Viral Fossil Brought Back To Life 320
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."
Andromeda strain (Score:3, Insightful)
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Really interesting (Score:2)
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because thats what we really need... (Score:4, Funny)
I mean - I was just saying the other day to a friend, I haven't
seen a new virus in ages... just the same old ebola, HIV,
flu, H5N1, herpes... I mean YAWN. Where's the excitement in
those?
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Very interesting (Score:5, Informative)
Viruses have a lytic cycle where they express nasty genes and build capsids inside you, and a lysogenic cycle, where they adopt a different strategy- they get into your DNA, become part of the junk DNA, and they replicate during normal cell division along with all the rest of your DNA.
Junk DNA has all sorts of nasty critters in it. One trick your body uses is to carpet especially infectious regions with methyl groups via cytosine methylation [wikipedia.org]. Basically the idea is that the methyl groups jam up the machinery that comes along to express proteins, so if the proteins are viral, you can "comment them out" that way. When a cell divides, both strands of its DNA have methylated cytosines in the same regions. After the DNA replicates you have two methylated daughter strands, each coupled with a brand new complimentary strand. This complimentary strand has no methyl groups on it. So a clever enzyme comes along, DNA methyltransferase. [wikipedia.org] It has a regulatory domain and a catalytic domain. The regulatory domain runs across the DNA feeling it for methyl groups. If it finds them on one strand, the catalytic domain deposits methyl groups on the other strand. That way, the stretch of DNA can be marked as "bad news" in a way that is heritable, despite the fact that no actual DNA sequence is being "inherited". As far as where the initial methylation signal came from, that can probably be put down to natural selection.
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Re:Very interesting (Score:4, Interesting)
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Was the original genome 1.0 written by Microsoft, by any chance? I suggest we start looking in our DNA for Bill Gates' copyright notices.
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Based on what? We only JUST mapped out the 3% that encodes protiens (the genes). Science does not know what the rest of the DNA does or does not do. There is certainly no study that I can find that offers proof that it is unused. It's the furthering of the trend of treating ignorance as if it were knowledge. If they had intellectual honesty, instead of proclaiming DNA 97% junk, they'd proclaim themselves 97% ignorant. Labeling of it as "junk," esp
Re:Very interesting (Score:5, Informative)
Dude, I'll just refer you to the Wikipedia page on Junk DNA [wikipedia.org] (the bold tags are mine):
And I didn't even edit that on Wikipedia before replying either.
You can call it something else if you're offended, but the DNA itself won't have its feelings hurt if you call it junk.
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Arguably, if a human is offended by the use of the term "Junk DNA", then the DNA's feelings were hurt, since the ability to even have that emotional response was coded for by the respondee's DNA.
But it's not whether the DNA's feelings are hurt, it's whether people are misled by the name. I agree with the grandparent, that using the term "junk" to refer to something that's mostly just not u
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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.
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It's also plausible that the viral sections you mention are kept so that the immune system can produce antibodies for them, by treating those sections of the genome as deactivated virus. This would give the organism as advantage to having those sections deactivated over not having them at all
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I'm actually scouring the net to see if anyone has found a way to unlock our "Hot Coffee" mod...
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So what are you saying....? Time to refactor? ;-)
Re:Very interesting (Score:5, Informative)
Well that's not the same kind of "reverse transcriptase".
TERT has the job of making DNA molecules longer after replication (telomere lengthening). It appends a sequence of 5'-TTAGGG (a telomere) over and over to the 3' end of a chromosome. To do this, it has an RNA template molecule inside itself with a sequence complimentary to TTAGGG, offset and repeated twice: 3'-CAAUCCCAAUC-5'. The left end of the template aligns to the end of the chromosome and hybridizes to the TTAGGG on the end. Then a new TTAGGG hybridizes to the second half of the template, is bound to the chromosome, and TERT disengages to repeat the process with another TTAGGG chunk. It's a pretty clever implementation actually. You could probably have it repeat any six base monomer other than TTAGGG by changing the RNA template molecule that it uses. Some other species use a different six base sequence for their telomeres.
