, which makes all of this very exciting and very much a small step towards an enormous goal. We're working on memristors, variability and other issues you mention, as well. However, implementing each mechanism or new technology in the laboratory takes a significant investment in time and energy, so achieving synaptic plasticity, for example, the next obvious step, is months away. comment Alice Parker - May 4, 2011  From Researchers create artificial synapses.

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

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

Tuszynski and his colleagues noted that the geometry of the CaMKII molecule was very similar to that of tubulin protein compounds. These tubulins are contained within microtubule protein structures, which in turn occupy the interiors of the brain’s neurons. They are particularly concentrated in the neurons’ axons and dendrites, which are active in the memory process.
The scientists wanted to understand the interaction between CaMKII, tubulin and microtubules, so based on 3D atomic-resolution structural data for all three protein molecules, they developed highly-accurate computer models. What they discovered was that the spatial dimensions and geometry of the CaMKII and microtubule molecules allow them to fit together. Furthermore, according to the models, the microtubules and CaMKII molecules are capable of electrostatically attracting one another, so that a binding process can occur between them.
This process takes place within the neurons, after they have been synaptically connected, to (in some cases) permanently store memories.
“This could open up amazing new possibilities of dealing with memory loss problems, interfacing our brains with hybrid devices to augment and 'refresh' our memories,” said Tuszynski. “More importantly, it could lead to new therapeutic and preventive ways of dealing with neurological diseases such as Alzheimer's and dementia, whose incidence is growing very rapidly these days.”
A paper on the research was recently published in the journal PLoS Computational Biology. Cytoskeletal Signaling: Is Memory Encoded in Microtubule Lattices by CaMKII Phosphorylation? Travis J. A. Craddock, Jack A. Tuszynski, Stuart Hameroff, mars 2012. Abstract: ...In long-term potentiation (LTP), a cellular and molecular model for memory, post-synaptic calcium ion (Ca2+) flux activates the hexagonal Ca2+-calmodulin dependent kinase II (CaMKII), a dodacameric holoenzyme containing 2 hexagonal sets of 6 kinase domains. Each kinase domain can either phosphorylate substrate proteins, or not (i.e. encoding one bit). Thus each set of extended CaMKII kinases can potentially encode synaptic Ca2+ information via phosphorylation as ordered arrays of binary ‘bits’. Candidate sites for CaMKII phosphorylation-encoded molecular memory include microtubules (MTs), cylindrical organelles whose surfaces represent a regular lattice with a pattern of hexagonal polymers of the protein tubulin. Using molecular mechanics modeling and electrostatic profiling, we find that spatial dimensions and geometry of the extended CaMKII kinase domains precisely match those of MT hexagonal lattices. This suggests sets of six CaMKII kinase domains phosphorylate hexagonal MT lattice neighborhoods collectively, e.g. conveying synaptic information as ordered arrays of six “bits”, and thus “bytes”, with 64 to 5,281 possible bit states per CaMKII-MT byte. Signaling and encoding in MTs and other cytoskeletal structures offer rapid, robust solid-state information processing which may reflect a general code for MT-based memory and information processing within neurons and other eukaryotic cells.
LTP is supported experimentally in vitro [2], [3], and may occur over many brain regions [4] as a common feature of excitatory synapses [5].

Source: University of Alberta, 

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Will I ever learn this?

Life is part of the environment.

Understanding how living organisms survive in an organized state despite the second law, is a common statement. But is this specific to life alone? Earth is highly differentiated, also into highly structured and ordered forms, and also form these forms. Snowflakes can have over 5000 fractal structural chrystal forms, (dendritic growth patterns, here a review), etc. Exchanges of energy with the environment constantly produce large amounts of entropy, to maintain the self-organized structure, negentropy, in Life. We say that Life creates entropy, in that way helping the second law,  but is that exactly what happens? What about the snowflakes? The time-aspect? The stability expressed as recreation?

