Draft 2: Quantum Coherence and Neurology

Quantum Coherence in Biology.

There is direct evidence for the presence of quantum coherence over appreciable length scales and timescales in the FMO pigment protein complex of the green sulphur bacteria.

It has also been theorised that magnetoreception (triggered by cryptocrhome or magnetite) is utilising quantum mechanical effects.   N Lambert – ‎2012.

The question has remained, how are such quantum effects generated?

One possibility is that the solid state photo-CIDNP effect, singlet and triplet states, ultra-fast electron transfer, and quantum coherence found in photosynthesis (and theorised in magnetorception) is due to the functioning of biological semiconductors within natural environments.

Certain organic semiconductors (OLEDs) exhibit magnetoelectroluminescence or magnetoconductance, the mechanism of which shares essentially identical physics with radical pairs in biology – specifically singlet and triplet states generated during magnetoreception. PJ Hore (2016).

During charge separation in biology, triplet states can react with molecular oxygen generating destructive singlet oxygen. The triplet product yield in bacteria and plants is observed to be reduced by weak magnetic fields.  It has been suggested that this effect is due to ‘solid-state photochemically induced dynamic nuclear polarization (photo-CIDNP), which is an efficient method of creating non-equilibrium polarization of nuclear spins by using chemical reactions, which have radical pairs as intermediates. A Marais – ‎2016

Biological materials implicated in quantum biology are similar in structure to organic semiconductors.

Organic molecules that serve as chromophores (of which flavins such as cryptochrome, are examples) consist of extended conjugated π-systems (the same structure as organic semiconductors) – which allow electronic excitation by sunlight and provide photochemical reactivity. …Ultrafast electron transfer mechanisms from an aromatic moiety to a photoexcited flavin are not only observed for riboflavin-binding proteins but for other flavoproteins, like for BLUF (blue light sensing using FAD) domains, cryptochromes, and DNA photolyases. H Staudt 2011. 

And in biology, evidence has been found that the existence of central aromatic acids can serve as stepping stones to support an electron hopping mechanism W Sun 2016.   J R Winkler 2015

These ideas are further explored in another posting – click here to find out more.

Is there evidence of similar effects in human beings?

J Kirschvink (Caltech) claims to have found evidence of magnetoreception in human beings (June 2016). A V Chervakov 2015 has recently explored possible mechanisms underlying the therapeutic effects of transcranial magnetic stimulation, and suggested magnetoreception may be implicated.

Evidence of reduced triplet product yield in brain tissue following exposure to magnetic fields would be required to demonstrate that the solid state photo CIDNP state effect was present in the brain.

A number of papers have proposed that oxidative stress could be caused by electro-magnetic fields e.g ELF-EMFs exposure (50 Hz, 0.1–1.0 mT) was shown to significantly affect antioxidant enzymatic capacity in both young and aged rat brains (S Falcone 2008).  However other studies suggest that magnetic fields could decrease oxidative stress and damage in rats and gerbils.  H Kabuto et al 2001 ,S R Balind 2014, I Tunez 2006, I Tasset 2010, 2013. Such studies show that the level and timing of exposure are critical factors impacting outcome measures. M Reale 2014.  

How Magnetism Could Be Interacting with Biological Processes

Transient receptor potentials 

The transient receptor potential (TRP) multigene superfamily encodes integral membrane proteins that function as ion channels. B Nilius 2011.

In mice, Ferritin nanoparticles associate with a camelid anti-GFP–transient receptor potential vanilloid 1 fusion protein, αGFP-TRPV1, and can transduce noninvasive RF or magnetic fields into channel activation, also showing that TRPV1 can transduce a mechanical stimulus. This, in turn, initiates calcium-dependent transgene expression.   S A Stanley 2015.   R Chen 2015.

It has been proposed that magnetic activation of TRPV4 channels enables remote control of cell function in the absence of chemical or biological agents (although this article has been withdrawn). O Lunov 2013. 

