Half the DNA on the NYC Subway Matches No Known Organism
February 6, 2015 7:55 AM Subscribe
The number of unknown species is not surprising, as the article says, most genomes are not mapped.
I just feel bad for the MTA, you can read their annoyance at the study. Bubonic plague! Anthrax! They had apparently always been present in the subway, but now people will panic and there is nothing to be done about it.
posted by blahblahblah at 8:03 AM on February 6, 2015 [6 favorites]
I just feel bad for the MTA, you can read their annoyance at the study. Bubonic plague! Anthrax! They had apparently always been present in the subway, but now people will panic and there is nothing to be done about it.
posted by blahblahblah at 8:03 AM on February 6, 2015 [6 favorites]
Gizmodo explains why it's unknown. Basically we haven't mapped every single type of bacteria on earth yet. So some sequences are unknown.
The problem, though, is that our genetic libraries are still incomplete. For example, if I don't know what the DNA sequences of a cockroach look like, how can I know my DNA sequence belongs to a cockroach? That's how why half the DNA found in the project matched no known organism.
This is especially true when it comes to bacteria that are being discovered for the first time in these new metagenomic analyses. And what does "associated with," when it comes to bacteria, really mean? Maybe we found a certain bacterium on cheese once, but maybe we never sampled its true native habitat?
posted by edbles at 8:05 AM on February 6, 2015 [3 favorites]
The problem, though, is that our genetic libraries are still incomplete. For example, if I don't know what the DNA sequences of a cockroach look like, how can I know my DNA sequence belongs to a cockroach? That's how why half the DNA found in the project matched no known organism.
This is especially true when it comes to bacteria that are being discovered for the first time in these new metagenomic analyses. And what does "associated with," when it comes to bacteria, really mean? Maybe we found a certain bacterium on cheese once, but maybe we never sampled its true native habitat?
posted by edbles at 8:05 AM on February 6, 2015 [3 favorites]
Basically we haven't mapped every single type of bacteria on earth yet.
Especially not Cthulhu bacteria.
posted by maxsparber at 8:06 AM on February 6, 2015 [4 favorites]
Especially not Cthulhu bacteria.
posted by maxsparber at 8:06 AM on February 6, 2015 [4 favorites]
Well, it's not like the non humans in these stories can get around by taxi.
posted by Buttons Bellbottom at 8:07 AM on February 6, 2015 [1 favorite]
posted by Buttons Bellbottom at 8:07 AM on February 6, 2015 [1 favorite]
I immediately went to the Smith-9th St station, and I wasn't surprised.
posted by 1970s Antihero at 8:10 AM on February 6, 2015
posted by 1970s Antihero at 8:10 AM on February 6, 2015
"Half the DNA on the NYC Subway Matches No Known Organism" - at first I thought it was going to be a posting about the riders.
posted by King Sky Prawn at 8:10 AM on February 6, 2015 [13 favorites]
posted by King Sky Prawn at 8:10 AM on February 6, 2015 [13 favorites]
Hey, bacteria are riders, too.
posted by limeonaire at 8:21 AM on February 6, 2015 [5 favorites]
posted by limeonaire at 8:21 AM on February 6, 2015 [5 favorites]
The bacteria under the Oil Cleanup tab sounds like it would thrive in New York:
Some strains can live on pure caffeine.
posted by clawsoon at 8:22 AM on February 6, 2015 [4 favorites]
Some strains can live on pure caffeine.
posted by clawsoon at 8:22 AM on February 6, 2015 [4 favorites]
Hey my stop's not too bad, mostly cheese.
Though the nurse at my baby's doctor told me this morning to take a hot shower and throw my clothes in a bag before touching my daughter after getting off the train because of measles. Cool thanks way to not induce panic.
posted by Potomac Avenue at 8:23 AM on February 6, 2015
Though the nurse at my baby's doctor told me this morning to take a hot shower and throw my clothes in a bag before touching my daughter after getting off the train because of measles. Cool thanks way to not induce panic.
posted by Potomac Avenue at 8:23 AM on February 6, 2015
Metafilter: Not too bad, mostly cheese.
posted by Tomorrowful at 8:25 AM on February 6, 2015 [13 favorites]
posted by Tomorrowful at 8:25 AM on February 6, 2015 [13 favorites]
#NotAllDNA
posted by infini at 8:30 AM on February 6, 2015 [2 favorites]
posted by infini at 8:30 AM on February 6, 2015 [2 favorites]
Lots of radiation resistance and toxic cleanup bacteria in Gowanus.
posted by grumpybear69 at 8:30 AM on February 6, 2015
posted by grumpybear69 at 8:30 AM on February 6, 2015
I pass through three, and sometimes four, subway stations in the course of a given day. And every single one of them is showing up as having some kind of "toxic cleanup".
