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Now that we know of bio/molecular tools that allow living organisms to deal with quantum computations e.g. the fancy proteins that allow birds to handle quantum coherence (e.g. The quantum needle of the avian magnetic compass or Double-Cone Localization and Seasonal Expression Pattern Suggest a Role in Magnetoreception for European Robin Cryptochrome 4) I wonder:

  • Are these tools already solving problems you (quantum computing researchers) have?
  • Is there any specific issue these tools 'must' be solving somehow that you are struggling with at your labs?
  • Could we use them (although this will imply a paradigm shift towards biotechnology)?
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"Is Quantum Biocomputing ahead of us?"

There has been some work done on biocomputing, quantum computing, spin chemistry, and magnetochemical reactions.

Correlated radical pairs — pairs of transient radicals created simultaneously, such that the 2 electron spins, one on each radical, are correlated — on photoactive magnetoreceptive proteins such as Cryptochromes does not constitute quantum computation.

See: "Light-dependent magnetoreception in birds: analysis of the behaviour under red light after pre-exposure to red light" by W. Wiltschko, Gesson, Noll, and R. Wiltschko in the Journal of Experimental Biology, 2004.

See the article "Vision-based animal magnetoreception" at the QuantBioLab website, Quantum Biology and Computational Physics research group, University of Southern Denmark (SDU):

Forward reaction MFeffect

Figure 6. Shown here is a semi-classical description of the magnetic field effect on the radical pairs between FADH and tryptophan in cryptochrome. The unpaired electron spins (S$_1$ and S$_2$) precess about a local magnetic field produced by the addition of the external magnetic field $B$ with contributions I$_1$ and I$_2$ from the nuclear spins on the two radicals. The spin precession continuously alters the relative spin orientation, causing the singlet (anti-parallel) to triplet (parallel) interconversion which underlies the magnetic field effect. Electron back-transfer from a tryptophan to FADH quenches cryptochrome's active state. However, this back-transfer can only take place when the electron spins are in the singlet state, and this spin-dependence allows the external magnetic field, $B$, to affect cryptochrome activation.

Retina Components

Figure 7. Schematic illustration of a bird's eye and its important components. The retina (a) converts images from the eye's optical system into electrical signals sent along the ganglion cells forming the optic nerve to the brain. (b) An enlarged retina segment is shown schematically. (c) The retina consists of several cell layers. The primary signals arising in the rod and cone outer segments are passed to the horizontal, the bipolar, the amacrine, and the ganglion cells. (d) The primary phototransduction signal is generated in the receptor protein rhodopsin shown schematically at a much reduced density. The rhodopsin containing membranes form disks with a thickness of ~20 nm, being ~15–20 nm apart from each other. The putatively magnetic-field-sensitive protein cryptochrome may be localized in a specifically oriented fashion between the disks of the outer segment of the photoreceptor cell, as schematically shown in panel d or the cryptochromes (e) may be attached to the oriented, quasi-cylindrical membrane of the inner segment of the photoreceptor cell (f).

In mathematical terms, the vision-based compass in birds is characterized by a filter function, which models the magnetic field-mediated visual signal modulation recorded on the bird's retina (see Fig. 8).

Filer Function

Figure 8. Panoramic view at Frankfurt am Main, Germany. The image shows the landscape perspective recorded from a bird flight altitude of 200 m above ground with the cardinal directions indicated. The visual field is modified through the magnetic filter function; the patterns are shown for a bird looking at eight cardinal directions (N, NE, E, SE, S, SW, W, and NW). The geomagnetic field inclination angle is 66°, being a characteristic value for the region.


A biomechanical computer has been created. Bio4Comp, an EU-funded research project, have created biomolecular machines each only a few billionths of a meter (nanometers) in size. The actin-myosin and microtubule-kinesin motility systems can solve problems by moving through a nanofabricated network of channels designed to represent a mathematical algorithm; an approach we termed “network-based biocomputation”. Whenever the biomolecules reach a junction in the network, they either add a number to the sum they are calculating or leave it out. That way, each biomolecule acts as a tiny computer with processor and memory. While an individual biomolecule is much slower than a current computer, they are self-assembling so that they can be used in large numbers, quickly adding up their computing power. An example of how this works is shown in the video on their website.

