His reply surprised me. Like most doctors, I thought of viruses as nothing more than parasites. I was taught modern Darwinian evolution as part of the core biology that underpins our understanding of medicine. Lay people often confuse viruses with bacteria but they are radically different organisms. Most viruses are a lot smaller than bacteria, so small in fact that most are completely invisible even under the highest magnifications of the light microscope. Only through more subtle detective work, using immunological probes, or molecular chemistry, or, ultimately, the vast magnification of the electron microscope, can we bring them into focus. In their genetic arrangements viruses also differ markedly from bacteria. Their DNA is usually packaged in the linear clusters we call genes, rather like our own, while the DNA of bacteria is packaged in a single ring. Viruses are also the ultimate masters of evolution through mutation. They mutate with astonishing speed, something like a thousand times faster than bacteria, which in turn mutate approximately a thousand times faster than we do. Mutation of this order is an important consideration for medicine since it is one of the ways in which bacteria and viruses become resistant to antibacterial and antiviral drugs. For example, it is the key to understanding resistance to therapy in conditions such as AIDS and tuberculosis, where the phenomenal mutational capacity of the HIV-1 virus and the tuberculosis bacterium means that we are obliged to prescribe a cocktail of different drugs to control them.

In this conversation with Terry Yates, I discovered that many different species of rodents around the world appeared to have hantaviruses that infected them. The first hantavirus ever discovered came from a rodent in Korea – it emerged close to the Hantaan River, which gave its name to the genus of viruses as well as to the human illness the virus caused, which is known as Hantaan fever. So when Yates told me he was looking into the evolutionary aspects of the hantaviruses, I presumed that he was talking about mutation. I knew nothing about the co-evolution of a virus in parallel with its host. Indeed, I was still thinking along the conventional medical and evolutionary lines when I asked him another question.

‘What do you perceive as a virus?’

‘That’s a good question. Some people will argue that viruses are not life. I disagree with that, certainly. Perhaps a more pertinent question to me is not “what is a virus?” but “what is a species as far as a virus goes?” Are there species of viruses analogous to mammalian species? Basically I am only recently into viruses. I became interested, almost accidentally, because of the work we do with mammals. It just happens that mammals are the main reservoirs of these viruses. So for me the question “what is a species when it comes to viruses?” is best understood in the context, are they evolving, and are they co-evolving with their reservoir organism? I think that viruses are lineages that have their own evolutionary trajectory and their own historical fate. By analysing the history of that evolution and studying the branching patterns of those viral lineages, we can define viruses based on the branches of the tree. And when we look across the board at these hantaviruses, our evolutionary analysis thus far has shown a very tight correlation between the evolutionary tree that illustrates the history of the mammalian host and the evolutionary tree that illustrates the history of the viruses.’

This still made little sense to me in the way I had been educated to think about viruses, not from the medical perspective and not, as I was already beginning to suspect, from the evolutionary perspective.

‘When you say you are studying the virus, do you imply studying its genome?’

Here I should explain, for my non-scientific readers, that a genome is the sum total of all the genes of a life form. While all other forms of life, including humans, have genes coded by DNA, viruses can be coded by DNA or, as in the case of the hantaviruses, by its sister molecule, RNA.

‘Studying its genome,’ he confirmed, ‘or any other characters that would be applicable. They are such simple organisms that – for example, in the case of hantavirus – to get enough characters to be able to understand the evolution of the virus, the best thing to use is the RNA sequences. So we’re having better luck with this because each of the bases in the RNA sequences is applicable.’

‘How do you manage to do that? Have you been studying the viral genome as and from when you first noticed it, or have you some way of going back in time to see what the virus was like some time ago?’

‘That’s a complicated subject and one that has been debated at the Natural History Museum at the exhibit on the evolution of man. We use a methodology called Cladistics. It’s basically a phylogenetic analysis [tree of life analysis] of the different lineages of viruses.’

‘This is where you observe them in different species?’

