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Biological semiconductors and quantum biology

INTRODUCTION

There are several evidenced examples in biology of processes which involve ultra-fast electron transfer, singlet and triplet spin mechanisms and quantum coherence.

These includes:

  1. Evidence of the solid state photo-CIDNP effect (via singlet and triplet states), ultra-fast electron transfer, and quantum coherence in photosynthesis.
  2. Evidence of the solid state photo-CIDNP effect (via singlet and triplet states) and ultra-fast electron transfer in flavoproteins.  In addition there are widely explored scientific theories of cryptochrome (a flavoprotein) triggering a quantum mechanical effect during ‘magnetoreception’.

There is also evidence of that the redox state of cysteine residues may support singlet and triplet states, and ultra-fast electron transfer in both flavoproteins and photosynthesis.  The coupling between circadian rhythms (providing periodicity) and redox could potentially influence the oxidative interface -consisting mainly of the redox regulation of redox-reactive cysteine residues on proteins. This may provide environmental support for quantum transport.

Consideration is also given to other environments where singlet and triplet states, ultra-fast electron transfer, and quantum coherence can be found – including at higher temperatures. Manifestations of quantum coherence in different solid state systems include semiconductor confined systems, magnetic systems, crystals and superconductors. Ultrafast electron transfer and charge separation is possible in semiconductors A Ayzner 2015, S Gélinas 2014, and work is currently being undertaken on semiconductor spintronic devices operating at room temperature. (N Thanh Tu 2016)

PJ Hore (2016) has pointed out that certain organic semiconductors (OLEDs) exhibit magnetoelectroluminescence or magnetoconductance, the mechanism of which shares essentially identical physics with radical pairs in biology. There are three main types of organic spintronic phenomena.  This includes a magnetic field effect in organic light emitting diodes, where spin mixing between singlet and triplet polaron pairs can be influenced by an external magnetic field leading to organic magnetoresistive effect.  E Ehrenfreund 2011F Geng 2016.   

J Vattay and S A Kaufmann (2015) have also suggested the existence of bio-conductor materials which neither metals nor insulators but new quantum critical materials which have unique material properties.  E Prati (2015) then used their work to explore room temperature solid state quantum devices at the end of chaos for long living quantum states.

The idea of biological semiconductors has been around for some years (e.g see A V Vannikov 1970). Several natural semiconductors have now been identified in biology.  Endogenous bioelectrical signals play critical roles in a near-infinite number of ubiquitous biological processes such as energy harvesting, rapid communications and inter/intra cellular synchronisation.  Specific examples include photosynthesis, vision, carbohydrate metabolism, neurophysiology, wound healing, tissue regeneration and embryonic development.  And several natural semiconductors have already been identified e.g melanin and peptides. Charge transport has been found in a variety of naturally-derived small molecule, semiconducting biological compounds – carotenoids (produced by plants and bacteria).  These include protection against oxidative species, pigmentation, and light havesting for photosynthesis.  The polyconjugated structure of this class of compounds suggests that the natural electronic activity of derivatives could be repurposed as an active semiconductor material for organic electron devices.   M Mukovich 2012.    And there are π-conjugated organic semiconducting materials. C Wang 2011.

It is of interest then that organic molecules that serve as chromophores (of which flavins such as cryptochrome, are examples) consist of extended conjugated π-systems, which allow electronic excitation by sunlight and provide photochemical reactivity. Eukaryotic riboflavin-binding proteins typically bind riboflavin between the aromatic residues of mostly tryptophan- and tyrosine-built triads of stacked aromatic rings…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.

Hopping conduction is widely considered the dominant charge transport mechanism in disordered organic semiconductors. A V Nenashev 2015.  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, including in flavins.

