Magnetoreception is an enigma. The problem is that the earth’s magnetic field is very weak—between 30 and 70 microtesla at the surface: sufficient to deflect a finely balanced and almost frictionless compass needle, but only about a hundredth the force of a typical fridge magnet. This presents a puzzle: for the earth’s magnetic field to be detected by an animal it must somehow influence a chemical reaction somewhere in the animal’s body—this is, after all, how all living creatures, ourselves included, sense any external signal. But the amount of energy supplied by the interaction of the earth’s magnetic field with the molecules within living cells is less than a billionth of the energy needed to break or make a chemical bond. How, then, can that magnetic field be perceptible to the robin?
Johnjoe McFadden, Life on the Edge. Kindle Edition. loc. 116-121. Accessed: 2/6/2018
All atomic nuclei are composed of two types of particles: protons and their electrically neutral partners, neutrons. If a nucleus has too many of one type or the other, then the rules of quantum mechanics dictate that the balance has to be redressed and those excess particles will change into the other form: protons will become neutrons, or neutrons protons, via a process called beta-decay. This is precisely what happens when two protons come together: a composite of two protons cannot exist and one of them will beta-decay into a neutron. The remaining proton and the newly transformed neutron can then bind together to form an object called a deuteron (the nucleus of an atom of deuterium), after which further nuclear reactions enable the building of the more complex nuclei of other elements heavier than hydrogen, from helium (with two protons and either one or two neutrons) through to carbon, nitrogen, oxygen, and so on.
Johnjoe McFadden, Life on the Edge. Kindle Edition. loc. 230-236. Accessed: 2/6/2018
We haven’t mentioned quantum entanglement yet because it is probably the strangest feature of quantum mechanics. It allows particles that were once together to remain in instant, almost magical, communication with each other, despite being separated by huge distances. For example, particles that were once close but are later separated so far apart as to be located at opposite sides of the universe can, in principle at least, still be connected. In effect, prodding one particle would prompt its distant partner to jump instantaneously.*5 Entanglement was shown by the quantum pioneers to follow naturally from their equations, but its implications were so extraordinary that even Einstein, who gave us black holes and warped space-time, refused to accept it, deriding it as “spooky action at a distance.” And it is indeed this spooky action at a distance that so often intrigues “quantum mystics” who make extravagant claims for quantum entanglement, for example that it accounts for paranormal “phenomena” such as telepathy. Einstein was skeptical because entanglement appeared to violate his theory of relativity, which stated that no influence or signal can ever travel through space faster than the speed of light. Distant particles should not, according to Einstein, possess instantaneous spooky connections. In this, Einstein was wrong: we now know empirically that quantum particles really can have instantaneous long-range links. But, just in case you are wondering, quantum entanglement can’t be invoked to validate telepathy.
Johnjoe McFadden, Life on the Edge. Kindle Edition. loc. 278-289. Accessed: 2/7/2018
Measurement is one of the most mysterious—and certainly the most argued about—aspects of quantum mechanics, as it relates to the question that we are sure has occurred to you already: Why don’t all objects we see do all these weird and wonderful things that quantum particles can do? The answer is that, down in the microscopic quantum world, particles can behave in these strange ways, like doing two things at once, being able to pass through walls, or possessing spooky connections, only when no one is looking. Once they are observed, or measured in some way, they lose their weirdness and behave like the classical objects that we see around us. But then, of course, this only throws up another question: What is so special about measurement that allows it to convert quantum behavior to classical behavior?*7 The answer to this question is crucial to our story, because measurement lies on the borderline between the quantum and classical worlds, the quantum edge, where we, as you will have guessed from the title of this book, are claiming life also lies.
Johnjoe McFadden, Life on the Edge. Kindle Edition. loc. 301-309. Accessed: 2/9/2018
Biology is, after all, a kind of applied chemistry, and chemistry is a kind of applied physics. So isn’t everything, including us and other living creatures, just physics when you really get down to the fundamentals? This is indeed the argument of many scientists who accept that quantum mechanics must, at a deep level, be involved in biology; but they insist that its role is trivial.
Johnjoe McFadden, Life on the Edge. Kindle Edition. loc. 345-347. Accessed: 2/9/2018
But life was different: although many animals fell, they also ran; plants grew upward and birds even flew around the earth. What made them so different from the rest of the world? An answer suggested by an earlier Greek thinker, Socrates, was recorded by his pupil Plato: “What is it that, when present in a body, makes it living?—A soul.” Aristotle agreed with Socrates that living beings possessed souls, but he claimed that they came in different grades. The lowliest were those that inhabited plants, enabling them to grow and obtain nourishment; animal souls, one rung higher, endowed their hosts with feeling and movement; but only the human soul conferred reason and intellect. The ancient Chinese similarly believed that living beings were animated by an incorporeal life force called Qi (pronounced “chi”) that flowed through them. The concept of a soul was later incorporated into all of the major world religions; but its nature and its connection with the body remained mysterious.
Johnjoe McFadden, Life on the Edge. Kindle Edition. loc. 498-505. Accessed: 2/22/2018
Life, it was generally believed, was indeed just elaborate thermodynamics.
