It's life, Jim, but not as we know it
March 25, 2011 11:09 AM   Subscribe

Could the three established domains of life - eukaryotes, bacteria and archaea - be joined by a fourth?
posted by Artw (53 comments total) 20 users marked this as a favorite

This is just advance viral hype for the live-action Smurfs movie, isn't it?

In all seriousness, this is pretty awesome. Looking forward to reading a more in-depth piece on it. And when I saw the post the first thing I thought of was the square-celled extremophile...
posted by jtron at 11:15 AM on March 25, 2011 [1 favorite]

Interestingly, if you visit UCSC's test genome browser, Craig Venter gets his own genome apart from humans. When we first saw how he is no longer listed as human life, it gave us all in the lab a bit of a laugh.
posted by Blazecock Pileon at 11:16 AM on March 25, 2011 [8 favorites]

Maybe this is too early.

Can't we have this thread when the journalists finally run out of breath, listen to scientists, and realize this dude has in fact discovered the fourth domain of life: viruses?
posted by Blasdelb at 11:17 AM on March 25, 2011 [3 favorites]

Incedentally, here is the actual paper
posted by Blasdelb at 11:20 AM on March 25, 2011

This Dr Venter, does he have two sons, Hank and Dean? But really, interesting post, and I look forward to reading more on this. And I agree with Blasdelb. When in biology class I learned that viruses do not meet the definition of life, my thought was, "Well they need to change the definition of life!"
posted by Yer-Ol-Pal at 11:28 AM on March 25, 2011 [4 favorites]

Yeah I was just going to link to the paper (well I did anyway :P) which I got off the author's blog. And here's a blog post about the paper. The blog post is a little more straight forward, from what I've read so far.
posted by delmoi at 11:28 AM on March 25, 2011

A fourth TLD for life (to join .eu, .ba and .ar)? Man, my HS biology is getting outer and outer of date.
posted by DU at 11:29 AM on March 25, 2011 [5 favorites]

From the blog:
Unfortunately, we do not actually know what is the source of these sequences. So we cannot determine which of the theories is correct. Obviously if there is a novel lineages of cellular organisms out there, well, that would be cool. But we have no evidence right now if that is what is going on. Personally, I think it is most likely that these novel sequences are from weird viruses. But as far as we can tell, they truly could be from a fourth major branch of cellular organisms and thus even though we did not have the story completely pinned down, we decided to finally write up the paper to get other people to think about this issue.
posted by delmoi at 11:29 AM on March 25, 2011 [5 favorites]

You mean a fifth, surely...
posted by aeshnid at 11:32 AM on March 25, 2011

I remember our team protesting a question at Science Bowl that still had 5 kingdoms as gospel. Thankfully one of us had some edition of Campbell with them. I could swear the common wisdom at the time was 7 kingdoms (archaebacteria and cyanobacteria in addition the traditional 5), but I'm not seeing anything online about cyano being classified as a separate kingdom at any time. Of course nowadays the whole kingdoms thing is pretty much gone too.
posted by kmz at 11:34 AM on March 25, 2011 [1 favorite]

In NZ we use .ac as an educational domain too.
posted by Samuel Farrow at 11:36 AM on March 25, 2011

Rearranging the early branches on the tree of life is a sure way to be forgotten in 30 years or so when someone else comes up with a good argument to do it another way. If you want longevity in science, go into chemistry and invent a new piece of glassware that's really handy.
posted by Kid Charlemagne at 11:39 AM on March 25, 2011 [23 favorites]

The blog post seems to be firmly in the camp of "I don't know what this is". The problem with "I don't know" means that it could be taken as "This could be anything!", which implies a new form of life which isn't all that different from viruses, but has an interesting taxonomic classification.

Cool discovery, and I think the method of collecting DNA will capture a lot more biodiversity (as noted in the article 97% of bacteria are unculturable, i.e. they won't grow in a petri dish) than we're currently aware, but let's not jump the gun by becoming enamored with possibilities.
posted by Turkey Glue at 11:40 AM on March 25, 2011

The problem with defining viri as life, is, if I go up in the lab, PCR up some of my own DNA totally en vitro, dried it down and put it in a little container, no one would say that container of DNA was alive. (At least no one I want to talk to about what we do at work.)

