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Why are evolutionary biologists bringing back extinct deadly viruses?
November 27, 2007 11:22 AM   Subscribe

Darwin's Surprise. "There may be no biological process more complicated than the relationships that viruses have with their hosts. Could it be that their persistence made it possible for humans to thrive?" [Via Disinformation.]
posted by homunculus (63 comments total) 11 users marked this as a favorite

 
A retrovirus stores its genetic information in a single-stranded molecule of RNA, instead of the more common double-stranded DNA. When it infects a cell, the virus deploys a special enzyme, called reverse transcriptase, that enables it to copy itself and then paste its own genes into the new cell’s DNA.

AIDS has been around for my entire life and this is the first time I've known what "retrovirus" meant. What a dumas I am.
posted by DU at 11:29 AM on November 27, 2007


IM IN UR DNA TRANSCRBNG UR BASES
posted by StickyCarpet at 11:51 AM on November 27, 2007 [10 favorites]


Yet nothing provides more convincing evidence for the “theory” of evolution than the viruses contained within our DNA. Until recently, the earliest available information about the history and the course of human diseases, like smallpox and typhus, came from mummies no more than four thousand years old. Evolution cannot be measured in a time span that short. Endogenous retroviruses provide a trail of molecular bread crumbs leading millions of years into the past.

Darwin’s theory makes sense, though, only if humans share most of those viral fragments with relatives like chimpanzees and monkeys. And we do, in thousands of places throughout our genome. If that were a coincidence, humans and chimpanzees would have had to endure an incalculable number of identical viral infections in the course of millions of years, and then, somehow, those infections would have had to end up in exactly the same place within each genome.


Can't wait for the pseudoscience explanation for this from the ID crowd, if they ever bother coming up with one.
posted by Artw at 11:52 AM on November 27, 2007 [1 favorite]


Can't wait for the pseudoscience explanation for this from the ID crowd

Deploy the Emergency Fallback Explanation: Satan is testing us.
posted by DU at 11:54 AM on November 27, 2007 [5 favorites]


I just finished reading Darwin's Radio and Darwin's Children by Greg Bear -- it's fiction but it deals with this science.
posted by garlic at 11:57 AM on November 27, 2007


Deploy the Emergency Fallback Explanation: Satan Kirk Cameron is testing us.
posted by billysumday at 11:58 AM on November 27, 2007


It was a result of especially malicious malware that Skynet became self aware at 2:14 am EDT August 29, 1997.
posted by Astro Zombie at 12:04 PM on November 27, 2007


Can't wait for the pseudoscience explanation for this from the ID crowd, if they ever bother coming up with one.

That one's not hard at all. No one is claiming that humans and apes don't share a lot of DNA, and why shouldn't we? We were made by the same designer using a lot of the same building blocks.
posted by tkolar at 12:19 PM on November 27, 2007


In fact, the complexity of the interrelation proves without a doubt that it couldn't have occurred naturally. This phenomenon is the smoking gun for intelligent design!
posted by tkolar at 12:22 PM on November 27, 2007


When did bevits learns to hack?
posted by jmd82 at 12:28 PM on November 27, 2007


Did the smoking gun inhale?
posted by srboisvert at 12:31 PM on November 27, 2007


A retrovirus stores its genetic information in a single-stranded molecule of RNA, instead of the more common double-stranded DNA. When it infects a cell, the virus deploys a special enzyme, called reverse transcriptase, that enables it to copy itself and then paste its own genes into the new cell’s DNA.

Undoubtedly it is more complicated than this, but could such a virus be engineered out of a patient's own RNA, but with certain specific genes altered to eliminate a genetic disorder or to do something as silly as change hair color? If this cannot be done, what part of the technology does not exist yet?
posted by Pastabagel at 12:45 PM on November 27, 2007


No one is claiming that humans and apes don't share a lot of DNA, and why shouldn't we? We were made by the same designer using a lot of the same building blocks.

To which I would reply that this is more than just "sharing some building blocks". That is, we are actually carrying the DNA for some viruses that our 40-million-year removed ancestors were infected with, and that other apes carry this same DNA as well, meaning that we almost certainly share a common ancestor.