Johnjoe McFadden, Life on the Edge. Kindle Edition. loc. 639-639. Accessed: 2/23/2018
One problem is the sheer complexity of biochemical reactions going on inside every living cell. When chemists artificially produce an amino acid or a sugar they almost always synthesize only a single product at a time, which they manage by carefully controlling the experimental conditions for the selected reaction, such as temperature and the concentrations of the various ingredients, to optimize the synthesis of their target compound. This is not an easy task and requires careful control of many different conditions inside customized flasks, condensers, separation columns, filtration devices and other elaborate chemical apparatus. Yet every living cell in your body is continually synthesizing thousands of distinct biochemicals within a reaction chamber filled with just a few millionths of a microliter of fluid.*7 How do all those diverse reactions proceed concurrently? And how is all this molecular action orchestrated within a microscopic cell? These questions are the focus of the new science of systems biology; but it is fair to say that the answers remain mysterious!
Johnjoe McFadden, Life on the Edge. Kindle Edition. loc. 682-690. Accessed: 2/23/2018
Another puzzle of life is mortality. A characteristic of chemical reactions is that they are always reversible. We may write a chemical reaction in the direction: substrates → products. But, in reality, the reverse reaction: product → substrate, is also always proceeding simultaneously. It’s just that, under a given set of conditions, one direction tends to dominate. However, it is always possible to find another set of conditions that favors the reverse chemical direction. For example, when fossil fuels burn in air, the substrates are carbon and oxygen and the sole product is the greenhouse gas carbon dioxide. This is normally considered to be an irreversible reaction; but some forms of carbon capture technology are working toward reversing that process by using a source of energy to drive the reaction backward. For example, Rich Masel from Illinois University has set up a company, Dioxide Materials, which aims to use electricity to convert atmospheric carbon dioxide into vehicle fuel.1 Life is different. No one has ever discovered a condition that favors the direction: dead cell → live cell. This was of course the puzzle that prompted our ancestors to come up with the idea of a soul. We no longer believe that a cell possesses any kind of soul; but what is it then that is irrevocably lost when a cell or a person dies?
Johnjoe McFadden, Life on the Edge. Kindle Edition. loc. 690-700. Accessed: 2/23/2018
The Nobel Prize–winning physicist Richard Feynman is credited with insisting that “what we can’t make, we don’t understand.” By this definition, we do not understand life because we have not yet managed to make it. We can mix biochemicals, we can heat them, we can irradiate them; we can even, like Mary Shelley’s Frankenstein, use electricity to animate them; but the only way we can make life is by injecting these biochemicals into already living cells, or by eating them, thereby making them part of our own bodies.
Johnjoe McFadden, Life on the Edge. Kindle Edition. loc. 714-717. Accessed: 2/23/2018
The first major breakthrough—the concept of the “quantum”—was made by the German physicist Max Planck, who presented his results in a seminar to the German Physical Society on December 14, 1900, a date widely regarded as the birthday of quantum theory. The conventional understanding at the time was that heat radiation traveled, like other forms of energy, through space as a wave. The problem was that the wave theory could not explain the way certain hot objects radiate energy. So Planck proposed the radical idea that the matter in the walls of these hot bodies vibrated at certain discrete frequencies, which had the consequence that the heat energy was only radiated in tiny discrete lumps, or “quanta,” that could not be subdivided. His simple theory was remarkably successful, but was a radical departure from the classical theory of radiation, in which energy was regarded as continuous. His theory suggested that energy, instead of flowing out of matter like water pouring continuously from a tap, came out as a collection of separate, indivisible packages—as if from a slowly dripping tap. Planck was never comfortable with the idea that energy was lumpy, but five years after he proposed his quantum theory, Albert Einstein extended this idea and suggested that all electromagnetic radiation, including light, is “quantized” rather than continuous, coming in discrete packets, or particles, which we now call photons. He proposed that this way of thinking about light could account for a long-standing puzzle known as the photoelectric effect, a phenomenon whereby light could knock electrons out of matter. It was this work, rather than his more famous theories of relativity, that would win Einstein the Nobel Prize in 1921.
Johnjoe McFadden, Life on the Edge. Kindle Edition. loc. 728-740. Accessed: 2/23/2018
Heisenberg was forced to conclude that the atomic world is a ghostly, insubstantial place that crystallizes into sharp existence only when we set up a measuring device to interact with it. This is the quantum measurement process that we briefly described in the last chapter. Heisenberg showed that this process reveals only those features that it is specifically designed to measure—much as the individual instruments on the dashboard of a car each give information about just one aspect of its operation, such as its speed, the distance traveled or the temperature of the engine. Thus we could set up an experiment to determine the precise position of an electron at some given time; we could also set up a different experiment to measure the speed of the same electron. But Heisenberg showed mathematically that it is impossible to set up a single experiment in which we can measure, as accurately as we wish, both where an electron is and how fast it is moving, simultaneously.
