What the hell?

I'm perfectly serious.

The nerdier elements amongst you will have heard of the seti@home project. They send data, radio waves, that they collect from the cosmos to your home computer, and your computer scans the data looking for patterns or messages that alien species beam off into the cosmos. It's pretty much a waste of time that is designed to keep beardy Trekkies off the streets. But it was the first example of people pooling their CPU power for a common cause. They did it with Mersenne prime numbers as well.

But fuck all that. This is much cooler.

The rosetta@home project is similar, yet much more useful. It is exactly the same structure of project (they create data, send them to your CPU, your CPU solves it and sends it back) but it does something more handy - determining the folding structure of a protein.

So who gives a shit about protein origami? Everyone in a white coat. Proteins, like all other natural systems, tend towards their natural equilibrium, their most stable state. Unfortunately that is very hard to determine because proteins are made out of many, many amino acids all of which fold up and behave differently. When you get a string of, say, 800 amino acids to make a protein, we have literally no fucking idea how the outside of the molecule looks unless we test them.

So, what does a large brute-force numerical solution to a problem need? Yes - masses and masses of computer power. Hence, this project. Here's the stuff they're working on:

"Malaria: We are part of a collaborative project headed by Austin Burt at Imperial College in London that is one of the Gates Foundation "Grand Challenge Projects in Global Health". Malaria is caused by a parasite that spends part of its life cycle inside the mosquito, and is passed along to humans by mosquito bites. The idea behind the project is to make mosquitoes resistant to the parasite by eliminating genes required in the mosquito for the parasite to live. Our part of the project is to use our computer based design methods (ROSETTA) to engineer new enzymes that will specifically target and inactivate these genes.

Anthrax: We are using ROSETTA to help John Collier's research group at Harvard build models of anthrax toxin that should contribute to the development of treatments. You can read the abstract of a paper describing some of this work at http://www.pnas.org/cgi/content/abstract/102/45/16409.

HIV: One of the reasons that HIV is such a deadly virus is that it has evolved to trick the immune system. We are collaborating with researchers in Seattle and at the NIH to try to develop a vaccine for HIV. Our role in this project is central--we are using ROSETTA to design small proteins that display the small number of critical regions of the HIV coat protein in a way that the immune system can easily recognize and generate antibodies to. Our goal is to create small stable protein vaccines that can be made very cheaply and shipped all over the world.

Other viruses: We have been collaborating with Pam Bjorkman's laboratory at Cal Tech to use the ROSETTA protein-protein docking methodology to build models of herpes simplex virus proteins in complex with human proteins.

Alzheimer's disease: Alzheimer's and many other diseases are likely to be caused by abberant protein folding in which proteins form large aggregated structures called amyloids rather than folding up into their normal biologically active states. A big advance was made recently by David Eisenberg's research group at UCLA in solving the first structure of an amyloid. We are collaborating with their research group to use the structure to predict which parts of proteins are likely to form amyloids, which will be a first step to blocking amyloid formation and hopefully disease.

Cancer: Cancer can be caused by mutations in key genes that disrupt normal cellular control processes. We are developing methods for cutting DNA at specific sites in the genome, and we will be targeting sites that are implicated in cancer. After these sites are cut, they should be repaired by the cell using a second, unmutated copy of the gene and the cell should no longer be cancerous. This is a very specific form of gene therapy that, if successful, will circumvent one the main objections to current gene therapy methods; namely, current methods insert the unmutated copy of a gene randomly into the genome, and if the insertion point happens to be near an oncogene, the gene therapy will cure one disease but cause another. Because our methods will target specific sites instead of random sites, they should avoid this pitfall.

Prostate Cancer: The androgen receptor (AR) binds testosterone and is responsible for normal male development. When the AR becomes hypersensitive to testosterone, prostate cancer is the result. The current treatment for prostate cancer, called "hormone therapy", involves lowering the amount of testosterone available (sometimes by castration). Many malignant tumors are resistant to this therapy, however, so we are applying our protein design methodology to find different ways to inhibit the AR and to treat prostate cancer. Specifically, we are trying to design proteins that will disable the AR even in the presence of testosterone. We are doing this by designing proteins that will prevent the AR from entering the nucleus of the cell (which is where it does its dirty work), and also preventing it from binding DNA and activating tumor-specific genes even if it does get into the nucleus."

If you're anything like me, you probably leave your computer on for several hours a day while you're not around it. So make it do something useful instead of display that Cephalic Carnage screensaver over and over again. This program does absolutely nothing but work on determining the structure of a protein while you're away from your PC.

