The Missing Transposable Link
March 6, 2011 10:47 PM Subscribe
In the 1940s Barbara McClintock discovered the remarkable phenomenon of mobile genetic elements, or transposons: parasitic DNA that makes up a significant fraction of the human genome. (Here is a video segment about McClintock: Part 1 & 2.) The discovery remains highly important: we now know that transposons play a role in driving genome evolution. Where do they come from? A compelling hypothesis is that some evolved from viruses.
Now a marine biology group at UBC has found a virus whose closest genetic relative is a type of transposon. (The paywalled paper's abstract is here.) But that is not even the interesting part.
It turns out that the virus in question is a type of virophage- reader, it infects other viruses. Previously, mimivirus was shown to be infected by the so-called Sputnik virophage. Makes for pretty pictures.
The new one they are calling mavirus. It infects Cafeteria roenbergensis virus, or CroV. CroV, in turn, infects a (eukaryotic) single-celled marine bicosoecid called, well, Cafeteria roenbergensis. Mavirus appears to protect C. roenbergensis from CroV, thus gaining a toehold in the genome: permanent incorporation of mavirus would confer permanent protection . If this explains the origins of transposons, it may be that they began with mutualistic host-virus interactions, and only later evolved into parasitic DNA.
Now a marine biology group at UBC has found a virus whose closest genetic relative is a type of transposon. (The paywalled paper's abstract is here.) But that is not even the interesting part.
It turns out that the virus in question is a type of virophage- reader, it infects other viruses. Previously, mimivirus was shown to be infected by the so-called Sputnik virophage. Makes for pretty pictures.
The new one they are calling mavirus. It infects Cafeteria roenbergensis virus, or CroV. CroV, in turn, infects a (eukaryotic) single-celled marine bicosoecid called, well, Cafeteria roenbergensis. Mavirus appears to protect C. roenbergensis from CroV, thus gaining a toehold in the genome: permanent incorporation of mavirus would confer permanent protection . If this explains the origins of transposons, it may be that they began with mutualistic host-virus interactions, and only later evolved into parasitic DNA.
I maintain one of these days we'll find out that viruses are in fact generated by the body as a mechanism for distributing genetic patches -- and that sometimes, those patches spread across the tribe (which has grown unexpectedly large).
It's a crazy batshit theory though :)
posted by effugas at 11:31 PM on March 6, 2011 [5 favorites]
It's a crazy batshit theory though :)
posted by effugas at 11:31 PM on March 6, 2011 [5 favorites]
"Cafeteria roenbergensis" would be a great name for a diner.
posted by Sys Rq at 11:51 PM on March 6, 2011 [1 favorite]
posted by Sys Rq at 11:51 PM on March 6, 2011 [1 favorite]
That's all well and good until someone decides to fork the project effugas.
posted by caution live frogs at 11:52 PM on March 6, 2011 [1 favorite]
posted by caution live frogs at 11:52 PM on March 6, 2011 [1 favorite]
A virus that infects a virus. I vote a rename to MetaVirus.
I know, right? Mind-blowing!!! Next they'll be telling us that there are mammals that eat mammals!
Oh, wait.
posted by Sys Rq at 11:53 PM on March 6, 2011
I know, right? Mind-blowing!!! Next they'll be telling us that there are mammals that eat mammals!
Oh, wait.
posted by Sys Rq at 11:53 PM on March 6, 2011
After McClintock found out about winning the Nobel, she said something grandmotherly like "Oh dear", and went to go work in her garden to calm down.
Not to go completely off-topic here (OK, actually to do exactly that), this brings to mind Doris Lessing's response to the news that she had won a Nobel. She was getting out of a cab in front of her house when a reporter asked her about it, she replied (in a slightly less grandmotherly fashion, "Oh, Hell!"
posted by deadbilly at 12:12 AM on March 7, 2011
Not to go completely off-topic here (OK, actually to do exactly that), this brings to mind Doris Lessing's response to the news that she had won a Nobel. She was getting out of a cab in front of her house when a reporter asked her about it, she replied (in a slightly less grandmotherly fashion, "Oh, Hell!"
posted by deadbilly at 12:12 AM on March 7, 2011
Actually after looking back, it was "Oh Christ!" not "Oh Hell!"
posted by deadbilly at 12:14 AM on March 7, 2011
posted by deadbilly at 12:14 AM on March 7, 2011
There is something beautiful and exciting about the idea that the tree of life is really a web - that besides the vertical links reaching up from our ancestors, there are horizontal links reaching across species and potentially joining every species that exists or has ever existed. We share DNA with other species that share DNA with others in their turn, thereby making us not only cousins but in-laws; part of a grand family of species that is only weakly reflected by our smaller intra-species relationships.
posted by Joe in Australia at 12:18 AM on March 7, 2011 [6 favorites]
posted by Joe in Australia at 12:18 AM on March 7, 2011 [6 favorites]
The word 'phage' means 'eater', but viruses infect other organisms. This is not the only virus that infects other viruses, but a) it is still super cool and b) coming from a transposon is additionally neat.
posted by Peter Petridish at 12:29 AM on March 7, 2011
posted by Peter Petridish at 12:29 AM on March 7, 2011
That's all well and good until someone decides to fork the project effugas.
too late
posted by effugas at 12:36 AM on March 7, 2011
too late
posted by effugas at 12:36 AM on March 7, 2011
But can it be used as a Soviet sanitizer?