Johnjoe McFadden, Life on the Edge. Kindle Edition. loc. 781-787. Accessed: 2/25/2018
In January 1926, at much the same time that Heisenberg was developing his ideas, the Austrian physicist Erwin Schrödinger wrote a paper outlining a very different picture of the atom. In it he proposed a mathematical equation, now known as the Schrödinger equation, which describes not the way a particle moves but the way that a wave evolves. It suggested that rather than an electron being a fuzzy particle in the atom, with an unknowable position as it orbits the nucleus, it is instead a wave spread throughout the atom. Unlike Heisenberg, who believed that it is impossible to have a picture of an electron at all when we are not measuring it, Schrödinger preferred to think of it as a real physical wave when we aren’t looking at it, which “collapses”*9 to a discrete particle whenever we do look. His version of atomic theory became known as wave mechanics and his famous equation describes how these waves evolve and behave over time. Today we regard both Heisenberg’s and Schrödinger’s descriptions as different ways of interpreting the mathematics of quantum mechanics and both, each in its own way, as correct.
Johnjoe McFadden, Life on the Edge. Kindle Edition. loc. 789-798. Accessed: 2/25/2018
When we wish to describe the motion of everyday objects, whether cannonballs or steam trains or planets, each one composed of trillions of particles, we solve the problem using a set of mathematical equations that date back to the work of Isaac Newton. But if the system we are describing resides in the quantum world, then we have to use Schrödinger’s equation instead. And here lies the profound difference between the two approaches, for in our Newtonian world the solution of an equation of motion is a number, or a set of numbers, that define(s) the precise location of an object at a given moment in time. In the quantum world, the solution of the Schrödinger equation is a mathematical quantity called the wave function, which does not tell us the precise location of, say, an electron at a particular moment in time, but instead provides a whole set of numbers that describe the likelihood of the electron’s being found at different locations in space if we were to look for it there.
Johnjoe McFadden, Life on the Edge. Kindle Edition. loc. 799-806. Accessed: 2/25/2018
The transformation of a tadpole into a frog involves a considerable amount of dismantling and reshaping of, for example, the animal’s tail, which is gradually reabsorbed into the body and its flesh recycled to form the frog’s new limbs. All of this requires the collagen-based extracellular matrix that supported the animal’s tail structure to be rapidly dismantled before being reassembled in its newly forming limbs. But, remember those sixty-eight million years under the Montana rocks: collagen fibers are not easily broken. Frog metamorphosis would take a very long time if it relied on the chemical breakdown of collagen solely by inorganic processes. Clearly an animal can’t boil its tough sinews in hot acid, and therefore needs a much milder means of dismantling its collagen fibers. This is where the enzyme collagenase comes in. But how does it—and all its fellow enzymes—work? The vitalist belief that enzyme activity was mediated by some kind of mysterious living force persisted until the late nineteenth century. At that point, one of Kühne’s colleagues, the chemist Eduard Buchner, demonstrated that nonliving extracts from yeast cells could stimulate precisely the same chemical transformations brought on by the live cells. Buchner went on to make the revolutionary proposal that the vital force was nothing more than a form of chemical catalysis.
Johnjoe McFadden, Life on the Edge. Kindle Edition. loc. 1143-1153. Accessed: 3/7/2018
Catalysts differ from the reactants (the initial substances participating in the reaction) because they help to speed up the reaction without taking part in it or being changed by it. Buchner’s claim was therefore that enzymes were no different in principle from the kind of inorganic catalyst discovered by Phillips.
Johnjoe McFadden, Life on the Edge. Kindle Edition. loc. 1160-1163. Accessed: 3/7/2018
So the key events of respiration actually have very little to do with the process of breathing, but consist instead of an orderly transfer of electrons through a relay of respiratory enzymes inside our cells. Each electron transfer event, between one enzyme and the next in the relay, takes place across a gap of several tens of angstroms—a distance of many atoms—much farther than was thought to be possible for conventional electron-hopping. The puzzle of respiration is how these enzymes are able to shift the electrons so quickly and efficiently across such big molecular gaps.
Johnjoe McFadden, Life on the Edge. Kindle Edition. loc. 1439-1443. Accessed: 3/10/2018
Consider the example of a ball being kicked up a small hill. In order for it to reach the top and roll down the other side it has to be given a firm enough kick. As it climbs the slope it will gradually slow down, and without sufficient energy (a hard enough kick) it will simply stop and roll back again the way it came. According to classical Newtonian mechanics, the only way a ball can get across the barrier is for it to possess sufficient energy to be lifted over the energy hill. But if that ball were an electron, say, and the hill a repulsive energy barrier, then there would be a small probability that the electron would flow through the barrier as a wave, essentially making an alternative and more efficient passage through. This is quantum tunneling
Johnjoe McFadden, Life on the Edge. Kindle Edition. loc. 1496-1501. Accessed: 3/10/2018
By quantum standards, living cells are also big objects, so at first glance it would seem unlikely that quantum tunneling would be found inside hot, wet living cells whose atoms and molecules would mostly be moving incoherently. But, as we have discovered, the interior of an enzyme is different: its particles are engaged in a choreographed dance rather than a chaotic rave.
