1. Quantum mechanical effects have been demonstrated in photosynthesis

Recent experiments on photosynthetic ‘Light Harvesting Complexes’ (LHC) and their constituents (e.g., the Fenna–Matthews–Olson (FMO) pigment-protein complex in green sulfur bacteria) have suggested that quantum coherence may play a role in one of the most fundamental and important of biological processes: energy transport and energy conversion. N Lambert – ‎2012. 

Evidence suggests a wavelike characteristic can explain the extreme efficiency of the energy transfer because it enables the system to simultaneously sample all the potential energy pathways and choose the most efficient one. This evidence includes detection of “quantum beating” signals, coherent electronic oscillations in both donor and acceptor molecules, generated by light-induced energy excitations.

There have also been indications of long-lived quantum coherence in the purple bacterium Rhodobacter sphaeroides pigment protein complex. H Lee 2007P Rebentrost. 2009Xian-Ting Liang 2010.  And quantum beats have been found in various photosynthetic systems LHC2 (in bacteria, spinach and potentially other plant photosystems), and the photosystem of a group of aquatic algae called cryptophytes. S Harrop 2014. 

A radical pairs mechanism has been found to operate in photosynthetic reaction centres.  The initial charge separation steps of bacterial photosynthetic energy conversion proceed via a series of radical ion pairs formed by sequential electron transfers along a chain of immobilised chlorophyll and quinone cofactors in a reaction centre protein complex.  Provided subsequent forward electron transfer is blocked, the recombination of the primary radical pair responses to magnetic fields in excess of ≈1 mT.  In unblocked reaction centres, 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 effect occur in plant photosystems. C T Rogers and P J Hore 2008.

During charge separation in photosynthetic reaction centres, 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 thought to involve radical pair mechanisms. 

A ‘solid-state photo-CIDNP effect’ has been observed in (J Matysik 2009)

Interestingly a magnetic-field effect has also been demonstrated on the photochemical yield of:

  • A flavin-tryptophan radical pair in Escherichia coli photolyase. K B Henbest 2008.
  • A mutant of the bluelight photoreceptor phototropin (LOV1-C57S from Chlamydomonas reinhardtii). S S Themarath 2010.
  • In the same way that photo-CIDNP MAS NMR has provided detailed insights into photosynthetic electron transport in Reaction Centres, it is anticipated in a variety of applications in mechanistic studies of other photoactive proteins. It may be possible to characterize the photoinduced electron transfer process in cryptochrome in detail. W Xiao-Jie12016.

It has been noted there seems to be a link between the conditions of occurrence of photo-CIDNP in RCs and the conditions of the unsurpassed efficient light-induced electron transfer in RCs. 

It has been pointed out that both the solid-state photo-CIDNP effect and the efficient light-induced electron transfer (ET) require optimized overlap of the wavefunctions (Jeschke and Matysik 2003) corresponding to moderate electron–electron coupling parameters… A clear picture of the required architecture of orbitals, however, is still missing. Such concept of overlapping static orbitals of the cofactors would be sufficient for the microscopic description of both the ET and the coherent origin of the solid-state photo-CIDNP effect. On the other hand, understanding of both processes on the protein level would allow for including the dynamic role of energy dissipation and entropy production in the transfer of electrons and polarization. It is possible that both ET and the solid-state photo-CIDNP effect require optimized dissipation channels J Matysik 2009. Efficiency of electron transfer and the general observability of the solid state photo CIDNP effect have one common feature: the short life time of the radical pair which reflects an optimised reaction channel avoiding side reactions as well as leading to broadening of the excitation held curve of the effect. I F Cespedes-Camacho and J Matysik 2014.  In various studies, it has been demonstrated that up to three mechanisms are involved to build up photo-CIDNP under continuous illumination, which may run in parallel. J Matysik 2009

Energy transfer and trapping in the light harvesting antennae of purple photosynthetic bacteria is an ultrafast process, which occurs with a quantum efficiency close to unity.  M Ferretti 2016Rienk van Grondelle has suggested that during photosynthesis, plants use electronic coherence for ultrafast energy and electron transfer and have selected specific vibrations to sustain those coherences. In this way photosynthetic energy transfer and charge separation have achieved their amazing efficiency. At the same time these same interactions are used to photoprotect the system against unwanted byproducts of light harvesting and charge separation at high light intensities.

Until recently solid-state photo-CIDNP effect has required high magnetic fields and cyclic electron transfer, which is reached, for example in RCs of Rb. sphaeroides by reduction or removal of the quinones.

But it has also been speculated that solid-state photo CIDNP effect at earth field plays a role in the magnetoreception of biological systems….Studies have found that the ‘solid-state photo-CIDNP’ effect allows for signal enhancement of factors of several 10000 s. Such strong signal enhancement allows for example selectively observing photosynthetic cofactors forming radical-pairs at nanomolar concentrations in membranes, cells, and even in entire plants. W Xiao-Jie12016.  Also see G Jeskchke 2011.  

Previously it had been proposed that such effects were a quantum zeno effect. E Daviso 2009A T Dellis and I K Kominis, 2009 A.T. Dellis, I.K. Kominis 2011,I K Kominis 2013,  R J. Usselman 2014, and M Goodman 2010. And perhaps this effect can be seen as analogous to the quantum zeno effect.

And beyond ultrafast charge separation in photosynthesis, there are similar dynamics in bond isomerization in sensory photoreceptors and repairing DNA damage.  It should be noted that in the DNA repair enzyme photolyase, it has been found that maximum efficiency was not enhanced by the ultrafast photoinduced process but by the synergistic optimisation of all steps in the complex repair reaction. C Tan 2015.

A Role for Cysteine Residues in Ultra-Fast Electron Transfer

In  order to understand reactive oxygen species ROS) regulation of signaling pathways it is necessary to understand the mechanism of how ROS alters protein function. The oxidative interface consists mainly of the redox regulation of redox-reactive cysteine residues on proteins by ROS. Findings indicate that the cysteine residues exposed on the surface of proteins are the dominant intracellular thiol and that they may play an important role in intracellular antioxidant defences. R Requejo 2010.  By specific and reversible oxidation of redox-sensitive cysteines, many biological processes sense and respond to signals from the intracellular redox environment. Redox signals are therefore important regulators of cellular homeostasis.  Oxidative modifications result in changes in structure and/or function of the protein.  P D Ray 2012.

It has been proposed that the side chains of tyrosine and cysteine residues can act as the relay stones of electron transfer in proteins.  The driving forces come from the loss of the active protons (protons link the ring oxygen of the tyrosine and the sulphur of the cysteine) in the appropriate protein environments, which lowers the reduction potentials of these two residues.  An example is the long distance electron transfer of the class I ribonucleotide reductase, involving four tyrosines and a cysteine residue. Additionally, the Giese Group, examined electron transfer along a series of polypeptides and demonstrated that the existence of central aromatic acids can serve as stepping stones to support the electron hopping mechanism. W Sun 2016.

