Sergey Brin’s Search for a Parkinson’s Cure
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This can't be overstated. The shear amount of data available for processing is huge. Google-scale. I'm not very familiar with GWAS studies (I'm more familiar with high-throughput sequencing), but these are O(N^m) scale problems (where m>=2).
Where I work, filesystem I/O is the rate-limiting step for most of my (next-gen sequencing) experiments...
OK, now that I've thought about it, the easiest way around this probably is throwing money at hardware (more disks) or optimizing the processing. However, this is only in the case of a true disk I/O bottleneck. If you're optimizing correctly then the disks should be reading 8GB blocks directly into memory and the CPU should be spitting them right out again. At the very minimum you should be using an optimized file system with large pages enabled in your kernel.
"What do you do for a living?"
"Exomes."
-spits drink out-
However, we just got our own instrument, so this will definitely be an issue, but our University knows a thing or two about dealing with big data (http://kb.iu.edu/data/avvh.html).
I've only dealt with a few GWAS style datasets, and the next-gen stuff dwarfs the GWAS data in terms of size. But when looking for linkages between variations, we're still talking more time than the universe is old level of calculations for more than 3 combinations. Which is really scary, because like you said, all the genetics people are going to be using sequencing for most things from here on out, so its like you have complexity on top of complexity...
I'd suggest getting involved in any lab doing any form of computer work. Lab meetings are a great place to find out what problems people are having, and most of the time you'll be able to use your skills to solve them. After taking on a few projects, people will start to realize what you can and can't do, and they'll start to give you a lot of related work.
Good luck!
Regarding massive information, I analyze a lot of the data we generate in order to optimize our delivery platform. Since there are few labs that do this kind of work, all the data I work with comes from us.
Isn't that enough?
First you see an object fall and them you wonder why. The same applies to birds flying, wood afloat, fire, atmospheric pressure... we observe(collect data) first, we make assumptions and look for more data later.
BUT, never underestimate the power of a GooglePlex for gathering and analysing data(like generic one). Never before we had used it, and so we could see things we never did before.
You know what happened when a man without studies created a miscroscope. The "scientist" of the time said that he didn't knew Latin, so he could not be called scientist, and that the microscope will only work for seeing the same things we already know bigger.
On a serious note, I hope they can find a cure for him and millions of others who can do nothing about their illness other than playing a waiting game.
They do. Aging may not technically be a disease, but it's currently unavoidable and cripples your body and often your mind. If I had a few extra billion dollars lying around, that's what I'd focus on.
>Many philanthropists have funded research into diseases they themselves have been diagnosed with. But Brin is likely the first who, based on a genetic test, began funding scientific research in the hope of escaping a disease in the first place.
Maybe there are bottlenecks that make it so more money wouldn't speed things up, but I bet there are ways to use resources to help alleviate or remove these bottlenecks.
Edit: I thought I'd add an example, since my father has Parkinson's so I know a little bit about it. One promising area of research is stem cell therapy. However, one known side effect of stem cell injection is cancer. (It takes years to develop but there have been enough studies already to show a strong correlation). Now, Parkinson's doesn't kill per se - it makes life miserable towards the end, but as a rule, people with Parkinson's live just as long as people without. So let's say you had really high net worth and wanted to spend it all to cure Parkinson's. Would you be able to "buy" people to trade a low chance of improvement in their lifestyle for a very real chance of cancer? I don't think so. Of course, this is just one example, however, it shows that things are not that simple.
Throwing money blindly at a problem doesn't always help, that's very true. But I'm sure there are many intelligent ways to use more than 50m effectively.
You mention stem cell therapies; helping get them to the point where they don't cause cancer anymore might be an area of research worth pushing, especially if some of it is under-funded. Giving out scholarships to people studying in areas related to the disease might be a way to help improve the supply of researchers. And when you can't hire more people, you can usually upgrade the equipment with faster/better stuff (shortening the upgrade cycle might help accelerate progress). You could help pay for conferences where the leading minds working on the problem can meet and exchange information (and if there's already enough of those, you can help make them better). You can probably find high-risk/high-reward research projects that aren't getting funded through the regular channels because those usually favor low-risk/low-reward projects. Etc.
But I repeat: What Brin did is awesome. Kudos to him. All I'm saying is maybe I'd do it differently if I was in his shoes.
This almost certainly will not represent the sum total of his donations.
one known side effect of stem cell injection is cancer.
I found that to be an incredibly interesting sentence, after having previously watched this video.http://www.ted.com/talks/eva_vertes_looks_to_the_future_of_m...
In addition, he'll probably continue investing in research going forward; $50M to date might eventually increase depending on what's found.
Specific conditions like Alzheimer's get massive research funding. But if the majority if that money had been invested in research targeted to expand basic knowledge of brain neurobiology, then we would be MUCH further along on real treatments that are actually effective.
When you invest heavily into research for one specific neurodegenerative disorder you are investing in specific and superficial symptom treatment. Investing in neurbio research expanding basic knowledge of the brain instead will give you more results in treating a wider range of neurodegenerative disorders.
A lot of money going to really good things is still better than a little money going to really good things.
We are not a bunch of 5-year olds around here, and I in particular am not so primitive as to think that the world revolves around me. There is nothing wrong with questioning mainstream journalism, especially when it's without citation and contradicts personal experience.
You can trivially find sources.
If so, wouldn't it be easy to paste a link, which is what I've requested in the first place? I hate the knee-jerk "google it" response - the person who gives it usually thinks that they are smarter than the person who asked for help in finding something, but all it shows is that you are (a) lazy and (b) disrespectful.
