The Language of the Genes

Another result which would have surprised Mendel is that one gene may control many characters. Thus, sickle-cell haemoglobin has all kinds of side-effects. People with two copies may suffer from brain damage, heart failure and skeletal abnormalities (all of which arise from anaemia and from the blockage of blood vessels). In contrast, some characters (such as height or weight) are controlled by many genes. What is more, Mendelian ratios sometimes change because one or other type is lethal, or bears some advantage.

All this (and much more) means that the study of inheritance has become more complicated in the past century and a half. Nevertheless, Mendel’s laws apply to humans as much as to any other creature.

They are beguilingly simple and have been invoked to explain all conceivable – and some inconceivable – patterns of resemblance. In the early days, long pedigrees claimed to show that outbursts of bad temper were due to a dominant gene and that there were genes for going to sea or for ‘drapetomania’ – pathological running away among slaves. This urge for simple explanations persists today, but mainly among non-scientists. Geneticists have had their fingers burned by simplicity too often to believe that Mendelism explains everything.

Mendel had no interest in what his inherited particles were made of or where they might be found. Others began to wonder what they were. In 1909 the American geneticist Thomas Hunt Morgan, looking for a candidate for breeding experiments hit upon the fruit fly. It was an inspired choice and his work, with Drosophila melanogaster (the black-bellied dew lover, to translate its name) was the first step towards making the human gene map.

Many fruit fly traits were inherited in a simple Mendelian way, but some showed odd patterns of inheritance. When peas were crossed it made no difference which parent carried green or yellow seeds. The results were the same whether the male was green and the female yellow, or vice versa. Some traits in flies gave a different result. For certain genes – such as that controlling the colour of the eye, which may be red or white – it mattered whether the mother or the father had white eyes. When white-eyed fathers were crossed with red-eyed mothers all the offspring had red eyes but when the cross was the other way round (with white-eyed mothers and red-eyed fathers) the result was different. All the sons had white eyes and the daughters red. To Morgan’s surprise, the sex of the parent that bore a certain variant had an effect on the appearance of the offspring.

Morgan knew that male and female fruit flies differ in another way. Chromosomes are paired bodies in the cell which appear as dark strands. Most of the chromosomes of the two sexes look similar but one pair – the sex chromosomes – are different. Females have two large X chromosomes; males a single X and a much smaller Y.

Morgan noticed that the pattern of inheritance of eye colour followed that of the X chromosome. Males, with just a single copy of the X (which comes from their mother, the father providing the Y) always looked like their mother. In females, the copy of the X chromosome from the mother was accompanied by a matching X from the father. In a cross between white-eyed mothers and red-eyed fathers, the female offspring have one X chromosome bearing ‘white’ and another bearing ‘red’. Just as Mendel would have expected, they have eyes like only one of the parents, in this case the one with red eyes.

The eye colour gene and the X chromosome hence show the same pattern of inheritance. Morgan suggested that this meant that the gene for eye colour was actually on the X chromosome. He called this pattern ‘sex-linkage’. Chromosomes were already candidates as the bearers of genes as, like Mendel’s hypothetical particles, their number is halved in sperm and egg compared to body cells.

Everyone has forty-six chromosomes in each body cell. Twenty-two of these are paired, but the sex chromosomes, X and Y, are distinct. Because the Y carries few genes, in males the ordinary rules of Mendelian dominance and recessivity do not apply. Any gene on the single X will show its effects in a male, whether or not it is recessive in females.

The inheritance of human colour blindness is just like that of Drosophila eye colour. When a colour-blind man marries a normal woman none of his children is affected, but a colour-blind woman whose husband has normal vision passes on the condition to all her sons but none of her daughters. Because all males with the abnormal X show its effects (while in most females the gene is hidden by one for normal vision) the trait is commoner in boys than in girls. Many other abnormalities show the same pattern.

