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

It takes less bits

[solevita]

To kill a Snow Leopard.

All depends on how you count, I guess...

Re:It takes less bits

[K. S. Kyosuke]

Bits are discrete.

Right, especially if the information transferred is a choice from N options, where N is not a power of two.

Re:It takes less bits

[Doggabone]

"fewer" not "less". Bits are discrete.

Well off topic and far too pedantic, but what the hell. A blog at http://itre.cis.upenn.edu/~myl/languagelog/archives/003775.html references Merriam-Webster's Concise Dictionary of English Usage (MWCDEU) to point out that "less" has been used before plural, countable nouns since the time of King Alfred. It was the opinion of Robert Baker, written in "Remarks on the English Language" in 1770, that "fewer" was preferable. It is unknown how this became the rule, but usage then and now do not conform to the rule.

From the MWCDEU:

If you are a native speaker, your use of less and fewer can reliably be guided by your ear. If you are not a native speaker, you will find that the simple rule with which we started is a safe guide, except for the constructions for which we have shown less to be preferred.

There's a scan of the MWCEDU available from the blog post. Make of it what you will, I found it interesting.

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

[Anonymous Coward]

It's like evolution is the demo coder and humans are the Amigas.

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

[cthulu_mt]

Pamela Anderson sure does get around.

Re:Increasing mortality is bad for business

[nickdwaters]

I don't think "successful" is the word I would use... It is a cliche' that the "course of history" is altered by X or Y events or Z disease. In motion, the future is. Disease is fundamental to evolution.

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

[nycguy]

Mod parent up, please.

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

[Jurily]

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

Did you just call the flu an unsuccessful virus? I dare you to show me two people in Europe or North America who never had it.

However, I'm still not afraid. TFA is right: this is one fast mutating virus. So much in fact, that every possible mutation has appeared already. I'm too lazy do back it up with math, but the numbers should be interesting.

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

[dwye]

> The second-most successful virus was the one that struck the
> Roman Empire circa 600 A.D. because if that virus had not struck,
> the Eastern Roman Emperor's army would have succeeded in his
> mission to reclaim Italy, Rome, and possibly France/Gaul too.

Was this after Narses the court eunuch and general conquered Italy, then let the Lombards attack the North to show the Emperor that he was needed (and committed suicide in shame when they succeeded)?

> he most-successful virus struck Europe in the mid-1200s,
> Thus the middle class was born.

The middle class existed for long before that. It merely improved the lot of peasants for about 60 years (until population levels came back) and created the "Rotten Boroughs" in England (abandoned towns that didn't lose their representation in Commons until the early 19th Century).

Anyway, the common cold beats them in almost any two year period. Further, people continue to catch colds all through their lives.

Now, if the goal of the virus were to wipe out humanity or at least change history, then your viruses would have won. Prove that either was deliberately weaponized, or introduced by aliens making a multi-sense recording for "viewers" in the Galactic Community (to make a season-ending cliffhanger, or else because a new bunch of writers wanted to "reboot" the franchise), and I will accept your definition of successful.

Re:Increasing mortality is bad for business

[dbet]

Did you just solve the unemployment problem? After all, they are the ones who won't get treated for the virus until it's too late.

I'll stop short of the conspiracy theories.

Re:Increasing mortality is bad for business

[gad_zuki!]

>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.

Right, but the modern world, at least in wealthier countries, are fairly hygienic. I dont think Ive ever seen a flea outside the woods. For a virus to be successful in today's world it would probably need to keep the host alive a lot longer. Perhaps this is why we just arent seeing pandemics on this level since around we got a good understanding of germ theory. Toss in modern quarantine options and a extra lethal virus might just burn itself out before it can spread.

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

[divisionbyzero]

Unless you are creating a weapon... Obviously killing someone instantly would be worthless (just use a bomb), but if they could increase the mortality rate while maintaining the contagious period, then some crazy people might find it interesting.

Re:Increasing mortality is bad for business

[PCM2]

Actually, for the Roman Empire one, he may be thinking of the Antonine Plague of 166 A.D., which may have wiped out up to a third of the population, and is believed to have been measles or more likely smallpox (both viruses). Still, I'm not sure if one pandemic outbreak is sufficient evidence for the success of a given disease on an evolutionary scale. After all, we were eventually able to wipe smallpox from the face of the Earth -- something we've tried doing to other diseases with only limited success -- so what does that say about the viability of smallpox overall?

Re:Increasing mortality is bad for business

[brainboyz]

No, he solved the middle class problem. The rich will be taxed to pay for the poor, but middle class will fall between the ability to afford it and the government program eligibility.

Re:Increasing mortality is bad for business

[brainboyz]

Never had it, or never experienced symptoms due to an immune system that squashes the bug before a symptom-causing response is necessary? unless you live in a bubble, I highly doubt you've never been immunized one way or the other.

Re:Increasing mortality is bad for business

[PCM2]

You've never had the flu? Ever? Come now. I had pneumonia when I was four years old, which was almost certainly a complication of the flu. I've probably caught it a dozen times since then.

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

[Volante3192]

I dont think Ive ever seen a flea outside the woods.

You've never had outdoor pets, have you?

Advantage is a wonderful thing...

Re:Increasing mortality is bad for business

[Darinbob]

Yes, let's not hurt the virus or its feelings.

Re:Increasing mortality is bad for business

[frosty_tsm]

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

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

Fixed it for you.

Re:Increasing mortality is bad for business

[antirelic]

Increase propaganda through FUD is pretty bad as well. In relation to the USA.

Regular Flu: Since January, more than 13,000 have died of complications from seasonal flu (April 2009)

Swine Flu: Since January, 10 reported deaths (May 2009)

In 1976, when 40 million people received the H1N1 vaccination over a period of a few months, the incidence of Guillain-Barre syndrome was about one out of 150,000.

http://en.wikipedia.org/wiki/Guillain-Barr%C3%A9_syndrome

"The flu season is upon us. Which type will we worry about this year, and what kind of shots will we be told to take? Remember the swine flu scare of 1976? That was the year the U.S. government told us all that swine flu could turn out to be a killer that could spread across the nation, and Washington decided that every man, woman and child in the nation should get a shot to prevent a nation-wide outbreak, a pandemic." (Mike Wallace, CBS, 60 Minutes, November 4, 1979)

http://www.globalresearch.ca/index.php?context=va&aid=14543

Old tricks with a new dog. Hope for Change. Got it. Is this administration just historically illiterate or are they up to something?

Re:Increasing mortality is bad for business

[profplump]

You're still assuming that "killing the host" happens some non-trivial amount of time after "infecting the host" -- at some point the host won't be able to travel far enough to infect anyone who wasn't also at risk from the original point of infection. Given modern travel speeds that threshold is pretty small, but it certainly still exists; a virus that killed people within 1 minute of infection would never make it out of the building where it was first encountered.

Re:Increasing mortality is bad for business

[Runaway1956]

"So much in fact, that every possible mutation has appeared already."

Even if such a statement could be verified mathematically AND historically - we still haven't seen every possible mutation in every possible situation in which it might be spread. The world has never before seen the population density we see today. Virulant outbreaks can span the globe in a week or less. The people at CDC are concerned for a reason.

Re:Increasing mortality is bad for business

[Splab]

The reason why they are scared aren't because it's ability to kill right now, the reason why they are scared and why you should be too is because:
1. it spreads like wildfire - off season, imagine what kind of havoc this will do when the flu season starts.
2. unlike most other, this will primarily hit young people, our immune system isn't geared for this, while this in the beginning wont cause many deaths, the consequences of having 20-30% of your working population off for a week or two due to sickness is really really bad for the economy and this will of course leads to all sorts of fun ways to drop dead without being sick.
3. While we in the western world right now are quite capable of handling the cases with complications, this will soon spiral out of control, right now we are seeing very low numbers of infections, compared to the expected numbers when the season gets going, this will lead to a lot more getting complications with their infections - and guess what, even here in the oh-so-civilized western, we can't handle that many complications - which will results in death counts matching that of Mexico.

In short, everybody PANIC!!!

Re:Increasing mortality is bad for business

[macraig]

I think the strains of HPV have that one beat hands down... they're the cause of ubiquitous warts, among many other persistent annoying things!

Re:Increasing mortality is bad for business

[Kral_Blbec]

Beware black guys who use a cane and own comic book galleries.

