Tuesday, February 10, 2009

"BioBricks" - Interview with Drew Endy from good.is

Designer Genes
Quoted from this post by: Rebecca Zcathcart on www.good.is March 20, 2008

When Drew Endy envisions the future, he sees giant gourds engineered to grow into four-bedroom, two-bathroom houses. He sees people alerted to nascent tumors in their bodies by internal biological sensors, and cars fueled by bacteria-produced gasoline. Endy, 37, is a pioneer in synthetic biology, a field that combines biology, chemistry, and engineering to remake biological systems to act according to human design.

For Endy, who has roots in civil and environmental engineering, biology offers the most sophisticated building materials in the world, potentially far more useful than anything created by modern technology. Endy is attempting to create a biological programming language by identifying, cataloging, and standardizing small sequences of DNA that tell a cell to perform a specific task.
After joining the faculty at MIT, in 2004, Endy co-founded the Registry of Standard Biological Parts, an open-source catalogue of DNA segments with specific functions, such as those that make DNA strands fold into shapes like microscopic origami or cause cells to change color. These “BioBrick” parts, as Endy calls them, are fitted with special links at either end where they may be easily connected with other DNA segments, much in the manner of lego blocks. The segments snap together to form more complex instructions, so that scientists can manipulate exactly what task a cell performs. “We’ve started to collect genetic words that speak to the cell and tell it to do something,” he says. For example, Endy’s colleague Jay Keasling has found a way to reengineer E. coli so that they naturally produce an anti-malaria drug. Soon, huge vats of bacteria will be making the medicine, at a fraction of the current cost. But that’s a fairly rare example.

For now, the use of BioBricks is limited, because making DNA is difficult. DNA synthesizers can use the genetic information of BioBricks to create new DNA—the idea is akin to the “replicators” from Star Trek that caused food to appear on command—but today’s machines are rudimentary; they work slowly and create only a small amount of DNA. We’re a long way from having Earl Grey tea materialize, mug and all. Though Endy—through Codon Devices, a biotech company he co-founded in 2004—is working to improve DNA replication technology, no one is yet close to assembling sophisticated biological systems.
But as the science and technology mature, the questions that surround biological engineering and DNA synthesis become more complex. Controversy already surrounds the genetic modification of crops, a relatively simple and straightforward process. Synthetic biologists, by contrast, aim to engineer life itself from whole cloth, which brings up obvious ethical questions, not to mention the possibility that deadly new pathogens could be created and released into the environment, intentionally or by mistake. Endy acknowledges that these risks are real, and even likely, but he believes they are outweighed by the possible benefits synthetic biology can bring to future generations. In fact, Endy believes that the best counter to these risks is for the synthetic biologists not to shy away from the potentially dangerous research, but rather to help ensure that it is used in the right way. Endy takes this a step further, by promoting a free, open exchange of information about DNA sequences, allowing synthetic biologists to focus on problems-solving rather than profit, and closely monitor any impending disasters. To that end, he also serves as president of the BioBricks Foundation, an organization of scientists and legal experts working to develop technical standards and legal protections for genetic sequences. “When we arrive at the future with a first generation of parts that can work together,” he says, “we’ll have the parts open and free, and people will be able to build what they want.” And Endy has many ideas about what that future will look like: “Imagine large-scale cities grown from bio-matter,” he muses. “Or, how about bacteria that smell like bananas? That sounds nice.”


• Rodney Brooks, MIT robotocist:
“Within 2-3 weeks, freshmen are adding BioBricks to the E.Coli bacteria chassis. They make oscillators that flash slowly and digital computation agents. But the digital abstraction may not be right metaphor for programming biology.”

“Polyclad flatworms have about 2000 neurons. You can take their brain out and put it back in backwards. The worm moves backwards at first, but adapts over time back to normal. You can rotate its brain 180 degrees and put it in upside down, and it still works. Biology is changing our understanding of complexity and computation.”

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