Sex-linkage leads to interesting differences between the sexes. For the X chromosome, females carry two copies of each gene, but males only one. As a result, women contain more genetic information than do men. Because of the two different sensors for the perception of red controlled by a gene on the X chromosome, many women must carry both red receptors, each sensitive to a slightly different point in the spectrum. Males are limited to just one. As a result, some women have a wider range of sensual experience for colour at least – than is available to any man.

Whatever the merits of seeing the world in a different way, women have a potential problem with sex-linkage. Any excess of a chromosome as large as the X is normally fatal. How do females cope with two, when just one contains all the information needed to make a normal human being (or a male)? The answer is unexpected. In almost every cell in a woman’s body one or other of her two X chromosomes is switched off.

Tortoiseshell cats have a mottled appearance, which comes from small groups of yellow and black hairs mixed together. All tortoiseshells are females and are the offspring of a cross in which one parent passes on a gene for black and the other transmits one for yellow hair. Because the coat-colour gene is sex-linked about half the skin cells of the kitten switch off the X carrying the black variant and the remainder that for yellow. The coat is a mix of the two types of hair, the size of the patches varying from cat to cat.

The same happens in humans. If a woman has a colour-blind son, she must herself have one normal and one abnormal colour receptor. When a tiny beam of red or green light is scanned across her retina her ability to tell the colour of the light changes as it passes from one group of cells to the next. About half the time, she makes a perfect match but for the rest she is no better at telling red and green apart than is her colour-blind son. Different X chromosomes have been switched off in each colour-sensitive cell, either the normal one or that bearing the instruction for colour blindness.

The inheritance of mitochondrial genes also shows sexual differences. When an egg is fertilised, much of its contents, including those crucial structures, is passed on to the developing embryo. Mitochondria have a pattern of inheritance quite different from those in the nucleus. They do not bother with sex, but instead are passed down the female line. Sperm are busy little things, with a long journey to make, and are powered by many mitochondria. On fertilisation these are degraded, so that only the mother’s genes are passed on. In the body, too, mitochondria are transmitted quite passively, each cell dividing its population among its descendants. Their DNA contains the history of the world’s women, with almost no male interference. Queen Elizabeth the Second’s mitochondrial DNA descends, not from Queen Victoria (her ancestor through the male line) but from Victoria’s less eminent contemporary Anne Caroline, who died in 1881.

Mitochondria, small as they are, are the site of an impressive variety of diseases. Their sixteen and a half thousand DNA bases – less than a hundredth of the whole sequence – were, a century after the death of Anne Caroline, the first to be read off. Every cell contains a thousand or so of the structures. They are the great factories of metabolism; places where food – the fuel of life – is burned. Mitochondrial genes code for just thirteen proteins, and about twice that number of the molecules that transfer information from the DNA to where proteins are made.

They are more liable to error than are others. Some of the mistakes pass between generations, while others build up in the body itself as it ages. Some of the two hundred known faults involve single changes in the DNA, others the destruction of whole lengths of genetic material. Some are frequent: thus, a certain change in one mitochondrial gene is present in about one in seven thousand births.

Mitochondrial disease involves many symptoms: deafness, blindness, or damage to muscles or the brain. Certain forms of diabetes are due to mitochondrial errors, as is an inherited muscle weakness and drooping of the eyelids. Different patients in the same family may have distinct problems; perhaps deafness in one child and brain damage in another. All this comes from the role of mitochondria in burning energy and from their random shuffling as cells divide. An egg may carry both normal and abnormal mitochondria. If, in an embryo, those with an error become by chance common in the cell lines that make brain tissue, that organ suffers; if in cells that code for insulin, then diabetes is the result. Mothers pass such genes to sons and daughters, but only daughters pass it to the next generation; a pattern quite different from sex-linked inheritance.