And trust me, if your computer figures out a dramatically effective way that antibodies stick to the HIV structure, and the data for the base structure for an AIDS vaccine starts in your CPU, you'll have your own special footnote in history.

"History was made today as an ugly spotty 16 year old metalhead discovered a key weakness in the human immunodeficiency virus. While he was dreaming about buying a better set of pickups and getting band groupies, his computer found an area on the virus where certain amino acids, when enzymatically bonded, would cause the body would generate normal antibodies and neutralise the virus. A vaccine is a few years away, but the discovery has the potential to save several million lives and all but eradicate AIDS from the planet. The metalhead, known only as "666slipkn0tkarnag3" could not be reached for comment but it is widely believed that somewhere he is playing power chords, chronically masturbating and unaware of the fact that he saved an entire generation of Africans."

But seriously... get the software and help. It's good for the soul.

__________________

Thats pretty cool, and a great idea. I'm all about it, because my computer is always on when I'm out getting stoned or chasing women.

(Downloads software)

__________________

that is one of the most interesting things i have read in a while. thanks FBS. so, let me get this correct, pretty much they are figuring out the amino acid structure and leaving it up to everyone elses computer to figure out how it crumples up?? THAT IS INSANE! i just dont see how that will work.....but then again, i don't think i care to either.
this kind of shit makes me want to start reading/studying biology again. i just fucking hate the chemistry aspect.

__________________

Yeah, that's close enough.

__________________

Its beautiful really

__________________

SETI

Search for Extraterestrial Intelligence also employs peoples computers at home to help sort data in the hopes of finding signals in space from intelligent life forms. They get more data than they can decode so a small prog is available for anyones home PC to lend a helping hand.

Thanks for overstating

I'm downloading it now. I'm going to be immortal GOD DAMNIT!!!!!

__________________

Thats insane

Yeah its really cool,they have the same type of program decyphering old WWII Codes, it sends them to your computer and you computer cracks it and sends it back, shame you dont get to see them.

__________________

This is awesome. Now I don't feel so bad about not being honest with all those women...

I remember SETI, it was cute. I always wanted to get it when I was younger but my computer couldn't handle it.

__________________

why would we still be decoding that stuff, completist collection of data or something? archiving?

__________________

I really wish that wasn't so long. I'll read it later.

__________________

i know someone that has the delta 32 mutation. lucky son of a bitch. very rare to find somone with the delta 32 mutation.
delta 32 makes u completely immune to aids/hiv and plague.

__________________

Am I the only one that finds it a bit amusing the the AIDS finding computer program is called BOINC?

__________________

I joined up for the Rosetta@home thing. Pretty fuckin cool idea i reckon.

And now i feel all tingly

Haha go into BOINC and select your project and show graphics... Look at the little suckers go!

__________________

That's the kind of thing that we're interested in here.

From memory, they also found a bunch of East African women several years ago who have similar or related mutations.

__________________

LOL

__________________

thats exactly what i was talking about. just i was referncing the plague incident.

__________________

Is he related to Andy Collyer?

hmm?

Oh deary me. FBS, good for the soul? Come on, don't let me down like this. But, at least I find it reassuring that you didn't mention yourself as the potential "discoverer". There is a limit to how many times the word, with variations, "FUCK" can be accepted in a respectable foot note of history.

And to all of you who have choosen to let your computers work on the defeat of AIDS, welcome aboard.
To the rest of you - take the time, download the software. It's good for your sex life.

__________________

I am actually, genuinely, real-world happy at the response to this thread so far. I hate you all way, WAY less than usual right now.



You know something? You are pretty much perfect. You combine being nice, being awful and torturing my beautiful language in almost equal amounts. I never have any idea exactly what you mean. It's fun and cool. You should keep posting here a lot.

(Also, if you were implying that I am somehow betraying myself by being pleasant, then you can take a running jump and fuck yourself. I am LOVELY AND NICE. Anyone who doesn't believe me will be killed.)

__________________

And just a couple posts ago you said you liked being a mean CUNT and a total BASTARD.

But I still love you, in a platonic way that is.

__________________

Literal translation: you're too fucking dumb to understand duality?

(No, seriously, I'm really nice. All puppies and shit.)

__________________

I understand duality. But I thought you were talking in absolute terms.
Offcoarse, since your all puppies and shit, here's a pretty flower.

__________________

I would really like to help this Rosetta project out. Minimum effort on my part now might mean a better world for me later. My only problem is I got fucking Windows ME but I meet the all the other requirements. I'm not sure I can use the BOINC program.

