Man Open Sources His Genetic Data 198
An anonymous reader writes "Manu Sporny, founder and CEO of Digital Bazaar, has decided to use GitHub to store a very interesting project. Rather than a piece of software, he is listing his own genetic data as an open source project. He has released all his rights to the data and made around 1 million of his genetic markers public domain. As to why he decided to do what many may feel is a risky sharing of data so personal and unique to himself, Manu explains: 'I've thought long and hard about each of those questions and the many more that you ask yourself before publishing this sort of personal data. There are large privacy implications in doing this. However, speaking solely for myself, I think the benefits outweigh the drawbacks.' Manu hasn't gone into great detail as to his thought processes yet, but promises to on his blog at a later date."
I was here first (Score:5, Funny)
I've been offering my DNA samples for at least 20 years now.
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I've been offering my DNA samples for at least 20 years now.
Propositioning someone is not the same as open sourcing you DNA sequence ;-)
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*sigh* the same old free as in beer vs free as in speech argument again...
Re:I was here first (Score:4, Funny)
Give me free beer and I'll give you free speech.
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I'm betting there would have to be free beer involved, and lots of it...
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share and share alike
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I've been trying to offer mine, but people lose interest when I make them read the GPL first.
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Thats because the GPL is viral!
You should try using the MIT or apache licence, chicks dig that.
Looking around... (Score:5, Funny)
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The main office on the top floor, take a right past the pearly gates...
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Say prayers to God? :)
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Where do we file bug reports?
You don't. Leave that to his mother in law.
Long term, not a good idea... (Score:4, Funny)
Re:Long term, not a good idea... (Score:5, Interesting)
That is one method of immortality.
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Why do you need the neural scanner for that? It's not her mind we're interested in!
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if you use a neural scan, then in the sim, like in reality, your answer would be the same:
"eww, get away from me, freak!"
Re:Long term, not a good idea... (Score:5, Interesting)
Then again, Lacks never gave consent for the cells to be used, whereas this guy chose to make this data available.
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Re:Long term, not a good idea... (Score:4, Informative)
Hela cells came from a cancer biopsy sample with a consent form
From the wiki page on HeLa cells I linked to above (emphasis mine):
The cells were propagated by George Otto Gey shortly before Lacks died in 1951. This was the first human cell line to prove successful in vitro, which was a scientific achievement with profound future benefit to medical research. Yet Gey freely donated both the cells and the tools and processes his lab developed to any scientists requesting them, simply for the benefit of science. Neither Lacks nor her family gave Gey permission, but, at that time, permission was neither required nor customarily sought.[4] The cells were later commercialized, although never patented in their original form. Then, as now, there was no requirement to inform a patient, or their relatives, about such matters because discarded material, or material obtained during surgery, diagnosis, or therapy, was the property of the physician and/or medical institution. This issue and Mrs. Lacks' situation was brought up in the Supreme Court of California case of Moore v. Regents of the University of California. The court ruled that a person's discarded tissue and cells are not their property and can be commercialized.[5]
Reference 5, "The Immortal Life of Henrietta Lacks" is an interesting read, I'm not done with it yet. The family though is upset due to the lack of consent, and the fact that others profited off of the thing that killed her.
No one should suggest that Henrietta Lacks is still around.
They are cancer cells derived from her, they're her genes. Those genes have been sequenced. Genes from HPV are detectable in the genome, so she had HPV, that's some very private information on her medical history that is public knowledge through HeLa cells. They're not Henrietta Lacks, but they are still cells from her, to imply it's not her at all is a mistake.
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>>>>>>e's going to find himself running over and over again in emulators in about 50 years.
>>
>>its insta-immortality right there.
Reminds me of the short story "Pretty Boy Crossover" from 1986. A young man converts himself to a virtual reality dance club, so he can remain young forever, and be part of the ultimate Remix video.
http://www.exampleessays.com/viewpaper/69933.html [exampleessays.com]
Creative Defense (Score:3, Funny)
"Your Honour, my client wasn't sexually assaulting the alleged victim, he was merely Open Sourcing his genetic data."
Re:Creative Defense (Score:5, Funny)
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You jest, but I really find the practice of using fingerprint and DNA evidence to prove guilt disturbing and flawed.
Lets say I were going to commit a crime.
I've seen many people who approximately match my description. It would take very little time for me to follow behind someone and nab their used drink cup and/or a few strands of their hair. After studying their routine I could schedule my crime to leave them with a very weak alibi (or none at all).