‘Not exactly, no. We’re talking about [analysing sequences over] enormous periods of time here. We have been successful in extracting viruses from our frozen tissue collection and we are having success with extracting DNA from fossil organisms. People have successfully amplified and sequenced DNA from plants that were embedded in Miocene rocks – these are 30-million-year-old plants. So what you can do with this phylogenetic analysis is take a viral sequence from a hantavirus of the Four-Corners deer mouse and compare that to other species of viruses that occur on other branches [of the parallel virus-rodent trees]. From this you can extrapolate what the historical condition was. So we can trace the evolutionary sequence back in time and make comparisons to other lineages that diverged from the lineage you are interested in, much earlier in time.’

The implications were slowly dawning on me. ‘So you see a link between the virus and the mammal that is very close?’

‘That’s right. For example, if we were looking at eutherian mammals [the placental mammals including humans], we might compare the sequences of eutherian viruses to those of the marsupials and egg-laying mammals, which are more ancient.’

‘Because they are similar, but not the same viruses, you raise the question that sometime in the past, just as the animals had a common ancestry, perhaps their viruses might also have had their own common ancestry?’

‘That’s right.’

A surprising idea had entered my mind. From my background knowledge of evolutionary biology, and in particular of evolutionary virology, I could assume that virologists, sharing the same conventional viewpoint as I had up to now, would assume that the viruses, given that they mutate at a vastly faster rate than the mammals, would fast-track their own evolutionary trajectories, to stay close to the evolutionary pathways of their mammalian hosts. But now, thanks to the surprising idea that Terry Yates had planted in my mind, I asked myself the question:

What if both the virus and its mammalian host are influencing one another’s evolution, one evolutionary tree interacting with the other, over the vast time periods of their co-evolution?

I spent a good deal longer than I had initially envisaged with Professor Yates, visiting the Sevilleta and enjoying the courtesy of a stay with him and his family, when I had ample opportunity to examine his work, and to think about his ideas in more detail. When I put my question to Yates himself, he could provide no definite answers other than the observation that viruses and hosts appeared to be following very close co-evolutionary trajectories. Nevertheless, over the months that followed, his explanation of virus-mammalian co-evolution intrigued me deeply and it caused me to look much harder at the relationships between viruses generally and their hosts. In particular I spoke to other biologists, and especially virologists, and I explored the literature far and wide. As far as I could determine, nobody was even thinking along the lines of viruses and hosts influencing each other’s evolution. And thus it would appear that, entirely by chance, I had stumbled across an idea that, if true, would have major implications. It was one of those exciting moments a scientist hopes will come along at some stage of his or her career, a new idea that makes you think long and hard, and even to question some of those ordinary assumptions you have carried with you since your undergraduate years.

What, then, is a virus?

Biologists will differ very widely in their answers to this question. Some will quote the distinguished immunologist and writer, Sir Peter Medawar, Nobel Laureate for his work on tissue transplantation, who caricatured the virus as a piece of bad news wrapped in a protein. But this definition, however whimsical, adds little to any real understanding. Others, usually molecular biologists or geneticists, will adopt a chemical perspective, while Darwinian evolutionists – and until recently symbiologists too – are inclined to see viruses as mere agents of “horizontal gene transfer” between different species. We saw a very interesting example of this with Elysia chlorotica, when the strange retroviruses in the slug’s genome appeared to enable the transfer of key genes “horizontally” across the kingdoms of plants and animals, as represented by the alga and the slug. Another interesting perspective is that of Eckard Wimmer, a professor in the Department of Molecular Genetics and Microbiology at Stony Brook, New York, who became famous in 2002 for reconstructing the polio virus from mail-order components back in his lab.⁶ This experiment provoked a good deal of interest and notoriety. But what Wimmer and his co-workers wanted to do, amongst other things, was to make a conceptual, and perhaps philosophical, point. If you know the genetic formula of a virus, you can reconstruct it. They even quoted an empirical formula for the polio virus, as follows:

