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<\/p>\n<\/div>\nLet\u2019s imagine planet Earth without viruses<\/a>.<\/p>\n<\/div>\n We wave a wand, and they all disappear. The rabies virus is suddenly gone. The polio virus is gone. The gruesomely lethal Ebola<\/a> virus is gone. The measles virus, the mumps virus, and the various influenzas are gone. Vast reductions of human misery and death. HIV is gone, and so the AIDS<\/a> catastrophe never happened. Nipah and Hendra and Machupo and Sin Nombre are gone\u2014never mind their records of ugly mayhem. Dengue, gone. All the rotaviruses, gone, a great mercy to children in developing countries who die by the hundreds of thousands each year. Zika<\/a> virus, gone. Yellow fever<\/a> virus, gone. Herpes B, carried by some monkeys, often fatal when passed to humans, gone. Nobody suffers anymore from chicken pox, hepatitis, shingles, or even the common cold. Variola, the agent of smallpox? That virus was eradicated in the wild by 1977, but now it vanishes from the high-security freezers where the last spooky samples are stored. The SARS virus of 2003, the alarm that we now know signaled the modern pandemic era<\/a>, gone. And of course the nefarious SARS-CoV-2 virus, cause of COVID-19<\/a> and so bewilderingly variable in its effects, so tricky, so dangerous, so very transmissible, is gone. Do you feel better?<\/p>\n<\/div>\n Don\u2019t.<\/p>\n<\/div>\n This scenario is more equivocal than you think. The fact is, we live in a world of viruses<\/a>\u2014viruses that are unfathomably diverse, immeasurably abundant. The oceans alone may contain more viral particles than stars in the observable universe. Mammals may carry at least 320,000 different species of viruses. When you add the viruses infecting nonmammalian animals, plants, terrestrial bacteria, and every other possible host, the total comes to \u2026 lots. And beyond the big numbers are big consequences: Many of those viruses bring adaptive benefits, not harms, to life on Earth, including human life.<\/p>\n<\/div>\n We couldn\u2019t continue without them.<\/a> We wouldn\u2019t have arisen from the primordial muck without them. There are two lengths of DNA that originated from viruses and now reside in the genomes of humans and other primates, for instance, without which\u2014an astonishing fact\u2014pregnancy would be impossible. There\u2019s viral DNA, nestled among the genes of terrestrial animals, that helps package and store memories\u2014more astonishment\u2014in tiny protein bubbles. Still other genes co-opted from viruses contribute to the growth of embryos, regulate immune systems, resist cancer\u2014important effects only now beginning to be understood. Viruses, it turns out, have played crucial roles in triggering major evolutionary transitions. Eliminate all viruses, as in our thought experiment, and the immense biological diversity gracing our planet would collapse like a beautiful wooden house with every nail abruptly removed.<\/p>\n<\/div>\n As a zebra shark cruises by, a diver at Aquarium of the Pacific in Long Beach, California, displays an image of a bacteriophage, a type of virus that infects bacteria. Harmless to plants and animals, bacteriophages are critical for healthy marine ecosystems. The Earth\u2019s oceans teem with these and other viruses. The aquarium\u2019s Tropical Reef Habitat and Soft Coral Garden hold 367,166 gallons of water, with an estimated 5.32 quadrillion viruses. If lined up side by side, those viruses would circle the Earth almost eight times.PHOTOGRAPH BY CRAIG CUTLER.<\/p>\n IMAGE OF BACTERIOPHAGE BY DOMINIK HREB\u00cdK AND PAVEL PLEVKA, LABORATORY OF STRUCTURAL VIROLOGY, CEITEC, MASARYK UNIVERSITY, CZECH REPUBLIC<\/p>\n<\/div>\n<\/figcaption><\/figure>\n A virus is a parasite, yes, but sometimes that parasitism is more like symbiosis, mutual dependence that profits both visitor and host. Like fire, viruses are a phenomenon that\u2019s neither in all cases good nor in all cases bad; they can deliver advantage or destruction. Everything depends: depends on the virus, on the situation, on your point of reference. They are the dark angels of evolution, terrific and terrible. That\u2019s what makes them so interesting.<\/p>\n<\/div>\n To appreciate<\/b> the multifariousness of viruses, you need to start with the basics of what they are and what they are not. It\u2019s easier to say what they are not. They are not living cells. A cell, of the sort assembled in great number to make up your body or mine or the body of an octopus or a primrose, contains elaborate machinery for building proteins, packaging energy, and performing other specialized functions\u2014depending on whether that cell happens to be a muscle cell or a xylem cell or a neuron. A bacterium is also a cell, with similar attributes, though much simpler. A virus is none of this.<\/p>\n<\/div>\n Saying just what a virus is<\/i> has been complicated enough that definitions have changed over the past 120-some years. Martinus Beijerinck, a Dutch botanist who studied tobacco mosaic virus, speculated in 1898 that it was an infectious liquid. For a time a virus was defined mainly by its size\u2014a thing much smaller than a bacterium but that, like bacteria, could cause disease. Still later, a virus was thought to be a submicroscopic agent, bearing only a very small genome, that replicated inside living cells\u2014but that was just a first step toward a better understanding. (See how viruses look up close.<\/a>)<\/p>\n<\/div>\n \u201cI shall defend a paradoxical viewpoint,\u201d wrote the French microbiologist Andr\u00e9 Lwoff in \u201cThe Concept of Virus<\/a>,\u201d an influential essay published in 1957, \u201cnamely that viruses are viruses.\u201d<\/i> Not a very helpful definition but fair warning\u2014another way of saying \u201cunique unto themselves.\u201d He was just clearing his throat before beginning a complex disquisition.