After finishing my dirty deed I could simply plant thei
how long befor some calms a IP rights to part of (Score:2)
how long before some calms a IP rights to part of the data and sues him?
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http://raines.wustl.edu/~anthro/articles/jensen2005intellectual.pdf [wustl.edu]
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Probably a while, but it's definitely possible. Michael Crichton wrote a rather dull book on the issue of corporations copyrighting DNS sequences:
http://en.wikipedia.org/wiki/Next_(novel) [wikipedia.org]
If it's IP, though, I'd like to point out the fact that you can't sue anyone for playing the twelve-bar blues in A because it's a traditional piece. Maybe this guy will become a 'traditional' DNA number.
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Next was about patenting, not copyrighting, gene sequences. Copyrighting a gene sequence would make it illegal for carriers of that gene to reproduce. Patents make it illegal for anyone to make money using that gene. And the trick with genes is that one does not patent the DNA at all, but the RNA, which is the 'negative' of the DNA sequence. The RNA is artificially produced, thus an invention. And to do any work with a sequence of DNA you always need RNA, so patenting the RNA gives the same result as patent
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What about people writing custom literature in their DNA?
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OK so I didn't pay attention. Like I said, the book was dull.
Another significant difference between IP and patents is that patents typically expire whereas IP rights may not, if owned by a corporation -- or at least that's my armchair lawyer's understanding. Feel free to pedantically correct me again.
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His post was definitely informative so I don't mind the pedantry which I detected in the section reading "please at least don't confuse copyright and patents...etc.". It's not so much a genuine plea as a hint of patronizing irritation followed by an ostensible clarification which is not clear at all. I appreciate the corrections. I'll tolerate the tone as long as I'm permitted to be snarky about it.
What about his relative's right to privacy (Score:3, Interesting)
Well, you could argue that anyone has the right to do this, but his DNA sequences will also be fairly close to his relatives DNA and you could probably make some assumptions about them and their predilection to certain diseases or whatever.
I wonder if he asked for his relative's permission?
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Well, you could argue that anyone has the right to do this, but his DNA sequences will also be fairly close to his relatives DNA and you could probably make some assumptions about them and their predilection to certain diseases or whatever.
I wonder if he asked for his relative's permission?
If every other person were uploading their DNA sequences...
His and his relatives' DNA literally pours off of their bodies as they walk about town. They haphazardly shed skin and hair every where they go, and toss disposable saliva laden cups into public waste bins.
YOUR DNA IS NOT PRIVATE INFORMATION; Neither are your fingerprints or the brand/size/color of your clothes.
Anyone who wants your DNA only has to wait till you've visited a public place, then clean up after you.
I only wished that courts would realise this too.
What about his race's right to privacy (Score:2)
His DNA sequence will also be fairly close to any ethnic group to which he belongs.
Thanks to DNA sequencing, it is known that Jewish women of Central and Eastern European origin [nytimes.com] have a higher than normal risk of getting breast cancer.
Should every one's right to information be limited by whatever group feels their "privacy" rights are more important?
Here's what he's doing (Score:5, Interesting)
He's establishing his DNA as "prior art".
Anyone who tries to patent some element of DNA (and there's plenty who will try to) now has a rather significant obstacle to overcome, especially since at least 99% of DNA is the same between people.
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They will just patent a 'method of using gene #456753 to test for risk of [disease X]'. Or 'an apparatus that treats [disease Y] by examining the patient's genetic profile and adjusting treatment accordingly; specifically, by use of gene #487532 to determine patient's likely reaction to [treatment Z]'.
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I don't see anything wrong with patenting a discovery that allows using the information from our DNA. There are huge issues with companies trying to patent the actual DNA because millions of people would infringe on it merely by existing.
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Thus why it's an extremely bad idea to allow ANY gene patents.
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and the ultimate evil:
http://en.wikipedia.org/wiki/Monsanto [wikipedia.org]
Patenting a plant, then suing people when nature happens and the plant is fertilized into their field.
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Monsanto is the Umbrella Corporation of the real world.
Re:Here's what he's doing (Score:4, Informative)
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So it does not cover the 99% of DNA that is the same between people
There's no need for it to cover that. The consensus DNA sequence (human genome reference sequence) is freely available from the NCBI [nih.gov] website [nih.gov].
