by Bryan Sykes
Many years later I had the good fortune to be invited to the opening of the new Egyptology gallery in the British Museum in London. At dinner that evening in the magnificent Egyptian Sculpture Gallery, my place was set directly opposite the huge granite statue of Rameses. He was looking down right at me with his unnervingly benign and omniscient gaze. I knew at once that he had heard about my joke at his expense, and that I was going to be in big trouble in the afterlife.
One of the most difficult things about getting ancient DNA out of old bones is that, unless you are extremely careful, you end up amplifying modern DNA, including your own, instead of the fossil’s. Even when it is present, the old DNA is pretty shattered. Chemical changes, mostly brought about by oxygen, slowly change the structure of the DNA so that it starts breaking down into smaller and smaller fragments. If even the tiniest speck of modern DNA gets into the reaction then the polymerase copying enzymes, which don’t realize that you are trying to amplify the worn out little scraps of ancient DNA, concentrate their efforts on the pristine modern stuff and, not knowing any better, produce millions of copies of that instead. So it looks as though the reaction has been a great success. You put a drop of ancient bone extract in at the beginning and get masses of DNA out at the end. Only when you analyse it further do you realize that it’s your own DNA, not that from the fossil at all.
Although we were fairly sure this hadn’t happened with the Abingdon bone, we thought one way of checking would be by getting DNA from old animal rather than old human bones. It would then be very easy to tell whether we had amplified animal DNA – the real thing – or human DNA, which would have to be a contaminant. The best source of sufficiently old animal bones we could think of was the wreck of the Mary Rose. This magnificent galleon had sunk during an engagement with a French invasion fleet off Portsmouth in 1545. Very few of the crew survived. For over four hundred years the wreck lay in the mud under 14 metres of water until it was raised in 1982 and put on display in a museum in Portsmouth harbour, where it is still being drenched with a solution of water and anti-freeze to prevent its timbers from buckling. As well as the skeletons of the unfortunate crew, hundreds of animal and fish bones were recovered from the wreck. The ship had been full of supplies when it sank, and among these were sides of beef and pork and barrels of salted cod. We persuaded the museum curator to let us have a pig rib to try. Because it had spent most of its life (after death, that is) buried in the oxygen-free ooze at the bottom of the Solent, the rib was in very good condition and we managed to get lots of DNA from it without much trouble. We analysed it – and there was no doubt at all that it was from a pig and not a human.
The point of telling you all this is not to take you through our experiments one by one, but to explain the reaction when the result was published. More phone calls and more headlines – of which my favourite is from the Independent on Sunday: ‘Pig brings home the bacon for DNA’. This was going to be fun.
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SO, WHAT IS DNA AND WHAT DOES IT DO?
All of us are aware, as people must have been for millennia, that children often resemble their parents and that the birth of a child follows nine months after sexual intercourse. The mechanism for inheritance remained a mystery until very recently, but that didn’t stop people from coming up with all sorts of theories. There are plenty of references in classical Greek literature to family resemblances, and musing on the reasons for them was a familiar pastime for early philosophers. Aristotle, writing around 335 BC, speculated that the father provided the pattern for the unborn child and the mother’s contribution was limited to sustaining it within the womb as well as after birth. This idea made perfect sense to the patriarchal attitudes of Western civilization at the time. It was only reasonable that the father, the provider of wealth and status, was also the architect of all his children’s features and nature. This was not to underestimate the necessity of choosing a suitable wife. After all, seeds planted in a good soil always do better than those put into a poor one. However, there was a problem and it was one that was to haunt women for a long time to come.
If children are born with their father’s design, how was it that men had daughters? Aristotle was challenged on this point during his lifetime, and his answer was that all babies would be the same as their fathers in every respect, including being male, unless they were somehow ‘interfered with’ in the womb. This ‘interference’ could be relatively minor, leading to such trivial variations as a child having red hair instead of black like his father; or it could be more substantial – leading to major ones such as being deformed or female. This attitude has had serious consequences for many women throughout history who have found themselves discarded and replaced because they failed to produce sons. This ancient theory developed into the notion of the homunculus, a tiny, preformed being that was inoculated into the woman during sexual intercourse. Even as late as the beginning of the eighteenth century the pioneer of microscopy, Anthony van Leewenhoek, imagined he could see tiny homunculi curled up in the heads of sperm.