WP4 SEM channels (full with scalebar corrected)

  • Are these tools already solving problems you (quantum computing researchers) have?

  • Is there any specific issue these tools 'must' be solving somehow that you are struggling with at your labs?

  • Could we use them (although this will imply a paradigm shift towards biotechnology)?

"The first step in solving mathematical problems with network-based biocomputation is to encode the problem into network format so that molecular motors exploring the network can solve the problem. We have already found network encodings for several NP-complete problems, which are particularly hard to solve with electronic computers. For example, we have encoded subset sum, exact cover, boolean satisfiability and travelling salesman.

Within the Bio4Comp project, we will focus on optimizing these encodings so that they can be efficiently solved with biological agents and be more readily scaled up. Analogous to optimized computer algorithms, optimized networks can greatly reduce the computing power (and thus the number of motor proteins) required for finding the correct solution." - Source: Bio4Comp Research.


Another interesting paper which supports my answer that radical pairs don't constitute a quantum computer, but is merely a quantum biochemical reaction demonstrating spin chemistry, is "Quantum probe and design for a chemical compass with magnetic nanostructures" by Jianming Cai (2018).

Introduction. — Recently, there has been increasing interest in quantum biology namely investigating quantum effects in chemical and biological systems, e.g., light harvesting system, avian compass and olfactory sense. The main motivation is to understand how quantum coherence (entanglement) may be exploited for the accomplishment of biological functions. As a key step towards this goal, it is desirable to find tools that can detect quantum effects under ambient conditions. The ultimate goal of practical interest in studying quantum biology is to learn from nature and design highly efficient devices that can mimic biological systems in order to complete important tasks, e.g. collecting solar energy and detecting weak magnetic field.

As an example of quantum biology, the radical pair mechanism is an intriguing hypothesis to explain the ability of some species to respond to weak magnetic fields, e.g. birds, fruit flies, and plants. A magnetochemical compass could find applications in remote magnetometry, in a magnetic mapping of microscopic or topographically complex materials, and in imaging through scattering media. It was demonstrated that a synthetic donor-bridge-acceptor compass composed of a linked carotenoid (C), porphyrin (P), and fullerene (F) can work at low temperature (193 K). It is surprising that such a triad molecule is the only known example that has been experimentally demonstrated to be sensitive to the geomagnetic field (yet not at room temperature). It is currently not known how one might construct a biomimetic or synthetic chemical compass that functions at ambient temperature.

...

Summary. — We have demonstrated that a gradient field can lead to a significant enhancement of the performance of a chemical compass. The gradient field also provides us with a powerful tool to investigate quantum dynamics of radical pair reactions in spin chemistry. In particular, it can distinguish whether the initial radical pair state is in the entangled singlet state or in the classically correlated state, even in the scenarios where such a goal could not be achieved before. These phenomena persist upon addition of partial orientational averaging and addition of realistic magnetic noise. The effects predicted there may be detectable in a hybrid system compass composed of magnetic nanoparticles and radical pairs in an oriented liquid crystalline host. Our work offers a simple method to design/simulate a biologically inspired weak magnetic field sensor based on the radical pair mechanism with a high sensitivity that may work at room temperature.

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Much has been written about Quantum Biology. A somewhat old -and yet, solid- take is that of Phillip Ball, The dawn of Quantum Biology (Nature 2011, 474, 271-274). For now, let's not review that and instead focus on your questions.


On the first question:(is it solving our problems?)