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(Never mind that SNPs aren't used in forensic DNA analysis)
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That's what I thought too. (Score:2)
Since a DNA sample is sequence tolerant, meaning it can occur just about anywhere in a DNA strand, trying to claim industrial-style ownership becomes damn near useless.
Researchers can claim that the sequence is open source and, apart from the portions that are unique to a specific individual, they'd be right.
Its also a means of giving himself immortality in the minds of all genetic researchers.
The name Manu Sporny may not roll off of the tongue as trippingly as Monsanto or Merk, but I'm already thanking him
Open Source? So that means we can fork him? (Score:3)
Add features that his users really want, like razor-sharp talons, wings, and burning laser X-ray eyes. I think that the future will be really interesting.
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Can we upgrade our calcium bones to a stronger metal?
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But in our bones it's calcium oxide.
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Does that mean our bones are rusted metal?
Rusting happens to ferrous materials such as iron, so our blood is rusty metal.
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Lawsuit Still Pending (Score:4, Funny)
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My mother is nagging me because of my derivative works.
Link To DNA Source (Score:3, Informative)
Makefile (Score:4, Insightful)
There's a Makefile in the source. I assume it's a symbolic link to the kamasutra.
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There's a Makefile in the source. I assume it's a symbolic link to the kamasutra.
There may be something to that.
# make love
Not war.
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I must be doing something wrong.
make: *** No rule to make target `love'. Stop.
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I get :
missing prereqs: buy dinner, send flowers
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Please merge with me! (Score:3, Funny)
Please merge with me! git pull https://github.com/nportman/dna [github.com]
Patented genes (Score:4, Interesting)
Haven't some genes been patented during the past years? How about the legal consequences of open sourcing these genes, which are part of his DNA?
Amateur genetics (Score:5, Interesting)
Hours after Joseph Pickrell put his genome on the internet, an anonymous blogger took the data and concluded that he came from Ashkenazi Jewish stock. Pickrell, a genetics graduate student at the University of Chicago, Illinois, was sceptical about the claim. But after talking to relatives, he discovered that he had a Jewish great-grandfather who had moved to the United States from Poland at the turn of the nineteenth century. "It was a part of my ancestry I was totally unaware of," he says. The blogger, who writes under the pseudonym Dienekes Pontikos at http://dodecad.blogspot.com/ [blogspot.com] had commandeered Pickrell's DNA as part of the Dodecad Ancestry Project, an ambitious project in which cutting-edge genomic analysis meets Web 2.0. Pontikos analyses genetic data submitted by followers of his blog to reconstruct personal ancestry and human population history — and reports his findings online. He is part of a small but growing group of 'genome bloggers', a mix of professional scientists and hobbyists proving that widely available tools for computational biology could enable recreational bioinformaticians to make new discoveries. "They are not amateurs. They are far from being amateurs," says Doron Behar, a population geneticist at Rambam Health Care Campus in Haifa, Israel, who studies human history. "I cannot stress enough the level of appreciation I have for their efforts." Pontikos has so far analysed several hundred thousand single-letter DNA variations from more than 2,200 individuals. That includes more than 200 submitted to him by readers of his blog, who had had their genomes analysed by genetics testing firms such as 23AndMe, based in Mountain View, California, with the remainder coming from publicly available datasets. The readers volunteering their genomes (identities stay private) are mostly keen to delve into their own ancestry. But Pontikos, who is from Greece and describes himself as an "anthropology dilettante", is more interested in unfurling the history of populations that tend to be overlooked by human-population geneticists. For instance, his analysis of genomes from people living in northern Eurasia reveals a genetic connection between populations in northern Finland and central Siberia (see 'Meet the ancestors'). David Wesolowski, a 31-year-old Australian who runs the Eurogenes ancestry project (http://bga101.blogspot.com), also focuses on understudied populations. "It's a response, in a way, to the lack of formal work that's been done in certain areas, so we're doing it ourselves," he says. Wesolowski and a colleague have drilled into the population history of people living in Iran and eastern Turkey who identify as descendants of ancient Assyrians, and who sent their DNA for analysis. Preliminary findings suggest their ancestors may have once mixed with local Jewish populations, and Wesolowski plans to submit these results to a peer-reviewed journal. But Pontikos sees little point in formally publishing his findings. "I can bypass them entirely, and have the entire world review what I write," he wrote in an e-mail. Indeed, comments on his blog — "could you please provide the eigenvalues for the principal component analysis", for instance — read like the niggling recommendations of a manuscript reviewer. ...