Re:Increasing mortality is bad for business

[PCM2]

Kinda thought that went without saying, judging from the number of viruses worldwide that exhibit the property of killing you one minute after infection (zero).

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

[Narpak]

If I were to speculate I would say that they are probably still around, just that many of those that didn't die had a higher resistance for that particular virus/disease; and that those people are our ancestors. That being said we also have things like hygiene now that might remove some of the factors contributing to a lower tolerance for diseases/viruses/etc.

Or maybe they have gone underground and is plotting their revenge.

Re:Increasing mortality is bad for business

[geekoid]

Daily news central? really? how about a decent cite?

The only reason eope are living longer s better medications.
Some poeple only need 1 pill a day, a huge improvement.
However, untreated, you ahve the same life expectancy you did 20 years ago.

Re:Increasing mortality is bad for business

[aethogamous]

Increase propaganda through FUD is pretty bad as well. In relation to the USA. Regular Flu: Since January, more than 13,000 have died of complications from seasonal flu (April 2009) Swine Flu: Since January, 10 reported deaths (May 2009) In 1976, when 40 million people received the H1N1 vaccination over a period of a few months, the incidence of Guillain-Barre syndrome was about one out of 150,000.

There has been a lot of discussion recently among public health officials about the 1976 outbreak and Guillain-Barre. It is estimated that modern flu vaccines produce Guillain-Barre at about 1 per 1,000,000 vaccinations http://www.cdc.gov/FLU/about/qa/gbs.htm

The H1N1 vaccines under development are essentially the same as the regular flu vaccine and can be reliably expected to produce Guillian-Barre at the same rate.

Oh - and the number of confirmed h1n1 deaths in the usa currently stands at 556 http://www.cdc.gov/h1n1flu/updates/us/#totalcases, which when I last checked was a wee bit bigger than 10.

Talk about spreading FUD.

Re:Increasing mortality is bad for business

[geekoid]

ONce tyou ahve spread, then the host can die and not impact the infection rate.
Of course, spreading it to multiple host sis better, but one will do.

Re:Increasing mortality is bad for business

[geekoid]

In your unrealistic example, yes you are correct. IN the real world the time you need to keep the host viable and be a year before symptoms emerge. As long as the host does whatever is needed to spread the virus, you will see virus growth.

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.

Success being growth of infected people. I don't want to imply some sort of thinking force behind the virus.

Re:Increasing mortality is bad for business

[CAIMLAS]

Provided the pre-symptom incubation period is fairly long, a deadly virus CAN spread far and wide.

Let's say there's a flu mutation which has a 3-month incubation period, give or take a couple weeks. It has a mortality rate of 50%. However, we don't know about it until three months after the first couple infections - by which time it's likely that the majority of people who will catch it, have caught it. Voila, you've got a pandemic on your hands to which there is no prevention: it's only a matter of time until you find out whether you're one of the lucky few who will die (and no, with 50% of the world's population dying, I do not say they are lucky with any humor).

Re:Increasing mortality is bad for business

[BluBrick]

You've never had the flu? Ever? Come now.

It's not that big a stretch. I had the 'flu this year and I don't think I had ever been so sick for so long in my life. (It's fair to say I have been sicker, but only very briefly) Then I realised that every illness that I had previously called 'flu was merely a common cold.

OTOH, are you sure that your "dozen times since then" have been 'flu and not a common cold? I always knew there was a difference between the common cold and the 'flu, but it took me 45 years to really understand that difference.

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

[cawpin]

I don't think anyone has actually every died FROM HIV have they? Or even AIDS for that matter? Haven't they basically all caught serious infections and died from that?

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

[maxwell demon]

Are you sure it was the flu and not just a common cold?

Re:Increasing mortality is bad for business

[Toonol]

Relatedly, I'm fascinated and a little creeped out by viruses, infections, and parasites that modify the behavior of the host in order to spread further. This seems to be more prevalent in simpler animals (such as insects), but I can't help but believe it happens (more subtly) in humans. Even if it's just 'make you itch so you spread the infection' type behavior.

I would think that STDs, for instance, would benefit immensely from heightening their host's sex drive.

Re:Increasing mortality is bad for business

[Jahava]

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?

Not that I disagree with your conclusion, but I do want to respond to your reasoning. The longer you live, the more you diarrhea, vomit, and get bitten. Over time, in that case, it seems (to me, at least) that a disease that keeps its host alive would reproduce more, and thus be more successful in the long run.

IANAD, but since this would all have been explored during the disease's evolution, I conclude that one of the following is the case:

• Those diseases didn't used to affect humans, so their evolution within the human species is still relatively primitive.
• The diseases themselves are relatively new, and thus not very mature
• There is some evolutionary advantage to specifically having a dead host
• The diseases have reached an equilibrium where the amount of time their host lives maximizes their efficiency versus other factors (e.g., the effort it takes them not to kill the host)
• I have no idea what I'm talking about

The list was fun, but the first paragraph was really what I was going for!

Re:Increasing mortality is bad for business

[UltimApe]

Deadliness of a virus is usually a side effect of the way that it approaches spreading. see http://www.ted.com/talks/lang/eng/paul_ewald_asks_can_we_domesticate_germs.html

Re:Increasing mortality is bad for business

[ceoyoyo]

There are subtleties, but malaria and cholera aren't nearly as deadly as they could be, nor kill as fast as they could.

In the case of cholera it definitely is a good idea not to have you drop dead before you manage to get to that nice waterway. Or maybe even two nice waterways. Ditto with malaria - if you stay alive for twice as long, that's twice as many opportunities for you to get bitten by a mosquito of the right type.

Both diseases are very widespread, have been around for a long time, and have found an equilibrium. Neither is going to kill off the human species.

Re:Increasing mortality is bad for business

[antirelic]

Talk about spreading FUD.

Read the quotes (May 2009) versus the regular "flu" in (April 2009). Talk about poor reading comprehension.

Re:Increasing mortality is bad for business

[antirelic]

I hope your the first to go.

Re:Increasing mortality is bad for business

[repapetilto]

look up toxoplasma gondii... actually here: http://en.wikipedia.org/wiki/Toxoplasma. People have tried to tie infestation with that parasite to increased car accidents, and even differences between cultures: Can the common brain parasite, Toxoplasma gondii, influence human culture?

Re:Increasing mortality is bad for business

[budgenator]

Actually a Mouse Pox virus was engineered to be so deadly and so virulent that the host would die even before it became contagious.

Re:Increasing mortality is bad for business

[budgenator]

That's the point, it's plausible that you can be partially immune to a flu strain and only get as sick as you'd expect from a cold and nobody would ever know unless you had expensive lab tests; likewise everybody calls a bad head-cold the flu. I notice when I've gotten my flu shot, I seem to miss out on two or three "cold" that people who don't get immunized get.

Re:Increasing mortality is bad for business

[infinitelink]

