13 ms·

A sample of the Ebola now raging in West Africa has, by recent count, 18,959 letters of code in its genome; this is a small genome, by the measure of living thi

A sample of the Ebola now raging in West Africa has, by recent count, 18,959 letters of code in its genome; this is a small genome, by the measure of living things. Does this mean mean Ebola is essentially about 38 kilobytes?

spacehome 12y ago
Yes. I wonder if being so incredibly small means that replication is more efficient and intense and is therefore a strong factor behind why it's so virulent.
- harshreality 12y ago
  I don't think that's the most important factor. Influenza, along with ebola and rabies, is small, while smallpox is big. http://www.lehigh.edu/~jas0/viralgenomes.html http://www.lehigh.edu/~jas0/viralgenomes.html
netcraft 12y ago
something like that: http://www.ncbi.nlm.nih.gov/nucleotide/NC_002549 http://www.ncbi.nlm.nih.gov/nucleotide/NC_002549 (I get 21K)
pygy_ 12y ago
4740 bytes, actually. There are only four nucleotides ("letters") in RNA. You can encode them with two bits.
throwaway_yy2Di 12y ago
38 kilobits = 4.7 kB, but yes. Here's the complete genome of the pandemic strain (scroll down a bit): http://www.ncbi.nlm.nih.gov/nuccore/KJ660346 http://www.ncbi.nlm.nih.gov/nuccore/KJ660346 Here's the paper sequencing it. ([edit]: I just realized the New Yorker article is largely about this exact paper -- I commented before reading, sorry). Note that five of the authors died before publication; there's a short tribute accompanying it. http://www.sciencemag.org/content/345/6202/1369.full http://www.sciencemag.org/content/345/6202/1369.full http://news.sciencemag.org/health/2014/08/ebolas-heavy-toll-study-authors http://news.sciencemag.org/health/2014/08/ebolas-heavy-toll-... Here's another phylogeny of this strain, including github repo: http://currents.plos.org/outbreaks/article/phylogenetic-analysis-of-guinea-2014-ebov-ebolavirus-outbreak-2/ http://currents.plos.org/outbreaks/article/phylogenetic-anal...
- ddlatham 12y ago
  Oops, thanks for the bits to bytes correction. It is simply incredible to me that it could be so small (in an information sense). This article (gzipped) is 22KB, more than 4 times as much information.
  - rads 12y ago
    Yeah, but don't forget the complexity of the hardware you need to run ebola versus a website. Our bodies provide most of the implementation details.
    - Florin_Andrei 12y ago
      Right. It's so much context dependent that the "hardware" of a different animal may react very differently to it - perhaps even ignoring it altogether. The genetic information is really the 4.8 kB of "code" PLUS the entire information already contained in the cellular hardware reading it. One doesn't make sense without the other. At the very bottom, the whole thing depends on the laws of quantum mechanics in this universe, governing the minute details of molecular interaction. That, too, should be considered to go into the "code". Make a tiny change to the Plank constant, and the Zaire ebolavirus code will do something very different.
    - JoeAltmaier 12y ago
      Thank you for saying that! Its so often repeated that our DNA contains the entire program for a human being. That's patently false. The cellular machinery provides almost all of the OS; DNA is just a script. I liken DNA to a paper tape containing one of two punches: MAN or MOUSE. Feed it into a bio-replicator and get a man or a mouse. Does the paper tape define the man? Of course not.
      - ghkbrew 12y ago
        > I liken DNA to a paper tape containing one of two punches: MAN or MOUSE I don't think that really captures it. Yes, it requires external machinery to actually do anything, but DNA is much more information dense and carries much more of an exact definition of the organism to be produced. Personally, I prefer the analogy of compiler source code. Sure, it can't do anything on its own. But it defines how an working external system (another compiler or an functional cellular environment) can produce a second possibly different system
deleted 12y ago
[deleted]
deleted 12y ago
[deleted]
scottious 12y ago
Yes, but also no. I work at The Broad Institute and I deal with these genomes all the time. Long story short: there's tons of redundant data in these genomes because of the imperfect nature of sequencing so the real file size is many times bigger than that. Though in theory if we had perfect sequencing then it'd be around that size.
- Terr_ 12y ago
  For some reason I think of X-ray crystallography: A large number of different pictures go into reaching a conclusion which is much simpler to convey.