I'd never heard of that before. So how long before the Zombocalypse when Monsanto makes a GM one?
posted by arcticseal at 1:10 AM on March 7, 2011
I'd never heard of that before. So how long before the Zombocalypse when Monsanto makes a GM one?
posted by arcticseal at 1:10 AM on March 7, 2011
Yo dawg we heard you like DNA
posted by Potomac Avenue at 3:43 AM on March 7, 2011 [7 favorites]
posted by Potomac Avenue at 3:43 AM on March 7, 2011 [7 favorites]
Does it 'infect' it...or eat it?
From one of the links above:
In their study, recently published in Nature, the researchers describe that Sputnik is unable to multiply in an amoeba on its own, but does grow rapidly when it can penetrate APMV's virus factory, where new viral particles are made. The hijacking of the factory's machinery results in the production of non-viable forms of APMV. Sputnik is therefore harmful to its host virus.posted by XMLicious at 4:23 AM on March 7, 2011
"There is something beautiful and exciting about the idea that the tree of life is really a web"
Oh yeah? Try telling that to Charles Koch.
posted by sneebler at 4:59 AM on March 7, 2011
Oh yeah? Try telling that to Charles Koch.
posted by sneebler at 4:59 AM on March 7, 2011
Describing a virus as "being infected" is kind of meaningless (and why viri are generally considered "not alive").
This needs a new verb.
posted by Kid Charlemagne at 5:35 AM on March 7, 2011
This needs a new verb.
posted by Kid Charlemagne at 5:35 AM on March 7, 2011
I think we should name them midi-chlorians.
posted by dances_with_sneetches at 5:48 AM on March 7, 2011 [1 favorite]
posted by dances_with_sneetches at 5:48 AM on March 7, 2011 [1 favorite]
Describing a virus as "being infected" is kind of meaningless (and why viri are generally considered "not alive").
This needs a new verb.
"Patched".
I think it fits flawlessly. The existing code is modified with new code. Patched.
posted by Netzapper at 6:00 AM on March 7, 2011 [14 favorites]
This needs a new verb.
"Patched".
I think it fits flawlessly. The existing code is modified with new code. Patched.
posted by Netzapper at 6:00 AM on March 7, 2011 [14 favorites]
Silliest girl in Rapture.
posted by BeerFilter at 6:51 AM on March 7, 2011 [1 favorite]
posted by BeerFilter at 6:51 AM on March 7, 2011 [1 favorite]
Like Patch Adams.
posted by blue_beetle at 7:40 AM on March 7, 2011
posted by blue_beetle at 7:40 AM on March 7, 2011
Does it "infect" it...or eat it? "Phage" tells me "eat".
Terminology is probably derived from "bacteriophage", which are viruses that infect and ultimately result in the lysis of eubacteria with release of hundreds of daughter viruses. It's an extension of "phage" to mean "consume" rather than literally "eat".
posted by overyield at 7:49 AM on March 7, 2011
Terminology is probably derived from "bacteriophage", which are viruses that infect and ultimately result in the lysis of eubacteria with release of hundreds of daughter viruses. It's an extension of "phage" to mean "consume" rather than literally "eat".
posted by overyield at 7:49 AM on March 7, 2011
Describing a virus as "being infected" is kind of meaningless (and why viri are generally considered "not alive").
This needs a new verb.
More to the point, Kid Charlemagne: viruses need a new adjective, if "living" is not acceptable to biologists.
They reproduce. They mutate. They pass on genetic changes. Caveat: they can only reproduce within and with aid from other living organisms, since they lack necessary materials and means for reproduction.
They're clearly quasi-alive, and certainly not lifeless. Science is so good at making up new, needed terms; why hasn't it done so for viruses?
posted by IAmBroom at 7:52 AM on March 7, 2011
This needs a new verb.
More to the point, Kid Charlemagne: viruses need a new adjective, if "living" is not acceptable to biologists.
They reproduce. They mutate. They pass on genetic changes. Caveat: they can only reproduce within and with aid from other living organisms, since they lack necessary materials and means for reproduction.