Off on its own, that's pretty much what a viri is. DNA (Or RNA) plus packaging.
posted by Kid Charlemagne at 11:42 AM on March 25, 2011 [2 favorites]

Prion rights! Misfolded proteins should be acknowledged as lifeforms too!
posted by Artw at 11:42 AM on March 25, 2011 [6 favorites]

This was a round-the-world cruise taken by Craig Venter on his yacht, Sorcerer II, which studied the diversity of micro-organisms in the Atlantic, Pacific and Indian oceans.

...shortly thereafter, he disappeared into his volcano fortress and reemerged later to threaten the free world as the head of SPECTRE.
posted by jquinby at 11:55 AM on March 25, 2011 [7 favorites]

The real problem is that, whenever we have meetings on new members, bacteria and archaea stick together and refuse to listen to reason. At the last meeting, they tried to vote in Legos.
posted by Halloween Jack at 11:56 AM on March 25, 2011 [15 favorites]

No no, Kid Charlemagne, you're missing what the virus is, that DNA in your container, like the DNA in viral particles, is undead.

I've isolated phage DNA, put it in an Eppendorf tube, let it sit for a week, and then transformed it into competent cells. Those phage pregnant cells were alive, and phages, but for that week (and the time before the extraction) my phages were AMONG THE UNDEAD.
posted by Blasdelb at 11:58 AM on March 25, 2011 [3 favorites]

posted by Artw at 12:06 PM on March 25, 2011

As noted in the article 97% of bacteria are unculturable

All of those bacteria have an order of magnitude more viral particles hunting for them and all of those particles have a much wider diversity of genetic materiel. Especially considering that he is looking at RecA, a recombinase.
posted by Blasdelb at 12:15 PM on March 25, 2011 [1 favorite]

On the article: Sounds like science by press release, though its nice that the paper is there too. I was under the impression that the 3 kingdoms were sufficiently broad to accept most non undead life.

On the issue of the undead: Those pesky things can be a real problem in labs. Took one of the labs in our building weeks to clean them out and they still get an outbreak now and again. We thought we'd gotten their issue as well, turns out it was just an incubator thinking that 37C=47C.
posted by Slackermagee at 12:16 PM on March 25, 2011

Could the three established domains of life - eukaryotes, bacteria and archaea - be joined by a fourth?

Oh yes definitely. It's called "conservatism". A very low parasitic form that sucks the life out of everything it touches - c. cameronensis being a particularly unctuous and unpleasant strain at large in the UK at present.
posted by MajorDundee at 12:59 PM on March 25, 2011 [3 favorites]

Is he undead?
posted by Artw at 1:00 PM on March 25, 2011 [1 favorite]

As an illustrator of scientific textbooks, I would just like to say: PROFIT!
posted by Kabanos at 1:05 PM on March 25, 2011 [9 favorites]

"Or are there other biological domains hiding in the shadows—missed, like the archaea were for so long, because biologists have been using the wrong tools to look?"

Sometimes it's best not to look.

Seriously, nobody else thought of Peter Watts?
posted by Guernsey Halleck at 1:09 PM on March 25, 2011

> Seriously, nobody else thought of Peter Watts?

Actually, ßehemoth was first thing I thought of. And then I tried not to think about it any more, because I have shit to get done today, and I can't afford a full-bore Category 5 Psychic Meltdown so early in the afternoon.
posted by pts at 1:29 PM on March 25, 2011

Shit, he's got worse stuff than that inside his leg.
posted by Artw at 1:32 PM on March 25, 2011

Thankfully the vast majority of them are not actually that scary in a laboratory setting, for the most part they desiccate and succumb to bleach like everything else. Your neighbor likely had a T1 phage infestation, and seriously, that shit is scary. They can be bone dry in aerosolized dust, T1 doesn't give a shit, they don't care much about bleach, and they can fucking fly. If you leave a plate with a lawn of sensitive E. coli out open on a bench in a contaminated lab they will fall into it. I've heard stories of whole labs (who couldn't use insensitive strains) going bust because they couldn't get rid of these things, careers ruined, people soaking laminar flow hoods in FORMALDEHYDE in desperation. You can clean EVERYTHING, bathe your whole lab in bleach and UV and then when you get back to work a tiny contaminated speck of dust in the fan of your spectrophotometer sets you back to square one. T1 is the fast zombie that keeps on coming even if you get it in the head.

