How Many Bits Does It Take To Kill You?

pegr writes "Andrew 'bunnie' Huang, Reverse Engineer, XBox hacker, and generally smart guy, muses over the H1N1/swine flu virus as only a reverse engineer can: 'I now know how to modify the virus sequence to probably make it more deadly.' Not that he would, of course. bunnie has consistently made the esoteric available to us mere mortals, and his overview of the H1N1 virus is a fascinating read from a unique perspective." (Seen today also at the top of Schneier on Security.)

Comments

Increasing mortality is bad for business

[7-Vodka]

Making a virus more 'deadly' is usually not very good for the virus. If it's host dies, so does it's habitat. Not to mention the host can no longer really spread it.

The Epstein-Barr virus, now there is a successful virus.

Re:Increasing mortality is bad for business

[binkzz]

It can be deadly and still be successful, just so long as it's not very fast (e.g. HIV).

Re:Increasing mortality is bad for business

[Mindcontrolled]

And, unfortunate for your vastly overrated modding, neither of those were viruses, but bacteria.

fascinating!

[Trepidity]

If only biologists had thought of the idea of treating DNA/RNA sequences as data, and then analyzing their properties statistically and computationally, with an eye towards what effects different modifications to the sequences might be predicted to have. We might call this field something fancy like "biological informatics".

Re:fascinating!

[Trepidity]

(Replying to my own comment.)

That said, it's a quite well-written tutorial-style article with engaging prose that tackles a number of the relevant issues. I just balked at the "reverse engineer takes on biology" angle, as if that were something biologists had never thought of.

Re:fascinating!

[RobertB-DC]

If only biologists had thought of the idea of treating DNA/RNA sequences as data, and then analyzing their properties statistically and computationally, with an eye towards what effects different modifications to the sequences might be predicted to have. We might call this field something fancy like "biological informatics".

Hahaha, I'm sure the biological informaticians are laughing their asses off. Kinda like we computer geeks did when the Not So Hon. Ted Stevens described the Internet as a "series of tubes".

Meanwhile, though, I'm really enjoying the analogies that "bunnie" draws between DNA/RNA and computer bits. You see, I know a thing or two about computer bits, and ports, and stuff like that. And I know that DNA encodes proteins. But I didn't make the connection the way "bunnie" does, with a simple statement like this:

If you thought of organisms as computers with IP addresses, each functional group of cells in the organism would be listening to the environment through its own active port. So, as port 25 maps specifically to SMTP services on a computer, port H1 maps specifically to the windpipe region on a human. Interestingly, the same port H1 maps to the intestinal tract on a bird. Thus, the same H1N1 virus will attack the respiratory system of a human, and the gut of a bird.

That's probably baby science to a biological informatician, just like mapping to port 25 is baby networking to many of us. But for me, it makes the concepts click.

Similarly, we all made fun of the "series of tubes" metaphor, without considering that for most of humanity, an electron is "the size and shape of a small pea" (Heinlein reference). If thinking of the Internet as a bunch of interconnected steampunk-style tubes that can get full (saturated bandwidth) helps a non-techie understand why they can't watch YouTube and play Halo at the same time... well, so much the better.

Re:fascinating!

[Sponge Bath]

Why not just call it "programming"?

To avoid 90 hour work weeks and lousy pay.

How many bits does it take to kill you?

[MBCook]

I don't know, go ask Mr. Owl.

Port H1 maps specifically to the windpipe region

[quatin]

Sounds like we need a firewall.

Re:Rats Leaving A Sinking Ship

[Lord Ender]

That's not how it works. Viruses don't all-of-a-sudden start to mutate when they "need" to. They mutate all the time. If a virus could "jump ship" to another species, it is most likely to do that when its first host species is common, not when that species is going extinct.

Your post is an example of a bad analogy substituting for intelligence. That's a common mistake. It's sort of like when your car won't start...

more bioinformatics for beginners

[cariaso1]

http://ds9a.nl/amazing-dna/ is a wonderful comparison of DNA to code

Re:It's humbling that I could be killed by 3.2kbyt

[interkin3tic]

It would actually take less than that, though it wouldn't spread the same way. Remember that prions are proteins that can kill you rather than whole viruses. The protein that gets misfolded in Bovine Spongiform Encephalopathy (or mad cow) seems to be called just Prion protein and is only 253 amino acids. If bunnie is correct and one amino acid = 6 bits, then thats 1,518 bits. "Bit calculator" tells me that would be 0.185 kbytes.

Granted, this wouldn't be airborne death, would be extremely slow, and wouldn't cause a pandemic, but still, far less data.

Even if you were to go the viral route, at least one virus is tricky in that it produces multiple proteins from overlapping reading frames. That is, the same sections of RNA genome (sendai uses RNA instead of DNA) is read in multiple ways to make different functional proteins, one protein might be formed from reading AUG GAU GGG CAG, which would make the amino acid sequence MDGQ, but that could aso be read as A UGG *AUG* GGC AG where the starred AUG is the start, making a protein of MG. I find that pretty cool, because as Carl Sagan pointed out, try doing that with english. "Romancement to get her" can be spaced differently to produce "roman cement together" is the longest he could come up with and it doesn't even make sense. Viruses make whole proteins that work. Anyway, the point of all that was that viruses can in some cases double up, so it would take even fewer nucleotides to produce the same amount of protiens.

Re:It's humbling that I could be killed by 3.2kbyt

[Ihmhi]

It's humblings that I could be killed by 3.2kbytes

3.2 kbytes should be enough to kill anyone.

Another interesting observation

[maxwell demon]

Looking at the amino acid and codon table I noticed another interesting point: The triples which code for the same amino acid typically differ only in the last base. Indeed, this can be made stronger: Except for the STOP codon, in each set of codons with no more than four members, the first two bases are always the same (for those with more than four codons that's of course not possible). Moreover, quite a few amino acids have exactly four codons which differ only in the last base, i.e. the amino acid is completely and unambiguously determined by the first two bases alone. Indeed, one can rearrange this into the following 16-entry table:

codon set ... amino acid(s)
  AA* ......... N (T/C) or K (A/G)
  AC* ......... T
  AG* ......... S (T/C) or R (A/G)
  AT* ......... I (T/C/A) or M (G)
  CA* ......... H (T/C) or Q (A/G)
  CC* ......... P
  CG* ......... R
  CT* ......... L
  GA* ......... D (T/C) or E (A/G)
  GC* ......... A
  GG* ......... G
  GT* ......... V
  TA* ......... Y (T/C) or STOP (A/G)
  TC* ......... S
  TG* ......... C (T/C) or W (G) or STOP (A)
  TT* ......... F (T/C) or L (A/G)

Note how many lines only have one entry on the right hand side. Could this mean the genetic code evolved from a two-base version (with only 15 amino acids) to the current three-base version?