I'm going to try it and see what happens.

Btw, why wasn't this Rosetta@home thing used to figure out the human genome? Anyone know?

Edit: Well, it seems to run just fine on Windows ME.

__________________

Oh, we understand duality alright. It's this scizophrenia I'm having trouble with. But thanks for starting this god-damnit-I-feel-stupid-for-not-having-started-this-myself-a-long-time-ago-thread.

__________________

Metaltabs now has a team you can join. This way we know who we are and can keep track of how much work our computers have done.

__________________

I didn't know about all that team mularkey existed. I tried joining. Did it work?

__________________

Umm, it doesn't look like it. Maybe it needs to update before new members show up?

__________________

Tried something else. Either way, it's going fiddly with a protein structure right now. That is very much the important thing.

__________________

I think I joined, though it didn`t even ask for a nickname or anything.

__________________

Puppy shit makes a great halloween treat.
Kids think it's Tootsie Rolls with the wrapper off.

...You truely can be a sick bitch... I guess thats why I like you

__________________

FBS this is really amazing. Interesting to watch, too. Glad I could add to the protein structure analysis.

__________________

Me too, dickface. Seriously, it's pretty testes-interferingly awesome.

P.S. I think this is Nomad's computer, but I don't want to change the settings because I might break something.

__________________

Soulinsanes's note on "our" teamsite of the Rosetta project:


You have my undying love for this text.
No you don't.
But I very much like you for it.

Come on people, join in, hands off the dick and on the mouse, where they belong.

__________________

Who is this? FBS?

__________________

More than likely. They went drinking together yesterday...

Is there a way to see who all's on the team? I joined it earlier, but I don't see any roster things anywhere, other than the five guys at the bottom.

__________________

sounds like they had a fun night. nice description!

__________________

Will it double my dating? hahaha.

EDIT: I'm in.

__________________

I think it takes a day or two for the server to load you in. I didn't see my name appear (Dylan. I'm in the lead!) untill the next night.

__________________

Holy crap, that's some crazy stuff! Most interesting thing I've seen all weekend! Deffo look into this!

__________________

Don't know. But don't get your hopes up. But, I shall correct myself:
Join in. It's good for my sex life.

__________________

We are doing really good for such a small team. My PC has been working on this monster fucking protein fold the last day, so I hope I don't fall to far behide in points. I have the slowest PC out of the whole team

__________________

Aw, poor you. But don't worry. I'm right at the bottom of the list, ready to catch you, throw you into the ground and kick gravel in your eyes.

__________________

I'm surprized my shit even runs the program correctly. Lol, Windows ME was never designed to be actually productive.

__________________

Just signed up, bitches. I'll soon get to the top spot on the team...my computer is on 24/7.

Yea, s'pse. But, at least I'm contributing.

__________________

This is weird...whenever I turn that BOINC program on, my laptop shuts down after 10 mins...

You assholes are kicking the shit out of me in points Most of the ones I get are only worth 10 points or less. I guess I'll get some good scoring proteins sooner or later.

__________________

Ok, I just got a great ideal. I'm going to see if I can't get the computers at my work (U.S. Navy) onto our team.

The worse that could happen is the program gets noticed and flaged as a danger ( in which case my ass will be in some deep shit ). More that likely, the network will never allow the program to download or to transmit data back, but its worth a try even if I get put in prison.

__________________

Don't put your ass on the line man.

__________________

I can always claim and honestly say I did it for aids and cancer research. Then I could retort by saying, "I guess the Navy just doesn't care about aids or cancer"

__________________

Haha they pretty much don't....


Want to hear some ridiculously crazy shit? This guy I know had skin cancer in his arm, and it got removed. He got a waiver for it.

Find out a year or so later that he's got very very minor asthma. Doesn't even need an inhaler. Guess what? They're kicking him out.

He's got a waiver for CANCER, but getting kicked out of the submarine force, where you don't run unless you like being unconcious, for fucking Asthma.
I love our military.

But yeah, anyway to be on topic, I'm sure there won't be any problems with the rosetta project. I'm sure if there was anything malicious behind it, it would have started with Seti, and I never heard of any significant problems with that.

__________________

Soulinsane, you still haven't got my undying love, but you are making a good run for it; "even though I might get thrown in prison for it" my my...

__________________

Darko, your computer is kicking protein ass

__________________

Yup, I'm the best philanthropist of you all. Now who said Altruism was bullshit?

This is great for me though. My computer is never off and BOINC stays on unless I'm doing recording.