Have to take issue with your guns comment. You see, Tuberculosis functions precisely in a fashion that's deadly: taking-up residence and wreaking havoc; from the human perspective that's all it is good for (though nowadays we've also put it to use fighting cancer in certain places--but it is totally unnatural to Tuberculosis). Something similar can be said of cancer: the cancer itself is the malfunction that is bringing disaster and eventual death (had cancer, by the way, but no treatment with Tuberculosis). Meanwhile, guns are a combination of different technologies, each of which in itself is useful for other ends, and the gun itself useful for other ends (hunting, etc.); it is not intrinsically people-designated, though it can so be put to use. Whereas from our view Tuberculosis and cancer are like automatons that will 'do their thing' whether or not we like it, guns are not: they are inert. They must be assembled by hand, loaded, and pointed: and pointing needn't be at a person. Those who use that phrase, even when people think 'ignorant rednecks' or other, aren't be overly literal, but making this exact point: and it's sad how many people, even cultured, educated ones, show either how ignorant and insensitive they are to understanding that point, or willfully ignoring the intent of the expression, in the case of the gun, that the person, not the gun, is responsible, whereas with Tuberculosis or cancer, the cellular organisms (and cancers pretty much are their own beasts too, not 'you' anymore) the person is not responsible: could people be responsible? Yes: they could willfully or negligently cause the illnesses, but then we wouldn't say 'Tuberculosis' or 'Cancer' 'killed him', we would lay the responsibility on the person who caused the condition in the other person, perhaps qualifying 'He used Tuberculosis/cancer to kill him', whereas with guns it's 'He used a gun/guns to kill him'. Get it? Stupid example, and awful reasoning: I hate how hyperliteral, or better put, 'verbal', people can be--especially the kind who'll trawl /., programmers (though more than I once thought are actually better than I was once prejudiced to think), etc.: oh yeah, and don't forget the liberals. (Also not a jab--I'm not a liberal, but have many liberal preferences, and respect quite a few dearly, though the classical as opposed to the freakishly extreme modernist/'progressive' sort, in most cases.) I would propose--and perhaps there's an old-school epistemologist who remains in this tradition, that the kind of thinking you've presented just now is a good example of reductionism: that powerful tool which scientifism has elevated to true knowledge, rather than a simple tool not to be believed--because it denies aspects. To give an example, modern day thinking goes 'logic is math', but prior to that sensational knee-jerk trajectory, a few good epistemologists (and logicians) left made a better case to the contrary, that this is inconsiderate of aspects, and that though math is logical, logic is not math. There's a reason philosophers, not mathematicians, still tend to be those at universities teaching formal (classical) logic. The computer-types just get logic embedded in math through their education, and come to reduce the two into one category. I find this type of thinking in modernity shallow, disturbing, and dangerous--not just to society, but science itself: it creates contradictions internal to the 'philosophy of science', the episteme upon which, and within which, it is built and framed: but most modern thinkers, whether Joe Bloe or Sam Scientist, no longer either know, or if they do, respect or care about consistency: pragmatism rules, and "I know...though I deny 'truth'" ('truth' in the sense that once held in philosophy, epistemology, etc., as the real as opposed to unreal, the genuine as opposed to ingenuine or mistaken, etc.). Thanks for reading my rant. : )

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

[jonadab]

I suppose it depends on how you define success, but I would have probably named the common cold and flu as the two most successful viruses of all time, based on the number of infections they've caused, which is significantly more than the total number of people who have ever lived, since they infect most people repeatedly over the course of their lives. This is especially true of the common cold, which infects the average person more than once per year. That's impressive.

Re:Increasing mortality is bad for business

[aethogamous]

Ah - my mistake, I will revise my opinion - I had thought merely that you had got some bad numbers - but I now see that you were really stupid enough to compare the number of deaths at the start of an epidemic with the number of deaths at the end of a different epidemic. Looks like I mistook you for being misinformed, rather than for being a moron. Thanks for fixing that for me.

Re:Increasing mortality is bad for business

[theheadlessrabbit]

good point.

any pathogen that is spread through water, mosquitoes, or other parasites wont face this sort of selective pressure, but something spread primarily through human contact will.

there was actually a TED talk video about this very phenomenon: can we domesticate germs?
http://www.youtube.com/watch?v=176adlNeRy8

Re:Increasing mortality is bad for business

[Metasquares]

If the immune system squashes it before it has a chance to cause symptoms, I'd call that an unsuccessful virus. Part of what makes a virus successful is the ability to evade the immune response.

Re:Increasing mortality is bad for business

[buchner.johannes]

Given that the first infects were recognized in 1984, I think the "selective pressure" is not a evolutionary one, as there just have not been enough generations. You have to factor in that the number of infected grew significantly, so the decrease of faster-killing virus variants may just stem from the fact that their hosts died earlier decreasing their share whereas that didn't happened for slower-killing virus.
That'd be without passing on to a newer generation of virii that has been selected due to fitting better (which will occur later, I'm sure).

Then on the other hand, I'm no biologist/physician :-)

Re:Increasing mortality is bad for business

[PCM2]

Pneumonia is a common complication of the flu, but not of common colds. So in my case, pretty sure, yes.

Re:Increasing mortality is bad for business

[cawpin]

No, it isn't stupid. HIV and AIDS let OTHER diseases attack your body. Tuberculosis and cancer both directly cause their damage. As for firearms, that is the most inaccurate of the examples as they are inanimate objects, like a hammer.

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:Increasing mortality is bad for business

[OeLeWaPpErKe]

You do realize exactly how fast viral reproduction is, right ? We're talking seconds to minutes inside an infected host. Hours (at best) outside of one.

Since HIV existed in living hosts continuously at the very least since 1954, it is (at the very least) the 14th million generation. Quite a bit could have happened in that amount of generations.

Re:Increasing mortality is bad for business

[mlush]

Given that the first infects were recognized in 1984, I think the "selective pressure" is not a evolutionary one, as there just have not been enough generations. You have to factor in that the number of infected grew significantly, so the decrease of faster-killing virus variants may just stem from the fact that their hosts died earlier decreasing their share whereas that didn't happened for slower-killing virus. That'd be without passing on to a newer generation of virii that has been selected due to fitting better (which will occur later, I'm sure).

Then on the other hand, I'm no biologist/physician :-)

(Very roughly) you only need about 10 generations so see a significant evolutionary change and HIV mutates at a frightening rate, (one of the reasons that it is so hard to treat is that if you treat a patent with a HIV drug there is always one virus in the patent with a protective mutation). Anyway getting back to the point its not just death that exerts a selective pressure its how ill it makes the patent. If your bed ridden with pneumonia your not out on the pull spreading viruses.

Re:Increasing mortality is bad for business

[R.Morton]

That's true but if I were going to die from a Virus I would want a good one ya know fast as hell !, so I will take Ebola Zaire any day of the week fast and effecient although a bit messy but it gets the job done.

R.Morton

Re:Increasing mortality is bad for business

[Nazlfrag]

The most succesful the would probably be bubonic plague used from the middle ages by Europeans and Mongols who hurled plague ridden corpses into besieged camps and towns, diseased clothing and blankets given to natives in the Americas, Australia, Africa and other colonial settlements, in WWI by Germany and others right up to WWII with the Japanese dropping infected fleas into Chinese towns, killing an aproximated 400,000.

Anthrax deserves a mention as one that many militaries vaccinate against, and though it's been used since WWI it's never seen large scale deployments, except perhaps in tests (especially WWII PoW tests), as does smallpox which was used on the French and various native populations by the British.

In the nonhuman realm, myxamitosis is probably the best known animal killer deliberately deployed by humans, while with plants it's use of wheat and rice blast during the cold war. Potato blight also deserves a mention as a plant weapon agent. From it's origin in the great Irish famine (where it wasn't used as a weapon, though some saw the British indifference as at least utilising it to weaken the Irish) it was extensively studied and stockpiled by the US and European powers, but I don't know of it ever being deployed.

Re:Increasing mortality is bad for business

[that IT girl]

It can be passed from a man to the person he's penetrating (female or male) quite easily on the first time.

Re:Increasing mortality is bad for business

[SQLGuru]

So, you're saying that nerds can't get HIV?!?

Re:Increasing mortality is bad for business

[OeLeWaPpErKe]

You don't get it. How does a virus reproduce outside of a host ? Simple : infection of another host. Infection takes time. You will find this part of viral reproduction to be a very necessary part of their survival.

So why the time limit ? Well the time between the creation of the virus particle by a mitochondrium and infection of a new host cannot, for nearly all diseases, exceed 2 hours. Virus particles are not very stable things in general. They don't do well at all, exposed to UV light, all sorts of reactive gases, ... generally anything you find in the athmosphere.

Re:Increasing mortality is bad for business

[Richy_T]

Lower risk of skin cancer too.

Re:Increasing mortality is bad for business

[Richy_T]

I think this is a little off the point of your last paragraph but I'd just point out that malaria is a multi-species disease and as such, it's possible it could reach an equilibrium that would quite happily wipe out the human species without affecting its own survivability

Re:Increasing mortality is bad for business

[brkello]

It's amazing how intelligent people become retarded when it comes to guns. They guy was just trying to counter someone saying that no one died from AIDS. Obviously, AIDS is the reason why many people die. Their lack of immune system allows them to contract a disease that we would be able to recover from typically.

We all know that it requires someone or something to fire a gun for it to kill you. The GP was responding to someone saying something like: "Even though Bob shot the guy with a gun, let's not fool ourselves. Bob did not kill him, nor did the gun. He died because he lost too much blood." Obviously, that is ridiculous. He died because someone shot him with a gun. Bob is to blame. The gun can actually be blamed as well since it is possible Bob would be to weak the kill person without the aid.

But saying AIDS doesn't kill people is just semantic garbage that detracts from actually talking about something meaningful. And focusing on the guns part of what they guy was saying shows you completely missed the point.

