Interesting analogy regarding the Java comparison. Sun Microsystems developed Java in order to sell more hardware and generate software-licensing revenue. The correct analogy would be: Dr. Endy develops a tabletop Biobrick synthesis and run-time machine, then develops XNA which only works in that machine, and the XNA only works with biological cells either purchased directly from him or licensed from him. In contrast, the real Biobricks only work with their compatible cells in their compatible structures, and are only available if you're a student at a University which has partnered with MIT.
Again, the journalist who wrote the original article needs to ask what the Yield of the system is, i.e. how successful any of the technology is, at doing what it claims.
## Jonathan Cline
## jcline@ieee.org
## Mobile: +1-805-617-0223
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On Thursday, April 25, 2013 2:09:19 AM UTC-7, eleitl wrote:
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http://www.wired.com/wiredenterprise/2013/04/bio- fab-open-source-language
Bioengineers Build Open Source Language for Programming Cells
BY DANIELA HERNANDEZ04.19.136:30 AM
Image: Steve Jurvetson/Flickr.
Drew Endy wants to build a programming language for the body.
Endy is the co-director of the International Open Facility Advancing
Biotechnology — BIOFAB, for short — where he's part of a team that's
developing a language that will use genetic data to actually program
biological cells. That may seem like the stuff of science fiction, but the
project is already underway, and the team intends to open source the
language, so that other scientists can use it and modify it and perfect it.
The effort is part of a sweeping movement to grab hold of our genetic data
and directly improve the way our bodies behave — a process known as
bioengineering. With the Supreme Court exploring whether genes can be
patented, the bioengineering world is at crossroads, but scientists like Endy
continue to push this technology forward.
Genes contain information that defines the way our cells function, and some
parts of the genome express themselves in much the same way across different
types of cells and organisms. This would allow Endy and his team to build a
language scientists could use to carefully engineer gene expression – what
they call "the layer between the genome and all the dynamic processes of
life."
According to Ziv Bar-Joseph, a computational biologist at Carnegie Mellon
University, gene expression isn't that different from the way computing
systems talk to each other. You see the same behavior in system after system.
"That's also very common in computing," he says. Indeed, since the '60s,
computers have been built to operate much like cells and other biologically
systems. They're self-contained operations with standard ways of trading
information with each other.
'In synthetic biology, the equivalent of a Java virtual machine might be that
you could create your own compartment in any type of cell, so your engineered
DNA wouldn't run willy-nilly.' — Drew Endy The BIOFAB project is still in the
early stages. Endy and the team are creating the most basic of building
blocks — the "grammar" for the language. Their latest achievement, recently
reported in the journal Science, has been to create a way of controlling and
amplifying the signals sent from the genome to the cell. Endy compares this
process to an old fashioned telegraph.
"If you want to send a telegraph from San Francisco to Los Angeles, the
signals would get degraded along the wire," he says. "At some point, you have
to have a relay system that would detect the signals before they completely
went to noise and then amplify them back up to keep sending them along their
way."
And, yes, the idea is to build a system that works across different types of
cells. In the 90s, the computing world sought to create a common programming
platform for building applications across disparate systems — a platform
called the Java virtual machine. Endy hopes to duplicate the Java VM in the
biological world.
"Java software can run on many different hardware operating system platforms.
The portability comes from the Java virtual machine, which creates a common
operating environment across a diversity of platforms such that the Java code
is running in a consistent local environment," he says.
"In synthetic biology, the equivalent of a Java virtual machine might be that
you could create your own compartment in any type of cell, [so] your
engineered DNA wouldn't run willy-nilly. It would run in a compartment that
provided a common sandbox for operating your DNA code."
According to Endy, this notion began with a group of students from Abraham
Lincoln High School in San Francisco a half decade ago, and he's now calling
for a commercial company to recreate Sun Microsystems' Java vision in the
biological world. It's worth noting, however, that this vision never really
came to fruition — and that Sun Microsystems is no more.
Nonetheless, this is what Endy is shooting for — right down to Sun's embrace
of open source software. The BIOFAB language will be freely available to
anyone, and it will be a collaborative project.
Progress is slow — but things are picking up. At this point, the team can get
cells to express up to ten genes at a time with "very high reliability." A
year ago, it took them more than 700 attempts to coax the cells to make just
one. With the right programming language, he says, this should expand to
about a hundred or more by the end of the decade. The goal is to make that
language insensitive to the output genes so that cells will express whatever
genes a user wants, much like the print function on a program works
regardless of what set of characters you feed it.
What does he say to those who fear the creation of Frankencells — biological
nightmares that will wreak havoc on our world? "It could go wrong. It could
hurt people. It could be done irresponsibly. Assholes could misuse it. Any
number of things are possible. But note that we're not operating in a
vacuum," he says. "There's history of good applications being developed and
regulations being practical and being updated as the technology advances. We
need to be vigilant as things continue to change. It's the boring reality of
progress."
He believes this work is not only essential, but closer to reality than the
world realizes. "Our entire civilization depends on biology. We need to
figure out how to partner better with nature to make the things we need
without destroying the environment," Endy says. "It's a little bit of a
surprise to me that folks haven't come off the sidelines from other
communities and helped more directly and started building out this common
language for programming life. It kind of matters."
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