by Steve Jones
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 charring 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. Kvcn 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 tor 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, iliey 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. Mosr families are roo small ro look for deviations from Mendel's rules and too few variants were known ro look for them. There seemed little hope that a genetic chart of humankind could be made.
The one exception to this terra incagnifii 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 19 ti, bur the first linkage on other chromosomes did nor 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 esrab-lished in rhe following year and rhe firsr non-sex linked gene mapped onro a specific chromosome in 1968.
Now, generics 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 rhe 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 prob
lems 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 rime 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 Irom the rest of the book. Electrophoresis Joes 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.
Another tool uses enzymes extracted from bacteria to divide the landscape into manageable pieces. Bacteria are attacked by viruses which insert themselves into their genetic message and force the host to copy the invader. They have a defence: enzymes which cut foreign DNA in specific places. These 'restriction enzymes' can be used to slice human genes into pieces. Dozens are available, each able to cut a particular group of DNA letters. The length of the pieces that emerge depends on how often the cutting-site is repeated. If each sentence in this volume was severed whenever the word land' appeared, there would be thousands of short fragments. If the enzyme recognised the word 'but', there would be fewer, longer sections; and an enzyme that sliced through the much less frequent word 'banana' (which, I assure you, does appear now and again) would produce just a few fragments thousands of letters long. The positions of the cuts (like those of the words and, but and banana) provide a set of landmarks along the DNA. To track them down is a first step to reconstituting the book itself. The process is close to that carried out by rlic students who stormed the American Embassy in Tehran after the fall of the Shah. With extraordinary labour they pieced together secret documents which had been put through a shredder. By putting the fragments together the students reconstituted a long, complicated and compromising message.
Molecular biology does much the same. First, it needs to multiply the number of copies of the message to allow each short piece to be surveyed in detail as a preliminary to the complete map. Various tricks allow cut pieces of DNA to be inserted into that of a bacterium or yeast. The DNA has been cloned. Whenever the host divides, it multiplies not only its own genetic message but the foreign gene. As a result, millions of copies of an original are ready for study in the exquisite detail needed for genetic geography.
Cloning has been supplemented by another contrivance, the polymerase chain reaction. This takes advantage of an enzyme used in the natural replication of DNA to make replicas of the molecule in the laboratory. To pursue our rather tortured literary analogy, the method is a biological photocopier which can produce many duplicates of each page in the genetic manual. The photocopying enzyme comes from a bacterium which lives in hot springs. The reaction is started with a pair of short artificial DNA sequences which bind to the natural DNA on either side of the length to be amplified. By heating and cooling the reaction mixture and feeding it with a supply of the four bases, the targeted strands of DNA unwind, copy themselves with the help of the enzyme, and re-form. Each time the cycle is repeated, the number of copies doubles and millions of replicas of the original piece of DNA are soon generated.
Another piece of trickery exploits DNA's ability to bind ro a mirror image of itself. DNA bases form two matched pairs; A with T and G with C. To find a gene, a complementary copy is made in the laboratory. When added to a cell this seeks out and binds to its equivalent on the chromosome. My computer can do tin- same. On a simple command, it will search for any word 1 choose and highlight it in an attractive purple. It does the job best with rare words (like 'banana'). A DNA probe labelled with a fluorescent dye shows up genes in the same way. The method is known as FISHing (for Fluorescent In-Situ Hybridisation) for genes. A modified kind of FISH involves unwinding the DNA before it is stained. This makes the method more sensitive.
All this and much more has revolutionised the mapping of human DNA. First, it has improved the linkage map. Patterns of inheritance of short sequences of DNA can be tracked through the generations just as well as can those of colour-blindness or stubby fingers. There are millions of sites which vary from person to person. All can be used in pedigree studies. Another scheme is to use the polymerase chain reaction to multiply copies of DNA from single sperm cells. The linkage map is made from a comparison of the reordered chromosomes in the sperm with that in the man who made them. This avoids the problem of family size altogether.
Linkage mapping in humans took a long time to get started and still has some way to go. Before the days of high technology the great problem was a shortage of differences; of variable genes, or segments of genetic material, whose joint patterns of inheritance could be studied. That problem has been solved. Our DNA is now known to be saturated with hundreds of thousands of variable sites, many based on individual variation in the numbers and positions of repeats of the two letters C and A. As a result, a whole new industry based on the most traditional kind of genetics has burst into existence.
It needs, like any industry, raw material. The French, together with the Americans, have identified sixty or so large families with long and complicated pedigrees, well suited for gene mapping. They come from various parts of the world, from Venezuela to Bangladesh. From each individual, lines of cells arc kept alive in the laboratory and thousands of variants have been identified, tightly packed along the entire length of the chromosomes. Patients with, say, heart disease can be screened to see whether they also tend to carry other inherited variants. If they do, there is a good chance that the actual gene involved is nearby, and is dragging its anonymous fellows along with it. To find such a milestone may be the first step to the gene itself.
The descendants of Morgan have at last managed to do for humans what was long ago achieved for the fruit fly, and a linkage map of man is close at hand. That of woman, it transpires, is rather longer. Such maps depend on the sexual reshuffling of genes. This takes place, for some reason, more in females than in males and, as a result, their chart works to a different scale.
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p; The human linkage map is useful, but biologists have always wanted to make a different kind of chart, one rather like that used by geographers, based on a straightforward description of the genetic material. Now, it is here. The approach was brutal: to assault the genome with time, money and tedium until the whole lot was read from one end to the other.
The first move in tying the linkage map to one based on the physical structure of DNA depended on a stroke of luck. Morgan noticed that in one of his fly stocks a gene which was usually sex-linked started behaving as if it was not on the X chromosome at all. A glance down the microscope showed why. The X was stuck to one of the other chromosomes and was inherited with it. A change in the linkage relationships of the gene was due to a shift in its physical position.
Such chromosomal accidents were used to begin the human physical map. Sometimes, because of a mistake in the formation of sperm or egg, part of a chromosome shifts to a new home. Any parallel change in the pattern of inheritance of a particular gene shows whav it must be. Now and again a tiny segment of chromosome is absent. That can lead to several inborn diseases at once. One unfortunate American boy had a deficiency of the immune system, a form of inherited blindness, and muscular dystrophy. A minute section of his X chromosome had been deleted. It must have included the length of DNA which carried these genes. He gave a vital hint as to just where the gene for muscular dystrophy — one of the most frequent and most distressing of all inherited diseases — was located. The absent segment was a landmark upon which a physical map of the area around this gene could be anchored.
