Introducing "Bi-Fi": The Biological Internet - Evolution News & Views

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Introducing "Bi-Fi": The Biological Internet

Imagine storing books in DNA and sending them across a biological Internet. It's already happening.

As we reported here back in May, bioengineers are realizing that DNA is an excellent storage medium. They've started writing books in DNA letters. Now a research team at Harvard has just announced in Science the "Next-Generation Digital Information Storage in DNA":

Digital information is accumulating at an astounding rate, straining our ability to store and archive it. DNA is among the most dense and stable information media known. The development of new technologies in both DNA synthesis and sequencing make DNA an increasingly feasible digital storage medium. We developed a strategy to encode arbitrary digital information in DNA, wrote a 5.27-megabit book using DNA microchips, and read the book by using next-generation DNA sequencing. (Emphasis added.)
The Harvard team even used modern programming techniques like addressable blocks and error correction at a substantially lower cost. In addition, their book included JPG images and software code. They see no reason that future attempts couldn't add other programming techniques like parity checks and compression. But do they really need compression? They already achieved 5 petabits per cubic millimeter! That's 1,000 terabits of data -- nearly twice the entire volume of digital records at the Library of Congress1 -- in a cube the size of the space between your thumb and forefinger when you hold them slightly apart.2

There are more reasons they think DNA storage is the wave of the future:

DNA is particularly suitable for immutable, high-latency, sequential access applications such as archival storage. Density, stability, and energy efficiency are all potential advantages of DNA storage, although costs and times for writing and reading are currently impractical for all but century-scale archives. However, the costs of DNA synthesis and sequencing have been dropping at exponential rates of 5- and 12-fold per year, respectively--much faster than electronic media at 1.6-fold per year. Hand-held, single-molecule DNA sequencers are becoming available and would vastly simplify reading DNA-encoded information.
Hand-held? You mean your smartphone might read and write documents in DNA? Why not?

Well, if DNA is the ideal storage medium, how about using it for the Internet? In fact, "Bi-Fi: The Biological Internet" is in development at Stanford School of Medicine.

Obviously DNA cannot travel through the air over many miles like electromagnetic waves do. DNA can, though, travel between cells in packets that carry signals. The Stanford team has made it possible to create arbitrary coded messages that one cell can send across a petri dish to another cell, which can read it.

To do this, researchers took an existing molecular machine, a neutral virus named M13 that parasitizes bacteria without killing them, and gave it a job: take this message and deliver it. Here's how it works:

M13 is a packager of genetic messages. It reproduces within its host, taking strands of DNA -- strands that engineers can control -- wrapping them up one by one and sending them out encapsulated within proteins produced by M13 that can infect other cells. Once inside the new hosts, they release the packaged DNA message.
This packetizing of information sounds eerily similar to our familiar Internet's TCP/IP protocol which puts wrappers around messages and sends them to a target address. The Internet protocol doesn't care about the message itself, just the source and the target addresses on the "envelope." That's true here, too:
The M13-based system is essentially a communication channel. It acts like a wireless Internet connection that enables cells to send or receive messages, but it does not care what secrets the transmitted messages contain. "Effectively, we've separated the message from the channel. We can now send any DNA message we want to specific cells within a complex microbial community," said [Monica] Ortiz, the first author of the study.
But if the DNA packets can't travel between cell phone towers through the air, how can they be useful for the Internet we all use? We're getting there. First, though, think of the possibilities for this inter-cell-net. The Stanford team has sent messages greater than 40,000 bits a distance of 7 centimeters. "That's very long-range communication, cellularly speaking," Ortiz said. So within a hand-held device, DNA storage could easily communicate and collaborate, using M13 packets.
"The ability to communicate 'arbitrary' messages is a fundamental leap -- from just a signal-and-response relationship to a true language of interaction," said Radhika Nagpal, professor of computer science at the Wyss Institute for Biologically Inspired Engineering at Harvard University, who was not involved in the research. "Orchestrating the cooperation of cells to form artificial tissues, or even artificial organisms is just one possibility. This opens a door to new biological systems and solving problems that have no direct analog in nature."
This is really cool. Now, let's put it together. The M13 network could be like a LAN that communicates in DNA packets. It could solve problems just like an in-house computer network, storage and all. Then, if DNA can be translated into electrons by an appropriate interface, the output could become input to the WAN -- the Internet at large -- and sent across the world.

This would provide seamless DNA-to-DNA networking. Note that conversion between dissimilar networks is common in the Internet; that's why Appletalk LANs can communicate with IPv4 or IPv6 and even older standards like IPX/SPX, provided they have the appropriate interfaces. The network protocol only affects the envelope around the message; the information inside the packet remains constant throughout the communication.

So, someday a DNA computer network inside your doctor's hand-held device could solve a complex diagnosis, send it to your smartphone through the air, which would retrieve it and send back your medical history stored in a DNA ebook. The possibilities cannot yet be foreseen:

Ortiz added: "The biological Internet is in its very earliest stages. When the information Internet was first introduced in the 1970s, it would have been hard to imagine the myriad uses it sees today, so there's no telling all the places this new work might lead."
The other thing that is seamless is the end-to-end intelligent design. As we asked earlier, what's the big problem with inferring an intelligent cause for the origin of the "natural" genetic code, since it also involves the encoding and storage of functional information?


1. A Library of Congress blog entry states current digital records amount to 74 terabytes, or 592 terabits converting from 8-bit ASCII bytes.

2. This represents just a small fraction of the information capacity of DNA. In the bonus features of Unlocking the Mystery of Life, Dr. Dean Kenyon states that a cubic millimeter of DNA could store 1018 bits (an exabit), 20 times more than the 5 petabits per mm3 density Harvard achieved.