Re:Increasing mortality is bad for business

[commodore64_love]

>>>>> Increasing mortality is bad for business. 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.
>>>>>

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

Or they can live in a host like a flea, while still killing humans quickly. 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. What did these viruses have in common? They were very virulent, killing the humans quickly, but it didn't matter because their code was spread via fleas.

Re:Increasing mortality is bad for business

[Garridan]

You are claiming that reproduction "outside of an infected host" takes place during the infection of another host. This is a most curious argument. In consideration of the scale, we should consider a single cell to be a "host". Either a cell contains a virus, or it isn't a host. A virus must be inside a cell to reproduce, and at the moment that the virus takes over the cell to the point that it can reproduce, the cell is infected. At the moment that a single cell is infected, we should consider the entire organism as infected.

Re:Increasing mortality is bad for business

[OeLeWaPpErKe]

we should consider the entire organism as infected.

No, we shouldn't, not in all cases at least. The last resort to prevent spread of a disease in an infected host, after all, is amputation. Several diseases, mostly wound infections (many of which have no treatment) necessitate this, some of them actually viral.

And yes, even in the very hospitable bloodstream of a human being*, virus particles are destroyed mostly within minutes, even if the imune system does not do anything.

* except, of course, for the immune system

(and sorry about the GP post, I claimed viruses are produced by the mitochondria, that should obviously have been ribosomes)

The point is that viral generations are very quick things indeed. The slowest form of viral reproduction (infection of a new organism) creates a new generation every two hours. All other forms are much faster, so the evolutionary speed of viruses is extremely fast, especially compared to other lifeforms (even though viruses are not uniformly considered to be lifeforms).

There are even theories that the more "low-level" evolution of humans, or even plants is not a part of actual evolution of the species, but that evolution really takes place in lower lifeforms, like cyanobacter for example, and spreads to plants, animals and even humans by viral infection of the reproductive organs. These theories explain why there is a "code-split" in all higher DNA : there are large sections dedicated to making specific, complicated proteins, with zero logic connecting them, and there are large sections that are basically programs that use the "protein section" as a sort of library by jumping into it. An unexplained question is why evolution would separate protein production from production control in so many species. Viral transmission of these production genes would explain it.

So viruses might actually be critical to evolution.

Re:Increasing mortality is bad for business

[RBanks84]

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.

What about Lysis? That's a pretty effective way for a virus to spread by destroying the host.

Re:Increasing mortality is bad for business

[StikyPad]

And there's more to it than just host-to-host infections. Many pathogens have natural reservoirs -- plants or animals that can host the pathogen without themselves becoming ill, or with only minor effects. While in the reservoir, the pathogen can still mutate by its normal mechanisms, and could become even more deadly to humans (or its reservoir.)

It's all a game of dice, and every once in a while you can, and probably will, roll snake eyes. Just because a mutation isn't good for the long-term viability of a pathogen doesn't mean it won't occur. It's not as if the pathogen has some sort of intelligent control that says "Woah, I'm killing my hosts way too fast.. I'd better slow things down a bit." Short term success is still success.

Consider that an oft-quoted statistic is that 99% of all species that have ever lived are now extinct. I'm not sure how accurate that figure is, but it only takes 1 to prove the point: Those extinct organisms were successful enough, until for whatever reason, they weren't.

Re:Increasing mortality is bad for business

[dwye]

> The most succesful the would probably be bubonic plague

> Anthrax deserves a mention as one that many militaries vaccinate against,

> In the nonhuman realm, myxamitosis is probably the best known animal killer deliberately deployed by humans,

As another reply to the post that I replied to pointed out, the above are all bacteria, whereas the article concerned viruses. Also, "successful" was originally defined in the virus's terms (lots of descendants and a population not resistant or immune due to the first exposure). Killing humans is only good if that helps spread the germs (like Ebola victims bleeding out does).

BTW, the blankets that Lord Amherst proposed (and only proposed) giving to the Indians to wipe them out were contaminated with smallpox, not bubonic plague.

Re:Increasing mortality is bad for business

[Garridan]

we should consider the entire organism as infected.

No, we shouldn't, not in all cases at least. The last resort to prevent spread of a disease in an infected host, after all, is amputation.

Ah! See, you just called the host "infected". This is my point. The host contains replicating bacteria, hence the host is infected. If you cut off the infected part of the host, you're merely re-defining "host". I'm curious if you'll agree with this:

John's toe is infected with a virus... say the exceptionally rare and deadly Picornavirus. This means that John is infected with the Picornavirus. If we amputate John at the waist, John's toe is still infected with the Picornavirus. However, John is not infected with the Picornavirus -- we've redefined "John" to be "The upper half of John".

Now, let's say that the affected body part is the head. If we amputate John's head, he is clearly cured of the virus. Here, we've redefined "John" to be "John, except the ugly bits".

In both cases, John still has body parts which are affected. But, since they have been detached, we decide not to keep calling those pieces by the name of John, since they're over here on the table and John is way over there, on the other table. Hence, John is no longer infected with the Picornavirus. Disaster averted!

I'm claiming that in these cases, we wouldn't have to go to such great lengths to combat the Picornavirus unless John was infected with it.

Re:Increasing mortality is bad for business

[Garridan]

... no idea the third sentence there says "bacteria". I'd change that to "virus"... if only I'd actually read the preview.

Re:Increasing mortality is bad for business

[PCM2]

Well, we're talking statistics here (and damned lies, and all that). If the chance of you catching the disease was 1 in ten million, you might still catch it the first time. That's the thing about statistics -- they're not prophecy.

But in strict point of fact... define "quite easily." Measles is incredible easy to catch. If I was giving a talk about measles and I had the disease and I coughed at the podium, more than likely every single person in the room would come down with measles within a week.

By comparison, the chance of catching HIV through vaginal intercourse is very, very low, no matter who has it and who doesn't. The chance of catching it through anal intercourse is much higher -- but only in a statistical sense. HIV is nowhere near as infectious as measles, or even chicken pox.

The difference, of course, is that HIV will kill the fuck out of you; chicken pox, less so. So who's willing to risk it?

Re:Increasing mortality is bad for business

[angel'o'sphere]

You are mixing up "human generations" with "virus generations". Since 1984 there might beonly 2 or 3 human generations but there are millions - if not billions - virus generations.

angel'o'sphere

Re:Increasing mortality is bad for business

[that IT girl]

I agree with you. Actually, my point (and I admit I didn't make it very clearly) was to point out that the partner being penetrated has a much higher rate of being infected than the person doing the penetrating. The parent to my post made it a point to say "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." as if that is the only side of the story. But if the man were the one infected, she's much more likely to be at risk the first time.

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!

[synthesizerpatel]

OH SNAP

Bunny got served

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!

[Anonymous Coward]

For someone who goes get off my lawn so much, it seems your understanding of other sciences is often at the level of a dorky scifi fanboy all the time, ponder that.

Re:fascinating!

[RobertB-DC]

Well, for my part, if I'd waited a couple of minutes I might have seen your reply to yourself where you noted that the article is better than it might have seemed! Ain't Slashdot great?

Re:fascinating!

[moon3]

Actually you are right, unfortunately for us they still booting their operating systems and learning SQL syntax, they had much trouble to read and sequence the DNA, now have PB of data waiting to be analyzed, it will take some years, decade or even decades, pretty likely our generation will not see any major and useful results from this DNA biology as this is just the very beginning of the research.

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!

[plasmacutter]

(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.

there are several instances in human history of inventions being developed independently in exactly at the same time.

this is far different than the sheer ignorance "max tedroom" displayed with his series of tubes speech.

Re:fascinating!

[Silas is back]

Ok, thanks for pointing this out. Like OP I was thinking "WTF does this kiddy try to conclude?", but if you see it from a purely computer scientist's side, it indeed might make sense.

Re:fascinating!

[Trepidity]

Yeah, it's true that there's some pretty lame stuff on the bioinformatics side too--- especially the early stuff has a feel of "hey guys what is computer", with books like Beginning Perl for Biologists.

Re:fascinating!

[Ubahs]

I don't know, yea it's in the early stages, but a lot of useful information is coming out of this mountain of data we have now.

Why was the Spanish Flu so deadly? ...The article actually nailed that on the head, it was a single nucleotide change that made it so deadly compared to the rest of the H1N1's at that time. That was from our PB of data.