And it has been reported that the side chains of tryptophan residue can speed up electron transfer rates as relay intermediates of long range electron transfer processes in many enzymes including DNA photolyases, where three Trp residues can form an electron transfer wire to facilitate electron hopping. W Sun 2016.  In the complex 1 of the respiratory chain on the inner membrane of the mitrochrondria, electrons are transferred over a cascade of iron-sulphur clusters from a Flavin adenine mononucleotide cofactor to a quinone binding set.  The overall pathway is nearly 10nm long and most likely to involve aromatic amino-acid residues as stepping stones to bridge the gaps between the iron-sulphur clusters.

It is interesting to note that extended electron-transfer in animal cryptochromes in mediated by a tetrad of aromatic amino acids.  D Nohr 2016.  Some photoreactive proteins, including those responsive to UV light, utilize characteristic aligned tryptophan residues for electron transfer.  Very fast photo electron transfer (PET) is feasible along the conserved linear tryptophan pathway found in the flavoproteins of the photolyase/cryptochrome family, including Arabidopsis UVR2 and UVR3…starting from the singly reduced (semiquinod) state of FAD, the overall photoreduction process is completed within 30ps, as has been shown by time-resolved optical absorption spectroscopy in E Coli DNA photolyase.  Dr T Biskup 2011.

For FAD in the fully oxidized state, PET generates a sequence of radical pair species. And in flavo-proteins (mutated in order to remove a cysteine residue next to the chromophore), it is possible to form a spin-correlated radical pair. Such radical pairs recombine, generally speaking, from both singlet and triplet states, giving rise to strong solid state-CIDNP. Because of the rigid environment, molecular mobility is strongly restricted; therefore, anisotropic spin interactions come into play and affect the evolution of the radical pairs… Presently, flavoproteins represent the only system, where both liquid state-CIDNP and solid state-CIDNP have been observed (even then, for slightly different flavoproteins).  Denis V. Sosnovsky.  2016.

Commonalities among flavin-based photo and redox receptors could reflect evolutionary relationships among them.  In the canonical LOV photocycle, a Flavin excited triplet state reacts with the thiol group of a conserved cysteine residue.  Bond formation likely proceeds via a redox process as supported by detection of a transient Flavin neutral semiquinone (NSQ) in C reinhardti phot1 LOV1, by indirect arguments from magnetic resonance experiments and by the general efficacy of Flavin photoreduction in the cysteine-devoid variants. Thus the NSQ is a likely intermediate in generating the adduct.  The BAT-LOV P1988C variant demonstrates that cysteines at the adduct forming position is an effective electron donor to the photo excited Flavin.  LOV signalling through the NSQ state has parallels to signal transduction in other flavin based photoreceptors including cryptochromes and BLUF.  There is strong evidence that the signalling state of cryptochrome involves reduction of the FAD to either NSQ or anionic semiquinone states.  A NSQ state may be populated transiently during the photocycle of a radical pair intermediate between the Flavin and a conserved Try. . E F Yee 2015.  Also see A Hense 2014.   A Czarna2013. R J Kutta 2015 for the role of cysteine residues in the generation of radical pairs in various flavoproteins.

Orf et al 2016 has recently demonstrated that an operative photoprotection mechanism exists in green sulfur bacteria and that this mechanism is activated by oxidation of two cysteine residues.  This new photoprotection mechanism identified by differs from more familiar motifs; the new mechanism employs amino acid residues instead of isomerization of dedicated photoprotective chromophores, such as carotenoids. It also seems to protect against damage from a single excitation (rather than multiple excitations). That is, the mechanism depends on redox potential, not light intensity….The system undergoes intersystem crossing into the triplet state after ~25% of excitations, and the lifetime of the triplet state is between 10-100 μs. The redox-sensitive cysteine residues in the protein,  modulate their redox state between free thiol and thiyl radical form to quench BChl excitations, probably via an electron transfer/ultrafast recombination mechanismOrf 2015.

2. How Might this Effect Arise: Environmentally Assisted Quantum Transport (ENAQT)

Several recent papers have suggested that optimally efficient networks are not purely quantum, but are assisted by some interaction with a ‘noisy’ classical environment. Y Li 2014. An overview of this approach is given in http://qubit-ulm.com/quantum-effects-in-biology/.

An important aspect of biological environments are vibrations which originate from proteins and embedded molecules. At specific frequencies this vibrational motion can be long-lived and interact in highly non-trivial fashion with electronic motion which could give rise to fast transport, molecular recognition or long-lived quantum coherence in biological systems.

Following this approach, if the oscillations of the exciton and the oscillations of the surrounding proteins are the same then when coherence gets knocked out of tune by white noise, it can be knocked back into tune by the protein oscillations….there would be a need to tune surrounding molecular white noise so that it would nudge the off-beat electrons into the same beat, but not too vigorously, or they would be knocked into different rhythms and coherence would be lost. Jim Al-Khalili, ‎- 2014.

It has also been proposed that the magnetoreception of organisms is caused by, or employs, the stochastic resonance mechanism. The effectiveness of detection of weak MF signals can be immproved through the action of noise factors. Vladimir N. Binhi – 2002. Stochastic resonance might help enable biological cells to respond to weak 50-60-Hz electromagnetic fields, far below the thermal noise level.  M. I. Dykman 1998.

It is known that circadian rhythms resulting from the transcription translation feedback loop  are not necessary for magnetoreception in cockroaches (O Bazalova 2016) or drosophila (R Gegear 2008).

The circadian clock of wild-type D. melanogaster is slowed (longer tau) in constant magnetic fields, in a dose dependent manner, but only in blue light and with a functional cry gene. Interestingly, cry-dependent magnetosensitivity does not require a functioning circadian clock, but it does require a functional cry gene.  cry’s functional requirement for blue light (<420nm) in phase shifting circadian clocks and in altering spatial orientation and taxis in several species relative to gravity, magnetic fields, solar, lunar, and celestial radiation  makes it the most interesting of the genes currently associated with both biological clocks and geotaxis.  D L Clayton 2016.

Also, as in the case of peroxiredoxin, flavoproteins such as cryptochrome in redox state may be exhibiting a circadian oscillation with a period of about 24 hours. Peroxiredoxin proteins may not be unique in their ability to undergo redox oscillations since many other proteins are susceptible to oxidation of their cysteine residues by peroxide.  S Ray 2016.

This may also involve interaction with an iron sulphur cluster.  One way to increase the strength of geomagnetic field effects in to use materials with a strong magnetic moment, such as iron oxides.  In the proper geometry, iron oxide clusters can behave like a compass need and magnetic bacteria can use such a compass needle mechanism to find up and down (T Ritz 2010).  Cysteine residues associated with iron sulphur clusters could also support a photochemical form of magnetoreception.  This may help explain the exhibiting of spontaneous alignment in magnetic fields (including that of Earth) of a newly discovered magnetosensing complex which has the attributes of both cryptochrome and iron based systems.

