These edits were proposed by Michael Cariaso, whom I met recently. Mike runs a cool site called http://snpedia.com.
SNPedia is like 23andme, except every night SNPedia reads PubMed abstracts to see if it can determine information about more SNPs. So, I believe it now gives information on 10x as many SNPs as 23andme, because it groks a lot more medical research.
SNPedia has a mode where you do not even need to upload your data to them, instead you simply download the program and run it locally. But, regardless, you need to get your DNA, and 23andme is the cheapest option for doing so.
with proper TDD (tests representing the environment) it should be possible to generate random commits and only commit them when they pass the test suite.
I would say it should make us realize we are no more than mere simulations in some huge computer about to have the power cable pulled by god's boss before he tells him to get back to work. (scifi book idea )
I'm pretty sure that was the plot of a fairly well know scifi book cough hhgttg cough. Except it wasn't God's boss that pulls the cable - Earth was demolished to make way for an intergalactic bypass.
That's kind of a stretch of an interpretation, don't you think? I always thought that the Earth was still physical in the way that we usually think of it, and humans were just part of its physical operation rather than being simulations.
This raises the possibility of us finding out that happiness/nirvana is NP-complete, leading to the mass suicide of the entire human race. That would suck.
Haha, that breeds all kinds of crazy ideas. If one could simulate the world's biosphere and its organisms at the genetic or even cellular level, we might one day be able to predict the effects of evolution on humans and other animals.
MAYBE even with bacteria and viruses to predict and then cure diseases before they even present themselves!
I doubt our understanding of genetics/biology is extensive enough for this yet, not to mention the computing power needed, but it seems quite possible.
There is this professor here at Oxford, Nick Bostrom, who argues that we are currently living in a simulation:
1) Moore's law holds across worlds.
2) People/beings will, for various reasons (historic, sociological, experimenting, play) want to simulate another world (at a social/molecular/submolecular, etc level).
3) If they simulate one, they'll likely do more.
4) Ergo, there will be more simulated worlds than real ones.
5) Therefore we are more likely to live in a simulated world/universe than in a first order one.
Also, he explicitly released it under the Creative Commons Public Domain License. Incidentally, I wonder if that has any patent implications? Does having genomes in the public domain prevent pharma companies from patenting their "discoveries"?
The cost of sequencing decreases by a factor of 10 (!) a year per base pair. I will wait until it's cheap to sequence my whole genome, before I'll shell out the money.
(Synthesizing also gets cheaper by around the same factor. But it started from a higher level of cost.)
I found all of it interesting, but I'm a bio geek. I'm also planning to have kids with my fiancé so it's also cool because of that.
Some highlights:
Both my fiancé and I are carriers for a mild form of Hemochromatosis, so we have a 1/4 chance of having a kid with it.
I am a little bit Asian! That's probably the Jewish ancestry. My fiancé thought he had a black ancestor but it turns out was 100% European. My best friend, whose father had always told her that her grandmother was Native American, found out he was lying to her (which did not surprise but did disappoint her.) Also the heat map of where your mitochondria are from is fun; it confirmed what I knew already but it was still really cool to see that the first migration of my maternal line out of Greece was with my grandmother.
But that's really just the tip of the iceberg. Part of what makes 23andme so fun is you get to learn a lot about biology from the framework of your own genes. Each SNP they report on has a bunch of information associated with it. It's only boring if you aren't interested in biology.
That sounds cool. Can they tell you from which European ethnic groups you come from too? How specific are they about this? Do they say French, German, etc...? Or do they say South of France Celtic, Germanic tribe from the North and so on?
Right now the only categories where they give you your percentage and paint your genome accordingly are European, Asian, and African.
The cool thing about 23andme though is that they're always rolling out new stuff. There is a separate, more detailed ancestry break-down in their "labs" (a part of the website for experimental stuff) but it's not very good. Part of the problem is that there isn't enough research pinning down large swaths of the genome to more specific areas. So what 23andme does is use user reported data- which is problematic due to globalization and limited by people's knowledge.
The only other things that are good and can really pin down geography are your mitochondrial DNA, like I mentioned, and the Y chromosome.
Aaaah, not very useful for me then. I live in Europe and doubt that I have any Asian or African ancestry. Maybe some Middle-Eastern or Sephardic Jew but I guess that falls in the same race as Europeans so they won't be able to tell me. $260 was going to be a big investment for me, I will wait until they can tell the difference between early Europe's ethnic groups: Celts, Germanic tribes, Iberians, Basques, "Roman", etc... They need to study people living in Europe in kind of isolated communities, remote mountains or whatever, then they will be able to tell the difference.
Just take the current price, and extrapolate. Not more than a few years for researchers. I don't know how retail will develop, since there may be regulations and other overheads.
For my friends in systems biology it's now almost cheaper to just send their microbes in for sequencing than doing their own gel electrophoresis.
(If you want to read around in Wikipedia, also have a look at Southern blots and Western blots, and DNA microarrays.)
In your README you state:
I find it fascinating that you can get a text file, roughly 25meg big that contains what I'd imagine to be terabtyes worth of data
I just thought I'd point out that you're really just getting a 25MB patch to a 3GB file (which is really duplicated to 6GB).
Sometimes I do not understand HN.
There is the original post of the guy that posted his DNA on github.com (with the link of course) and a decent discussion on
I don't read HN much, but I thought that in theory that's something you would expect of reddit and not HN? Isn't HN supposed to be above that kind of stuff?
Which is odd because starting from the blog you get the author's take on it AND a link to the code. It's not like you just get one or the other. I would think HN would (should?) be more interested in the whole story and not just a link to a codebase whenever possible.
