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Still sick...

...and I've got just two words for that. Code signing.

Seriously. Code signing.

Viruses work because our cells contain machinery which will read, accept, and translate any RNA strands they see into proteins. Any RNA strands they see. Including RNA strands injected into our cells from viruses, or RNA strands transcribed from DNA injected into our cells from viruses.

Which is, from a security standpoint, pretty fracking stupid.

Code signing, I'm telling you. If our genetic material were signed with some sort of unique code that means "yes, this really does come from us, it's safe to translate this RNA and build this protein," and the transcribing and translating machinery would refuse to process RNA that wasn't signed, then viruses could inject their bits into our cells from now 'til Doomsday and it wouldn't mean diddly.

Code signing. Just one more reason why if we were designed by some Grand Creator, he wasn't very good at his job.



( 25 comments — Leave a comment )
(Deleted comment)
Dec. 22nd, 2008 10:08 pm (UTC)
Yep, Shelly is. Think I'll tell her to get on it as soon as she's back from visiting her mom.
Dec. 22nd, 2008 09:48 pm (UTC)
Maybe the Grand Creator simply used a poor uniqueness-generator, or an insufficient number of unique bits - brute force heaven! :)

Hope you feel better!
Dec. 22nd, 2008 10:11 pm (UTC)
Considering how many problems regular old SSL causes at times, I'm happy this ISN'T the case.
Dec. 22nd, 2008 10:17 pm (UTC)
What we need is RNA restriction endonucleases. Bacteria evolved DNA restriction enzymes for precisely the function you mention, although they took the "negative" approach; i.e., to slice up foreign DNA molecules that do have a particular nucleotide sequence that the host cell lacks. However, they only work on double-stranded DNA.
Dec. 23rd, 2008 03:59 pm (UTC)
That's a great idea! Custom-tailor an enzyme to recognize certain potentially harmful sequences in a strand of RNA and chop it to pieces before it gets translated.

RNA carrying the sequence for reverse transcriptase would be a logical bet, since reverse transcriptase is not (to my knowledge) coded for or used anywhere in our cells. If you see it, you know it's from a retrovirus.
Dec. 22nd, 2008 10:17 pm (UTC)
Viruses work because our cells contain machinery which will read, accept, and translate any RNA strands they see into proteins.

1. Things like viruses "shouldn't" have been able to enter the cell itself. Each cell is surrounded by a cell wall, which has protein receptors that determine whether something should be able to enter the cell.

2. Even when a virus is inside a cell, cells have some protection in lysosomes. These organelles DO the code-signing that you're looking for, and digest things that they don't recognize (like viruses).

3. Feel free to describe a code signing algorithm that's as parallelizable as what our cells use to replicate RNA.

Edited at 2008-12-22 10:19 pm (UTC)
Dec. 23rd, 2008 10:51 am (UTC)
Actually, only plant and some fungus species have a cell wall. All others only have a semi-permeable cell membrane which is where the protein receptors are located. Viruses bypass the protein receptors entirely and inject their nucleic acid of choice by chemically splitting a section of the membrane itself.
Dec. 23rd, 2008 04:04 pm (UTC)
A simple code-signing mechanism might be a "primer string" attached to each molecule of mRNA that prepares a ribosome for translation; absent the primer string, the RNA won't be translated. It wouldn't take much rejiggering; strands of mRNA coding for specific protiens already carry pre-defined START and STOP codons. Make the START codon longer and species-specific and there you go! Viral RNA carries conventional START codons but without the correct "extended START" codon it wouldn't be translated--the ribosome simply wouldn't recognize it as valid.
Dec. 22nd, 2008 10:23 pm (UTC)
The method through which cells determine whether or not to accept chemical signals is actually negotiated at the cell membrane (call it a firewall). There is, as far as I remember, no 'code signing' inside of the cell. Such things have developed so that the body can react quickly to certain stimuli (Adrenaline, go! Melatonin, go! Testosterone, go!)


The way the viruses have evolved is to imitate the natural signal compounds the body produces and latch onto the cells through the receptors that the hormones need to signal. I guess you could argue that 'code signing' is used there; the virus has to have the proper code to get through the cell membrane to begin with, which explains why we don't all have feline AIDS. (note: hopefully other things explain that as well.) With this code signing, certain viruses don't spit their RNA into us at all.

This part is fuzzy, ask Shelly: 'Code signing' isn't used in RNA transcription since DNA can be split at (almost) any point, which is where the DNA = coding analogy breaks down. When I start Photoshop, it goes through verification before it opens the program. When I make a certain protein in a cell, there can be multiple places on the DNA strand that may code for that certain protein (yay redundancy!)