It may be the case that levels of conductivity could change/adapt within biology.  This is explored in more depth towards the end of this article. Biology could draw on a complex system of interfaces between different types of conductors (from flavins to iron sulphur clusters which are ubiquitous in biology) and insulators, periodic oscillations (biological rhythms), redox systems, and generated magnetism (biological organisms also produce tiny electrical currents exist due to the chemical reactions that occur as part of the normal functions, even in the absence of external electric fields). There will also be responses to changes in the environment (e.g temperature and external magnetic fields).  

For example redox doping could increase the conductivity of a material – and in biology such redox doping could be provided by the biological redox state – including the redox state of cysteine residues.  It might also be the case, that in certain conditions, there could be a transition to superconducting (e.g  E H Halpern 1972.

‘RADICAL PAIRS’ MECHANISMS IN MAGNETORECEPTION AND PHOTOSYNTHESIS

In chemical reactions involving transient radical pairs (singlet and triplet states), quantum effects are proposed to induce a sensitivity to the intensity and/or orientation of external magnetic fields. The governing principle of these phenomena is the magnetic field dependent interconversion between quantum-coherent and often entangled states of electronic spin pairs.

When activated by light, it is theorised that cryptochromes undergo a redox cycle, in the course of which radical pairs are generated during photo-reduction as well as during light-independent re-oxidation. 

In biology a ‘radical pair’ is a short-lived reaction intermediate comprising 2 radicals formed in tandem whose unpaired electron spins may be either antiparallel (↑↓, a singlet state, S) or parallel (↑↑, a triplet state, T). C T Rogers 2008.  It is proposed that in magnetoreception the absorption of a photon raises a receptor molecule into an excited state and leads to a light-activated electron transfer from a donor to an acceptor, thus generating a spin-correlated pair. By interconversion, singlet states radical pairs with an antiparallel spin are transformed into triplet states with parallel spin and vice versa. The singlet/triplet ratio depends on, among other factors, the alignment of the receptor molecule in the external magnetic field and could thus mediate information on magnetic direction. R Wiltschko 2014. 

A well-studied precedent for magnetically sensitive radical pair chemistry is provided by the initial charge separation steps of bacterial photosynthetic energy conversion, which proceed via a series of radical ion pairs formed by sequential electron transfers along a chain of immobilized chlorophyll and quinone cofactors in a reaction center protein complex. Provided subsequent forward electron transfer is blocked, the recombination of the primary radical pair responds to magnetic fields in excess of ≈1 mT. In unblocked reaction centers, spin correlation can be transferred along the electron transport chain from the primary to the secondary radical pair, whose lifetime is also magnetically sensitive. Similar effects occur in plant photosystems. C T Rogers 2008. 

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Good Timing: The Synchronisation of Neural Networks in Computing and Implications for Neurology

A symbiotic relationship now exists between the study of neural networking in computing, and neurology.  Artificial neural networks were originally inspired by neuroscience, although major developments have been guided by insights into the mathematics of efficient optimization, rather than neuroscientific findings.  A H Marblestone 2016.  Now neurology is looking towards the development of neural networks to increase our understanding of how the brain works.  There is the possibility that  the two fields will increasingly merge – with particular recognition of the importance of bio-physics in the study of intelligence.

For a long time, the accepted model of memory formation was linear. Short term memories were thought to directly transform into long term memory in a classical, mechanistic fashion. But this model has been challenged.

The new model emerging is complex and non-linear.  The brain is starting to be seen as ‘more than the sum of its parts’ – analogous to a parallel computer (with many interconnected networks), artificial neural networks/deep learning, or a ‘network of networks (such as the Internet), with all the problems (cascading failures) and solutions (built in redundancy) that are associated with such a model.

