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Programming Life

July 21, 2016

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A new programming language developed at the Massachusetts Institute of Technology (MIT) enables virtually anyone to take control of a bacteria cell's functions to generate plans for a genetically encoded circuit.

The new technique takes only moments to create the sequencing for a DNA-encoded circuit, which previously took years to create.  It also is accessible to virtually anyone.

"You could be completely naive as to how any of it works; that’s what’s really different about this," says Chris Voigt, a professor of biological engineering at MIT.  "You could be a student in high school and go onto the Web-based server and type out the program you want, and it spits back the DNA sequence."

The heart of Voigt's tool is Cello, a system that takes an electronic circuit created in a hardware description language called Verilog, and auto-converts it into plans for a DNA sequence.  Once a researcher has the sequence, creating a new function for E. Coli, for example, is as simple as having a gene synthesis firm to cook up the new DNA sequence and inserting it into an E. coli cell.

Voigt and his team developed the tool in part to free up researchers from the generally laborious, multi-year task of developing DNA circuits.  With Cello, researchers can instead focus on what they are really after: changing the way a cell functions. Programming bacteria to produce an anti-cancer drug when they detect a tumor; creating cells that can halt their own fermentation process if too many toxic by-products build up; altering bacteria to degrade oil when there is an oil spill—these are scenarios researchers now can pursue much more easily.

"It is literally a programming language for bacteria," Voigt says. "You use a text-based language, just like you’re programming a computer; then you take that text and you compile it and it turns it into a DNA sequence that you put into the cell, and the circuit runs inside the cell."

The prospect of giving everyone the ability to re-engineer life at the DNA level may seem frightening so some, but do not expect to see a modern-day Frankenstein monster emerge from a lab any time soon.

For starters, Voigt's tool currently only works on one, very simple life form: E. coli bacteria.  Also, while the goal is to expand the tool's use to more complex life forms, getting there will take some doing.

"Some people have shown basic circuit functions in mammalian cells," Voigt says,  "but we are a long ways from having the underlying principles that would be required to automate design."

Even if one can find a firm capable of generating a strand of DNA, "For a gene sequence of just 5,000 base pairs, that's $1,150 or more outsourced to, say, Genscript (a gene synthesis firm)," says Brian Hanley, founder of gene therapy firm Butterfly Sciences.  "Genscript might get it to you in three to six months? You can get faster, but it'll cost you."

Voigt's work may one day be seen as a turning point in synthetic biology: the day when people who really have no idea what they are doing were given the ability to alter life at the DNA level.

That is fine if you are a scientist like Voigt, and your only ambitions are to improve things for everyone else. However, one wonders what would happen if a terrorist organization were to get wind of Cello and start playing around with the functions of E. coli to weaponize it in  some fashion.

"I am sure that the first thought most people who understand the new technology might have is something along the lines of, 'if anyone can do it, what's to stop malicious people, or those too ignorant of molecular biology, from creating a DNA program with drastic consequences?'" says Steven Umbrello, managing director of the Willington, CT-based Institute for Ethics and Emerging Technologies.

As with most scientific developments, Umbrello says, it is all about maintaining the delicate balance of allowing researchers to do their work, while ensuring that work is not put to malicious use.

"Programming DNA circuits may now have become easier," Umbrello says.  "But the manufacturing of the circuits, the devices themselves, could be themselves created with constraints to limit the production to produce predetermined outputs.

"Our laws must work hard to ensure that research and development can take place in science and engineering without putting an undue burden on them, while simultaneously making sure that there are enough 'teeth' in the statutes to ensure deterrence of malicious use."

Joe Dysart is an Internet speaker and business consultant based in New York City.


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