But even with all of this terror there are still crazy motherfuckers who actually work with this, which leads to my favorite T1 story. Way back in the day there was a lowly post-doc who was really interested in studying T1 genetics. The only problem was that the small field was dominated by this one old dude who had a big collection of mutants and was infamously curmudgeoney about sharing them. Everyone thought this was, if not rude, certainly self defeating, but they were his mutants. So this post-doc figures that he could either spend a year making the mutant he needed or somehow get it from this guy, and he came up with a beautifully brilliant plan. He decided to write the dude a snail mail letter, even though by this point that was a bit odd, asking him for the strain knowing exactly what would happen. The guy then writes back a hostile, mean, dismissive and generally unkind letter back to the post-doc telling him, essentially, to fuck off and let him monopolize the work. So as soon as the letter comes in to the department mail, the post-doc comes down with gloves, reads the letter briefly to confirm what it said, cuts it up and then soaks it in phage buffer. In the end he was able to isolate the strain he needed from the phage buffer and publish nice papers based on what he wanted to do, everyone just laughed at the old curmudgeon.
posted by Blasdelb at 1:34 PM on March 25, 2011 [194 favorites]

Yeah, you can safely chloroform cells and the phage (well, lambda at least) survives happily enough in solution. We do this routinely to eliminate yeast contamination from our phage plates.

I am currently working with phage, E. coli, and yeast at a bench with no flame. I am not thrilled with this situation.
posted by maryr at 2:47 PM on March 25, 2011

Someone told me today that some of Venter's students or employees (whoever he takes with him on his trip) were thinking of programming DNA samples in the lab and then tossing them out in front of the ship; when de-coded they'd read, "CRAIGVENTERISGOD."
posted by you're a kitty! at 5:32 PM on March 25, 2011 [2 favorites]

"Someone told me today that some of Venter's students or employees (whoever he takes with him on his trip) were thinking of programming DNA samples in the lab and then tossing them out in front of the ship; when de-coded they'd read, "CRAIGVENTERISGOD.""

Oh God, you could totally spell that in amino acids. That made my day.
posted by Blasdelb at 5:41 PM on March 25, 2011

You can't spell that in amino acids - there is no O.
posted by maryr at 11:09 PM on March 25, 2011

maryr: You can't spell that in amino acids - there is no O.

O is pyrrolysine. But it is a bit of a special case.
posted by Mitrovarr at 11:17 PM on March 25, 2011 [1 favorite]

Secret Messages Coded Into DNA Of Venter Synthetic Bacteria
posted by Blazecock Pileon at 11:21 PM on March 25, 2011 [1 favorite]

With every passing year, I know less and less biology.
posted by Carius at 1:43 AM on March 26, 2011 [6 favorites]

So long as this is getting attention, I should mention that T1, like all phages, are not the least bit dangerous to humans or any eukaryotes for that matter. They are only the sprinting deathless contagious horde to E. coli, which it grows exponentially at the expense of, and only if it has the FhuA iron transporter intact and unaltered to bind to.
posted by Blasdelb at 1:29 PM on March 26, 2011 [1 favorite]

You realize that's exactly what the scientists say in horror movies right before the unkillable poomonster slaughters everyone in the lab, right?
posted by elizardbits at 3:56 PM on March 26, 2011 [6 favorites]

Most characters in those movies don't walk around with over 1014ish villains on and in them at all times though.
posted by Blasdelb at 5:27 PM on March 26, 2011

T1, like all phages, are not the least bit dangerous to humans or any eukaryotes for that matter.

But what about this? If I'm reading it right, it seems to suggest that some phages can lead bacteria to do weird things, like produce toxins they wouldn't otherwise. Is that correct?

Note: The last time I took a biology class was 12 years ago.
posted by limeonaire at 7:29 PM on March 26, 2011 [1 favorite]

If you want longevity in science, go into chemistry and invent a new piece of glassware that's really handy.