A Goldbeter 2007 sets out the sheer diversity of biorhythms. Much as spatial structures arise in chemical systems beyond a critical point of instability with respect to diffusion, biological rhythms correspond to a temporal organisation that appear beyond a critical point of instability of a non-equilibrium steady state. These type of non equilibrium dissipative structures can only be maintained by the energy dissipation associated with the exchange of matter between the chemical system and its environment. Sustained oscillations of the limit cycle type can thus be viewed as temporal dissipative structures…The onset of sustained oscillations generally corresponds to a passage through a Hopf bifurcation point. Before this point, the system displays damped oscillations and eventually realises the steady state, which is a bistable focus. Beyond the birfurcation point, a stable solution arises in the form of a small amplitude limit cycle surrounding the unstable steady state…sometimes a mix of positive and negative feedback can produce a relaxation oscillation based on bistability and when coupled to the negative feedback loop, this results in repetitive cycles of hysteresis.

Unlike ordinary chemical oscillators, the dichotomic molecular noise of gene state switching in gene oscillators affects the stochastic dephasing in a way that may not always be captured by phenomenological limit cycle-based models. D A Potoyan 2014.

  1. Circadian Rhythms and the Redox Link

Circadian Rhythms are Emerging as Central to All Aspects of Photosynthesis.

Evidence suggests that circadian clocks control a number of biological processes through an organism. ….. recent advances demonstrate that interactions occur between the circadian clocks of cells of individual tissues, different tissues, and different organs. AN Dodd – ‎2015. Whole-transcriptome analyses have established that the plant circadian clock regulates virtually every plant biological process.  C. Robertson McClung 2010.  Overall it has been found that plant circadian clocks increase photosynthesis, growth, survival, and competitive advantage. A N Dodd 2005. To this day, circadian clocks remain one of the most robust experimental systems wherein perturbations of genetic background or environmental state can be directly linked to changes in physiology and behaviour. Lisa Wulund 2015.

Rhythmic environmental cues create a periodic life-strategy that starts from oscillations in metabolism, primarily photosynthesis. Light absorption during the warm day leads to carbon fixation. The assembly of carbon thus occurs in the context of an assault on biological molecules from irradiation. The clock functions to prime resistance to the oxidation reactions that occur during light harvesting. As the day warms, the clock controls abscisic acid signalling and stomatal aperture to maximise water-use efficiency from the molecular to the whole-leaf level. Towards the end of the light period, a plant can expect a cooler night and the depletion of starch depots and consumption of soluble carbohydrates, which are timed by the clock. These are coincident processes with a preparation for a cold-stress response. Added to these issues of rhythmic carbon metabolism and abiotic stress actions, other aspects of plant nutrition are under clock control, including nitrogen metabolism and mineral nutrition. A relationship between root uptake of required elements is associated with a reciprocal connection of the clocks in the leaf and the root. Such a connection is associated with a homeostatic relationship of tissues, which work in source-sink connections to drive growth in a turgor and hormonally driven fashion. Water trafficking through aquaporins and cell division and elongation intervals are thus also clock-controlled processes. A variety of hormonal pathways driving growth, including gibberellins, brassinosteroids, auxins and jasmonates are markedly under direct clock control. Many of these hormones also function in disease resistance, and as microbial and herbivore pathogens are themselves often clock-controlled, it is perhaps not surprising that much of disease-resistance signalling is also a diurnally-driven reaction coordinated by the circadian clock. Together, the molecular oscillator sets a prevalent transcriptional landscape that potentiates homeostasis from the cellular to the whole-plant level. In this a coordination of rhythmic metabolism overlays plant nutrition and stress resistance to biotic and abiotic cues. Frontiers.  It seems that the interlocking of circadian regulation with carbohydrate biochemistry in terms of photosynthesis, starch accumulation and feedback to the circadian clock maximizes the efficiency of the capture and utilization of solar energy by plants. A N. Dodd 2014,AN Dodd – ‎2015 and Maria L. Guerriero et al 2014.

Cryptochromes appear to mediate blue light induction of changes in gene expression via both the transcriptional and post transcriptional mechanisms. Cryptochromes mediate blue light induction of nuclear genes that encode plastid proteins required not only for photosynthesis and other functions of plastids, such as chlorophyll a/b binding, but also for components of the plastid transcription apparatus. (Loredana Lopez 2013). Expression of the light-harvesting complex protein genes (Lhc) is under the control of a circadian clock. B Piechulla 1998. CryB in Rhodobacter sphaeroides has been shown to undergo a photocycle – it does not only affect gene expression in response to blue light illumination but also in response to singlet oxygen stress condition. Geisselbrecht – ‎2012Hendrischk et 2009.  S Metz 2012.

In analyzing the photosynthesis CR of Gonyaulax. It was found that the supramolecular organization of the pigment-protein-complexes changes periodically. These organisms provide a demonstration of the power of membranes to generate circadian rhythmicity (possibly together with a cytoplasmic protein). T. Vanden Driessche 1996.

Beyond the known redox regulation of phosphorylation of the D1 photosystem II reaction center protein, the overriding control is exerted by an internal, circadian clock. Diurnal rhythm of D1 phosphorylation follows parameters that are fundamental to circadian rhythms i.e. it has a 24-h periodicity and can be entrained..It is possible that circadian oscillations in D1 phosphorylation are part of a regulatory system controlling the operation of the photosynthetic apparatus, as well as a signal to alter the metabolism of the D1 protein. I S. Booij-James 2002.

Rubisco Activase and chlorophyll a/b binding protein of photosystem H (Cab) are also known to exhibit a circadian rhythm (S Martino-Catt 1992, B Watillon 1993, M L pilgrim 1993) although these do not result in any detectable oscillation at protein level.

Dissipation of excess excitation energy in the light harvesting antenna of Photosystem II (PSII) givesphotosynthetic organisms an evolutionary advantage by reducing damage in fluctuating light conditions.  The details of quenching process are not well understood, but Effective quantum yield (ΔF/F′) and non-photochemical quenching have been found to vary with circadian rhythms.  A McMinn 2013.

Models of Circadian Clocks

Circadian clocks exhibit stochastic noise due to the low copy numbers of clock genes and the consequent cell-to-cell variation: this intrinsic noise plays a major role in circadian clocks by inducing more robust oscillatory behavior. The importance of stochasticity in genetic networks is well known, and arises from the fact that the molecules involved are generally present in very low concentrations. This kind of stochasticity, referred to as intrinsic noise, has been observed in circadian clock networks of animal, plant, and fungal species, and has been shown to increase the robustness of oscillations in the concentrations of network components.  Maria L. Guerriero et al 2014.

It has been argued that the collective rhythmcity of circadian clocks may be best obtained by studying it at its outset,that is treating it as a kind of phase transition or bifurcation or self-synchronization transition (Y Kuramoto 1984). Working within the framework of a mean-field model, Winfree discovered that such oscillator populations can exhibit a remarkable cooperative phenomenon. As the variance of the frequencies is reduced, the oscillators remain incoherent, each running near its natural frequency, until a certain threshold is crossed. Then the oscillators begin to synchronize spontaneously… Winfree pointed out that this phenomenon is strikingly reminiscent of a thermodynamic phase transition, but the oscillators align in time, not space. In addition, biological clocks can be stopped by relatively mild perturbations – with a stimulus of appropriate timing and duration can drive the clock to a “phase singularity,” – a point at which phase is ambiguous and near which phase takes on all values.  S Strogatz 2016. Other explanations for this effect (an unstable steady state) have also been put forward.

