The Living Matrix

giving up space and time as fundamental constituents of nature.. figuring out how the Big Bang and cosmological evolution of the universe arose out of pure geometry.

“In a sense, we would see that change arises from the structure of the object, but it’s not from the object changing. The object is basically timeless.”

– Arkani-Hamed, on the amplituhedron.

 

Fractal sets underlay the geometry of complex dynamics, and hence are the universal ordering principle in living systems. Fractal geometries are not only the universality at the transition to chaos (unpredictable systems, like life), they also endow our physical universe with infinite diversity, from simple functions. Viewing the time-evolution (iteration) of a fractal system, one can almost see the living nature of our fundamental mathematical/geometric matrix – the living universal matrix.

This underlying geometric order of complex systems is very different from the present paradigm of random topological fluctuations that predominate the Field. This “seething” sea of quantum energy fluctuations – may actually have a specific, yet not entirely predictable (fractal), ordering. An intelligence inherent in the fundamental mechanics of space-time-matter.

Random quantum oscillations fluctuate in and out of existence within the lowest energy state (the zero point field) of the quantum vacuum. The lowest quantum energy state should have virtually no energy associated with it, however what is found is that the vacuum actually has an infinite potential energy density, and this energy is nontrivial – meaning that it has demonstrable physical effects. In fact, it is actually an infinite reservoir from which all physical phenomena emanatize – and as a resevoir it is very much like a fluid medium. However unlike the random fluctuations of quantum harmonic oscillators pictured above, there are membranes upon which the vacuum forms ordered phases where all of the quantum fluctuations oscillate coherently.

Hamiltonian Quantum Oscillation

It is the ordered phases of the vacuum that we are concerned with – as it produces the morphogenetic field of living systems, the advanced wave propogation of consciousness, and even anti-gravity (levitic) effects.

Water – The Key to Life

 

 

 

 

 

 

 

 

 

 

 

 

 

Far from the conventional paradigm of water in the biological system, in which it is only an inert medium for biochemical reactions to take place, the highly structured phase of water within the cellular environment orders the biochemical reactions through interaction with the quantized electromagnetic field. The quantum magneto-electrodynamics of water are directly related to its interaction with the quantum vacuum as described through Quantum Field Theory. The propensity of water to be coherently structured at the molecular level from the quantum vacuum and electromagnetic fields suggests that it may be the information-carrying medium from which biochemical reactions are ordered within the biological system.

This has been demonstrated empirically by Montagnier et al through the ability of aqueous nanostructures of water to carrier unique electromagnetic signature frequencies of specific DNA sequences, and for those EMS-carrying aqueous nanostructures to reconstitute the same specific DNA sequence from the base constituent biomolecules of DNA.

These and other observations suggest that it is highly probable that an atomically-ordered coherent phase of water is involved in directing the activity and state of biomolecules within the biological system. These observations become particularly pertinent when considering the close association of nuclear DNA (chromatin) with water and how that interplay may affect the epigenetic expression of genetic elements of the chromatin. This would imply that not only is the genetic expression of the chromatin modules directed by the electromagnetic frequencies specific to the associated molecular nanocomplex of the aqueous matrix, but that the epigenetics could potentially be altered or modulated by the introduction of aqueous nanostructures with a different electromagnetic signature frequency.

This is especially pertinent when considering aspects of information processing and cognitive function in the living organism. For example, at the core of the brain is a water filled ventricular space that circulates throughout the entire brain as the cerebrospinal fluid.

This system is not just for cushioning the brain or for the diffusion of neurotransmitters, hormones, cytokines, etc.. – it is the primary reception center of the brain for consciousness. Concrete examples of this occur in hydrocephaly, where in some cases the cortical tissue of the brain will be completely lost and yet the individual is able to function completely normally (http://www.foxnews.com/story/0,2933,290610,00.html).

In the above MRI image it is seen that most of the bran has experienced neurodegeneration to be replaced predominantly by the lumen of the vetricular cavities. Many times in this situation the individual displays completely competence in cognitive functioning.

 

 

 

 

 

The most advanced technological equipment today cannot detect or fully harness the incredible information and energy density of the quantum vacuum. There is an amazingly coherent and superbly efficient system that may very well access this infinitely deep reservoir of information and energy on a routine basis as a matter of normal functioning – and that is the living biological system. As such, it is possible that the biological system is the most technologically advanced form of matter yet achieved, and more importantly it provides a model by which this sublime living technology can be reverse engineered and hybridized for unimagined advances in our own externalized technologies.