A single-component, magnetically sensitive actuator, “Magneto (comprising the cation channel TRPV4 fused to the paramagnetic protein ferritin) has also been created. Scientists validated noninvasive magnetic control over neuronal activity by demonstrating remote stimulation of cells using in vitro calcium imaging assays, electrophysiological recordings in brain slices, in vivo electrophysiological recordings in the brains of freely moving mice, and behavioral outputs in zebrafish and mice. Results present Magneto as an actuator capable of remotely controlling circuits associated with complex animal behaviors. M A Wheeler 2016.

In C Elegans, a pair of neurons called AFD neurons are equivalents to TRPs. Theser carry information about temperature and chemical stimuli from the environment, but are also critical for magnetic navigation. C H Rankin 2015.

In transgenic C Elegans, using the magnetoreceptor MagR in myo-3-specific muscle cells or mec-4-specific neurons, application of an external magnetic field triggered muscle contraction and withdrawal behaviour of the worms, indicative of magnet-dependent activation of muscle cells and touch receptor neurons. X Long 2015

A Clock-Compass System

Mechanistic links between the redox state and the Transcriptional, translational, feedback loop (TTFL) framework of circadian rhythms have been identified in a variety of organisms, including mammals.  (Wulund and Reddy 2015).

The Cryptochrome protein (CRY) in Arabidopsis, Drosophila, and mouse provide the most direct path by which redox status can interact with the core components of the transcription–translation feedback loop (TTFL).  Lisa Wulund 2015. The redox cofactor FAD (also implicated in magnetoreception) stabilises the clock protein cryptochrome (CRY), modifying rhythmic clock gene expression. A Hirano 2017.

In Drosphila it has been proposed that CRY activation involves intramolecular electron transfer and presumably subsequent confirmational changes, thus, the cellular redox status also regulates the transfer of photic information and CRY stability.  Results suggests that the cellular redox status and electron transfer modulate the light dependent activation of CRY, which in turn affects the subsequent transmision of the light signal to TIM and the degradation of CRY itself, with subsequent clock setting….Research on Zebrafish cells suggests the altered redox state triggers the transduction of photic signals that regulate and synchronize the circadian clock.  M L Fanjul-Moles 2015. 

It has been proposed that a Cryptochrome/Radical Pair Mechanism signalling is a fundamental component of the robustness and temperature insensitivity of circadian systems.  J Close 2014   

There are a number of other examples in nature, where cryptochrome may be operating in a way that integrates the clock and compass mechanisms – find out by clicking here for a separate posting.

A Clock-Compass System Interface with the Metabolism 

In nature such as system could able optimal alignment between the animal and their environment.

Circadian clocks regulate different aspects of sleep, suggesting that redox and metabolism may affect sleep homeostasis through their impact on the state of the circadian system…Binding of certain clock proteins may be regulated by intercellular redox potential, indicating the potential for cross-talk between the circadian clock machinery, energy metabolism and sleep regulation. (Ray and Reddy 2016).

Implications for Neurology 

Recent results indicate a key role of cryptochrome proteins in Time and place learning (TPL)  CK Mulder 2016 .   

Studies provide much evidence that a functional circadian clock is required for optimal memory formation and persistence. A Malik 2015.

It is known that circadian rhythms influence learning, cognitive performance, and memory formation across different species. Studies describe disruption of circadian rhythms altering learning and memory performance, spatial learning, intra and intersession habituation, place learning, long-term potentiation, and trace fear memory (A Jilg 2010 (implicating Per 1), A A Kondratova 2010, E A Van der Zee 2008).  

Further links between circadian rhythms, redox and neurology (particularly memory) are explored in a separate posting.

It is suggested that a classical dissipative system could support short term linear memory (as such memory can be created within a reaction diffusion process), coupled with a long term spin based associative memory (e.g the Hopfield model).

