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Distributed Computing Attacking SARS
fwc writes "D2OL has added a SARS Target to it's distributed computing project which locates potential drug candidates for several viruses. At this point, I've replaced SETI@Home at least temporarily on all of my Boxen. There are clients available for Linux, Solaris, Mac OS X, and of course Windows."
I wonder when my United Devices client (ud.com) is gonna add that project... It's currently working on smallpox and cancer...
;)
Should I change projects? Switch UD in favor of D2OL or what? And why?
Any technology distinguishable from magic, is insufficiently advanced.
I'm not sure that this project (as it is now) will be all that useful. Alot of it appears to be hinging on generous speculation.
I'm not a virologist, but as far as I remember, drug-directed approaches haven't been notably successful with attacking coronaviruses (ever hear that "medicine can't cure the common cold", anyone?) -- and to confuse things more, this one seems to be very atypical.
Also, from what I know about the anti-virals that have shown some efficacy against these type of SS-RNA viruses, they've been directed at nucleic acids, not at product-proteins. Ribavirin, which was initially hoped to be the "magic bullet" to stop SARS is a nucleoside analogue (purine? I don't remember). I haven't heard of an effective intervention that disrupts the protein envelope or synthesis.
Additionally, this group is assuming that the causitive agent of SARS has correctly been isolated and identified in the first place, which isn't certain by any means.
Aiming computing power towards a worthy goal like this can't hurt, but I question how effective it really will be. I guess the computer-types can just tweak the parameters as the biomed-folks find out more on their end.
Sony has actually decided to adopt this model with the (eventually) upcoming Playstation 3. The idea is that users will leave their PS3 running all the time, game or no, and Sony will use the extra processing power to do whatever it is they do...spy on us or something. Of course, in order for this to work to their advantage we'll all have to use our PS3s to connect to the Net or some similar service. The only thing I hope is that Sony actually has an option to turn off processor sharing, just in case us hapless users don't want to support whatever cause it is that they are studying at the moment.
In order to be immortal you must be organize
While much of the public fears of SARS is definitely overplayed in the short term, in the long term there is a justifiable fear of the risks posed by a fast-spreading, lethal, and poorly understood pathogen. Especially one that coincides with the cold and flu season (thus masking the symptoms of a more severe disease), and may share similar traits in terms of easy transmission via airborne droplets. Remember, highly infectious pathogens are much more dangerous to the world population than they were prior to the jet age (think Ebola...)
SARS stands for Senior-citizen Accelerated Reduction Scheme. Anyone at a 3-feet radius around a SARS patient will be sprayed with thousands of droplets from his/her mouth. Medical mask alone is not enough to stop the spread you'll survive better with a pair of goggles and a detail aseptic training. Motality rate is about 5% in Asia, 10% in Canada. If 10 million got the disease, you will find 1 million graves more somewhere. A little bit more than the Hiroshima blast.
At first no one will believe it, it's just common cold flu. Then people start to cough and cannot breath. Next, you'll find the ICU in the hospital is jammed with respiratory patient and to make the matter worse, the medical front-line is collapsing one after the other.
Please study the disease and avoid it before it ever begin in your city.
SARS kills, SARS also kill your tourism, restaurant, hotel flat. Business will go down 90%. By all means, avoid SARS.
If we had lived in that time, SARS would probably have killed a similar percentage of the population. Nowadays we have modern concepts of hygiene, we know what bacteria and viruses are, etc. so we know how to contain epidemics. That doesn't mean that the disease is any less worth of fear. It's that fear that motivated humanity to get to this level of medical knowledge in the first place.
that all these distributed projects are actually doing what they're supposed to?
Would you notice it if my long-lasting-no-results-yet-but-soon-for-sure distributed project for an AIDS vaccine were actually a rendering farm for animated kiddie porn movies?
How small a thought it takes to fill a whole life
Biologists have to find target. Produce the protein artificialy, study it and validate it (=conclusive evidence that blocking it will blocks the virus). Ten they have to develop a reliable high-throughput assay and huge collections of chemicals are screened to see if there is any decent inhibitor found. Chemists select the most reasonable candidates and start elaborating them (=derivatomania). Once they get very potent inhibitors, they do a lot of other optimisation - to get drug candidate that is cell-permeable cells, not metabolized/excreeted too fast, has low protein binding and good distribution, is not toxic and is preferably oraly available. At this point a lot of detailed biology research has to be done in animals, which is slow. Then there is study on healthy volunteers (subject of government aproval), then pilot clinic study just to see if they can get decent dosing in patients, then second large double-blind clinical study to see efficiency and the third phase even larger study to compare the drug with other therapies. Human trials are extremely costly.