 

Fascinating and Highly Elucidative Study on Protoplasmic Water –

This is a study conducted by  Martina Havenith, with colleagues Martin Gruebele and David Leitner. The following is an excerpt from their report and can be found in full at the following site:

http://www.hfsp.org/frontier-science/hfsp-success-stories/water-and-biological-molecules-probed-terahertz-spectroscopy

What are the properties of water in a living cell?  With a cytoplasmic packing density of up to 400 mg/ml of protein, nucleic acids, lipids, carbohydrates and small molecules or ionic compounds, there is little distance from any one molecule to its nearest neighbors – only about 20-30 Å, depending on the molecular size.  The roughly 10 layers of water molecules that can  fit into these spaces have entirely different properties from water in “bulk” due to its interactions with cellular components.  Water as we know it, that hydrogen-bonded bulk liquid melting at 0 °C and boiling at 100 °C, may not exist within cells.  Recently, a new technique has provided a means to observe water dynamics. i.e. the fast collective motion of water molecules, around biological molecules.  Terahertz light, at frequencies between microwaves and the infrared (1012 Hertz = 1 Terahertz), can excite collective motions of solvent molecules and of biomolecules whose time scales are on the order of a picosecond.  This corresponds to the important time scales for hydrogen bond rearrangement in water and collective, functionally important motions of large biomolecules such as proteins and nucleic acids.  In fact, the motions of the protein or nucleic acid and the hydrogen bond rearrangement of water are coupled.  Modern terahertz instrumentation, building on decades of progress in far infrared spectroscopy of solid samples and films, is now powerful enough to penetrate water layers and look at fully solvated proteins, carbohydrates, lipids, and nucleic acids.

With THz technology and computer simulations now at a stage where spectra of solvated biomolecules could be obtained and interpreted, our groups sought support from the Human Frontier Science Program to initiate a series of studies on biomolecule-solvent interactions and dynamics.  We hoped that THz technology would shed light on motions on that critical time scale of hydrogen bond breaking and formation coupled to functionally important dynamics of biomolecules that cannot be accessed by other methods, such as nuclear magnetic resonance (NMR).  Since THz technology was new, there was considerable risk that the method would not be sensitive enough to provide the information we were seeking – others told us that it would be impossible or even hopeless. We were extremely thrilled that HFSP supported our high-risk endeavor in 2004.  With HFSP funding we have been able to establish THz spectroscopy as a now blossoming and widely used tool in the study of biomolecule-solvent dynamics and interactions.

At first glance, there appeared to be little information contained in the THz spectrum of a biomolecule.  The frequency dependence of the absorbance is largely featureless in the THz regime.  However, with the help of the HFSP support we soon discovered that measurements of the THz absorbance as a function of biomolecule concentration in solution provides clues about the extent of the hydration layer, i.e., the number of water molecules around the biomolecule that are dynamically distinct from bulk water, as well as giving information on the dynamic coupling between the biomolecule and water.  Two kinds of water, bulk water and hydration water, each with distinct absorption coefficients, were identified to account for the variation of the absorbance with biomolecule concentration.   By studying the change in absorbance with concentration we could deduce the size of the hydration layer.  In combination with molecular dynamics simulations modeling the same system, we explored at the molecular level the biomolecule-solvent dynamics underlying the THz spectra.

As our work developed, several novel key concepts in the Terahertz spectroscopy of biomolecules in water emerged, with major implications for our investigation of the interaction between water and biological macromolecules.  (a) “Terahertz defect”:  Biomolecules absorb less THz light than water over part of the frequency range, and when biomolecules are dissolved in water, the absorption coefficient of the solution often decreases at certain frequencies  (e.g. 2.5 THz for proteins in water).  (b) Another key concept is the “Terahertz excess”. Despite the fact that pure biomolecule solids or films generally absorb less than bulk water between 1 – 3 THz, there are still many situations where the biomolecule+water mixture absorbs more than either the biomolecule or a bulk water sample. This can be explained only by invoking a third substance: biological or hydration water.  If the presence of biomolecules perturbs nearby water molecules, this could have an effect on many of the measurable properties of water: density, relaxation rates, reorientation rates.