Cryptochrome’s role in Vision

Cryptochrome is found throughout adult human retina. CRY2 is localized throughout the cytoplasm of cells in the ganglion cell layer as well as within nuclei… C L Thompson et al 2003.

Human cryptochrome 2 protein (hCRY2), can sense magnetic fields when implanted into Drosophila. LE Foley – ‎2011.    However in mammalian clock neurons, they cannot. Consequently, the EMF responsiveness of cryptochrome is determined by its intracellular environment, suggesting that other, unknown molecules that interact with cryptochrome are also very important.  G Fedele 2014.

In experimental studies, it has been shown that the human visual threshold can be influenced by the geomagnetic field. One of the results was that the threshold shows periodic fluctuations when the vertical component of the field is reversed periodically. The maximum of these oscillations occurred at a period duration of 110 s. After optimization of the parameters, the oscillations of FAD and FADH* show maximal amplitude at a period duration of 110 s, as was observed in the experiment. This makes it most likely that the signal, which influences the visual system, originates from FADH* (signalling state).  F Thoss 2017

Electrophysiologic responses to magnetic fields have been detected in several parts of the avian nervous system that receive projections from the visual system.  Response to changes in magnetic field has been demonstrated in some neurons of the basal optic root and the optic tectum. Responses to magnetic fields in both locations disappeared when the optic nerves were cut. These results suggest that one locus of magnetoreception in birds is in the visual system (perhaps in the photoreceptors).  Sönke Johnsen 2004.

Characterisation of the space-coding properties of gamma-band neural oscillations in the avian optic tectum lays the foundation for understanding the role of these oscillations in spatial localisation and spatial attention across different classes of vertebrate animals…In the optic Tectum this corresponds to a high resolution topological, multimodal map of space.  D Sridharan et al 2011.  Sridharan 2014 

In the Ansell’s mole rat (a mammal) It has been shown that magnetic information is integrated with multimodal sensory and motor information into a common spatial representation of allocentric space within the superior colliculus, the head direction system and the entorhinal–hippocampal spatial representation system (Nemec et al.,2001; Burger et al., 2010). “The specific mechanisms underlying this integration have yet to be identified and characterized”. Ludmila Oliveriusová et al 2012

It is suggested that gamma oscillations may be the result of magnetoreceptive sensoring (via the superior colliculus or optum tectum).

Gamma Oscillations

Evidence suggests that successful memory performance requires coupling of 30–100 Hz gamma rhythms to particular phases of the theta cycle.  L L Colgin 2015J Lisman 2013,  T K Rajji 2016.

Gamma Oscillations and Microsaccades. 

Findings some gamma oscillations may only exist as a result of microsaccades (very small eye movements) has led to some questioning of the importance of gamma oscillations in neural processing and memory. S Yuval-Greenberg et al 2008 found that no gamma band activity was observed on trials without any saccades whatsoever, indicating that the gamma band activity observed at the scalp might solely reflect saccade-related muscle activity. Also see C A Bosman et al (2009).  

Microsaccades are thought to contribute to foveal and peripheral vision and to trigger perceptual transitions in a number of bistable illusions, including binocular rivalry. 

They may drive perceptual flips in binocular rivalry. Bistability may be of particular relevance to biological systems that switch between discrete states, generate oscillatory responses, or production of self-sustaining biochemical “memories”.  D Angeli 2003.

Turing Patterns in Vision: Phosphenes

Phosphenes can be stimulated by flickering light, and both electricity and magnetic fields (e.g TMS). Perceived phosphenes can occur through ionizing radiation, electrical, or magnetic stimulation of the visual cortex. Magnetophosphenes have been found to occur also in strong magnetic field during movement of the head and in transient fields during energising or deenergising of high-field magnets. PC Talyor 2010.

