Category Archives: DNA

Good Regulators: The Weakness of 1Password and Its Progeny

There’s a math theorem that I rather like because I think it appeals to so many situations. I feel this way about that quote from Frankenstein, “And now, once again, I bid my hideous progeny go forth and prosper… blahblah;” I used that repeatedly in school essays, on entrance exams, in acceptance speeches. Some things make little sense to you in-situ but come to mean much more when you apply them to other scenarios. In the Good Regulator Theorem, good regulators are a model of systems that they regulate, and if the model is not a performant echo, then the system is weak, unregulated, and welcome to compromise. In some ways, I feel passwords are “good regulators,” things that model what they manage, because they protect memory (stores of information that you might like to keep private), and in a meta-way, they rely on your memory to ensure their utility.

We often write weak passwords because we have weak memories. So then we write frameworks around them that weaken their ability to perform, their ability to echo the system they model, and thus we introduce our human weakness into an already crippled model of protection. We “salt” and “hash” our passwords but we are still distant from a happy breakfast, to a happy progeny, a product of our genius and not simply an echo of our faults. So what can be done about passwords? What can be done about the memory they protect? How does the weakness of passwords, and of “good regulation,” affection the bio-politics of our contemporary world?

Password Strength XKCD

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Is Beating a DNA Test Possible?

ralph

 

Humans contain about 25,0000 protein coding genes and much more non-protein coding DNA, all of which uniquely identifies us. Because of this, DNA tests have become the standard is criminal forensics for identification of individuals at the scene of a crime. When done properly these tests can identify individuals with a theoretical probability of 1 in 10,000,000,000,000,000,000(1018). These statistics come from using the Combined DNA Index System or CODIS and focuses on identity through only 13 genes (alleles). Well, it is not actually 13 genes, it is only small parts of 13 genes. To me this seems like a very breakable and hackable system so let’s talk think about that for a minute or seven.

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Sci-Fi Crime Drama With A Strong Black Lead

Published 7/6/15 by The New Inquiry

The practice of rendering appearance from forensic samples is called “Forensic DNA Phenotyping” (FDP) or “molecular photofitting,” and there are a handful of scientists and companies around the world trying to make this not only scientifically possible, but also a useful law enforcement tool. FDP has already been used to create a new kind of police sketch.

While there are a few traits like eye and hair color that can be predicted from DNA with a high degree of certainty, the bulk of FDP relies on algorithmically derived statistical composites. We tend to look at technical systems as neutral black boxes, but if you open them up and look at the component parts, you find that they reflect the assumptions and motivations of their designers.

FDP begins with a dataset of 3D facial scans and DNA samples taken from research participants. These scans are processed to create what’s called “face space,” a probabilistic representation of all possible faces drawn from, and limited by, this set of 3D scans. Finally, the data is mined for correlations between DNA and facial shape by examining characteristics that are assumed to be opposite ends of a spectrum, like masculine and feminine or “European” and “African.”

The act of creating computational averages and looking for correlated features in large datasets has an air of authenticity and scientific validity, but what this actually does is create a system of types — you might call them stereotypes.

Continue Reading: Sci-Fi Crime Drama With A Strong Black Lead at The New Inquiry.

The Future of Microbiome Forensics

bacteriaEverywhere we go we leave microscopic traces of ourselves, and we collect microscopic traces of others. Microscopic DNA left at the scene of a crime is commonly used to identify criminals and substantiate evidence against them. What about other microscopic traces humans leave behind or even collect, can we be identified or tracked based solely on the bacteria that inhabit our body?

Yes.

Everyone’s skin is covered in bacteria, it is all over you and the surfaces you interact with. Scientists call each community of bacteria a microbiome. Until the past few years this knowledge was little more than a curiosity as Scientists attempted to understand if this population of bacteria on our bodies affected us in any way. Then some studies came around which suggested that bacteria influence things like mammalian circadian clocks and appetites. Some others attempted to quantify the types and amounts of bacteria on our skin, inside our body, and in our environments. From all of this, Scientists began to see that both the microbiome of our environments and our bodies have unique qualities.

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Response to the “Face of Litter”

Yes, this looks very familiar…

No I had nothing to do with it, I was not consulted or cited, and I’m not surprised.

It isn’t surprising that an ad agency copied an artist’s work with no remuneration or citation.

And it isn’t surprising that an ad agency press release was recycled from one media outlet to the next as “news” without research or problematization of the obvious issues here around surveillance, genetic privacy, and public shaming as a technique of social control.

Finally, it isn’t surprising that DNA might be used to monitor, survey, and publicly shame individuals deemed deviant.

But what is the “face of litter” campaign really? DNA phenotyping isn’t cheap, and it’s telling to contemplate why a Parabon Nanolabs, a small biotech startup, would donate this expensive technology to an ad agency for a pro bono ecological project. It’s called PR.

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How Apple, Google, and Microsoft are trying to get inside your genes

re-posted from the Council for Responsible Genetics, and fusion

by Daniela Hernandez 

Not satisfied by having our emails, chats, status updates, search histories, clicking behaviors, and shopping preferences, some of Silicon Valley’s most powerful tech titans are in an arms race to get access to your most personal information:
your DNA.