Many mathematical models have been proposed to understand the molecular regulatory mechanisms that account for circadian dynamic properties including temperature compensation, entrainmment by light dark cycles, phase shifts by light pulses, rhythm splitting, robustness to molecular noise, and intercellular synchronisation. …It has been proposed that the circadian system needs to integrate interlocked feedback loops, inter-cellular coupling and stochasiticity). D Gonze 2011.  Circadian rhythms can be mathematically modeled by reaction and reaction-diffusion systems e.g T Vejchodsky 2013, J Eliaš – ‎2014A Zakharov 2014T Hinze 2011. and potentially be described by limit cycles/periodic orbits. e.g D. Gonze 2015T Hinohara 2007.  The fact that the circadian network relies on multiple interlocked feedback loops allows the generation of complex dynamic behaviours such as chaotic oscillations. This kind of irregular behaviour is often considered as pathologic. There are however theoritical analyses which show that such behaviour may provide the system with advantages, namely in the adaptation of the oscillator to various conditions, by selecting an appropriate circadian period. D Gonze 2011.  Also see Y Suzuki 2016, J C Leloup and A Goldbeter 1999.

Redox and Photosynthesis

Photosynthesis functions as a sensor for light signals, and the redox state of photosynthetic electron transport components and redox-active soluble molecules act as regulating parameters. This provides a feedback response loop in which the expression of photosynthesis genes is coupled to the function of the photosynthetic process, and highlights the dual role of photosynthesis in energy fixation and the reception of environmental information. T Pfannschmidt 2003.

Environmental stresses, such as rapid and dynamic changes in light intensity and quality, temperature, relative humidity, water and CO2 availability, cause excess absorption of light energy (EEE) and induce chlorophyll fluorescence and heat dissipation, which lead to the generation of singlet stages of dioxygen, chlorophyll and carotenoid molecules. These primary quantum events in photosynthesis induce secondary redox reactions in photosystems, e.g. electrical charge separation, chloroplast lumen acidification and activation of the xanthophyll cycle by means of non-photochemical quenching (NPQ), redox reactions between the photosynthetic electron carriers (electron transport), and formation of reactive oxygen species. These, in turn, induce cascades of physiologically regulated redox reactions in the chloroplast stroma metabolism. S Karpiński 2012.

All photosynthetic RCs, regardless of their source, use light energy to create a charge-seperated state by moving electrons along a chain of carriers away from the oxidized P+, which is ultimately reduced by a neighbouring electron donor rather than by a back reaction. The use of multiple cofactors seperated by <14-15 Å ensures that electron tunnelling is a much more efficient mechanism of transfer than is catalytic turnover. The protein matrix arranges the redox co-factors along the desired transfer pathway, with specific positions, orientations, and turned redox potentials in order to induce directional electron transfer and avoid charge recombination. The result is a charge-seperated state in which the oxidized and reduced cofactors are located on opposite sides of the protein…. How the protein environment controls the redox properties of the cofactors is fundamental to the understanding of ET. R Razeghiford and T J Wydrzynski 2005.

Cellular ROS sensing and metabolism are tightly regulated by a variety of proteins involved in the redox (reduction/oxidation) mechanism. Molecular mechanisms through which ROS directly interact with critical signaling molecules to initiate signaling in a broad variety of cellular processes include proliferation and survival (MAP kinases, PI3 kinase, PTEN, and protein tyrosine phosphatases), ROS homeostasis and antioxidant gene regulation (thioredoxin, peroxiredoxin, Ref-1, and Nrf-2), mitochondrial oxidative stress, apoptosis, and aging (p66Shc), iron homeostasis through iron–sulfur cluster proteins (IRE–IRP), and ATM-regulated DNA damage response…in order to understand ROS regulation of signaling pathways it is necessary to understand the mechanism of how ROS alters protein function. The oxidative interface consists mainly of the redox regulation of redox-reactive cysteine residues on proteins by ROS. Oxidation of these residues forms reactive sulfenic acid that can form disulfide bonds with nearby cysteines or undergo further oxidation to sulfinic or sulfonic  acid; if nearby nitrogen is available sulfenic acid may also form a sulfenamide. These oxidative modifications result in changes in structure and/or function of the protein. With the exception of sulfonic acid, and to a lesser degree sulfinic acid, these redox modifications are reversible by reducing systems such as thioredoxin and peroxiredoxin. P D Ray 2012.

Results strongly suggest that the circadian clockwork is involved in complex cellular programmes that regulate endogenous ROS and also defend the organism against exogenous oxidative challenge. Current evidence seems to support the conclusion that the responses to ROS are mediated both through the regular function of the molecular clockwork and the involvement of the TTFL genes in extra-circadian pathways. Lisa Wulund 2015. Photosynthesis is regulated by metabolic and environment controls that balance energy supply and demand in order to optimize photosynthetic efficiency while minimizing back reactions that favour the production of reactive oxygen species (ROS).

A number of antioxidative enzymes including catalase (Cat3), SOD (Cu/Zn SOD) and glutathion reductase show circadian oscillations in their activity. Finally, the disulfide-thiol interchange activity of a particular plasma membrane NADH oxidase from plant and animal cells showed an ultradian pattern. H Asard 2000.

The coupling of circadian rhythms and redox

Circadian rhythms organise processes such as gene transcription, mitosis, feeding, and rest at different times of day and night. These rhythms are orchestrated by a network of core ‘clock genes’ that are organised into transcription–translation feedback loops (TTFLs), producing oscillations with a period of approximately 24 h. The modern understanding of circadian timekeeping has revolved around the TTFL paradigm. Recently, however, this has been challenged by new findings that redox reactions persist in the absence of gene transcription, and that cycles of oxidation and reduction are conserved across all domain of life. These results suggest that non-transcriptional processes such as metabolic state may interact and work in parallel with the canonical genetic mechanisms of keeping circadian time….Although a single model has yet to emerge, studies strongly suggest that redox state may be an oscillation that feeds back upon the TTFL, whereby a cell’s redox state may alter clock gene expression and the clock genes, in turn, regulate redox state. Lisa Wulund 2015, A Stangherlin – ‎2013, K Nishio 2015, N B Milev 2015. There are also examples of redox that exhibit circadian rhythms. A Stangherlin 2013. N P Hoyle 2015. 

In animals, the current understanding of cellular circadian rhythms throughout an organism is that while the core clock genes are oscillating in most tissues and in the midst of enormous environmental pressures, metabolic circadian oscillations are strongly shaped by the environment. There can also be circadian rhythms in redox proteins e.g peroxiredoxins – and peroxiredoxin proteins may not be unique in their ability to undergo redox oscillations since many other proteins are susceptible to oxidation of their cysteine residues by peroxide. S Ray 2016.

There is also a growing realisation in biology that transcription based 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).