A system (or process) described by Quantum Biology is non-trivially quantum-mechanic, and therefore interesting, but to the best of my knowledge it is also not multi-qubit, so not really what quantum computing is about. In particular: currently known quantum biological processes do not present scalability, and neither do they present quantum logical gates (or not in the way we understand them at least), much less so quantum algorithms. So, as an answer, that's mainly a no: these tools are not solving our problems.


On the second question:(is it solving a specific issue we're struggling with?)

Reliable quantum coherence on the solid state, in complex structured systems and at high temperature is something we all would like to see solved, and, at least to some point, this is what Quantum Biology is about. So, as far as the current understanding of the field goes, this is indeed a specific issue that people in labs are working on and which seems solved in Biology (since molecules are complex nanostructures). Whenever we are able in our labs to reliably achieve quantum coherence in the solid state, in complex structured systems and at high temperature, we will jump much closer to usefulness and cheapness. So, as an answer, that is a yes.


On the third question:(could we use biomolecules as quantum hardware?)

They are not in the main league yet, to say the least. Even as an optimistic speculation, I'd say that they will not be competing with the big players any time soon, but I do believe that, as research advances past DNA origami (and related strategies) in Molecular Biology and Synthetic Biology, at some point biomolecular qubits will play a role within the subset of molecular spin qubits. In particular, the keys to relevance would be to combine the (seemingly proven) coherence in unusual conditions (warm, wet), with the unmatched ability of biomolecules for extremely complex self-organisation into functional structures. Since (coherent, organized) molecular spin qubits are my field of research, let me link to a couple of relevant papers. First, a first reaction on the first magnetic molecule that was competitive in terms of coherence with regular solid-state candidates, and thus how magnetic molecules are back in the race toward the quantum computer. And also, this proposal (disclosure: I'm an author) on the arXiv on why and how one could use peptides as versatile scaffolds for quantum computing.

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There has been a great deal of scientific debate over evidence of quantum effects in biology due to the difficulties of reproducing scientific evidence. Some have found evidence of quantum coherence while others have argued this is not the case. (Ball, 2018).

The most recent research study (in Nature Chemistry, May 2018) found evidence of a specific oscillating signal indicating superpositioning. The scientists found quantum effects that lasted precisely as expected based on theory and proved that these belong to energy superimposed on two molecules simultaneously. This resulted in the conclusion that biological systems exhibit the same quantum effects as non-biological systems.

These effects have been observed in the Fenna-Matthews-Olsen reaction centre of the bacteria - Chlorobium Tepidum (Borroso-Flores, 2017).

Research evidences the dimensions and time scales of the photosynthetic energy transfer processes puts them close to the quantum/classical border. There are various explanations for this, but they seem to indicate energetically noisy quantum/classical limit is ideal for excitation energy transfer control. Keren 2018.

Quantum Biology as Biological Semiconductors

Such dynamics in biology rely on spin chemistry (radical pairs), and it is has been recognised that “Certain organic semiconductors (OLEDs) exhibit magnetoelectroluminescence or magnetoconductance, the mechanism of which shares essentially identical physics with radical pairs in biology”

 PJ Hore (2016).

The terms 'spin singlets' and 'triplets' are used in spintronics (in investigating semiconductors) and the term radical pairs (including spin singlets or triplets) are used to discuss spin chemistry in biology. But all the terms are describing the same phenomena (just in different disciplinary realms). Recently there has been interdisciplinary calls for the integration of spin chemistry and spintronics in recognition of this J Matysik (2017).

Biological semiconductors that have already identified by scientists include melanin and peptides, and peptides are now being explored as scaffolds for quantum computing.

UltriaFast Electron Transfer, and Storing Electronic Spin Information in a Nuclear Spin

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

Rienk van Grondelle.

In 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 an efficient method of creating non-equilibrium polarization of nuclear spins by using chemical reactions, which have radical pairs as intermediates (Adriana Marais 2015). Within biology such as mechanism could increase resistance to oxidative stress.