The integration of the organism and the biosphere is important for 'What is Life' and how living matter differ from ordinary matter. Life is generally said to be an open thermodynamic system, and so thermodynamic principles should not be able to use, because in open systems we get no stable, final equilibrium state. In spite of this fact there are suggestions how thermodynamics could work in living, open systems (non-equilibrium thermodynamics) using also physical descriptions as entanglement, formations of clusters etc..Clusters and networks are the same kind of phenomenon. In what degree ordinary matter is a closed system, and whether Universe is closed or not has also been debated. In fact we have difficulties telling exactly ‘What is Matter’, also considering it make up only about 5% of total matter, where most matter is non-interactive dark matter and (dark) energy. If it is so, but the calculations are more and more exact, so today we have no reason to doubt this?

Open systems mean that we must include interference from environment, which includes environmental and also social  aspects, biometeorology, geomedicine, chronobiology, psychosomatics, consciousness, homeopathy, acupuncture, yoga, meditation, transpersonal psychology, suggests D.Rakovic 2009.

It is not only energy that flows through living matter-systems, also ordinary matter do, and especially carbon as CO2 in/out (carbon interference) and competition between N and C in metabolic chains, expressing space changes and perturbations (the ‘real’ structure formation). Life is based on carbon. But there is also some kind of Silicon based life seen in diatomeers, plants ex.

This open system is easily realized in epigenetics, as markers from environment, the Nurture-aspect, and a pool of freely exchangeable genes (transposons and circulating nucleotides and DNA islands as ALU or CGislands) and DNA (the Nature-aspect or analog for ‘Self’) between individual organisms. Nucleic acid trafficking may be involved in intercellular signalling during development, in epigenetic remodelling, tissue regeneration and fine tuning of the adaptive immune system. It may also be involved in cancer development and immune surveillance. Also rewrite the genetic text in brain developement using tunneling nanotubes? DNA-trafficking or horizontal transfer of DNA may be important during tumour progression. The hidden Markov Models are such an model approach, using the CG-island signal.

Perineural nets as stabilizers and barriers of/to the extracellular environment and neurons are another couple. The neuronal activity (but not GA-activity) forms PN-sheets. Epigenetic markers also stabilize the genome and build a barrier? Development can be thought of as the stabilization of connections to match the current environment but with considerable residual plasticity that can be revealed if there is a shift in the excitatory: inhibitory balance or the removal of the structural stabilizers. The laminal structure of the basement membrane and its importance for developement is another similar question.In fact almost every atom is exchanged in the body in the growing/repair process by time, turnover, metabolism.

So how is the body described physically then? Complexity networks describes memory or dissipation holding the body together, as negentropy, but neither matter nor energy is iniert? Everything comes from outside and rearrange itself. Or can reorganizations within the borders create iniert energy? This is why a body has to move and change in order to live? A fight between change and stability? I have a strong feeling our blind fixation on the second law, although fundamental, has made us forget the stability and conservation aspect, also fundamental. Like Life would be intermediate between first and second law? Third law (The entropy of a perfect crystal at absolute zero is exactly equal to zero, or zero at the absolute temp.), or a fourth law (there have been dozens of various supposed "fourth laws")? Onsager's fourth law of thermodynamics with symmetry relation? Symmetry and asymmetry?  Including "quasi-thermodynamic" theories by Thomson and Helmholtz respectively. Life rocks.

Onsagers fourth law express the equality of certain ratios between flows and forces in thermodynamic systems out of equilibrium, but where a notion of local equilibrium exists."Reciprocal relations" occur between different pairs of forces and flows in a variety of physical systems. For example, consider fluid systems described in terms of temperature, matter density, and pressure. In this class of systems, it is known that temperature differences lead to heat flows from the warmer to the colder parts of the system; similarly, pressure differences will lead to matter flow from high-pressure to low-pressure regions. What is remarkable is the observation that, when both pressure and temperature vary, temperature differences at constant pressure can cause matter flow (as in convection) and pressure differences at constant temperature can cause heat flow. Perhaps surprisingly, the heat flow per unit of pressure difference and the density (matter) flow per unit of temperature difference are equal, as a consequence of the time reversibility of microscopic dynamics (microscopic reversibility).