<\/p>\n<\/div>\n Lwoff knew that viruses are easier to describe than to define. Each viral particle consists of a stretch of genetic instructions (written either in DNA or that other information-bearing molecule, RNA) packaged inside a protein capsule (known as a capsid). The capsid, in some cases, is surrounded by a membranous envelope (like the caramel on a caramel apple), which protects it and helps it catch hold of a cell. A virus can copy itself only by entering a cell and commandeering the 3D-printing machinery that turns genetic information into proteins.<\/p>\n<\/div>\n If the host cell is unlucky, many new viral particles are manufactured, they come busting out, and the cell is left as wreckage. That sort of damage\u2014such as what SARS-CoV-2 causes in the epithelial cells of the human airway\u2014is partly how a virus becomes a pathogen.<\/p>\n<\/div>\n But if the host cell is lucky, maybe the virus simply settles into this cozy outpost\u2014either going dormant or back-engineering its little genome into the host\u2019s genome\u2014and bides its time. This second possibility carries many implications for the mixing of genomes, for evolution, even for our sense of identity as humans, a topic to which I\u2019ll return. One hint, for now: In a popular 1983 book the British biologist Peter Medawar and his wife, Jean, an editor, asserted, \u201cNo virus is known to do good: It has been well said that a virus is \u2018a piece of bad news wrapped up in protein.\u2019 \u201d They had it wrong. So did a lot of scientists at the time, and it remains a view still embraced, understandably, by anyone whose knowledge of viruses is limited to such bad news as the flu and COVID-19. But today some viruses are known to do good. What\u2019s wrapped up in the protein is a genetic dispatch, and that might turn out to be good news or bad, depending.<\/p>\n<\/div>\n Where did the first viruses<\/b> come from? This requires us to squint back almost four billion years, to the time when life on Earth was just emerging from an inchoate cookery of long molecules, simpler organic compounds, and energy.<\/p>\n<\/div>\n Let\u2019s say some of the long molecules (probably RNA) started to replicate. Darwinian natural selection would have begun there, as those molecules\u2014the first genomes\u2014reproduced, mutated, and evolved. Groping for competitive edge, some may have found or created protection within membranes and walls, leading to the first cells. These cells gave rise to offspring by fission, splitting in two. They split in a broader sense too, diverging to become Bacteria and Archaea, two of the three domains of cellular life. The third, Eukarya, arose sometime later. It includes us and all other creatures (animals, plants, fungi, certain microbes<\/a>) composed of cells with complex internal anatomy. Those are the three great limbs on the tree of life, as presently drawn.<\/p>\n<\/div>\n But where do viruses fit? Are they a fourth major limb? Or are they a sort of mistletoe, a parasite wafted in from elsewhere? Most versions of the tree omit viruses entirely.<\/p>\n<\/div>\n Jason Shepherd, a neuroscientist at the University of Utah, holds an image of a three-dimensional reconstruction of a virus-like protein capsule that plays a critical role in cognition and memory. The ARC <\/i>gene, which carries the code to create this spherical marvel, was acquired by terrestrial vertebrates\u00a0from a viral-like ancestor about 400 million years ago. The capsule, which resembles the capsids that surround viral genomes, ferries genetic information between neurons in the human brain as well as in the brains of many other animals. PHOTOGRAPH BY CRAIG CUTLER. PHOTOGRAPH OF PROTEIN CAPSULE BY SIMON ERLENDSSON, MRC LABORATORY OF MOLECULAR BIOLOGY<\/span>\u00a0(LEFT) AND PHOTOGRAPH BY ROBERT CLARK (RIGHT)<\/span><\/p>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n <\/p>\n One school of thought asserts that viruses shouldn\u2019t be included on the tree of life because they aren\u2019t alive. That\u2019s a lingering argument, hinging on how you define \u201calive.\u201d More intriguing is to grant viruses inclusion within the big tent called Life, and then wonder about how they got in.<\/p>\n<\/div>\n There are three leading hypotheses to explain the evolutionary origins of viruses, known to scientists as viruses-first, escape, and reduction. Viruses-first is the notion that viruses came into existence before cells, somehow assembling themselves directly from that primeval cookery. The escape hypothesis posits that genes or stretches of genomes leaked out of cells, became encased within protein capsids, and went rogue, finding a new niche as parasites. The reduction hypothesis suggests that viruses originated when some cells downsized under competitive pressure (it being easier to replicate if you\u2019re small and simple), shedding genes until they were reduced to such minimalism that only by parasitizing cells could they survive.<\/p>\n There is also a fourth variant, known as the chimeric hypothesis, which takes inspiration from another category of genetic elements: transposons (sometimes called jumping genes). The geneticist Barbara McClintock deduced their existence in 1948, a discovery that earned her a Nobel Prize<\/a>. These opportunistic elements achieve their Darwinian success simply by bouncing from one part of a genome to another, in rare cases from one cell to another, even one species to another, using cellular resources to get themselves copied, over and over. Self-copying protects them from accidental extinction. They accumulate outlandishly. They constitute, for instance, roughly half of the human genome. The earliest viruses, according to this idea, may have arisen from such elements by borrowing proteins from cells to wrap their nakedness inside protective capsids, a more complex strategy.<\/p>\n<\/div>\n![\"Picture](\"https:\/\/www.nationalgeographic.com\/content\/dam\/magazine\/rights-exempt\/2021\/02\/viruses\/viruses-aquarium-sharks-bacteriophage.adapt.133.1.jpg)
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