EPIGRAPH

fn1 Max Delbrück, Transactions of the Connecticut Academy of Arts and Sciences, vol. 38, 173–90 (December 1949)

WHAT IS LIFE?

fn1 Vitalism also suffered from being too close in concept to another nineteenth-century fad – spiritualism, with its bizarre stories of ectoplasm and aetheric bodies.

fn2 This is a simplification: different organs die at different rates, and the bacteria that inhabit the mouse may live on for ever.

fn3 Lee Cronin of the University of Glasgow has proposed a measure of chemical complexity based on the number of steps needed to produce a given large molecule.

fn4 When information from DNA is transcribed into RNA, T is substituted for a slightly different molecule labelled U, which stands for uracil.

fn5 A terminological point: scientists cause much confusion when they refer to an organism’s ‘code’ when they really mean coded genetic data. Your genetic data and mine differ, but we have the same genetic code.

fn6 A nanometre is one billionth of a metre. ‘Nanotechnology’ refers to engineered structures on this molecular scale.

ENTER THE DEMON

fn1 I’m ignoring here the mass-energy of matter, which is mostly inert, and the mysterious dark energy of empty space. They are far more abundant.

fn2 The first law of thermodynamics is just the law of conservation of energy when heat is included as a form of energy.

fn3 The great British astronomer Sir Arthur Eddington once wrote: ‘The law that entropy always increases, holds, I think, the supreme position among the laws of Nature. If someone points out to you that your pet theory of the universe is in disagreement with Maxwell’s [electromagnetic field] equations – then so much the worse for Maxwell’s equations. If it is found to be contradicted by observation – well, these experimentalists do bungle things sometimes. But if your theory is found to be against the second law of thermodynamics I can give you no hope; there is nothing for it but to collapse in deepest humiliation.’ (Arthur Eddington, The Nature of the Physical World (Cambridge University Press, 1928), p. 74)

fn4 Maxwell assumed that the demon and the shutter are perfectly functioning devices with no friction or need for a power source. This is admittedly an idealization, but there is no known principle preventing an arbitrarily close approach to such mechanical perfection. Remember, friction is a macroscopic property where ordered motion, e.g. a ball rolling along the floor, is converted to disordered motion – heat – in which the ball’s energy is dissipated among trillions of tiny particles. But on a molecular scale, all is tiny. Friction doesn’t exist. Later I will describe some practical demonics.

fn5 The general formula is n = −log₂p, where n is the number of bits and p is the probability of each state. That must be a number between 0 and 1, hence the need for a minus sign.

fn6 It certainly is. I wrote this section of the book sitting on a beach near Sydney. When I got to the part about surprise, a stray dog walked unannounced over the keyboard. Here is what it had to add to the discussion: ‘V tvtgvtvfaal.’ I leave it to the reader to evaluate the information content of this canine interjection.

fn7 The impressive data-storage properties of DNA have created something of a cottage industry among scientists uploading poetry, books and even films into the DNA of microbes (without killing them). Craig Venter pioneered the field by inserting ‘watermarks’ in his creation, including a pertinent quotation by the physicist Richard Feynman embedded into the customized genome of a microbe that he re-engineered in his lab. More recently, a group of Harvard biologists encoded a digitized version of the famous galloping-horse movie made by Eadweard Muybridge in 1878 (to demonstrate that all four legs could be off the ground simultaneously) and embedded it into the genomes of a population of living E. coli bacteria. (See Seth L. Shipman et al., ‘CRISPR–Cas encoding of a digital movie into the genomes of a population of living bacteria’, Nature, vol. 547, 345–9 (2017).) These feats were more than a bit of recreational tinkering; they provide a graphic demonstration of a technology that could pave the way for inserting ‘data recording’ devices into cells to keep track of vital processes.

fn8 To carry this point to the extreme, let me return to the coin example. Every atom of the coin has a position in space. If you were able to measure where every atom is located, the information acquired would be astronomical. If we ignore quantum mechanics, a particle such as an electron, which for all we know has no size at all (it is a point), would represent an infinite amount of information because it would take a set of three infinitely long numbers to specify its exact location in three-dimensional space. And if just one particle has infinite information, the total information content of the universe will certainly be infinite.

fn9 Like Schrödinger and many others, Szilárd eventually fled Nazi Europe. He travelled to England and then the United States – which was fortunate for the Allies, as he was involved in early experiments with nuclear fission. It was Szilárd who, foreseeing the possibility of a German atomic bomb, persuaded Einstein to sign a joint letter to President Roosevelt in 1939, urging the US to develop its own nuclear weapons.

fn10 Because thermal fluctuations are random, the molecule will often move slower or faster than average, but one could imagine a large ensemble of identical single-occupant boxes, and, once equilibrium had been established between the molecular inhabitants of the boxes and the heat source, the distribution of velocities of the ensemble of molecules would precisely mirror those of a gas at the same temperature.