That is so true.
posted by Civil_Disobedient at 8:36 PM on March 26, 2011

Yes, the Jack in the Box E. coli O157:H7 as well as Shigella, cholera, botulism, diphtheria, scarlet fever, and a whole bunch of described shrimp and insect diseases are associated with prophages. Essentially, all "live" phages can go through what is called a lytic life cycle when they infect a cell, shut down host metabolism and substitute their own, replicate their DNA, construct and pack viral particles, and then lyse the cell for the new particles to hunt for more cells. Some phages (known as temperate phages and analogous to retroviruses) can also go through a lysogenic life cycle where instead of shutting down the hosts metabolism, they insert their genomes into the host chromosome and wait. This creates what are call lysogens, sort of a phage/bacteria hybrid, where the phage hides and lets the host replicate it with its own chromosome when it divides. Now these temperate phages have an interest in their hosts doing well and sometimes have exotic genes, which get expressed independently of the host lethal ones, that often contribute to host success in weird situations, like pathogenesis. However, as the phages become more beneficial to their hosts the need for virulence decreases and they begin to lose the genes necessary to enact a lytic life cycle, and becoming what are often called cryptic prophages. These kinds of degraded helpful viruses are critical in evolution, more than 8% of the human genome is immediately recognizable as viral and undoubtedly most of it has at least distant viral origins while an even greater portion of the coli genome is. It is, for the most part, these cryptic prophages that cause pathogenesis though there are still active phages described.

When doing phage therapy, people only use oligately lytic phages unable to go through a lysogenic life cycle, not so much because they could be particularly dangerous, but because they are more unpredictable and generate lysogenic immunity, where prophages often grant mechanisms of immunity to other phages like it to prevent lysis by its sisters.

Thankfully T1 is an extremely lytic phage, otherwise crazy Soviet generals might have wanted to have weaponized it somehow long ago. Even if you were to somehow jam a virulence cassette into its rigid unexpandable capsid, if any native promoter were expressed (and they all are) it would make immediately host lethal genes preventing the expression of anything nasty. This is really one of those things we couldn't fuck with if we tried.
posted by Blasdelb at 10:55 PM on March 26, 2011 [7 favorites]

A phage could easily (contain DNA to) produce a substance that is non-lethal to the host but lethal to humans. Cholera toxin doesn't bother Vibrio cholerae. In fact, Wikipedia suggests that non-toxic strains can become toxic by acquisition of a lysogenic phage, "CTXf or CTXφ". Or am I misunderstanding?
posted by maryr at 8:27 PM on March 27, 2011

Yes wikipedia is correct*, it would have been more accurate for me to have said that "T1, like all obligately lytic phages, are not the least bit dangerous". The CTXφ phage produces a somewhat more complex example of lysogeny where excision, particle production, and lysis requires initiation by a satellite phage. As a prophage, CTXφ produces a repressor which strongly prevents the expression of all the host lethal genes necessary to make particles but not the virulence cassette. It is only excised in the presence of an anti-repressor from the satellite phage and if anything the cholera toxin is likely to produce a benefit to Vibrio cholerae.

*Or at least it is now now that I've fixed a quibble, phage nomenclature is a bit complicated to get used to, even some respected phage researchers regularly confuse the hell out of people with improper use. A phage able to go insert its genome into a host chromosome is a temperate phage, while dormant it is called a prophage and the bacteria is then called a lysogen or a lysogenic cell. This is by the logically consistent nomenclature from the old literature, it makes sense when you think about it, since all phages are lysogenic as lysis is an inherent part of the process that makes the phage independent from its host. Max Delbrück** only used the term lysogen to refer to cells that would produce a plaque on a lawn of similar cells. By this logic a temperate phage would need to be a lysogengen.

**Also the badass who fist isolated T1.
posted by Blasdelb at 10:40 PM on March 27, 2011

I hate to quibble with a pile of favorites and a sidebarred post, but I think the T1 phage story is an urban legend. I'd heard this story years ago in grad school and alway wondered if it was true -- it seemed a bit too neat to be real, and my first impression upon hearing it was "what a great story, I've got to repeat it", which always seems like a red flag for an urban legend in the absence of actual names, dates, and evidence.