C332,652H492,388N98,245O131,196P7,501S2,340

It is strange to think of an organism, even if exceedingly small, being reduced to a list of atoms. One is reminded of the bitter opposition of the gentle French naturalist, Jean-Henri Fabre, the so-called poet of entomology, who, although he greatly respected Darwin as a man and fellow scientist, opposed Darwin’s line of thinking. In Chapter VIII of his book, More Hunting Wasps, Fabre described a ‘nasty and seemingly futile’ experiment he had conducted, rearing caterpillar-eating wasps on a ‘skewerful of spiders’. We need not consider the experiment in detail here, only Fabre’s conclusion, which led him to dismiss the concept of evolution through natural selection. In Fabre’s own words, ‘It is assuredly a majestic enterprise, commensurate with man’s immense ambitions, to seek to pour the universe into the mould of a formula … But … in short, I prefer to believe that the theory of evolution is powerless to explain [the wasp’s] diet.’

It is perfectly true that, in certain circumstances, viruses do behave like inert chemicals. Indeed, I once performed a series of experiments that proved this. When I was a medical student at Sheffield University, I was interested in how our mammalian immune system would respond to viral invasion. The penetration of such alien organisms into our bloodstream – literally the very heart of our being – would be a major, and extremely threatening, event. With the help of my mentor, Mike McEntegart, Professor of Microbiology, I set up an experiment in which I injected viruses into the bloodstream of rabbits. Some readers might react with concern about hurting experimental animals, but the virus I used was a bacteriophage, known as ΦX174 – a virus that only attacks bacteria – so the rabbits suffered no illness. Yet their adaptive immune system responded in exactly the way it should to any alien invader, with a build-up of antibodies in two waves, rising to a peak by 21 days, where a single drop of their serum would be seen to inactivate a billion viruses in mere moments.

The point I am making is that this experiment, by its very design, did not really reproduce the living behaviour of viruses. Injecting a virus into such a host was the virological equivalent of landing people, unprotected, on the surface of Mars. The circumstances were unnatural to the virus and it could neither survive nor respond, in the behavioural sense, and so it died. Had I injected smallpox, or influenza, or HIV-1, into people, the result would have been altogether different. The virus would have come alive in its natural host and a fearsome interaction, virus-with-human, would have followed. As this suggests, it is a waste of time, from the definitional perspective, to consider viruses outside of their natural ecology. Outside the host, it could be argued that a virus really does behave much as Professor Wimmer’s formula – as an inert assemblage of genes and proteins. Only in the real circumstances of its life cycle, when it interacts with its natural host, do we witness the real nature of viruses.

This is why, like Terry Yates, I take the view that viruses, in their natural life cycles, should be regarded as life forms. In this sense the extreme reductionism of depicting a virus as a list of chemicals is implicitly absurd. We might similarly contrive a chemical formula for a human being, when we would end up listing a similar collection of atoms, albeit their numbers would be far more gargantuan. People who view viruses only as chemical assemblages miss the vitally important point that viruses have arrived on the scene through a vast, and exceedingly complex, trajectory of evolution, much as we have ourselves. And though Professor Wimmer might seem to be promoting the viewpoint of a virus as inert, this is not his thinking at all. His view of viruses is much the same as my own, and that of the majority of biologists. A virus may appear inert outside its host, but when it enters the host cell, he too regards it as coming alive. And what an extraordinary life form it turns out to be – for here, in the landscape of the host cell, it has the unique ability of taking over and driving the host genome to make it manufacture new viruses.

Here, in the cells of their natural hosts, viruses are born, like all other life forms. Moreover, they can die. When we treat viral illness with viricidal drugs, our purpose is to kill viruses, much as we use bactericidal drugs to kill bacteria. And, perhaps most important of all, the powerful forces of evolution apply to viruses, just as they do to all other life forms. That is why it is so difficult to cure people infected with viruses. If a virus was nothing more than an inert collection of chemicals, there would never have been an AIDS pandemic. The human immune system would have mopped them up from the circulation without any difficulty.