spacehome 12y ago

Yes. I wonder if being so incredibly small means that replication is more efficient and intense and is therefore a strong factor behind why it's so virulent.

harshreality 12y ago
I don't think that's the most important factor. Influenza, along with ebola and rabies, is small, while smallpox is big. http://www.lehigh.edu/~jas0/viralgenomes.html http://www.lehigh.edu/~jas0/viralgenomes.html

netcraft 12y ago

something like that: http://www.ncbi.nlm.nih.gov/nucleotide/NC_002549 http://www.ncbi.nlm.nih.gov/nucleotide/NC_002549 (I get 21K)

pygy_ 12y ago

4740 bytes, actually. There are only four nucleotides ("letters") in RNA. You can encode them with two bits.

throwaway_yy2Di 12y ago

38 kilobits = 4.7 kB, but yes. Here's the complete genome of the pandemic strain (scroll down a bit): http://www.ncbi.nlm.nih.gov/nuccore/KJ660346 http://www.ncbi.nlm.nih.gov/nuccore/KJ660346 Here's the paper sequencing it. ([edit]: I just realized the New Yorker article is largely about this exact paper -- I commented before reading, sorry). Note that five of the authors died before publication; there's a short tribute accompanying it. http://www.sciencemag.org/content/345/6202/1369.full http://www.sciencemag.org/content/345/6202/1369.full http://news.sciencemag.org/health/2014/08/ebolas-heavy-toll-study-authors http://news.sciencemag.org/health/2014/08/ebolas-heavy-toll-... Here's another phylogeny of this strain, including github repo: http://currents.plos.org/outbreaks/article/phylogenetic-analysis-of-guinea-2014-ebov-ebolavirus-outbreak-2/ http://currents.plos.org/outbreaks/article/phylogenetic-anal...

ddlatham 12y ago
Oops, thanks for the bits to bytes correction. It is simply incredible to me that it could be so small (in an information sense). This article (gzipped) is 22KB, more than 4 times as much information.
- rads 12y ago
  Yeah, but don't forget the complexity of the hardware you need to run ebola versus a website. Our bodies provide most of the implementation details.
  - Florin_Andrei 12y ago
    Right. It's so much context dependent that the "hardware" of a different animal may react very differently to it - perhaps even ignoring it altogether. The genetic information is really the 4.8 kB of "code" PLUS the entire information already contained in the cellular hardware reading it. One doesn't make sense without the other. At the very bottom, the whole thing depends on the laws of quantum mechanics in this universe, governing the minute details of molecular interaction. That, too, should be considered to go into the "code". Make a tiny change to the Plank constant, and the Zaire ebolavirus code will do something very different.
  - JoeAltmaier 12y ago
    Thank you for saying that! Its so often repeated that our DNA contains the entire program for a human being. That's patently false. The cellular machinery provides almost all of the OS; DNA is just a script. I liken DNA to a paper tape containing one of two punches: MAN or MOUSE. Feed it into a bio-replicator and get a man or a mouse. Does the paper tape define the man? Of course not.
    - ghkbrew 12y ago
      > I liken DNA to a paper tape containing one of two punches: MAN or MOUSE I don't think that really captures it. Yes, it requires external machinery to actually do anything, but DNA is much more information dense and carries much more of an exact definition of the organism to be produced. Personally, I prefer the analogy of compiler source code. Sure, it can't do anything on its own. But it defines how an working external system (another compiler or an functional cellular environment) can produce a second possibly different system

deleted 12y ago

[deleted]

deleted 12y ago

[deleted]

scottious 12y ago

Yes, but also no. I work at The Broad Institute and I deal with these genomes all the time. Long story short: there's tons of redundant data in these genomes because of the imperfect nature of sequencing so the real file size is many times bigger than that. Though in theory if we had perfect sequencing then it'd be around that size.

Terr_ 12y ago
For some reason I think of X-ray crystallography: A large number of different pictures go into reaching a conclusion which is much simpler to convey.