fn11 Using Shannon’s formula, I can be more precise about the demon. In Szilárd’s engine, the molecule is equally likely to be on the left of the box or on the right. By observing which, the demon reduces the uncertainty from fifty:fifty to zero, thus (according to Shannon’s formula) acquiring precisely one bit of information. When this solitary bit is used to lift a weight, the amount of energy extracted from the heat reservoir depends on the temperature, T. It is a simple calculation to work out the force on the screen due to its bombardment by the confined molecule; the higher the temperature, the greater the force. From that calculation one soon finds that the theoretical maximum amount of work extracted by Szilárd’s engine is kT ln 2. Here the quantity k (known as Boltzmann’s constant) is needed to express the answer in units of energy, such as joules. Putting in the numbers, at room temperature, one bit of information yields 3 x 10−21 joules.

fn12 A much-discussed example is bitcoin mining, which is estimated to consume more power than Denmark.

fn13 There is an important difference between physically eliminating the 1s and 0s and resetting the state of the computer’s memory to some reference state, such as all 0s, creating a ‘tabula rasa’. It was the latter that Landauer studied.

fn14 His examples of how to do it were highly idealized and need not concern us here.

fn15 For example, 0 could stand for dot and 1 for dash in Morse code.

fn16 When the physicist Richard Feynman died, he left a famous aphorism on his blackboard: ‘What I cannot build, I cannot understand.’ (It was these words that Craig Venter inscribed into his artificial organism – see p. 39.) Today, scientists are building Maxwell demons and information engines, and elucidating their operating principles. The place of information in the eternal tussle between order and chaos is finally being revealed in a practical way.

fn17 In a related experiment on the trade-off between information and heat flow, performed as part of the Brazilian National Institute of Science and Technology for Quantum Information programme, it was reported that heat was induced to flow from a colder to a hotter system (i.e. refrigeration) by using entangled quantum particles, a subject I shall explain in Chapter 5.

fn18 A process known as rectification.

fn19 Like all physical processes, even this fix occasionally goes wrong. In humans, for example, the proofread and edited RNA transcript still contains about one mistake in every 100 million letters.

fn20 You might be wondering how on Earth England could calculate the reproduction entropy, given the complexity of a bacterial cell. He is able to do it because of a fundamental connection between the entropy generated by a physical process and the rate at which the process proceeds compared to the reverse process. For example, the reverse process to synthesizing a strand of RNA from its components is destroying the said strand of RNA in similar circumstances. How might that happen? In water, RNA disintegrates spontaneously in about four days. Compare that to the roughly one hour it takes for it to be synthesized. From this ratio, the theoretical minimum entropy production can be calculated for this piece of the action. Taking all the relevant factors into consideration leads to England’s quoted estimate.

THE LOGIC OF LIFE

fn1 An axiom is a statement taken to be obviously true – such as ‘if x = y, then y = x’, which is to say that if on a farm there are the same number of sheep as goats, then there are the same number of goats as sheep.

fn2 The origins of the Entscheidungsproblem can be traced back to an earlier address by Hilbert, delivered in 1900 to the International Congress of Mathematicians at the Sorbonne in Paris.

fn3 Charles Babbage, a century earlier, arrived at the same basic concept, but he made no attempt to offer a formal proof of universal computability.

fn4 As usual, things are a bit more complicated, because both read-out and replication can occur at the same time, sometimes in the same region, risking traffic accidents. To minimize the potential chaos, genomes organize things to avoid RNA and DNA polymerases going opposite ways. In von Neumann terms, this means that life makes sure the tape moves in only one direction when the system needs to be both hardware and software at the same time.

fn5 Which raises a rather deep question about the nature of life. Everyone agrees life is complex, but is its complexity because it is the product of a complex process, or might it be the outcome of successive simple processes, as in the Game of Life? I am grateful to Sara Walker for stressing the distinction between a complex process and a complex state.

fn6 There is no mystery about correlation without causation. Let me give a simple example. Suppose I email my friend Alice in London the password protecting a secret bank account, which she immediately accesses, and a few moments later I send the same message to Bob in New York, who follows suit. A spy monitoring the account might jump to the erroneous conclusion that Alice had given Bob the password, that is, that the information about the password had passed from London to New York, thus causally linking Alice to Bob. But, in fact, Alice’s information and Bob’s information are correlated not because one caused the other but because they were caused by a common third party (me). Conflating correlation with causation is an easy trap to fall into.

fn7 There is an inevitable downside to all this, which is the possibility of bio-hacking for reasons of control or genocide.

fn8 The issue of the biological clock is a fascinating separate story. As I have mentioned, bacteria going flat out can go through the whole cycle in twenty minutes, but hardy microbes living at sub-zero temperatures, called psychrophiles, may take hundreds of years.

fn9 Simple networks like this are referred to as Boolean, after George Boole, who introduced the idea of an algebra of logical operations in the nineteenth century. They are ideal for applying Shannon’s measure of information, and elaborations thereof, based on binary (0 and 1) choices (see p. 36).

fn10 Another common communication strategy for ants is stigmergy – communication via the environment by depositing and sensing pheromones.

fn11 A scaling law is a mathematical relationship describing how a quantity increases or decreases with scale. For example, in the solar system there are a much greater number of smaller objects like asteroids and moons than there are planets.

fn12 Some cells, pluripotent stem cells, remain only partially differentiated and have the potential to become cell types of different varieties.

