From now on I will be posting content to my new shared blog biononymous.me
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Here is the presentation I gave on SNPs and ancestry
Here is the bricoBio Kevin Chen from Bricobio gave on DNA and DIY bio
Here are Yves Amyot from Turbine’s 3Dprinting
I am putting together a Stranger Visions workshop to take place at Studio XX in Montreal next weekend (Sunday Oct 8) in collaboration with Turbine and bricobio
We will be taking found genetic data files, creating phenotype profiles, generating 3d models interpreting those phenotypes and 3d printing miniature versions of these portraits. Here are some of the resources we will be using:
Found data files
Look on github.com a code sharing website for people who have posted 23andme files
Look on the Personal Genome Project for volunteers who uploaded 23andme data
Here are some examples which I have pre-processed for a later step, cooking show style:
Upload your 23andme file as a zip to the website gedmatch to get admixture information
(this part can take quite a while so I pre-uploaded several files for us to work with)
alternatively you can use the more visual and less quantitative results from Stanford’s Interpretome
Get your mtDNA haplogroup
gedmatch gives eye color prediction
The easiest and most intuitive way to translate a phenotype profile into a model of a face is using the commercial software facegen this program will let you export a watertight 3d printable head, you just have to install the additional model set how to video here.
Here is code I wrote in python to generate a phenotype profile from a user-customizable SNP base
here is a worksheet I made which you can use to help create your profile/sketch and document the details of the sample
PRISM Break Up
October 3-6, 2013
New York, NY
Request for Proposals
DEADLINE: MIDNIGHT August 25
On October 3-6, 2013, Eyebeam Art and Technology Center will host the first event of its kind PRISM Break Up, a series of art and technology events dedicated to exploring and providing forms of protection from overreaching surveillance. The gathering will bring together a wide spectrum of artists, hackers, academics, activists, security analysts and journalists for a long weekend of meaningful conversation, hands-on workshops and art installations.
Why does it matter?
In the contemporary digital era, privacy has become a luxury for the initiated. Google and Facebook mine your personal data for a profit, the government monitors your phone calls, even shopping malls track the mobile phones connected to their wifi. In the wake of revelations about the NSA PRISM program, many citizens are left wondering what they can do to protect their privacy. We believe everyone has a right to define their own digital privacy, understand how it is being compromised, and feel empowered to protect it.
Initiatives like Prism Break (http://prism-break.org/), the Locker Project (http://lockerproject.org/), and Security in a Box (https://securityinabox.org/) have attempted to combat privacy violations, but the process continues to be complex and inaccessible to the general population. We also recognize that security and privacy, especially at the hardware level, is tricky, but that’s not going to stop us from trying to determine how it can best be protected.
Thursday Oct. 3 – Kickoff party and art opening.
Friday Oct. 4 – Evening lectures/discussions, screening party.
Saturday Oct. 5- Day of workshops.
Sunday Oct. 6- Lectures/discussions, wrap up, help cafe, cryptoparty.
There are three categories of participation: talks, workshops and art:
Do you have an idea for a lecture, panel discussion or other type of talk you would like to give about privacy, security, surveillance or PRISM related issues? Submit your idea! Talks will take place Friday, Oct. 4th.Topics can be from 15-20 minutes in length, variable if a panel discussion is implied. From the submissions, we will select between 6-8 talks and a maximum of 2 panels.
The goal of these workshops is to share security techniques with the general public. Want to teach people how to secure their communications? Is it possible to get off Google? How do we avoid being tracked? If you know how to do so in a fun and engaging way, propose a workshop! We are also looking for people to assist during our Sunday help cafe.
Initial workshop ideas include implementing any of the PRISM-break technologies (https://prism-break.org/), mobile encryption, building affinity groups, evading hardware level surveillance, steganographic tools, submitting FOIA requests, and generally getting over Google. Workshops will be around 45 minutes in length and take place on Saturday, Oct. 5th.
Do you create works dealing with issues of privacy and surveillance? Submit your work to the PRISM Break Up exhibition taking place Oct. 3-6. Installations and collaborations, non-traditional and experimental work is encouraged.
Is your work ephemeral, hard to transport or located far from New York? We can’t cover transportation but we are having a screening party. Submit a video work or documentation of your privacy themed art to our screening taking place Friday Oct. 4.