It would be a very odd (almost sinister, I might say) "intelligent designer" who would create several unrelated species but then insert pathological DNA to make it appear that they all had the same ancestor. But thats the nice thing about religion, you don't need a logical explanation when all you can say is "Lo, these are great mysteries".
posted by Avenger at 12:46 PM on November 27, 2007


FWIW, in my adult Sunday school program, our current Bible study is working its way thru Genesis. Based on how the classroom discussions have gone, I can say pretty confidently that my classmates who are most prone to insisting on the simplistic, literalist "understanding" of the creation myths (the same one's in there, twice, with some variation -- betcha didn't know that, haters!) are least likely to have a friggin' clue about what Darwin actually said about natural selection nor what viruses, DNA, RNA, and reverse transcriptase do.
posted by pax digita at 12:59 PM on November 27, 2007


Great post! I never thought of viruses infecting gametes (or gametocytes?). Can someone with a biology background comment on that?
posted by fleetmouse at 1:03 PM on November 27, 2007


“No one is claiming that humans and apes don't share a lot of DNA, and why shouldn't we?”

I’d like to share some DNA with an ape, give them a virus, if you know what I mean.
posted by Smedleyman at 1:13 PM on November 27, 2007 [1 favorite]


but could such a virus be engineered out of a patient's own RNA, but with certain specific genes altered to eliminate a genetic disorder or to do something as silly as change hair color? If this cannot be done, what part of the technology does not exist yet?

The technology for this exists already (using both viral and non-viral methods). It's called gene therapy.
posted by RichardP at 1:16 PM on November 27, 2007


pastabagel, it kind of can be done in a way, but with bacteria and their little satellite DNA rings known as plasmids. We can insert a desired gene into a plasmid and insert the plasmid into the bacterium, and some times it "sticks", and we can create recombinant treatments (aka biologics).

I think though, in the future, this will be a hot area of research for gene therapy.
posted by Mister_A at 1:21 PM on November 27, 2007


Undoubtedly it is more complicated than this, but could such a virus be engineered out of a patient's own RNA, but with certain specific genes altered to eliminate a genetic disorder or to do something as silly as change hair color? If this cannot be done, what part of the technology does not exist yet?

Can be done, has been done (first and most famous was for SCID).

There are at least two major problems at this point regarding administering it in the manner you suggest. One is that the transduction efficiency is still quite low, so in your example only patches of the head will change colour. The other problem is that viruses are immunogenic. i.e. the immune system will see them and attack the infected cells. So the cells that would have made a different hair colour would be destroyed before they had a chance.
posted by kisch mokusch at 1:22 PM on November 27, 2007 [1 favorite]


In the future, I will learn to preview, too.
posted by Mister_A at 1:22 PM on November 27, 2007


Until recently, the earliest available information about the history and the course of human diseases, like smallpox and typhus, came from mummies no more than four thousand years old. Evolution cannot be measured in a time span that short.

That's completly incorrect, especially for viruses and bacteria. For example, researchers can use the genetic changes in HIV to track it's "Family Tree" across the past few decades, to see how it spreads.

It's an interesting article, but I wonder how many other errors the author makes.

Anyway, if you like this kind of stuff you'll love the blog the loom if you don't know of it already.
posted by delmoi at 1:24 PM on November 27, 2007


That is, we are actually carrying the DNA for some viruses that our 40-million-year removed ancestors were infected with, and that other apes carry this same DNA as well, meaning that we almost certainly share a common ancestor.

Exactly. I forget the figure, but a fair amount of our DNA is never actually transcribed.

Undoubtedly it is more complicated than this, but could such a virus be engineered out of a patient's own RNA, but with certain specific genes altered to eliminate a genetic disorder or to do something as silly as change hair color? If this cannot be done, what part of the technology does not exist yet?

My biochem education's a few years old, but I understand that our cells don't typically utilize reverse transcriptase in the fashion you desire. Most studies would be in line with how to deliver DNA to the cell so our own polymerases can transcribe- not on genetically modifying our DNA through RNA. It's kind of a reverse way of going about things. RNA is used in transcription for various tasks, but not as the actual DNA enzymatic template disorders may arise from. Your body sees your RNA acting in aways it doesn't normally function as? That's asking for an autoimmune issue.

However, in lab settings, RNA sequences can be utilized quite a bit, particularly in RT-PCR- a process to create cell cultures from RNA.
posted by jmd82 at 1:28 PM on November 27, 2007


I just finished reading Darwin's Radio and Darwin's Children by Greg Bear -- it's fiction but it deals with this science.

