The Mysterious World of the Human Genome

Scientists who have laboured long and hard at a difficult but eventually rewarding line of research are usually happy to talk about it – if not to the media or ordinary social channels, certainly to colleagues. They travel to scientific symposia. They take part in conferences. They enjoy the camaraderie that comes from sharing the same interests. In the words of Frank Portugal, ‘wide-ranging discussions with peers both individually and at meetings are part and parcel of the scientific process. It is an important component of how collaborations are formed and scientific advances are made and respected.’ Most scientists are only too glad to accept the, often rare, honours and distinction their work brings their way. Not so Oswald Avery.

In 1944 Avery was proposed for an honorary degree at Cambridge University, a recognition most scientists would cherish. The following year he was awarded the Copley Medal by the Royal Society of London. Avery’s roots were English – in the late nineteenth century his family had emigrated to Canada from the city of Norwich – but he refused to visit England even on such prestigious occasions, putting forward the excuse that his state of health did not permit it except by travelling first class. In Dubos’ opinion, this was disingenuous, since the respective foundations would have funded the flights. That he might have felt nervous, claustrophobic, on the lengthy flight is possible. Recalling those dark moods in which Avery might mumble to himself about the damaging inflictions of resentment, it seemed more than likely to Dubos that he might have been unable to suppress lingering anger at the hurtful controversy provoked years ago by his polysaccharide typing of pneumococci. Whatever his reasons, Avery refused both honours.

An incident highlighted just how strong was Avery’s aversion to such formal acknowledgement of his work. Sir Henry Dale, who was President of the Royal Society in England, took it upon himself to bring the Copley Medal to the Rockefeller Institute, there to confer it on the shy and retiring Avery in person. Dale was accompanied by a Dr Todd, who knew Avery personally. The two highly respected English visitors arrived at the Institute in New York unannounced and went directly to Avery’s department in the main hospital building. But when they saw Avery working in his lab, through the ever-open door, they retreated without intruding on his presence.

Dr Todd would later recount how Sir Henry Dale said simply: ‘Now I understand everything.’

Bizarre as this behaviour would appear, it was in keeping with Avery’s increasingly reclusive personality: a man who avoided any of the normal personal contacts outside of immediate family and work colleagues. Genius can be strange. Yet such idiosyncratic behaviour apart, it was this son of an evangelical Baptist preacher who first discovered that DNA was the molecule of heredity. And putting such personal matters aside, the question remains: why was such a fundamental discovery not recognised by the awarding of the Nobel Prize?

In his letters to his brother, Avery retained a modest outlook. Could it be that a combination of Avery’s innate conservatism, his tendency to over-caution, and his downplaying of the implications of his discovery in the paper of 1944 might have contributed to his being overlooked? In Dubos’ words, the paper … ‘did not make it obvious that the findings opened the door to a new era of biology’. Dubos wondered if the Nobel Committee, unaccustomed to such restraint and self-criticism ‘bordering on the neurotic’ might have caused them to wait a while for both confirmation of the discovery and to see what the broader implications might be. To put it another way, Dubos questioned if the paper might have been a failure not in its own merits, as a scientific communication, but from the public relations point of view.

This lack of recognition is made all the more puzzling by the fact that, if the importance of the 1944 paper was not universally recognised when it was published, it became more and more obvious with the passage of time. The Hershey and Chase paper was published in 1952. And although he was retired by the time Crick and Watson published their famous discovery of the three-dimensional chemical structure of DNA in 1953, Avery was still alive. He wouldn’t die until two years later, in 1955.

More recently the Nobel authorities have allowed open access to their earlier thinking, and this has confirmed much of what Dubos had concluded. As part of the system for deciding who should get Nobel Prizes, the Nobel Committee receives proposals from leading experts around the world. In the words of Portugal, who reviewed their working and archives, ‘It seems that key biological chemists were not convinced by Avery’s claim that DNA was the basis of heredity.’ Not a single geneticist nominated Avery for the Nobel Prize. In part this may have reflected a difficulty in extrapolating his discovery in a single type of bacterium to genetics more widely, but even those colleagues who did nominate him for the Nobel Prize tended to overlook his work on DNA in favour of his immunological typing of the pneumococcal capsule. Portugal also wondered if Avery’s own idiosyncratic behaviour, including his reluctance to meet with and exchange findings with colleagues, and in particular geneticists, at scientific meetings had unintentionally confounded the acceptance of his groundbreaking discovery.

