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Crowdsourcing HIV Research

timothy posted more than 3 years ago | from the work-backwards-to-zero dept.

Biotech 52

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."

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AIDS (0)

Anonymous Coward | more than 3 years ago | (#32104022)

You have AIDS from reading this.

Correction (0)

Anonymous Coward | more than 3 years ago | (#32104252)

It's Drexel University, not DREXLER.

Wow (2, Insightful)

phantomfive (622387) | more than 3 years ago | (#32104102)

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.

Re:Wow (3, Informative)

Capt.DrumkenBum (1173011) | more than 3 years ago | (#32104276)

Well you could get involved with:
http://www.worldcommunitygrid.org/ [worldcommunitygrid.org]
and donate some processor time to FightAIDS@Home

Just a thought.

Re:Wow (2, Funny)

Chris Burke (6130) | more than 3 years ago | (#32106224)

But I already fight AIDS at home by engaging in an alternative to one of the most common transmission methods.

Why, I've probably prevented over 100 cases of HIV in just this year to date!

Re:Wow (0, Flamebait)

ooshna (1654125) | more than 3 years ago | (#32106996)

Lol the only way what you did prevented AIDS is if you were HIV+ and every time you engaged in your alternate solution there was a different person who at that time would have engaged in actual sex. Chances a /.er could get 100+ women in a year without it including cash changing hands or a rape trial are nil.

Re:Wow (1, Interesting)

drinkypoo (153816) | more than 3 years ago | (#32109736)

I find this kind of stuff amazingly ironic. We're going to burn more fuel and produce more cancer-causing emissions so that we can produce more CPU cycles to fight illness. I don't know about you but my operating systems send HLT instructions to my processors when they're idle.

Re:Wow (2, Insightful)

tignet (1303483) | more than 3 years ago | (#32110308)

Now that you mention it, all research requires fuel that, at some level, produces cancer-causing emissions. All research should be stopped! We've known about this [wikipedia.org] for a long time, why produce all those cancer-causing emissions looking for 'better' treatments?

Although, I suggest that instead of sending HLT instructions to the processors as part of the idle loop, you should turn your computer off when it's idle. Think about all the energy you're using; the cancer-causing emissions are too much to bear. Wait! Go check the electricity meter on your house! Your entire house is burning energy even while you sleep. Oh no! We should all go completely off the grid and stop all research. That's definitely the best way of fighting cancer.

While it's interesting that you "find this kind of stuff amazingly ironic," you may want to keep that irony and associated comments to yourself in the future. You may think your opinion is insightful or particularly interesting, but, to me, the following quote comes to mind:

'Tis better to be silent and be thought a fool, than to speak and remove all doubt. - Abraham Lincoln

Re:Wow (1, Insightful)

Anonymous Coward | more than 3 years ago | (#32104304)

I'm not convinced you NEED any knowneldge of AIDS. At the end of the day, it's just a data mining problem.

Re:Wow (1)

interkin3tic (1469267) | more than 3 years ago | (#32105248)

Unfortunately I don't really have the expertise to do ANYTHING related to it, and I'm not sure many do.

Judging from TFA, if you're posting here you probably have at least most of the expertise to do it, quoting:

Models can be trained using the records of 1,000 patients. To predict an improvement in a patient's viral load, competitors will be provided with data on the nucleotide sequences of their Reverse Transcriptase (RT) their Protease (PR) and their viral load and CD4 count at the beginning of therapy. There is a brief discussion of the science of these variables in the Background section, but no knowledge of biology is necessary to succeed in this competition. Competitors' predictions will be tested on a dataset containing 692 patients.

Sounds like they give you the data and tell you what you're looking for, and then you tell them when you've found them.

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.

That may be why they don't, but "biolgeek" does. The page specifically calls it a "competition" and "contest." No mention of crowdsourcing, which doesn't mean a lot to most people.

Re:Wow (1)

biolgeek (1804468) | more than 3 years ago | (#32105578)

People often refer to 99designs logo competitions as crowdsourcing designs (http://webworkerdaily.com/2008/04/28/99designs-crowdsourcing-works/). On that basis, I think this classifies as crowdsourcing.

Re:Wow (1)

Yvanhoe (564877) | more than 3 years ago | (#32109124)

I have the feeling that you are only 3 hours of wikipedia-surfing away from being able to translate it into a pattern-matching and algorithm-finding problem. If you know how to code and are good at algorithms, you could help.

