Scientists Build Biocomputer That Runs on Bacteria to Solve Hard Problems

Move over, microchips. The next generation of supercomputing might just run on living bacteria. For 20 years, an international team of scientists has been developing a biocomputer that uses bacteria to process information. Scientists from McGill University in Montreal announced their findings on Nov. 3 and published a paper detailing the results earlier this year in Nature. 

Researchers from Canada, Europe, the United Kingdom and Australia contributed to this work, which combines biology with computer science and engineering. The researchers say the resulting biocomputer could be used to solve problems that give standard computers a hard time. 

“Electronic (sequential) computers are not meant, or designed, to solve decision trees,” Dan Nicolau, a McGill bioengineering professor and senior author for the research paper, told CNET via email. 

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Nicolau noted that if electronic computers are to solve these types of problems, the computers will need a lot of RAM.

The study relied on the bacterium Escherichia coli and Vibrio natriegens to run the calculations. The researchers used E. coli because it moves through fluid in a predictable, measurable way and V. natriegens because it reproduces very quickly.

Changing math into tunnels for bacteria to explore

The researchers tested the biocomputer with a seemingly simple math problem called the Subset Sum Problem, which famously becomes exponentially harder as the number of inputs increases. 

When the Subset Sum Problem inputs grow too large, the problem is known to give traditional computers issues, such as taking centuries, or even millions of years, to solve the problem.

The researchers translated the problem into a graph that branches off into each possible combination of inputs. Next, the team created a tiny physical structure that mirrored the Subset Sum Problem graph. 

Inside the structure, they built a network of tunnels to mirror the graph branches. Each fork in the tunnels represents a decision point, and every possible route through the tunnels represents a different solution to the problem. 

Making processing units the old-fashioned way

The researchers unleashed bacteria, which rapidly reproduce, inside the tunnels. The fast-growing bacteria moved through the tunnels, exploring many routes to the solution simultaneously. 

Compared to digital processing, the bacteria are slow. But rather than tackling a problem sequentially, as traditional computers do, the bacteria can examine many solutions at once. And if you need more computing power, bacterial reproduction within the tunnels creates additional processing units to help solve the problem. 

The team used automated image analysis to follow the bacteria through the correct tunnels. In this way, the researchers were able to tell which paths through the network satisfied the problem’s constraints. 

The researchers were also able to adjust temperatures to prevent bacteria overcrowding while traveling through the network.

Yes, it can run Doom

Enterprising fans have figured out how to run Doom, the groundbreaking 1993 first-person shooter video game, on everything from E. coli to a thermostat. Nicolau says Doom could probably run on the new system, with an important caveat concerning the biocomputer’s size.

“(The biocomputer) must be huge!” Nicolau said. Because bacteria make slow processors, you would need a massive biocomputer to host enough bacteria to run a video game. 

But because no RAM is needed, Nicolau said biocomputing could help to solve the global RAM shortage, and even broaden our understanding of what a computer could be. 

“A computer is a device which accepts (input) numbers and gets out (output) numbers. Full stop,” he said. “All other uses of the word computer (are) from our point of view, well, poetical.”

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Julian is a contributor and former staff writer at CNET. See full bio