DEADLINE: MIDNIGHT August 25
Please copy the template below into a blank email and answer in full. Email your proposal to firstname.lastname@example.org with subject line [workshop] [talk] [art] or to specify what you are applying to propose. You may submit multiple proposals.
What is it? (pick all that apply)
– Artwork (if video for screening please specify)
URL of the work/documentation of the work (if applicable):
Details of implementation (for workshops):
Who is your intended audience? (for workshops):
What will your proposed contribution add to this event?
What do you hope to get out of this experience?
Have a question about the application? Want to help fund this exciting endeavor? Or would you like to volunteer food/drinks/money/time? If you want to help out but don’t have a specific idea, email us and we can figure it out together. Email us at email@example.com with subject line [volunteer] to get involved!
Allison Burtch, Aurelia Moser, Heather Dewey-Hagborg, Ramsey Nasser
Come by QF gallery tomorrow evening for my closing party!
98 Newtown Lane
East Hampton, NY 11937
Saturday, July 20
gallery opens at noon
closing reception 6-8pm
This is the first in a series of technical posts I hope to put together over the coming weeks about the process of creating Stranger Visions. Starting from the lab end I will describe in detail how I create these portraits from DNA.
The first step of course is extracting DNA from a sample, that can be done with a kit readily obtainable from Qiagen, the “DNA Investigator Kit”.
After I extract the DNA* I do a test PCR for a specific alu insertion using a primer (full kit is also available) from Carolina. This gives me an idea of whether I successfully extracted chromosomal DNA or not. If the results look bad on this there is probably no reason to go further with this sample.
If all these results look good I continue to look at 3 SNPs associated with particular traits and 1 region on the y chromsome:
rs12913832 – for eye color
SRY gene – present on Y chromosome, I use to indicate gender
rs9939609 – as one of many indicators of obesity
rs4648379 – preliminary research, correlated with the size of the nose
I have been using a free tool on IDT for designing primers to target these regions using PCR. If the result of the reactions looks good in a gel I send them for sequencing.
So those are SNPs I have had success so far analyzing in the lab myself, but there are a whole lot more clues I have on a “master list”, the things I can find out from a 23andme profile for example. In addition to SNPs related to specific traits this includes Y chromosome haplogroup information from males to get an idea of paternal ancestry, as well as Ancestry Informative Markers, specific SNPs that are correlated with population studies giving an overall picture of ancestry beyond the direct maternal and paternal lineage. I am pasting my master list here below (excluding the ancestry info I just mentioned and linked to above as that would increase the list a thousand fold). Also, here is a link to appearance related SNPs on snpedia.
*I have recently discovered that whole genome amplification can also be performed after the extraction step and isn’t as expensive as I previously though – I will likely pursue this in future experiments.
|rs1426654||AA||light skinned european|
|rs17646946||GG||curlier hair in europeans|
|rs12896399||TT||blue eyes vs green if not brown – prelim research|
|rs1426654||AA||euro ancestry – light skinned|
|rs1667394||CC||decreased odds blond hair|
|rs1805007||TT||higher odds red hair|
|rs1851665||AA||greater chance of obesity|
|rs3827760||AG||thinner hair (asian)|
|rs1393350||AA||blue eyes rather than green IF non-brown – preliminary research|
|rs1533995||AA||more pronounced crypts|
|GG||less pronounced crypts|
|AC,CC||less iris furrows|
|rs12896399||GG||more pronounced pigementation rings|
|TT||absent pigmentation rings|
|CT||slightly higher odds red hair|
|TT||increased odds brown hair|
|rs1042602||AA||absence of freckles|
|CT;TT lighter skin|
|rs1800414||C||each c -> 1.3 melanin unit lighter skin in east asians|
|rs16891982||GG||european light skinned|
|preliminary facial research||source|
|rs4648379||C/T||edge of nostril -> tip of lower nose|
|rs974448||C/T||mid eye to top of nose|
|rs17447439||A/G||distance between eyes|
|rs6555969||C/T||distance between cheekbone and nose, ALSO distance between eye and top nose|
|rs805722||C/T||distance between eye and top of nose|
|Eye and Skin color||source|
Kari Mulholland over at TED made a short behind-the-scenes documentary about Stranger visions, check it out!
I am very excited about this event I am participating in on Monday afternoon:
It’s a policy discussion in DC about the bioethical and privacy issues raised by Stranger Visions. If you are in or near DC come by! I will have some work on display, give a short presentation and then we will have an interactive discussion.