Why are some people immune to HIV? Why do those people tend to be of European descent?

Why is this strain of Pseudomonas fluorescens more able to prevent a plant disease than that strain?

Very recently, why does that dog have curly hair and another dog have short hair and a 'mustache'? Three genes, that on the DNA level are different.

Most of the work just doesn't get publicized except in obscure journals, where only a hundred or so people read the work.

I dunno, I think a farmer who is able to keep their Canola crop growing because of hand-picked bacteria to kill off some fungus/bacteria/nematode/what-have-you is a pretty major thing. ...And, we're just starting.

Re:fascinating!

[Ubahs]

Bioinformatics is no actual work with chemicals or lab, it's almost 100% computers and stats. ...And a lot of file-conversion and a lot of making crappy web pages to show data in a pretty way to non-scientists and scientists. You program computers, but you also deal with 10 year old programs that can't handle the data size now, tons of Java or Perl and any problems there, etc.

Some people are programming along the lines of what you ask, however, there is even a fancy UI that you click and tell a machine what type of what-have-you pathway you want and *spoot* out comes a bacteria that does what you want.

Very close to being out and about in the world...the link below is a tad old, they've gotten further then what Venter said at the time.

http://www.ted.com/index.php/talks/craig_venter_is_on_the_verge_of_creating_synthetic_life.html

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...

Re:fascinating!

[Carewolf]

Why not just call it "programming"? Whether you're writing code for machine made of sand (silicon) or chemicals should not matter one bit. Ya know in Babylon 5, the Vorlons and Shadows didn't just "grow" their ships. They programmed the DNA to produce the desired result. I see no reason why we humans can't do the same.

Because computer science has next to nothing to do with programming. Informatics is another name for Computer Science, so Biological Informatics is abstractly Computer Science applied in Biology, like BioChemistry is Chemistry applied to Biology. Both studies however require enough specialized knowledge that they are fully separate from Computer Science and Chemistry, which is why they have their own names. Though at least at my CS department I've been able to takes classes in protein folding, which was a fancy name for advanced techniques for optimizing string search.

Andrew "Davros" Huang

[Anonymous Coward]

http://video.google.com/videoplay?docid=7026801162637347552

Oh noes! He's got teh pig flu!

[RingDev]

Error establishing a database connection

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.

Re:How many bits does it take to kill a human?

[clone53421]

Yeah... the flu virus is a kill routine written in assembly language source. In a sufficiently high-level language, executed by the correct interpreter, it could be done in much less space.

Now... sic 'em, butch!

Re:How many bits does it take to kill a human?

[Juba]

640 bits ought to be enough for anyone...

Re:How many bits does it take to kill a human?

[ACMENEWSLLC]

1 bit is all it takes. Just beam one bit using the Star Trek transporter into the heart of a human and you have a dead human.

Or another way; 0 bits. All humans already die. It is a built in feature. No add-ons are required.

Re:How many bits does it take to kill a human?

[Pingmaster]

I guess it would depend on the computer, i mean, if one bit carries 1mA, then you'd only need about 100 bits, but if it were 1μA, then you'd need about 100,000

Re:How many bits does it take to kill a human?

[Thuktun]

How many bits does it take to kill a human?

Only 1, the evil bit.

Re:How many bits does it take to kill a human?

[krewemaynard]

640K of anything should be enough for anybody.

Re:How many bits does it take to kill a human?

[ceoyoyo]

One bit. And it's a one. The executioner pushing the on button on the electric chair.

Re:How many bits does it take to kill a human?

[pclminion]

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

The question is meaningless, because bits have no unit. They are dimensionless. This is easily seen by looking at Shannon's definition of information entropy. The average entropy in bits of a random source is a weighted sum of logarithms. Logarithms are dimensionless. Therefore, the bit is also dimensionless.

An analogous physical quantity would be angle. Angle has no unit (and the unit is not "angle," there simply isn't one). Note that you can take the sine of an angle. You couldn't do that if angle had a unit associated with it.

Now, there are different scalings possible for quantities of information. Instead of bits (base 2) you could use bans (base 10) or nats (base e). But these are analogous to measuring angles in radians vs. degrees. The underlying quantity is dimensionless no matter how you scale it.

Re:How many bits does it take to kill a human?

[noidentity]

Besides, you don't need a complex virus to kill a human; some very simple compounds will do.

Re:How many bits does it take to kill a human?

[domatic]

Yeah, but the output peripheral is a real bitch and it can even share error codes with old high speed line printers: ElectricalLoad1: is on fire!

Re:How many bits does it take to kill a human?

[Teresita]

Mad cow disease, caused by prions, all self-assembling, self-replicating protein, no DNA, no RNA, answer: zero bits.

Re:How many bits does it take to kill a human?

[R2.0]

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

Stupidity: it only takes one small little bit to kill you.

How many bits does it take to kill you?

[MBCook]

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

Re:How many bits does it take to kill you?

[MrBulwark]

one, two-hoo, three

Re:How many bits does it take to kill you?

[Mal-2]

I would, but he's currently in the clutches of an evil futon.

Mal-2

Re:How many bits does it take to kill you?

[Sabathius]

A-one, a-two, a-three...*crunch*! A-three!

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.

Re:Rats Leaving A Sinking Ship

[Darkness404]

Well of course they will have stronger immune systems, but will they get sick as much? Its kind of comparing someone active with strong bones compared to someone inactive with weaker bones. If the most activity you do is go up and down stairs, your risk of breaking a leg is probably less than someone who is into extreme sports, even if the person is healthier and has stronger bones than the person who does little activity.

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: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:Rats Leaving A Sinking Ship

[PCM2]

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

Trust me on this one: "Our obsessive need for antibiotics" isn't going to affect viruses in the slightest.

and wiping all indoor surfaces down with lethal cleaners.

If you're suggesting that disease pathogens get stronger when subjected to chemical microbicides, that's about as silly as suggesting we could breed a race of superhumans who are immune to poisoning by feeding people arsenic and letting the survivors breed.

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.

You'll have to clarify what that means. Does "stronger immune system" mean more antibodies were found in their bloodstreams? That just means they have been exposed to more pathogens. Which is only natural -- since, like you say, the majority of diseases are believed to be zoonotic in origin. Hang around animals, get exposed to animal diseases. Eventually some will mutate and cross the species barrier. The only way to avoid it would be to exterminate the animals -- because contrary to your analogy, when an animal dies, all the diseases it carries do not suddenly leap from its body and go scurrying off looking for new kinds of animals to infect. They pretty much just die with the animal.

Re:Rats Leaving A Sinking Ship

[Lord Ender]

Your insults are really odd. Are you translating them verbatim from another language?

PS: Sorry the facts got in the way of your karma. You sure take things hard, though.

Re:Rats Leaving A Sinking Ship

[geekoid]

No, it doesn't.

Interaction with humans and human viruses are need for a virus to mutate(adapt) to a new for of cross species virus.

A virus alone in anhost will not utate to jump species. It needs another virus.

Re:Rats Leaving A Sinking Ship

[geekoid]

Your original post is wrong. Animals dying won't cause there virus to suddenly mutate to adapt to a near by potential hiost.

You are both wrong, but it's funny to watch both of you vehemently defend and argue while both being wrong

Re:Rats Leaving A Sinking Ship

[pwfffff]

Right...

"Fall had come to an end, and as the bitter, cold winds of Winter came sweeping through what was left of the once great forest, the last of the rare northern striped bunny rabbits fought in vain to keep warm. With no shelter left in the clear-cut forest their days were few, and soon they had all succumbed to the biting cold. A great loss, truly, but it was not the only tragedy to befall our Earth that day, for something sinister still stirred among the fallen corpses: a virus!

  Sensing that its host population had become extinct, it swarmed from the rabbity remains in search of a new host. Crawling slowly but surely over the frostbitten ground, it encountered first the very creatures that had annihilated its original host's habitat. Sensing the evil that had destroyed its former life, the virus began to attack the humans, mutating until the first of us had fallen to the now infamous H2N1 bunny flu of 2083."

^ How parent thinks the world works.

