"biotechnology" entries

Open source lessons for synthetic biology

What bio can learn from the open source work of Tesla, Google, and Red Hat.


When building a biotech start-up, there is a certain inevitability to every conversation you will have. For investors, accelerators, academics, friends, baristas, the first two questions will be: “what do you want to do?” and “have you got a patent yet?”

Almost everything revolves around getting IP protection in place, and patent lawyer meetings are usually the first sign that your spin-off is on the way. But what if there was a way to avoid the patent dance, relying instead on implementation? It seems somewhat utopian, but there is a precedent in the technology world: open source.

What is open source? Essentially, any software in which the source code (the underlying program) is available to anyone else to modify, distribute, etc. This means that, unlike typical proprietary development processes, it lends itself to collaborative development between larger groups, often spread out across large distances. From humble beginnings, the open source movement has developed to the point of providing operating systems (e.g. Linux), Internet browsers (Firefox), 3D modelling software (Blender), monetary alternatives (Bitcoin), and even integrating automation systems for your home (OpenHab).

Money, money, money…

The obvious question is then, “OK, but how do they make money?” The answer to this lies not in attempting to profit from the software code itself, but rather from its implementation as well as the applications which are built on top of it. For the implementation side, take Red Hat Inc., a multinational software company in the S&P 500 with a market cap of $14.2 billion, who produce the extremely popular Red Hat Enterprise Linux distribution. Although open source and freely available, Red Hat makes its money by selling a thoroughly bug-tested operating system and then contracting to provide support for 10 years. Thus, businesses are not buying the code; they are buying a rapid response to any problems.

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BioBuilder: Rethinking the biological sciences as engineering disciplines

Moving biology out of the lab will enable new startups, new business models, and entirely new economies.


Buy “BioBuilder: Synthetic Biology in the Lab,” by Natalie Kuldell PhD., Rachel Bernstein, Karen Ingram, and Kathryn M. Hart.

What needs to happen for the revolution in biology and the life sciences to succeed? What are the preconditions?

I’ve compared the biorevolution to the computing revolution several times. One of the most important changes was that computers moved out of the lab, out of the machine room, out of that sacred space with raised floors, special air conditioning, and exotic fire extinguishers, into the home. Computers stopped being things that were cared for by an army of priests in white lab coats (and that broke several times a day), and started being things that people used. Somewhere along the line, software developers stopped being people with special training and advanced degrees; children, students, non-professionals — all sorts of people — started writing code. And enjoying it.

Biology is now in a similar place. But to take the next step, we have to look more carefully at what’s needed for biology to come out of the lab. Read more…

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Cheese, art, and synthetic biology

Christina Agapakis discusses the intersection of art and science in the new edition of BioCoder.

We’ve published the second issue of BioCoder! In this interview excerpt from the new edition, Christina Agapakis talks with Katherine Liu about the intersection of art and science, and the changes in how we think about biotechnology. It’s one of many reasons we’re excited about this new issue. Download it, read it, and join the biotechnology revolution!

Katherine Liu: What can art and design teach us about biology and synthetic biology?

Christina Agapakis: That’s a great question. There are two different ways you can think about it: first as a way to reach different groups of people and have a different kind of conversation or debate around biotechnology. The second way that you could think about it is more interesting to me as a scientist because I think using art and design helps us ask different questions and think about problems and technological solutions in different ways. To make a good technology, we need to be aware of both the biological and the cultural issues involved, and I think the intersection of art and design with science and technology helps us see those connections better.

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Craig Venter on moving at the speed of light

My discussion with Venter left me with a sense of wonder and excitement for biotechnology and the future.

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. Read more…


The biocoding revolution

The potential for synthetic biology and biotechnology is vast; we all have an opportunity to create the future together.

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. Read more…

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