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Viral Fossil Brought Back To Life
hey hey hey writes "In a controversial study, researchers have resurrected a retrovirus that infected our ancestors millions of years ago and now sits frozen in the human genome. Published online by Genome Research this week, the study may shed new light on the history of these genomic intruders, as well as their role in tumors. Although this particular virus, dubbed Phoenix, is a wimpy one, some argue that resuscitating any ancient virus is inherently risky and that the study should have undergone stricter reviews."
In this particular case, there were 30 copies of the virus in the genome. They worked backward to create the original virus. The resultant virus was disabled so that, after replicating once in a cell, the daughter viruses could not replicate. So there was no risk.
In the human genome, the researchers point out, are the pieces from other viruses. 8% of the human genome codes for HERV proteins or their regulatory subunits. If these pieces are activated, they can reassemble to create a new, working virus. This happens naturally.
All of these HERVs are viruses that, throughout human evolution, we and our ancestors have more or less come to terms with. At some point, many of them were probably devastating. But those that caught the virus, survived, and reproduced were able to mitigate the effects of the virus. These are viruses we've reached a "détente" with. They no longer rampage through the population. In fact, some of the proteins they produce are vital to our survival. One of these retroviral proteins permits implantation of the placenta. Without it, we'd all have placentas that don't attach to the uterine lining -- like mice, which as a result, aren't very complex when they have to be born.
Yes, HERVs are related to cancer. This occurs naturally. They act in a transposon-like manner, and they can pop into areas where they either damage mechanisms that prevent cancer or control cell replication. If we don't study these viral remains, we won't learn about them, won't learn what we can safely disable further -- and what we don't dare eliminate from our genome because we are dependent upon it.
These researchers were not Dr. Frankensteins, messing with things man was not meant to know. They were careful, they were deliberate, and theya re beginning the investigation into what could be an incredibly crucial topic in molecular biology.
Remember -- these are viruses that we learned to live with, more or less. By studying them, we can learn to mitigate the damage they still present.
This sig seemed like a good idea at the time....
I had read recently in Popular Science that said researchers discovered that alot of what we thought was junk DNA is actually regulatory code that operates in coordination and in response to the environment of protiens and enzymes to turn genes on and off and change the folding of the DNA structure itself. I think they called the idea, the epigenome, if anyone else knows more. (I forget which issue. It may have been Scientific American instead.)
Demented But Determined.
I'm reminded of this short story.
THE HOLE MAN
One day Mars will be gone.
Andrew Lear says that it will start with violent quakes, and end hours or days later, very suddenly. He ought to know. It's all his fault.
Lear also says that it won't happen for from years to centuries. So we stay, Lear and the rest of us. We study the alien base for what it can tell us, while the center of the world we stand on is slowly eaten away. It's enough to give a man nightmares.
It was Lear who found the alien base.
We had reached Mars: fourteen of us, in the cramped bulbous life-support system of the Percival Lowell. We were circling in orbit, taking our time, correcting our maps and looking for anything that thirty years of Mariner probes might have missed.
We were mapping mascons, among other things. Those mass concentrations under the lunar maria were almost certainly left by good-sized asteroids, mountains of rock falling silently out of the sky until they struck with the energies of thousands of fusion bombs. Mars has been cruising through the asteroid belt for four billion years. Mars would show bigger and better mascons. They would affect our orbits.
So Andrew Lear was hard at work, watching pens twitch on graph paper as we circled Mars. A bit of machinery fell alongside the Percival Lowell, rotating. Within its thin shell was a weighted double lever system, deceptively simple: a Forward Mass Detector. The pens mapped its twitchings.
Over Sirbonis Palus, they began mapping strange curves.
Another man might have cursed and tried to fix it. Andrew Lear thought it out, then sent the signal that would stop the free-falling widget from rotating.
It had to be rotating to map a stationary mass.
But now it was mapping simple sine waves.
Lear went running to Captain Childrey.
