I'm Joining PGP

As of today, I'm an official participant in the Personal Genome Project (PGP). Ever since reading an article about the program last fall, I've been fascinated about the potential of PGP. Given my professional interest in large-scale data analysis and my personal interests in data liberation and the quantified self movement, PGP is the perfect program for me to contribute to. For over a decade, since first reading about DNA replication in AP Biology, I've been fascinated by the limitations of traditional genetics and the promise of epigenetic research. I had a couple friends who were twins, and I can still remember asking my high school biology teacher about why genetically identical organisms weren't always phenotypically the same. It seems like we're not that much closer to the answer ten years later.

For people unfamiliar with the program, it's the spiritual successor to the Human Genome Project, focused specifically on producing a publicly available database of genomic, phenotypic and environmental information with the intent of providing a rich source of input data for epigenetic research. However, unlike most similar programs, PGP's data is available to the public. George Church, the lead researcher in the study, has his data here; mine is available here. While I don't have any professional experience in the space, the narrative of researchers having to spend most of their time recruiting participants for a single study resonated with me. Research is tough enough when you can collect data reliably - I can't imagine having to spend time recruiting human subjects for every new study.

In addition to my general curiosity about altruistic participation in genetic research, the program had a couple of other fascinating attributes.

1) The organizers decided against locking down data and opted to make it publicly available. 

In order to get this program approved by Harvard's Institutional Review Board, the researchers made the choice to opt for a program that emphasizes informed consent as opposed to data protection. In order to enroll, I had to spend an hour reading about possible risks associated with participation and answer dozens of questions about the consent process. The most interesting risks felt like they were coming right out of science fiction:

• Someone could use my genetic information to create clones.
• I could be convicted of crimes based on synthetic DNA that matches mine.
• In the future, insurance companies might be able to discriminate based on my genome to charge me higher, risk-adjusted rates

2) I was required me to talk with my parents and siblings before finalizing my application.

The application process required me to certify that I had talked with my nuclear family about the risks that my participation would expose them to; because I share my genetic information with my parents and siblings, making my genome public would implicitly release some of their personal genetic information. 

3) Going through the application forced me to think about what the future of genetic research might hold.

The eventual use of the data is complete unregulated and impossible to predict. We have no way of knowing what we will be able to do with genetic data in a decade, and participation now exposes me to a number of completely unknowable risks that may arise in the future.

4) Many genetic studies aren't performed on representative human populations.

Though it's obvious after thinking about how most human genetic research is performed, I was surprised to discover that many participants are recruited from the community around the research center, often a university campus. As such, we don't have many of genetic studies that analyze longitudinal differences across demographic and regional groups, the precise studies required to make any serious breakthroughs in epigenetics. 

Finally, in the course of evaluating the program, I've come to the conclusion that it's surprisingly difficult to do effective longitudinal genetic research. This type of research doesn't generate results quickly, and it requires a coordinated effort from funding organizations, study participants and researchers. Documenting every aspect of the study, especially variables that may only be relevant in hindsight, is an arduous task, but one that has proven effective in the past; the Framingham Heart Study, which has been running for close to 70 years, has spawned over 1,000 research papers and dramatically changed our understanding of the relationships between diet, exercise, and heart disease. I hope that the data made available as part of PGP will yield similarly impressive results.

In either case, next time I'm in Boston, MA, I'll be getting blood work done and making my genome available to any of you weirdos who want to check it out! Hope to hear from some other people who decide that this is an interesting way to become a naked mole rat and altruistically contribute to the future of human genetic knowledge!

Economist Redux #5: February

The past three weeks have been pretty wild for me, and so I'm falling a bit behind on my blogging goal and my goal of reading The Economist every week. I spent today catching up on the past few weeks, and here are some articles I enjoyed!

• Some interesting point/counter-points about teaching recruitment and how teacher's unions in the US make it difficult to attract really high-performing students. There was also a good follow-up piece about different methods of training teachers that focused on TFA specifically.
• Starting the piece about the alfalfa farmer in Catch 22, this piece about farm subsidies was a pretty good analysis of different ways in which the current programs are generally wasteful and inefficient. Nothing really new here, but a good piece.
• This article about crowdfunding was focused on a game called Star Citizen (Kickstarter here), that's raised over $72 million. Cool thoughts about how this could be an effective way to pay for blockbuster films, with a pithy quote about an example that's near and dear to my heart: "if Joss Whedon wanted to do another series of ‘Firefly’, I bet he could raise a hell of a lot of cash.”
• Gentrification is a huge part of the national dialogue about urbanization, with most people assuming that it's a hugely negative trend. This article talks a lot about the positives of gentrification, which, whether or not you agree with them, are worth considering.
• Totally agree with this article; shutting down the DHS is definitionally bad for national security and is a lame attempt at governance. 
• Generally good article about Apple's risky plan to enter the car market, but I think the line about how "the technology firms have no manufacturing culture" falls pretty flat in the face of any basic interrogation of the complex supply chains and manufacturing requirements of complex modern electronics.
• An awesome article about Kaspersky Labs, an organization that has time and time again been ahead in the digital arms race over cyber security
• In an article very close to my heart, the newspaper tackles the furious battle for talent in Silicon Valley. Nothing particularly novel here, but I will say that I was disappointed that they didn't mention anything about the way developers at tech firms are in the front office, not the back office. I think that's also a huge part of why it's so hard to attract tech talent in more traditional industries.
• Cool article about the Supreme Court, and how it's the final frontier of grey, distinguished politics where disagreement doesn't make anyone enemies. Having been listening to Amicus, a podcast from Slate, I think there's a lot that I have to learn about the court.
• I highly recommend this article about North Korea's economic policies and how they end up making their economy chug along (albeit terribly). There are a couple of really interesting discussions about the differences between the North and South and some good commentary on the damage that the nuclear arms program has on the North Korean economy.
• Not particularly interesting on its own, but this article about bottled water in China resonated with me after having just finished reading How to Get Filthy Rich in Rising Asia.
• This article, about how eyelashes actually create aerodynamic turbulence that prevents eye infection, was just a great reminder that science is always moving forward, and that very few things evolve for no reason. 
• My college roommate and I used to talk for hours about using viral methods to attack antibiotic-resistant bacteria, as well as a ton of other tactics, but it sounds like we might be getting closer to this actually becoming a reality.