Hippocrates, whose name is commemorated in the oath that newly qualified doctors used to take (some still do), had a less extreme view than Aristotle which did give women a role. He believed that both men and women produced a seminal fluid, and that the characteristics of the baby were decided by which parts of the fluid prevailed when they mixed after copulation. A child might have its father’s eyes or its mother’s nose as a result of this process; if neither parent’s fluid prevailed for a particular characteristic, the child might be somewhere in between, having, for example, hair of a colour that was intermediate between the two parents.
This theory was much more obviously connected to most people’s experience of real life. ‘He’s just like his father’ or ‘She’s got her mother’s smile’ and other similar observations are repeated millions of times every day throughout the world. The idea that the parents’ characteristics are somehow blended in the offspring was the predominant belief among scientists until the end of the nineteenth century. Darwin certainly knew no better, and it was one reason why he could never find a suitable mechanism to explain his theory of natural selection; for anything new and favourable would be continually diluted out by the blending process at each generation. Even though geneticists today scoff at such apparent ignorance among their predecessors, I wouldn’t mind betting that a theory of blending is, even now, a perfectly satisfactory explanation for what most people observe with their own eyes.
Eventually, two practical developments in the nineteenth century provided key clues to what was really going on. One was the invention of new chemical dyes for the textile industry, and the other was a change in the way microscope lenses were ground which made big improvements in their performance. Greater magnification meant that individual cells were now easily visible; and their internal structure was revealed when they were stained with the new dyes. Now the process of fertilization, the fusion of a single large egg cell and a single small, determined sperm, could be observed. When cells divided, strange thread-like structures could be seen assembling and then separating equally into the two new cells. Because they stained very brightly with the new dyes these curious structures became known as chromosomes – from Greek, meaning literally, ‘coloured bodies’ – years before anyone had a clue about what they did.
During fertilization, one set of these strange threads seemed to come from the father’s sperm and another set from the mother’s egg. This was just what had been predicted by the man universally acknowledged as the father of genetics, Gregor Mendel, a monk in the town of Brno in the Czech republic who laid the foundation for the whole of genetics from his experimental breeding of peas in the monastery garden in the 1860s. He concluded that whatever it was that determined heredity would be passed on equally from both parents to their offspring. Unfortunately he died before he ever saw a chromosome; but he was right. With the important exception of mitochondrial DNA (of which we shall have much more to say later) and the chromosomes that dete
rmine sex, genes – specific pieces of genetic coding that occur in the chromosomes – are inherited equally from both sets of parents. The essential part played by chromosomes in heredity and the fact that they must contain within them the secrets of inheritance was already well established by 1903. But it took another fifty years to discover what chromosomes are made of and how they worked as the physical messengers of heredity.
In 1953 two young scientists working in Cambridge, James D. Watson and Francis Crick, solved the molecular structure of a substance which had been known about for a long time and largely thought of as dull and unimportant. As if to emphasize its obscurity, it was given a really long name, deoxyribonucleic acid, now happily abbreviated to DNA. Although a few experiments had implicated DNA in the mechanism of inheritance, the smart money was on proteins as the hereditary material. They were complicated, sophisticated, had twenty different components (the amino-acids) and could assume millions of different forms. Surely, the thinking went, only something really complicated could manage such a monumental task as programming a single fertilized egg cell to grow into a fully formed and functional human being. It couldn’t possibly be this DNA, which had only four components. Admittedly it was in the right place, in the cell nucleus; but it probably did something very dull like absorbing water, rather like bran.
