Part 1. Genomics, Bioinformatics, & Bio-Hacking

What I am about to describe is what happens when an extremely curious ex-financial analyst discovers a public company while reading a nerdy periodical (the MIT Tech Review).  My goal is to use my story to highlight some interesting content on gene sequencing, biohacking, open source dna, and bioinformatics.

Introduction:

I’m an avid reader of the MIT Tech Review, recently I came across an article titled, Does Illumina Have the First $1,000 Genome?. The article is about Illumina’s new dna sequencing machine that can supposedly map “whole genomes” for less than $1000. People have been talking about crossing the $1,000.00 sequencing milestone for many years – the idea being that as the costs of dna sequencing decline more genetic data will lead to a better understanding of diseases and genetic variation. What caught my attention while reading this MIT piece was my recall of article I read by Kevin Kelly called “Open Source DNA” and a recent post by hacker who is open sourcing his genetic “code” (repo available here). This hacker was following the footsteps of ManuSporny who was the first person to publish his genetic data to the massively popular GitHub (which is a decentralized source control system used by programmers). You can read about ManuSporny’s motivations for releasing his genome publicly via this blog post. After thinking about all of these connections I started to search the web  to learn about gene sequencing. Below is some of the stuff I learned along the way.

Part 1. Background & Context

Genomics 101

According to Wikipedia,  genomics is,

“a discipline in genetics that applies recombinant DNA, DNA sequencing methods, and bioinformatics to sequence, assemble, and analyze the function and structure of genomes (the complete set of DNA within a single cell of an organism). The field includes efforts to determine the entire DNA sequence of organisms and fine-scale genetic mapping.”

Let’s follow this with two  introductions to Genomics via Ted.com:


BioInformatics

According to Wikipedia bioinformatics is,

An interdisciplinary scientific field that develops methods for storing, retrieving, organizing and analyzing biological data. A major activity in bioinformatics is to develop software tools to generate useful biological knowledge.

Bioinformatics uses many areas of computer science, statistics, mathematics and engineering to process biological data. Complex machines are used to read in biological data at a much faster rate than before.

Here are three videos covering the basics of bioinformatics.

Biohacking

Biohacking is a movement about engaging biology with the hacker ethic. This relates to Illumina as several do it yourselfers are building machines to sequence genomes for trivial sums (or at least at the cost of building the machine). One of the popular home brew solutions is called OpenPCR which was launched alongside a kickstarter campaign in 2010. From an analytical perspective the diy movement is interesting because it has the potential to challenge Illumina’s pricing power.  Most diagnostic companies make money from closed end systems that work much like expensive printers requiring proprietary ink  (or in this case tests/reagents/etc). To be fair it seems very unlikely that a diy machine will rival the speed, accuracy, and reliability of a high end machine – but you never know.  To learn more about biohacking start with this piece from Wired Magazine followed by this article from Aljazerra.

Below are two ted talks on biohacking:

Here is another example of open source biohacking equipment.

As with most entrepreneurial activities there are now spaces dedicated for biohackers to get together. Below are two videos featuring biohacking spaces. The first video is about BioCurious a hackerspace based in the bay area. The second video is about GenSpace a biohacker lab in NYC.

Open-Source DNA

After reading about biohacking I turned to investigating Open-Source DNA. One of my favorite papers on Open-Source DNA is by Eugene Thacker (you can access it here). One of my favorite paragraph’s from Eugene’s paper is:

“In the same way that open source has contributed to a DIY computer culture and various types of hacker ethics, could the design of innovative bioinformatics software apps, combined with public access to the genome, spawn a DIY biotech culture? Could an increase demand on public access medical data, combined with advances in telemedicine, generate a new type of homeopathic health care? At the furthest reaches of the extreme, how might this “open source DNA” movement affect areas such as media art, education, body performance, regenerative medicine, body art, and wet computing?”

As a follow up to Eugene Thacker’s paper I also recommend reading Keving Kelly’s piece on Open-Source DNA (you can access it here). Some of my favorite bits from Kevin Kelly’s piece are:

“Because DNA is seen as conveying not only paternity, and sexual activity,  but also the blueprints to each person’s persona, the idea of someone else “capturing” it feels wrong.  We currently perceive our DNA to be a personal code that contains our past, present and future. If we could just unlock it, we’d know our destiny. And at the same time, we’d better understand our current identity.”

“Your DNA is not really yours, either. That statement is counterintuitive for some and stake-burning heretical for others. First, we know that 99.99% of the code in your cells is also in mine. We are 99.99% identical.”

“Right now, laws can regulate DNA sequencing because this work must be done by big machines owned by legit companies: the Navigenics of the world. Think gigantic printing presses. But these large, capital-intensive, and easily regulated machines will be disappearing as the price of DNA sequencing keeps dropping. Sequencing is dropping in prices as fast as computer chips (because that is what powers them). The price of gene code is plunging in half every 20 months, which is roughly the 18 months of Moore’s Law. In about 25 years, it will cost only a few cents to get your entire chromosomes done. At first we’ll decipher them once in our life, then once a year and then once a day, in order to detect the effects of environmental  toxins.”

“The only way we’ll decipher genes is through the brute force mapping of genes to bodies and behavior, which will require disclosing and sharing our genetic codes. Mapping genes without tracing their effects upon a body will not be very valuable. But each time a person reveals their genes to the science collective and starts to correlate their genes to their own bodies and behavior, the more valuable their sequence gets. This is the very recipe for the increasing returns and “network effects” that we’ve seen unleash the internet, the web and cell phones. The more who join, the better it gets. The more folks that sequence and share, the more valuable your sequence becomes. Increasing returns and network effects penalize early adopters and favors the late, but once the cycle quietly begins, it can suddenly pass the tipping point and gallop into a stamped”

I also found an interesting video rant about Open Source DNA.

Legal Issues & Sequencing

Below is an interesting video via the ACLU on the fight over BRCA gene mapping. BRCA genes are responsible for a large share of hereditary breast cancers and ovarian cancer. A company was granted patents on the discovery and mapping of BRCA genes and was suing for patent infringement.

This concludes part 1 stay tuned for part 2 which will be posted soon.

About Miguel Barbosa

I run this site.

14. March 2014 by Miguel Barbosa
Categories: Science & Technology | Leave a comment

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