Re:Rats Leaving A Sinking Ship

[mindbrane]

No dickwad, I'm not translating my insults from another language, just another field, biology. And no, dickwad, I don't take things hard, mostly I let them slide but instead of your parent post making a point you followed it up with a gratuitous insult, so, I gave you a couple in return. I don't like the sort of tribal shit you spewed out. As for /. I've an account from the late 90's I can't be bothered to reactivate because it's more fun to see how little tribal boys and girls like yourself have changed the site. As to my karma, I'm back at /. after a 3 year hiatus and am just hanging around to play while I get other things done.

having trouble with penis fencing and flatworm men? Try the videos "The Shape Of Life"

Lastly, you didn't make any points, you, like me, just made an unsupported comment and the little troll, tribal, dog moderators did what they've always done. As I used to strongly advocate: Keel haul the /. weenies.

Re:Rats Leaving A Sinking Ship

[Lord Ender]

a gift to you: http://www.buddhanet.net/e-learning/index.htm

Re:Rats Leaving A Sinking Ship

[mindbrane]

My middle class upbringing demands a gift be given in return:

May you never know more of life than you now know.

Port H1 maps specifically to the windpipe region

[quatin]

Sounds like we need a firewall.

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:It takes only 1 bit to kill a human

[ceoyoyo]

Nope. DNA bases come in pairs. Change a single base and it's partner won't stick. If that error correction mechanism doesn't work, there are others built into the genome. If that doesn't work, there's a good chance a gene with a single base pair error will still work. If not, there's conveniently a second copy.

Also, for a cancer to develop you have to disable multiple safeguards AND cause the cell to decide to divide out of control.

I very much doubt that any single base mutation would kill.

Cached link

[Laxori666]

Google cached link

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.

Just one

[tmosley]

A big ol' bit out of the jugular vein is enough to kill anyone.

Re:Port H1 maps specifically to the windpipe regio

[TheSpoom]

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.

Nanoprobe-supported organs. Once again, Star Trek has beaten us to it.

Or to bring down a government?

[Jeff Carr]

32 bytes, 256 bits..

Don't you think she looks tired?

Re:Mr. Huang: If you don't know biology, STFU!

[ThePeices]

Oh noes! his analysis wasnt biologically perfect, therefore everything else he has stated is instantly rendered completely and utterly wrong!

See what you did there ACoward? yup, a nice big fat logical fallacy, thats what you did.

more bioinformatics for beginners

[cariaso1]

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

Re:more bioinformatics for beginners

[maxwell demon]

Nice link. One thing I noted:

The human genome is about 3 gigabases long, which boils down to 750 megabytes. Depressingly enough, this is only 2.8 Mozilla browsers.

Now that's an argument that Mozilla is bloated! :-)

Re:more bioinformatics for beginners

[geekoid]

Here is another comparison of DNA to Code:
http://lifestreamblog.com/wp-content/uploads/2008/03/apples_oranges1.jpg

Re:Mr. Huang: If you don't know biology, STFU!

[Bakkster]

Yup, to follow his (strained) analogy, 6-bits of RNA encode into 5-bits of amino acid (with 10 invalid encodings).

But really, anyone who could follow his analogies should be smart enough to learn the actual biology, so why bother with a broken analogy?

Re:Mr. Huang: If you don't know biology, STFU!

[Volante3192]

Umm, I'm confused by this ranting.

FTFA: As you can see, we have 'GAA' coding for 'E' (Glutamic acid). To modify this genome to be more deadly, we simply need to replace 'GAA' with one of the codes for Lysine ('K'), which is either of 'AAA' or 'AAG'.

Article author points out that TWO triplets both translate into Lysine. OP's ability to RTFA is bunk. Learn to not troll.

The question he should have asked...

[amRadioHed]

is how many bits would it take to kill his server.

Re:The question he should have asked...

[geekoid]

One, if it's the evil bit.

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.

All of these bit measures are misleading.

[Estanislao Mart�nez]

The 26,000-some bit virus only exists in the context of a host that contains considerably more DNA information than that. To use the awful computer analogies, it's like running a 26K program on a 300MB interpreter system; the small program just calls some combination of really complex, pre-built functions that shouldn't be called in that combination.

And keep in mind that the 300MB interpreter is meaningless without the context in which it executes: some physical machine.

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:Port H1 maps specifically to the windpipe regio

[Kjella]

Not to mention a rather nifty virus scanner in the transporter buffer... Oh yeah and you can patch it too. They even unintentionally made a backup copy of commander Riker. It's easy when you can just throw out every crazy idea you got.

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

[Culture20]

That's being bit 3.2*1024*8 times! Or 3.2*1000*8 times if you're into distinguishing between kibiytes/kilobytes. But that's still a lot. Imagine that many mosquitoes...

Just one bit can be enough

[TheLink]

All depends on which bits you can change.

If you can change the constants of the universe I'm sure you only need to change one bit to kill everyone :).

Re:Just one bit can be enough

[Kratisto]

If you can change the constants of the universe, you probably already killed everyone an infinite number of times, preemptively.

Re:Just one bit can be enough

[fractoid]

If you can change the constants of the universe, you probably already killed everyone an infinite number of times, preemptively.

Yeah but you do that anyway no matter what you do.

Re:Just one bit can be enough

[kmoser]

If you can change the constants of the universe, you probably already killed everyone an infinite number of times, preemptively.

What is the sound of an infinite number of voices crying out and suddenly silenced?

Re:Just one bit can be enough

[rant64]

There was never anybody to kill in the first place.

Re:Just one bit can be enough

[sexconker]

0

Filter error: You can type more than that for your comment.

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

[CarpetShark]

If you throw in Meme Theory, humans would be more like two Amigas: one running a demo which makes it think its running the other demo by choice, when actually neither were a choice.

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

[jack2000]

I see it now.
We are bio servers and this whole virus thing is just people from the demo scene trying to outcode each other!

Re:Mr. Huang: If you don't know biology, STFU!

[maxwell demon]

Although for many unwashed masses your ramblings look quasi-brilliant, your analysis has WAY too many holes. Each triplet is translated into ONE of TWENTY amino acids. You know what? Some triplets are translated to the SAME amino acids. Your analysis is bunk. Learn your biology.

Yes, each triplet is translated into one amino acid (OK, there are a few which are translated into none). There's no single triplet which is translated into two or more amino acids. The fact that several triplets are translated into the same amino acid doesn't change that (even if you shout). Learn your logic.

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

[geekoid]

The fact that you are not modded funny shows how little most people understand what a proper study is.

That sentence ended poorly.

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.

How any bits ?

[Conditioner]

How many bits make up cyanide ? it like 4 or 5 molecules, and has a lovely almond smell to it. or so iv heard.

Link is down

[geekoid]

" 'I now know how to modify the virus sequence to probably make it more deadly.' "
I have some serious doubt. Ignoring the fact that 'make it more deadly' is a bit(lot) vague, it's not a pile of bits.
Also, there is a long way between designing a virus, and being able to make it.

OTOH, he does hack a trivial easy piece of hardware, so maybe he did it with dust tape, spit and MacGyvers seman.

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

[geekoid]

This is the internet, censorship is easy to get around, post a link, you whack job.

300% mortality makes no sense and add to the suspicion that you are a loon that can't think for themselves.

No one is forgetting about the Swine flu scare in 70.

in 1970 the virus was engeneered? something thats only doable on a priomative scale with todays technology?

You ahve gotten sucked into the 'world cons;piracy' meatal state. Logically waht you are saying make no sense, so instead of realizing that, you ahve created an invisible secret conspiracy. One that would profit a lot more if it actually had the technology from above board uses.

"My main /. account is posting at -1 just because of my critical thoughts of EVER finding myself dependent on my fellow man. I want independence; Wisdom decides what knowledge I seek, so as to not have an untactical command of random unsorted information."

You need to log into some psychiatric help.
  Seriously, uyou are sounding non sensicle. I know it makes sense to you, but to most people it's jibberish. This is a bad sign.

No one is out to get you,
There is no conspiracy
You need help.

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: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

Re:Another interesting observation

[nateb]

It would be interesting to know if the amino acids at the "wobble possitions" were isomers of each other. Do you happen to know?

I find it interesting that there are two encodings for STOP, as well.

