ENTRIES TAGGED "science"

DIYbio and the hacking metaphor

Definitive answers require further testing

The following is from the second issue of BioCoder, the quarterly newsletter for synthetic biologists, DIY biologists, neurobiologists, and more. Download your free copy today.


Within DIYbio, one cannot escape the hacking metaphor. The metaphor is ubiquitous and, to a point, useful. The term connotes both productive play with an existing technology aimed at improvement and, at the same time, play with sinister undertones. In this sense, hacking captures the promise and pitfalls of the dual uses any mature technology might be put to, whether that technology is as dramatic as nuclear power/weapons or as mundane as a free/premium software license. But every metaphor has its limits. Pushed too far, metaphors break down, and instead of illuminating, they obscure. Which brings me to ask: how far can the hacking metaphor be pushed within DIYbio—at least the part of DIYbio falling in line with synthetic biology?

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Handling Data at a New Particle Accelerator

Unlocking Scientific Data with Python

dust_accelerator

Most people working on complex software systems have had That Moment, when you throw up your hands and say “If only we could start from scratch!” Generally, it’s not possible. But every now and then, the chance comes along to build a really exciting project from the ground up.

In 2011, I had the chance to participate in just such a project: the acquisition, archiving and database systems which power a brand-new hypervelocity dust accelerator at the University of Colorado.

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DNA: The perfect backup medium

DNA storage could change the way we store and archive information.

It wasn’t enough for Dr. George Church to help Gilbert “discover” DNA sequencing 30 years ago, create the foundations for genomics, create the Personal Genome Project, drive down the cost of sequencing,  and start humanity down the road of synthetic biology. No, that wasn’t enough.

He and his team decided to publish an easily understood scientific paper (““Next-generation Information Storage in DNA“) that promises to change the way we store and archive information. While this technology may take years to perfect, it provides a roadmap toward an energy efficient, archival storage medium with a host of built-in advantages.

The paper demonstrates the feasibility of using DNA as a storage medium with a theoretical capacity of 455 exabytes per gram. (An exabyte is 1 million terabytes.) Now before you throw away your massive RAID 5 cluster and purchase a series of sequencing machines, know that DNA storage appears to be very high latency. Also know that Church, Yuan Gao, and Sriram Kosuri are not yet writing 455 exabytes of data, they’ve started with a more modest goal of writing Church’s recent book on genomics to a 5.29 MB “bitstream,” here’s an excerpt from the paper:

We converted an html-coded draft of a book that included 53,426 words, 11 JPG images and 1 JavaScript program into a 5.27 megabit bitstream. We then encoded these bits onto 54,898 159nt oligonucleotides (oligos) each encoding a 96-bit data block (96nt), a 19-bit address specifying the location of the data block in the bit stream (19nt), and flanking 22nt common sequences for amplification and sequencing. The oligo library was synthesized by ink-jet printed, high-fidelity DNA microchips. To read the encoded book, we amplified the library by limited-cycle PCR and then sequenced on a single lane of an Illumina HiSeq.

If you know anything about filesystems, this is an amazing paragraph. They’ve essentially defined a new standard for filesystem inodes on DNA. Each 96-bit block has a 19-bit descriptor. They then read this DNA bitstream by using something called Polymerase Chain Reaction (PCR). This is important because it means that reading this information involves generating millions of copies of the data in a format that has been proven to be durable. This biological “backup system” has replication capabilities “built-in.” Not just that, but this replication process has had billions of years of reliability data available.

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Science Hack Day goes global

Science Hack Day goes global

A new grant will help Science Hack Day set up shop around the world.

The just-announced Science Hack Day Ambassador program will bring 10 people to Science Hack Day San Francisco 2011. The idea is to spread the model to more cities and countries.

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