Johnjoe McFadden, Life on the Edge. Kindle Edition. loc. 1515-1518. Accessed: 3/10/2018
There are several mechanisms responsible for significant kinetic isotope effects, and one of them is quantum tunneling, which, like cycling, is extremely sensitive to the mass of the particle that is trying to tunnel. Increasing the mass makes the particle’s behavior less wave-like and hence less likely to be able to seep through an energy barrier. So doubling the mass of the atom, for example changing from normal hydrogen to deuterium, causes its probability of quantum tunneling to plummet. Finding a big kinetic isotope effect may therefore be evidence that the reaction mechanism—the route between reactants and products—involves quantum tunneling. However, it would not be conclusive since the effect might be attributable to some classical (non-quantum-driven) chemistry. But if quantum tunneling is involved, then the reaction should also show a peculiar response to temperature: its rate should plateau out at low temperatures, just as DeVault and Chance had demonstrated for electron tunneling. This is precisely what Klinman and her team discovered for the ADH enzyme; and the result provided strong evidence that quantum tunneling was involved in the reaction mechanism.
Johnjoe McFadden, Life on the Edge. Kindle Edition. loc. 1597-1606. Accessed: 3/13/2018
THE MASSACHUSETTS Institute of Technology, better known as MIT, is one of the world’s scientific powerhouses. Founded in 1861 in Cambridge, Massachusetts, it boasts nine current Nobel laureates among its one thousand professors (as of 2014). Its alumni include astronauts (one-third of NASA’s space flights were manned by MIT graduates), politicians (including Kofi Annan, former Secretary-General of the United Nations and winner of the 2001 Nobel Peace Prize), entrepreneurs such as William Redington Hewlett, cofounder of Hewlett-Packard—and, of course, lots of scientists, including the Nobel Prize–winning architect of quantum electrodynamics, Richard Feynman. Yet one of its most illustrious inhabitants is not human; it is in fact a plant, an apple tree. Growing in the President’s Garden in the shadow of the institute’s iconic Pantheonesque dome is a cutting from another tree kept at England’s Royal Botanic Gardens, which is a direct descendant of the actual tree under which Sir Isaac Newton supposedly sat when he observed the falling of his famous apple.
Johnjoe McFadden, Life on the Edge. Kindle Edition. loc. 1690-1698. Accessed: 3/13/2018
There is an aspect of that famous scene that went unnoticed by Newton and has gone unremarked upon ever since: What was the apple doing up in the tree in the first place? If the apple’s accelerated descent to the ground was puzzling, then how much more inexplicable was the bolting together of Lincolnshire air and water to form a spherical object perched in the branches of a tree? Why did Newton wonder about the comparatively trivial matter of the pull of the earth’s gravity on the apple and overlook entirely the utterly incomprehensible puzzle of the fruit’s formation in the first place?
Johnjoe McFadden, Life on the Edge. Kindle Edition. loc. 1701-1705. Accessed: 3/13/2018
What we now find is that, with each firing of the atom gun that is accompanied by the appearance of a bright dot on the screen, either the left or the right detector beeps, never both. Surely we now have proof at last that the interfering atoms do indeed go through either one slit or the other, but not both simultaneously. But, be patient and keep watching the screen. As lots of individual flashes of light build up and coalesce, we see that what is produced is no longer an interference pattern. In its place are just two bright bands, indicating the collection of a pile of atoms behind each slit, just like we had in the experiment with bullets. The atoms are now behaving like conventional particles throughout the experiment. It is as though each atom behaves like a wave when it is confronted by the slits, unless it is being spied upon, in which case it innocently remains as a tiny particle.
Johnjoe McFadden, Life on the Edge. Kindle Edition. loc. 1844-1850. Accessed: 3/17/2018
How is it that atoms behaved as particles when the detector over the left slit was switched on, but as soon as it was switched off they behaved like waves? How does a particle going through the right slit know that the detector over the left slit is switched on or off?
Johnjoe McFadden, Life on the Edge. Kindle Edition. loc. 1864-1866. Accessed: 3/17/2018
So instead of individual atoms going through the two-slit experiment we have to consider the wave function traveling from source to back screen. On encountering the slits, the wave function splits in two, with each half going through one of the slits. Note that what we are describing here is the way an abstract mathematical quantity changes in time. It is pointless to ask what is really going on, since we would have to look to check. But as soon as we try to do so we alter the outcome. Asking what is really going on between observations is like asking whether your fridge light is on before you open the fridge door: you can never know because as soon as you peek you change the system.
Johnjoe McFadden, Life on the Edge. Kindle Edition. loc. 1885-1890. Accessed: 3/17/2018
We can imagine following the wave function describing the single atom as it leaves the source. It behaves just like a wave that flows toward the slits, so, at the level of the first screen, it will be of equal amplitude in each slit. If we place a detector on one of the slits, then we should expect equal probabilities: 50 percent of the time we will detect the atom at the left slit and 50 percent of time we will detect it at the right slit. But—and this is the important bit—if we don’t try to detect the atom at the level of the first screen then the wave function flows through both slits without collapsing. Thereafter, in quantum terms we can talk of a wave function describing a single atom that is in a superposition: of its being in two places at the same time, corresponding to its wave function going through both the left and right slits simultaneously.
Johnjoe McFadden, Life on the Edge. Kindle Edition. loc. 1898-1904. Accessed: 3/17/2018
It is important to remember that this reinforcement and cancellation process—quantum interference—takes place even when only a single particle is involved. Remember that there are regions of the screen that atoms, fired one at a time, could reach with just one slit open but that were no longer reachable when both slits are open. This only makes sense if each atom released from the atom gun is described by a wave function that can explore both paths simultaneously. The combined wave function with its regions of constructive and destructive interference cancels out the probability of the atom being found in some positions on the screen that it would reach if only one slit were open.