A bit of searching found an alt.folklore.urban post from 1996 that debunks the story, or at the least, calls it into question as anything more than scientific gossip (I'm reposting the bulk of it here due to Google's spotty service on the Usenet archive):
The story goes that scientist A. had published a paper on some particular DNA that he'd cloned into a phage. The accepted mores of science mean that, once the system was published, Dr A was obligated to provide the phage to anyone else interested in it; so Dr B wrote to him and asked for the DNA.

Dr A wrote back and gave some excuse - I've heard different versions, ranging from outright refusal to claiming he no longer had it - but anyway, did not provide the phage. Dr B looked at this refusal letter and reasoned that it had probably been written in Dr A's lab; and from that, he wondered if any phage had been floating around in the lab on the day A wrote the letter. Dr B soaked the letter in medium, added it to some bacteria, and lo and behold out grew a phage - which, sure enough,turned out to be the one Dr A supposedly didn't have.

So that's the story. It's classic UL material: a lovely moral, a nice plot twist, short and snappy. It's neither obviously false (the trick could be done) nor obviously true (I'd bet that 99% of the time, if you tried that, you'd come up empty). It's reasonably well-known among the geek crowd I hang out with.

Most of the people I've talked to only know the version I give above:let's call it the vanilla version. Last night, I went out with a bunch of friends, had a Vietnamese dinner that couldn't be beat, saw the Best of Spike and Mike's Animation festival, and got some more versions of this.The contributor (Paul) was formerly a professor at Harvard and now works in biotech. The first version he heard was in the spring of 1979, and he's heard two other versions since.

Paul's first version was rather different in that it wasn't M13, but was a phage of Corynebacterium parvum. (C. parvum is now reclassified as Propionibacterium acnes. I don't know a lot about it. Phages are used in studies of most bacteria, but not as a tool for DNA manipulation but rather for examining the bacterium.) He said that he heard it with a lot of detail, but (significantly) without any identification of the labs involved.

His second version was the vanilla one. The third took it out of science altogether and into beer (not that the two are entirely unconnected): it involved a brewer writing to a commercial brewery and asking for their yeast strain, getting a refusal letter and you know the rest.
A fourth version was provided a while ago by yet another Paul. Paul Tomblin had heard the M13 version with a twist: in his, Scientist A wanted to give the phage to B, but lawyers were involved and refused to allow it. Dr A wrote a regretful refusal to B, but hinted between the lines that the phage was in the letter and B caught on. In this version,the moral is still there but is pointed at the lawyers instead of the scientists, which changes the flavour quite a bit. There's also a new conspiracy element which wasn't in any other version I've heard.
However, this version is reminiscent of something Jan Harold Brunvand talks about in _Curses! Broiled Again!_ (ISBN 0-393-30711-5, WW Norton,New York, 1989) - pp 73-75 in my paperbound version: The Message Under The Stamp --:

... In 1943, his [Brunvand's correspondent] recounted in a letter a story that was going around about another sailor stationed in the Pacific. ...after a time, his letters stopped arriving. His mother was distraught. And she was well-nigh inconsolable after Navy authorities contacted her and reported that her son had been taken prisoner by the enemy. The mother eventually received a letter from her son. He was confined to a Japanese prisoner-of-war camp, he said, but he was safe and was being treated well. When the mother steamed off the stamp, though, she found a hidden message from him: "They've cut off my hands!" ... [another version about the Gestapo having cut off the prisoner's hands.] I've heard versions of the story that try to explain what led the mother to remove the stamp. In these versions, the son suggests in his letter that she should steam off the stamp for "little Alf" or "little Johnny" to add to his collection. But there is no little Alf or Johnny in the family. Nor are there any stamp collectors. The mother finally realizes this is a clue and steams the stamp off the envelope, finding the message. Given its wartime setting, it's not surprising that one variation pushes the origin of the story back from the Second World War to the First. In his autobiography _Exit Laughing, publishes in 1941, Irwin S. Cobb describes a "sad little tale which sprang up 24 years ago and now is enjoying a popular revival. It's the heart-moving one about the German housewife who writes a letter to her kinfolks in America that everything is just dandy [soaks off stamp and] underneath are the words "We are starving." I don't know how we'd get along without that standby every time war breaks out in Europe," Cobb adds.

