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.

Re:Increasing mortality is bad for business

[Anonymous Coward]

The second-most successful virus was the one that struck the Roman Empire circa 600 A.D. and wiped-out about a third of the population.

The most-successful virus struck Europe in the mid-1200s, killed 40% of the people

Maybe. But where are they now?

Re:Increasing mortality is bad for business

[Otto]

Depends on how you define "deadly", of course. Making it more easily transmitted would be better for the virus, for example.

Re:Increasing mortality is bad for business

[Beardo the Bearded]

Actually, HIV has become less deadly as time goes by. There's been selective pressure for it to kill the hosts less slowly:

http://health.dailynewscentral.com/content/view/1716/

Re:Increasing mortality is bad for business

[PCM2]

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.

Be careful with that kind of thinking, because it's not strictly true. There's an oft-repeated saying that all diseases will naturally become less deadly over time because it doesn't pay to kill your host -- but in some cases it does pay.

Consider something like cholera. Cholera gives you horrific diarrhea and vomiting, and the resulting dehydration can kill you pretty quickly, especially if you're very young or otherwise infirm. Going by the above-stated theory, that would normally be bad -- except that cholera exists in all your excretions, and other people can catch it from coming into close contact with those excretions. What's more, the normal route of infection is via contaminated water supply -- so if your excretions can make it back to the water supply, more's the better for cholera. Who cares if you drop dead?

Similarly, malaria doesn't need you up and walking around to infect people. You can be lying on your deathbed and a mosquito can still fly in through the window, bite you, and then fly off and bite someone else. That's why, though malaria has been known since the dawn of human history, it never seems to become less of a health threat to humans. There's simply no evolutionary pressure in that direction.

True, neither cholera or malaria is caused by a virus. But I just wanted to point out that the "evolution favors keeping your host alive" theory is rather too simplistic for the bigger picture of human disease.

 

Re:Increasing mortality is bad for business

[bcmm]

A number of people doubt the bacterial bubonic plague/rats/fleas explanation due to the rapid manner of spread of the disease. A viral haemorrhagic fever, possibly airborne, is given as a more likely alternative.

The rapid spread would have been in part due to refugees fleeing the infected areas, unaware that they were incubating the disease. The plague is also potentially airborne, spreading to the lungs in severe cases and thereby allowing direct transmission between humans, which would allow the refugees to infect locals very fast.

Also, the reason the Black Death is thought to have been caused by bubonic plague is that there are many contemporary illustrations and descriptions of the victims, and they look a lot like modern plague victims. In an admittedly brief search, I couldn't find any reference to VHF producing buboes. Any alternative cause for the Black Death would surely have to produce those in at least a very sizable proportion of cases.

Re:Increasing mortality is bad for business

[Beardo the Bearded]

You don't know what the phrase "selective pressure" means, do you?

Viral strains that are less deadly will reproduce for a longer time in the host before the host dies. In the case of HIV, that means the host will have more sexual partners, giving that less deadly strain more hosts to infect. This less deadly strain then has more hosts with a longer lifespan, developing a cycle of selective pressure upon HIV wherin those strains that are less virulent become more likely to reproduce.

Re:Increasing mortality is bad for business

[danudwary]

While that's true, it's kind of stupid. You might as well say guns don't kill people, they shoot bullets that break important organs. Tuberculosis doesn't kill you, the lack of functioning lungs did. It wasn't that brain cancer that got you, it was the lack of a a cerebellum. Come on.

Re:Increasing mortality is bad for business

[FiloEleven]

In the case of HIV, that means the host will have more sexual partners, giving that less deadly strain more hosts to infect.

So, wait...getting the HIV will guarantee you more sexual partners? No wonder it's so popular!

Re:Increasing mortality is bad for business

[TaggartAleslayer]

You started off strong enough, then held on ok for a bit, then lashed out at programmers, logic, and liberals while being apologetic at the same time and never really making a strong point other than when you got to your defense of philosophy as you see it at the end. All, in all, I give it a B-. Now find your enter key and someone other than me might actually read that long son of a bitch of a paragraph you just shat out.

Re:Increasing mortality is bad for business

[PCM2]

For AIDS, you only need to have unprotected sex a few times and the virus will be successful. SO if you don't notice symton for a coupl of years, and you are sexually active, that's more then enough for the virus to propagate.

Actually, AIDS is not considered a highly infectious disease. Seriously. If you're having unprotected vaginal sex, it might take a great many times before the virus is successfully transmitted from a woman to a man. Scientists believe the actual rate of infection in such cases may be less than 1 percent. Sooooooooo.... feel better? Wanna risk it? Didn't think so.