Despite the general lack of interest in this substance shown by most of their scientific contemporaries, Watson and Crick felt sure it held the key to the chemical mechanism of heredity. They decided to have a crack at working out its molecular structure using a technique that was already being used to solve the structure of the more glamorous proteins. This entailed making long crystalline fibres of purified DNA and bombarding them with X-rays. As the X-rays entered the DNA, most went straight through and out the other side. But a few collided with the atoms in the molecular structure and bounced off to one side where they were detected by sheets of X-ray film – the same kind of film that hospital radiographers still use to get an image of a fractured bone. The deflected X-rays made a regular pattern of spots on the film, whose precise locations were then used to calculate the positions of atoms within the DNA.
After many weeks spent building different models with rods and sheets of cardboard and metal to represent the atoms within DNA, Watson and Crick suddenly found one which fitted exactly with the X-ray pattern. It was simple, yet at the same time utterly marvellous, and it had a structure that immediately suggested how it might work as the genetic material. As they put it with engaging self-confidence in the scientific paper that announced the discovery: ‘It has not escaped our notice that the specific pairings we have postulated immediately suggest a possible copying mechanism for the genetic material.’ They were absolutely right, and were rewarded by the Nobel Prize for Medicine and Physiology in 1962.
One of the essential requirements for the genetic material had to be that it could be faithfully copied time and again, so that when a cell divides, both of the two new cells – the ‘daughter cells’, as they are called – each receive an equal share of the chromosomes in the nucleus. Unless the genetic material in the chromosomes could be copied every time a cell divided it would very soon run out. And the copying had to be very high quality or the cells just wouldn’t work. Watson and Crick had discovered that each molecule of DNA is made up of two very long coils, like two intertwined spiral staircases – a ‘double helix’. When the time comes for copies to be made, the two spiral staircases of the double helix disengage. DNA has just four key components, which are always known by the first letters of their chemical names: A for adenine, C for cytosine, G for guanine and T for thymine. Formally they are known as nucleotide bases – ‘bases’ for short. You can now forget the chemicals and just remember the four symbols ‘A’, ‘C’, ‘G’ and ‘T’.
The breakthrough in solving the DNA structure came when Watson and Crick realized that the only way the two strands of the double helix could fit together properly was if every ‘A’ on one strand is interlocked with a ‘T’ directly opposite it on the other strand. Just like two jigsaw pieces, ‘A’ will fit perfectly with ‘T’ but not with ‘G’ or ‘C’ or with another ‘A’. In exactly the same way, ‘C’ and ‘G’ on opposite strands can fit only with each other, not with ‘A’ or ‘T’. This way both strands retain the complementary coded sequence information. For example, the sequence ‘ATTCAG’ on one strand has to be matched by the sequence ‘TAAGTC’ on the other. When the double helix unravels this section, the cell machinery constructs a new sequence ‘TAAGTC’ opposite ‘ATTCAG’ on one of the old strands and builds up ‘ATTCAG’ opposite ‘TAAGTC’ on the other. The result is two new double helices identical to the original. Two perfect copies every time. Preserved during all this copying is the sequence of the four chemical letters. And what is the sequence? It is information pure and simple. DNA doesn’t actually do anything itself. It doesn’t help you breathe or digest your food. It just instructs other things how to do it. The cellular middle managers which receive the instructions and do the work are, it turns out, the proteins. They might look sophisticated, and they are; but they operate under strict directions from the boardroom, the DNA itself.
Although the complexity of cells, tissues and whole organisms is breathtaking, the way in which the basic DNA instructions are written is astonishingly simple. Like more familiar instruction systems such as language, numbers or computer binary code, what matters is not so much the symbols themselves but the order in which they appear. Anagrams, for example ‘derail’ and ‘redial’, contain exactly the same letters but in a different order, and so the words they spell out have completely different meanings. Similarly, 476,021 and 104,762 are different numbers using the same symbols laid out differently. Likewise, 001010 and 100100 have very different meanings in binary code. In exactly the same way the order of the four chemical symbols in DNA embodies the message. ‘ACGGTA’ and ‘GACAGT’ are DNA anagrams that mean completely different things to a cell, just as ‘derail’ and ‘redial’ have different meanings for us.