Brunvand points out a bunch of things showing that the first version is clearly nonsense, and Cobb clearly didn't believe the second (civilian)version.
The secret hidden in the letter, and especially the hint by which the sender points to the secret, sound a lot like the phage (remember the phage? This here's a post about phages) story. If so, then this relatively recent science geek legend has antecedents going back at least 80 years.

Ian "FAQ: U" York
The only thing more tenacious than phages are urban legends, which in its own way is kind of awesome. Borges would be proud: a story that purports to be about a novel method of transmitting a virus, is itself the virus mutating and being transmitted as it's told.
posted by benzenedream at 11:45 PM on March 27, 2011 [111 favorites]

Thanks! I just scraped a phage off of that post.
posted by wayland at 7:10 AM on March 28, 2011 [10 favorites]

There are in fact a lot of people who doubt the story as it is generally told, particularly Dr. Kropinski, a respected Canadian phage PI who did some minor tracking down of it a while ago. Its unfortunate that the other of the two debunkings he links to is dead, though I read it a while ago. It points to a few more flaws in the story as it is generally told.

The mutant is generally described as an amber mutant, or something recombineered somehow, but then how would our plucky hero isolate the mutant he wanted and not the many other phages the curmudgeon presumably worked with? Particularly during the ancient days of the 70s and 80s before PCR and easy sequencing. However, it is clear that this story has been passed down and changing for a for even longer than that, I heard it from my old PI who herself heard it from Roger Christian as having happened in the early 60s when she was a graduate student at the University of Rochester before 1968. As she told it to me, it makes significantly more logical sense. The T1 strain that the plucky hero was looking for was an expanded host range mutant, something particularly valued at the time, one that could successfully infect a wider range of bacteria than the wild-type. The hero simply plated the phage buffer on a lawn of the unique host to isolate it.

It makes sense that the story would survive for so long, its a really good one, but it also makes sense that it would divorce from its origins over time and mutate. Phage research starting in the late 60s and early 70s started to die and disperse for a variety of reasons and has only really come back recently starting in the early 90s. This has led to a large disconnect between the modern and original phage communities with precious few bridges left. Hell, I once saw a paper published recently in a good journal where a graduate student more or less ripped of work published in the early 70s in a reasonably obscure journal, that I only happened to have access to going back that far from my unusually large institution's library. The bastard cited it but everything he did was a nearly exact replica of the old work with only very minor modifications and similar results. Almost no one would have memory of the old paper much less have access to it.

I've been hoping to have an excuse to actually track this down, and this afternoon I'll send emails to the people I can think of who were involved in that community who are still alive and to any graduate students of Roger Christian I can find. It should in fact be easier now than it would have been in the last 20 years or so with better indexing of papers and everyone being online. I'll report back when I find the people involved, or of course the original joker.
posted by Blasdelb at 10:47 AM on March 28, 2011 [1 favorite] also makes sense that it would divorce from its origins over time and mutate.

So you're saying that the story has...evolved?

Nonsense. How come we still have the original story then? I am a firm believer in creative writing.
posted by maryr at 10:55 AM on March 28, 2011 [2 favorites]

Eventually, after multiple rounds of bleaching, UV light treatment every night for 6 months after the initial contamination, conversion to T1-resistant strains, and about 2 years, T1 is not detectable in the lab.

T1 Phage don't care. T1 Phage don't give a shit.
posted by Kabanos at 2:11 PM on March 28, 2011 [3 favorites]

This thread is awesome and I'm glad both the original (allegedly) urban legend tale and the rebuttal have been posted. There's something I haven't seen on Snopes, that's for sure.

I'd also like to say that I've been rightfully accused (not in this thread, in general) of being an annoying know it all. Well, 70% of this thread reads like alien gibberish to me. I have absolutely no idea what most of you are talking about - and that's great. I keep having to look up stuff on wikipedia to even grasp most of it. The way I figure it if I ever start actually feeling like I've got most of it figured out I'll be figuratively or literally dead.