Pre-clinical development can take several years, as it was case with AIDS, clinical trials 4-6 years. It goes this fast only if there is a big profit potencial(to justify $400M cost of development), which so far there is not.
Government now tests a collection of *all* known approved drugs (concidered reasonably safe) to see if any of them has any effect. If we get lucky on this - slim chances - it would cut the development time and the clinical testing too, since only 1-2 studies would be needed.
I doubt that we will ever figure out - and I suspect that even if we did figure out we couldn't do much about it
You can argue patents all you want but in order for the pharmaceutical industry to function the intellectual property right of drug research companies most be sacrosanct. Billions of dollars are spent every year on pharmaceutical research and if the is no return on investment then there won't be billions of dollars to spend next year. I realize that there are government grants but that is not were most of the money to fund research comes from most if it comes from the money made from the previous successful drug. I know it sounds cruel to say you can't make this drug because you can't afford the patent rights but its better then having there be no drug research at all.
Just so you all know, this is about as fruitful as SETI, so don't go giving up on that just because this "sounds" like it'll be more important or yield a more relevant result. It won't. I work on this type of protein modelling and drug-protein interaction research. The state of the art is that anything produced by your client is going to be at best a wild guess at what the protein looks like or what interactions the drug will make with the protein.
The "scoring" that your results are based on is just how nice the energy is of the final folded protein. This is flawed in a couple of ways, first it means that we need to know nearly everything about protein folding energetics and calculate it with a tidy formula (not yet...but we're getting there) and it means that the folds chosen by the algorithm to test for these energies are all the possible folds (last best guess is that we only know about 80% of all folds)...and then if you're going to try to use this for docking a drug molecule...you open a whole new can of drug-protein interaction knowledge necessary.
SETI actually has a better scoring method for finding a "hit" and while the result (hey, look radio from space) isn't as tangible as killing a virus...I'd say stick with the SETI or try and break the XBox number....or find some more prime numbers. At this point, distributed protein folding/docking isn't just fishing in the dark, it's fishing in the dark in Death Valley.
Mordor...a magical, mythical land where women are more rare than dragons--but where every man would rather find a dragon
What if governments payed for the research? Finding treatments and preventions for diseases seems like it would be in the best interest of a nation. Alas, helping people does not seem to be on the agenda of many governments or the pharm. co.'s.
It does cost the companies a lot of money to make the new drugs, but they easily make that money back and then some through defending patents that keep the price of the drug artificially high, even after the research is payed off. Pharmcos are a two sided coin: on one side they help people through tough times, on the other side they make money off of people's pain.
-dr. layyze f. tooth PhD
SARS has a mortality rate of more than 10% so far in Singapore.
In the past century, there has not been any other infectious disease that has spread so fast and consumed medical and political resources of affected countries so fast.
Just because your country has not been significantly affected (so far) does not mean that this is a minor problem.
It's still early in the progression of SARS. If there are no good public health measures to limit the spread of SARS, it's entirely conceivable that the entire world would be infected by 2005. Even assuming that the mortality sticks at 10% or so, that's a heck of a lot of dead people.
I read that an exotic open-air animal market in Guangzhou, China is being investigated by WHO as possibly having something to do with the origin of the illness. (That story taught me a new word I didn't even know- zoonosis. It sounds like a good name for a band.)
Which isn't too hard to believe. Anyone who has watched any Nature episode on an endangered animal species has seen the part at the end that goes like this:
Unfortunately, the future of the [insert weird species here] is far from certain, because it is considered a delicacy in certain Asian countries.
(There's also a less common variant of the Nature show ending, where the species is an aphrodisiac and not a delicacy.)
Basically, the issue is that in Guangzhou, China there is a famous wet market where dozens of different animal species are for sale- rodents, birds, alligators, cats, badgers, dogs, porcupines, pigs, snakes, turtles, and other delicacies. They come from all over the world. They aren't frozen and packed or anything like that- they're running and fluttering around in their cages when you pick them out. Some of them have chewed their limbs off in attempts to escape traps. They are either butchered on the spot or you take them home still alive and kill them yourself. The emphasis is on freshness.
Of course this grossed out the tourists, not to mention the people who make Nature documentaries. So the Chinese authorities (in typical fashion) cracked down on the market two years ago by forcing it to move out of sight of foreigners. It was moved from an outdoor park setting into an enclosed building two years ago. WHO thinks the move to an indoor setting would have made the risk of zoonosis worse.
The first known SARS patient got sick in November. He lived 12 miles away, but had been in Guangzhou and received treatment there.