The foundations of the coupling between redox and the circadian system may have been laid down around the time of the Great Oxidation Event (GEO) approximately 2.5 billion years ago. The increase in atmospheric oxygen levels as a result of the newly acquired ability of photosynthetic bacteria to use water as the main electron donor are thought to have created a strong selective pressure on anaerobes to evolve defense systems to deal with this harsh and unprecedented oxidizing environment. Rhythmic photosynthesis, and thus oxygen production as a function of the changing day and night, as well as the generation of reactive oxygen species (ROS) by metabolic reactions, or directly by UV radiation, could have forced the coevolution of the circadian and redox systems. Thus, the generation of ROS and those processes sensitive to oxidation were temporally segregated, preventing harmful oxidative stress that would otherwise have led to cell dysfunction and death….Temporal separation of cellular metabolism might be an adaptation to prevent the simultaneous occurrence of mutually-antagonistic reactions that would otherwise result in energetically-wasteful futile cycles.  N B Milev 2015. Also see R Hardeland and T Vanden Driessche et al 2000.

Could this “circadian/redox system” be providing that “same beat” that is needed to get the whole system “in tune”.

Examples of the Redox-Circadian Coupling in nature:

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). CRY shares homology with a phylogenetically ancient enzyme family that repairs DNA in response to ultraviolet light known as the photolyases, leading to speculation that redox is therefore crucial to CRY function. Indeed, the CRY protein does contain motifs that bind the flavins, a group of organic compounds known for their prominent role in electron transport in many metabolic reactions and also their ability to be reduced by the incidence of light. Lisa Wulund 2015.   CryB in Rhodobacter Sph (the only bacterial cryptochrome with a clear biological function) has an iron sulphur cluster and is a member of a group of FeS-BCP proteins. mFeS-BCP ( bacterial cryptochromes and photolyases)) sequences have also been found in hundreds of bacterial organisms.

Since cyanobacteria obtain their energy through photosynthesis, it has been proposed that the cyanobacterial clock must then sense cellular redox state. Although it had been assumed that metabolic rhythms are a functional readout of the circadian clock, the activity of the quinones in cyanobacteria suggests that redox states likely play an integral role in circadian timing. Lisa Wulund 2015. Light dependent protein A (LdpA) a component of the cyanobacterial circadian clock, has been proposed to act as a redox sensor and to be used by the clock to adjust the period length. LdpA contains iron-sulfur centers and can sense the redox state of the cell, which correlates with the amount of light (high light correlates with a reduced redox state, whereas low light is associated with an oxidized redox state. The effects of altered ROS and the circadian clock have also been observed in N. crassa and in the cyanobacterium Microcystis aeruginosa, in which HO has been shown to impact on the daily expression pattern of clock genes as well as clock-controlled genes, including those involved in coordinating photosynthesis. These results clearly show that fluctuations in the redox state of the cells have an impact on the expression of clock-related genes in multiple diverse systems.   A Stangherlin – ‎2013.    M Katayama – ‎2003.  NB Ivleva 2005, NB Milev – ‎2015 .

A protein disulfide isomerase (PDI) from Chlamydomonas reinhardtii (CrPDI2) is involved in the circadian signaling pathway and, together with the night phase-specific interaction of CrPDI2 and a peroxiredoxin, findings suggest a close coupling of redox processes and the circadian clock in C. reinhardtii. A Filonova 2013.

  1. The Need for Good Timing 

A link from circadian rhythms (a global clock) to photosynthesis also offers a way in which to ensure the convergence of timescales and wider environment. The initial absorption of a photon and creation of an exciton in a chromophore is a fast process, taking only a few femtoseconds. By contrast, the exciton lives for several nanoseconds before decaying. So there is a six order of magnitude separation of time scales between absorption and decay. The physiological benefits of this particular separation of time scales is easy to see: fast absorption arises from strong coupling of the chromophore to light, and to absorption over a broad band of frequencies, both desirable characteristics. Long lifetimes increase the chance that the exciton will make it to the reaction center. All other time scales in the excitonic transport process, however – coupling constants, energy differences, decoherence rates, and environmental correlation times – converged to the scale of a picosecond or so. S Lloyd 2011.

  1. A Effect Analogous to a Quantum Zeno Effect?

It had been proposed (Eugenio Daviso 2009A T Dellis and I K Kominis, 2009) that radical-ion-pair reactions form a biochemical system that exhibits the quantum Zeno effect .

Quantum measurements allows, in principle, for a quantum system to be “frozen” by repeated measurements. This is called a quantum zeno effect, and have been demonstrated experimentally with the “spins” of subatomic particles. When a system couples very strongly to its environment through certain degrees of freedom, it can effectively “freeze” other degrees of freedom by a sort of quantum Zeno effect, enabling coherent superpositions and even entanglement/coherence to persist. Quantum measurements allows, in principle, for a quantum system to be “frozen” by repeated measurements. There are a number of manifestation of the quantum zeno effect, and the external system performing the observation need not be a bona fide detection system… P Facchi 2003.

Here it is suggested that the circadian-redox system (with its multiple feedback loops and links through to a range of other biological rhythms) could potentially support a quantum zeno effect.

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. 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.

Biological clocks and switches (which exhibit bistability) have been explored by A Goldbeter 2008.

Such an effect could:

  • offer a form of antioxidant – reducing singlet oxygen production (e.g see Marais et al 2015), and so be integrated into (and perhaps emerging from) that wider circadian-redox-antioxidants cycle (R Hardeland and T Vanden Driessche 2000).
  • support environmentally-assisted quantum transport. Quantum transport via the quantum zeno effect could be used to exclusively direct a quasi particle such as the exciton to propagate uninterrupted in a pre-selected route. T Kobayashi 2012. Also see. J J. J. Roden 2015Thilagam 2013G Vattay 2013Yu-Ran Zhang 2015.
  • support both photosynthesis and magnetoreception. When the quantum zeno effect is manifested (i.e. when the recombination rates are asymmetric), the reaction’s magnetic and angular sensitivity is practically independent of the presence or not of exchange and/or dipolar interactions A.T. Dellis, I.K. Kominis 2011.

Altering Transcription and Translation.

There is evidence in various species that transcription – translation machinery can be magnetically sensitive. AC MFs of moderate flux density (200 660 μ T, 50 Hz) alter the transcription rate of the lac operon in E. coli. Sharp “amplitude windows” are observed for this effect, which are a hint on a non-linear dose dependence. Furthermore while a field strength of 300 μ T suppresses transcription, a field strength of 550 μ T results in a substantial increase. Investigations using HeLa cells, though of human origin, generated data that was highly pertinent to the problem of magnetically induced gene expression. Lin et al. were able to show that weak, alternating, magnetic fields (8 and 80 μ T, increased the transcription of mouse or human c- myc genes. This effect was dependent on the presence of specific electromagnetic response elements located between − 353 and − 1257 bp relative to the promoter. Similar response elements were also detected in the promoter region of the heat shock gene hsp70. Strong magnetic fields (14.1 T) caused the transcriptional up-regulation of 21 genes, and the down-regulation of 44 genes, in Shewanella oneidensis.

In the photosynthetic bacterium, Rhodobacter sphaeroides , magnetic fields of 0 . 13 − 0 . 3 T induced a 5-fold increase in porphyrin synthesis, and enhanced expression of the enzyme 5-aminolevulinic acid dehydratase, which may be caused by elevated gene expression. Very strong DC fields (0 . 13 0 . 3 T) induce, in Rhodobacter sphaeroides , an increase of 5-aminolevulinic acid dehydratase concentration predominantly at the magnetic North pole, an effect that was paralleled by increased porphyrin production. The fact that Magnetic fields can modulate enzyme activities in vitro is a crucial observation, because it indicates that enzymes may function as magnetoreceptors. A Pazur 2007.