How describe this in spacelike, timelike or lightlike cones?
Is the living matter a subsystem of ordinary matter or contrarily? The matter flows through, and the energy, both irreversibly. Like the arrow of time. The organism border is no real border. Why do we then need borders and selves? For the big principle of self-organization? The networks are? Like the Hopf fibration neural networks and MRI, magnetic resonance? Neuronal networks are most longlived structures (= analog for Self?, Big CD-diamond?). Still synapses are born /deleted at a big pace, so not even them are completely inner structures. This allow the spaces to pass through each other, like galaxies travel through each other.? See Mathematical Methods for Neurosciences,
Time is coded by asymmetry, as is gravity? L-formations of sugars are also asymmetric.
Hopf Fibration and Quantum Entanglement in Qubit Systems (entanglement in high dimensional systems are problematic, topology and transmission requires entanglement)
Basically, a Hopf fibration is a map from a higher dimensional unit sphere to a lower dimensional unit sphere which is not null-homotopic. The simplest example of a Hopf fibration is a map from a three-sphere into a two-sphere in three dimensional Euclidean space S3 S1→ S2, which helps to define the well known Bloch sphere as the representation of one pure qubit. In this case, two complex numbers are necessary for the normalization condition that depends on four real parameters. These real numbers define a three-sphere and using the Hopf fibration, all the states differing by a global phase are identified with a unique point in the two-sphere. (Mosseri R. and Dandoloff R., J. Phys. A: Math. Gen 34, 10243 (2001)).
Epigenome as external world, fixed into small molecules inside the cell? So the external world lies tight against the Self, and regulate it? The same is seen in perineural sheet and neuron. Cancers too? Glia cells are responsible for the extracellular homeostasis, and relay light etc. Is there an intracellular homeostasis too? "There are many "pumps" that function in the cell membrane to supply the intracellular environment with these substances. The pump is inhibited when a cells has a sufficient amount of a given substance." This was better. Membranes again! So, what regulates the epigenome? Time? Almost everything, is it holistic, like light? Light is massless? As is magnetic extremals?

An interesting study of this system/subsystem question is the system approach of cancer. Cancers are usually seen as ’anarchistic’ conglomerates expressing opportunism. Glioblastoma  tumors are responding to multiple signals, as one is inhibited the signal is delivered another route. The secret was that they used the cytosceleton for the message delivery, not membrane impulses. DC cells (dendritic immune cells) act like patrolling sentries, prowling boundaries between the body and the outer world on and under skin, within the epidermis and within mucous membranes in the mouth, nose, ear and colon. Glucosensing cells form a network important for the regulation of Self seen as homeostasis, etc. Social interaction is seen in memory and EGO (socially constructed Self)?

If we look at the total abundance of atoms in Universe those describing Life is in big majority. So Life was maybe prior to ordinary matter? Organic molecules are also generally found in space. There is something fundamental missing here? Water forms entropy and order, both, says Gerald Pollack. This is also what Life does in photosynthesis. So, Life is about membranes and surfaces? "As you lower the temperature the liquid crystal starts to become organized and imprints that order into the surfactant itself, causing it to self assemble," about liquid chrystals. This can be called memory?

To understand the energy-aspect (chi?) we must understand
1) its interactions on matter (relativistic GR) or What is Matter,
2) resonant wave-wave interactions through a massless system (as stochastic resonance, biophotons emission, charge exchange).
3) the epigenetics as a regulating outer, bigger system, and its relation to the smaller gene pool (Self),  the causative force,
4) the changes and homeostasis/allostasis, expressed as diseases, invoke on the whole, (as in the Yin/Yang principle?)
5) psychosomatic disease. On energy dispersion, under stress we tend to focus more on the rewards than on the risks of any decision. Intention and free will. Riskmanagement.
6) psychosis and schizophrenia etc, neurological disorders, the uttermost effect of inner noise, but also very much outer noise when the 'antenna' in and metals become too strong. extracellular matrix. As for MultipleSclerosis the Fe-content is strongly linked to expression of the disease.