Re:Another interesting observation

[sFurbo]

Well, it is an intriguing idea, and one I have seen suggested before. But it is hard to get from a two-base to a three-base representation. You would need to change a lot of things in one go (inserting 50% more bases, changing the RNA, changing the proteins etc.), which isn't that easy to do in a evolutionary environment. I think it has more to do with redundancy. Changing one base have about a 1/3 chance of not causing a mutation, and the t-RNA doesn't have to be nearly as selective (it doesn't matter if it gets the last base wrong). You could even imagine a start where there were only one t-RNA for each amino acid, and it simply ignored the last base (well almost, with the obvious exceptions)

Re:Another interesting observation

[thepotoo]

The third position will often code for the same amino acid no matter it is (IE, only the first two matter), and if it codes for a different aa, it's often one which is functionally similar (both will be polar, or nonpolar).

Also, all amino acids are D-isomers in life forms.

I'm sure there's a fascinating story behind the multiple stop codons, too, but I don't know it off the top of my head.

Re:Another interesting observation

[Nazlfrag]

If we rule out T/C winning as there is no stop codon when we use only those from that group, we can go with A/G winning instead. This works out better, but there is still ambiguity. I'll just go with my arbitary instinct and pick only one stop codon, leaving G as the winner as follows:

codon set, G wins
    AA ........... K
    AC ........... T
    AG ........... S
    AT ........... I
    CA ........... Q
    CC ........... P
    CG ........... R
    CT ........... L
    GA ........... E
    GC ........... A
    GG ........... G
    GT ........... V
    TA ........... STOP
    TC ........... S
    TG ........... W
    TT ........... L

Though perhaps it's two stop codons (A wins), or something completley different. However it might work, its a brilliant idea.

Re:Another interesting observation

[Elven Thief]

I'll respond with a question - why is that we can produce 64 different codon combinations, but only evolutions only has us code 20 amino acids?
I have a professor who theorized that our current genetic code evolved from another 3 base code which was palindromic. AAC and CAA would produce the same amino acid. Additionally, their complements would do the same. AAC, CAA, TTG, GTT would all be the same amino acid. This would allow you to read the DNA backwards and forwards and get the same amino acid structure (perhaps backwards, but there's evidence that it could be worked around).
If you accept a palindromic 3-base code, you'll get:

AAA = TTT
AAT = TAA = TTA = ATT
AAC = CAA = TTG = GTT
AAG = GAA = TTC = CTT
ATA = TAT
ATC = CTA = TAG = GAT
ATG = GTA = TAC = CAT
ACA = TGT
ACT = TCA = TGA = AGT
ACC = CCA = TGG = GGT
ACG = GCA = TGC = CGT
AGA = TCT
AGC = CGA = TCG = GCT
AGG = GGA = TCC = CCT
GGG = CCC
GAC = CAG = CTG = GTC
GAG = CTC
GTG = CAC
GCC = CCG = CGG = GGC
GCG = CGC

Which can represent exactly 20 different amino acids, using all 64 combinations. It's a little too pretty to be a coincidence.
I don't know how easy it would be to find on the internet, but this is all listed in this paper: Beland P. and T. F. H. Allen. 1994. The origin and evolution of the genetic code. Journal of Theoretical Biology 170:359-365.
They attempted to map what amino acids the old codons represented and there are some strikingly interesting graphs. I wish I had pictures I could link to, but the gist of it was that the 64 codons could be put on a graph where codons that produced the same amino acid are placed next to each other in a grid. The "old code" had vertical matches, where our current code has horizontal matches. Supposedly, at some point, there was a switch over in representation.
One thing to note is that this potential "old code" didn't have stop codes like we do now. It's possible that the stop codes evolved to break anything that attempted to use the old code in favor of the new interpretation.

Who is the host.

[pavon]

You are assuming that humans are the primary host. That's what's scary about these cross-species viruses. Even if a strain were to mutate that killed every single human it infected within hours, as long as it is harmless to it's original animal host then it will continue to spread just fine. And if that species shares a close environment with humans (rats, birds, etc), then it will continue spreading to us as well.

That's nothing.

[pavon]

Bruce Schneier can kill a man with a single 0 bit.

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

[Anonymous Coward]

The protein that gets misfolded in Bovine Spongiform Encephalopathy (or mad cow) seems to be called just Prion protein [nih.gov] and is only 253 amino acids. If bunnie is correct and one amino acid = 6 bits, then thats 1,518 bits.

But the same sequence of amino acids exists normally in us, as a useful protein. What makes the prion variant dangerous is that the amino acid chain has folded slightly differently, to form a different shape - so it's in the file metadata, not the file itself.

Website appears to be down

[MHolmesIV]

So how many bits does it take to kill Andrew Huang's web server?

Example backwards?

[sp332]

"To ground this in a specific example, six bits stored as âoeATGâ on your hard drive (DNA) is loaded into RAM (RNA) as âoeAUGâ (remember the T->U transcription). When the RNA program in RAM is executed, âoeAUGâ is translated to a pixel (amino acid) of color âoeMâ, or methionine (which is incidentally the biological âoestartâ codon, the first instruction in every valid RNA program). " I think this is a little backwards, because the letters match A-T and G-C, so when "ATG" is copied to RNA it would be "UAC". Or is there a double-reversal somewhere?

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

[Enter the Shoggoth]

Or we can try a modern day example: expertsexchange
experts-exchange
expert-sex-change

I remembered in the good old days, my network access got suspended once because they triggered a naive web url history scanner....

I assume they also blocked the partner sites:

amateursexchange.com

and

diysexchange.com

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

[interkin3tic]

That's a good point although in looking up the size of prion protein I found some articles suggesting that there are some mutant forms which cause it. Presumably those mutations predispose the protein to fold the wrong way. You're right, folding wasn't represented by bits, but the same goes for bunnie's avian-swine flu virus. Simply typing out the nucleotide or amino acid code won't do anything, neither will actually generating a stretch of DNA or RNA that is the virus' genome, the virus still needs proteins to activate, so it's not just data that kills you.

If I'm not mistaken, there are some plant viruses that are only RNA. I don't know a whole lot about them, but I think there's probably some RNA enzyme activity that goes on there, so again it's not quite "data" that kills there.

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

[inKubus]

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

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.

Mr. Owl, how many bits does it take to kill you?

[AlpineR]

Boy has joined the chat.
[Boy] Mr. Owl, how many bits does it take to kill you?
[MrOwl] A good question. Let's find out. A one... A two-HOO... A three...
MrOwl has left the chat.
[Boy] Three!

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

[PachmanP]

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

Well 11 posts into a twitter feed and I'm willing to kill myself, so yeah...

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

[Ubahs]

I believe that RNA can just kill you - or the DNA - if it gets inside your cells (the hard part - but can happen easily sometimes). Your cell will just pick up the DNA/RNA and do whatever it says, usually along the lines of make more virus. The outer coating (proteins) are just the vessel to carry the DNA into your cells. Some, however, come with their own spiffy enzymes that embed the DNA into your genome so you can make plenty more...years later (retro) - maybe generations later, but I don't know if that's actually been documented in people (plants, this has been seen). All this is generalized and there are distinct types of virii (viruses? Hate the Latin stuff...) that each do their own thing, but it's the "data" you want to worry about for the most part. Mileage may vary, I'm not a virologist, etc.

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

[BrokenHalo]

If bunnie is correct and one amino acid = 6 bits...

Well, you could possibly argue that it isn't. I haven't read bunnie's argument, because his blog is slashdotted at the moment, so here's my reasoning FWIW: OK, it takes 3 codons (base pairs) to make one amino acid, but there are 4 bases in DNA or RNA. So in the first place we are working from a tetragesimal code rather then binary. If we assigned numerical values for these (0 to 3) then you obviously need more than two bits to represent a value of 2 in base 4.

Misleading sig

[The Monster]

What do you call a hockey Mom that preaches 'Abstinence only'? ... A grandma!

If the grandma you're thinking of is the former Governor of Alaska, you're thinking wrong:

"I'm pro-contraception, and I think kids who may not hear about it at home should hear about it in other avenues," she said during a debate in Juneau. . . . Palin spokeswoman Maria Comella said the governor stands by her 2006 statement, supporting sex education that covers both abstinence and contraception.

But don't let the facts get in the way of The Narrative.

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

[DarkSabreLord]

They've been doing that on Celebrity Jeopardy for years!

"I'll take Catch the semen for $800"

The interesting part for a bioinformatics person

[tlambert]

The interesting part for a bioinformatics person should be the application of reverse engineering techniques and abstraction to the problem space.

With respect, you're not really thinking like a Craig Venter or Sam Levy, or like a reverse engineer.

