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.)

Rats Leaving A Sinking Ship

[mindbrane]

As we extinguish species by the ark load it's worth musing where all their on board viruses and bacterium will land when they jump ship onto a new species. Reminds me of the ship of sick sailors who landed in Italy with the first boat load of rats bearing the plague. Supposedly many of the viruses that now plague us have adapted to us by way of our domestic livestock, especially fowl. We may be setting the table for the little critters with our obsessive need for antibiotics and wiping all indoor surfaces down with lethal cleaners. The Swiss did some research and found that farm kids raised tending livestock had stronger immune systems than Swiss city kids raised in sanitized urban housing.

It takes only 1 bit to kill a human

[aepervius]

Change 1 of the DNA base and the embryo cannot grow to completion. Change a base and a cancer can suddenly develop and go awry (for example, kill the apoptose system of the cells). Kill one bit in the mytochondrial DNA and you probably get the same. I am not a biologist , and I am sure there are a lot of redundant gene, but some might not.

Re:Increasing mortality is bad for business

[Mindcontrolled]

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

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.

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:Rats Leaving A Sinking Ship

[Lord Ender]

Beneath your amusing impotent rage, it looks like you still don't understand. Let me explain: More viruses -> more mutations -> more likely to jump species. Therefore, a higher population of the original host animal means a higher probability of cross-species mutations.

Re:Increasing mortality is bad for business

[godel_56]

The most-successful virus struck Europe in the mid-1200s, killed 40% of the people, and created a shortage of labor that allowed the serfs to free themselves and demand pay. Thus the middle class was born.

What did these viruses have in common? They were very virulent, killing the host quickly, but it didn't matter because their RNA code was spread via fleas.

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.

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

[inKubus]

Coral Cache [nyud.net] of the site, not running super fast but it'll get there.

One bit

[russotto]

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

Re:Another interesting observation

[Dungbeetle]

Actually, it's more about efficiency and called the "wobble position". Here's a wikipedia paste since i'm lazy:
--
In the genetic code there are 4^3 = 64 possible codons (tri-nucleotide sequences). For translation each of these codons requires a tRNA molecule with a complementary anticodon. If each tRNA molecule paired with its complementary mRNA codon using canonical Watson-Crick base pairing, then 64 types (species) of tRNA molecule would be required. Since most organisms have fewer than 45 species of tRNA[1], some tRNA species must pair with more than one codon. In 1966 Francis Crick proposed the Wobble hypothesis to account for this.
--
http://en.wikipedia.org/wiki/Wobble_base_pair [wikipedia.org]

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.

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

[interkin3tic]

The coat proteins do more than just carry the DNA to your cells, they allow the virus to actually get inside the cell. That's a pretty major part of a virus, the DNA itself is not going to get inside a cell to produce an infection. There are also more proteins inside many viruses that are essential HIV has several for example. [doctorspiller.com] Influenza does too [respirator...sts.com.sg]. So it requires more than just the data to kill you.

Viroids [wikipedia.org] are infectious particles that are just nucleotides, just the data. All the viroids that we know of though infect plants, not humans. That wiki page mentions Hepatitis D as viroid like, but it hitches a ride on another hepatitis, without the viral proteins of that virus it can't infect.

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

[Ubahs]

You're right, of course, everything you said I pretty much hinted at, however. I wasn't wanting to go too in debt (my mistake).

"The coat proteins do more than just carry the DNA to your cells, they allow the virus to actually get inside the cell." == "The outer coating (proteins) are just the vessel to carry the DNA into your cells"
The protein coat, quite often, mimics a molecule that triggers a cell to eat the virus. Granted, that's just one of the methods various virii (viruses?) use.

"There are also more proteins inside many viruses that are essential HIV has several for example." == "Some, however, come with their own spiffy enzymes that embed DNA into your genome so you can make plenty more..."
This being the exact mechanism that HIV embeds itself into a genome. I'm sure you know that an enzyme is a protein (although, technically a RNA enzyme is not a protein...)

I was poorly arguing that it's the data that one has to be worried about in this case. Free-floating DNA can make its way into a cell, it's rare, but it can happen ("the hard part - but can happen easily sometimes"). I should have been a proper biologist and clarified we're talking eukaryotic cells, bacteria pick up random DNA all the time and do it gleefully (note: bacteria do not contain glee). Bacteria then can run the DNA, eat the DNA, whatever it wants to do.

Once there, the data/DNA then creates havoc by existing, the cell's machinery follows the destructive data and starts to build until it dies (doesn't always die). It builds proteins, which are used to build more virii (viruses?) duplicates more DNA/RNA, the virus self-assembles, leaves and continues on with a nice and shiny protein-coat (or whatever it wants to coat itself with, sometimes parts of you).

Much like a computer virus (DNA) embedded in a program (cell). Normal program instructions are ran, the CPU comes across viral opcodes - runs those too - then continues on like nothing happened...assuming it's a well written computer virus. All the business about transferring a virus via flashdisk, floppy, email, etc (protein coat) - while essential - is secondary to the viral payload itself, the code/data/dna/rna. In my opinion...