Scientists and engineers bent on developing data storage technology have increasingly experimented with biology in their attempt to find solutions to digital problems. The latest breakthrough in this line of experimentation took place at Harvard, where a team of researchers led by geneticists Seth Shipman and Jeff Nivala have developed a way to write chunks of digital information into the genetic code of living bacteria cells. The cells then become living memory sticks, which pass data onto their descendants that can be read later by genotyping the bacteria.
Scientists made headlines some time ago when it was revealed to be possible to synthetically manufacture DNA and write into it basically anything, including a full-length science book. Shipman and Nivala’s team have taken that discovery a step further.
“Working within a living cell is an entirely different story and challenge,” Shipman explained. “Rather than synthesizing DNA and cutting it into a living cell, we wanted to know if we could use nature’s own methods to write directly onto the genome of a bacterial cell, so it gets copied and pasted into every subsequent generation.”
The process is thought of as uploading information into a living cell, and before Shipman and Nivela’s experiment, the most information that had ever been “uploaded” was 11 bits. That’s not enough bits to code two alphabetic letters. The technique developed by the Harvard scientist allows for 100 bytes of data to be uploaded, shattering the previous record.
While that is still a relatively tiny amount of space in terms of what would be needed to convey more than a sentence worth of data, it demonstrates the momentum that the Harvard scientists have created in terms of encoding information into living organisms. In order to move from bits to bytes of information transferred, the research team utilized an immune response that certain bacteria have developed in order to protect themselves against viral infections. The response, called the CRISPR/Cas system, occurs when the bacteria are invaded by viruses and in response they physically cut out a segment of the attacking virus’s DNA and paste it into a specific region of the bacteria’s own genome. Then the bacteria can recognize that particular virus in the future and react appropriately, plus the bacteria can pass along that information to its progeny.
The Harvard scientists created synthetic DNA onto which information was coded, then disguised it to look like viral DNA to a colony of bacteria that had the CRISPR/Cas system. When the bacteria believed the DNA to be viral, they incorporated it into their genetic code, effectively uploading the information into their DNA and the DNA of their progeny.
Perhaps most importantly in terms of the CRISPR system being used to transmit information, the bacteria in question store their new immune system memories sequentially. In other words, viral DNA from earlier infections are recorded in their DNA before those of more recent infections.
According to Shipman, “That’s quite important… If the new information was just stored randomly, that wouldn’t be nearly as informative. You’d have to have tags on each piece of information to know when it was introduced into the cell. Here it’s ordered sequentially, like the way you write down the words in a sentence.”
There are some obstacles to the process, however. When scientists introduce coded messages of faux-viral DNA, not every bacteria eats up and copies every part of the message. If the message was “My dog bites people who can’t read,” some bacteria would have “Bite people who can’t read” and others would have “My dog can’t read” and still others wouldn’t have copied anything at all. However, Shipman explained that because they introduce the message to so many bacteria to begin with, looking at an entire colony ultimately makes the full message obvious.