They're clearly quasi-alive, and certainly not lifeless. Science is so good at making up new, needed terms; why hasn't it done so for viruses?
posted by IAmBroom at 7:52 AM on March 7, 2011
They're clearly quasi-alive, and certainly not lifeless. Science is so good at making up new, needed terms; why hasn't it done so for viruses?
Living vs. not living is not really an issue for science. Viruses are what they are. It is really just an issue if you want to divide science up into compartments.
posted by Mental Wimp at 9:05 AM on March 7, 2011 [1 favorite]
Living vs. not living is not really an issue for science. Viruses are what they are. It is really just an issue if you want to divide science up into compartments.
posted by Mental Wimp at 9:05 AM on March 7, 2011 [1 favorite]
Living vs. not living is not really an issue for science.Sure it is, if only by implication. It was scientists who gave viruses a taxonomic classification system that, at the low levels, is the same as that which they gave to... other things. Order, family, genus, species. And the reasoning that leads to some two viruses being placed in the same order, or family, or whatever, is the same reasoning that leads to two other things being placed into the same order, or family, or whatever.
And I imagine that you could, and perhaps that they do, group orders of viruses into some higher level group, using the same reasoning that you would use to group orders of other things into "classes".
But they're unwilling to say that orders of viruses can be grouped into "classes" of viruses. Why not?
I'm no biologist, but from my uneducated vantage point, it seems pretty arbitrary, and the reason that I can't help imagining is that they don't want to say "classes" because they don't want to say "phylums", and they don't want to say "phylums" because they don't want to say "kingdom", and they don't want to say "kingdom" because they don't want to invite placement into the tree of life.
posted by Flunkie at 10:14 AM on March 7, 2011 [1 favorite]
Flunkie, everything you say is true. But it all works whether or not you designate viruses as "living" or "not living", doesn't it? Let's say, for the sake of argument, that there is no absolute dividing line between "living" and "not living". How does that affect how the science would proceed. Things like family, genus, and species aren't the stuff of science, they're just organizing bins. Ultimately, it is the process of becoming those things that is the goal of science and the bins are an intermediate step to learning those processes. They were originally developed based on morphological features, whereas now the genetic history is considered more definitive. It is a testament to the power of the original taxonomy, as well as the strength of the genetic model, that the revisions necessary due to this shift are few.
But we can't confuse the tools of science with science itself, which is the deeper and deeper modeling of the physical world.
posted by Mental Wimp at 10:22 AM on March 7, 2011
But we can't confuse the tools of science with science itself, which is the deeper and deeper modeling of the physical world.
posted by Mental Wimp at 10:22 AM on March 7, 2011
Sure, they're just organizing bins. But:
* For certain things being classified, scientists group them into a kind of bin that they call X. They're doing that grouping for some reason - used to be morphological, now genetic, doesn't really matter for the purposes of my point.
* For certain other things being classified, scientists group them into a kind of bin that they call X. They're doing so for the exact same reason that they're grouping those other things into a kind of bin that they call X.
* For the first kind of thing, they group X bins into other types of bins, that they call Y bins. They're doing this grouping for some reason.
* For the second thing, I imagine that X bins can be grouped into some other kind of bin, for the exact same reason that you would group the other things' X bins into Y bins.
* But they don't. Or, if they do, they don't call those bins "Y bins".
Why not?
I think it's merely because they're making an implicit value judgment on what is "life".
Obviously viruses are what they are and other things are what they are no matter whether you think either or both or neither "alive", and so yeah, of course the mere word "alive" is not relevant to the physical world, but that hasn't stopped scientists from implicitly giving it importance within science.
posted by Flunkie at 10:34 AM on March 7, 2011 [1 favorite]
* For certain things being classified, scientists group them into a kind of bin that they call X. They're doing that grouping for some reason - used to be morphological, now genetic, doesn't really matter for the purposes of my point.
* For certain other things being classified, scientists group them into a kind of bin that they call X. They're doing so for the exact same reason that they're grouping those other things into a kind of bin that they call X.
* For the first kind of thing, they group X bins into other types of bins, that they call Y bins. They're doing this grouping for some reason.
* For the second thing, I imagine that X bins can be grouped into some other kind of bin, for the exact same reason that you would group the other things' X bins into Y bins.
* But they don't. Or, if they do, they don't call those bins "Y bins".
Why not?
I think it's merely because they're making an implicit value judgment on what is "life".
Obviously viruses are what they are and other things are what they are no matter whether you think either or both or neither "alive", and so yeah, of course the mere word "alive" is not relevant to the physical world, but that hasn't stopped scientists from implicitly giving it importance within science.
posted by Flunkie at 10:34 AM on March 7, 2011 [1 favorite]
Flunkie,
I don't think that there is a conspiracy by biologists who study viruses to keep them out of the tree of life to avoid questions as to whether they are alive or not. The biologists who study viruses are unlikely to update their classifications of viruses to use classes or phylums because they are are interested in the movement of DNA sequences. They are not going to sit around and argue about what class are a new population of viruses is, they are going to get some samples, sequence them, look for markers and propose some clades. Sure it will get a Linnaean name but no real interest in King Phillip etc for them.