Olde School HIV cure crowdsourcing... (4, Funny)

jameskojiro (705701) | more than 3 years ago | (#32104156)

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!

Re:Olde School HIV cure crowdsourcing... (3, Insightful)

Saishuuheiki (1657565) | more than 3 years ago | (#32104278)

I was under the impression that some African countries are more or less doing this with little to no success in gaining immunity.

Re:Olde School HIV cure crowdsourcing... (1)

Locke2005 (849178) | more than 3 years ago | (#32104578)

Actually, we've already bred people with HIV resistance [wikipedia.org]. Why nobody is intensively studying these people to document WHY they remain asymptomatic for so long is beyond me.

Re:Olde School HIV cure crowdsourcing... (0)

Anonymous Coward | more than 3 years ago | (#32104638)

"They have been the subject of a great deal of research, since an understanding of their ability to control HIV infection may lead to better anti-HIV drugs or a vaccine against HIV.[1]" ... this is from the article you provided a link to.

Re:Olde School HIV cure crowdsourcing... (3, Informative)

Anonymous Coward | more than 3 years ago | (#32104648)

We are being intensively studied. See www.zephyrfoundation.org .

Re:Olde School HIV cure crowdsourcing... (1)

Locke2005 (849178) | more than 3 years ago | (#32104816)

I stand corrected, and thank you for doing so. The study of Elite Controllers sounds very promising; I'm surprised I've never heard of the Zephyr Foundation before. Also, the fact that the Elite Controllers they were studying were all infected by transfusions destroys the myth that HIV is spread through "irresponsible behavior", as well as my personal theory that long-term non-progressors developed immunity though exposure to low levels of the virus over an extended period of time. So it looks genetic -- somehow, the descendants of survivors of some plague in the past still carry within them genetic mutations that enable them to better fight HIV. Has anybody done a genealogy study on these people to see if they come from common roots?

Re:Olde School HIV cure crowdsourcing... (0)

Anonymous Coward | more than 3 years ago | (#32107278)

Zephyr is a fairly small organization so far, but growing.
I personally wasn't infected by transfusion. Ultimately, though, it doesn't matter how one was infected. It is an illness. There is no need to blame the victims. The cure is needed for everyone.
There are definitely some genetic markers. We already know of a few of them. CCR5 and HLA B*5701 . The first usually prevents transmission of some strains of HIV altogether, the second slows disease progression. I have this second marker.

Re:Olde School HIV cure crowdsourcing... (1)

Locke2005 (849178) | more than 3 years ago | (#32107854)

Thousands of children have been born infected... I find this just a little bit difficult to blame on their own behavior. If you've been infected for more than 22 years, you can plead ignorance. How you got infected doesn't matter now that you are infected, but it does matter for educating other people on how to slow the spread of the disease -- e.g. mandatory prenatal screening of mothers for HIV, and precautions to safeguard the blood supply and health care workers that have already been put in place in most countries.

Re:Olde School HIV cure crowdsourcing... (1)

madbrain (11432) | more than 3 years ago | (#32108112)

It's not just children. I reiterate that there is no need to blame anyone here. I'm sick of this stigma. Having the disease is bad enough. Do people need to justify themselves for how they got it too ?
I got it from sex (gosh, I know, so rare on slashdot!), and I have no shame in it. If somebody wants to cast the first stone, I will listen only if they have never had sex.

I agree with you about education, but unfortunately this is not sufficient. I was fully aware of HIV but still caught it. I think most people who get it have heard of it before as well.
Sometimes bad circumstances will still occur - condoms don't work 100% of the time, they don't get used 100% of the time, and occasionally low risk sex acts still cause transmissions. It only takes one mistake. And often you have no idea that it happened.

What we really need is a vaccine or a cure, and preferably both. Education alone is not going to stop the epidemic, unfortunately.

Re:Olde School HIV cure crowdsourcing... (-1, Flamebait)

Anonymous Coward | more than 3 years ago | (#32104922)

Do you ever try sleeping with desperate AIDS girls to see if you're REALLY immune? C'mon, don't lie...

Re:Olde School HIV cure crowdsourcing... (0)

Anonymous Coward | more than 3 years ago | (#32105128)

If they did, they would have used a condom. Too bad your parents didn't think of that!