Research on astronauts experiencing phosphenes found that frequency [of phosphenes] was up to 25 times higher near the magnetic poles than in equatorial latitudes”. Photic stimulation within a specific frequency and luminance range also causes them in control subjects. D H Ffytche 2008.

Oster 1970 also connected phosphenes to the retrieval of memory. Stimulating the visual cortex at the extreme rear of the brain interrupts the patient’s normal vision and causes him to see specks of light. When electrodes are moved to the adjacent region, the visual associative area, the patient reports seeing phosphenes of geometric design. When the electrodes are moved father forward, the patient frequently reports a visual scene of some past experience that is so vivid as to be current (Oster 1970:86).

Further images of phosphenes can be found on a site by Dr Ida Pearce. They seem to resemble phase transitions, and have been compared to BZ reactions by a number of scientists. It asked whether this patterning could be related to other non linear activity in the retina and critical brain dynamics (e.g Janina Hesse 2014). 

The Patterns Produced by Phosphenes

Klüver (1926) reported that the mescaline-induced imagery (form constants) could be observed with the eyes either closed or open and that with the eyes open it was impossible to look at a blank wall without seeing it as being covered with various forms (Siegal, 1977:132). He defined four main types of constantly occurring hallucinations:

  1. grating, lattice, fretwork, filigree, honeycomb and chessboard
  2. cobwebs
  3. tunnel, funnel, alley, cone and vessel; and
  4. spirals.

The Maths Behind Phosphenes

Ermentrout and Cowan, and  Bressloff, have explored diffusion-driven Turing instabilities in the Wilson–Cowan neural field equations supporting formation of stationary activity patterns that have been likened to visual hallucinations. E Negahbani 2014.  Also see  P Bressloff 2002,  Kilpatrick and Ermentrout, 2012a,b; Froese et al., 2013, V A Billock – ‎2012  and P Tass 1995.




Bressloff, Cowan, Golubitsky, Thomas, Wiener, ‘What Geometric Visual Hallucinations Tell Us about the Visual Cortex’. Neural Computation 14 (2002) 473–491.

Symmetric bifurcation theory has been used to explain how low frequency flicker should produce hexagonal patterns while high frequency produces pinwheels, targets, and spirals (M Rule et al 2011).

Phosphenes and Consciousness

It should be emphasised that such geometric patterns are common to human beings and do not have to be drug and diseased induced. They can also be perceived  during meditation,  upon entering sleep, in lucid dreams and on awakening.  They are more common in childhood (Oster 1970:83).

I have seen the following phosphenes as I go into the waking state.  Initially I see luminous ‘bubbling’ which shifts in a chaotic manner (this can remind me of liquid crystal going through phase transitions), but this then changes to form clear geometric shapes including pinwheels and grids.  On one occasion I saw a snowflake like visual, on another occasion they looked very similar to a BZ reaction.  I have often found that these phosphenes are associated with times when I have undertaken substantial meditation or computer time.  Both of these activities are likely to have influenced my eye movements.


Descriptions of phosphenes can also be found in lucid dreamers. “Although I have often seen darkness in a (lucid) dream, it was not until I began to examine darkness closely that at times I came across faintly seen patterns. The time I saw the patterns most distincly.  My view was divided into possibly eight to twelve irregularly shaped sections. Each contained its own pattern. Each section of pattern seemed to vibrate or twitch within itself, though the section divisions remained stable. I was able to examine the whole display, scanning right to left and back again. Most of the sections had line or herring bone designs; one had all dots close together; and one had a chess board pattern. The chess board and dot designs I have seen often in hypnopompic experiences, though not the parallel lines. Sometimes I see only swiftly moving patterns covering my visual field and appearing to surround me. They are constantly changing versions of lattices, lines, dots, and colors”.  G Gillespie, University of Pennsylvania – taken from a lucid dreaming site.

Phosphenes and Retinal Prosthesis

Phosphenes are already routinely being used as part of the design of retinal prosthesis systems.

