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Science Essays 
Book 4

Endogenous Retroviruses and Evolution 
Stephen Darksyde, Science Writer

"More than a hypothesis, it's a theory!"

Every winter as the season turns and Santa comes to visit, a less welcomed traveler makes the rounds. It's influenza, a truly horrid little critter. And right now, in the throes of delirium, flush with fever and cold, I confess; I really despise influenza. I go to sleep feeling chipper and wake up feeling beaten with baseball bats and heated by a microwave to a toasty 103 degrees.

This damn flu is caused by a virus, of course, just one of many viral pathogens that curse mankind. No one knows how these quasi-living, self-replicating packets of genetic material first came to be. Perhaps they're a vestigial remnant of a long-gone RNA-based world that thrived in the nearly boiling sea of a planet unrecognizable as Earth, billions of years ago. Maybe they're errant bits of code from a more traditional bacterial microbe that began freelancing on its own.

However they arose, the viral vector is here to stay.

They all have the same grisly modus operandi. First, the dastardly buggers break through the cell wall. Some pick the lock of an existing portal and sneak past the molecular doorman disguised as legitimate cargo. Others are constructed like an off-shore drilling platform. They land on jointed legs, drop a drill bit onto the exterior of their target, and then begin boring in for all they're worth.

Once the membrane is breached by whatever means, viruses inject a packet of trouble into the interior, which makes for the nucleus and commandeers the genetic machinery to make more viruses. The end result is a person who sickens, and sometimes dies.

But there is a consolation prize. Geneticists have found that this viral scourge is incredibly useful in shedding light on all manner of mysteries biological.

Viruses Are Our Friends, Part 1

Some of these little influenza bugs are retroviruses like HIV and feline leukemia.

retrovirus (n): genes carried on single-stranded RNA, which co-opts the nucleus of the infected cell to convert itself into DNA. This DNA sometimes inserts itself into the cell's chromosomal DNA.

These viruses are RNA, and typically "reverse-transcribe" their RNA into DNA for integration into the host's genome. When that happens, they snip the DNA and insert themselves surreptitiously into the host's chromosome, where they lie dormant, sometimes for years, before activating. Later, they activate and begin making more RNA, which in turn inserts itself into the genome, until the entire cell basically falls apart. Then the RNA retroviruses are off to seek new, healthy cells for more viral adventures.

But if the retrovirus doesn't reactivate, this life cycle fails. While the infection is contained, the cell is left with inert viral sequences scattered throughout its genome. They can cause problems. The inert sequences may disrupt a key gene, for example, and uncontrolled replication may ensue-the beginning of cancer. Or it could spark an autoimmune disorder like multiple sclerosis, or exotic forms of painful, debilitating inflammatory disease. But often the retrovirus simply sits in the chromosome, inert and disregarded.

Now consider inheritance. Sometimes, by a stroke of fate, the infected host is a sperm or egg cell, which becomes a child. That child has those inert viral sequences in every single cell of his body. If those sequences happen to lie near an allele (one member of a pair of genes) that becomes ubiquitous in the population through natural selection, then all members of the species will carry the same genetic "signature" in every cell of their body. These ghosts of infections past are called endogenous retroviruses, or more affectionately, ERVs.

An ERV found in the same DNA location in two people provides powerful evidence, admissible in court, that they share a common ancestor. All humans share many ERVs in identical locations, which is no surprise. We all have common ancestors if one looks far enough back. But here's where it gets interesting: Chimps and humans also have ERVs in common. If identical ERVs serve as evidence of relatedness in court, then ERVs are equally convincing evidence that chimps and humans are related!

The human and chimp genomes have been sequenced over the last decade, and we've found a dozen separate ERVs (hundreds of repeats each) identical in both genomes, in exactly the same locations. When these sequences are checked for time of introduction, they indicate a common ancestor five to seven million years ago. That is consistent with other molecular divergence studies and the fossil record.

But wait, there's more!

Consider a repeat sequence of base pairs like an ERV-or any other nonfunctional DNA sequence for that matter-found in the same locations in the genome between two species. Geneticists have looked at shared sequences between humans and mice, and compared those to the shared sequences between humans and chimps. They found that in humans and chimps, the same mouse sequences have been overwritten, just like a new CD recorded over an old one. This is exactly what we'd expect if ancestors of chimps and humans diverged more recently than primates and rodents diverged.

Creationists hate ERVs. They usually ignore them, or recursively label them "intelligent common design." ERVs have no known function. They code for viral proteins used only by viruses. Even if these things did have a function to us, common descent (common ancestors) explains how they got where they are in both species. The odds against two species by sheer chance being identically infected are enormous: one in ten followed by a hundred zeros. You have a better chance of winning the lottery ten times in a row than of being infected by a dozen distinct ERVs in the same hundreds of locations in your genome as any other individual or creature.

Viruses Are Our Friends, Part 2

Viruses do more than shed light on evolutionary relationships. Their study holds great promise for novel health therapies. We may someday tailor viruses that eat only cancer cells. And since a virus can literally perform nano-surgery on the chromosomes of a cell without so much as breaking the patient's skin, we might enlist them to remove genetic abnormalities and replace the pathological sequences with healthy ones. Inherited susceptibility toward cardiopulmonary disease, diabetes, and cancer-the three greatest killers of humanity-might be permanently eliminated. Afflictions like sickle-cell anemia, lupus, irritable bowel syndrome, muscular dystrophy, Lou Gehrig's disease, and on and on, would all become words found only in history books. What a wonderful gift of health to bestow on our children!

Science is slowly but surely domesticating the virus. This is only fair. We've suffered from these little beasts for way too long. A little payback is overdue. At least that's my firm opinion as I lie here immobilized with flu on the couch, temporarily lucid between waves of total mental incapacitation. God, my body aches...Where the hell did I put that aspirin?

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