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World of Science: 50% of DNA from NYC subways unknown

 
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Darqcyde



Joined: 11 Jul 2006
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PostPosted: Fri Feb 06, 2015 2:20 am    Post subject: World of Science: 50% of DNA from NYC subways unknown Reply with quote

Half the DNA on the NYC Subway Matches No Known Organism

Sarah Zhang Today 7:40pm

Quote:
The results of a massive new DNA sequencing project on the New York City subway have just been published. And yup, there's a lot of bacteria on the subway—though we know most of it is harmless. What's really important, though, is what we don't know about it.

The PathoMap project, which involved sampling turnstiles, benches, and keypads at 466 stations, found 15,152 life-forms in total, half of which were bacterial. The Wall Street Journal has created a fun, interactive microbial map of the subway out of the data, showing where on the lines the bacteria "associated with" everything from mozzarella cheese to staph infections was found.

But "associated with" is a pretty fuzzy term that runs up against the limits of science. In the past few years, genetic sequencing has become vastly more powerful and cheap, making metagenomic analyses possible. This means we can take all of the DNA in an environmental sample—human, plant, bacteria, cockroach, whatever—and sequencing the hell out of it.

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?

Even the best technologies we have now are ultimately crude tools to grope at a vast, unseen world. It maybe be hard to intuit whether it make sense for Acinetobacter or Enterococcus to be on the subway, but the research team found plenty of non-microbial DNA, too, and a lot of it didn't make sense. According to the WSJ, human DNA was prevalent, as were beetle and fly DNA. Those make sense. (We actually don't know about cockroaches because their genome hasn't been sequenced yet.)


Full story: http://gizmodo.com/half-the-dna-on-the-nyc-subway-matches-no-known-organis-1684045880
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Dogen



Joined: 10 Jul 2006
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PostPosted: Fri Feb 06, 2015 2:50 am    Post subject: Reply with quote

That interactive map is pretty cool. I started out clicking on stations I'd been to, and then to stations I'd heard on Law & Order, and then I started looking for the one with the most human DNA. Fun times.
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Sam



Joined: 09 Jul 2006
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PostPosted: Fri Feb 06, 2015 3:38 am    Post subject: Reply with quote

yeah don't worry, we got some lovecraftian Old God shit all over the MBTA that can be used to battle this MTA shit if it starts congealing into a macrobiome

and trust me

our shit will win
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KillAllMen



Joined: 24 Mar 2014
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PostPosted: Fri Feb 06, 2015 3:49 am    Post subject: Reply with quote

Sam wrote:
some lovecraftian Old God shit all over the MBTA


Poo'thulhu strikes again!
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Sam



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PostPosted: Fri Feb 06, 2015 7:58 am    Post subject: Reply with quote

If I say that my somewhat extravagant imagination yielded simultaneous pictures of the red line, a blue line, and a grotesque caricature of mass transit what the green line, nominally, affirms itself as, I shall not be unfaithful to the spirit of the thing. A pulpy, tentacled head surmounted a grotesque and scaly body with rudimentary wings... It represented a monster of vaguely anthropoid outline, but with an octopus-like head whose face was a mass of feelers, a scaly, rubbery-looking body, prodigious claws on hind and fore feet, and long, narrow wings behind. This thing, which seemed instinct with a fearsome and unnatural malignancy, was at least nineteen minutes late, and God pity that who got on for Braintree when was for Alewife they intended... You fear the latent creatures of New York? It is to laugh. Believe me when I say, no matter what macrobiome the unknown MTA bacteria might foment and congeal itself into, it shall find itself no match for what sightless horrors shall conflict with its spread into the darkly waiting North.
— H.P. Lovecraft, "The Call of the MBTA"
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mouse



Joined: 10 Jul 2006
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PostPosted: Sat Feb 07, 2015 1:37 am    Post subject: Reply with quote

Quote:
Initial database searches with subway DNA, for instance, turned up false matches to the Tasmanian devil, the Himalayan yak and the Mediterranean fruit fly—all creatures highly unlikely to be found in a New York transit system.


well, now, i'm highly disappointed - from the stories i had heard, i thought things like yaks would be among the less-surprising subway denizens.

(but just to note: mediterranean fruit flies are a common pest on fruit here in CA - someone may have just been munching on imported citrus)
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