We are left with a lingering sense of regret that Avery was not accorded the recognition he deserved. He was 67 years old when his iconoclastic paper was published. It was, in the words of the eminent biochemist Erwin Chargaff, the rare instance of an old man making a major scientific discovery. ‘He was a quiet man: and it would have honoured the world more, had it honoured him more.’

But there is a greater acknowledgement of discovery than the awarding of a prize, no matter how respected and prestigious. In the words of Freeland Judson, ‘Avery opened up a new space in biologists’ minds.’ By space he meant he had unravelled a major truth, revealing new unknowns and raising important new questions. Avery himself had, with quintessential modesty, touched upon those important new questions in his letter to his brother:

If we are right, and of course that is not yet proven, then it means that nucleic acids are not merely structurally important but functionally active substances in determining the biochemical activities and specific characteristics of cells – and that by means of a known chemical substance it is possible to induce predictable and hereditary changes in cells. This is something that has long been the dream of geneticists … Sounds like a virus – may be a gene. But with mechanisms I am not now concerned – one step at a time – and the first is, what is the chemical nature of the transforming principle? Someone else can work out the rest …

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The Story in the Picture (#ulink_1f573ad9-98b3-558a-8d1f-470d1b6d5745)

You look at science (or at least talk of it) as some sort of demoralising invention of man, something apart from real life, and which must be cautiously guarded and kept separate from everyday existence. But science and everyday life cannot and should not be separated.

ROSALIND FRANKLIN

The discovery of the ‘transforming substance’ by Avery, MacLeod and McCarty, confirmed by Hershey and Chase’s elegant experiment with the bacteriophage, proved that DNA was the molecule of heredity. But both groups were working with microbes, bacteria and viruses, which were known to be much simpler in their hereditary nature than, say, animals and plants. This left huge unknowns that needed to be explored. Was DNA the key to the heredity of all of life, or was it just relevant to bacteria and viruses? By the early 1950s, work in many different laboratories had confirmed that DNA was a major ingredient in the nuclei of animals and plants. This supported the idea that DNA was the coding molecule of life. But if so, how did it really work? How, for example, did a single chemical molecule code for the complex heredity of a living organism?

Biologists, doctors, molecular biochemists and geneticists were now asking themselves the same, or similar, questions. Critical to any such understanding was the precise molecular structure of DNA. If, for example, we were to regard the role of DNA as akin to a stored genetic memory, how did that molecular structure enable the quality of such a phenomenally complex memory? How was that genetic memory transferred from parents to offspring? How did the same stored memory explain embryological development, where a single cell arising from the genomic union of a paternal sperm and maternal ovum gives rise to the developing human embryo and future adult human being?

There was another profoundly important question.

Darwinian evolution lay at the heart of biology. To put it simply, Darwin’s idea of natural selection implied that nature selected from a range of variations in the heredity of different individuals within a species. The way in which it worked was exceedingly simple, if brutal. Those individuals, and by inference their variant heredities, who carried a small advantage for survival and thus a better chance of giving rise to offspring, would therefore be more likely to contribute to the species gene pool. In reality natural selection worked more through a process of attrition. Those less advantaged individuals who did not carry the advantage for survival, were more likely to perish in the struggle for existence, and thus they were less likely to contribute to the species gene pool.

This is what Darwinian evolutionary biologists refer to as ‘relative fitness’. It is the measure of the individual’s contribution to the species gene pool. Certainly it has nothing to do with racist notions of superiority and inferiority attached to ‘survival of the fittest’ – a term introduced not by Darwin but by the social philosopher Herbert Spencer. But if we take a pause and think about it, such variant heredity, essential for natural selection to work, must also come about through mechanisms involving this wonder molecule, DNA, which must lie not only at the heart of heredity but also at the absolute dead centre of evolution. All of these questions needed to be answered by the scientists now struggling to understand the structure and, assuming structure was function, the properties of this remarkable chemical, DNA.

In fact the first step towards answering these questions had already been taken back in 1943, in what might appear unlikely circumstances. It was taken not by a biochemist, biologist or geneticist, but by an Austrian physicist. The spark was lit when, at 4.30pm on Friday 5 February, Erwin Schrödinger stepped up to the podium in Dublin to deliver a lecture that is now seen as a landmark moment in the history of biology. Schrödinger had been awarded the Nobel Prize in 1933 for work in quantum physics that expanded our understanding of wave mechanics – but I won’t confuse myself or my readers by entering further into the physics. The simple facts were that Schrödinger had exiled himself from his native Austria in protest at human rights abuses and had been given sanctuary in neutral Ireland by its President, Eamon de Valera. In Dublin Schrödinger had helped found the Institute for Advanced Studies. As part of his duties in support of the Institute, he had agreed to give a series of three lectures in which he developed a central theme: ‘What Is Life?’

