Scientific American; Dec2004, Vol. 291 Issue 6, p100-105, 6p, 1 diagram, 4c
"Impact on Evolution DEBATES OVER WHETHER to label viruses as living lead naturally to another question: Is pondering the status of viruses as living or nonliving more than a philosophical exercise, the basis of a lively and heated rhetorical debate but with little real consequence ? I think the issue is important, because how scientists regard this question influences their thinking about the mechanisms of evolution.
Viruses have their own, ancient evolutionary history, dating to the very origin of cellular life. For example, some viral-repair enzymes which excise and resynthesize damaged DNA, mend oxygen radical damage, and so on [see box below] are unique to certain viruses and have existed almost unchanged probably for billions of years.
Nevertheless, most evolutionary biologists hold that because viruses are not alive, they are unworthy of serious consideration when trying to understand evolution. They also look on viruses as coming from host genes that somehow escaped the host and acquired a protein coat. In this view, viruses are fugitive host genes that have degenerated into parasites. And with viruses thus dismissed from the web of life, important contributions they may have made to the origin of species and the maintenance of life may go unrecognized. (Indeed, only four of the 1,205 pages of the 2002 volume The Encyclopedia of Evolution are devoted to viruses.)
Of course, evolutionary biologists do not deny that viruses have had some role in evolution. But by viewing viruses as inanimate, these investigators place them in the same category of influences as, say, climate change. Such external influences select among individuals having varied, genetically controlled traits; those individuals most able to survive and thrive when faced with these challenges go on to reproduce most successfully and hence spread their genes to future generations.
But viruses directly exchange genetic information with living organisms--that is, within the web of life itself. A possible surprise to most physicians, and perhaps to most evolutionary biologists as well, is that most known viruses are persistent and innocuous, not pathogenic. They take up residence in cells, where they may remain dormant for long periods or take advantage of the cells' replication apparatus to reproduce at a slow and steady rate. These viruses have developed many clever ways to avoid detection by the host immune system-essentially every step in the immune process can be altered or controlled by various genes found in one virus or another.
Furthermore, a virus genome (the entire complement of DNA or RNA) can permanently colonize its host, adding viral genes to host lineages and ultimately becoming a critical part of the host species' genome. Viruses therefore surely have effects that are faster and more direct than those of external forces that simply select among more slowly generated, internal genetic variations. The huge population of viruses, combined with their rapid rates of replication and mutation, makes them the world's leading source of genetic innovation: they constantly "invent" new genes. And unique genes of viral origin may travel, finding their way into other organisms and contributing to evolutionary change.
Data published by the International Human Genome Sequencing Consortium indicate that somewhere between 113 and 223 genes present in bacteria and in the human genome are absent in well-studied organisms--such as the yeast Saccharomyces cerevisiae, the fruit fly Drosophila melanogaster and the nematode Caenorhabditis elegans--that lie in between those two evolutionary extremes. Some researchers thought that these organisms, which arose after bacteria but before vertebrates, simply lost the genes in question at some point in their evolutionary history. Others suggested that these genes had been transferred directly to the human lineage by invading bacteria.
My colleague Victor DeFilippis of the Vaccine and Gene Therapy Institute of the Oregon Health and Science University and I suggested a third alternative: viruses may originate genes, then colonize two different lineages--for example, bacteria and vertebrates. A gene apparently bestowed on humanity by bacteria may have been given to both by a virus.
In fact, along with other researchers, Philip Bell of Macquarie University in Sydney, Australia, and I contend that the cell nucleus itself is of viral origin. The advent of the nucleus-which differentiates eukaryotes (organisms whose cells contain a true nucleus), including humans, from prokaryotes, such as bacteria--cannot be satisfactorily explained solely by the gradual adaptation of prokaryotic cells until they became eukaryotic. Rather the nucleus may have evolved from a persisting large DNA virus that made a permanent home within prokaryotes. Some support for this idea comes from sequence data showing that the gene for a DNA polymerase (a DNA copying enzyme) in the virus called T4, which infects bacteria, is closely related to other DNA polymerase genes in both eukaryotes and the viruses that infect them. Patrick Forterre of the University of Paris-Sud has also analyzed enzymes responsible for DNA replication and has concluded that the genes for such enzymes in eukaryotes probably have a viral origin.
From single-celled organisms to human populations, viruses affect all life on earth, often determining what will survive. But viruses themselves also evolve. New viruses, such as the AIDS-causing HIV-1, may be the only biological entities that researchers can actually witness come into being, providing a real-time example of evolution in action.
Viruses matter to life. They are the constantly changing boundary between the worlds of biology and biochemistry. As we continue to unravel the genomes of more and more organisms, the contributions from this dynamic and ancient gene pool should become apparent. Nobel laureate Salvador Luria mused about the viral influence on evolution in 1959. "May we not feel," he wrote, "that in the virus, in their merging with the cellular genome and reemerging from them, we observe the units and process which, in the course of evolution, have created the successful genetic patterns that underlie all living cells?" Regardless of whether or not we consider viruses to be alive, it is time to acknowledge and study them in their natural context--within the web of life."
My micro professor told us that the debate whether or not they are alive is a waste of time, but we should focus more on their obligately parasitic lifestyle.
I hope that helps somewhat...I couldn't find a journal article.