  1. Bacteria and Plant Growth

Plant growth and development are regulated by both hormone and circadian signaling pathways. The growing number of signaling molecules whose syntheses are circadian-regulated (e.g. jasmonic acid, auxin) and the time-of-day-specific transcripts of cytochrome P450 monooxygenases (P450s) involved in their syntheses and catabolisms suggest an interactions between hormone signaling network and circadian signaling network. P Yinghong 2013

Plant CRYs are blue, green, and UV-A light photoreceptors responsible for photomorphogenesis, a phenomenon in which growing plants under light leads to chloroplast differentiation, chlorophyll accumulation, leaf expansion, and inhibition of stem elongation. Moreover, CRYs are involved in circadian, developmental, and adaptive growth regulation of plants. P Zu 2009

Growth can also be altered by magnetic fields, through a link to photosynthetic equipment. Magnetic fields accelerate the growth of the cynanobacterium S. platensis associated with activation of light excitation in the photosynthetic electron transfer system and increase in phycocyanin contents, and that these effects are maximal at magnetic flux densities of around 100 gauss.  M Hirano 1998.

It is likely that the recently discovered stimulation of plant growth by magnetic fields (Florez et al. 2004, 2007, Martınez et al. 2009) can be explained by decrease in the production of reactive singlet oxygen in chloroplasts. However, alternative explanations of the growth stimulation cannot be fully excluded, as magnetic field of approximately 0.5 mT has recently been shown to inhibit hypocotyl growth in Arabidopsis (Ahmad et al. 2007) due to an effect on a radical pair located in cryptochrome. ,Marja Hakala-Yatkin 2014

Spin-radical pair products are modulated by the 7 MHz RF magnetic fields that presumably decouple flavin hyperfine interactions during spin coherence. RF flavin hyperfine decoupling results in an increase of H2O2 singlet state products, which creates cellular oxidative stress and acts as a secondary messenger that affects cellular proliferation. Research has demonstrated the interplay between O2•- and H2O2 production when influenced by RF magnetic fields and underscores the subtle effects of low-frequency magnetic fields on oxidative metabolism, ROS signaling, and cellular growth. R J Usselman 2014.

ROS is a byproduct of many cellular metabolic processes, such as photosynthesis and respiration. Recent evidence suggests that ROS are not only byproducts but also signaling molecules in various biological processes, including biotic and abiotic stress responses, stomatal movement, development, and cell expansion. J Sung Shim 2015.

Massimo E Maffei (2014) has undertaken a full review of research on the effects of altering magnetic field (MF) conditions on plants by considering plant responses to MF values either lower or higher than those of the GMF. The possible role of GMF on plant evolution and the nature of the magnetoreceptor is also discussed. Magnetoreception in plants has already been explored by several authors including P Garland 2005 and FC Stormer – ‎2014, mainly drawing on findings relating to plant sensitivity to magnetism.

Another of my postings explores how the circadian rhythms/redox system might support growth.

  1. Quantum Correspondence

According to this principle, if quantum mechanics were to be applicable to macroscopic objects, there must be some limit in which quantum mechanics reduced to classical mechanics. Bohr’s principle demands that classical physics and quantum physics give the same answer when systems become large.

Bohr assumed that, even for moderately excited states, the probability of a given quantum jump was approximately given by the intensity of the ‘corresponding’ harmonic component of the motion in the initial stationary state…The fundamental insight of Bohr’s correspondence principle is that even these quantum transitions are determined in a surprising way by the classical description of the electron’s motion….Bohr uncovered the remarkable fact that, despite these striking differences between the quantum and classical theories, there is nonetheless a deep relation between the quantum frequency, and the harmonic components of the classical motion….each allowed quantum transition is determined by the presence of a “corresponding” harmonic component in the electron’s classical motion; if a harmonic is missing from the classical motion, then that quantum transition is not allowed.  Alisa Bokulich 2009.

The equivalence of the Agarwal equation with Redfield theory shows they satisfy a surprising level of classical – quantum correspondence. D Kohen, (1997).

The Redfield equation (a microscope semi-classical theory of spin relaxation in which the spin system is treated quantum mechanically whilst the coupling of the spin with the lattice is treated classically ), is one of the few viable paths to explore quantum coherence. Akihito Ishizaki 2009.  The conditions for generation and preservation of the Agarwal-Fano noise induced coherence in multi-level quantum systems has obvious relevance to photosynthetic light harvesting and photovoltaics. V Timur 2014

In addition the FKPP Equation could be relevant in bring to model the coming together of biorhythms, magnetic fields, and particle physics:

  • Reaction diffusion fronts in an RD system propagate (biorhythms can be modeled on reaction diffusion). Strands of DNA can be used to generate waves of chemical reactions with programmable shape and velocity. Such models can be in agreement with a generalized FKPP analytical model. A S Zadorin – ‎2014
  • Dynamo theory and the azimuthal magnetic field (which, can be reduced to the classical FKPP equation) .  S Fedotov et al 2003.
  • The same FKPP (reaction diffusion) type of equation appears in various fields of statistical physics and, recently, in the domain of Quantum Chromodynamics (QCD), the interaction theory of quarks and gluons. Higher order corrections to the Colour Glass Condensate (a universal form of matter) evolution equations, include the BK and JIMWLK equation. F Gleis 2010Robi Peschanski 2008Charles R. Doering,  Giuseppe Marchesini 2015H Weigert 2004.

If the classical treatment of the FKPP equation (due to Freidlin) is expanded to include the phenomenon of anisotropic diffusion with a finite velocity, in the long-time large-distance asymptotic limit the Hamiltonian dynamical system associated with the anisotropic reaction–diffusion equation has a structure identical to that of general relativity theory. The function determining the position of the reaction front and its speed is nothing else but the action functional for a particle in both gravitational and electromagnetic fields. S Fedotov et al 2000.

  1. Quantum Mechanics in a Warm Wet Environment.

Electron transfer in photosynthesis does not slow down significantly (and in some cases increases) as temperature is lowered. K Schulten 1991.  But nature needs to find various balances in the case of photosynthesis, and such electron transfer must be able to take place at higher temperatures.

One central key characteristic of all circadian rhythms is “temperature compensation”, which allows organisms to maintain robust rhythms with a period close to a diel cycle over a broad range of physiological temperatures.

The mechanism for temperature compensation is not yet understood, however it is possible that cryptochrome is implicated in this.

A 2010 study showed that in Drosophila, whose protective heat and stress response has been inhibited, the clock hardly shifts with temperature changes. Since the conventional model predicts that everything is temperature sensitive, no single pathway should be this influential. Recent findings suggested that temperature-induced shifts of the clock involve genetic pathways separate from the molecular cycles at the core of the clock, but linked to them, and that the core clock is actually insensitive to temperature. P B. Kidd 2015.