Last week, for instance, the MIT Technology Review reported that Apple was looking to integrate genetic data into studies that run atop its new open-source research platform, ResearchKit. That should come as no surprise. There’s a national focus on personalized medicine, and since DNA information is becoming cheaper to get and store, the healthcare industry is hoping that personalized medicine will be part of the solution to rising costs.

Here’s a look at how three tech companies are preparing to dominate your DNA:

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After Genetic Privacy: an Interview with Yaniv Erlich

In 2013, Yaniv Erlich’s genetics lab at MIT (now at Columbia) called the entire possibility of genetic anonymity into question when they discovered the identities of DNA donors by cross-referencing their genetic data with publicly available information from genealogy databases. Their article “Identifying Personal Genomes by Surname Inference”(1) published in Science created a stir across privacy and medical research communities.

Heather Dewey-Hagborg: In your own words, can you give us a brief explanation of the study? What did you do and what did it mean to you?

Yaniv Erlich: We showed that it is possible in some cases to infer the surnames of males from their allegedly de-identified DNA samples. In most societies, a male receives his surname from his father, who received his surname from his own father and so own. Now, since males receive their Y chromosome from their father and the father of their father, this process creates a correlation between surnames and y chromosomes.

Our technique exploits this correlation to identify the surname of individuals and uses open genetic genealogy databases to infer the right surname. Surnames are strong identifiers. Correctly inferring them dramatically narrows the search space. We specifically showed that if the age and state of the targeted individual are known (HIPAA does not protect these two identifiers), then a surname inference can virtually resolve the identity of the person.

To show that this technique works, we were able to identify with extremely high probabilities close to 50 people that were part of a large scale study, called the 1000 Genomes.

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Forensic DNA Phenotyping in the news

From NYTimes. Original caption read: The police in Columbia, S.C.,  released this sketch of a possible suspect based on DNA left at the crime scene. Parabon NanoLabs, which made the image, has begun offering DNA phenotyping services to law enforcement agencies.

From NYTimes. Original caption read: The police in Columbia, S.C., released this sketch of a possible suspect based on DNA left at the crime scene. Parabon NanoLabs, which made the image, has begun offering DNA phenotyping services to law enforcement agencies.

Lots of media attention recently to a new company Parabon NanoLabs who is offering a forensic DNA phenotyping service (creating 3d virtual portraits from DNA) apparently to police nationwide. Popular Science broke the story as far as I can tell and I received a lot of email this week when the New York Times put their own story about the service on their homepage Monday. There are so many issues that went unaddressed in these articles which focus primarily on discussing this as a *technology*. I wrote a letter to the editor of the New York Times addressing one aspect of this I felt went far under-discussed: the way in which it forms a supposedly scientific basis for a new form of racial profiling. Here is the letter I wrote, we’ll see if they respond or publish it.

Update 3/5/15 – The New York Times did not publish or respond to my letter.

TO THE EDITOR:

In “Building a Face, and a Case, on DNA” (NYT, Feb. 23, 2015) Andrew Pollack describes how police departments are mining DNA evidence to create police sketches. Since 2012 I have been creating life size full color 3D portraits from DNA in chewing gum, cigarettes and hair I found on New York’s streets for an art series called Stranger Visions that has shown in locally and internationally from the New York Public Library, to the Science Gallery in Dublin and Ars Electronica, Linz.

Through my own work in the molecular biology lab, I discovered that this science is still in its infancy. As noted in your article, there are few facial characteristics that can be known for certain, lending the practice a speculative nature. While eye and hair color can be guessed with a strong probability, skin color and race, hidden behind the term “ancestry,” are much more problematic.

Rather than producing a useable sketch, the technology allows police departments to hide the practice of racial profiling beneath a veneer of “legitimate” science. After years of controversy, racial profiling has been widely controversial and rejected by the public. But if you glance at the profile that is actually generated by Identitas and Parabon, you see a composite model based on very few genetic variables that relate to facial features. It’s a portrait of a generic African American male—a visualization of a stereotype.

The real question here is whether scientists and society in general is willing to accept a new form of racial profiling that masquerades as science?

Sincerely,
Heather Dewey-Hagborg
Assistant Professor of Art and Technology Studies, School of the Art Institute of Chicago

Newborn DNA Storage Raises Serious Privacy Concerns

Before they are even a week old, ninety-eight percent of the 4.3 million babies born annually in the United States have a small sample of blood taken from their heels. These newborn bloodspots (NBS) are then screened for a variety of inherited conditions and are often later stored in state-operated databases. Newborn screening itself is an important public health program and some have described these residual sample “biobanks” in equally positive terms. Although there are concrete benefits of newborn testing, there are also troubling consent and privacy issues raised by the screening, storage and use of the samples.

 

Newborn screening began in the United States as a series of state level pilot programs in the 1960s to test for PKU, a rare genetic condition that is easily treatable if caught early. The success of these early programs led to rapid adoption of newborn screening among all states in the US and the number of conditions screened for has grown progressively since with additional funding at the Federal level. Because of the singular history of newborn screening, it remains the only widespread health testing in the US conducted not by an individual’s doctor, hospital, or health care provider but by individual state departments of public health. This singular history can also account for a wide disparity in state law and policy with regards to parental consent, sample storage and use.

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