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.
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
researchers
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 DNAcopying 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 orig
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.

3Expand

Are Viruses Alive?: Scientific American

Tags: science on 2008-08-19 -All Annotations (0) -About

more fromwww.sciam.com

Impact on Evolution
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 infl uences as, say, climate change. Such external infl uences 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.

3Expand

Are Viruses Alive?: Scientific American

Tags: science on 2008-08-19 -All Annotations (0) -About

more fromwww.sciam.com

A precise scientifi c defi nition of life is an elusive thing, but most observers would agree that life includes certain qualities in addition to an ability to replicate. For example, a living entity is in a state bounded by birth and death. Living organisms also are thought to require a degree of biochemical autonomy, carrying on the metabolic activities that produce the molecules and energy needed to sustain the organism. This level of autonomy is essential to most definitions.
Viruses, however, parasitize essentially all biomolecular aspects of life. That is, they depend on the host cell for the raw materials and energy necessary for nucleic acid synthesis, protein synthesis, processing and transport, and all other biochemical activities that allow the virus to multiply and spread. One might then conclude that even though these processes come under viral direction, viruses are simply nonliving parasites of living metabolic systems. But a spectrum may exist between what is certainly alive and what is not.

A rock is not alive. A metabolically active sack, devoid of genetic material and the potential for propagation, is also not alive. A bacterium, though, is alive. Although it is a single cell, it can generate energy and the molecules needed to sustain itself, and it can reproduce. But what about a seed? A seed might not be considered alive. Yet it has a potential for life, and it may be destroyed. In this regard, viruses resemble seeds more than they do live cells. They have a certain potential, which can be snuffed out, but they do not attain the more autonomous state of life.
Another way to think about life is as an emergent property of a collection of certain nonliving things. Both life and consciousness are examples of emergent complex systems. They each require a critical level of complexity or interaction to achieve their respective states. A neuron by itself, or even in a network of nerves, is not conscious—whole brain complexity is needed. Yet even an intact human brain can be biologically alive but incapable of consciousness, or “brain-dead.” Similarly, neither cellular nor viral individual genes or proteins are by themselves alive. The enucleated cell is akin to the state of being braindead, in that it lacks a full critical complexity. A virus, too, fails to reach a critical complexity. So life itself is an emergent, complex state, but it is made from the same fundamental, physical building blocks that constitute a virus. Approached from this perspective, viruses, though not fully alive, may be thought of as being more than inert matter: they verge on life.