AC fields (14.6 mT, 60 Hz) can provide protection for Salmonella typhimurium from heat stress and magnetic field exposure can induce the heatshock protein HSP70 in Drosophila A Pazur 2007. In Drosophila, brief, noxious heat pulses (37°C) have also been demonstrated to cause dramatic decreases in Per and Tim protein abundance and phase shifts in locomotor activity rhythms. This phenomenon is not entirely understood, but likely involves disruption of the Per-Tim complex via a Cry-dependent mechanism. A Bellemer 2015. Findings indicate a role for CRY in circadian temperature as well as light regulation and suggest that these two features of the external 24-h cycle normally act together to dictate circadian phase. R Kaushik 2007. Different subsets of clock neurons operate at high and low temperatures to mediate Drosophilia clock synchronization to temperature cycles, suggesting that temperature entrainment is not restricted to measuring the amplitude of such cycles. CRY dampens temperature input to the clock and thereby contributes to the integration of different Zeitgebers. C Gentile 2013.

It has been proposed that a Cryptochrome/Radical Pair Mechanism signalling is a fundamental component of the robustness and temperature insensitivity of circadian systems. RPM/CRY is an ideal biophysical candidate for temperature insensitive signalling within the phosphorylation processes of multimeric post-translational circadian clocks. The biological outcome is to influence circadian behaviour in a manner that is independent of the influences of temperature and molecular environment on kinetic constants, thus further contributing to the robustness of circadian systems.  J Close 2014 .

Perhaps a similar mechanism is used in quenching within photosynthesis.

Some further ideas for how a quantum process might take place at room temperature are set out below.

  • Fluctuation-dissipative theory.

Such theorum has been applied to circadian rhythms by Xiao et al (2009), M Baiesi and C Maes 2013, and electromagnetic fluctuations. M Eckhardt 1982.

A central finding of equilibrium statistical physics is that fluctuations inevitably induce dissipation in a system with many degrees of freedom. This is the content of the well-known fluctuation-dissipation theorem. For a system at thermal equilibrium, it relates the fluctuations in the system with its dissipative response to sufficiently weak external perturbations. Dario Bercioux 2015.

In thermal equilibrium the fluctuation-dissipation theorem relates the linear response and correlation functions in a model and observable independent fashion. Out of equilibrium, these relations still hold if the equilibrium temperature is replaced by an observable and frequency-dependent parameter (effective temperature). When the system achieves a long time thermal state all of these effective temperatures should be equal and constant. T. S. Bortolin 2014.

  • Quantum Squeezing

In the case of a pair of driven quantum oscillators that are entangled and which sit in a hot environment, two processes are competing with each other (1) the way the entanglement leaks into the hot environment; and (2) the way that the process of driving these oscillators also squeezes their state and this helps preserve entanglement. This competition dramatically increases the temperature at which entanglement can occur. Galve et al 2010.

Quantum squeezing is found to be able to induce, enhance and even preserve entanglement in decohering environments. Lock Yue Chew 2014.

This could be further influenced by interaction between quantum and classical oscillators e.g For oscillators with equal unperturbed frequencies, i.e., at resonance, the uncertainties exhibit a time-dependent quantum squeezing which can be extreme. RM McDermott – ‎2004. Quantum squeezing can be implicitly linked to the local classical dynamical behavior via the paradigm of quantum–classical correspondence. SK Joseph – ‎2014 

The Agarwal/Redfield equation indicates that squeezed states emerge naturally during the relaxation process, even if the initial state is unsqueezed, provided that the counter rotating terms are included in the harmonic oscillator master equation. D Kohen – ‎1997

Recently evidence has been found of two possible quantum mechanical processes taking place during magnetoreception S Qin – ‎2015, which would require the coupling of those processes (either cooperatively or in competition) – add nonlinearity, and this could further change the dynamics of quantum squeezing. For example in the asymptotic entanglement of two quantum harmonic oscillators nonlinearly coupled to an environment, the asymptotic negativity as function of temperature, initial squeezing, and coupling strength, is considerably more robust that for linearly damped cases compared to results for systems with linear system-reservoir coupling. A Voye 2015

  • Topological Insulation

Such materials can occur naturally e.g kawazulite, and aleksite. Oxides with heavy transition metal ions, which often host a competition between electron interactions and spin–orbit coupling, are possibilities for unusual topological phenomena and other unconventional phases.

The electrons flowing over the surface of a topological insulator are all aligned in a specific way. Their “spins” are locked at right angles to their direction of motion. This spin-momentum locking means that the electrons are immune from the buffeting they would get inside an ordinary conductor. Instead, the electrons can move through perfect topological insulators with 100 percent efficiency, even at room temperature. Recently evidence has emerged of the electrical accessibility of spin currents on topological insulator surfaces up to room temperature. A Dankert 2015. It had previously been thought that only magnetic fields could destroy the mobility offered by topological insulators, but this theory has been disproved e.g see J Sanchez-Barriga 2016.

  • Organic Semisuperconductors and 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.

Superconductors could also provide an environment in which ultra fast electron transfer, radical pairs, and quantum coherence could all arise, including at room temperature.

London speculated that superconductivity might exist in certain biological systems and specifically in the aromatic organic long-chain molecules which have conjugated double bonds containing itinerant electrons (π electrons).  Utilising this speculation of London and BSC theory of coupled electrons Little postulated the existence of an organic polymer that might be a superconductor at room temperature.  E H Halpern 1972.

The search for organic superconductors had been boosted in the 1960s by the idea that conductive polymer chains with polarizable molecular groups may provide for electrons running along the polymer chains a highly effective Cooper pair coupling by means of an energy exchange via localized excitons  Since the first discovery of an organic superconductor in 1980 [13] Tc >10 K has been achieved.  However, the origin of superconductivity has turned out to be far from the suggested excitonic mechanism. Electric conduction stems here from π- electrons in stacked aromatic rings forming one-dimensional or two-dimensional (2D) delocalized electron systems. This restriction of the effective dimensionality and strong Coulomb repulsion effects push the systems toward metal-insulator, magnetic, and SC transitions. R Hott 2011

It has also been proposed extreme sensitivity of some organisms to weak magnetic fields  may relate to the superconductive junction phenomena  in these biological systems. A weak magnetic field effect on probable Josephson junctions have been observed in carbon films at 25℃.  Electron tunnelling through these junctions take place in response to the very small magnetic fields.  Freeman W Cope 1979.   Freeman W Cope 1975 reviewed the evidence for solid state physical processes in diverse biological systems. He found that  semiconduction of electrons across the enzyme particles as the rate-limiting process in cytochrome oxidase is evidenced by the peculiar kinetic patterns of this enzyme and by microwave Hall effect measurements. PN junction conduction of electrons is suggested by kinetics of photobiological free radicals in eye and photosynthesis. Superconduction at physiological temperatures may be involved in growth and nerve. Phonons and polarons seem likely to be involved in mitochondrial phosphorylation.

E D Giudice 1989 also made the proposal of coherent electromagnetic processes as the engine for biological dynamics suggests that Josephson effects could be present in living cells and claimed that there was evidence for this. And it has been proposed that the quantum like transition that realizes the stable state of living matter at room temperature is similar to the non conventional BCS-like transition as seen in high Tc superconductors. N Poccia 2009. 