I know biology has been getting weird and freaky over the last few decades, but apparently I had no idea exactly how weird and freaky it's been.

Oh my god there are billions and trillions of tiny little bugs crawling all over me and inside me. I'm never going swimming in anything but household bleach ever again. *scratches fitfully*
posted by loquacious at 7:50 PM on March 28, 2011 [2 favorites]

The Message Under The Stamp

Far afield from the phage legend, but potentially relevant because some urban legends can start out as truthful stories somewhere....

Corrie Ten Boom recounts in her autobiography that her sister sent her a message under a stamp to escape the notice of the Germans when Holland was being occupied.
posted by jeanmari at 12:38 AM on March 29, 2011

There have been Metafilter posts about sports that I have understood better than this. SPORTS.

This fourth domain: do we have a name for it yet? I pored over the Economist article and it doesn't seem to cite one, but then again, I keep getting confused and then cursing my sub-par, vintage 1980s high school science education.

And do the phages belong to it, or was that just an urelated conversational tangent?

("Derail" seems a little harsh for what has been a very interesting, entertaining, and educational conversation to eavesdrop upon.)
posted by ErikaB at 1:55 PM on March 29, 2011


As Jonathan Eisen, the author, makes much more clear in the paper and on his much less technical blog post, he hasn't actually found any unknown life forms, just genomic evidence for them. Essentially, he amplified DNA for two specific genes found in almost all life from organisms living in seawater around the world. Because he was looking at DNA directly from seawater and not pure cultures of organisms isolated from the seawater, he cannot say which organisms the DNA came from. However in exchange, he can say that it is representative of everything out there, and not biased by the fact that we haven't figured out how to artificially grow most of life.

Because the two genes he looked at are ubiquitous, or found everywhere, we have a lot of information about the diverse sequences of DNA that make them and the kinds of organisms they are found in. Thus, he was able to make a phylogenetic tree, grouping together similar sequences that he found in the seawater and label them as belonging to known groups. However, he found two groups of sequences that were fundamentally different from anything we had sequenced before and he couldn't match them to known organisms.

While it is distinctly possible that the novel sequences he found are from a fundamentally new domain of cellular life unlike anything we have grown in culture before as the Economist breathlessly proclaims, it is extremely unlikely. Most of the diversity found in the different types of the two genes he was looking at are in bacteriophages, the viruses of bacteria called phages for short. Thus he has likely discovered a new type of phage that has not yet been sequenced (Its really cheap and easy to sequence them but there arn't many people doing it) I find this really exciting, but it is unlikely to change high school textbooks. It is also very possible, but less likely, that he has found uncultured cellular life belonging to one or two of the three known domains.

tl;dr: The Economist article is, sadly like a great deal of science journalism, complete bullshit. The authors blog explains it better, and the paper itself is worthy and well written, even if the title is irresponsible.
posted by Blasdelb at 7:26 PM on March 29, 2011

For an update!

After some amount of looking around, it looks like this story did originate as a good natured joke in the early sixties. A bunch of people who should know the origin if it were real didn't, and the one person who as replied so far who would know first heard it told as fun. I still haven't heard back from the one person left who aught to know the original teller, though I have some ideas. If he never emails me back I should see him at the next conference in August.

It is however important to keep in mind that not everything that can be Googled is worthwhile and not everything that is worthwhile can be Googled. I'll paypal $50 to anyone who can send me a copy of Amiran Meipariani's thesis, easily one of the most important works of the era, within the life of this thread.

I also wanted to mention that the bit with the stamp doesn't make so much sense for inspiration. Back in the day, people used to send cultures of bacteria and phages by letter all the time. You'd soak some filter paper in the culture, attach it to a letter, and send it so that the receiver could grow it up and isolate a single colony or plaque. This was especially easy for phage labs because you could use different phages (which have specific host ranges) to make sure you had the right bacteria, and different bacteria to make sure you had the right phages, it didn't need to be perfectly sterile.
posted by Blasdelb at 11:33 PM on April 13, 2011

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