Archive | October 2016

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 […]

Is the Coupling of Circadian Rhythms and Metabolism/Redox Regulating Morphogenesis

Self Organisation Far from Equilibrium

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).  Also see J England 2015 on ‘dissipative adaptation in driven self-assembly’.

Dissipative processes are present in biology.  It is asked whether these could be contributing to morphogenesis.

Stochastic reaction-diffusion simulations have been successfully used in a number of biological applications. Formation of skin patterns and the biochemical processes in living cells (like gene regulatory networks), the cell cycle, circadian rhythms, signal transduction in E Coli chemotaxis, MAPK pathway, oscillations of Min proteins in cell division, and intracellular calcium dynamics are examples of processes mathematically modelled by reaction and reaction-diffusion systems. T Vejchodsky 2013, J Eliaš – ‎2014A Zakharov 2014T Hinze 2011. Read More…