Maybe he is opening his genome to anybody who wants to study it. Since it is the only Open Source genome, I'm sure there will be plenty of research, and he could benefit from it (not financially, but it's a nice relief to be assured that you can not have alzehimer, diabetes or whatever.)
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They are not amateurs. They are far from being amateurs," says Doron Behar, a population geneticist at Rambam Health Care Campus in Haifa, Israel, who studies human history.
Does that mean that they don't enjoy what they do ? If they hate it so much why don't they just stop doing it ?
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I suppose it is the only "open source" genome, unfortunately the label seems to have no meaning whatsoever in this context, and the whole thing is just a cheap publicity stunt.
Essentially all data produced in academic labs is created as part of government-funded projects or is deposited in government funded databases when it's published - all of these are in the Public Domain, always have been, always will be.
The 1000
Future of gaming (Score:2)
step 1 - buy video game and install it
step 2 - load your sequenced genes
step 3 - play the game as yourself
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Genotype-Phenotype (Score:2)
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...
Guess he shouldn't date geneticists.
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Free samples (Score:2)
Don't you lose your proprietary rights over your genetic material if you give away free samples? I've been giving them away for years and I can't be surprised should a recipient have them sent to a lab and tested. I've never requested an NDA be signed by any women.
Assuming that anyone has default proprietary rights over this information opens up some interesting questions about everything from paternity testing to the possibility of a DMCA takedown notice should someone make an unapproved copy of my gene
Personal Genome (Score:4, Informative)
Forks & merges (Score:2)
As of now, he's got already 26 forks [github.com], so he's been cloned several times.
But what will be impressive is having merges (via pull requests) accepted into the master branch. Crowd-sourced gene therapy (or mutation) anyone?
I skipped to the end and read a bit. (Score:2)
That certainly one way to replicate your genes. (Score:2)
Seriously.
Prepare to be sued (Score:2)
Jailbroken (Score:2)
I can run his code on my pet turtle. Man.
All genetic data is public domain* (Score:2)
All genetic data is public domain*. You're merely the temporary custodian of your particular permutations, combinations, and mutations.
* yes. I know it probably isn't in a legal sense - but I've yet to see a convincing explanation of why it shouldn't be. We don't earn it or create it. We just pass it on or not.
Large Privacy Implicatons? (Score:2)
Can we build our of instance of Manu Sporny now? (Score:2)
All we would need is complete neural map of his brain and way to clone him and imprint that neural map intot he cloned brain and we could essentially duplicate this guy.
Since his "source" would be GPL, does that mean anyone could enslave him after cloning him????
Who wrote this crap code? (Score:4, Funny)
How this stuff compiles and runs I don't know, it's clearly NOT intellegent design!
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Largely, I'm with you.. but I think it's more about things in the future like 'oh.. you are gonna have prostate cancer and will be prone to clinical depression, and this here genetic marker indicates you will be homosexual, and this one says you have a small penis and offensive body-odor'..
Based on those things, persons might choose to treat him different.. I guess?
Until we find the gene sequence that shows you're more prone to effective advertising or that you're better at paying your mortgage on time, it'
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and offensive body-odor'
God, I'd hate for my DNA to be sequenced and get out into the public so that people would know my secret: that I have HORRIBLE BO! Then I wouldn't be able to lure people into sniffing my armpit anymore and finding out the easy way!
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Why do people treat genetic data as though it's the most confidential document in history? It's just a long string of base pairs, amirite?
Are you kidding? This could lead to the ultimate identity theft.
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Oh and gattaca http://www.imdb.com/title/tt0119177/ [imdb.com]
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They already can't: http://en.wikipedia.org/wiki/Genetic_Information_Nondiscrimination_Act [wikipedia.org]
Why has no one hard of this?
Fun fact: Ron Paul was the only vote against this bill, in both the House and the Senate.
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Re:That's silly (Score:5, Insightful)
He is most certainly releasing the source code. In his case, it's a reverse-compile, so the code is messy and doesn't have any documentation, and probably has lots of GOTO loops in it.
However, like most open-source objects, he's not including the compiler. You have to find or build your own compiler to compile the source into another being.
I'm only aware of one compiler, but I can't figure out the make file format for 100% predictable results, and speculating as to its exact nature of this compiler is a matter of biology, philosophy, or religion, depending on which "man" file you open.
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