A Gazillion Tiny Avatars
By OLIVIA JUDSON
Viruses have a bad reputation: in humans, they cause illnesses as varied as colds, flu, cervical cancer, polio and ebola. But to focus exclusively on the harm they cause is to do them an injustice, for viruses are also fascinating, mysterious and powerful forces of nature.
First things first: what is a virus?
Viruses are different from all other life forms. Whereas the rest of us — whether we’re talking humans, mushrooms, petunias or bacteria — are made of one or more cells, viruses are not. They haven’t got a cell, with all that machinery for detecting, and interacting with, the outside world. Instead, viruses are just sets of genes packed inside a capsule, or “capsid,” that is usually made out of protein molecules. (Depending on the virus, the capsid will take one of a number of forms. Some look like 20-sided dice. Others resemble moon landers — tiny containers on a set of legs.)
Many viruses have unorthodox genetics: instead of using DNA to store their genetic information, they use a related molecule, RNA. Moreover, while in its capsid, a virus is inert: it does not eat, it does not breathe. And all viruses are parasites. That is, they cannot reproduce — make more viruses — unless they are within the cell of a “proper” organism.
I say “proper” because many people argue that viruses aren’t alive, that they mark the boundary between living and non-living. And it is true that they don’t fit into the tree of life — that map of ancestry by which the rest of us can trace our lineages back to LUCA, the last universal common ancestor. (LUCA is the being to which all living organisms can, in principle, trace their family trees.) The tree of life only covers cell-based life forms.
An ability to resist viral attack has sculpted the genomes of all known organisms, from bacteria to humans.
Indeed, the origins of viruses are shrouded in mystery. Are most viruses descended from a virus that appeared long ago, the viral version of LUCA? (This would give viruses their own tree of life.) Or have viruses originated several, even many, times during the history of life? No one knows. Despite these difficulties, I put viruses among the living, myself, on the grounds that they are discrete entities that reproduce, mutate, experience natural selection and evolve, just as the rest of us do.
But whether you count viruses as living or not, there’s an awfully large number of them: a single drop of seawater may contain more than 10 million viral particles. That’s more than 10 billion in a liter (two-and-a-bit pints) of ocean. Some people have estimated that, in the oceans, there’s more carbon stashed away in viruses than there would be in 75 million blue whales.
Moreover, viruses are extremely diverse; there are zillions of different kinds. Some, such as MS2, a virus that attacks bacteria like Escherichia coli, have as few as four genes. Others, such as the gargantuan Mimivirus, have more than 900. (Mimivirus mostly attacks amoebae, although it is also suspected of occasionally causing pneumonia in humans.) And each time we look in a new place, we find more and more viruses that are different from those we have known before.
Fortunately for us, most viruses don’t attack humans; they attack bacteria and other microbes, which they kill on a colossal scale. In the oceans alone, viruses are reckoned to kill about 100 million metric-tons’-worth of microbes every minute. One hundred million metric tons! Given that a typical bacterium only weighs a tiny, tiny fraction of a gram (and there are a million grams in a ton), that is one huge number of dead microbes. (For anyone who doesn’t use the metric system, one metric ton is a little bigger than the American short ton; there are just over 28 grams in an ounce.) Viruses are thus important, if tiny, avatars of the grim reaper.
Which has several interesting consequences.
One is that viruses play a fundamental role in regulating the food chain. This is because death-by-virus is different from death-by-predator. When a predator kills a microbe, it consumes it: the microbe’s cell is incorporated into the predator’s body. In contrast, when a virus kills a microbe, the microbe’s cell bursts open, or “lyses,” releasing new viruses and a lot of cellular debris back into the environment. This debris can then be consumed by other microbes. In other words, by lysing their victims, viruses are constantly making food available to other life forms.
A second consequence of all this viral activity is the role viruses play in evolution. An ability to resist viral attack has sculpted the genomes of all known organisms, from bacteria to humans. (Why, then, do viruses remain dangerous? The answer to this is complex, but part of the reason is that they are often able to stay one step ahead of their hosts, because viruses tend to evolve very fast. So if the host evolves a new way to detect and disable an intruder, sooner or later the virus will evolve a new way to evade the trap. This is one reason viral diseases are so hard for us to treat.)
But here’s what I find most interesting of all. Viruses don’t just cause other organisms to evolve. They are also important sources of new genes. The reason is that as viruses move in and out of host cells, they sometimes take a few host genes with them, or leave some of their own behind. Thus, although viruses are among the most destructive forces of nature, they are also among the most potent forces of creation.