It is clearly important that we take the trouble to understand viruses. We all know that this is important to medicine in combating viral illness in people. It is important also to veterinary medicine in combating diseases in animals, as it is to agriculture in combating diseases in plants. But there is another, even more profound, reason why we should take the trouble to understand viruses. My subsequent researches, and those of virologists such as Luis Villarreal and Marilyn Roossinck, have made it increasingly evident that viruses have played a key role in the evolution of life, from its very beginnings on Earth to the magnificent diversity we see today. Nowhere has the contribution of viruses been more significant than in the evolution of the human species. Perhaps most amazingly of all, this creative role in human evolution and disease has been played by viruses with a very close resemblance to HIV-1.

I realise that these will appear to be startling claims. When I first proposed such novel concepts, they provoked a heady mixture of bafflement and denial. The reaction was hardly surprising since, if I was right, it appeared to threaten the hegemony of the so-called “synthesis theory”, the trilogy of principles that has stood fast for more than seventy years as the theoretical foundation of modern Darwinism.

2
A Crisis in Darwinism

What [The Double Helix] conveys … is how uncertain it can be, when a man is in the black cave of unknowing, groping for the counters of the rock and the slope of the floor, listening for the echo of his steps, brushing away false clues as insistent as cobwebs to recognise that something important is taking shape.

HORACE FREELAND JUDSON¹

A key proposition that has been almost universally misinterpreted among non-scientists as the core of Darwin’s theory is the concept known as the “survival of the fittest”. Nothing could have more alienated religious sensibility, with its potential for misapplication to society, for example its misuse in condoning laissez-faire politics in relation to poverty and hunger, and worst of all its extrapolation to racial and ethnic abuse. It is important, therefore, to clarify the fact that Darwin did not invoke the term. On the contrary, the concept of survival of the fittest was the brainchild of the social philosopher Herbert Spencer, who first proposed it in his book, Principles of Biology, published in 1864.² Spencer had been developing his own thread of thought even before he read Darwin’s Origin of Species, which was published some five years before his own Principles of Biology, but the social philosopher was not educated in biology, and, although his concept was widely seen as synonymous with, or even a clearer exposition of, what Darwin was supposed to have meant by his term “natural selection”, Spencer misunderstood Darwin’s scientifically grounded theory, and he misapplied it as an endorsement of his sociological philosophy. The scientific historians, and philosophers, who have examined Spencer’s ideas have concluded that he saw evolution as a purposeful progression of the physical world, including all biological organisms, the human mind, and human culture and society. Unfortunately it was Spencer’s sociological concept of survival of the fittest, as opposed to Darwin’s scientific concept of natural selection, that led to the inaptly named Social Darwinism of the early nineteenth century, with all of its unfortunate ramifications.

There was never any true scientific foundation to Spencer’s ideas, but since they conveniently fitted with some of the prevailing prejudices of class, and the ethnic and racial bias of the late nineteenth century, extending into the first half of the twentieth century, they became deeply ingrained and influenced political and social belief. It is tragic that Spencer’s ideas still influence a lot of non-scientists today, so that one frequently hears the expression “survival of the fittest” raised in defence or excuse of some prejudicial action. So ingrained did Spencer’s ideas become that, during his lifetime, Darwin himself was put under a lot of pressure, by Spencer and others, to change his basic premise, but, although he briefly flirted with Spencer’s idea, he quickly recovered his senses and returned to his original concept.

Why am I making such a fuss of this when it might be argued that a similar concept of “fitness” is central to Darwinian theory even today? Of course fitness is a core concept to evolutionary biology, but this Darwinian expression is far from the judgemental notion proposed by Spencer. What then did Darwin really imply with his theory of evolution by means of natural selection, and how does the Darwinian concept of “fitness” differ from Spencer’s notion of “the survival of the fittest”?