Re:Olde School HIV cure crowdsourcing... (1)

lakeland (218447) | more than 3 years ago | (#32105270)

No, it's going fairly well from a long term perspective.

Just seems that some people object to the pain and suffering necessary for this method to work.

Re:Olde School HIV cure crowdsourcing... (2, Insightful)

the_humeister (922869) | more than 3 years ago | (#32104768)

Or just produce people with the CCR5-32 gene variant.

Re:Olde School HIV cure crowdsourcing... (1)

interkin3tic (1469267) | more than 3 years ago | (#32105312)

Or just produce people with the CCR5-32 gene variant.

Didn't we find out that would work through a screening process in humans pretty similar to what jameskojiro suggested? In other words, do we know that people with the CCR5-32 gene variant are immune because out of the millions of people with HIV, there are a few people we've found are immune and those people have that gene variant?

Re:Olde School HIV cure crowdsourcing... (1)

roman_mir (125474) | more than 3 years ago | (#32105830)

so I see. A giant 'catch a bug' party for everyone? Do you think majority would do this to themselves maybe to solve the problem for the future generations? Why would anyone sacrifice themselves for the future generations ever, that's a stupid thing to do.

Lowest bidder ... (4, Insightful)

DeadDecoy (877617) | more than 3 years ago | (#32104262)

They're really going for the lowest bidder if they want to crowd source this problem:

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.

Re:Lowest bidder ... (1)

SomeJoel (1061138) | more than 3 years ago | (#32104344)

$500 amounts to around a week or so worth of work

Yeah, they can't afford much. The budget is kind of small - most of the money was allocated to fighting baldness and impotence.

The Internet Has No Quality Control (1, Offtopic)

ObsessiveMathsFreak (773371) | more than 3 years ago | (#32104316)

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.

What will happen when I find the answer? (1)

houghi (78078) | more than 3 years ago | (#32104318)

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?

Re:What will happen when I find the answer? (1)

Judowill (1805142) | more than 3 years ago | (#32104742)

The algorithm will be published as an open-source paper ... likely BMC Bioinformatics but I guess that depends on any number of factors. btw. This is Will Dampier, I'm hosting the competition with Kaggle.com and Drexel University

Gross (2, Funny)

davidbrit2 (775091) | more than 3 years ago | (#32104358)

This strikes me as the sort of disease where you'd want to stay away from phrases like "viral load".

Re:Gross (1)

treeves (963993) | more than 3 years ago | (#32105086)

Is there a sort of disease where you *wouldn't* want to stay away from phrases like "viral load"?

Re:Gross (0)

Anonymous Coward | more than 3 years ago | (#32107352)

What about an STD that causes breast growth and selective mutism in women?

Its actually "Drexel University" (2, Informative)

Judowill (1805142) | more than 3 years ago | (#32104790)

A small typo, its actually "Drexel University" in the Philadelphia Area

Fontanelles is not in the running (1)

Okian Warrior (537106) | more than 3 years ago | (#32105254)

From the forum page [kaggle.com] over at Kaggle:

The Fontanelles is a group which does HIV research professionally and so has some specialized information in this area. We're disqualifying our entry, but have put it in just for fun as a target. We may be back if someone beats it.

So despite the appearance of the professional entry, this looks like an interesting contest that anyone might enter.

To help more people join in (1)

Judowill (1805142) | more than 3 years ago | (#32105322)

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

Interesting approach. (2, Interesting)

jd (1658) | more than 3 years ago | (#32106598)

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. Ignore the implementation details of the virus (which changes too often to seriously fingerprint) and focus on the attack vector. It's a bottleneck that all the mutations in the world can't bypass.

What's more, assuming the assumption of it being a common bottleneck is correct, this would allow the two largest-funded groups of researchers (AIDS and cancer) to pool resources, thus improving odds on managing a task neither has succeeded in doing alone.

Re:Interesting approach. (0)

Anonymous Coward | more than 3 years ago | (#32107862)

Perhaps you should host a competition?

Re:Interesting approach. (1)

jd (1658) | more than 3 years ago | (#32113798)

Tell you what, you figure out a way for me to have several millions (after tax), and I'll set up X-Prizes on a whole slew of areas that I think are of exceptional interest, of which some form of analysis of IT security techniques in a biological system would be one. (Both founders of modern technology - Alan Turing and Von Neumann - started by treating computers as equivalent to idealized biological systems. This is precisely why Alan Turing worked on the question of whether the human brain was a Turing Machine, and why Von Neumann wanted to figure out the abstract model for a DNA-like system - before DNA had even been identified.)