Like ID?
posted by ersatz at 1:43 PM on November 27, 2007 [1 favorite]


A note on the title:

These shouldn't be thought of as deadly viruses, as they integrated into the host's genome without killing him or her, or at least without killing the host instantly and preventing the transmission of the newly-integrated DNA to progeny. So deadly viruses, well, maybe some of these viruses killed some monkey-men, but I think it is a bit hyperbolic.
posted by Mister_A at 1:43 PM on November 27, 2007



That's completly incorrect, especially for viruses and bacteria. For example, researchers can use the genetic changes in HIV to track it's "Family Tree" across the past few decades, to see how it spreads.

It's an interesting article, but I wonder how many other errors the author makes.

Anyway, if you like this kind of stuff you'll love the blog the loom if you don't know of it already.


Worst. Plagiarist. Ever.
posted by srboisvert at 2:11 PM on November 27, 2007


Darwin's Radio was one grrrreat book, in my opinion. Highly recommended. I didn't know there was a sequel. Time to check my library system! (Amazon.com for researching books + library with a website for requesting books = cheap entertainment.)

Seems like the U.S. is one of the few countries still debating the validity of evolution; most of the others, and virtually all of the other industrialized nations, have accepted it, more or less, as fact. As they should, since there's such an overwhelming body of evidence to support it, spanning a multitude of fields.
posted by jamstigator at 2:12 PM on November 27, 2007


Amazon.com for researching books + library with a website for requesting books = cheap entertainment.

Hey - that's my system!
posted by Artw at 2:15 PM on November 27, 2007


Interesting stuff in the article.

Seems like the U.S. is one of the few countries still debating the validity of evolution

Thet's cuz weer a Christean nashun!
posted by Doohickie at 2:19 PM on November 27, 2007


These shouldn't be thought of as deadly viruses

Good point. Also interesting to note that the general consensus is our mitochondria- the powerplant of the cell- was bacteria which started out in symbiosis with our ancestors and became fully integrated in our DNA over the millennium.
posted by jmd82 at 2:23 PM on November 27, 2007



That one's not hard at all. No one is claiming that humans and apes don't share a lot of DNA, and why shouldn't we? We were made by the same designer using a lot of the same building blocks.

And some of those building blocks include mistakes such as pseudogenes?
http://en.wikipedia.org/wiki/Pseudogene
posted by francesca too at 2:26 PM on November 27, 2007


Getting into most of the cells you want is very difficult. Reverse transcriptase just makes the DNA; integrase (and some others) put it into the cell's DNA. Getting it where you want it is quite tricky; getting it expressed in the amount that you want even worse. Then, t-cells come along and spy non-self peptides and go apeshit. There's plenty of hope for gene therapy, but there have also been trials which ended in complete disaster.
posted by a robot made out of meat at 2:28 PM on November 27, 2007 [1 favorite]


Seems like the U.S. is one of the few countries still debating the validity of evolution

Thet's cuz weer a Christean fundahmenteleest nashun!


(Or at least allow Fundamentalists to define the debate.)

Fixed that for you.
posted by Hactar at 2:29 PM on November 27, 2007


francesca: the easy answer is that you just don't know what they do, or that they became inactivated post-creation. IIRC there are pseudogenes which gain promoters in some mutations and get expressed. Copy-number variation is important. Pseudogenes might also serve a regulatory purpose since they are so similar to an actual gene.
posted by a robot made out of meat at 2:31 PM on November 27, 2007


These shouldn't be thought of as deadly viruses

Why would you say that? Most deadly viruses do not have 100% kill rates.
posted by srboisvert at 2:46 PM on November 27, 2007


Everyone responding to tkolar's ID-ish answer with rational argument misses the point of ID entirely. The point of ID isn't to successfully win arguments. The point is to give fundamentalists that first thing to say so that there is an argument, and therefore a 'controversy' that validates teaching ID. Therefore tkolar's response, as shallow and poorly-fleshed-out as it is, is sucessful.
posted by shakespeherian at 2:47 PM on November 27, 2007 [1 favorite]


It would be a very odd (almost sinister, I might say) "intelligent designer" who would create several unrelated species but then insert pathological DNA [...]

------

And some of those building blocks include mistakes such as pseudogenes?