Now, if you can provide sources, please do, and if you cannot, I respectfully ask that you please leave this thread to people who care to contribute something other than "google it, stupid".
Your choice of words aside, I care about this forum, and I don't want it to become the usual deal where people assert their ego at the expense of actual discussion. My intent was not confrontation, it was cooperation.
Edit: Never mind. I see from your "ha ha ha" post below that you are trolling. I guess that answers my question.
http://news.wustl.edu/news/Pages/20150.aspx
Doing the math (450,000 cases out of 36,000,000 million Medicare recipients in the US), the adult incidence rate of Parkinson's is 0.0125, or 1.25%.
Sadly, I can't find a full copy of the study which isn't behind a pay wall. But, from the summary, it appears Parkinson's has some "clustering" based on both genetic and environmental factors. The text under the map on the article indicates areas in red have an adult incidence rate of 13.8% or more, so experiences such as yours are normal (albeit frightening).
So, yes, you're right to question that 1% statistic. It isn't sufficient to describe the situation at all when standing by itself.
I wonder if with the "graying" of baby boomers, the statistic is going to shoot up. I wouldn't be surprised if by 2020 the numbers would double, along with the projected retirement numbers. Of course, that would mean that the cluster areas would see rates close to 1 in 4 older adults, which would be truly scary!
(For reference: "I am well aware of the various ways to look at statistics." from http://news.ycombinator.com/item?id=1421249)
http://plosgenetics.org/article/info:doi/10.1371/journal.pge...
When the response to new and cool is "you didn't do it according to protocol", something is definitely wrong.
It's a good thing that someone is thinking about how all this stuff is going to be protected.
The protocol there is one of ensuring anonymity for people that want to remain anonomous. Making sure that that sentiment is retained moving forward is not a bad thing.
IRBs are designed to protect the subjects/patients, the researchers, and the institutions. To skip that step is pretty unusual, and some hoops had to be jumped through in order to deal with it. I think the fact that the 23andMe study was published at all was a big leap, and represents the flexibility inherent in the scientific community.
The response to "new and cool" wasn't "you didn't do it according to protocol". It was: since you didn't do it according to protocol, we need to verify that you did this ethically.
Imagine what would have happened if they used someone's DNA in their study without their knowledge. When you're talking about publishing links between diseases and people's DNA, you better be damn sure you have permission to use their genetic data. That is what IRBs are good for.
In a world where movies constantly are pointing out how scary/evil/unethical scientists can be (Andromeda strain, Splice), these checks are very important, even if it slows things down a little.
Apart from privacy and "ownership of one's genetic material", why?
Saying "Joe Smith's DNA contains a vital clue to solving parkinson's" doesn't affect Joe's ability to monetize.
Saying the same about "unspecifed_37" doesn't affect anyone's privacy.
http://en.wikipedia.org/wiki/Henrietta_Lacks
There was a good episode of Radiolab about her, as well as a good interview on Dr Kiki's Science Hour with the author of the book written about her life and legacy.
Her family was deeply disturbed by what was happening at first. Progress is necessary, but so is people's dignity.
I don't want to be callous, but look at the cost-benefit calculation:
Cost: One disgruntled family.
Benefit: Polio vaccine. Treatments for cancer, HIV, various toxins, and other stuff I don't know about in the 50,000 research papers on HeLa. I am not exaggerating. There really are over 50,000 papers about HeLa.
I think the system worked very well in this case.
I think this is a case where the system didn't work... but more because the science got ahead of the ethics. Sure, excellent science has been done with HeLa cells, but it all started with an ethically ambiguous beginning. For example: why do we know her name? This alone should never have happened.
Excuse me? It was the first human cell line that could grow in culture indefinitely. Doctors and researchers immediately recognized the potential of HeLa cells. It took less than three years before the cells were used to mass-produce Jonas Salk's polio vaccine.
I am not exaggerating when I say that millions of people today owe their lives to HeLa. Had doctors been forced to do what you call ethical, those people would be dead. With so many lives at stake, the objections of the family (or the individual) simply don't matter.
For example: why do we know her name? This alone should never have happened.
Originally she was anonymized. Later, researchers wanted to get genetic information from her living relatives. Somehow the press found out. Perhaps a relative told them.
As I said, apart from privacy and monetization, so what?
Note - I think that her family should be paid. I also think that she had some privacy rights that were violated.
I do not read the editorial you linked as saying, "You didn't do it according to protocol." The editorial, in fact, is explaining why PLoS Genetics thought the study was okay to publish, how the 23andMe study strictly complied with existing protocol and went above and beyond its requirements, and how the IRB system needs to be improved to deal with GWAS.
I realize it's not really a science article (it's even possible all the information on Parkinson's came directly from Brin himself), but they didn't say cigarette smoking staved off Parkinson's completely - they said it lowered the odds of it developing.
Thing is, the human body is so complicated, you can do all the right things and still come up on the short end. Load up on omega-3s and still get clogged arteries. Eat a well balanced diet and still get cancer.
Doing the "right" things can only improve the odds - something's going to get to you in the end.
It's complicated, but it's not magic. If you are doing things to avoid a problem and you get the problem, then you were not doing "all the right things" - your understanding was wrong.
Nope. "All the right things" isn't a guarantee and since you can't do anything about your dna, some folks are going to have risks no matter what they do.
For example, you can get unlucky wrt a mutation or a cosmic ray.