Modern neuroscience is going through a renaissance of its own – moving away from mechanistic views of the brain, to focus on connectivity.  It recognises some networks may be particularly important for such connectivity e.g the default mode network – which is effected in various neurological conditions such as Alzheimer’s, as well as altered states of consciousness such as meditation and psychedelic drug use.
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Biological Clocks and Ageing

Intraterrestrial life extends down at least 5 km and animals are found even in the deepest oceans. The biosphere is, therefore, dominated by dark, largely “arrhythmic” habitats, and in terms of biomass, most of life on earth resides in places isolated from the direct effects of the sun…studies of species that live away from the sun […]

Multi-model Oscillation Based Connectivity Theory Applied to the Integration of Bio-Sensory Data

1. Global Clock Synchronisation 

In computing many emerging sensor network applications require that the sensors in the network agree on the time. A global clock in a sensor system will help process and analyze the data correctly and predict future system behavior. For example, in the vehicle tracking application, each sensor may know the time when a vehicle is approaching. By matching the sensor location and sensing time, the sensor system may predict the vehicle moving direction and speed. Without a global agreement on time, the data from different sensors cannot be matched up. Other applications that need global clock synchronization include environment monitoring (for example, temperature), navigation guidance, and any other application that requires the coordination of locally sensed data and mobility.  Q Li 2004.

In these systems various approaches have been taken to temperature compensation  e.g Q Li 2004. S Chauhan 2012.   J M Castillo-Secilla 2013. 

A similar approach could potentially be taken to synchronising biosensors. A Prindle 2015T Danino 2009. J Hasty 2008,  J V Selinger 2003,

This posting considers whether a similar mechanism to global clock sychronisation could be connecting together biological sensors (using  the Transient Receptor Potential (TRP) superfamily of ion channels), and supporting temperature compensation.

Another posting on this site explores how this could also support the operational of neural networks. Read More…

Applying Universality to Systems Biology

Over recent years, the field of “systems biology” has been emerging.  It is throwing light on areas that have long been a mystery.  There are also vast back catalogues of biological research that need to be reviewed from the perspective of systems biology. Read More…

Biological Clocks, Reaction-Diffusion, Self Organisation and Quantum Biology

1.Introduction

New states can arise from far from equilibrium, possessing an extraordinary degree of order, whereby trillions of molecules coordinate their actions in space and time. Under certain circumstances, entropy producing processes are able to organise themselves in the presence of noise, in a way that so called dissipative structures are formed (Prigogine and Lefever 1975, and Nicolis and Prigogine 1977).  G Bodifee 1986.

Dissipation-driven adaptation has already been explored by a number of well known scientists i.e I Progogine, R Lefever and G Nicolis 1975, M Eigen 1971.  J England 2013, 2014, 2015.

This post seeks to describe a self organising dissipative system which supports biomass/information processing.

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Superconductivity and the Self Organisation of the Universe

Emergence

New states can arise from far from equilibrium, possessing an extraordinary degree of order, whereby trillions of molecules coordinate their actions in space and time.  Prigogine coined the term “dissipative structures” to describe them, since they result from the exchange of matter and energy between system and environment, together with the production of entropy (dissipation) by the system.  The complex and mutually dependent processes leading to the formation of structures, collectively called “self organisation”…in such a universe, irreversible non-equilibrium thermodynamics allows for the possibility of self organisation leading to structures ranging from planets and galaxies to cells and organisations.  R Highfield and P Coveney 2015.

According to Masser (2006), it would be appropriate to represent the Big Bang not as a single event, but as an on going process of gradual formation out of chaos.  In other words the evolution of the universe is a continuous self organisation process that has led to its currently observed structure with a host of galaxies, galaxy clusters and planetary systems.

In some materials, the strong electron-electron correlations to other degrees of freedom with the complex many body quantum system lead to new, emergent properties that are controlled by a competition of fluctuation effects, characterised by phase transitions at critical temperature, where correlations lead to coordination with a macroscopic region – resulting in the breaking of a symmetry of the system.

Below the transition temperature, a new broken-symmetry ground state is found, which can possess a variety of novel, emergent properties that are macroscopically observed.  In condensed-matter physics, the complex interaction of many degrees of freedom, such as electrons, ions and spins leads to the formation of properties such as superconductivity, magnetism, charge density waves and orbitally ordered states.