Someone please tell me that all this means is someone spilled a bottle of bleach or something.
posted by EmpressCallipygos at 8:31 AM on February 6, 2015 [1 favorite]
Someone please tell me that all this means is someone spilled a bottle of bleach or something.
posted by EmpressCallipygos at 8:31 AM on February 6, 2015 [1 favorite]
"Especially not Cthulhu bacteria."
Cthulhicobacter pylori, cause of Deep Ulcers.
posted by komara at 8:31 AM on February 6, 2015 [7 favorites]
Cthulhicobacter pylori, cause of Deep Ulcers.
posted by komara at 8:31 AM on February 6, 2015 [7 favorites]
The next thing Weill Cornell oughta track is the epidemiology of their findings turning up as setups at NYC open mics.
posted by EatTheWeek at 8:32 AM on February 6, 2015 [2 favorites]
posted by EatTheWeek at 8:32 AM on February 6, 2015 [2 favorites]
The next thing Weill Cornell oughta track is the epidemiology of their findings turning up as setups at NYC open mics.
No, these guys are bacteriologists--that will have to wait for the virologists.
posted by yoink at 8:43 AM on February 6, 2015 [1 favorite]
No, these guys are bacteriologists--that will have to wait for the virologists.
posted by yoink at 8:43 AM on February 6, 2015 [1 favorite]
Probably makes more sense if you take into account that 10-20% of NYC subway trains are actually cunningly disguised shoggoths just waiting for the stars to come right.
posted by McCoy Pauley at 8:46 AM on February 6, 2015 [2 favorites]
posted by McCoy Pauley at 8:46 AM on February 6, 2015 [2 favorites]
Just pointing out that bacteria can differ by 25% of their genome and still be of the same species.
posted by halifix at 8:55 AM on February 6, 2015 [2 favorites]
posted by halifix at 8:55 AM on February 6, 2015 [2 favorites]
Oh yeah, my local stop is associated with mozzarella. I can live with that. *drops metrocard in vat of warm milk, waits*
posted by moonmilk at 9:01 AM on February 6, 2015 [4 favorites]
posted by moonmilk at 9:01 AM on February 6, 2015 [4 favorites]
My money is on C.H.U.D.
posted by bottlebrushtree at 9:07 AM on February 6, 2015 [3 favorites]
posted by bottlebrushtree at 9:07 AM on February 6, 2015 [3 favorites]
I can't believe I didn't go for the CHUD joke before the Cthulhu joke. I feel like such an idiot.
posted by maxsparber at 9:11 AM on February 6, 2015 [4 favorites]
posted by maxsparber at 9:11 AM on February 6, 2015 [4 favorites]
Some of it probably belongs to the patrons of the Midnight Meat Train.
posted by mephron at 9:11 AM on February 6, 2015 [2 favorites]
posted by mephron at 9:11 AM on February 6, 2015 [2 favorites]
That's a better reference too! God damn it, I have to step up my game.
I think it's a mix of alligator DNA and cells from the surviving abortions that live in the sewers in Harlan Ellison's Coratoan.
posted by maxsparber at 9:17 AM on February 6, 2015 [1 favorite]
I think it's a mix of alligator DNA and cells from the surviving abortions that live in the sewers in Harlan Ellison's Coratoan.
posted by maxsparber at 9:17 AM on February 6, 2015 [1 favorite]
Nope. That was just upsetting.
posted by maxsparber at 9:17 AM on February 6, 2015 [1 favorite]
posted by maxsparber at 9:17 AM on February 6, 2015 [1 favorite]
That's your issue with my joke?
posted by maxsparber at 9:21 AM on February 6, 2015 [1 favorite]
posted by maxsparber at 9:21 AM on February 6, 2015 [1 favorite]
I think I was getting confused between the Ellison story and the movie Alligator too and oh god I just can't
posted by maxsparber at 9:22 AM on February 6, 2015 [1 favorite]
posted by maxsparber at 9:22 AM on February 6, 2015 [1 favorite]
It's Q the Winged Serpent bacteria.