“Visual prostheses have the potential to restore partial function to individuals by electrically stimulating different parts of the visual pathway (retina, optic nerve, or cortex) and have become an increasingly prominent topic in the field of neural prosthetics.  A prosthesis may provide useful visual percepts in the form of spots of light called phosphenes.

These phosphenes form rudimentary building blocks in prosthetic vision that can be used to realize more complex patterns representing visual scenes. The possibility of restoring vision by using multiple simultaneously elicited phosphenes with a microelectronic prosthesis is the foundation for current clinical trials and is the general assumption made in prosthetic visual simulations.  S C Chen 2009.

Holographic optogenetic stimulation of patterned neuronal activity is also being explored for vision restoration.  Again such systems make use of phosphenes to deliver information to the visual system. G A Goetz et al 2013.

In non linear optics, information can be coded and processed as an optical pattern.  These patterns can include hexagons, spiral and complex geometries –  including the coexistance of different patterns.  The capacity of such systems is determined by the number of different pattern models that can exist and interact as a system. Mikhail A. Vorontsov 1995.    Information processing in the retina has been modeled as cellular automata e.g  F Devillard – ‎2014,  S Gobron 2007.  M Beigzadeh et al 2013.

Phosphenes May Be Used as Coding to Create Visual Imagery

It is proposed that the brain is using the black and white elements of phosphenes as universal code in order to encode ‘visual scenes’.

The patterns of light and dark that fall on the retina provide a wealth of information about the world around us, yet scientists still don’t understand how this information is encoded by neural circuits in the visual cortex. But it has been found that the majority of neurons in visual cortex respond selectivity to light vs dark, and they combine this information with selectivity for other stimulus features to achieve a detailed representation of the visual scene.. In short, it has been discovered that information about dark and light is preserved in the responses of most neurons in visual cortex, and it is an integral part of the neural code that cortical circuits use to represent our visual world.  J Kremkow 2016.    G B Smith 2015.   Kuo-Sheng Lee 2016.

Instead, the cortex’s primary organizational principle is to create a giant switchboard that pits light vs dark at every position in the visual scene.

Orientation and direction maps would originate in a sensory map that is represented as continuously as possible.  In the visual cortex this continuous representation could be accomplished by precisely matching response properties of on and off thalamic afferents.  The same principle may apply to other sensory spaces and afferents feeding other cortical areas that have maps for touch, hearing and spatial navigation.  J Kremkow 2016.

Why does a phosphene resemble an optical illusion and why do both of these resemble a phase mask used in a process to produce an optical vortex?


Figure 1: Phosphene image from What Geometric Visual Hallucinations Tell Us about the Visual Cortex. Bressloff, Cowan, Golubitsky, Thomas, Wiener; Neural Computation 14 (2002) 473–491.


Figure 2: A flickering wheel illusion.  Such illusory motion has been found to be driven by microsaccades (with their close links to gamma, and possibly alpha neural oscillations) e.g see the work of Martinez-Conde (2012), and J Lange – ‎2014.  Perception of illusory movement is not specific to humans.


Figure 3: A schematic diagram of dynamic holographic optical tweezers creating an optical vortex. The SLM imposes the phase   on the incident TEM  beam, converting it into a helical beam that is focused into an optical vortex. The inset phase mask encodes an optical vortex.    http://physics.nyu.edu/grierlab/vortex5c/

Vision in a Holographic Universe

Phosphenes might also be a mechanism by which we would translate data generated by a holographic universe into the three dimensions we directly perceive.

A hologram is essentially a phase mask but instead of a single luminous point, all the points on the surface or surfaces of an entire three dimensional object or scene act as sources of light.   

