The Gene Machine and its control

Survival machines began as passive receptacles for the genes, providing little more than walls to protect them from the chemical warfare of their rivals and the ravages of accidental molecular bombardment. In the early days they ‘fed’ on organic molecules freely available in the soup. This easy life came to an end when the organic food hi the soup, which had been slowly built up under the energetic influence of centuries of sunlight, was all used up. A major branch of survival machines, now called plants, started to use sunlight directly themselves to build up complex molecules from simple ones, re-enacting at much higher speed the synthetic processes of the original soup. Another branch, now known as animals, ‘discovered’ how to exploit the chemical labours of the plants, either by eating them, or by eating other animals. Both main branches of survival machines evolved more and more ingenious tricks to increase their efficiency in then- various ways of life, and new ways of life were continually being opened up. Sub-branches and sub-subbranches evolved, each one excelling in a particular specialized way of making a living: in the sea, on the ground, in the air, underground, up trees, inside other living bodies. This sub-branching has given rise to the immense diversity of animals and plants which so impresses us today.

Both animals and plants evolved into many-celled bodies, complete copies of all the genes being distributed to every cell. We do not know when, why, or how many times independently, this happened. Some people use the metaphor of a colony, describing a body as a colony of cells. I prefer to think of the body as a colony of genes, and of the cell as a convenient working unit for the chemical industries of the genes.

Colonies of genes they may be but their behaviour, bodies have undeniably acquired an individuality of their own. An animal moves as a coordinated whole, as a unit. Subjectively I feel like a unit, not a colony. This is to be expected. Selection has favoured genes that cooperate with odiers. In the fierce competition for scarce resources, in the relentless struggle to eat other survival machines, and to avoid being eaten, there must have been a premium on central coordination rather than anarchy within the communal body. Nowadays the intricate mutual co-evolution of genes has proceeded to such an extent that the communal nature of an individual survival machine is virtually unrecognizable. Indeed many biologists do not recognize it, and will disagree with me.

 

The control of the survival machines

The apparatus they use for timing their movements has more in common with an electronic computer, although it is stricdy different in fundamental operation. The basic unit of biological computers, the nerve cell or neurone, is really nothing like a transistor in its internal workings. Certainly the code in which neurones communicate with each other seems to be a little bit like the pulse codes of digital computers, but the individual neurone is a much more sophisticated data-processing unit than the transistor. Instead of just direct connections with other components, a single neurone may have tens of thousands. The neurone is slower than the transistor, but it has gone much further in the direction of miniaturization, a trend which has dominated the electronics industry over the past two decades. This is brought home by the fact that there are some ten thousand million neurones in the human brain: you could pack only a few hundred transistors into a skull.

Neurones are basically just cells, with a nucleus and chromosomes like other cells. But their cell walls are drawn out in long, thin, wirelike projections. Often a neurone has one particularly long ‘wire’ called the axon. Although the width of an axon is microscopic, its length may be many feet: there are single axons which run the whole length of a giraffe’s neck. The axons are usually bundled together in thick multi-stranded cables called nerves. These lead from one part of the body to another carrying messages, rather like trunk telephone cables. Other neurones have short axons, arid are confined to dense concentrations of nervous tissue called ganglia, or, when they are very large, brains. Brains may be regarded as analogous in function to computers.* They are analogous in that both types of machine generate complex patterns of output, after analysis of complex patterns of input, and after reference to stored information.

The main way in which brains actually contribute to the success of survival machines is by controlling and coordinating the contractions of muscles. To do this they need cables leading to the muscles, and these are called motor nerves. But this leads to efficient preservation of genes only if the timing of muscle contractions bears some relation to the timing of events in the outside world. It is important to contract the jaw muscles only when the jaws contain something worth biting, and to contract the leg muscles in running patterns only when there is something worth running towards or away from. For this reason, natural selection favoured animals that became equipped with sense organs, devices which translate patterns of physical events in the outside world into the pulse code of the neurones. The brain is connected to the sense organs—eyes, ears, taste-buds, etc.—by means of cables called sensory nerves. The workings of the sensory systems are particularly baffling, because they can achieve far more sophisticated feats of pattern-recognition than the best and most expensive man-made machines; if this were not so, all typists would be redundant, superseded by speech-recognizing machines, or machines for reading handwriting. Human typists will be needed for many decades yet.