This technically counts as converting RNA to DNA, so the enzyme is called "telomerase reverse transcriptase". But it's not appending any coding DNA, it's just adding TTAGGG over and over again to give structural integrity to the chromosome. Usually "reverse transcriptase" refers to a family of enzymes with a viral origin that share ancestry and work by converting viral coding RNA into DNA with no proofreading mechanism and a high rate of error.
It's most commonly used by retroviruses along with integrase (used by viruses to splice crud into your DNA) but retrotransposons [wikipedia.org] also use it to jump around. These are genetic parasite sequences that can move around in the genome and use reverse transcriptase to make copies of themselves. LINE (long interspersed element) is a retrotransposon about 5000 bases long that inserts copies of itself all over the place. The human genome now has about 900,000 copies of LINE- fully 21% of the genome. Another 11% of the genome is SINE (short interspersed element) elements. SINE is a 500 base or less sequence. LINE has actual coding DNA in it for something that works like integrase and reverse transcriptase. That lets it copy itself along with its adjacent sequence, and insert the copy in some random place in your DNA. SINEs don't have any coding DNA- they hitch a ride along with the LINEs when they get copied, so they're parasitizing the parasites.
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Revival being controversial? (Score:2)
Revival or restoration... I think that a fully restored 1967 Hemi Barracuda is a very nice car!
Anyways, I was more expecting that the focus of controversy here would be evidence or other implications indicative of Nature's myriad ways to encourage evolution.
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Link to the Original Article in Genome Research (Score:3, Informative)
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Biowarfare labs already know how to take a mild virus and amp up its virulence. Now scientists are digging up agents that are known to be infectious... You see where I'm going?
Put it in that context, it's easy to see why TFA says that this type of lab work should be authorized at the (inter)national level & done under the highest level of containment.
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I think it made the news because of the concern that the work should have been subject to greater review. The research was normal enough stuff, but nobody likes a mad scientist. Nobody. NOBODY you hear! HAHAHAHAHAhahahah........
I'm not a mad scientist, honest. I'm being a penguin today.
Not very Intelligent design (Score:3, Insightful)
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Re:Not very Intelligent design (Score:5, Informative)
My problem with evolution is that it doesn't explain the beginning.
Then you need not have a problem with evolution. Evolution and abiogenesis (life from non-life) are two separate questions and topics. Evolution tells us that descent with modification is the current best explanation for the species and forms we see today. It does not purport to tell us what the first life form(s)? were or how they came to be. That is a separate and far more speculative field of study.
Even Darwin understood this way back when. His first attempt to systemize evolution was NOT called "Origin of Life". It was called "Origin of Species". Evolution operates on extant forms of life. If it operates in the processes that lead to life starting in the first place, the mechanisms involved are likely different from the ones creationists and (reputable) biologists argue all the time. Evolution presupposes entities capable of self-reproduction. You need replicators of some sort to even talk about evolution in the first place. Once the first replicator either spontaneously arrives or is created (and no this need not be dismissed out of hand but if the only case for it is faith-based then we aren't talking science.....) then evolution can take over and eventually bring about forms vastly more varied and different from the starting point.
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Umm... In the beginning, there weren't "more species," there were very few.
These few species became many through mutation and/or selective environmental pressures.
It isn't that hard of an idea to wrap your head around, even if you believe that God created everything 6000 years ago. 6000 years is plenty of time for microevolution & speciation to occur.
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My problem with creationism is that it doesn't explain the beginning. It starts under the assumption that this divine being already exists, and the heaven and the earth was created. But what exactly were heaven and earth created from, and where did all this space come from to put this stuff in. And considering this, what about this magical being that ignores the laws of thermodynamics. Where did HE come from anyway. And
HERVs: 8% of Human Genome (Score:5, Interesting)
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 [nature.com]. 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.
Re:HERVs: 8% of Human Genome (Score:4, Interesting)
Re:HERVs: 8% of Human Genome (Score:5, Funny)
Hell yes! I removed all that crap and compiled my DNA with -O4 -funfold-proteins -march=ubermensch and now I can flip a VW bus with one hand and paint fences with my mind! w00t!