As you lie in bed with flu, or sit at your desk sneezing with a cold, it may be hard to appreciate the wonder of viruses. Yet, just as much of the beauty we see around us — the length of a hummingbird’s beak, the speed of the gazelle — is an evolved response to other life forms (the depth of a flower, the leap of a cheetah), so too at the level of the cell, much of the intricacy we see is due to evolution in response to viruses. It’s an intricacy that we are still unraveling: we have much to learn in the years ahead. Perhaps one day, we’ll be able to use our knowledge to beat viruses at their own game.
Notes:
It is surprisingly difficult to write a water-tight definition of life. But for a vigorous attack on the idea that viruses count as living, see Moreira, D. and López-García, P. 2009. “Ten reasons to exclude viruses from the tree of life.” Nature Reviews Microbiology 7: 306-311. These authors also provide a historical overview of definitions of life; they argue against a single-common ancestor of all viruses. For an alternative opinion of whether viruses are alive, see Brüssow, H. 2009. “The not so universal tree of life or the place of viruses in the living world.” Philosophical Transactions of the Royal Society of London B 364: 2263-2274. For the view that viruses are ancient and have their own tree of life, see Forterre, P. and Prangishvili, D. 2009. “The origin of viruses.” Research in Microbiology 160: 466-472; see also Filée, J., Forterre, P. and Laurent, J. 2003. “The role played by viruses in the evolution of their hosts: a view based on informational protein phylogenies.” Research in Microbiology 154: 237-243. These authors also provide data showing that viruses are important sources of new genes for cell-based life forms.
When I say a “drop” of seawater, I am using that as shorthand for a milliliter — which is around a fifth of a teaspoon. For viral abundance in the oceans, and for the estimate that marine viruses are equivalent to 75 million blue whales, see Suttle, C. A. 2005. “Viruses in the sea.” Nature 437: 356-361; this paper also includes an interesting discussion of how death by virus is different from death by predator. For the estimate that viruses kill 100 million metric tons of microbes in the ocean every minute, see Rohwer, F., Prangishvili, D. and Lindell, D. 2009. “Role of viruses in the environment.” Environmental Microbiology 11: 2771-2774. For an excellent review of the importance of marine viruses, see Fuhrman, J. A. 1999. “Marine viruses and their biogeochemical and ecological effects.” Nature 399: 541-548.
For the small genome of MS2, see Fiers, W. et al. 1976. “Complete nucleotide sequence of bacteriophage MS2 RNA: primary and secondary structure of replicase gene.” Nature 260: 500-507. For the giant genome of mimivirus, see Raoult, D. et al. 2004. “The 1.2-megabase genome sequence of Mimivirus.” Science 306: 1344-1350. For the role of Mimivirus in pneumonia, see Raoult, D., La Scola, B. and Birtles, R. 2007. “The discovery and characterization of Mimivirus, the largest known virus and putative pneumonia agent.” Clinical Infectious Diseases 45: 95-102. For an example of novel viruses from novel environments, see López-Bueno, A. et al. 2009. “High diversity of the viral community from an Antarctic lake.” Science 326: 858-861.
For an interesting discussion of the evolution and counter-evolution between bacteria and viruses, see Comeau, A. M. and Krisch, H. M. 2005. “War is peace — dispatches from the bacterial and phage killing fields.” Current Opinion in Microbiology 8: 488-494. For viruses shuffling genes to and from bacteria, see for example, Lindell, D. et al. 2007. “Genome-wide expression dynamics of a marine virus and host reveal features of co-evolution.” Nature 449: 83-86; Lindell, D. et al. 2004. “Transfer of photosynthesis genes to and from Prochlorococcus viruses.” Proceedings of the National Academy of Sciences, USA 101: 11013-11018; and Canchaya, C. et al. 2003. “Prophage genomics.” Microbiology and Molecular Biology Reviews 67: 238-276.
Many thanks to Dan Haydon and Jonathan Swire for insights, comments and suggestions.
Olivia Judson, an evolutionary biologist, is the author of “Dr. Tatiana’s Sex Advice to All Creation: The Definitive Guide to the Evolutionary Biology of Sex.” Ms. Judson has been a reporter for The Economist and has written for a number of other publications, including Nature, The Financial Times, The Atlantic and Natural History. She is a research fellow in biology at Imperial College London.
Source: NY Times Opinion Column, 12/16/09.
http://opinionator.blogs.nytimes.com/category/olivia-judson/