It is a common misconception that because a machine such as a guided missile was originally designed and built by conscious man, then it must be truly under the immediate control of conscious man. Another variant of this fallacy is ‘computers do not really play chess, because they can only do what a human operator tells them’. It is important that we understand why this is fallacious, because it affects our understanding of the sense in which genes can be said to ‘control’ behaviour. Computer chess is quite a good example for making the point, so I will discuss it briefly.

Computers do not yet play chess as well as human grand masters, but they have reached the standard of a good amateur. More strictly, one should say programs have reached the standard of a good amateur, for a chess-playing program is not fussy which physical computer it uses to act out its skills. Now, what is the role of the human programmer? First, he is definitely not manipulating the computer from moment to moment, like a puppeteer pulling strings. That would be just cheating. He writes the program, puts it in the computer, and then the computer is on its own: there is no further human intervention, except for the opponent typing in his moves. Does the programmer perhaps anticipate all possible chess positions, and provide the computer with a long list of good moves, one for each possible contingency? Most certainly not, because the number of possible positions in chess is so great that the world would come to an end before the list had been completed. For the same reason, the computer cannot possibly be programmed to try out ‘in its head’ all possible moves, and all possible follow-ups, until it finds a winning strategy. There are more possible games of chess than there are atoms in the galaxy. So much for the trivial non-solutions to the problem of programming a computer to play chess. It is in fact an exceedingly difficult problem, and it is hardly surprising that the best programs have still not achieved grand master status.

The programmer’s actual role is rather more like that of a father teaching his son to play chess. He tells the computer the basic moves of the game, not separately for every possible starting position, but in terms of more economically expressed rules. He does not literally say in plain English ‘bishops move in a diagonal’, but he does say something mathematically equivalent, such as, though more briefly: ‘New coordinates of bishop are obtained from old coordinates, by adding the same constant, though not necessarily with the same sign, to both old x coordinate and old y coordinate.’ Then he might program in some ‘advice’, written in the same sort of mathematical or logical language, but amounting in human terms to hints such as ‘don’t leave your king unguarded’, or useful tricks such as ‘forking’ with the knight. The details are intriguing, but they would take us too far afield. The important point is this. When it is actually playing, the computer is on its own, and can expect no help from its master. All the programmer can do is to set the computer up beforehand in the best way possible, with a proper balance between lists of specific knowledge, and hints about strategies and techniques.

The genes too control the behaviour of their survival machines, not directly with their fingers on puppet strings, but indirectly like the computer programmer. All they can do is to set it up beforehand; then the survival machine is on its own, and the genes can only sit passively inside. Why are they so passive? Why don’t they grab the reins and take charge from moment to moment? The answer is that they cannot because of time-lag problems.

Genes work by controlling protein synthesis. This is a powerful way of manipulating the world, but it is slow. It takes months of patiently pulling protein strings to build an embryo. The whole point about behaviour, on the other hand, is that it is fast. It works on a time-scale not of months but of seconds and fractions of seconds. Something happens in the world, an owl flashes overhead, a rustle in the long grass betrays prey, and in milliseconds nervous systems crackle into action, muscles leap, and someone’s life is saved—or lost. Genes don’t have reaction-times like that.

 

 

The Origin of ‘Life’

It is no good taking the right number of atoms and shaking them together with some external energy till they happen to fall into the right pattern, and out drops Adam! You may make a molecule consisting of a few dozen atoms like that, but a man consists of over a thousand million million million million atoms. To try to make a man, you would have to work at your biochemical cocktail-shaker for a period so long that the entire age of the universe would seem like an eye-blink, and even then you would not succeed. This is where Darwin’s theory, in its most general form, comes to the rescue. Darwin’s theory takes over from where the story of the slow building up of molecules leaves off.

The account of the origin of life that I shall give is necessarily speculative; by definition, nobody was around to see what happened. There are a number of rival theories, but they all have certain features in common. The simplified account I shall give is probably not too far from the truth.