According to the biological signal-processing model presented, the visual system uses neural matrixes functioning as spatial filters in a holographic form, and the CNS acts as a Fourier analyzer. Thus, it can be assumed that, if this model is a functionary one indeed, nonspecific stimuli (e.g., electric or magnetic stimulation, etc.) when acting on such a function group, may result in a visual pattern sensation characteristic to the filter pattern the CNS used in its signal processing. Such so-called “subjective light patterns of the second kind” are not unknown in physiology (phosphenes) and in psychiatry (hallucinations). Some of them might be regarded as a perceived filter pattern“. Pal Greguss 1999.

In holographic data storage technology, holographic data can be encoded onto a signal beam using a spatial light modulator.  This translates electronic 0’s and 1’s into an optical checkboard pattern of light and dark pixels. A hologram is formed in the light sensitive storage medium at the point where a reference beam and signal beam intersect.  Chemical reactions occur causing the light distribution to be recorded as a permanent polymerisation pattern.

Interaction Between the Classical and Quantum May Create An Effect Analogous to a Quantum Zeno Effect

Efstratios Manousakis has given a quantum mechanical description of the phenomena of binocular rivalry. It rests heavily upon the quantum Zeno effect, which is a strictly quantum mechanical effect that has elsewhere been proposed as the key feature that permits the free choices on the part of an observer to influence his or her bodily behavior.. Within the von Neumann dynamical framework this intervention can, with the aid of quantum Zeno effect, cause a person’s brain to behave in a way that causes the body to act in accord with the person’s conscious intent (Henry P Stapp. 2013).   Further explanation of Strapp’s theory of how the QZE would effect consciousness can be found by clicking here.

A theoretical approach to describe the dynamics of alternating perceptive configurations was proposed in terms of the so-called Necker-Zeno model. This model is inspired by the Zeno effect for unstable quantum states  and describes the perceptual instability of ambiguous stimuli in a formal fashion. .  H. Atmanspacher et al 2007.

During rivalry, transitions in dominance from one stimulus to the other can appear highly ordered. Rather than constituting an abrupt transition from one view to the other, one experiences waves of dominance whereby one stimulus sweeps the other out of conscious awareness. These waves of dominance are particularly prominent with larger rival patterns subtending several degrees of visual angle. Every few seconds the perceptual every few seconds the perceptual dominance will dominance will switch switch….

The Coupling of Classical and Quantum Systems Resulting in a QZE

It has been suggested that a mechanism leading to the Quantum Zeno Effect (QZE) could be analysed within a model interaction between a classical and a quantum system. The Zeno’s effect then appears when a classical device, that is able to high frequency switching between two alternate states (i.e bistability), is strongly coupled to a quantum system prepared in an appropriate initial state. The Hamiltonian evolution of the quantum system is then slowed down, and it stops completely in the limit of infinite coupling constant.    P Blanchard 1993,  19952003., 2013.

Recent results show that a simple dissipative time evolution can result in a dynamical exchange of information between classical and quantum levels of Nature. With a properly chosen initial state the quantum probabilities are exactly mirrored by the state of the classical system and moreover the state of the quantum subsystem converges for t → +∞ to a limit which agrees with that required by von Neumann-Luders standard quantum measurement projection postulate.  P Blanchard 2013.

Within biology, quantum mechanics (through an organic superconductor) could potentially interface with the classical mechanics of biological clocks and switches (which exhibit bistability).

Other Models

The approach taken in this posting could complement a number of other models of quantum consciousness including:

  1. The dissipative brain (W J Freeman and G Vitiello).
  2. Spin based consciousness.
  3. Consciousness on the poised state (S Kauffman and Vattay)
  4. The holonomic brain, with phospenes providing a platform for perception of holographic information as ‘normal visual imagery’.
  5. Quantum consciousness (Hameroff and Penrose)

More information on these models is available from www.slideshare.net/accipio/quantum-physics-in-consciousness-studies-dirk-k-f-meijer-and-simon-raggett

2016. This article merely joins up other peoples work into an overall system.  These works have been referenced so it is clear that others have provided the individual pieces of evidence that have been used to shape a specific systems approach.    







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