Admirers of David Attenborough’s Blue Planet series will have observed how, in the warmth of summer, the female Atlantic lobster, a species that can grow up to 20 kilograms in weight, decides that the time has come to lay her eggs. She has already mated – often this happens as soon as she has moulted – but for seven months she has skulked from view in the freezing, deeper waters of the ocean, safe from predators and winter storms and patient in her determination to choose the most opportune moment for her offspring. But now her mind is made up, she is obliged to trudge her month-long marathon to the sandbanks of the warmer, surface waters, where, on her arrival, she must first do battle, claw for claw, with other lobsters to take control of her favoured sheltered pit. Here at last, some eight months after first fertilisation, she deposits her 20,000 or so eggs, which tumble into the pit from grape-like clusters beneath her abdomen, and from which her young emerge within minutes to take advantage of the warmth and limited shelter afforded by their mother’s endurance, discrimination and fortitude in battle. In the case of other marine invertebrate animals, such as sea urchins, and certain species of fish, a single spawning may give rise to millions of eggs. This behaviour, and the very production of vast numbers of potential offspring, is closely linked to what biologists actually mean when they talk about fitness in its true evolutionary meaning.

Fitness, from the Darwinian perspective, is a measure of how successful an individual is in his or her ability to reproduce and thus to contribute to the broad genetic pool of the species. It is a very simple, non-moralistic and non-judge-mental concept, the real emphasis of which is on reproduction. But, as we see with the lobster, this is more complex than merely laying eggs, or, in the case of human beings, bearing young in a womb. The individual has first to survive in the competitive theatre of life and then to compete with others of the same species for reproduction, and further to make possible, even in such limited life histories as that of the lobster, the survival of as many offspring as possible. In fact evolutionary biologists will usually measure comparative fitness of an individual within a species and what they look for is the proportional contribution of an individual’s genes to the species gene pool in a single generation.

Humans do not give birth to millions of eggs at a very early stage of embryological development, but rather to highly developed infants, which demands that they be nurtured for a very long period of time in the womb. For this purpose evolution has designed the human uterus as a single chamber, roughly the shape of an inverted pear, which is optimally designed for bearing a single foetus. The highest recorded number of living offspring born to a human mother in a single pregnancy is the eight babies born to an American mother in January 2009, all of whom lived. They were not conceived in the normal way but through assisted fertility treatment, and it is unlikely that all would have lived without the assistance of modern obstetric care. Indeed, obstetricians rightfully regard any increase above the normal single offspring as carrying an increased risk to both mother and offspring, even for twins.

Fitness, in human terms, is clearly more complex than we see in lobsters, but nevertheless the same basic non-Spencerian considerations apply, in terms of relative fitness.

The modern Darwinian concept of natural selection is brutally simple and depends on a system of probability, amenable to calculus. Where an individual of any species acquires some slight advantage in terms of survival over its fellows, it is more likely to survive long enough to have offspring, and if the advantage is hereditary, the offspring in turn will enjoy the same advantage over their own generation, so the advantage in time becomes part of the evolving species. From the fitness point of view, the hereditary advantage gives the individual, and its offspring at every subsequent stage of reproduction, the chance of making a bigger contribution to the species gene pool than the average member of the species. It’s really that simple. We can see, from the Darwinian standpoint, that relative fitness is a way of measuring advantage from a natural selection point of view. In time, particularly if the affected group within a species is isolated, geographically or otherwise, from the remainder of the species, an accumulation of such hereditary changes – or a rapidly developing major change – will so alter the affected group that they are no longer capable, or likely, to reproduce with members of the original species. This is the perfectly reasonable Darwinian explanation of how new species arise in a linear-with-branching pattern from ancestral species.

The creation of new species from old is termed “speciation”. Spencer, who was influenced by the French evolutionary biologist, Lamarck, believed that evolution was driving all of life, and most particularly the human species, towards a higher, utopian, destiny. But it is clear that Darwin’s theory of evolution by means of natural selection embraces no such ideal. On the contrary, selection works through the biological necessities of survival and comparative success in reproduction, which have nothing to do with morality, and have no in-built drive towards a philosophic, or religious, ideal of individual or societal perfection.

