Notes, thoughts, and news on synthetic biology.

Communicating with Aliens through DNA


DNA encodes the information for all the proteins inside the cell, their amino acid sequence, when and where to turn them on, and a whole lot of other things that we probably don't fully understand yet. With the ability to write DNA, to synthesize our own arbitrary stretches of A's, T's, C's, and G's, we can create our own instructions for cellular proteins or we can encode sequences that would be "junk" to a cell but that we could read as a message. This week, George Church, Yuan Gao, and Sri Kosuri published a short paper demonstrating that not only could we encode a few phrases here and there, but write a whole book in DNA. The book, Church's Regenesis: How Synthetic Biology Will Reinvent Nature and Ourselves, which will be published using more traditional means this fall, includes 53,426 words, 11 jpgs, and one JavaScript program. The text and images were converted to html format and then read as bits, 1's and 0's that can be easily encoded into DNA: A or C for 0 and T or G for 1. Having two possible letters for each bit means that the sequence won't end up with long stretches of any single letter, a challenge for chemical DNA synthesis. The perl code they used to covert bits to DNA is available in the paper's supplementary information (PDF).

This is by far the largest amount of non-biological information synthesized and stored in DNA—a total of 5.27 megabits, way beyond the 7,920 bit record previously held by the Venter Institute's watermarks in their chemically synthesized genome (written using an undisclosed code for each letter and punctuation mark).

The sequence of Watermark 4 in the Venter Institute's synthetic genome

While news reports about the DNA book often acknowledge this previous DNA message, as well as a 1999 paper encoding the World War II spy message "JUNE 6 INVASION: NORMANDY" in DNA (PDF), they don't mention the very first synthetic DNA message cited in the paper. In 1988, Joe Davis, an artist collaborating with molecular biologist Dana Boyd in Jon Beckwith's lab at Harvard Medical School (and currently a research affiliate in George Church's lab), designed and synthesized an 18 base-pair message encoding the image of the ancient Germanic rune representing life and the female earth. The Microvenus message was then pasted into a vector and transformed into E. coli, creating a living work of art.

Microvenus--The first non-biological message encoded in DNA, by Joe Davis

The Arecibo Message

The coding scheme for Microvenus was inspired by the binary message sent by Carl Sagan and Frank Drake from the Arecibo radio telescope in 1974, an attempt to open up communication with extraterrestrial intelligence (as well as demonstrate the capabilities of the newly remodeled telescope). The image is a 23x73 rectangle (having the dimensions be two prime numbers makes it easier to decode the single stream of binary digits) showing pictures of the telescope, a person, and information about our solar system and our DNA. Microvenus is coded with a similar principle, the lines of the image translated to ones and zeros in a 5x7 grid, converted to DNA with phase-change values rather than numerical values. The DNA bases are arranged by size — C= 1, T=2, A =3, G=4 — and represent the number of bits needed before you switch to the opposite bit. For example, 10101 translates to CCCCC because each digit occurs once before it switches, and 00011 would be AG because there are three 0 before it switches to two ones.

Despite its tendency to mutate and evolve as cells divide, DNA is a remarkably inert and stable chemical on its own, lasting long enough for archeologists to be able to sequence strands of DNA many thousands of years old. In a microbial spore hurtling through space, DNA could theoretically last long enough to be found by an extraterrestrial civilization that could sequence it and decode the message inside. In the late 1970's, some scientists even hypothesized the inverse possibility—that viruses on Earth could have been sent as messages from extraterrestrials. Attempts to decode the φX174 viral genome sequence into two dimensional images of course didn't yield any striking alien messages, but did open up the possibility of sending out different kinds of messages of our own.

For Davis, the messages that we send to aliens aren't just about sending out a friendly description of life, art, and science on Earth, but of better understanding those things ourselves. He writes in his paper describing the Microvenus project:

By sending messages to extraterrestrial intelligence, human beings are importantly engaged in a search for themselves. They must first reveal themselves to themselves before they can reveal themselves to anyone else. This has not only been a central dilemmain the search for extraterrestrial intelligence, but it has also been an essential element of art, history, psychology, and classical philosophy.

Thus, the image encoded in Microvenus also represents some of the anatomical detail left out of the female figure on the Pioneer plaque, omitted out of a fear that a more accurate image might lead the perhaps puritanical NASA bureaucracy to block the addition of the plaque. While Carl Sagan has said that in retrospect this fear may have been unfounded, we ended up sending not just an image of the human form, but a very specific image of what we find "acceptable." If this is how we communicate with aliens, what does it mean about us?

These are recurring themes in Davis's work, which constantly jumps from the microscopic to the interstellar at the interface of art, science, and philosophy. Davis draws from and influences both art and science, collaborating with researchers in many fields to show the connection of aesthetics and values with science and technology. Microvenus, he writes, "is a work of art, a poetic image, yet the project to create it originated as a collaborationin both art and science. Now, like the particle/wave duality, neither explanation seems completely adequate."

Joe Davis is also a fascinating person, and I highly recommend the documentary about his life and work, Heaven and Earth and Joe Davis by Peter Sasowsky. Here's a short preview:

The views expressed are those of the author and are not necessarily those of Scientific American.

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