Phase transitions can have a wide variety of important implications including the formation of topological defects , or it may even trigger a period of exponential expansion.

In current physics, from a theoretical perspective, insights from black hole physics and string theory indicate that our ‘macroscopic’ notions of spacetime and gravity are emergent from an underlying microscopic description in which they have no a priori meaning. Read More…

Reaction Diffusion and Self Organisation of the Brain

INTRODUCTION

Interactions between biochemical and mechanobiological activity and feedback loops

It is proposed that the formation and workings of the brain are influenced by an interplay between oscillatory biochemical (reaction-diffusion) and mechanobiological activity (including in response to external stresses), feedback loops, and stochastic resonance.

This relationship between biochemistry and mechanobiology has already been explored in other areas of science.  Waves in the BZ reaction in gels cause deformation, which in turn affects the spiral wave dynamics. Furthermore, a ‘‘chain reaction’’ of spiral wave births and deaths can result from an externally controlled deformation of a medium A. V. Panfilov 2005.  A Adamatsky (2010) describes a propagating excitation wave front inducing an associated mechanical wave of contraction.  Oscillatory dynamics have been found in organs e.g deformation can create spiral waves, and this has been explored in cardiac dynamics. Louis D. Weise et al 2011A. V. Panfilov 2005.

These types of interactions in biology can resemble “chicken or an egg” relationships, as a simple chain of cause and effect is not apparent.  In this paper, it is suggested that this relationship is taking place within a dissipative clock system linking circadian rhythms and cell cycles/oscillations and redox/the metabolism and using positive and negative feedback.  Circadian clocks do not operate in isolation, but rather are mutually dependent upon intrinsically rhythmic cytosolic signals (cAMP, Ca2+, kinases) such as that the cell as a whole has a resonant structure tuned to 24 hour operations. (Hastings et al 2008 in C Colwell 2015).

A fuller range of biological rhythms are explored by Goldbeter 2007.

Biological Rhythms –  (Goldbeter 2007). Period
Neural rhythms 0.001 s to 10 s
Cardiac rhythms 1 s
Calcium Oscillations Sec to min
Biochemical oscillations 30 s to 20 min
Miotic Oscillator 10 min to 24 h
Hormonal rhythms 10 min to 3-5 h (24 h)
Circadian rhythms 24 h
Ovarian cycle 28 days (human)
Annual Rhythms 1 year
Rhythm in ecology and epidemiology years
Segmentation Clock 90 mins
Biological Regulations Examples of Associated Cellular Rhythms
Ion Channel Neural and Cardiac rhythms
Transport Ca2+ oscillations
Gene expression Circadian rhythms, segmentation clock.

Under certain circumstances, entropy producing processes are able to organise themselves in the presence of noise, in a way that so called dissipative structures are formed (Prigogine and Lefever 1975, and Nicolis and Prigogine 1977).  Necessary conditions for the occurance of dissipative structure are that the system is open , that it is in a state far from equilibrium and that non linear processes occur within the system.  In these  conditions, internal small fluctuations may be amplified non linearly by a flow of mass and energy from the surroundings.  The system is then removed irreversibly from its initial state, in particular from any homogeneous or unorganised state that is characteristic for equilibrium conditions.  Therefore the new state is characterised by a more organised internal distribution of matter, energy and process rates.  G Bodifee 1986Goldbeter 2007.

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Quantum Consciousness Supported by Semiconduction and Superconduction

COULD CONSCIOUSNESS DRAW ON BIOLOGICAL MATERIALS WHICH ACT AS ORGANIC SEMICONDUCTORS AND/OR SUPERCONDUCTORS?

Manifestations of quantum coherence can be found in different solid state systems including semiconductor confined magnetic systems, crystals and superconductors.

PJ  Hore (2016) has pointed out that 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. 