All 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. Mechanistically, fast electron transfer from the aromatic moiety to the riboflavin has been proposed to quench the excited state of riboflavin by building a couple of a positively charged amino acid radical and a negatively charged flavin semiquinone . 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.

Superconductors allow interplay between superconductivity and magnetism.   A complete synergy between superconducting and magnetic orders turns out to be possible through the creation of spin-triplet Cooper pairs, which are generated at carefully engineered superconductor interfaces with ferromagnetic materials. It is fascinating to consider what relationship/interaction radical pairs might have with cooper pairs.

Radical pairs.  When radicals are formed, they are created in pairs and spin is conserved in the reaction process e.g a singlet molecule dissociates to form a singlet ‘spin-correlated radical pair’ in which the electron spins on the two radicals are opposite. a triplet molecule dissociates to yield a pair with identical spins. But reaction has a strict selection rule, normally only radicals with opposite electron spins can combine to form products.

Cooper pairsUsually, the Cooper pairs form in a singlet state, where the electrons have opposite spins, so that the Cooper pairs have zero spin overall. On rarer occasions, Cooper pairs to form in a triplet state with parallel spins. Due to the Pauli exclusion principle, which requires that the pairing wave function is antisymmetric upon exchanging the electrons, the singlet state has even parity and the triplet state has odd parity…in the case of unconventional superconductors, spontaneous appearance of magnetic fields below superconducting transition can taken place.

In unconventional superconductivity a complex of phases has been found in new materials, such as the strong correlation of electrons in curpate HISCs  Organic superconductors have also been identified, including copper oxides, iron arsenides/selendas, and heavy fermions compounds.   It has been found that the key fundamental properties – transition temperature and magnetic field penetration depth of these complex superconductors are dependent on composition and the degree of disorder in the material structure.

If flavins and iron sulphur clusters  were found to be organic superconductors, this might explain quantum biology taking place at room temperature.

Iron Sulphur Clusters

Their most common oxidation states are paramagnetic and present significant challenges for understanding the magnetic properties of mixed valence systems . Charge distribution in the clusters depends on coordination number of the metals and the extent of the magnetic coupling between them- with ferromagnetic coupling favouring charge doclocalisation, and anti-ferromagnetic coupling appearing to give rise to charge localisation.

Although in most magnetotactic microorganisms, the geomagnetic field is detected by magnetic particles with a permanent magnetic moment, a magnetic iron-sulphur crystals have also been found in microorganisms. The magnetosomes are found in planar groups inside the cytoplasm of each cell in the aggregate.  M Farina 1990.  Ferrimagnetic greigite (Fe3S4) occurred in all types of sulfide-producing magnetotactic bacteria examined.  Mackinawite (tetragonal FeS) and, tentatively, sphalerite-type cubic FeS were also identified. Mackinawite converted to greigite over time within the bacteria that were deposited on electron microscope grids and stored in air.  Orientation relationships between the two minerals indicate that the cubic-close-packed S substructure remains unchanged during the transformation; only the Fe atoms rearrange. Neither mackinawite nor cubic FeS are magnetic, and yet they are aligned in chains such that when converted to magnetic greigite, the probable easy axis of magnetization, is parallel to the chain direction. The resulting chains of greigite are ultimately responsible for the magnetic dipole moment of the cell. Both greigite and mackinawite magnetosomes can contain Cu, depending on the sampling locality.  M Posfai 1998.  T Kasama 2006 .

Up to now, at least four structure types of iron-based superconductors have been developed, including the discovering of superconductivity in tetragonal FeS  (mackinawite-type FeS, is now confirmed as a superconductor and not a magnetic semiconductor) although its Tc is only 5K, it is seen to provide a new platform to realise high temperature superconductors. It has been found that the substantial difference in magnetic and superconducting behaviour in different FeS phases is directly tied to the crystal structure details and compositions. S J Kuhn 2016.  E E Rodriguez 2016.   Results both indicate the existence of strong itinerant spin fluctuations in mackinawite, and mackinawite exhibits the magnetic characteristics of the high temperature Fe-based superconductors with which it is isostructural. If strong spin fluctuations are the mediators of electron pairing in these Fe-based superconductors. Mackinawite may be one of the simplest Fe-based superconductors.  K D Kwon 2011.  Unlike its heavier analogs FeSe and FeTe, however, mackinawite is metastable and therefore cannot be synthesized from their respective elements using solid state methods, unless it is alloyed with significant amounts of Co, Ni, or Cu.  C K H Borg 2016.

Iron sulphur clusters are also found throughout biology, for example CryB in Rhodobacter Sph (the only bacterial cryptochrome with a currently known biological function) has an iron sulphur cluster and is a member of a group of FeS-BCP proteins.  mFeS-BCP (bacterial cryptochromes and photolyases with iron sulphur clusters) have been found in hundreds of bacterial organisms.

The Fe-S cluster is capable of transferring electrons in electron transfer chains (for photosynthesis and respiration) and of catalysing redox reactions.  Additionally Fe-S Clusters act as catalytic centres, regulators of gene expression and sensors off iron and oxygen.  The simplest Fe/S clusters are of the (2Fe-2S and 4Fe-4S) types which contain either ferrous or ferric iron and sulphide and which are usually integrated into proteins via coordination of iron ions by cysteine or histidine residues.  John H. Golbeck 1993.

10. Chaos and Quantum Entanglement

If environmentally assisted quantum transport is exploiting circadian rhythms, then this could potentially be an example of a relationship between quantum entanglement and choas. Natural rhythms can be either periodic or irregular over time and space. M A Savi 2005). The fact that the circadian network relies on multiple interlocked feedback loops allows the generation of complex dynamic behaviours such as chaotic oscillations. This kind of irregular behaviour is often considered as pathologic. There are however theoritical analyses which show that such behaviour may provide the system with advantages, namely in the adaptation of the oscillator to various conditions, by selecting an appropriate circadian period. D Gonze 2011.  Also see Y Suzuki 2016, J C Leloup and A Goldbeter 1999.

Theoritically and experimentally it has been observed that, there exist a clear relationship between quantum entanglement and classical chaos (Miller and Sarkar 1999, Ghose and Sanders 2004, Chaudbury et al 2009, Lombardi and Marzkin 2011, Lakshminarayan 2001)…the connection between the degree of chaos and entanglement enhancement via squeezing has been explored. S K Joesph 2015.  Also see G Wang 2014, Signatures of chaos in the entanglement dynamics persist in the presence of decoherence. In addition, the classical chaos affects the decoherence rate itself. S Ghose 2008. S. Chaudhury 2009. Research has shown signatures of ergodicity and “islands of stability in a sea of chaos” in Quantum mechanical systems…and a 2016 paper shows that even isolated quantum systems can shown ergodic dynamics. Maps of the entanglement entropy bear a strong resemblance to the phase space dynamics in the classical limit; classically chaotic motion coincides with higher entanglement entropy. C Neill 2016.

Understanding of biology (including within a natural environment) can assist in the understanding and application on physics, and visa versa. The days when disciplines could simply be separated are gone. But the cross over between the disciplines opens a whole new vision of our universe and we are just on the edge of that.

Feb – Oct 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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