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Crowdsourcing HIV Research
biolgeek writes "In recent years, HIV has been managed with a collection of therapies. However, the virus will likely evolve around these drugs, making it crucially important to get a better understanding of the virus itself. An important step in understanding the virus is to get a handle on its genetic blueprint. William Dampier of Drexler University is taking a novel approach to this research by crowdsourcing his problem. He is hosting a bioinformatics competition, which requires contestants to find markers in the HIV sequence that predict a change in the severity of the infection (as measured by viral load). So far the best entry comes from Fontanelles, an HIV research group, which has been able to predict a change in viral load with 66% accuracy."
You have AIDS from reading this.
Wow, I would love to get involved with this and help find the cure for AIDS. Unfortunately I don't really have the expertise to do ANYTHING related to it, and I'm not sure many do.
I'm not sure you can call it crowdsourcing when the number of people who can get involved are so small. Maybe a contest or an open research project or something. Either way, I wish them luck.
Qxe4
Isn't this what caused so many people to come down with it in the first place?
Tsukasa: All I really want, is to be left alone...
Infect Huge Numbers of people with HIV and after 10 years breed the survivors and infect them again, after 100 years the crowds are dwindled down and whomever remains is immune, HIV epidemic, SOLVED!
Tsukasa: All I really want, is to be left alone...
AIDs? That is so 1990s. Cancer is so in right now!
It's Drexel University, not DREXLER.
There is $USD500 up for grabs, and the winner(s) will also have the opportunity to co-author a paper with the competition host. The winner must supply their methodology before any prize money is awarded.
$500 amounts to around a week or so worth of work, not counting resources used like hardware and computing time. And also, the prize is you get to be a coauthor? If you develop a novel algorithm that has a statistically significant improvement over prior methods, you should damn well be the first author with the host being the coauthor. A more interesting crowd-sourced competition should involve a >$100k prize with a publication in some significant journal like nature, bioinformatics, or new england journal. That would at least attract the hardcore statisticians to your cause.
If you crowdsource AIDS Research/Treatment, you'll find that upwards of 50% of treatments will be complete crackpottery/homoeothermy/witch doctors, 45% of finds will be from religious groups/AIDS denialists, and the remaining 5% will be paid astroturfing from pharmaceutical companies. A vanishingly small percentage of suggestions will be from actual medical researchers.
The internet is a cesspool of misinformation, junk and lies. Sorry but that's just the way it is. If you give everyone on earth their own personal, worldwide soapbox, don't expect quality content on average. I'm not saying there isn't quality information out there. I'm just saying that it is very, very difficult to find without trustworthy quality control, or which there is precisely none whatsoever at this point in time.
Sure we can talk about a "marketplace of ideas", but as anyone with three brain cells and the attention span of a goldfish can attest, marketplaces are neither rational, efficient or likely to work without moderating forces. Left to the crowds in their clouds, the HIV virus is going to remain even more inscrutable than if it was just left to professional researchers. People will turn up so many loose ends and red herrings that the whole enterprise will be a giant waste of time.
May the Maths Be with you!
Will the solution be mine, his or some company who will charge money for it and say they invested a LOT in it and make profit from it?
Don't fight for your country, if your country does not fight for you.
This strikes me as the sort of disease where you'd want to stay away from phrases like "viral load".
A small typo, its actually "Drexel University" in the Philadelphia Area
From the forum page over at Kaggle:
So despite the appearance of the professional entry, this looks like an interesting contest that anyone might enter.
In an effort to actually decrease the barrier for entry I'm working on a quick example function for predicting the dataset. I'm hoping to have it posted in a day or so. I'm actually defending my PhD thesis within the next few weeks so I'm kinda pressed for time. btw: This is Will Dampier, I'm hosting this competition at Kaggle.com
Can't help but wonder, though, if they're trying to solve the wrong problem. There's research out that suggests that virus-related cancers are exploiting what are effectively a small set of security holes in the way DNA handles the "junk" portions. HIV is a retrovirus, IIRC, which also means it installs itself into the DNA. The first line of attack I'd have thought of, based on those two pieces of information alone, would be to see if the SAME security holes are responsible for both the virus-caused cancers and HIV breaking into the DNA. If there is a common attack vector, across multiple viruses, then that attack vector becomes far more interesting than the specifics of each virus.
Assuming the attack vector cannot actually be patched in mainstream cells, to fix the flaw, then perhaps it can be fixed in T-Cells, which are essentially disposable and it doesn't matter a whole lot if they're non-standard. HIV crashes the immune system through a massive DDoS attack via the immune system itself, by using the T-Cells. If the T-Cells are closed to that specific attack, then the virus can mutate all it likes but it can't crash the immune system. IF it is invariant across multiple viruses, then it's likely invariant across all of HIV strains. Merely preventing a DDoS on the immune system should massively slow the virus down and improve the chances of additional treatments actually ridding the body of the virus.
The ideal would be to fix the security hole in total, for all cells. I'm not sure that's possible, as evolution has required the mechanism to inject new code into the DNA strands. Indeed, a lot of evolution would be impossible without such a mechanism, and you can't exactly install X.509 certificates into all harmless or potentially beneficial RNA and DNA sources on the off-chance they need to integrate. Besides, cell defenses don't usually include SSL. The best I think you can probably do is bio-engineer a new DNA strand, which you can install in an organelle (organelles are just places where cells used to have DNA before all the useful bits were pushed over into the nucleic DNA), which provides some sort of Intrusion Detection System. As I see it, you've two options - a honey-pot (an extra-vulnerable DNA strand that causes the whole cell to self-destruct if infected by a retrovirus), or a Tripwire-like IDS that looks for mutations in any given strand of nucleic DNA =and= monitors for virus-production. If both conditions are satisfied (ie: it's not a benign insert, but a malign one), then the strand is broken up.
Again, not sure if this is remotely possible. Sure, there are enzymes which break up DNA - they're used all the time for sequencing, as you can't sequence long strands. But to identify a malign region in the DNA =and= have the enzyme only break the DNA at that point =and= have this done in a way that won't cause the end result to do strange and undesirable things -- that's going to be tough.
So if this approach is so tough, why go for it? Because researchers have tried targeting the virus directly and have failed utterly. Deactivating it only results in it reactivating itself, making vaccines extremely hard to produce. When they are produced, the virus has mutated and the vaccine is useless. In other cases, the virus has even used the immune response to hijack more immune system cells, so as to spread faster. It also mutates so fast that what worked one week won't work the next. Direct attacks have no serious shelf-life and just won't work.
That leaves indirect attacks. To beat the mutation problem, you need some aspect of the virus that will never change. If one such aspect is the mechanism for breaking into nucleic DNA and inserting rogue sequences, controlling that entry-point will not only beat AIDS, but it will beat some cancers too. Since uncontrolled entry into DNA is why some gene therapies cause cancers, controlling the entry point will also be critical to gene therapy being successful for a wide range of conditions.
Thus, this is the obvious place to focus on. Ign
It's a small world and it smells funny; I'd buy another if it wasn't for the money; Take back what I paid (SoM)
Isn't this what caused so many people to come down with it in the first place? Brac Apartments
The research is actually being done at Drexel University in Philadelphia PA. If anybody was wondering...