It has been noted there seems to be a link between the conditions of occurrence of photo-CIDNP in reaction centres and the conditions of the unsurpassed efficient light-induced electron transfer in reaction centres. J Matysik 2009, I F Cespedes-Camacho and J Matysik 2014. 

A CIDNP effect has been observed in the Fenna-Matthews-Olsen reaction centre (Roy et al 2006).

A CIDNP effect has also been observed in flavin adenine dinucleotide (FAD) (Stob 1989).

FAD is implicated in quantum effects theorised in cryptochrome and other biological redox reactions. The widely accept theory is that during response to magnetic fields, the photo-excitation of the non-covalently bound flavin adenine dinucleotide (FAD) cofactor in Cryptochrome leads to the formation of radical pairs via sequential electron transfers along the “tryptophan-triad”, a chain of three conserved tryptophan residues within the protein. This process reduces the photo-excited singlet state of the FAD to the anion radical, 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 Xiao-Jie (2016).

'until now, no CIDNP phenomenon has been observed in spintronics , although the possibility of obtaining such effects has been mentioned “If nuclear spin resonance is found to have an impact on the spin-dependent electron transport due to the hyperfine interaction, ultimately the opposite process may become possible: storing electronic spin information in the nuclear spin.”

 J Matysik (2017).

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Extension of Anin Post above (I havent been able to login back into that account, so set up a new one)

Limits of the Quantum Biology as Biological Semiconductor Approach

Quantum biology cannot simply solve the practical concerns of quantum computing as they stand - as biology is not simply a form of semiconductor or quantum computer.

I note that leading scholars such as P J Hore (quoted above) working on the radical pair mechanism in biology have been strongly connected to NMR research from the start. These scholars may well be aware of both the benefits and pitfalls of interdisciplinary work. One of the major risks within academic study, is that in drawing parallels across disciplines, we can ignore differences. It unlikely that the complex adaptive systems of biology will simply fit to existing conceptualisations within computing or physics. It requires scholars examine the phenomena as something unknown and holding many possibilities - some of which may challenge any preconceptions they already have.

For example, focusing on the radical pairs mechanism alone in research into quantum efficiency (within biological processes) will be of limited use without understanding their wider context.

Understanding Context

There is research evidencing the interaction of cryptochrome with redox and biological timing mechanisms in mice models (Harino et a, 2017). And more widely there is a growing literature on the interaction of redox and circadian rhythms (including through circadian gating) across many plant (Guadagno et al, 2018) and animal species.

Recent work has investigated circadian rhythms of Reactive Oxygen Species (ROS) generation and ROS-scavenging enzymes, and circadian rhythms of ROS-generating photosynthesis. It has been suggested that

'given that changes in the rate of photosynthesis lead to alterations in the production of singlet oxygen, circadian regulation of photosynthesis might give rise to rhythms of singlet oxygen production'. (Simon et al, 2019).

If you want to understand more about circadian rhythms then I would suggest checking out Alfred Goldbeters work.

Biology doesn't Separate Everything into Individual Components

The operation of such timing mechanisms have implications for quantum efficiency [Garzia- Plazaola et al, 2017; Schubert et al, 2004) within biology. Sorek and Levy (2012) have also researched relationships with temperature compensation.

All known circadian clocks have an endogenous period that is remarkably insensitive to temperature (Kidd et al, 2015)

From the above research, it would also seem that biology can treat light and temperature signalling as integrated rather than separated (Franklin et al, 2014).

And this isn't just about response to magnetic fields or light. The cry gene alters blue-light (<420 nm) phototransduction which affects biological clocks, spatial orientation and taxis relative to gravity, magnetic fields, solar, lunar, and celestial radiation in several species (Clayton, 2016)

Possible Role for Quantum Scarring

Associations between periodic orbits and quantum have been made in quantum scarring - where systems are prevented from reaching thermalisation. It may explain why equations that can be used to model dissipative structures which have been used to model biological oscillations (Alfred Goldbeter) can also be applied to other fields. For example the FKPP equation can be used to model dissipative structures arising through reaction-diffusion (the propagation of unstable non-linear wave fronts/population dynamics), but also quantum chromodynamics (Mueller and Munier, 2014) and the speed at which magnetic fronts propagate in a turbulent electrically conducting fluid. The diffusion approximation for transport admits an infinite speed of propagation (Fedotov et al).