These, then, are the rules of the genetical game. From here on, the rest is molecular biology: mechanics rather than physics. The notion that life is chemistry came first from humans. In 1902, just two years after the rediscovery of Mendelism, the English physician Sir Archibald Garrod noticed that a disease called alkaptonuria – at the time thought to be due to an intestinal worm – was more frequent in the children of parents who shared a recent ancestor than in those of unrelated people. Its symptoms, a darkening of the urine and the earwax, together with arthritis, followed that of a recessive. The disease was, he thought, due to an inherited failure in one of the pathways of metabolism, what he called a “chemical sport’ (Darwin’s own word for a deviation from the norm). It was the first of many inborn errors of metabolism. The actual gene itself was found just four years before the century ended. The key to its discovery showed how wide the genetical net must spread. An identical was found in a fungus, and that piece of damaged DNA used to search out its human equivalent.

What genes are made of came from the discovery it was possible to change the shape of bacterial colonies by inserting a ‘transforming principle’ extracted from a relative with different shaped colonies. That substance was DNA, discovered many years before in some rather disgusting experiments using pus-soaked bandages. It was the most important molecule in biology.

The story of how the structure of DNA, the double helix, was established is too well known to need repeating. The molecule consists of two intertwined strands, each made up of a chain of chemical bases – adenine, guanine, cytosine and thymine – together with sugars and other material. The bases pair with each other, adenine with thymine and guanine with cytosine. Each strand is a complement of the other. When they separate, one acts as the template to make a matching strand. The order of the bases along the DNA contains the information needed to produce proteins. Every protein is made up of a series of different blocks, the amino acids. The instructions to make each amino acid are encoded in a three-letter sequence of the DNA alphabet.

The inherited message contained within the DNA is passed to the cytoplasm of the cell (which is where proteins are made) through an intermediary, RNA. This ribose-nucleic acid comes in several distinct forms, each involved in passing genetic information to where it is used.

The DNA molecule – the agent of continuity between generations – has become part of our cultural inheritance. The new ability to read (and to interfere with) its message has transformed our vision of our place in nature and our dominion over its inhabitants. It is, nevertheless, worth remembering that the laws of genetics were worked out with no knowledge of where or what the inherited units might be. Like Newton, Mendel had no interest in the details. He was happy with a universe of interacting and independent particles which behaved according to simple rules. These rules worked well for him, and often work just as well today.

Again like Newton, Mendel was triumphantly right, but only up to a point. Molecular biology has turned a beautiful story based on peas into a much murkier tale which looks more like pea soup. The new genetical fog is described in the next chapter.

Chapter Three HERODOTUS REVISED

The Greek traveller Herodotus felt that he knew the world well. He voyaged around the Mediterranean and heard much of the Phoenicians’ journeys into Africa. By putting what he knew of the globe’s landmarks together he came to the conclusion that ‘Europe is as long as Africa and Asia put together, and for breadth is not, in my opinion, even to be compared with them.’ Herodotus had things in about the right places in relation to each other but the physical distances between them were hopelessly wrong.

For two thousand years maps could only be made in the Greek way. They were relative things, made by trying to fit landmarks together, with no measure of the absolute distances involved. Familiar bits of the countryside loomed far larger than they deserved. Mediaeval charts were not much better. Although the shape of Africa is recognisable it is much distorted. The cartographers’ perception of remoteness was determined by how long it took to travel between two points rather than how far apart they really were.

Genetics, like geography, is about maps; in this case the inherited map of ourselves. Not until the invention of accurate clocks and compasses two thousand years after Herodotus was it possible to measure real distances on the earth’s surface. Once these had been perfected, good maps soon appeared and Herodotus was made to look somewhat foolish. Now the same thing is happening in biology. Geneticists, it appears, were until not long ago making the same mistakes as the ancient Greeks.

Just as in mapping the world, progress in charting genes had to wait for technology. Now that it has arrived the shape of the biological atlas has been revolutionised, with a change in world-view far greater than that which separates the geography of the Athenians from that of today. What, even three decades ago, seemed a simple and reliable chart of the genome (based, as it was, on landmarks such as the colour of peas or of inborn disease) now looks very deformed.