Hey, ID just posits a designer. It doesn't say anything about a *good* designer.
posted by tkolar at 3:15 PM on November 27, 2007


Evolutionary Strategy No. 8737437:
Hide inactive copies of yourself in the germline DNA of host. Wait for host's evolutionary descendants to evolve intelligence and invent science so they can recreate you.

For my favorite way to win evolution, I think this beats that Venter guy making sure his genes the ones that will be mirrored perpetually as the first-ever-sequenced.
posted by TheOnlyCoolTim at 3:38 PM on November 27, 2007 [1 favorite]


No one is claiming that humans and apes don't share a lot of DNA

That would be an impossible claim, since humans are apes.
posted by grouse at 4:13 PM on November 27, 2007 [1 favorite]


I really wish people would stop saying "Darwin never expected this. Surprise, Darwin!" It's such terrible writing. Of course he didn't expect it. He died in 1884. The fact that we're still building on evolutionary theory is the thing to marvel at. As for what he expected, his work and Mendel's weren't integrated until after they were both dead, so we have a lot more basic knowledge to work with than either of them did. We know about DNA, which they didn't. And empirical evidence to support the germ theory of disease is rather handy, too.

Also interesting to note that the general consensus is our mitochondria- the powerplant of the cell- was bacteria which started out in symbiosis with our ancestors and became fully integrated in our DNA over the millennium.

Endosymbiosis, if anyone's interested. It's very neat.
posted by Tehanu at 4:24 PM on November 27, 2007 [2 favorites]


Damn. It was 1882, says Wikipedia.
posted by Tehanu at 4:26 PM on November 27, 2007


[quote of my comment] Worst. Plagiarist. Ever.

Huh?? Are you talking about me or Carl Zimmer?
posted by delmoi at 4:49 PM on November 27, 2007


robot- what you are describing is a mutation of an already mutated chunk of DNA, rare but not impossible, even if to occur it would involve a chromosomal translocation or insertion. There is already a lot of solid research that has been done on pseudogenes for me to accept speculation on their possible functions. I believe that the similarity is a priori: they are so similar to functioning genes because originally they were that gene, which became disfunctional and deactivated because of mutations.
posted by francesca too at 4:54 PM on November 27, 2007


Rous, who as a young man worked on a Texas cattle ranch, was mystified. He extracted cancer cells from the sick bird, chopped them up, and injected the filtered remains into healthy chickens: they all developed tumors. A virus had to be the cause, but for years no one could figure out how the virus functioned.

Also not true, some cancers do spread from animal to animal. Rather then a virus attacking new cells and turning them cancerous, the cancer cells literally become pathogens, integrating into the new hosts body, but carrying the DNA of the origional host. An example would be Sticker's sarcoma in dogs.
posted by delmoi at 4:56 PM on November 27, 2007


Oooo, viruses.

Makes me wonder about the origin of viruses.

I don't agree with the article's notion that non-retroviral viruses don't "possess the evolutionary power to influence humans as a species—to alter our genetic structure." If some aspect of a human's genes conferred resistance to deadly viruses in a populace, wouldn't that particular genotype become more prevalent over time? Or do all viruses kill too quickly and occur in populations that are too small?

Time to do some reading!
posted by Mister Cheese at 4:59 PM on November 27, 2007


Makes me wonder about the origin of viruses.

While people used to speculate that life evolved from viruses, many now believe that the viruses we have today actually evolved from life. Probably just what you were thinking.
posted by grouse at 5:08 PM on November 27, 2007


Also not true, some cancers do spread from animal to animal.

Actually, the article has it right. Rous filtered the chopped tumors to remove all cells, meaning that a non-cellular agent was responsible, making this different from Sticker's Sarcoma. He got the Nobel for it in 1966.
posted by Llama-Lime at 5:12 PM on November 27, 2007


Actually, the article has it right.

The mistake is this

...they all developed tumors. A virus had to be the cause, but for years no one could figure out how the virus functioned....

A virus wouldn't have "had" to be the cause.
posted by delmoi at 5:28 PM on November 27, 2007


Oh, I guess that peer review, the Nobel committee, and the whole scientific community screwed the pooch on that one.