Water has a built-in probe of its orientation: its dipole moment, with a negative charge at the oxygen end and positive charge at the hydrogen end of the molecule.  The dynamical reorientation of the water dipole moment turns out to be affected over particularly long distances, up to several nanometers from the surface of a biomolecule.  This reorientation arises as water molecules within the hydrogen bonding network tumble around and diffuse, constantly making and breaking hydrogen bonds.  Couple that with the radius-squared increase of the number of water molecules as one moves outward to more remote solvation shells, huge numbers of water molecules can be affected, each a little bit, by a single biomolecule.

 

Dynamical hydration layer around a protein.  The five helix bundle protein known as  λ*6-85  is shown surrounded by 1000 water molecules in the dynamical hydration shell. All of them are shown to be affected by a single protein in their picosecond hydrogen bond dynamics

A simple picture of a biomolecule in water thus has to include the protein, nucleic acid or carbohydrate (causing a Terahertz defect), bulk water (if far enough away), and, in between, hydration water with new physical properties, including a propensity for enhanced Terahertz absorption – the Terahertz excess.  The hydration water defined in this way is not the same as the sterically bound water molecules probed by X-ray crystallography, NMR or neutron crystallography.  We have therefore detected a dynamical hydration shell, which includes all water molecules that show water network dynamics distinct from the bulk, and thus a distinct THz absorbance.  The influence of the biomolecule can reach much further than the static hydration radius since it involves only a change in the motions and not a fixed H-bond to the protein.

Our work has shown that this simple picture works quantitatively in some cases with a homogeneous surface, for instance water molecules surrounding small sugar molecules, but breaks down in other cases, for instance hydration water around crowded proteins. In the latter case, the effect of proteins on the surrounding water shell reaches out so far that water molecules begin to “see”more than one protein. In addition, the influence of the protein will now be governed by several key parameters such as hydrophobicity and hydrophilicity of the side chains and steric hindrance. In addition, many-body interactions become important, so the influence of the hydration bond dynamics of water in the hydration shell becomes more complex. Molecular dynamics simulations of the solvation water around biomolecules shows a retardation of the H-bond dynamics for hydrophilic as well as hydrophobic protein surface areas. Whereas the first is explained by H-bond with the proteins, the retarded hydrogen bond dynamics around hydrophobic residues is at first glance surprising and can be explained by the additional imposed steric constraints on the water molecules at hydrophobic sites.

A detailed analysis using ab initio molecular dynamics simulations revealed a fundamental mechanistic difference between correlated molecular dipole oscillations at infrared and THz frequencies. While at infrared frequencies beyond 1000 cm-1 (30 THz) the molecular dipoles of neighbouring water molecules are correlated purely due to electronic polarization effects, at THz frequencies the nuclear motion of neighbouring water molecules are responsible for the observed correlated oscillation of molecular dipoles. While the vibrational motion of atoms is strictly localized on single molecules at infrared frequencies, at frequencies below 1000 cm-1, the onset of truly correlated, and thus collective nuclear motion of neighbouring water molecules is observed. In particular at THz frequencies, below 200 cm-1 (6 THz), the collective vibrational motion included water molecules significantly beyond next neighbours.

What is the role of the dynamical hydration shell? In order to address this, kinetic studies are necessary on the interactions between protein and water detected by THz absorption. As a first proof of principle experiment we have now visualized the changes in THz absorption during the protein folding process and recorded changes in the THz absorption with millisecond time resolution. This new method has been called kinetic terahertz absorption (KITA) spectroscopy.

 

For more on the implications of these findings – see also the Institute for Science in Society: Electronic Induction Animates the Cell –

http://www.i-sis.org.uk/Electronic_Induction_Animates_the_Cell.php

The interaction of unfolded protein chains with water is particularly significant. When protein chains are unfolded, their peptide bonds -CONH- become exposed, forming an alternating chain of negative (CO) and positive (NH) fixed charges that is very good at attracting polarized multilayers (PM) of oriented water molecules (see Figure 2). I have referred to this water as ‘liquid crystalline water’ on grounds that it forms dynamically quantum coherent units with the macromolecules ([17] The Rainbow and the Worm, The Physics of Organisms, ISIS publication), enabling them to transfer and transform energy seamlessly with close to 100 percent efficiency. And it is this liquid crystalline water that gives the cell all its distinctive vital qualities (see [18] Life is Water’s Quantum Jazz, ISIS Lecture).