Such was Schrödinger’s fame that the lecture theatre, which had a seating capacity for 400, could not accommodate all who wished to attend the lectures – this despite the fact that they had been warned in advance that the subject matter was a difficult one and that the lecture was not going to be pitched at an easy or popular level, even though Schrödinger had promised to eschew mathematics. De Valera himself was present in the audience, as were his cabinet ministers and a reporter for Time magazine. One wonders what these politicians and journalists made of Schrödinger’s focus on ‘how the events in space and time which take place within the spatial boundary of a living organism can be accounted for by physics and chemistry’.

Schrödinger subsequently extrapolated the three lectures into a book of less than a hundred pages with the same title: What Is Life? This was published the following year. In what is now a very famous book, Schrödinger popularised a quantum mechanics interpretation of the gene that had been proposed earlier by another distinguished physicist, the previously mentioned Max Delbrück.

In the opening pages of the first chapter, Schrödinger posed the question: ‘How can the events which take place within a living organism be accounted for by physics and chemistry?’ Admitting that at the time of writing the prevailing knowledge within the disciplines of physics and chemistry was inadequate to explain this, he nevertheless hazarded the opinion that ‘the most essential part of a living cell – the chromosome fibre – may suitably be called an aperiodic crystal’. The italicisation is Schrödinger’s to emphasise, as he further explained, that the physics up to this time had only concerned itself with periodic crystals, the kind of repetitive atomic structures seen, for example, in very obvious crystalline compounds such as gemstones.

What did he mean by an ‘aperiodic crystal’?

He explained this with a metaphor. If we examined the images within the pattern of a wallpaper, we could see how the pattern was repeated, over and over. This was the equivalent of a periodic crystal. But if we examined the complex elaboration of a Raphael tapestry, we saw a pattern of images that did not repeat themselves, yet the pattern was coherent and meaningful.

Schrödinger intuited further.

It was the chromosomes, or more likely an axial fibre much finer than what was visible under the microscope, that contained what he termed ‘some kind of code-script’ that determined the blueprint of the individual’s development from fertilised egg to birth – and further determined the functioning of what we would now term the genome throughout the lifetime of the individual.

That intuition would provide the drive for a naïve but highly inquisitive young American, called James Dewey Watson, to join forces with a slightly older but equally inquisitive Englishman, Francis Crick, and form what is now seen as one of the most famous partnerships in scientific history. Both men would take their inspiration from Schrödinger to search for the aperiodic crystal that coded for DNA.

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Watson was an exceptionally bright child who lived at home with his family in Chicago while attending the local university. He enrolled when aged just 15 and he graduated, aged 19, in 1947 with a bachelor’s degree that included a year studying zoology. His teacher of embryology would remember him as a student who showed little interest in lectures and made no notes whatsoever, so it was all the more puzzling when he graduated top of his class. Watson would subsequently admit to a habitual laziness. Though vaguely interested in birds, he had deliberately avoided any courses that involved chemistry or physics of ‘even medium difficulty’. This self-indulgent student left Chicago with only a rudimentary knowledge of genetics or biochemistry. As part of his education he had attended lectures by the geneticist Sewall Wright, who had devised a mathematical system of studying population genetics. Wright’s course included a discussion of Avery’s work, but Watson would subsequently confess that he took little notice. He would also confess that the inspiration for his subsequent interest in the ‘mystery of the gene’ was Schrödinger’s book, What Is Life?

Inspired by this book, Watson landed a research fellowship at Indiana University, at Bloomington. He was delighted by the move because Nobel Laureate Hermann Joseph Muller was the local Professor of Zoology. As early as 1921 Muller had observed that the genes of the fruit fly underwent mutations – as did the genes of the bacteriophages – the viruses that had inspired Hershey and Chase. Watson was intrigued by the fact that phage viruses could be manipulated in test tubes. Their reproductive cycles were extremely brief – an important consideration for an impatient young scientist. There were simple test systems that could be employed to follow their life cycles, and numbers, in a way that would open up new angles from which to attack the gene problem. All you had to do was carefully design an experiment aimed at probing some particular aspect of the gene problem and the whole shebang could be completed in a matter of days. This intimate, if brutal, interplay between phage viruses and their host bacteria allowed scientists to figure the complex chemistry of genes, genetics and chromosomes.