The concept of natural selection, as proposed by Darwin, was both logical and amenable to experimental confirmation, so that, in spite of considerable opposition from both Church and rivals within his own field, it appealed to the majority of scientists, and eventually to the educated society of his day. However, it embodied a weakness of which Darwin himself was well aware. For selection to work, it demanded a source, or sources, of hereditary change, which would give rise to the key advantages in survival, and thus relative fitness, of one individual, or group, over the others of its own species. Today we know that this implies some sort of genetic, or genomic, innovation, but Darwin was hampered by the ignorance of the mechanisms of heredity in his day. The very concept of genetics was unknown and the enlightenment of DNA would be unavailable until almost a century after publication of The Origin of Species. What Darwin achieved, given the science of his day, was, without exaggeration, world-changing. We cannot criticise him if he was obliged to fall back on now-outmoded concepts of parental mixing, or blending, as if the quaint notion of pedigree could somehow supply what we now realise to be the vast genetic and genomic change necessary to give rise to biodiversity. It was an inherent weakness in his theory that was unlikely to go away.

Thus it was not altogether surprising that, at Oxford, in 1894, during his presidential address to the British Association for the Advancement of Science, the Marquis of Salisbury attacked the concept of natural selection. The distinguished Thomas Henry Huxley was in the audience – cast by his critics as Darwin’s bulldog – but in reality one of the most objective, and formidable, biologists of his day. Huxley was faced with the fact that, where many earlier critics had attacked Darwinism from a religious perspective, adopting the Procrustean stance of faith, Salisbury was a highly educated man, an ex-Prime Minister and amateur scientist, and his attack was based in logic. He did not doubt the reality of evolution and he praised Darwin for convincing science, and the more educated levels of society, of this – rather, it was Darwin’s mechanism of evolution, natural selection, on which he focused his criticism. To date no scientist had ever proved in scientific experiment or observation that natural selection could produce a new species from an ancestral one. Moreover, Darwin’s theory assumed a very slow and gradual change in the evolution of life, and biodiversity, implying that the history of the Earth extended, say, to something like a billion years. Meanwhile Lord Kelvin, widely regarded as the foremost physicist in the world, had calculated the presumed age of the Earth from the physics of a cooling body, and pronounced that it could be no more than a million years old – too little time for life’s diversity to have evolved.

Although Huxley defended Darwin as best he could, he was hampered by the prevailing lack of hard evidence, and so inevitably he lost the battle to the scientific methodology of Kelvin. Darwinism had fallen to its lowest point, a nadir that would subsequently be recalled by Huxley’s own grandson, Julian, as “the eclipse of Darwinism”. Indeed, Julian Huxley would go on to describe the pressures on Darwinism that arose about the end of the nineteenth century and extended into the twentieth, when they were compounded by the growing dichotomy of many of the core disciplines of the biological sciences. In a great series of scientific publications, author after author would simply assume that their observations implied evolutionary adaptations, and thus the influence of natural selection, with ‘little contact of [such] evolutionary speculation with the concrete facts of cytology and heredity, or with actual experimentation’. The new generation of selectionists ignored the rising field of genetics, as pioneered by the writings of the Bavarian monk, Gregor Mendel, and they ignored the discovery of mutation by the Dutch botanist, Hugo de Vries. Evolutionary biology fragmented into three different factions – the selectionists, who had an undying conviction in natural selection, Mendelians (what we would now call geneticists), and mutationists, inspired by de Vries – and for several decades the discord continued.

In the opening chapters of his book, Evolution: The Modern Synthesis, Julian Huxley put his finger on the heart of the problem: ‘The really important criticisms have fallen upon Natural Selection as an evolutionary principle and centred round the nature of inheritable variation.’³

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