Life on the Edge: The Coming of Age of Quantum Biology

by Johnjoe McFadden

Which came first: the DNA gene, the RNA, or the enzyme? If DNA or RNA came first, then what made them? If the enzyme came first, then how was it encoded?

The RNA world hypothesis, as it came to be known, proposes that primordial chemical synthesis resulted in the generation of an RNA molecule that could act as both gene and enzyme, and thus could both encode its own structure (like DNA) and make copies of itself (like enzymes) out of the biochemicals available in the primordial soup.

Although simple biochemical reactions may be catalyzed by ribozymes, self-replication of a ribozyme is a far more complex process involving recognition by the ribozyme of the sequence of its own bases, identification of identical chemicals in the ribozyme’s environment, and assembly of those chemicals in the correct sequence to make a replica of itself.

There is no known nonbiological mechanism by which the ribose sugar can be generated on its own.

The Scottish chemist Graham Cairns-Smith estimated that there are about 140 steps necessary for the synthesis of an RNA base from simple organic compounds likely to have been present in the primordial soup.

For each step there is a minimum of about six alternative reactions that need to be avoided.

So, the odds of any starting molecule eventually being converted into RNA is equivalent to throwing a six 140 times in a row.

relying on chance alone, each of the 140 necessary steps would have yielded the right one of six possible products: it is one in 6140(roughly, 10109). To have a statistical chance of making RNA by purely random processes you would need at least this number of starting molecules in your primordial soup. But 10109 is a far bigger number than even the number of fundamental particles in the entire visible universe (about 1080).

Since we seem to be having such fun with big numbers, we can work it out. It turns out that 4100 individual strings of RNA 100 bases long would have a combined mass of 1050 kilograms. So this is how much we would need, in order to have a single copy of most strings and therefore a reasonable chance that one of them would have all its bases arranged correctly to be a self-replicator. However, the entire mass of the Milky Way galaxy

Can any of these devices make a copy of itself? Probably the closest is a 3-D printer such as one of the RepRap (short for Replicating Rapid prototyper) printers that are the brainchild of Adrian Bowyer at the University of Bath in the United Kingdom. These machines can print their own components, which can then be assembled to make another RepRap 3-D printer.

However, the situation is radically different if we consider the 64 key particles in the proto-enzyme to be electrons and protons that can tunnel between their alternative positions.

In its 64-qubit state, the quantum proto-replicator molecule could repeat its search for self-replication in the quantum world continuously.

But there is one event that will terminate the quantum coin-tossing. If the quantum proto-replicator molecule eventually collapses into a self-replicator state, it will start to replicate and, just as in the starving E. coli cells we discussed in chapter 7, replication will force the system to make an irreversible transition into the classical world.

We have already explored part of the answer. Erwin Schrödinger pointed out more than sixty years ago that life is different from the inorganic world because it is structured and orderly even at a molecular level. This order all the way down endows life with a kind of rigid leverage that connects the molecular to the macroscopic, such that quantum events taking place within individual biomolecules can have consequences for an entire organism: the kind of amplification from the quantum to the macroscopic asserted by that other quantum pioneer, Pascual Jordan.

They showed that transporting the quantum coherent exciton can be either retarded or assisted by environmental noise, depending on just how loud that noise is. If the system is too cold and quiet, then the exciton tends to oscillate aimlessly without actually getting anywhere in particular; whereas in a very hot and noisy environment something called the quantum Zeno effect kicks in, which retards quantum transport. Between these two extremes is a Goldilocks zone where vibrations are just right for quantum transport.

The quantum Zeno effect, as it came to be known, describes how continuous observations can prevent quantum events from happening. For example, a radioactive atom, if observed closely and continuously, will never decay—an effect often described in terms of the old adage “the watched pot never boils.”

This is the quantum Zeno effect: constantly collapsing the quantum wave into the classical world.

Two recent papers from Martin Plenio’s group at the University of Ulm in Germany in 2012 and 2013 demonstrated that if the oscillation of the exciton and the oscillations of the surrounding proteins—the colored noise—are beating to the same drum then, when the coherent exciton gets knocked out of tune by the white noise, it can be knocked back into tune by the protein oscillations.5

Order from chaos is conceptually quite similar to Erwin Schrödinger’s “order from disorder,” which, as we have already described, lies behind the motive force of steam engines. But, as we have discovered, life is different. Although there is plenty of disorderly molecular motion inside living cells, the real action of life is a tightly choreographed motion of fundamental particles within enzymes, photosynthetic systems, DNA and elsewhere. Life has built-in order at a microscopic level; and so “order from chaos” cannot be the only explanation for life’s fundamental distinguishing features. Life is nothing like a steam train.

But in the photosynthetic reaction center of a plant or microbe, energy is used to pluck electrons right out of water molecules in which the electrons are far more tightly bound. Essentially, a pair of H2O molecules is split to produce one O2 molecule, four positively charged hydrogen ions and four electrons. So, since water molecules lose their electrons, the reaction center is the only natural place where water is oxidized.

To do this, molecular noise is used to nudge an electron into a superposition of two energy states at the same time. When this electron then absorbs the energy of a photon and is “excited,” it will remain in a superposition of two (now higher) energies at once. Now the probability of the electron falling back to its original state and losing its energy as wasted heat can be reduced, thanks to the quantum coherence of its two energy states—this is similar to the example of the interference pattern produced by the double-slit experiment we described in chapter 4. There, certain positions on the back screen that are available to the atom when just one slit is open become inaccessible owing to destructive interference when both slits are open. Here, the delicate collaboration between molecular noise and quantum coherence tunes a quantum heat engine to reduce inefficient wastage of thermal energy and thereby increase its efficiency beyond the quantum Carnot limit.

They are all equipped, not with a single chlorophyll molecule that might be able to operate a straightforward quantum heat engine, but with a pair of chlorophyll molecules known as a special pair.

Although the chlorophyll molecules in the special pair are identical, they are embedded in different environments in the protein scaffold, which makes them vibrate at slightly different frequencies: they are slightly out of tune. In their later paper, Scully and his colleagues pointed out that this structure provides photosynthetic reaction centers with the precise molecular architecture needed for them to work as quantum heat engines.

The researchers showed that the chlorophyll’s special pair appears to be tuned to exploit quantum interference to inhibit inefficient wasteful energy routes and thereby deliver energy to the accep...