Curiously it would not be Muller but another phage researcher, Salvador Luria, who would now give shape and direction to the young scientist’s growing infatuation with the gene.

The Italian-born Luria was another European scientist – a microbiologist, like Avery – who found refuge in America from the European war zone. By now he had entered into a working collaboration with Max Delbrück, who was Professor of Biology at the California Institute of Technology. In 1943 Luria and Delbrück designed and conducted an experiment that demonstrated that genetic inheritance in bacteria followed precise evolutionary principles. This experiment became one of the foundation stones of modern Darwinism. That same year Delbrück befriended another microbiologist called Alfred Hershey, who would subsequently write the key DNA paper with Martha Chase. In a letter to Luria, Delbrück summarised Hershey as follows: ‘Drinks whiskey but not tea. Likes living in a sailboat … Likes independence.’ The three scientists joined forces to become the nucleus of a cooperating and mutually supportive network of scientists that would become known as the ‘phage group’. Delbrück would subsequently explain that they would be a group only in the sense that they communicated freely on a regular basis, and that they told one another what they were thinking and doing. In this way a loose creative movement grew around the two European expatriate scientists, all working towards the common ambition of figuring out how genes worked.

Luria, Delbrück and Hershey now posed some interesting questions. How does the phage virus actually get into the bacterium? How, once inside, does it multiply? Does it multiply like a bacterium, growing and budding off daughter viruses? Or does it multiply by an entirely different mechanism? Is this multiplication some complex physical or chemical process that could be understood in terms of known physical and chemical principles? Through making use of the phage reproductive system, they hoped to solve the mystery of the gene. To begin with it all seemed simple in principle, but as experiment followed experiment and year followed year, they found themselves no closer to the answer.

Up to 1940 or so, people like Delbrück and Luria had assumed that viruses were simple. They had little to go on since the majority of viruses were so minuscule they could not be seen with any clarity through the ordinary light microscope. They would even talk about them as if they were akin to protein molecules. Luria would come to define phage viruses, in a misleading oversimplification, as extensions of the bacterial genome. But with the invention of the electron microscope, by the German company Siemens, even the smallest viruses, including bacteriophages, would soon become visible for the first time. And when they did become visible, they proved to be more complex than the two scientists had initially conceived.

Many phages had a head that was cylindrical in shape, with a narrow sheath below it, as tall as the head, and a base plate with six spikes with fibres attached. Now that they could visualise phages in the process of infecting their host bacteria, something struck Delbrück and Luria as exceedingly odd. The viruses didn’t actually pass through the bacterial cell wall. What they appeared to do was to squat down against the wall and inject their hereditary material into the cell. In 1951 a phage researcher called Roger Herriott would write to Hershey, ‘I’ve been thinking that the virus may behave like a little hypodermic needle full of transforming principles.’ This became the background to Hershey and Chase’s experiment in which they confirmed that that was precisely what happened. The virus behaved exactly like a hypodermic syringe; the tail and its elongated fibrils would attach to the bacterial wall and the phage would then inject its viral DNA in through the bacterial wall to take over the bacterium’s own genetic machinery, the viral genome compelling the bacterial genome to construct what was necessary for the generation of daughter viruses. In effect, the infected bacterium became a factory for the production of daughter viruses.

It would be this discovery, together with many associated extrapolations to microbiology and genetics, that would lead to all three scientists – Delbrück, Luria and Hershey – sharing the Nobel Prize in 1969.

Meanwhile, back in 1947, it was the dynamic energy and infectious charm of Luria, and the innovative genius of Delbrück, that proved most influential to the youthful Watson after his arrival into Indiana University. Still fascinated by the mystery of the gene, it was his hope that the mystery might be solved without his bothering to learn any of the complex physics or chemistry.

It is instructive to discover, from conversations between Luria and Watson, that there was no ignorance at Bloomington about Avery’s discovery of DNA. Luria had visited Avery in 1943, prior to the publication of the key paper, when he had the opportunity of discussing Avery’s findings in detail. He would recall Avery to Watson as an utterly non-pompous scientist, precise in his language, with a tendency as he spoke to close his eyes and rub his bald head – ‘every bit of a chemist, even though he was an MD’. Watson would take his cue from Luria, writing, in The Double Helix, how Avery had shown that hereditary traits could be transmitted from one bacterial cell to another by purified DNA molecules. Given the fact that DNA was known to occur in the chromosomes of every type of living cell, ‘Avery’s experiments strongly suggested that … all genes were composed of DNA.’