Running? It was more like trapeze artistry. Lear pulled himself along by handholds, kicked off from walls, braked with a hard push of hands or feet. Moving in free fall is hard work when you're in a hurry, and Lear was a forty-year-old astrophysicist, not an athlete. He was blowing hard when he reached the control bubble.
Childrey--who was an athlete--waited with a patient, slightly contemptuous smile while Lear caught his breath.
He already thought Lear was crazy. Lear's words only confirmed it. 'Gravity for sending signals? Dr. Lear, will you please quit bothering me with your weird ideas. I'm busy. We all are.'
This was not entirely unfair. Some of Lear's enthusiasms were peculiar. Gravity generators. Black holes. He thought we should be searching for Dyson spheres:
stars completely enclosed by an artificial shell. He believed that mass and inertia were two separate things: that it should be possible to suck the inertia Out of a spacecraft, say, so that it could accelerate to near lightspeed in a few minutes. He was a wide-eyed dreamer, and when he was flustered he tended to wander from the point.
'You don't understand,' he told Childrey. 'Gravity radiation is harder to block than electromagnetic waves. Patterned gravity waves would be easy to detect. The advanced civilizations in the galaxy may all be communicating by gravity. Some of them may even be modulating pulsars--rotating neutron stars. That's where Project
Ozma went wrong: they were only looking for signals in the electromagnetic spectrum.'
Childrey laughed. 'Sure. Your little friends are using neutron stars to send you messages. What's that got to
"No Risk"
By no means do I suggest that these researchers necessarily acted dangerously or that their research and research like it should be stopped, but I have to say that complex efforts with potentially "devastating" [your term] results should not be reassured against with phrases like "there was no risk". Your explanation of "The resultant virus was disabled so that, after replicating once in a cell, the daughter viruses could not replicate" only inspires a dubious curiosity for how this was done.
Indeed, also hearing the allegation that "the researchers couldn't be absolutely sure about Phoenix's infectivity" and that only biosafety level 3 was used while a level 4 was recommended, a layperson is left to wonder. (What the hell is a biosafety level in the first place, ?)
These researchers are Dr. Frankensteins in their pursuit of knowledge. And let them be! The pursuit of knowledge is unquestionably good! Just let them be careful while doing it, or they may also be Dr. Frankensteins in their poor safeguarding, Unleashing The Ritz on us.
Biodiversity & Nanomachines
In support of the investigation, let me say that I recently wondered, on the tail of some ethics reading regarding ecology, what other utility values nature could provide us beyond simple resources and recreation. Thinking of how proteins are basically nanomachines; and how much of the unused portions of our genome may be disused codes for once-useful, now-retired proteins; and how hard it must be to design a working nanomachine (just look at how hemoglobin contorts so bizarrely with the simple addition of an oxygen molecule); I came to wonder whether there might be a goldmine of blueprints for tested nanomachines in us. In us and every species we destroy.
Yes, please figure out how to mine genomes for molecular machines. In the meantime we'll see about preserving all these genomes.
Ob. Plural Of 'Virus'
Don't say 'virii'. That isn't even just wrong yet. You probably mean 'viri', which is just wrong. It wasn't used in the plural (being a mass noun, not a count noun) and there may not have been a proper plural form of it in Latin. My guess is that it is actually a 4th declension neuter with a plural of 'virus' (long 'u' sound), but what the hell do I know? Well, more than someone saying 'virii', by a long shot. Be safe, inflect it in English rather than classically: viruses.
Knowing the details of the debate makes you a pedant. I mean, how important is it really? But using the certainly wrong classical form makes you ignorant.
http://en.wikipedia.org/wiki/Plural_of_virus
As a bioinformatician who recently published a paper in Nature Genetics on Conserved Non Coding regions (non gene regions that are more highly similar than expected - the base pairs are the same), I'd have to call "Bullshit!" on this wikipedia article.
Please don't believe everything you read on wikipedia. It might have been right if I'd read that 5 years ago, but my work, and other people's work says otherwise.