Grid Computing Saves Cancer Researchers Decades 149
Stony Stevenson writes "Canadian researchers have promised to squeeze "decades" of cancer research into just two years by harnessing the power of a global PC grid. The scientists are the first from Canada to use IBM's World Community Grid network of PCs and laptops with the power equivalent to one of the globe's top five fastest supercomputers. The team will use the grid to analyze the results of experiments on proteins using data collected by scientists at the Hauptman-Woodward Medical Research Institute in Buffalo, New York. The researchers estimate that this analysis would take conventional computer systems 162 years to complete."
Re:I used to run Folding@... (Score:1, Interesting)
It just feels too much like an economic scheme based in pseudo-science and half truths. "The world is doomed, here's how you as a consumer can spend your way to salvation! Buy a new car and light bulbs filled with mercury!"
It's poster child, Al Gore, uses the word "if" too much. It's an old debating trick, to say "if X, then Y", and focus on the terrible consequence Y, and completely avoid the debate - which is over the validity/scope/level/definition of X.
At the end of the day, and back on topic, I know cancer is absolutely real, and I also know that real cures and treatments are buried in the mountains upon mountains of data in hospitals, schools and research centers.
So, I'm maybe gonna pick a horse I think has a chance of crossing the finish line.
This is great and all but... (Score:5, Interesting)
Re:I used to run Folding@... (Score:1, Interesting)
Don't buy a Prius, it may get better mileage - though if you convert to gallons per mile - a true meter of energy cost, it doesn't look so good. Never mind the fact it runs on laptop batteries, which makes it a disposable vehicle at the end of the day.
Or go to a "super efficient" diesel engine. Well, there's reasons we restrict the numbers of diesels that can be put on the road, and that's those huge plumes of black smoke that puff out are full of nasty shit. Remember acid rain? You may not be old enough - it was the source of our ecological doom in the 80s, and is the byproduct of sulphur dioxide. Despite the industries claims of super-low-sulphur diesels, the amount in the fuel is not insignificant.
The fact is, modern engines are quite well designed, and with regular maintenance could easily last your entire life. So what does the auto industry do now? Appeal to vanity, sure - you don't want to be seen in the same old rig, do you? They've now found a way to appeal to your innate sense of guilt. Buy a Prius, save this baby seal from clubbing!
I also see the government mandating switches to compact flouros, being absurd. The quality of light is terrible, they dont handle slight power fluctuations all that well, even the ones that are "dimmable", really aren't, and don't work in the cold. We don't want all that mercury in our groundwater when those things start hitting the dumpster en masse. Besides, switching would just mean people leave the lights on longer. If you're used to paying 150 bucks a month, you'll keep paying it, just a weird sociological quirk., in the vein of "some snack has half the calories, so fatty eats 3, and thinks he's dieting".
All this over CO2, a benign non-toxic gas, which has a small contribution to "the greenhouse effect", although it's been shown that the real major cause is water vapor in the atmosphere - but we have no way to track that.
All the while we search for imaginary mystery energy sources - we're almost there, just need a huge breakthrough in physics/chemistry/biology/astrology - we completely ignore the fact that nuclear fission can supply our energy needs, no need to dig up and burn dinosaurs.
But what of the radioactive waste? Well holy fuck, we can stand around masturbating waiting for a magical breakthrough bacteria that turns garbage into gold-plated hydrogen for our fuel-cell car of tomorrow, but this great global scientific community cant figure out how to throw out some gunk? How about this, I'll figure it out for them.. Pulverize it and release it into the atmosphere, it'd be less radioactive material than comes out of a typical coal plant in a year.
My point is, there are sensible, practical, answers - but they aren't all futuristic and neat and don't involve funky lightbulbs and throwaway cars, and would (gasp) preserve the american lifestyle that it's become so vogue for the left to hate, despite living the exact same way.
All I see are ivory tower assholes using this current round of paranoia to line their pockets. I distrust any solution that involves me "buying new things".
So, lets cure cancer.
Patents? (Score:3, Interesting)
Because that would make me feel a little less charitable with my computing power. (Only a little, though.)
I can see it now (Score:3, Interesting)
I OBJECT!! (Score:5, Interesting)
Let me back up and explain what the project is doing. To simplify a little bit, the vast majority of "work" in the cell is done by proteins. While DNA can be thought of as something like a simple "string", proteins have complex three-dimensional shapes. Knowing those 3D shapes is of great interest to biologists. There are several reasons for that. One is that it can allow easier design of drugs targeted at a specific part of the protein. Another is that by seeing the shape, we can understand how all the mutations that occur in disease might be affecting its function.
The primary way to determine the shape of the protein is to take the protein and to grow it into an ordered crystal. You can then shine an x-ray beam through the crystal, and the diffraction pattern that emerges can be, through some very complex math, reverse-engineered into a 3D structure. Typically the most difficult part of this process is finding the specific chemical conditions that will allow a crystal to grow. These conditions differ from protein to protein.
This project is not "solving cancer", by any means. Rather, the people in Buffalo have generated a high-throughput way of screening different chemical conditions to determine which ones might allow a protein to grow. They use robotics to screen about 1000 conditions, and take pictures of each condition. The question then becomes: can you automatically process the pictures to find crystals. That's the goal of this project, to help automatically identify crystals in this screen.
So why do I object so strongly to this work? There are three reasons.
First, the project has nothing to do with cancer. In fact, the proteins being analyzed are not in any way "cancer-specific proteins" -- many of them are not even human!! This "cancer" pitch is a sales job, and nothing but a sales job. As a cancer researcher, it offends me that people try to use the disease to justify research that is this unrelated.
Second, the project is ill-conceived, technically. In no way did the group in question (Igor Jurisica's lab, in Toronto) carefully select a machine-learning approach to identify good ways of analyzing images. Instead, they have just selected something like 1000 different techniques, and are running *all* of them on every image they have. It's a fishing expedition, with the hope that one of those thousand metrics they return will be a useful predictor.
Third, the techniques selected are basically arbitrary. Most egregiously, there appear to be NO Fourier transforms included in the analysis!! Further, the images generated by the software appear to be transforms of something called "gray level cooccurrence matrices", and the computation of those can be estimated in no more than five minutes. So why are they taking 5 hours per unit? It appears that they have chosen to implement an exhaustive GLCM search that is an order of magnitude slower, rather than using existing estimation procedures that are ~98.5% accurate. Is that an excuse to use more computer time? Is there any scientific merit to that? Why aren't Fouriers included, since they are a standard technique for image analysis?
I have a number of computers that I run various BOINC projects on, but this will NEVER be one. It's a fishing expedition, being sold as cancer research, and that is a sad way to deceive the public.
Re:I used to run Folding@... (Score:3, Interesting)
Meanwhile, since I live in Canada and by this time of year I do need heating, I have my boinc client running at 100%, I'm doing some good, and (since the peak capacity of the machine is justified in other ways) it's not costing a penny. The heating here is electric anyway; it may as well do some computation on its way into my home!
Doing whatever@home in the winter is just good sense.
Now what's needed is a distributed computing client that is controlled by a room thermostat. No, really, I'm totally serious.
Re:I OBJECT!! (Score:3, Interesting)
Or, as a lot of molbio automation companies are offering, actually shine an X-ray beam through the putative crystal onto a detector and see if it diffracts.
Fully automated high-throughput crystal growing strikes me as a bit of a boondoggle; the sophisticated robots required for the last steps of automation are an order of magnitude more expensive than having three shifts of trained Indian or Chinese workers moving plates around and looking through microscopes.