Whew. Hail mary-ed it.
posted by maxsparber at 9:23 AM on February 6, 2015
Whew. Hail mary-ed it.
posted by maxsparber at 9:23 AM on February 6, 2015
Let's talk about sex baby
It's about G, A-T-C,
Let's talk about all the good genes and the bad genes in this petri sea
Bacteria: we do it horizontally. Jeff Ross has a somewhat bad joke about wishing he could transfer and obtain skills from sex. Bacteria do it errrday, it occerrd to may
posted by aydeejones at 9:40 AM on February 6, 2015 [3 favorites]
It's about G, A-T-C,
Let's talk about all the good genes and the bad genes in this petri sea
Bacteria: we do it horizontally. Jeff Ross has a somewhat bad joke about wishing he could transfer and obtain skills from sex. Bacteria do it errrday, it occerrd to may
posted by aydeejones at 9:40 AM on February 6, 2015 [3 favorites]
"My money is on C.H.U.D."
The smart money is always on C.H.U.D.
posted by komara at 9:42 AM on February 6, 2015 [1 favorite]
The smart money is always on C.H.U.D.
posted by komara at 9:42 AM on February 6, 2015 [1 favorite]
Makes one pause and reconsider riding the subway with no pants.
posted by ZeusHumms at 9:54 AM on February 6, 2015 [7 favorites]
posted by ZeusHumms at 9:54 AM on February 6, 2015 [7 favorites]
But how does this unknown DNA react to the presence of positive or negative emotion, particularly Jackie Wilson?
posted by fifteen schnitzengruben is my limit at 9:59 AM on February 6, 2015 [4 favorites]
posted by fifteen schnitzengruben is my limit at 9:59 AM on February 6, 2015 [4 favorites]
Oh that's also good
posted by maxsparber at 10:00 AM on February 6, 2015
posted by maxsparber at 10:00 AM on February 6, 2015
Link to the paper (likely paywalled, sorry!)
The "half couldn't be assigned to an organism" thing is maybe a little misleading. It's probably not the case that these reads are mapping to some completely unknown group of microbes. They actually did shotgun sequencing here, which is awesome and more powerful than previous approaches that only look at a single highly conserved gene (often the 16S subunit of the ribosome), but what that means is they get tiny fragments of the entire genome. So half of those fragments didn't align to a genome -- but for them to align to anything we'd have to have a close-ish homolog of that gene already sequenced in existing databases. That's still very cool and means we aren't close to having a full repertoire of gene families sequenced, which means there's a ton to learn about what biochemistry (and other functions) these microbes are actually performing. But it's also in line with other things we know: we know the number of sequenced whole microbial genomes is tiny relative to the total, and probably non-representative of the diversity present in the environment (historically there's been a strong bias towards lab-culturable organisms, for obvious reasons), and other metagenomic analyses (e.g.) have found similar percentages of unmapped reads looking at, for example, gut metagenomes.
Still a very interesting study and I'd love to look at their data.
posted by en forme de poire at 10:37 AM on February 6, 2015 [1 favorite]
The "half couldn't be assigned to an organism" thing is maybe a little misleading. It's probably not the case that these reads are mapping to some completely unknown group of microbes. They actually did shotgun sequencing here, which is awesome and more powerful than previous approaches that only look at a single highly conserved gene (often the 16S subunit of the ribosome), but what that means is they get tiny fragments of the entire genome. So half of those fragments didn't align to a genome -- but for them to align to anything we'd have to have a close-ish homolog of that gene already sequenced in existing databases. That's still very cool and means we aren't close to having a full repertoire of gene families sequenced, which means there's a ton to learn about what biochemistry (and other functions) these microbes are actually performing. But it's also in line with other things we know: we know the number of sequenced whole microbial genomes is tiny relative to the total, and probably non-representative of the diversity present in the environment (historically there's been a strong bias towards lab-culturable organisms, for obvious reasons), and other metagenomic analyses (e.g.) have found similar percentages of unmapped reads looking at, for example, gut metagenomes.
Still a very interesting study and I'd love to look at their data.
posted by en forme de poire at 10:37 AM on February 6, 2015 [1 favorite]
Half the DNA on the NYC Subway Matches No Known Organism
During the avian flu crisis a few years back I happen to board a plane with an infection disease specialist from the Mayo Clinic and started asking him about his take on the feared epidemic. I also asked him a question I had been curious about for some time and that was to what extent did we know whether we had identified all the microorganisms in our environment, since there may be many that can't be cultured or that haven't been identified with a disease. He was quite frank about the fact that we have no idea. There may be hundreds of thousands of significant microorganisms that have never been recognized. When we look for their presence in disease, we are looking for those already identified and tend to ignore any that don't conform to our expectations. So perhaps this would not be so surprising even if we had genotyped all known organisms.