How are biologists who study viruses making a judgment about what is and isn't life? Are you assuming that biologists only study life?
posted by bdc34 at 3:16 PM on March 7, 2011
I don't think that there is a conspiracy by biologists who study viruses to keep them out of the tree of life to avoid questions as to whether they are alive or not. The biologists who study viruses are unlikely to update their classifications of viruses to use classes or phylums because they are are interested in the movement of DNA sequences. They are not going to sit around and argue about what class are a new population of viruses is, they are going to get some samples, sequence them, look for markers and propose some clades. Sure it will get a Linnaean name but no real interest in King Phillip etc for them.
How are biologists who study viruses making a judgment about what is and isn't life? Are you assuming that biologists only study life?
posted by bdc34 at 3:16 PM on March 7, 2011
IAmBroom wrote: Caveat: they can only reproduce within and with aid from other living organisms
Well, the same goes for me, and I'm alive.
posted by Joe in Australia at 3:24 PM on March 7, 2011 [3 favorites]
Well, the same goes for me, and I'm alive.
posted by Joe in Australia at 3:24 PM on March 7, 2011 [3 favorites]
I wasn't saying that there was some grand conspiracy where they sit around in some dark room and laugh evilly, bdc34.
posted by Flunkie at 4:12 PM on March 7, 2011
posted by Flunkie at 4:12 PM on March 7, 2011
"Describing a virus as "being infected" is kind of meaningless (and why viri are generally considered "not alive")."
OO OO, I'm a Phage Biologist, I can answer this! According to Didier Raoult and Patrick Forterre, the two guys who are really leading the work with this sort of thing, really we should think of a virus not as the viral particle but as the virus pregnant cell. You wouldn't count the number of frogs in a lake by including the number of frog eggs would you? Similarly if you wanted to count the number of phages in a lake you should count the number of phage pregnant cells not the particles. Thus the true Mimivirus, by which I the Mimivirus pregnant cell, is what gets infected by Sputnik. Patched doesn't really quite work as Sputnik really is an autonomous entity, it doesn't alter the Mimivirus, it takes over and replaces it.
Flunkie, you might be interested in these publicly available papers 1 2 3. They pretty much answer most of your questions and are an awesome and entertaining example of how scientists can only call each other names carefully and obliquely.
Also, the way this FPP is framed its not really complete without this paper
"I'd never heard of that before. So how long before the Zombocalypse when Monsanto makes a GM one?"
Theres a really awesome Scottish company working on using them as vaccines for otherwise difficult diseases?
I'll stick around if people have more questions.
posted by Blasdelb at 9:48 AM on March 8, 2011 [4 favorites]
OO OO, I'm a Phage Biologist, I can answer this! According to Didier Raoult and Patrick Forterre, the two guys who are really leading the work with this sort of thing, really we should think of a virus not as the viral particle but as the virus pregnant cell. You wouldn't count the number of frogs in a lake by including the number of frog eggs would you? Similarly if you wanted to count the number of phages in a lake you should count the number of phage pregnant cells not the particles. Thus the true Mimivirus, by which I the Mimivirus pregnant cell, is what gets infected by Sputnik. Patched doesn't really quite work as Sputnik really is an autonomous entity, it doesn't alter the Mimivirus, it takes over and replaces it.
Flunkie, you might be interested in these publicly available papers 1 2 3. They pretty much answer most of your questions and are an awesome and entertaining example of how scientists can only call each other names carefully and obliquely.
Also, the way this FPP is framed its not really complete without this paper
"I'd never heard of that before. So how long before the Zombocalypse when Monsanto makes a GM one?"
Theres a really awesome Scottish company working on using them as vaccines for otherwise difficult diseases?
I'll stick around if people have more questions.
posted by Blasdelb at 9:48 AM on March 8, 2011 [4 favorites]
bdc34,
Phage nomenclature is, at the moment, kind of a mess. So far they have only really been grouped by the morphology of the particle and the molecule carrying the genetic information (dsDNA, ssRNA, ext..). This paper describes the current problem of phage names and presents the solution we are working towards.
posted by Blasdelb at 9:57 AM on March 8, 2011
Phage nomenclature is, at the moment, kind of a mess. So far they have only really been grouped by the morphology of the particle and the molecule carrying the genetic information (dsDNA, ssRNA, ext..). This paper describes the current problem of phage names and presents the solution we are working towards.
posted by Blasdelb at 9:57 AM on March 8, 2011
I'm software, and I can reproduce without any outside help at all. w00t!
posted by Goofyy at 10:58 AM on March 9, 2011
posted by Goofyy at 10:58 AM on March 9, 2011
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