In this way, the viruses use our natural machinery against us. Now, this is natural machinery that works very well for us. I thoroughly enjoyed the effects of puberty (and still do!). To fight these viruses, our body has developed various and sundry ways to fight it.

This is why vaccines and flu shots are good: because they're like adding extra definitions to your body's anti-virus program. Sickness occurs only when your body can't respond fast enough, and is, actually, a very good thing. It means your body will react faster next time. In fact, having a small amount of ever-evolving harmful viruses and bacteria in your body at all times is a wonderfully good idea, as it keeps all your systems up and running at full strength.

I always blamed my good health on growing up on a chicken farm. I breathed in so much shit growing up, my body's ready for whatever can be thrown at it. XD
Dec. 22nd, 2008 10:24 pm (UTC)
Ha. The guy above me beat me to it. XD
(Deleted comment)
Dec. 23rd, 2008 04:05 pm (UTC)
True. But bugger evolution--we're near the point now when we can take over from the blind watchmaker anyway. :)
Dec. 23rd, 2008 12:45 am (UTC)
This is going to be really random. But I was talking to a partner of mine today and he was going on about this game that he wanted to play. I about fell over in surprise to see you listed as the creator. It's a small small world.
Dec. 23rd, 2008 04:05 pm (UTC)
Very cool! Onyx, by any chance?
Dec. 23rd, 2008 05:32 pm (UTC)
Yes It would be. I should add that i am some random person who used to comment to you a lot in sextips and lurks your journal.
Dec. 23rd, 2008 01:44 am (UTC)
I'm thinking that lack of some such measures are why we continue to evolve.

But then, we have a HUGE lack of good security, and this is only one way...
Dec. 23rd, 2008 02:33 pm (UTC)
Genetic research appears to support your thinking. The development of the first placenta is speculated to be the result of a viral rewrite, for example.

Dec. 23rd, 2008 04:07 pm (UTC)
Yep, the lack of basic DNA security is in fact one of the things that make evolution possible. But bugger that, I say. Evolution is a blind, non-goal-directed process that's just as happy producing beetles as people. It may be speciesist of me to say, but human beings are unique among all the animals in that we have, theoretically, the ability to take over from this blind process and do things a little more intelligently.

Besides, if it means I never catch a cold again, I'm fine telling evolutionary forces to bugger off. :)
Dec. 23rd, 2008 09:54 pm (UTC)
There's a lot to be said for the intelligent approach, and we've yet to see any other species apply it to the level some humans have displayed. It's still worth noting how often the intelligent approach has benefitted from the occurence of fortunate accidents.

Having said that, I'd rather not leave things up to the accidents either. The phrase, "Let nature take its course," gives me the willies.
Dec. 24th, 2008 02:16 am (UTC)
ooooo.... hubris, hardly ever the downfall of civs that think they have got it all figured out...
Dec. 24th, 2008 03:18 am (UTC)
Downfalls of civilizations? Piffle. Civilizations are nothing on evolutionary timelines. Left to its own devices, the blind forces of evolution will wipe the human species right out of the universe in time. evolutionary forces don't care, and they've got a pretty good track record so far of wiping out entire ecosystems in the blink of an eye.

We don't have it all figured out, but we are unique in the history of the world in that we alone of all species that has ever existed on the face of the planet can have some say in shaping our destiny. I say that's a good thing.

Edited at 2008-12-24 03:18 am (UTC)
Dec. 23rd, 2008 05:15 am (UTC)
I agree. I was constantly fighting various colds this semester, since I was at a school several days a week and children are filthy little germ vectors. I wish my cells had code signing.
On a slightly different note, you must get better soon so we can go for sushi! My offer of chicken soup still stands.
Dec. 23rd, 2008 04:08 pm (UTC)
Dunno if we're likely to make sushi, but you're welcome to stop by nonetheless!
Dec. 24th, 2008 02:21 am (UTC)
Dennis and I may stop by to say hi sometime.
Dec. 23rd, 2008 08:20 am (UTC)
I see what you're getting at, but the analogy really does break down at a number of places. First, I'm not sure that DNA/RNA can be shown to be Turing Complete. Second, it's a fairly well-known-and-popular fact that the DNA/RNA transcription mechanisms are quite prone to error by omission, substitution or repetition. How can you do any sort of signing of a key of any useful length when tolerance or acceptance of a key that is "mostly correct" is a design requirement of any signing system you develop. How do you do key revocation ?

Dec. 23rd, 2008 04:09 pm (UTC)
By making the key not code for production of anything. We've already got well-defined codons that mean START and STOP; add a bit of complexity and robustness to the START codons and set it up so that RNA without the proper START sequence doesn't get translated.
( 25 comments — Leave a comment )