VIII. Quantum Biology – Noisy, Warm, Dynamical Quantum Systems

Quantum Biology is a field that has come out of nowhere to be at the forefront of pioneering science. But 20 years ago, virtually no one thought quantum mechanics had anything to do with biological organisms. On the scale of living things quantum effects just didn’t matter. Nowadays quantum effects seem to appear all over biological systems. The book “Life on the Edge: The Coming Age of Quantum Biology” by J. McFadden and J. Al-Khalili (2014) is a New York Times bestseller and gives a great comprehensive introduction. Another, slightly more technical introduction, is this paper “Quantum physics meets biology” by M. Ardnt, T. Juffmann, and V. Vedral (2009), and more recently this paper
Quantum biology” (2013) by N. Lambert et al. A summary of the major research follows:

Photosynthesis: Photosynthesis represents probably the most well studied of quantum biological phenomenon. The FMO complex (Fenna-Mathews-Olsen) of green-sulphur bacteria is a large complex making it readily accessible. Light-harvesting antennae in plants and certain bacteria absorb photons creating an electronic excitation. This excitation travels to a reaction center where it is converted to chemical energy. It is an amazing reaction achieving near 100% efficiency – nearly every single photon makes its way to the reaction center with virtually no energy wasted as heat. Also, it is an ultrafast reaction taking only about 100 femtoseconds. Quantum coherence was observed for the first time in “Evidence for wavelike energy transfer through quantum coherence in photosynthetic systems” by Engel et al. (2007). The energy transfer seems to involve quantum exciton
delocalization that is assisted by quantum phonon states and environmental noise. It is believed that coherent interference may guide the excitations to the reaction centers. This paper proves unequivocally that photosynthesis uses quantum processes – something that there is surprisingly strong resistance to by classicists.

Enzyme Catalysis:
Enzymes catalyze reactions speeding up reactions rates by enormous amounts. Classical factors can only explain a small fraction of this. Quantum tunneling of hydrogen seems to play an important role. Enzymes are vibrating all the time and it is unclear what role coherence and superposition effects may also contribute to reaction rate speed-ups.

Avian Compass: Several bird species, including robins and pigeons, are believed to use quantum radical-pair production to sense the Earth’s magnetic field for migratory purposes (the avian compass). Pair production involves the protein cryptochrome and resides in the bird’s eye.

Olfactory sense: Traditional theories of olfaction describe a “lock & key” method where molecules (the key) are detected if they fit into a specific geometric configuration (the lock). We have about 400 differently shaped smell receptors, but recognize 100,000 different smells. For example, the human nose can distinguish ferrocene and nickelocene which both have similar geometry. It has been proposed that the olfactory sense uses quantum electron tunneling to detect the vibrational spectra of molecules.

Vision receptors: One of the key proteins involved in animal vision is called retinal. The retinal molecule undergoes conformational change upon absorption of a photon. This allows humans to detect even just a handful of emitted photons. The protein rhodopsin, active in octopi in the dark ocean depths, may be able to detect single photons.

Consciousness: R. Penrose was the first to propose that quantum mechanics had a role in consciousness in his book “The Emperor’s New Mind” (1989). Together with S. Hameroff, he developed a theory known as Orch-OR (orchestrated objective reduction) which has received much attention. While the theory remains highly controversial, it has been instrumental in jump starting research into possible relationships between quantum mechanics and consciousness. The compelling notion behind this has to do with quantum’s departure from determinism – a.k.a. the “annihilation operator” of freewill, i.e. quantum probabilities could potentially allow freewill to enter the picture. Generally, the thinking is that wave function collapse has something to do with conscious choice. The conversation about consciousness is a deeply fascinating subject unto itself and we will address this in a subsequent supposition.

Mutation: In 1953, shortly after discovering DNA, J. Watson and F. Crick proposed that mutation may occur through a process called tautomerization. The DNA sequence is comprised of nucleotides: cytosine, adenine, guanine and thymine. The only difference between guanine and thymine is the location of a hydrogen atom in the molecular structure. Tautomerization is a process by which the hydrogen atom quantum tunnels through the molecular structure to allow guanine to transform into thymine, and similarly adenine into cytosine. Only recently have quantum simulations become sophisticated enough to test this hypothesis. This paper “UV-Induced Proton Transfer between DNA Strands” by Y. Zhang et al. (2015) shows experimental evidence that ultraviolet (UV) photons can induce tautomerization. This is a very important mechanism we will return into later.

Even with the growth and success of quantum biology, and the advances in sustaining quantum entanglement (e.g. 10 billion ions entangled for 39 minutes at room temperature – 2013), some scientists look at the warm, wet environment of living organisms and conclude there is no way “to keep decoherence at bay” in such an environment. Such arguments are formidable in the context of static quantum systems – like those used for developing present day quantum computers. But, biological systems tend to be dynamical, operating far from thermal equilibrium, with lots of noise and many accessible quantum rotational, vibrational, torsional and quasiparticle states. Moreover, we have discussed the importance of managing complexity in machine learning (chapter II and III), science has had a lot of success with classical molecular chemistry (balls and sticks), and, classical calculations are much simpler than quantum calculations. Shouldn’t we cling to this simpler approach until it is utterly falsified? Maybe so, but while quantum mechanical calculations are certainly more computationally intensive, they may not be more complex as a theory. More importantly, classical science is simply struggling to correctly predict observed results all over biological systems. A thorough study of quantum biological processes is deservedly well underway.

In 2009 J. Cai, S. Popescu, and H. Briegel published a paper entitled “Dynamic entanglement in oscillating molecules and potential biological implications” (follow-up enhancements in 2012 are here) which has shown that entanglement can continually recur in biological molecules in a hot noisy environment in which no static entanglement can survive. Conformational change is ubiquitous in biological systems – this is the shape changing that many proteins rely on to function. Conformational change induced by noisy, thermal energy in the environment repetitively pushes two sites of the bio-molecule together entangling them. When the two sites come together, they “measure” each other. That means that their spins must either line up together, or be opposite. The system will sit in a superposition of both, with each spin dependent upon the other, i.e. entangled, during at least a portion of the oscillation cycle. If the conformational recurrence time is less than the decoherence time, entanglement may be preserved indefinitely. Entanglement can be continually restored even in the presence of very intense noise. Even when all entanglement is temporarily lost, it will be restored cyclically. We wonder if there were not only two sites, but a string of sites, could a wave of entanglement spread, via this method, throughout the system? Followed by a wave of decoherence. In such a circumstance, perhaps an “envelope” of entanglement might cascade through the system (as we discussed in chapter VI). Such a question could be addressed in the context of quantum dynamical models as in the solution to the quantum measurement problem.

Figure 19: “Conformational changes of a bio-molecule, induced, for example, by the interaction with some other chemical, can lead to a time-dependent interaction between different sites (blue) of the molecule.” – from “Dynamic entanglement in oscillating molecules and potential biological implications” by J. Cai, S. Popescu, and H. Briegel (2009)

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