I'll throw in a bonus. Find me $100,000,000,000, a few thousand pure mathematicians, a few thousand Software Architects/Engineers, and as many programmers as mathematicians and SA/Es combined, and I can have Linux A1/CC7-compliant and nine 9's reliable within a year - guaranteed.

The problem is not one of thinking of ways to do things. That's never the problem. It's not even a case of it being a problem thinking of ideas that are highly valuable and beneficial. The problem is that most ideas will never get any kind of time or money invested in them, and that of the ideas explored, only one in a thousand will ever be implemented in a way that works (lack of money, lack of interest, lack of supporting technology, lack of ideas to bridge the gap between start and finish), and of those ideas that are implemented soundly, perhaps one in a thousand will ever find its way to anyone who can actually make any real use of it.

This is why patent-farms and patent-trolling are extremely popular. It's very very easy to churn out enough of a game plan to file a patent. You don't have to actually build it or even know how to, since the patent system works entirely on a good-faith principle. Then when someone actually DOES build the idea, either the patent or a license can be sold. If the patent-farm is run well, the fee for the inventor just buying the patent will be less than the cost of overturning the patent and filing a new one. Totally immoral, certainly unethical, probably in violation of some patent law or other, possibly in violation of laws the courts actually take seriously, but it's a huge revenue stream for many corporate giants.

Garage developers can do a hell of a lot - and often do. These people, though, rarely do the fundamental research. They're taking that fundamental research and making it practical, but they're not where you see the blue-sky work being done.

"Blue-sky" Armchair Inventors and Armchair Investigators are confined to those armchairs. They will never have the means to actually do the work, their personal merit and the merit of their ideas are worth NOTHING to the outside world. What can, sometimes, happen though is that those ideas (when circulated) can trigger thoughts by others - essentially a mental version of the Butterfly Effect. (This is always going to be true, which is why meritocracies will never actually exist - you will never be able to reliably associate the merit with the person. Chaotic systems can't be reversed.)

The original thoughts may or may not (in themselves) ever get used, but so long as they feed into a cascade, where one or more branches within that cascade actually DOES produce something viable, the original thought was worth expressing.

The problem of simply collecting such thoughts into some giant thought-pool is that there's going to be a lot of crap and a few gems. Even those ideas that are good, if they're not created by someone with deep understanding, they will have a good deal of crap surrounding the nuggets of gold. Nobody would trawl through Sourceforge looking for brilliant algorithms, although I can guarantee that there are going to be absolute gems somewhere in there.

So either you'd need experts to wash the crud off, so that all that was left was the prize stuff (but you'd need so many experts that the only way to make this pay for itself would be to actually build the ideas, making the pool pointless as an ideas oasis), or you forget pooling the ideas and opt instead for a good old-fashioned message in a bottle. Throw out enough messages in enough bottles and you'll either be nicked for dumping at sea or you'll eventually get a bottle to someone uncynical enough to read it and in a position to do something. You just have to hope that the bottle they find had one of your better ideas.

Re:Interesting approach. (1)

comm2k (961394) | more than 3 years ago | (#32108442)

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.

There are some approaches with modified/fine-tuned Zinc-fingers cleaving (your own) DNA - one example see this article: http://www.health.am/aids/more/proteins-put-personalized-hiv-therapy-within-reach/ [health.am]

Re:Interesting approach. (1)

jd (1658) | more than 3 years ago | (#32112838)

Again, this is exceptionally interesting and because it doesn't directly attack the virus itself but attacks a vector being used, there is a greatly reduced risk of the virus mutating to work around the fix. It's a relatively novel approach, which in my opinion is critical to any actual solution. And because it's effectively for building a bullet-proof T-Cell, it shows that my thinking wasn't totally off in left field, that closing attack vectors is an area researchers consider interesting.

I don't know how long people have known enough to work with Zinc fingers or have even known the mechanism existed, that's not something I've looked at outside the linked article, but I do know that most of what we know about the epigenome and the non-encoding regions has been learned very very recently. They're all very fresh areas with vast amounts of promise, making them ripe for major discoveries.

If they ran an X-Prize-style contest on the most creative use of Zinc fingers in intra-cellular medicine, I think it far more likely you'd get results that could be used to fight AIDS than with the contest being run.

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