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. Eukaryotic riboflavin-binding proteins typically bind riboflavin between the aromatic residues of mostly tryptophan- and tyrosine-built triads of stacked aromatic rings…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, including in flavins, with suggestions that a redox doping type mechanism may be in operation (also see Orf 2015 and 2016 

These ideas are further explored in another posting – click here to find out more.  This includes evidence of solid state photo-CIDNP and its involvement in ultra-fast electron transfer, singlet and triplet states and quantum coherence within biology (and therefore at high temperatures).

IS THERE EVIDENCE OF MAGNETORECEPTION AND THE PHOTO CIDNP EFFECT IN HUMANS?

J Kirschvink (Caltech) claims to have found evidence of magnetoreception in human beings (June 2016).

He has used a Faraday cage to demonstrate that human brains can be influenced by magnetic fields.  When the magnetic field is rotating counterclockwise, there’s a drop in participants’ alpha waves. The suppression of α waves, in the EEG world, is associated with brain processing: a set of neurons were firing in response to the magnetic field, the only changing variable.

Kirschvink’s experiments found that when magnetic field is rotating counterclockwise, there’s a drop in participants’ alpha waves.  Existing research suggests there is a mutual relationship between gamma and alpha oscillations in the visual cortex.  K Hepp (ed P Blanchard and J Frohlich 2015).

Currently the sample size is very small (24 participants) and the results need to be peer reviewed for publishing, but it will be interesting to see further information on this in the future.

The mechanism behind such magnetoreception is unknown, however recently it has been found that a polymer-like protein, dubbed MagR (Drosophila CG8198)  forms a complex with a photosensitive protein called Cryptochrome (Cry).  The MagR/Cry protein complex, the researchers found, has a permanent magnetic moment, which means that it spontaneously aligns in the direction of external magnetic fields. This is the only known protein complex that has a permanent magnetic moment. Cry likely regulates the magnetic moment of the rod-shaped complex, while the iron-sulfur clusters in the MagR protein are probably what give rise to the permanent magnetic polarity of the structure. S Qin – ‎2016.

In transgenic C Elegans, expressing this magnetoreceptor 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. It was also found that the magnetoreceptor could evoke membrane depolrisation and action potentials, generate calcium influx, and trigger neuronal activity in both HEK-293 cells and cultured primary hippocampal neurons when activated by a remote magnetic field. The magnetogenetic control of neuronal activity could be dependent on the direction of the magnetic field and exhibits on-response and off-response patterns for external magnetic fields applied. The group also screened other species’ genomes and showed variants of both proteins were highly conserved across several animals, including pigeons, monarch butterflies, whales and even humans. X Long 2016

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 such findings have been contradicted in other studies.   H Kabuto et al 2001 demonstrated that no ROS generation nor lipid peroxidation could be detected in brain homogenates of exposed mice. Interestingly, they observed a slight decrease in oxidative damage in mice exposed to static field (2–4 mT). S R Balind 2014  also found extremely low frequency magnetic field (50 Hz, 0.5 mT) reduces oxidative stress in the brains of gerbils.  ELF-EMF exposure, in the form of transcranial magnetic stimulation (60-Hz, 0.7 mT) applied to rats for 2 hr twice daily, can prove neuroprotective. Extremely low-frequency EMF can mitigate oxidative damage, elevate neurotrophic protein levels in brain and ameliorate behavioral deficits in rats (I Tunez 2006, I Tasset 2010 and 2013 found that EMFs activated the antioxidant pathway Nrf2 in a Huntington’s disease-like rat mode), Extremely low-frequency electromagnetic fields land   as well as potentially augment neurogenesis. Such studies reiterate that the level and timing of exposure are critical factors impacting outcome measures. M Reale 2014.  

A V Chervakov 2015 has recently explored possible mechanisms underlying the therapeutic effects of transcranial magnetic stimulation. Read More…