__________________

I'm sigining up right now, although its taking forever to download because I have 56K. I figure this will make up for that one time I gave that guy AIDS. I'm not gay or anything he was just bending over and i acicidentally walked into him. Man was he pissed when he got AIDS

oh well i'm redeeming myself

__________________

I was doing kinda well, but turns out BOINC was using a lot of my international traffic. I have it back on now tho

__________________

2000 credits mofo's!

__________________

I thought it just took a little bit of CPU power, and some more when the PC is idle, but I just found out it takes about 90% of mine, even when the PC is activley used.

__________________

Yeah, I've noticed that.

But check the priority in the system queue - it should be on "low". It shouldn't get in the way of other applications.

BIG SMILES!!!

__________________

Considering my piece of shit conputer is only about 0.01% efficient in the first place I'm not losing much If it cures AIDS I will give it to a museum.

__________________

If it cures aids I shall build a shrine for it.



Smile returned.

__________________

If my computer finds the cure for AIDS, I want to have sweet hot monkey sex with it.

__________________

If you do that, I shall build a sanctuary for you. Asylum Sanctuaries Inc.

__________________

There's that "disk space" section, and mine is at 29.69. What's everbody else's disk space? My computer runs BOINC and other apps just fine. And I'm almost in first, goddamn Oli.

And this is what I'm giving my computer if it cures AIDS: http://oz.irtc.org/ftp/pub/stills/1996-06-30/shrine.jpg (early computer model build)

__________________

I honestly hope our computers never will be appreciative of such gestures.

I'm allocating a bit more than fifty to Rosetta and about twenty to World Community Grid.


Hut hut hut, if any of you apes haven't joined yet, then step into line right now!

__________________

Yay, I finally broke 1000 credits

__________________

I turn off my computer for a day and FBS and Soul are both ahead of me. You cunts.

__________________

I'm giving you "the look." I don't think I need to say anymore except --ooo ooo ee ee RAW RAW!

I'm doing it now. wally did it so I will.

__________________

It's really for a good cause. If you're not doing this and you own a PC then I will not feel sorry for you when you die of AIDS.

__________________

I've quit this fucking thing. I just cannot get it to work for more than 15 minutes, at which point my computer shuts down.

Oh, don't you feel bad about that; pretty women are giving me "looks" all the time.

__________________

The fan broke on my PC and it's in an un-air-conditioned, poorly insulated Chicago building, so I quit doing this. But you'd damn well better pity me if I die of AIDS. That pity will make it all okay.

If you need a transfusion, I'm a universal donor and I'm clean. Lemme know!

__________________

Why would I want a transfusion? I want pity.

You'd get more pity--at least from these guys --if you had my blood in your veins. Just trying to help.

__________________

More pity than if I had AIDS and the primary reason it hadn't been cured by then was because my fan broke and I couldn't fix it? I doubt it. I'm also not sure why I'd want a blood transfusion, even if I did have AIDS (they're known as the occasional cause, not the cure, of that particular affliction), or why I'd have to get it from Ohio when I have a non-rare blood type and live in the third largest city in the US. So let me say now that your offer makes no sense given any criteria I have to judge it.

You're rubbish! I'll have to fly the flag for the UK on my own then

__________________

Just being neighborly. I know that crap. I worked with diseased people.

__________________

Everybody knows that crap (though that's a funny response to a post in which the only assertation is that your last few posts were nonsense and shouldn't have been written). I was just pointing out the various ways in which you weren't being neighborly, unless 'being neighborly' means 'making an irrelevant and useless comment over the internet to somebody you've never seen.' I'll admit to being out of touch if that's what 'being neighborly' now means.

Well, get with the program. I guess you speak a different language in Chi-town than we do over here.

__________________

My neighbors here are mostly black and on welfare. Being neighborly with them means having a beer on the stoop, which is actually a kind of being neighborly I can get behind.

But I'm pretty sure that Chicago, as a big and important city, is superior to the rest of America, and therefore its denizens are superior to people living in, say, Ohio.

or you could buy a fan for 5 dollars

__________________

$2, but it's not that simple. It's not a hardware problem. The software is fucked up, and though I've replaced it several times under the directions of HP professionals, it continues to die on me. I have to use ice packs to be able to use the computer for longer than a half hour at a time, but they melt pretty quickly.

Hey! At least I got some credits...

0.42

Well, we're ranked 381 now

__________________

Anyone who hasn't seen this thread, well, see it now.

There are almost no good things you can do that are easy, effortless and entirely free. But this is one of them.

__________________

An example of the difficulties and also the promise of this kind of research.

__________________