Johnjoe McFadden, Life on the Edge. Kindle Edition. loc. 1912-1917. Accessed: 3/17/2018
In fact, the transfer of captured photon energy from a chlorophyll antenna molecule to the reaction center boasts the highest efficiency of any known natural or artificial reaction: close to 100 percent. Under optimal conditions, nearly every energy parcel absorbed by a chlorophyll molecule makes it to the reaction center.
Johnjoe McFadden, Life on the Edge. Kindle Edition. loc. 2051-2053. Accessed: 3/24/2018
As we discovered in the last chapter, the capturing of electrons from any substance is called oxidation, and it is the same process that takes place during burning. When wood burns in air, for example, oxygen atoms pull electrons from carbon atoms. The electrons in the outer orbit of carbon are fairly loosely attached, which is why carbon burns easily. However, in water they are held very tightly: photosynthesis systems are unique in that they are the only place in the natural world where water is “burnt” to yield electrons.
Johnjoe McFadden, Life on the Edge. Kindle Edition. loc. 2117-2120. Accessed: 3/24/2018
By comparing photosynthesis in plants with the respiration (burning our food) that takes place in our own cells, discussed in the last chapter, you can see that, under the skin, animals and plants are not so different. The essential distinction lies in where we, and they, get the fundamental building blocks of life. Both need carbon, but plants obtain it from air whereas we get it from organic sources, such as the plants themselves. Both need electrons to build biomolecules: we burn organic molecules to capture their electrons, while plants use light to burn water to capture its electrons. And both need energy: we scavenge it from the high-energy electrons that we obtain from our food by running them down respiratory energy hillsides; plants capture the energy of solar photons. Each of these processes involves the motion of fundamental particles that are governed by quantum rules. Life seems to be harnessing quantum processes to help it along.
Johnjoe McFadden, Life on the Edge. Kindle Edition. loc. 2138-2145. Accessed: 3/24/2018
Still, the quantum world appears very strange to us and it is often claimed that this strangeness is a symptom of a fundamental split between the world we see around us and its quantum underpinnings. But in reality there is only a single set of laws that govern the way the world behaves: quantum laws.*8 The familiar statistical laws and Newtonian laws are, ultimately, quantum laws that have been filtered through a decoherence lens that screens out the weird stuff (which is why quantum phenomena appear weird to us). Dig deeper and you will always find quantum mechanics lurking at the heart of our familiar reality.
Johnjoe McFadden, Life on the Edge. Kindle Edition. loc. 2159-2164. Accessed: 3/24/2018
As a freshman, Axel threw himself into the intellectual maelstrom of university life in the 1960s. But to support his party-going lifestyle he took a job washing glassware in a molecular genetics laboratory. He became fascinated by this emerging science, but remained hopeless at glass washing, so was sacked from that job and rehired as a research assistant. Torn between literature and science, he eventually decided to enroll in a graduate genetics course but then switched to studying medicine to escape the Vietnam draft. He was apparently as bad at medicine as he’d been at glass washing. He couldn’t hear a heart murmur and never saw the retina; his glasses once fell into an abdominal incision and he even managed to sew a surgeon’s finger to his patient. He was eventually allowed to graduate only on condition that he promise never to practice medicine on living patients. He returned to Columbia to study pathology, but after a year the chairman of the department insisted that he should never practice on dead patients either.
Johnjoe McFadden, Life on the Edge. Kindle Edition. loc. 2378-2385. Accessed: 3/25/2018
Using a Pavlovian conditioning setup, the researchers even managed to train the flies to associate certain forms of chemicals with punishment: a mild electric shock to their feet. The team was then able to perform an even more remarkable test of the vibration theory. They first trained flies to avoid compounds with the carbon–deuterium bond, with its characteristic vibration at 66 terahertz. They then wanted to discover whether this avoidance could be generalized to very different compounds that happened to possess a bond vibration at the same frequency. And it could. The team discovered that the flies trained to avoid compounds with the carbon–deuterium bond also avoided compounds called nitriles whose carbon–nitrogen bond vibrates at the same frequency, despite being chemically very different. The study provided strong support for a vibration component of olfaction, at least in flies, and was published in the prestigious science journal Proceedings of the National Academy of Science in 2011.
Johnjoe McFadden, Life on the Edge. Kindle Edition. loc. 2645-2652. Accessed: 3/25/2018
They proposed that the binding pocket of the olfactory receptor works like a swipe-card machine. Swipe cards have a magnetic strip that is read to generate an electric current in the swipe-card machine. But not everything fits into a swipe-card reader: the card has to be the right shape and thickness, with its magnetic strip in the right place, before you can even use it and check whether the machine recognizes it. Brookes and her colleagues proposed that olfactory receptors work in a similar way. An odorant molecule, the team postulated, must first fit into a left- or right-handed chiral binding pocket, rather like a credit card fitting in a card reader. So odorants with the same bonds but different shapes, such as a left-handed and a right-handed version of the same molecule, will be picked up by different receptors. Only after either odorant has fitted into its complementary receptor does it have the potential to stimulate the vibration-induced electron tunneling event to make the receptor neuron fire; but because the left-handed molecule will be firing a left-handed receptor, it will smell different from a right-handed molecule firing a right-handed receptor.
