In 2004, these early principles were tried out by students during a synthetic biology competition, now known as the International Genetically Engineered Machines (iGEM) contest, an effort that grew out of Endy’s and Knight’s labs. Teams from five U.S. universities vied to build a biological system using standardized parts. In 2013, more than 200 undergraduate teams from around the world competed in iGEM, creating novel biological systems (such as an E. coli-based sensor to detect arsenic in drinking water) using BioBrick parts made and freely shared by previous iGEM students, and stored and distributed from the freezers at iGEM headquarters in Cambridge, Mass.
Despite the dramatic growth in such student-led efforts, many still doubted whether the principles of standardization and abstraction were applicable to biology. Endy recalls a 2006 New York Times article on synthetic biology in which Frances Arnold, a distinguished professor of chemical engineering at Caltech, said, “There is no such thing as a standard [biological] component, because even a standard component works differently depending on the environment. … The expectation that you can type in a [DNA] sequence and can predict what a [genetic] circuit will do is far from reality and always will be.”
Endy paid heed to such criticism, and it weighed on him. “I have been carrying a technical, scientific burden,” he says. “It’s hard to ignore when smart people say what you are trying to do is impossible.”
Engineering a Transistor
As far as Endy is concerned, that burden has lifted somewhat in the past two years. In June 2012, his Stanford lab published what would turn out to be the first of three key papers that advanced the cause of computing inside cells using standardized parts. In the first paper, a team led by postdoc Jerome Bonnet showed how information could be stored inside a cell. Granted it was just a single bit of memory, but there it was: the ability to store either a 0 or 1, and flip the bit at will.
To do this, the team borrowed know-how perfected by bacteriophages — viruses that can infect bacteria by inserting their viral genome into the bacterial genome. At the heart of the “bit” of memory is essentially a fragment of DNA called a promoter, which enables the machinery of a cell to make a given protein. In this case, if the promoter faced one way (0), it would enable the production of a green fluorescent protein inside E. colicells. If the promoter were facing the other way (1), a red fluorescent protein would be produced.
The team showed how they could flip the direction of this promoter using bacteriophage enzymes, whose levels inside the cells they controlled using chemicals. Once flipped, the DNA sequence would continue to be replicated by the bacteria, thus maintaining the bit as 0 or 1 until it was flipped again. It had been a long, draining effort to get this simple element working. “It took three years to get a single bit of memory out of the lab,” says Bonnet.
Later that year, the team built another cog in the wheel of biological computing: the ability to send arbitrary messages between cells, again with help from a bacteriophage called M13. This wondrous virus can package its DNA into “particles” and send them to other cells without killing the host cell. Endy and his student Monica Ortiz tweaked M13 to send arbitrary DNA messages of their own choosing, instead of viral DNA, from one cell to another.
But the singular achievement in Endy’s eyes came in 2013, when his team built its first biological amplifying logic gate. In conventional digital electronics, the key to building logic gates is the transistor, a component in which a modest control signal can regulate the flow of a large electric current. Their biological transistor, which they named the “transcriptor,” is a device made from an engineered sequence of DNA. The “current” is the flow of a molecule called RNA polymerase, which moves along the DNA “wire” and transcribes it, allowing the cell to make the relevant protein. The key here was to create a control signal that could let the RNA polymerase transcribe or stop it from doing so.
To do this, they embedded within the DNA strand another bit of DNA called a transcription terminator. They then used bacteriophage enzymes to flip the direction of this terminator — technology perfected while creating the 1-bit memory. In one direction, the terminator allowed the RNA polymerase to zip across the DNA sequence and transcribe downstream genes. Flipped, it prevented transcription. Endy and his team had their basic biological transistor, and they used it to implement a variety of Boolean logic gates, such as AND and OR.