Generative Code?

You might which to give consideration to how quantum biological systems could be associated with code. The photon is a proposed resource in quantum computation and communication.

Photons represent the natural flying qubit carriers for quantum communication, and the presence of telecommunications optical fibres makes the wavelengths of 1,310 nm and 1,550 nm particularly suitable for distribution over long distances. However, qubits encoded into alkaline atoms that absorb and emit at wavelengths around 800 nm have been considered for the storage and processing of quantum information (Tanzili et al, 2005)

Within biology there is a mechanism known as spontaneous chemiluminescence (and by a number of other names including ultraweak photon emissions and biophotons).

It is generally accepted that (these) photons are emitted (1) at near UVA, visible, and near IR spectral ranges from 350 to 1300 nm and (2) at the intensity of photon emission in the range of several units to several hundreds (oxidative metabolic process) and several hundreds to several thousands (oxidative stress process) photons s−1 cm−2. (Cifra and Pospíšil, 2014)

This mechanism is widely found across biology (both in plants and animals) and takes place where electronically excited species are formed during oxidative stress processes (Cifra et al, 2014), which are associated with the production of ROS (Pospíšil et al, 2014). They can be generated and influenced by various stimuli including magnetic fields (Li, 2012)

The thinking is that

various molecular processes can emit photons and that these are transported to the cell surface by energy carrying excitons. A similar process carries the energy from photons across giant protein matrices during photosynthesis (MIT technology review, 2012).

This mechanism has been linked to systematic changes in energy metabolism inherent to a circadian cycle in both animals and plants (Footitt et al, 2016 and Kobayashi et al, 2009). It has also been noted that a clear advantage of this mechanism is that it provides spatiotemporal information (Burgos et al, 2017)

It has been proposed that phosphenes (which can be generated in our visual cortex in response to various stimuli including light and magnetic fields) are the result of Ultra Weak Photon Emissions Császár et al, 2015. The exact mechanisms behind this are still under investigation, but we have various proteins including cryptochrome in our own retinas (Foley et al, 2011). Phosphenes generate a large range of geometrical shapes and colours. These could potentially act as code/memory.

The Geometries of Nature and the Chiral-induced Spin Selectivity Effect

The geometries of nature (including rotating spiral waves and chiral structures) are worth exploring further e.g see www.nature.com/articles/s41570-019-0087-1. It has been speculated that

'Many biological electron transfer processes occur through chiral systems, and the role of the chiral-induced spin selectivity effect has not yet been considered. The benefits of reducing backscattering and directing charge flow along chiral structures offer compelling possible reasons for why nature might use spin-selective electron transfer in biology' (Ron Naaman and David. H. Waldeck, 2015).

You might also want to check out literature on 'Redox-Triggered Chiroptical Switching'.

What might be the outcome of collapsing superpositioning

If the superpositioning of 1 and 0 can be generated, the question then needs to be asked what is the outcome of collapsing this.

A metaphor for this might be the collapsing of multi-stable visual illusions - such as the Necker cube. These present the possibility of multiple images and have been explored as a quantum effect.

We can collapse such illusions by deciding to give our attention to a particular possibility/image. Choice of which image we attend varies across individuals and such choices are preferences. Choosing one image does not validate that image above all others. It is merely a choice.

What we end up with is just one choice/interpretation from multiple possibilities. As such the application of both memory and prediction result in interpretations or constructions (with prediction drawing heavily on memory) rather than a correct answer.

The collapsing of super-positions might then be prevented through avoidance of such choice or superpositioning could established again through new possibilities - for example as generated through environmental change.

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