Johnjoe McFadden, Life on the Edge. Kindle Edition. loc. 2671-2679. Accessed: 3/25/2018
So let’s imagine you try the same trick, as above, but somehow arrange for one die to be thrown on earth and the other to be thrown simultaneously on Mars. Even at its closest distance from earth, light takes four minutes to travel between the two planets, so you know that any synchronizing signal must suffer a similar delay. To beat it, you simply arrange for the two dice to be thrown at intervals more frequent than this. This should prevent any signal from synchronizing the dice between throws. If they continue to fall on matching numbers, then there would seem to have to be an intimate connection between them that ignores Einstein’s famous limitation. Although the above experiment hasn’t been performed with interplanetary dice, analogous experiments have been performed with quantum-entangled particles on earth, and the results show that separated particles can perform the same kind of trick that we imagined for our dice: their state can remain correlated irrespective of the distance between them. This bizarre feature of the quantum world seems not to respect Einstein’s cosmic speed limit, for a particle in one place can instantaneously influence another, however far apart the two may be. The term “entanglement” to describe this phenomenon was coined by Schrödinger who, along with Einstein, was not a fan of what Einstein referred to as “spooky action at a distance.” But, despite their skepticism, quantum entanglement has been proved in many experiments and is one of the most fundamental ideas in quantum mechanics, with many applications and examples in physics and chemistry—and, as we shall see, possibly in biology too.
Johnjoe McFadden, Life on the Edge. Kindle Edition. loc. 3038-3050. Accessed: 3/26/2018
But remember that the Vostok organisms have been locked under the ice for many hundreds of thousands of years. The similarity of their DNA sequences to those of organisms that live above the ice is thus a consequence of shared ancestry from organisms that must have lived among the flora and fauna of Antarctica before the lake and its inhabitants were locked away beneath the ice. The gene sequences of those ancestral organisms were then copied, independently, both above and below the ice, for thousands of generations. Yet despite this long chain of copying events, the twin versions of the same genes have remained nearly identical. Somehow, the complex genetic information that determines the shape, characteristics and function of the organisms that live both above and beneath the ice has been faithfully transmitted, with hardly any errors, over hundreds of thousands of years.
Johnjoe McFadden, Life on the Edge. Kindle Edition. loc. 3305-3311. Accessed: 3/26/2018
We tend to take for granted the ability of living organisms to replicate their genomes accurately, but it is in fact one of the most remarkable and essential aspects of life. The rate of copying errors in DNA replication, what we call mutations, is usually less than one in a billion. To get some idea of this extraordinary level of accuracy, consider the one million or so letters, punctuation marks and spaces in this book. Now consider one thousand similarly sized books in a library and imagine you had the job of faithfully copying every single character and space. How many errors do you think you would make? This was precisely the task performed by medieval scribes, who did their best to hand-copy texts before the invention of the printing press. Their efforts were, not surprisingly, riddled with errors, as shown by the variety of divergent copies of medieval texts. Of course, computers are able to copy information with a very high degree of fidelity, but they do so with the hard edges of modern electronic digital technology. Imagine building a copying machine out of wet, squishy material. How many errors do you think it would make in reading and writing its copied information? Yet when that wet squishy material is one of the cells in your body and the information is encoded in DNA then the number of errors is less than one in a billion.
Johnjoe McFadden, Life on the Edge. Kindle Edition. loc. 3321-3330. Accessed: 3/26/2018
Schrödinger was right: genes are written in quantum letters, and the fidelity of heredity is provided by quantum rather than classical laws. Just as the shape of a crystal is determined ultimately by quantum laws, so the shape of your nose, the color of your eyes and aspects of your character are determined by quantum laws operating within the structure of a single molecule of DNA that you inherited from one or other of your parents. As Schrödinger predicted, life works via order that goes all the way down from the structure and behavior of whole organisms to the position of protons along its DNA strands—order from order—and it is this order that is responsible for the fidelity of heredity.
Johnjoe McFadden, Life on the Edge. Kindle Edition. loc. 3397-3401. Accessed: 3/26/2018
Once again, this process of adaptation through mutation (DNA replication errors) within Lake Vostok is a microcosm of the process that has been taking place around the globe for billions of years. The earth has suffered many major catastrophes throughout its long history, from huge volcanic eruptions to ice ages and meteor impacts. Life would have perished if it hadn’t adapted to change via copying errors. Just as important, mutations have also been the driver of the genetic changes that turned the simple microbes that first evolved on our planet into the hugely diverse biosphere of today. A little infidelity
Johnjoe McFadden, Life on the Edge. Kindle Edition. loc. 3409-3414. Accessed: 4/1/2018
Once again, this process of adaptation through mutation (DNA replication errors) within Lake Vostok is a microcosm of the process that has been taking place around the globe for billions of years. The earth has suffered many major catastrophes throughout its long history, from huge volcanic eruptions to ice ages and meteor impacts. Life would have perished if it hadn’t adapted to change via copying errors. Just as important, mutations have also been the driver of the genetic changes that turned the simple microbes that first evolved on our planet into the hugely diverse biosphere of today. A little infidelity goes a long way, given sufficient time.