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"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."
I'd be willing to guess that you'd have quite a different creature on your hands.
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I'd like to know whether it's possible to strip out the transposons and transposon-like sequences - if they can insert into cell-management areas, causing cancer, then if we genetically modified ourselves to not have them, or not to express them, incidence of cancer should plummet.
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Something like 40% of the population has it, whereas only like 10% of people that have it get the traditional symptoms and pass it on.
I bet a lot of virii are like this.
They are one of the strongest proofs of evolution (Score:2)
See this paper [pnas.org] for a detailed treatment of how the family tree of the primates can be reconstructed by the retrovirus sequences in our genes.
Pretty much the only available response from the ID crowd is that God created false evidence to test our faith.
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Life will find a way.... have you learnt nothing?
Re:HERVs: 8% of Human Genome (Score:4, Funny)
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Deactivating the method of this virus's reproduction is not quite akin to ripping out its lungs, as it doesn't 'die', but it's damned close.
"no risk"; biodiversity & nanomachines; pl. vi (Score:2, Interesting)
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.
Indee
Re:"no risk"; biodiversity & nanomachines; pl. (Score:2)
About grammar, probably. But I'm willing to bet you don't know shit about virii
We say virii because our professors said virii. That's just the way it is.
Re:"no risk"; biodiversity & nanomachines; pl. (Score:2)
I'm not offended. That's why I put the "smilie" in there. I was pointing out, in a vague way, the joy of specialization. While doing that I am reminded of the old joke "A specialist is someone who knows a great deal about very little". I had no idea what a declension plural is until I met you. Actually - thanks for the eduation!
Re:"no risk"; biodiversity & nanomachines; pl. (Score:2)
Re:"no risk"; biodiversity & nanomachines; pl. (Score:2)
This is Slashdot.
Re:"no risk"; biodiversity & nanomachines; pl. (Score:2)
I think it's the "what if you're wrong" question that worries people.
Sure, if your calculations are correct then yes, there is no risk, but if not.....
Re:"no risk"; biodiversity & nanomachines; pl. (Score:2)
No one worries about people writing kernel code, accusing them of being "Dr. Frankensteins" because they might accidentally create a virus that will escape their machine, infect the Pentagon, and launch all our nuclear missiles.
Biological viruses aren't any more magic than their machine counterparts.
Re:"no risk"; biodiversity & nanomachines; pl. (Score:2)
We did not create life, it's something that cannot be entirely understood by humans.
For every question abut kernel issues, someone knows the answer. The same is not true of biological scenarios. In this way, biological viruses are more mysterious, and that mystery opens the margin of error wider than some believe acceptable.
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Better: So the only risk was that someone messed up and the disabling mechanism didn't work.
(Sorry, I've been a software engineer for too long, pessimism comes with the trade I guess)
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In working with fissionables, the usual goal is 3 fault tolerance. In other words, you make three mistakes and they don't combine to create "bad." A P3 lab is, in and of itself, 3 fault tolerant, the damage done to the virus was simply an added, extra layer.
If anything, it was overkill on the safety measures. I can't blame them for that.
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Unfortunately, they used African sex-changing frog DNA to fill in the gaps and the daughter viruses chemically adjusted themselves to reproduce! Fortunately, the resultant virus is only dangerous to users of AOL and Xanga.
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No? Well, TFA says
"Richard Ebright, a molecular biologist at Rutgers University in New Jersey, says any study that creates new viruses or activates old ones should be subject to a special review at the national or international level. What's more, he says, because the researchers couldn't be absolutely sure about Phoenix's infectivity, the study should have been carried out under Biosafety level 4 conditions--t
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The researchers weren't sure about the infectivity of the virus...they weren't sure it would be infective at all. This is a virus that was beaten by evolution and became a pet:
Relax... (Score:2, Funny)
Junk code (Score:2)
Human ROOT KIT! (Score:2, Funny)
Of course it's always safe to run AdAware[ http://www.lavasoft.com/ [lavasoft.com] ] and if you have the budget, purchase WebRoot[ http://www.webroot.com/ [webroot.com] ] for a fast, centralized cleaning in the enterprize environment.