The great age of cartography was driven, in the end, by economics: by the desire to find new materials and new markets. The mappers’ Columbian ambitions needed a Ferdinand and Isabella. Even fifty years ago, to those in the know, there seemed to be money in DNA, and many great foundations gave cash to the subject. Not until the 1980s did it seem feasible to chart the whole lot and, even then, it seemed that the task would take decades. Such is the rate of progress that the job is now, just after the millennium, in effect complete. The politician’s ear and the scientist’s ego shifted cash into Programs, Institutes and Centres as the free market in science was abandoned in favour of the planned economy; but, in the end, the Human Genome Project worked and at last we have the map of ourselves. Taxpayers (most of them American) played an important part, but in its latter days the job was split, with some acrimony, between governments in consort with charities (such as the Wellcome Foundation at its campus near Cambridge) and private institutions, the biggest run by a defector from an American government laboratory. There was a mad rush to patent genes. Large sums changed hands. The rights to one technology were sold to a Swiss company for three hundred million dollars. At the end of the DNA bonanza the altruists were ahead and large parts of the information were fed onto the internet, where it is available to all.

The idea of a gene map came first not from technology but from deviations from Mendel’s laws. Morgan, with his flies, found lots of inherited attributes that followed the rules. Their lines of transmission down the generations were not connected to each other; like pea colour and shape the traits were independently inherited. There was one big exception. Certain combinations of characters, those on the sex chromosomes, did not behave in this way. Soon, they were joined by others.

Mendel found that the inherited ratios for the colour of peas were not affected by whether the peas were round or wrinkled. Morgan, in contrast, discovered that, quite often, pairs of characteristics (such as eye colour and sex) travelled down the generations together. Soon, many different genes (such as those for eye colour, reduced wings and forked body hairs) in flies were found to share a pattern of inheritance with sex and, as a result, with the X chromosome. They were, in flagrant disregard of Mendel’s rules, not independent. To use Morgan’s term, they were linked.

Within a few years, many other traits turned out to be transmitted together. Experiments with millions of flies showed that all Drosophila genes could be arranged into groups on the basis of whether or not their patterns of inheritance were independent. Some combinations behaved as Mendel expected. For others, pairs of traits from one parent tended to stay together in later generations. The genes involved were, as Morgan put it, in the same linkage group. The number of groups was the same as the number of chromosomes. This discovery began the ‘linkage map’ of Drosophila and became the connection between Mendelism and molecular biology.

Linkage is the tendency of groups of genes to travel together down the generations. It is not absolute. Genes may be closely associated or may show only a feeble preference for each other’s company. Such incompleteness is explained by some odd events when sperm and egg are formed. Every cell contains two copies of each of the chromosomes. The number is halved during a special kind of cell division in testis or ovary. The chromosomes lie together in their pairs and exchange parts of their structure. Sperm or egg cells hence contain combinations of chromosomal material that differ from those in the cells of the parents who made them.

That is why, within a linkage group, certain genes are inherited in close consort while others have a less intimate association. If genes are near each other they are less likely to be parted when chromosomes exchange material. If they are a long way apart, they split more often. Pairs of genes that each follow Mendel are on different chromosomes. Recombination, as the process is called, is like shuffling a red and a black hand of cards together. Two red cards a long way apart in the hand are more likely to find themselves split from each other when the new deck is divided than are two such cards close together. Such rearrangements mean that each chromosome in the next generation is a new mixture of the genetic material made up of reordered pieces of the chromosome pairs of each parent.

Recombination helped make the first genetic maps. Like the cards in a hand held by a skilled player, genes are arranged in a sequence. Their original position can be determined by how much this is disturbed each generation as the inherited cards are shuffled. By studying the inheritance of groups of genes Morgan worked out their order and their relative distance apart. Combining the information from small sets of inherited characters allowed what he called a ‘linkage map’ to be made.