DARWINISM 2.0

fn1 Although electricity is key, the morphogenetic field here is not an electric field in the normal sense, extending across the developing tissue. Instead, it is a field of electric cell polarization. ‘Polarization’ is the term given to describe the voltage difference across the cell’s membrane. If that voltage drop varies from cell to cell and place to place, it may be said that there is an electric polarization field spread throughout the developing tissue. Physicists will recognize that the polarization is a scalar field, whereas electric fields are vector fields.

fn2 There have been no tests yet to see whether baby deer inherit the change.

fn3 The word ‘stress’ here, and in what follows in this chapter, doesn’t of course refer to a mental state but to circumstances in which a cell or organism is threatened or challenged in some way, for example, by starvation or wounding.

fn4 Recently a fourth line of attack – immunotherapy – has received a lot of attention. It involves supercharging the body’s immune system to destroy cancer cells. Early results we promising, but it is too soon to know if this technique will transform the field.

fn5 Multicellularity arose independently several times. True multicellularity is restricted to eukaryotes. However, bacteria can aggregate into colonies that sometimes display cancer-like phenomena.

fn6 When is that? When little caps on the end of chromosomes, called telomeres, are worn down.

fn7 The use of the term ‘stress’ here, as previously, refers to a threatening micro-environment, e.g. carcinogens, radiation or hypoxia. The widespread belief that people who feel stressed may get cancer is not obviously related to the physical stress I am discussing here.

fn8 The distinction between trigger and root cause is analogous to running a basic and well-used computer software package, e.g. Microsoft Word. The ‘open’ command triggers Word, but the ‘cause’ of the ‘Word phenomenon’ is the Word software, which has its origin in the dim and distant past of the computer industry.

fn9 Defined in this study to be those genes demonstrated to be causally implicated in cancer.

fn10 Technically, they are termed ‘orthologs’ of those genes.

SPOOKY LIFE AND QUANTUM DEMONS

fn1 We now know that quantum mechanics does not permit faster-than-light communication, undercutting Einstein’s objection.

fn2 This oft-repeated description must be interpreted cautiously. The electron doesn’t literally bifurcate. Any experiment to determine its precise location will always find it in one place or the other. But in the absence of such a measurement, there are definite physical effects stemming from its indeterminate position.

fn3 Some years ago a physics colleague of mine claimed he could sense north even when blindfolded and disoriented. He attributed it to an ability to detect the Earth’s magnetic field. As far as I know, there have been no systematic tests of this unusual ability in humans.

ALMOST A MIRACLE

fn1 When the astrophysicist Thomas Gold suggested in the late 1980s that there may exist a deep, hot biosphere, he received nothing but ridicule. Yet he was absolutely right.

fn2 There is a long history of what might be called ‘molecular Darwinism’ in which ‘naked’ molecules are able to replicate with varying efficiency and natural selection filters out the best. The so-called RNA world theory falls into this category. Though these studies are instructive, they are very contrived and require carefully managed human intervention (e.g. to prepare materials, to do the selecting) to accomplish anything. Relevance to the natural world is far from obvious.

THE GHOST IN THE MACHINE

fn1 A high-profile case occurring at the time of writing was that of Charlie Gard, a baby born with an apparently incurable syndrome that left him largely unresponsive. A legal decision was made to terminate life support rather than permit experimental treatment.

fn2 There was a famous legal test in Britain in 1973: the case of the Eyemouth prawns. A sixteen-year-old girl was charged with cruelty to animals for cooking live prawns on a hotplate. The case was eventually dropped, but not before it attracted the attention of the Soviet media. At that time Britain was going through a period of industrial turmoil and economic decline. Moscow cited the prawn case as an example of Western decadence: how could the British people be preoccupied with such trivia when the workers were in revolt against the collapsing capitalist system?

fn3 That being the title of the recent movie about Turing’s life.

fn4 ‘Computer’ is a poor choice of word here as what we today think of as a computer almost certainly couldn’t simulate consciousness.

fn5 Psychology experiments with small children suggest that full self-awareness does not develop until the age of about two.

fn6 It seems fair to say that if a neural network becomes disintegrated – if you carry on snipping – it will stop thinking altogether. Giulio Tononi’s formula for measuring consciousness adopts this basic idea. However, there may be other formulae that would work better.

EPILOGUE

fn1 The word ‘evolve’ has a very different meaning in physics from the one in use in biology, which can cause confusion.

fn2 Irreversibility arises because the information about the phases of the various branches of the wave function has been destroyed by the act of measurement.

fn3 Many scientists (de Duve included) support the idea of a cosmic imperative without feeling the need for novel laws or principles to fast-track life’s genesis. They appeal to the generality of the laws of known chemistry and eschew parochialism – why should we/Earth be so special? But this has an air of wishful thinking to it. I am totally sceptical that known chemistry embeds a life principle, for known chemistry offers no conceptual bridge between molecules and information.