We do not know what chemical raw materials were abundant on earth before the coming of life, but among the plausible possibilities are water, carbon dioxide, methane, and ammonia: all simple compounds known to be present on at least some of the other planets in our solar system. Chemists have tried to imitate the chemical conditions of the young earth. They have put these simple substances in a flask and supplied a source of energy such as ultraviolet light or electric sparks—artificial simulation of primordial lightning. After a few weeks of this, something interesting is usually found inside the flask: a weak brown soup containing a large number of molecules more complex than the ones originally put in. In particular, amino acids have been found—the building blocks of proteins, one of the two great classes of biological molecules. Before these experiments were done, naturally-occurring amino acids would have been thought of as diagnostic of the presence of life. If they had been detected on, say Mars, life on that planet would have seemed a near certainty. Now, however, their existence need imply only the presence of a few simple gases in the atmosphere and some volcanoes, sunlight, or thundery weather. More recently, laboratory simulations of the chemical conditions of earth before the coming of life have yielded organic substances called purines and pyrimidines. These are building blocks of the genetic molecule, DNA itself.

Processes analogous to these must have given rise to the ‘primeval soup’ which biologists and chemists believe constituted the seas some three to four thousand million years ago. The organic substances became locally concentrated, perhaps in drying scum round the shores, or in tiny suspended droplets. Under the further influence of energy such as ultraviolet light from the sun, they combined into larger molecules. Nowadays large organic molecules would not last long enough to be noticed: they would be quickly absorbed and broken down by bacteria or other living creatures. But bacteria and the rest of us are late-comers, and in those days large organic molecules could drift unmolested through the thickening broth.

At some point a particularly remarkable molecule was formed by accident. We will call it the Replicator. It may not necessarily have been the biggest or the most complex molecule around, but it had the extraordinary property of being able to create copies of itself. This may seem a very unlikely sort of accident to happen. So it was. It was exceedingly improbable. In the lifetime of a man, things that are that improbable can be treated for practical purposes as impossible. That is why you will never win a big prize on the football pools. But in our human estimates of what is probable and what is not, we are not used to dealing in hundreds of millions of years. If you filled in pools coupons every week for a hundred million years you would very likely win several jackpots.

Should we then call the original replicator molecules ‘living’? Who cares? I might say to you ‘Darwin was the greatest man who has ever lived’, and you might say ‘No, Newton was’, but I hope we would not prolong the argument. The point is that no conclusion of substance would be affected whichever way our argument was resolved. The facts of the lives and achievements of Newton and Darwin remain totally unchanged whether we label them ‘great’ or not. Similarly, the story of the replicator molecules probably happened something like the way I am telling it, regardless of whether we choose to call them ‘living’. Human suffering has been caused because too many of us cannot grasp that words are only tools for our use, and that the mere presence in the dictionary of a word like ‘living’ does not mean it necessarily has to refer to something definite in the real world. Whether we call the early replicators living or not, they were the ancestors of life; they were our founding fathers.

The next important link in the argument, one that Darwin himself laid stress on (although he was talking about animals and plants, not molecules) is competition. The primeval soup was not capable of supporting an infinite number of replicator molecules. For one thing, the earth’s size is finite, but other limiting factors must also have been important. In our picture of the replicator acting as a template or mould, we supposed it to be bathed in a soup rich in the small building block molecules necessary to make copies. But when the replicators became numerous, building blocks must have been used up at such a rate that they became a scarce and precious resource. Different varieties or strains of replicator must have competed for them. We have considered the factors that would have increased the numbers of favoured kinds of replicator. We can now see that less-favoured varieties must actually have become less numerous because of competition, and ultimately many of their lines must have gone extinct. There was a struggle for existence among replicator varieties. They did not know they were struggling, or worry about it; the struggle was conducted without any hard feelings, indeed without feelings of any kind. But they were struggling, in the sense that any mis-copying that resulted in a new higher level of stability, or a new way of reducing the stability of rivals, was automatically preserved and multiplied. The process of improvement was cumulative. Ways of increasing stability and of decreasing rivals’ stability became more elaborate and more efficient. Some of them may even have ‘discovered’ how to break up molecules of rival varieties chemically, and to use the building blocks so released for making their own copies. These proto-carnivores simultaneously obtained food and removed competing rivals. Other replicators perhaps discovered how to protect themselves, either chemically, or by building a physical wall of protein around themselves. This may have been how the first living cells appeared. Replicators began not merely to exist, but to construct for themselves containers, vehicles for their continued existence. The replicators that survived were the ones that built survival machines for themselves to live in. The first survival machines probably consisted of nothing more than a protective coat. But making a living got steadily harder as new rivals arose with better and more effective survival machines. Survival machines got bigger and more elaborate, and the process was cumulative and progressive.