Linkage maps, based as they are on exceptions to Mendelism, are very useful. They have been made for bacteria, tomatoes, mice and many other beings. Thousands of genes have been mapped in this way. In Drosophila almost all have been arranged in order along the chromosomes and in mice almost as many.

Because this work needs breeding experiments, the human linkage map remained for many years almost a perfect and absolute blank. Most families are too small to look for deviations from Mendel’s rules and too few variants were known to look for them. There seemed little hope that a genetic chart of humankind could be made.

The one exception to this terra incognita was sex linkage. If genes are linked to the X chromosome, they must be linked to each other. It did not take long for dozens of traits to be mapped there. To draw the linkage map for other chromosomes was a painfully slow business. The gene for colour-blindness was mapped to the X in 1911, but the first linkage on other chromosomes did not emerge until 1955, when the gene for the ABO blood groups was found to be close to that for an abnormality of the skeleton. The actual number of human chromosomes was established in the following year and the first non-sex linked gene mapped onto a specific chromosome in 1968.

Now, genetics has been transformed. The technology involved is as to linkage mapping as satellites are to sextants. It does not depend on crosses and comes up with much more than a biological chart based on patterns of inheritance. Geneticists have now made a more conventional (but much more detailed) kind of chart, a physical map of the actual order of all the bases along the DNA. The new atlas of ourselves has changed our views of what genes are.

In the infancy of human genetics, thirty years ago, biologists had a childish view of what the world looks like. As in the mental map of an eleven year-old (or of Herodotus) linkage was based on a few familiar landmarks placed in relation with each other. The tedious but objective use of a measure of distance changed all that. Thirty years ago, molecular biologists were full of hubris. They had, they thought, solved the problems of inheritance. The new ability to read the DNA message would do the job that family studies and linkage mapping had failed to complete; it would show where all our genes were in relation to each other. The edifice whose foundations were laid by Mendel would then be complete. Optimism was, at the time, reasonable. It seemed a fair guess that the physical map of the genes would look much like a biological map based on patterns of inheritance and might in time replace it.

Such optimism was soon modified. The first explorations of the unknown territory which lay along the DNA chain showed that the physical map was quite different from the linkage map as inferred from peas or fruit-flies. The genes themselves are not beads lined up on a chromosomal string, but have a complicated and unexpected structure.

The successes of the molecular explorers depended, like those of their geographical predecessors, on new surveying instruments which made the world a bigger and more complicated place. The tools used in molecular geography deserve a mention.

The first device is electrophoresis, the separation of molecules in an electric field. Many biological substances, DNA included, carry an electrical charge. When placed between a positive and a negative terminal they move towards one or the other. A gel (which acts as a sieve) is used to improve the separation. Gels were once made of potato starch, while modern ones are made of chemical polymers. I have tried strawberry jelly, which works quite well. The gel separates molecules by size and shape. Large molecules move more slowly as they are pulled through the sieve while smaller ones pass with less difficulty. Various tricks improve the process. Thus, a reversal of the current every few seconds means that longer pieces of DNA can be electrophoresed, as they wind and unwind each time the power is interrupted. The latest technology uses arrays of fine glass tubes filled with gel, into each of which a sample is loaded. With various tricks the whole process becomes a production line and tens of thousands of samples can be analysed each day.

The computer on which I wrote this book has some fairly useless talents. It can – if asked – sort all sentences by length. This sentence, with its twenty words, would line up with many otherwise unrelated sentences from the rest of the book. Electrophoresis does this with molecules. The length of each DNA piece can be measured by how far it has moved into the gel. Its position is defined with ultraviolet light (absorbed by DNA), with chemical stains, fluorescent dyes that light up when a laser of the correct wavelength is shone on them, or with radioactive labels. Each piece lines up with all the others which contain the same number of DNA letters.