I thought they found that the ability to delay gratitude is largely genetic? That's still a long way from identifying the particular gene responsible (or even knowing that there is a particular gene, and it's not a combination of a large number of unrelated genes), but it does make it plausible that this will be possible one day.
There's a huge difference between releasing his fully sequenced dna and the data from a genotyping chip.... I went to the github site expecting to see several large fasta files for each chromosome.
I don't see why Github couldn't be used to version track actual genomes of engineered small organisms... It would be great, you could curate changes that are 'virtual', changes that have been made, tested, and validated.
79 comments
[ 2.5 ms ] story [ 127 ms ] thread(rhetorical musing question)
And also we'll see more people asking for changes on appearance than health.
"No instructions on how to build"
https://github.com/msporny/dna/issues#issue/2
https://github.com/cariaso/dna
These edits were proposed by Michael Cariaso, whom I met recently. Mike runs a cool site called http://snpedia.com.
SNPedia is like 23andme, except every night SNPedia reads PubMed abstracts to see if it can determine information about more SNPs. So, I believe it now gives information on 10x as many SNPs as 23andme, because it groks a lot more medical research.
SNPedia has a mode where you do not even need to upload your data to them, instead you simply download the program and run it locally. But, regardless, you need to get your DNA, and 23andme is the cheapest option for doing so.
Given how that works out for the world we live in, there really would be more bugs than anything else....
http://www.si.edu/Encyclopedia_SI/nmnh/buginfo/bugnos.htm
MAYBE even with bacteria and viruses to predict and then cure diseases before they even present themselves!
I doubt our understanding of genetics/biology is extensive enough for this yet, not to mention the computing power needed, but it seems quite possible.
1) Moore's law holds across worlds. 2) People/beings will, for various reasons (historic, sociological, experimenting, play) want to simulate another world (at a social/molecular/submolecular, etc level). 3) If they simulate one, they'll likely do more. 4) Ergo, there will be more simulated worlds than real ones. 5) Therefore we are more likely to live in a simulated world/universe than in a first order one.
http://www.simulation-argument.com/
Think about this when you unplug something in the future...
- The human species is likely to go extinct before reaching a stage where it can simulate its ancestors.
- Future humanity will have no interest in simulating its ancestors.
- We are almost certainly living in an ancestor simulation now.
http://help.github.com/pull-requests/
makes sense now, pretty funny comment about the nipple.
"That ugly nose is your father's"
"Your mother is the one that gave you X disease."
[1] http://manu.sporny.org/2011/public-domain-genome/
Also, he explicitly released it under the Creative Commons Public Domain License. Incidentally, I wonder if that has any patent implications? Does having genomes in the public domain prevent pharma companies from patenting their "discoveries"?
msporny created dna and everyone else forked it. This is the family tree.
The cost of sequencing decreases by a factor of 10 (!) a year per base pair. I will wait until it's cheap to sequence my whole genome, before I'll shell out the money.
(Synthesizing also gets cheaper by around the same factor. But it started from a higher level of cost.)
If and when they offer the service for a complete sequence, I'll probably pay the money again, just to have a complete record.
Some highlights:
Both my fiancé and I are carriers for a mild form of Hemochromatosis, so we have a 1/4 chance of having a kid with it.
I am a little bit Asian! That's probably the Jewish ancestry. My fiancé thought he had a black ancestor but it turns out was 100% European. My best friend, whose father had always told her that her grandmother was Native American, found out he was lying to her (which did not surprise but did disappoint her.) Also the heat map of where your mitochondria are from is fun; it confirmed what I knew already but it was still really cool to see that the first migration of my maternal line out of Greece was with my grandmother.
But that's really just the tip of the iceberg. Part of what makes 23andme so fun is you get to learn a lot about biology from the framework of your own genes. Each SNP they report on has a bunch of information associated with it. It's only boring if you aren't interested in biology.
The cool thing about 23andme though is that they're always rolling out new stuff. There is a separate, more detailed ancestry break-down in their "labs" (a part of the website for experimental stuff) but it's not very good. Part of the problem is that there isn't enough research pinning down large swaths of the genome to more specific areas. So what 23andme does is use user reported data- which is problematic due to globalization and limited by people's knowledge.
The only other things that are good and can really pin down geography are your mitochondrial DNA, like I mentioned, and the Y chromosome.
For my friends in systems biology it's now almost cheaper to just send their microbes in for sequencing than doing their own gel electrophoresis.
(If you want to read around in Wikipedia, also have a look at Southern blots and Western blots, and DNA microarrays.)
I just thought I'd point out that you're really just getting a 25MB patch to a 3GB file (which is really duplicated to 6GB).
http://news.ycombinator.com/item?id=2211334
(5 hours ago)
and still this post is the most upvoted
http://twitter.com/#!/schwa/status/36618789894361088
Lame.
Imagine how much money the people who discovered it would end up making!
And they'd start making it right away ;)
For more information about the raw format used by 23 and Me: http://www.snpedia.com/index.php/23andMe
==== http://vurl.me/YDW ====
Christan Audigier bikini $23
Ed Hardy Bikini $23
Smful short_t-shirt_woman $15
ed hardy short_tank_woman $16
Sandal $32
christian louboutin $80
Sunglass $15
COACH_Necklace $27
handbag $33
AF tank woman $17
puma slipper woman $30
==== http://vurl.me/YDW ==== ----- ~ ¤ ╭⌒╮ ╭⌒╮ ╭⌒╭⌒╮╭⌒╮～╭⌒╮ ,））））,''）~~ ,''~） ╱◥█◣ ╱◥█◣ ｜田｜田｜｜田｜田｜ ╬╬╬╬╬╬╬╬╬╬╬╬╬╬
ie: removed increased risk of coronary artery disease at rs1333049
Pretty awesome
In the future, common practice.