That, or reading popular science articles very narrowly leads to misconceptions. There's a lot more evidence that went into this, and I thank the author for not overburdening the sentence with information that detracts from the point.
posted by Llama-Lime at 5:33 PM on November 27, 2007


I'm not a creationist. I'm saying that IDers, which are people rationalizing creationism, would answer back that they do have functions and therefor it makes sense for them to be the same in similarly designed animals. Alternatively, they would say that they used to do something, and that our genome has degenerated since its inception. I say this having heard these words come out of a creationist's mouth. These aren't fantastic answers, but they're adequate for audiences who don't know what they're talking about. The point is that common pseudogenes isn't a real show stopper for IDers.
posted by a robot made out of meat at 7:47 PM on November 27, 2007


[...]a real show stopper for IDers.

Now there's a thought. Is there anything short of God appearing in Times Square and saying "I invented evolution so I wouldn't have to do it all by hand, you jackasses" that would actually be a show stopper for IDers?

I'm pretty sure not.
posted by tkolar at 7:55 PM on November 27, 2007


That's completly incorrect, especially for viruses and bacteria. For example, researchers can use the genetic changes in HIV to track it's "Family Tree" across the past few decades, to see how it spreads.

As one of Zimmer's readers suggests, the paragraph as a whole sounds like the author probably meant that the evolution of humans and apes from a common ancestor can't be measured in that time span.
posted by homunculus at 8:10 PM on November 27, 2007


Deploy the Emergency Fallback Explanation: Satan is testing us.

Step 2: Launch JibJib Attack.
posted by homunculus at 8:23 PM on November 27, 2007


Or JibJab Attack. Whatever works.
posted by homunculus at 8:27 PM on November 27, 2007


What a dumas I am.
père or fils?

posted by kirkaracha at 9:22 PM on November 27, 2007


I’d like to share some DNA with an ape, give them a virus, if you know what I mean.

Just who are you flirting with?
posted by peeedro at 9:25 PM on November 27, 2007


Someone with lovely ginger hair from Borneo perhaps?
posted by Artw at 9:38 PM on November 27, 2007


I realize that these guys are doing really useful work that will help us to understand ourselves and to combat diseases, but I can't help but get creeped out by the fact that they are bringing million year old viruses to life.

What if someone who isn't quite so smart tries to reproduce their work and makes some critical mistakes? Or maybe a researcher has a really bad year and decides he hates the world, then realizes he knows how to exact his revenge.
posted by eye of newt at 10:35 PM on November 27, 2007


Amen, eye of newt. The way I look at it, at least the authors of the post-disease-holocaust novels and screenplays will no longer have to resort to the lame rationale, "they accidentally created the super-plague when they were doing some experiments on animals!" That always totally shatters my suspension of disbelief. At this point they're so embarrassed at having resorted to it as a plot device that they try to brush right past it.

I imagine a bored lab tech rubbing mascara in a bunny's eye... close-up on the bunny's eye as it turns an infernal red (not Vizine red but the Al Pacino in The Devil's Advocate red!)... the lab tech melodramatically clutches at his throat when the deus ex machina super-plague takes him down, barely managing to stagger over and hit the convenient large red button that sets off all of the klaxons in the bunker (why were they doing animal experiments in an underground bunker again?), camera cuts to someone gratuitously shouting "containment breach!"

(So of course another thumbs-up to Darwin's Radio for sparing us.)
posted by XMLicious at 11:10 PM on November 27, 2007


Fascinating.

Can I point out though, that the post is not about creationism. If we automatically start talking about ID every time someone mentions evolution, the loonies have won.
posted by Phanx at 12:15 AM on November 28, 2007 [1 favorite]


If we automatically start talking about ID every time someone mentions evolution, the loonies have won.

The right to teach and talk about evolution in the US was hard won. The pendulum could swing back at any time.

Which isn't to say that we have to have an ID derail in every thread that mentions evolution, but it's not particularly surprising that we do.
posted by tkolar at 12:50 AM on November 28, 2007


It'd be nice if we could have science articles that didn't derail into 'suck it, religionists'.
posted by garlic at 7:11 AM on November 28, 2007


Oh, I guess that peer review, the Nobel committee, and the whole scientific community screwed the pooch on that one.

Are you saying the author of this article won a Noble prize? I didn't say a virus wasn't a cause, I'm just saying there are other ways that cancers can be communicated, so that the one bit of the essay was wrong.
posted by delmoi at 3:00 PM on November 28, 2007


The Poo Theory of Life
posted by homunculus at 10:55 PM on December 5, 2007


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