Was there to be any end to the gradual improvement in the techniques and artifices used by the replicators to ensure their own continuation in the world? There would be plenty of time for improvement. What weird engines of self-preservation would the millennia bring forth? Four thousand million years on, what was to be the fate of the ancient replicators? They did not die out, for they are past masters of the survival arts. But do not look for them floating loose in the sea; they gave up that cavalier freedom long ago. Now they swarm in huge colonies, safe inside gigantic lumbering robots,* sealed off from the outside world, communicating with it by tortuous indirect routes, manipulating it by remote control. They are in you and in me; they created us, body and mind; and their preservation is the ultimate rationale for our existence. They have come a long way, those replicators. Now they go by the name of genes, and we are their survival machines.

We are survival machines, but ‘we’ does not mean just people. It embraces all animals, plants, bacteria, and viruses.

Different sorts of survival machine appear very varied on the outside and in their internal organs. An octopus is nothing like a mouse, and both are quite different from an oak tree. Yet in their fundamental chemistry they are rather uniform, and, in particular, the replicators that they bear, the genes, are basically the same kind of molecule in all of us—from bacteria to elephants. We are all survival machines for the same kind of replicator—molecules called DNA—but there are many different ways of making a living in the world, and the replicators have built a vast range of machines to exploit them. A monkey is a machine that preserves genes up trees, a fish is a machine that preserves genes in the water; there is even a small worm that preserves genes in German beer mats. DNA works in mysterious ways.

For simplicity I have given the impression that modern genes, made of DNA, are much the same as the first replicators in the primeval soup. It does not matter for the argument, but this may not really be true. The original replicators may have been a related kind of molecule to DNA, or they may have been totally different. In the latter case we might say that their survival machines must have been seized at a later stage by DNA. If so, the original replicators were utterly destroyed, for no trace of them remains in modern survival machines. Along these lines, A. G. Cairns-Smith has made the intriguing suggestion that our ancestors, the first replicators, may have been not organic molecules at all, but inorganic crystals— 3 minerals, little bits of clay. Usurper or not, DNA is in undisputed charge today, unless, as I tentatively suggest in Chapter 11, a new seizure of power is now just beginning.

A DNA molecule is a long chain of building blocks, small molecules called nucleotides. Just as protein molecules are chains of amino acids, so DNA molecules are chains of nucleotides. A DNA molecule is too small to be seen, but its exact shape has been ingeniously worked out by indirect means. It consists of a pair of nucleotide chains twisted together in an elegant spiral; the ‘double helix’; the ‘immortal coil’. The nucleotide building blocks come in only four different kinds, whose names may be shortened to A, T, C, and G. These are the same in all animals and plants. What differs is the order in which they are strung together. A G building block from a man is identical in every particular to a G building block from a snail. But the sequence of building blocks in a man is not only different from that in a snail. It is also different—though less so—from the sequence in every other man (except in the special case of identical twins).

Our DNA lives inside our bodies. It is not concentrated in a particular part of the body, but is distributed among the cells. There are about a thousand million million cells making up an average human body, and, with some exceptions which we can ignore, every one of those cells contains a complete copy of that body’s DNA. This DNA can be regarded as a set of instructions for how to make a body, written in the/i, T, C, G alphabet of the nucleotides. It is as though, in every room of a gigantic building, there was a book-case containing the architect’s plans for the entire building. The ‘book-case’ in a cell is called the nucleus. The architect’s plans run to 46 volumes in man—the number is different in other species. The ‘volumes’ are called chromosomes. They are visible under a microscope as long threads, and the genes are strung out along them in order.