Many recent findings lend support to Ling’s hypothesis and the liquid crystalline cell, and I shall mention them in context.

PM water molecules are highly polarized and oriented. According to Ling [4], they are restricted in motion, and have shortened nuclear magnetic resonance relaxation times. (This is the basis of nuclear magnetic imaging that detects cancerous tissues by their longer relaxation times, as indicative of less structured water.) PM water does not freeze at the temperature of liquid nitrogen, and it tends to exclude solutes, which accounts for the apparent diffusion barrier for many molecules that are erroneously attributed to the cell membrane.  In fact, the cell membrane offers very limited restriction to diffusion, and it is the PM water that excludes them.

PM water resembles supercooled water that has been identified in recent years as hydration water of proteins (see [19] Dancing with MacromoleculesSiS 49). A similar phase of water has been found on surfaces of hydrophilic gels, most recently by Gerald Pollack’s research team at University of Washington, Seattle in the United States (see [20] Water Forms Massive Exclusion ZonesSiS 23), which indeed excluded all solutes tested: including albumin, and pH sensitive dyes.

In addition, though not mentioned by Ling, PM is expected to be extremely good at resonant energy transfer over long distances, even better than bulk water at ambient temperatures, and to conduct positive electricity by jump conduction of protons (see [21] Positive Electricity Zaps Through Water ChainsSiS 28).

A cell with 80 percent water content would have polarized multilayers of water some 4 molecules thick that anastomose and surround the abundant cytoplasmic proteins such as those of the ubiquitous cytoskeleton.  This is also precisely the thickness of the highly polarized water around proteins identified in Terahertz absorption spectroscopy within the past several years [22].

Surprisingly, an opinion review article published in 2005 stated [23]: “Recent progress in predicting protein structures has revealed an abundance of proteins that are significantly unfolded under physiological conditions. Unstructured, flexible polypeptide are likely to be functionally important and may cause local cytoplasmic regions to become gel-like.” This is another indication that Ling may well be right.

Ling sees his proposed ‘cardinal sites’ on proteins to include the ubiquitous receptor sites of cell biology, but going beyond them [4]. For example, ATP and 2,3 diphosphoglycerate (2,3 DPG), are essential for the action of haemoglobin, the iron-containing oxygen carrier protein in red blood cells. Binding of ATP and 2,3 DPG reduces the affinity of haemoglobin for oxygen, so that haemoglobin can deliver the oxygen to the lungs [24, 25]. ATP is therefore not the only cardinal adsorbent. Drugs, hormones, 2,3-DPG, Ca2+, and other potent agents at very low concentration may interact with cardinal sites to sustaining the resting living state of the protoplasm or bring about changes [16].

Thus, electronic induction is essentially the mode of action in cell [4]. The ‘cardinal adsorbents’ are electron-donating or electron-withdrawing. Induction happens via the polypeptide chain, which possesses a partially resonating structure as the peptide bond is 40 percent double bond and 60 percent single bond [26] (see Figure 3), and is therefore highly polarisable, enabling it to transfer energy and information over long distances [16].

As the PM water is highly ordered and polarized if not quantum coherent [15, 17, 27] (Quantum Coherent Water and Life,  SiS 51), I would expect it, too, to be equally adapt at resonant energy and information transfer, if not more so, and over the widely anastomosing networks that ultimately connect up the whole cell via the cytoskeleton.

Indeed, the major cytoskeletal proteins – actin, tubulin and intermediate filament proteins – polymerize into extended fibrous networks throughout the cell in the presence of ATP (GTP, guanosine triphosphate in the case of tubulin) [28, 29], and hence expected to support polarized multilayers of water. The cytoskeletal proteins are also all highly acidic, with glutamate and aspartate carboxylate side-chains and termini exposed and organised in clusters that are expected to show considerable preference for binding K+ over Na+ [7] in the resting polymerized state, not unlike the picture Ling had in mind. When stimulated into activity, the depolymerisation of the cytoskeletal proteins would release ATP or bound ADP and Pi, thereby bringing about a change in protein conformations that also alters the state of cell water, and with that, membrane depolarization and new chemistry due to influx of previously excluded solutes and ions [4, 7, 30] (The Importance of Cell WaterSiS 24).

Suddenly, a whole new vista has opened up. The coming decade could be the most exciting in the history of cell biology.

 

 

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