Johnjoe McFadden, Life on the Edge. Kindle Edition. loc. 3409-3414. Accessed: 4/1/2018
We have explored many of these revelations in earlier chapters, but all those we have so far discussed, from magnetic compasses to enzyme action, from photosynthesis to heredity to olfaction, can be discussed in terms of conventional chemistry and physics. While quantum mechanics may be unfamiliar, particularly from many biologists’ perspectives, it nevertheless fits completely within the framework of modern science. And although we may not have an intuitive or commonsense grasp of what is going on in the two-slit experiment or quantum entanglement, the mathematics that underpins quantum mechanics is precise, logical and incredibly powerful. But consciousness is different. Nobody knows where or how it fits in with the kind of science that we have discussed so far. There are no (reputable) mathematical equations that include the term “consciousness,” and unlike, say, catalysis or energy transport, it has not, so far, been discovered in anything that isn’t alive. Is it a property of all life? Most people would think not, and would reserve consciousness for those creatures that possess nervous systems; but then how much of a nervous system is necessary? Do clownfish yearn for their home reef? Did our European robin really feel an urge to fly south for the winter, or was she on automatic pilot like a drone aircraft? Most pet owners are convinced that their dogs, cats or horses are conscious; so did consciousness emerge in mammals? Many people who keep budgerigars or canaries are equally sure that their pets also have their own personalities and are just as conscious as the cats that chase them. But if consciousness is common to both birds and mammals, then both probably inherited the property from a common conscious ancestor, perhaps something like the primitive reptile called an amniote that lived more than three hundred million years ago and appears to be the ancestor of birds, mammals and dinosaurs. So, did the Tyrannosaurus rex that we met in chapter 3 experience fear as it sank into the Triassic swamp? And are more primitive animals really unconscious? Many aquarium owners would insist that fish or molluscs such as octopi are conscious; but to find an ancestor to all these groups we have to go back to the emergence of vertebrates in the Cambrian period five hundred million years ago. Is consciousness really that ancient?
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Consciousness allows our mind to be driven by ideas and concepts, rather than mere stimuli.
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For example, adding one more bit to an 8-bit classical computer will increase its power by a factor of one-eighth; to double its power, the number of bits will have to be doubled. But simply adding one qubit to a quantum computer will double its power, leading to the same kind of exponential increase in power that the emperor saw running away with his rice grains. In fact, if a quantum computer could maintain coherence and entanglement within just 300 qubits, which could potentially involve just 300 atoms, it could outperform, on certain tasks, a classical computer the size of the entire universe!
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Urey was initially skeptical about his enthusiastic student’s plans to put the Oparin–Haldane theory to the test: it might, he reckoned, take millions of years for inorganic chemical reactions to generate a sufficient number of organic molecules to be detected, while Miller had just three years to get his PhD! Nevertheless, Urey was prepared to give him the space and resources he needed for six months to a year. That way, if the experiments were not going anywhere, Miller would have time to switch to a safer research project. In his attempt to replicate the conditions in which life originated on the early earth, Miller simulated the primordial atmosphere by simply filling a bottle with water, to represent the ocean, topped up with the gases that he thought would have been present in the atmosphere: methane, hydrogen, ammonia and water vapor. He then simulated lightning by igniting the mixture with electric sparks. To Miller’s surprise, and to the general astonishment of the scientific world, he discovered that after only a week of sparking his primordial atmosphere the bottle contained significant quantities of amino acids, the building blocks of proteins. The paper describing this experiment was published in the journal Science in 19531—with Miller as sole author, Harold Urey having adopted the highly unusual position of insisting that his PhD student gain full credit for the discovery.
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Returning then to our origin-of-life problem, although a living cell as a whole is a self-replicating entity, its individual components are not; just as a woman is a self-replicator (with a little “help”), but her heart or liver is not. This creates a problem when trying to extrapolate backward from today’s complex cellular life to its much simpler noncellular ancestor. If you put it another way, the question becomes: 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?
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The idea that a world of self-replicating RNA molecules preceded the emergence of DNA and cells is now almost dogma in origin-of-life research. Ribozymes have been shown to be able to perform all the key reactions expected of any self-replicating molecule. For example, one class of ribozymes can join two RNA molecules together, whereas another can break them apart. Yet another form of ribozyme can make copies of short strings (just a handful of bases long) of RNA bases. From these simple activities we can imagine a more complex ribozyme able to catalyse the complete set of reactions necessary for self-replication. Once self-replication kicks in, then so too does natural selection; so the RNA world would have been set on a competitive path that led eventually, or so it is argued, to the first living cell.
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However, chemists are able to synthesize the RNA bases from simple chemicals by going through a very complex series of carefully controlled reactions in which each desired product from one reaction is isolated and purified before taking it on to the next reaction. 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.2 For each step there is a minimum of about six alternative reactions that need to be avoided. This makes the chemical synthesis easy to visualize, for you can conceive of each molecule as a kind of molecular die, with each step corresponding to a throw where the number six represents generating the correct product and any other number indicates that the wrong product has been made. So, the odds of any starting molecule eventually being converted into RNA is equivalent to throwing a six 140 times in a row.