posted by Mental Wimp at 12:55 PM on February 6, 2015
During the avian flu crisis a few years back I happen to board a plane with an infection disease specialist from the Mayo Clinic and started asking him about his take on the feared epidemic. I also asked him a question I had been curious about for some time and that was to what extent did we know whether we had identified all the microorganisms in our environment, since there may be many that can't be cultured or that haven't been identified with a disease. He was quite frank about the fact that we have no idea. There may be hundreds of thousands of significant microorganisms that have never been recognized. When we look for their presence in disease, we are looking for those already identified and tend to ignore any that don't conform to our expectations. So perhaps this would not be so surprising even if we had genotyped all known organisms.
posted by Mental Wimp at 12:55 PM on February 6, 2015
I'm just gonna leave this here
posted by feckless fecal fear mongering at 4:48 PM on February 6, 2015 [2 favorites]
posted by feckless fecal fear mongering at 4:48 PM on February 6, 2015 [2 favorites]
I got home just now and reached into the fridge for a snack. I was pulling apart some fresh mozzarella with my bare fingers when I realized - my god, I'm the one contaminating 7th Av with Italian Cheese Bacteria!
posted by moonmilk at 5:22 PM on February 6, 2015 [1 favorite]
posted by moonmilk at 5:22 PM on February 6, 2015 [1 favorite]
They still haven't found the Wookie have they?
That was BART. Other coast.
posted by radwolf76 at 5:59 PM on February 6, 2015 [1 favorite]
That was BART. Other coast.
posted by radwolf76 at 5:59 PM on February 6, 2015 [1 favorite]
EmpressCallipygos: I pass through three, and sometimes four, subway stations in the course of a given day. And every single one of them is showing up as having some kind of "toxic cleanup".
Don't forget us when you're a mutant!!!!! <3333
posted by Deoridhe at 6:26 PM on February 6, 2015
Don't forget us when you're a mutant!!!!! <3333
posted by Deoridhe at 6:26 PM on February 6, 2015
Enterococcus gallinarum
Associated with Heart-valve infections
Oh, for fuck's sake.
Alright, I'll file it under "things I'll worry about next time I get a little hearburn."
posted by mandolin conspiracy at 7:09 PM on February 6, 2015
Associated with Heart-valve infections
Oh, for fuck's sake.
Alright, I'll file it under "things I'll worry about next time I get a little hearburn."
posted by mandolin conspiracy at 7:09 PM on February 6, 2015
I'm just gonna leave this here
posted by feckless fecal fear mongering
Eponysterical?
posted by gusandrews at 8:11 PM on February 6, 2015 [4 favorites]
posted by feckless fecal fear mongering
Eponysterical?
posted by gusandrews at 8:11 PM on February 6, 2015 [4 favorites]
I was thinking more like eponyvomitous, but eh.
posted by feckless fecal fear mongering at 9:19 PM on February 6, 2015
posted by feckless fecal fear mongering at 9:19 PM on February 6, 2015
This guy in my writers group writes unfortunate sex scenes from a woman's point of view. Last month I said the harsh but maybe true thing that the sex scenes felt like a male fantasy rather than being true to the characters.
So, this week's submission, he wrote about a romance blossoming when a dude gets a blow job on the Philly El. I don't even know what to say about that. Somebody threw up on me once on the Philly El. The idea of exposed genitals on the El is a little terrifying. Although somebody gave birth on the El a few weeks back. Still, not an advertisement for fucking on the el.
posted by angrycat at 4:20 AM on February 7, 2015
So, this week's submission, he wrote about a romance blossoming when a dude gets a blow job on the Philly El. I don't even know what to say about that. Somebody threw up on me once on the Philly El. The idea of exposed genitals on the El is a little terrifying. Although somebody gave birth on the El a few weeks back. Still, not an advertisement for fucking on the el.
posted by angrycat at 4:20 AM on February 7, 2015
Cue John Carpenter. The plot nearly writes itsself.
posted by Nanukthedog at 3:27 PM on February 7, 2015
posted by Nanukthedog at 3:27 PM on February 7, 2015
MIB.
posted by SteveLaudig at 5:01 AM on February 8, 2015
posted by SteveLaudig at 5:01 AM on February 8, 2015
« Older ENDLESS AMUSEMENT | "Just a Little Heart Attack" Newer »
This thread has been archived and is closed to new comments
posted by infini at 8:01 AM on February 6, 2015 [4 favorites]