If I were attempting to reverse engineer the ability to program a computer, for example mitochondrial ribosomes, with an unknown instruction set, for example mRNA, and all I knew was how to make random sequences of mRNA, not how the equipment itself actually functioned, then I'd get a bunch of equipment (cells) together and throw random mRNA at it until I could make statistical correlations between the input (the mRNA) and the output (the proteins). And I would do this in parallel, on as much equipment as I could afford to get together, to shorten the amount of time it took me to get to the desired result. From an engineering perspective, that's the output, not how to create a cycle-accurate simulator or document the entire instruction set by sending the computer off to ChipWorks in Canada. We don't have the tools to do that right now.

However, it turns out that I do not need to have knowledge of how the computer works to get useful work out of it. A lot of nominally computer people program in high level languages, and have absolutely no idea what a compiler is doing behind the scenes, or that there's an assembler involved at all, or a linker. If they learned on Java, they might not even understand pointers. Now I'm not claiming that their work is optimal, or even necessarily efficient, but the point is that their work can be *effective* without them understanding the steps in between the input and the output, other than what input to give it to get a desired output. And if that happens at a low enough relative cost compared to the work product, it can be good enough to be economically viable.

This should be your take-away: We have a compiler. We do not need to understand it to create working programs. It is enough that we can do so.

PS: Yes, I realize that this is somewhat antithetical to the bioinformatics goal of managing and analyzing the data, thereby increasing our understanding of biological processes. But we aren't actually talking so much about doing science here, as we are talking about doing engineering.

-- Terry

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

[interkin3tic]

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

BSE destroys your brain. Do most twitterers' first 11 posts show signs of brain activity?

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. Influenza does too. So it requires more than just the data to kill you.

Viroids 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.

Obligatory

[magnus.ahlberg]

http://xkcd.com/435/

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

[mestar]

not to mention

www.oddsexchange.com (a real site)

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

[thunderclap]

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

It already has. Look at DJ AM.

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

[MenThal]

3.2 kbytes should be enough to kill anyone.

Remind me again; how big is the JPG on goatse?

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...

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

[squizzar]

I thought experts exchange http://www.experts-exchange.com/ has a hyphen for similar reasons. I can just imagine the google typo suggestion popping up...

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

[sFurbo]

In the case of prions, what kills you is not the sequence of amino acids, but the folding. You already have the proteins in your body, just folded the right way. And coding protein folding is tricky, do you need to specify every bond angle and length, or are there just 2 positions(folded right, folded wrong), making it one bit? Both are too extreme, but a wide array of foldings will collapse to the sick one, and a wide array will collapse to the healthy one. So, I suppose the question becomes, what is the proportion of the number of foldings collapsing to the sick one to the number of possible foldings. Or, more precisely, the logarithm of that proportion.

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

[Ubahs]

...too in depth. Not that I want to go too in debt, either.

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

[OeLeWaPpErKe]

Yeah, but what causes what ? Does twitter cause brain shutdown, or does brain shutdown cause twittering ... or perhaps it's a combination ?

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

[kohaku]

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

Or a single ethernet frame!

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

[Cyberax]

It was expertsexchange.com (without the hyphen) for several years. Can't imagine why they have changed that.

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

[Keeper Of Keys]

Correlation is not causation.

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

[OeLeWaPpErKe]

Great soundbite. But correlation DOES equal causation. One of three causal relations to be exact.

A and B correlate IF AND ONLY IF
1) A causes B
2) B causes A
3) There is a third variable C that causes both A and B

Note that obviously and unfortunately you need infinite data series to be sure.

Because one cannot differentiate between these 3 the soundbite "correlation is not causation" was created. But it is one of those "technically not a lie" you know like if you drive over someone saying it wasn't your car that killed him (it was the impact, you see).

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

[that IT girl]

Don't worry... you're not the only one who thinks outside the box. And you're not the only one who gets flamed for it, either. But... "All great truths begin as blasphemies." -George Bernard Shaw
Truth passes through three stages: First it is ridiculed, second it is violently opposed, and third, it is accepted as being self-evident. We'll get there eventually--hopefully without becoming one of the casualties.

Best part of the article

[Osurak]

The best part of the article is the random "All Your Base" reference.

Researchers are still discovering more about the H5 port; the Nature article indicates that perhaps certain human mutants have lungs that do not listen on the H5 port. So, those of us with the mutation that causes lungs to ignore the H5 port would have a better chance of surviving an Avian flu infection, whereas as those of us that open port H5 on the lungs have no chance to survive make your time / all your base pairs are belong to H5N1.

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

[Volante3192]

See, there's so much wrong with the OP that it's not even worth trying to correct him.

Swine Flu has existed for, likely, thousands of years although we only have proof of it since 1930. To say that a vaccine existed before the outbreak, therefore, is ignoring nature's years and years of work on influenza.

Second, the whole 300% baloney. Obviously, numbers like '25 vaccine related deaths to 1 influenza related death' doesn't exactly have shock factor. And 2500% mortality compared to the flu...well, that'll set off even more bullshit alarms.

In fact, even 25 deaths from a vaccine seems downright tame considering the regular flu outbreak takes out ten thousand annually (well, it's either 10 or 20 thou, but either way, we're talking magnitudes of difference. Another point ALWAYS overlooked by fearmongers).

It's just it's not worth trying to point out the flaws in their pseudologic; they're like birthers or moon landing hoax believers. A divine being could materialize in front of them with whatever evidence they want to disprove the outlandish belief, basically flat out go "Look, you're just wrong," and still nothing would change.

So, in the long term, better to just go for the +Funny

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

[BoothbyTCD]

'Viruses' is correct. The Latin plural of virus is just 'virus.'

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

[brkello]

The problem that you don't realize and probably can't realize is that you are messed up in the head. While human history has show awful things have been done, believing fringe conspiracy theories shows that your brain is susceptible to garbage. You probably consider yourself to be more open minded than others...why can't we understand the truth you are saying? In reality, being open minded means that you can consider a thought, but still be able to dismiss it when it doesn't prove itself out.

Let's consider your ideas. On one hand, you have a vaccine that kills a certain percentage of people (let's assume it is less than 300% since I would hope that is a typo). On the other hand, you believe people are creating vaccines for diseases that don't exist yet. The problem is if that were true, why aren't we being vaccinated every month with all these new diseases coming out? I haven't required any strange vaccines for a new disease, have you? H1N1 is just the flu that is slightly more deadly. It has been shown that these things can alter without scientific human intervention. It just changes as it goes from species to species and mutant strains can take off due to natural selection.

But you want to believe that the military complex designed these things. Is this some sort of backward Intelligent Design theory you have?

If everyone is modding you down, it isn't because you see things more clearly. It is because your mind is broken. It is unfortunate that when you are insane, everyone seems against you. You can't see that you fail to see the world correctly since you have some sort of chemical imbalance. So your life is full of anger and mistrust. The problem is you can't trust your own perception. You have to trust others and let them help you. But your insanity doesn't allow you to trust. It's sad.

You claim to want independence, but that is a lie. You don't come to an online forum to find independence. You obviously are here because you want to find others that share your viewpoints so you don't feel so alone. Unfortunately, your viewpoints are wrong and extreme. Until you get past your ego and realize you know nothing and that you need help, your existence will be lonely.

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

[sexconker]

When the shitty trance/techno/house/whatever music kicks in, I'm going to kill myself.

They did a nice job on the 3D fractal video though.

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

[treeves]

Well, if you decide to call amino acids "bits", then I could do you one better and call atoms or functional groups "bits", and replace a methyl with a cyano (or three hydrogens with a nitrogen), and that would be quick death.
I know viruses reproduce and cyanide does not, so it's not a matter of changing literally one molecule, but from an information perspective (e.g. there's cookbook for humans that includes a recipe for hemoglobin that I could change) it makes some sense.

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

[sexconker]

No. "Meta" is the most overused bullshit term ever.

It simply means "about".

Any "mata" data has to be external.
You can't have an object with internal meta data (about itself) because that data's existence (regardless of it's content) alters the object, and is part of it.

Even if it were self-referential, it's not meta.
And even if you want to use the word meta to describe it, the shape of a physical object is certainly not meta data. If we're referring to an object as data, then the entirety of the object's physical state must be described as such.

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

[sexconker]

Uh...

4) There is no causal relation, and your sample is shitty.

5) There is no causal relation, your sample is good, and it's just a coincidence.