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Of course, chemists improve these stupendous odds by carefully controlling each step, but the prebiotic world would have had to rely on chance alone. Perhaps the sun came out at just the right time to evaporate a little pool of chemicals surrounding a mud volcano? Or perhaps the mud volcano erupted to add water and a little sulphur to create another set of compounds? Perhaps a lightning storm stirred up the mix and accelerated a few more chemical changes with the input of electrical energy? The questions could go on and on; but it’s easy enough to estimate the probability that, 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). The earth simply did not have enough molecules, or sufficient time, to make significant quantities of RNA in those millions of years between its formation and the emergence of life at the time suggested by the Isua rocks.
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If a molecule is not behaving quantum mechanically and finds itself, as it almost certainly will, with the wrong arrangement of atoms that is unable to self-replicate, trying out a different configuration would have to involve the geologically slow process of dismantling and rearranging molecular bonds. But, after decoherence of the equivalent quantum molecule, each of the 64 electrons and protons of our proto-enzyme will, almost instantaneously, be ready to tunnel again into a superposition of both of their possible positions to reestablish the original quantum superposition of 264 different configurations. In its 64-qubit state, the quantum proto-replicator molecule could repeat its search for self-replication in the quantum world continuously. Decoherence will rapidly collapse the superposition once again; but this time the molecule will find itself in another of its 264 different classical configurations. Once again, decoherence will collapse the superposition, and once again the system will find itself in another configuration; and this process will continue indefinitely. Essentially, in this relatively protected environment, the making and breaking of the quantum superposition state is a reversible process: the quantum coin is being continually tossed by the processes of superposition and decoherence, processes that are far more rapid than the classical making and breaking of chemical bonds. 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. The quantum coin will have been irreversibly thrown, and the first self-replicator will have been born into the classical world. Of course, this replication will have to involve some sort of biochemical process within the molecule, or between it and its surroundings, that is distinctly different from those that took place before the proto-replicator arrangement was found. In other words, there needs to be a mechanism that anchors this special configuration in the classical world before it is lost and the molecule moves on to the next quantum arrangement.
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Of course, any scenario involving quantum mechanics in the origin of life three billion years ago remains highly speculative. But, as we have discussed, even classical explanations of life’s origin are beset with problems: it isn’t easy to make life from scratch! By providing more efficient search strategies, quantum mechanics may have made the task of building a self-replicator a little easier. It almost certainly was not the whole story; but quantum mechanics could have made the emergence of life in those ancient Greenland rocks a lot more likely.
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The three strata of reality. The top layer is the visible world, filled with objects such as falling apples, cannonballs, steam trains and airplanes, whose motions are described by Newtonian mechanics. Lying beneath is the thermodynamic layer of billiard-ball-like particles whose motion is almost entirely random. This layer is responsible for generating the “order from disorder” laws that govern the behavior of objects such as steam engines. The next layer down is the layer of fundamental particles ruled by orderly quantum laws. The visible features of most of the objects that we see around us appear to be rooted in either the Newtonian or thermodynamic layers but living organisms have roots that penetrate right down to the quantum bedrock of reality.
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There are two complementary approaches to synthetic biology. The top-down approach is the one we have already met in the course of discussing how the genome-sequencing pioneer Craig Venter constructed so-called “synthetic life” by replacing the genome of a bacterium called mycoplasma with a chemically synthesized version of the same genome. This genome swap allowed his team to make relatively minor modifications to the entire mycoplasma genome. Nevertheless, it was still a mycoplasma: they did not introduce any radical changes into the bacterium’s biology. Over the coming years Venter’s team plans to engineer more radical changes; but these changes will be introduced step-by-step in this top-down synthetic biology approach. The team did not make new life: they modified existing life. The second approach is bottom-up and is far more radical: rather than modifying an existing living organism, bottom-up synthetic biology aims to engineer completely new life forms out of inert chemicals. Many would consider such an endeavor dangerous, even sacrilegious. Is it even feasible? Well, living organisms, like us, are extraordinarily elaborate machines. Like any machine, they can be reverse-engineered to discover their design principles; and those design principles can then be harnessed to build even better machines.
Johnjoe McFadden, Life on the Edge. Kindle Edition. loc. 5105-5114. Accessed: 4/18/2018
Life, we believe, depends on quantum mechanics. But are we right? As we have already discussed, this is hard to prove with the technology we have today, because you can’t just turn quantum mechanics off and on in a living cell. However, we predict that life, whether natural or artificial, is impossible without the strange features of the quantum world we have discussed in this book. The only way to find out if we are right is to make synthetic life with and (if possible) without quantum weirdness and see which one works best.
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Of course, as we have emphasized in previous chapters, we cannot yet be sure that all the features we have just described are quantum mechanical. But there is no doubt that much of what is or was wonderful and unique about robins, clownfish, bacteria that survive beneath the Antarctic ice, dinosaurs that roamed the Jurassic forests, monarch butterflies, fruit flies, plants and microbes derives from the fact that, like us, they are rooted in the quantum world. There is much that remains to be discovered; but the beauty of any new area of research is the sheer unknown. As Isaac Newton said: I do not know what I may appear to the world, but to myself I seem to have been only like a boy playing on the sea-shore, and diverting myself in now and then finding a smoother pebble or a prettier shell than ordinary, while the great ocean of truth lay all undiscovered before me.
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