In the autumn of 1947, Watson, still just 19, took Luria’s course in bacteriology and Muller’s in X-ray-induced gene mutation. Faced with the choice of entering into research with Muller on Drosophila or with Luria on microbes, he plumped for Luria, despite the fact that the Italian scientist had a reputation among the graduate students for having a short fuse with dimwits. Watson would subsequently adopt his patron’s example. Delbrück was a heroic figure to Watson because he had inspired Schrödinger’s ideas in the inspirational book. Watson was delighted when Luria introduced him to Delbrück when the eminent German physicist paid a visit to Bloomington.

Luria set Watson a PhD dissertation on the pathological effects on phage of exposure to X-rays. The work proved so mundane that Watson would barely mention it in his biography. But his obsession with the gene was undimmed. By the summer of 1949, his thesis nearing completion, he had the itch to travel to Europe. Luria arranged a Merck Fellowship from the National Research Council – three thousand dollars for the first year, potentially renewable. In May the following year, with his PhD under his belt, he sailed for Denmark, where he had been assigned to study nucleotides with a biochemist named Herman Kalckar. Kalckar was a gifted scientist but his interest was neither the gene nor the bacteriophage. A disenchanted Watson switched his attentions to another Dane, and a member of the phage group, Ole Maaløe, who was working on the transfer of radioactively-tagged DNA from phages to their viral offspring.

Out of the blue, Kalckar accepted a short-term project in the Zoological Station in Naples. He suggested that Watson might tag along. Though he had little interest in marine biology, Watson was delighted to acquiesce. He hoped to warm himself in the Italian sun. But he was disappointed to find Naples chilly, with no heater in his room on the sixth floor of a nineteenth-century house. ‘Most of my time I spent walking the streets or reading journal articles … I daydreamed about discovering the secret of the gene, but not once did I have the faintest trace of a respectable idea.’

Here, by happenstance, he attended a lecture in the Zoological Station given by an English scientist named Maurice Wilkins. The lecture could hardly have excited him in prospect, knowing that most of it would be about the biochemistry of proteins. ‘Why should I get excited learning boring chemical facts as long as the chemists never provided anything incisive about the nucleic acids?’

But he took the risk and attended anyway.

Tall, bespectacled, asthenic and somewhat diffident in manner, you might have expected Wilkins’ presentation to bore the restless and impatient Watson. But it did not. To begin with, it was delivered in a language that Watson readily understood. And for all of his diffident manner, Wilkins kept to the point. Then suddenly, close to the end of the lecture, a projected slide jarred Watson to full attention. On the screen was a photograph that showed something Wilkins called an X-ray diffraction pattern of DNA that had been taken in the King’s College laboratory in London. Watson would subsequently admit that he knew nothing about X-ray crystallography. He hadn’t understood a word of what he had read about it in the scientific journals and he thought that much of what the ‘wild crystallographers’ were claiming was very likely baloney.

But now here was Wilkins mentioning in passing that this was the clearest picture of DNA that he and his colleagues had yet obtained from their X-ray studies. In the same audience was the Leeds-based English physicist, William Astbury, who had pioneered X-ray diffraction studies of biological molecules, and who had produced the first X-ray pictures of DNA. Astbury would subsequently confirm that no one had ever shown such a sharp, discrete set of reflections from the DNA molecule as Wilkins then projected onto the screen. ‘There was nothing like it in the literature.’ In explaining the picture, Wilkins suggested that DNA might be thought of as a crystalline substance.

Watson was electrified to hear Schrödinger’s prophecy confirmed. He sat in a daze of wonderment as Wilkins went on to explain that if and when we understood the structure of DNA, then we might be in a better position to understand how genes worked. Watson was now asking himself some pertinent questions. Who was this interesting English scientist, Wilkins? And how could he get to join his team at King’s College in London?

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Maurice Hugh Frederick Wilkins was not, in fact, English, as Watson initially surmised. He was born in Pongaroa, New Zealand, where his father, Edgar Henry, was a practising doctor. The family were Anglo-Irish in origins, hailing from Dublin, where Maurice’s paternal grandfather had been headmaster of the high school and his maternal grandfather chief of police. On leaving New Zealand the family first returned to Ireland, then headed for London, where Dr Wilkins was later to do his pioneering work in public health.