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November 08 2013

Craig Venter on moving at the speed of light

Last week I had the privilege of speaking with J. Craig Venter at the Hillside Club in Berkeley, as part of the Bay Area Science Festival. Dr. Venter is a pioneer in biotech, from sequencing the Human Genome to creating a synthetic organism. It was an exciting moment for me, personally, as he thinks in terms of moonshots and succeeds often (through the failures).

Dr. Venter was in Berkeley as part of his tour to promote his new book, Life at the Speed of Light, which was inspired by Erwin Schroedinger’s question in 1943, “What is Life?” That question set Dr. Venter off on a life-long quest: first, to first take life apart and then rebuild it; to test his understanding of the machinery of life; and, ultimately, prove that he and humanity could rebuild life from scratch. The machinery of life still involves a lot of mystery, even for the simplest synthetic organisms. When when they were building the first synthetic organism, they focused on the minimum number of genes needed to create a viable life form. They found that they needed to include 50 genes with unknown functions. Without these genes, they couldn’t get the organism to “boot up.” They are clearly necessary, but why? What do they do? We still don’t know.

Venter also shared his thoughts on life on Mars. He thinks it is likely that life has existed on Mars, as Earth and Mars regularly exchange large amounts of particulate matter filled with bacteria. He’s planning a project to sequence Martian DNA (which he believes exists), with a plan to send the digital DNA sequence back to Earth for re-synthesis. His ultimate aim is to rebuild Martian bacteria on Earth for further study. Venter’s joy in exploring the domain of life rang through. With the rapidly decreasing costs of genetic sequencing and the tiny fraction of bacterial species that we have sequenced, anyone can now be an explorer. In every breath of air or every clump of dirt we grab, there are a multitude of new bacterial species waiting to be discovered.

At the end of Venter’s talk, I was able to ask him, “Where do you think the next moonshots in biotechnology will be?” His answer left me excited about the future. He said that the world’s population is rapidly rising; there are now seven billion people out there who desperately need access to medicine, food and energy. For humanity to live sustainability on this planet, we need revolutions in all of these areas, and those revolutions will be driven by new biotechnologies. His advice to any burgeoning scientist was that there is no area of human endeavor that will be left untouched by biotechnology, and all of these areas are fine areas to pursue.

As we’re all exploring, playing, biohacking DNA in front of computers, in labs, garages or at home, I look forward to the day when an innovation in biotechnology is just as likely to come from an industrial biotech lab in San Francisco as it is from the mind of a young biohacker in a home DIY Biolab. Venter left me with a sense of wonder and excitement for biotechnology and the future; I can’t wait to see what he sequences on Mars!

October 21 2013

The biocoding revolution

What is biocoding? For those of you who have been following the biotechnology industry, you’ll have heard of the rapid advances in genome sequencing. Our ability to read the language of life has advanced dramatically, but only recently have we been able to start writing the language of life at scale.

The first large-scale biocoding success was in 2010, when Craig Venter (one of my scientific heroes) wrote up the genome of an entirely synthetic organism, booted it up and created de novo life. Venter’s new book, Life at the Speed of Light, discusses the creation of the first synthetic life form. In his book and in video interviews, Venter talks about the importance of ensuring the accuracy of the DNA code they designed. One small deletion of a base (one of the four letters that make up the biological equivalent of 1s and 0s) resulted in a reading frame shift that left them with gibberish genomes, a mistake they were able to find and correct. One of the most amusing parts of Venter’s work was that they were able to encode sequences in the DNA to represent each letter of the English alphabet. Their watermark included the names of their collaborators, famous quotes, an explanation of the coding system used, and a URL for those who crack the code written in the DNA. Welcome to the future — and let me know if you crack the code!

Biocoding is just the beginning of the rise of the true biohackers. This is a community of several thousand people, with skill sets ranging from self-taught software hackers to biology postdocs who are impatient with the structure of traditional lab work. Biohackers want to tinker; do fun science; and, in the process, accelerate the pace of biotech innovation. There are plenty of differences between writing computer code and writing code in the building blocks of life, but the important thing is that it can be done and is being done now by citizen scientists working both from shared biohacker labs (like BiocuriousGenspace, and Counter Culture Labs) and at home (for example, Cathal Garvey, who works out of a spare bedroom in his mother’s home). Drew Endy’s short video about Engineering Biology gives a great overview of what we can accomplish when we start programming the genetic code. One of his projects is genetically encoded data storage — but it’s not just about replacing dry silicon with wet carbon; it’s about what can happen when you can do computing in an environment where you couldn’t possibly place silicon: inside a living cell.

Biotech is the wet nanotech we’ve been waiting for. It’s a little less logical and a lot buggier than we’d like, but we now have the tools to write DNA, insert this code into a cell, reboot the cell and make those cells produce custom-designed proteins and substances, and engineer biology. The potential for synthetic biology and biotechnology is vast. The biocoding era will be as transformative as the computer era, and we all have an opportunity to create the future together.

Biocoder is a new O’Reilly quarterly newsletter chronicling the rise of DIY bio, synthetic bio, biohackers, Grinders, and the new innovations being developed at the edges of the biotech industry. Check out Biocoder and download it for free.

February 25 2013

Four short links: 25 February 2013

  1. Xenotext — Sci Foo Camper Christian Bök is closer to his goal of “living poetry”: A short stanza enciphered into a string of DNA and injected into an “unkillable” bacterium, Bök’s poem is designed to trigger the micro-organism to create a corresponding protein that, when decoded, is a verse created by the organism. In other words, the harmless bacterium, Deinococcus radiodurans (known as an extremophile because of its ability to survive freezing, scorching, or the vacuum of outer space), will be a poetic bug.
  2. Notes on Distributed Systems for Young Bloods — why distributed systems are different. Coordination is very hard. Avoid coordinating machines wherever possible. This is often described as “horizontal scalability”. The real trick of horizontal scalability is independence – being able to get data to machines such that communication and consensus between those machines is kept to a minimum. Every time two machines have to agree on something, the service is harder to implement. Information has an upper limit to the speed it can travel, and networked communication is flakier than you think, and your idea of what constitutes consensus is probably wrong.
  3. Lemnos Labs — hardware incubator in SF. (via Jim Stogdill)
  4. OLPC Built the Young Lady’s Illustrated Primer — Neil Stephenson imagined it, OLPC built it. Science fiction is a hugely powerful focusing device for creativity and imagination. (via Matt Jones)
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