So, how is the message written and how is it read? DNA is confined to the chromosomes, which never leave the cell nucleus. It is the proteins that do all the real work. They are the executives of the body. They are the enzymes which digest your food and run your metabolism; they are the hormones that coordinate what is happening in different parts of your body. They are the collagens of the skin and bone, and the haemoglobins of the blood. They are the antibodies that fight off infection. In other words, they do everything. Some are enormous molecules, some are tiny. What they all have in common is that they are made up of a string of sub-units, called amino-acids, whose precise order dictates their function. Amino-acids in one part of the string attract amino-acids from another part, and what was a nice linear string crumples up into a ball. But this is a ball with a very particular shape, that then allows the protein to do what it was made for: being a catalyst for biological reactions if it is an enzyme, making muscles if it is a muscle protein, trapping invading bacteria if it is an antibody, and so on. There are twenty amino-acids in all, some with vaguely familiar names like lysine or phenylalanine (one of the ingredients of the sweetener aspartame) and others most people haven’t come across, like cysteine or tyrosine. The order in which these amino-acids appear in the protein precisely determines its final shape and function, so all that is required to make a protein is a set of DNA instructions which define this order. Somehow the coded information contained in the DNA within the cell nucleus must be relayed to the protein production lines in another part of the cell.
If you can spare one, pluck out a hair. The translucent blob on one end is the root or follicle. There are roughly a million cells in each hair follicle, and their only purpose in life is to make hair, which is mainly made up of the protein keratin. As you pulled the hair out, the cells were still working. Imagine yourself inside one of these cells. Each one is busy making keratin. But how do they know how to do it? The key to making any protein, including keratin, is
just a matter of making sure that the amino-acids are put in the right order. What is the right order? Go and look it up in the DNA which is on the chromosomes in the cell nucleus. A hair cell, like every cell in the body, has a full set of DNA instructions, but you only want to know how to make keratin. Hair cells are not interested in how to make bone or blood, so all those sections of DNA are shut down. But the keratin instruction, the keratin gene, is open for consultation. It is simply the sequence of DNA symbols specifying the order of amino-acids in keratin.
The DNA sequence in the keratin gene begins like this: ATGACCTCCTTC…(etc. etc.). Because we are not used to reading this code it looks like a random arrangement of the four DNA symbols. However, while it might be unintelligible to us, it is not so to the hair cell. This is a small part of the code for making keratin, and it is very simple to translate. First the cell reads the code in groups of three symbols. Thus ATGACCTCCTTC becomes ATG–ACC–TCC–TTC. Each of these groups of three symbols, called a triplet, specifies a particular amino-acid. The first triplet ATG is the code for the amino-acid methionine, ACC stands for threonine, TCC for serine, TTC for phenylalanine and so on. This is the genetic code which is used by all genes in the cell nuclei of all species of plants and animals.
The cell makes a temporary copy of this code, as if it were photocopying a few pages of a book, then dispatches it to the protein-making machinery in another part of the cell. When it arrives here, the production plant swings into action. It reads the first triplet and decodes it as meaning the amino-acid methionine. It takes a molecule of methionine off the shelf. It reads the second triplet for the amino-acid threonine, takes a molecule of threonine down and joins it to the methionine. The third triplet means serine, so a molecule of serine gets tacked on to the threonine. The fourth triplet is for phenylalanine, so one of these is joined to the serine. Now we have the four amino-acids specified by the DNA sequence of the keratin gene assembled in the correct order: methionine–threonine–serine–phenylalanine. The next triplet is read, and the fifth amino-acid is added, and so on. This process of reading, decoding and adding amino-acids in the right order continues until the whole instructions have been read through to the end. The new keratin molecule is now complete. It is cut loose and goes to join hundreds of millions of others to form part of one of the hairs that are growing out of your scalp. Well, it would if you had not pulled it out.