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!

[Trepidity]

Yeah, I probably should've been nicer. =] The Slashdot summary is actually more objectionable than the article is: as you point out, the metaphors in the article are quite well done. If you don't view it as "l33t XBox hacker discovers how to haxx0r viruses", but instead as "engaging tech writer uses computer terminology to explain how viruses work", it's much better.

Re:fascinating!

[Sponge Bath]

Why not just call it "programming"?

To avoid 90 hour work weeks and lousy pay.

Re:fascinating!

[Bakkster]

>>>"biological informatics".

Why not just call it "programming"? Whether you're writing code for machine made of sand (silicon) or chemicals should not matter one bit.

Probably for the same reason we separate mathematicians from physicists, and chemists from biologists. There's a lot of specificity in each field that makes specialization worthwhile. Sure, biology is 'just' macro-scale chemistry (which, in turn, is 'just' macro-scale physics), but there are special cases that only happen in cells, as well as a lot of things that never happen in cells.

That doesn't mean that it's a bad thing to have someone with a foot firmly in both fields (computational physics, or biochemistry), but specializing is what allows computer engineers to spend more time on transistors than proteins, while the bioinformatics students learn about RNA without needing to bother with JAVA.

Re:fascinating!

[Vornzog]

I just balked at the "reverse engineer takes on biology" angle, as if that were something biologists had never thought of.

Interesting that you should say that - the traditional biologists, by and large, don't think of doing things like this. Bioinformatics is a catch-all for any number of different disciplines, all in relative infancy, and almost always pioneered by people outside the traditional biology arenas.

I studied biochemistry in college, with a ton of extra math, physics, and computer science. Then I did a PhD developing DNA diagnostics for flu (awarded by the chem department, but I was a full time programmer and part time bench chemist).

My first paper was applying Shannon informational entropy theory to big alignments of flu DNA to look for conserved regions. No one around me had a clue what the hell I was on about. The code I wrote for that paper is still used by the Flu Division at CDC.

The only place where this article went wrong was in assuming that traits are trivially mapped to sequences. In practice, it almost always turns out to be extremely non-trivial, and in flu it almost doesn't work at all (the biologist figured out the easy cases years ago). Never the less, most really good science starts with some assumption that looks to be extremely over-simplified, and turns out to be very predictive.

There is going to be a lot of room for hackers and coders in the biological sciences in coming years - computer science has solutions to problems the traditional biologists haven't even realized are problems yet. Data storage and retrieval to support high-throughput sequencing labs, new algorithms for large-scale data analysis, instrument networking for lab automation. The job postings will go up just as soon as the biologists figure out that they have a problem...

How many bits does it take to kill a human?

[itsybitsy]

How many bits does it take to kill a human? Bits of what is the real question?

Bits of information? Bits of bullets? Bits of concrete? Bits of glass? Bits of a virus?

They can all get the job done given the right, er wrong, context.

3.2KiB of data with the flu eh?

How about three bytes, 24 bits, uttered from the mouth of Bush? "War"! That killed a whole bunch of people with a lot less information. Ok, sure there was lots of supporting info.

Many people have died from a lot fewer bits than the flu needs.

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...

Re:Port H1 maps specifically to the windpipe regio

[2names]

Only if the firewall also performs deep packet inspection. Many bad critters (viruses/bacteria) enter the system by making our firewall(s) think they are innocuous by externally looking link other good critters. It is the payload that is the real problem. If we could teach the body to somehow read the payload before docking with the receptors we could be disease (contracted from viruses/bacteria) free.

more bioinformatics for beginners

[cariaso1]

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

Re:The best book is still the one not on the shelv

[Volante3192]

Yes, troll feeding is bad, but honestly,

that there was a Swine Flu vaccine back in the 1970's that caused a 300% mortality rate on all the "volunteers,"

This alleged vaccine killed the subject, revived them, killed them a second time, revived them again, and finally killed them off (for good) a third time?

Math is hard, clearly.

Re:The best book is still the one not on the shelv

[mikael_j]

Actually, they had a control group who were given a placebo who also died even though they had not even been given the vaccine. Also, the researchers died and through luck these two groups were each the exact same size as the group given the vaccine, thus the 300% mortality rate.

/Mikael

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?

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

[fractoid]

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.

So you're saying that it would take just 11 posts on Twitter to kill someone?

One bit

[russotto]

I'm pretty sure one bit can kill you... if your logic levels are 50,000V and -50,000V, anyway.