Hanta Virus...? (Score:2)
Say what!?!!?!!?!!! (Score:2)
(OK, I don't know how to continue from here....)
Viruses aren't alive. (Score:2)
They don't eat, excrete, convert energy, grow, reproduce or respond to stimuli.
So they can't be brought back to life.
Here's an anolgy (Score:2)
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Any genetic defences we got are probably only good against the historical variants of the virus (and might not work against the one the French scientists hacked together by some clever guesswork). Some evidence suggests si/ miRNAs are part of defences that kept the virus dormant, in which case if Heidmann made a single wrong guess about the original sequence
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Especially, considering how it is usually transmitted... :-(
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Way ahead of you (Score:4, Funny)
As a side note, tonight I am sleeping on the couch: got busted typoing a Google image search for 'Large Hadron Collider.'
Still way ahead of you! :) (Score:2)
Hi, meet "humor" (Score:2)
Leave the jokes to the professionals.
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The mistake you're making is trying to do the calculation with Earth's mass and zero radius. But the thing is the gravity doesn't come from a tiny point in the center, that's just a simplification. As you go inside the earth, there's going to be more and more matter over you pulling in the opposite direction. Were you to end up in the center there would be no gravity at all, as the matter around you wo
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Bigellow, meet the laws of motion. A body at rest remains at rest unless acted on by a force. The gravitational pull at the earth's centre is (or pretty much) because there is (pretty much) an equal amount of force acting in every direction. That's a net force of zero. Let's not get sidetracked by common sense - we don'
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no it couldnt. each time you moved up a layer, you would be increasing the amount of mass on one side of you and reducing the amount on the other side, thereby gradually increasing the amount of acceleration in one particular direction you would experience due to gravity, ie. your weight.
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Not sure what you're smoking on that one.
If you were at the center of the earth, you would feel no net gravitational pull from the earth (i.e., you would experience weigtlessness), however, the earth would feel your gravitational pull.
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Nope. At the center of Earth, gravity is zero. The formula of gravity inside a massive body is F=GrMm/R^3, where r is the distance from center, and R the radius of the (sperical) body.
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Right.
If the black hole was created at the center of the Earth, no problem. It's when it is created at the surface and falls down, and through the center, eating a little bit of matter on the way down, then back up the other side, then down again, and up, and down, and up... Then we have a problem.
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It should. Larry Niven did it to Mars back in 1973 (the January '74 edition of "Analog") with "The Hole Man", and won the Hugo for it.
Thanks for the link, BTW. I hadn't heard of Escape Pod. Yet another market, if a small one. (The sketch on the page is an interesting coincidence -- I just started my NaNoWriMo [nanowrimo.org] novel, "The Martian War" (aka "The War of the Worlds: The True Story"). Earth wasn't quite so defenseless as Wells lets on, and Nikola Tesla is implicated in both att
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not sure... (Score:4, Funny)
I'm not sure, but I'm sure Mohinder Suresh would be interested in this information.
doesn't it bother you (Score:2)
Horrible writing flaw. I'm still watching it because it's X-Men on TV (but I don't know the plotline!) but that piece of writing seemed really fucking lazy to me and bodes ill for the series.
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sigh - no (Score:2)
He speaks broken english to him, able to communicate exactly what he wants to ("your secret is safe with me, can I get a ride?") even though up to then it was a major plot point that he COULDN'T speak English and that's why the junkie kept hanging up on him.
That's a major fucking hole, and it bugs me that anyone let it
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Someone get these guys a copy of "Night of the Living Dead"!
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Inheritable diseases and legacy code. (Score:2)
So are recessive traits that might express themselves in our children.
So are many inactive things that aren't usually expressed. Think of it as legacy code that would never be called by a sane programmer.
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Greg Bear has already done this. (Score:2)
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And they were waiting for Duke Nukem Forever...
Answers here (Score:2)
They wanted to know more than what's enough to ensure it could only replicate once.