Deinococcus radiodurans, the 'toughest bacterium on the planet.'

Deinococcus radiodurans, the 'toughest bacterium on the planet.'

The prose at the end of the universe

Programming 'indestructible' bacteria to write poetry.

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    For over a decade, Canadian poet Dr. Christian Bök has toiled to create living prose. Bök calls the project The Xenotext and, should he be successful in his attempts, he will have done something truly special. The idea, at its core? To encipher poetry within an immortal bacterium's genome. Poetry that will last forever.

    "A big concern is the protection of valuable information in the case of a nuclear catastrophe," Pak Chung Wong told the New Scientist in 2003. Wong, then an information technologist at the Pacific Northwestern Laboratory, had just enciphered some lyrics from "It's a Small World" into the genome of Deinococcus radiodurans, a bacterium that can survive in extreme conditions. Wong theorized that the DNA of bacteria, and perhaps even hardy organisms like cockroaches and types of weed, could be used to preserve our data for future generations.

    Wong's work made waves, but the full concept for The Xenotext didn't come until later. Shortly after the paper was published, astrophysicist Paul Davies mused that SETI's efforts to discover extraterrestrial intelligence through radio waves might be misguided. Davies posited that, due to the vastness of space, the most astute way to communicate across interstellar distances would be to build self-replicating and -maintaining robots that could slowly explore the universe.

    The idea wasn't particularly novel, but Davies' interpretation of it was: He said there were already such "robots" on our planet. Viruses and bacteria, he suggested, were capable of replicating and repairing themselves using resources in close vicinity. What if an alien had, in fact, programmed information into a hardy bacterium and sent it across the universe? What if sitting on our planet, neatly gift-wrapped in a bacterial casing, was a message from the stars, waiting for a lifeform of sufficient intelligence to recognize and decode it? Bök was enthralled by the possibility. "I thought both of these speculations were extremely extravagant, but yet, the technology that would be involved in this endeavor works," he told me.

    What if sitting on our planet, waiting to be decoded, was a message from across the universe?

    Current research suggests that Earth was in the first eight percent of habitable planets to form. We may be one of the first civilizations to leave our atmosphere in search of the unknown. If Davies' hypothesis is possible, humans could be the first civilization to put it in motion. But what might that communication look like? NASA's Voyager probe famously included a Golden Record -- a message in a bottle with a map to our planet and an audio snapshot of our world. If and when it's discovered by intelligent lifeforms, our world may be long gone. But they will know that we once existed.

    A single bacterium can store vastly less information than NASA's Golden Record. If we as a species can leave a single message behind, what text should we choose to represent our world? "Surely poetry should be at the core of such an experience, such a technological advancement," Bök said. And so The Xenotext was born.

    Bök

    Christian Bök is not a typical poet. His work is beautiful, of that there can be no doubt, but it's perhaps better described as fastidious, or even self-flagellatory. He calls his first major work, Crystallography, "a pataphysical encyclopedia about the metaphor of crystals as a conceit for poetry." Bök was fascinated with crystals as a lyric poet, leaning on them for imagery and metaphors, and the book is both a thorough study of that fascination and a beautiful collection of poetry in its own right.

    After Crystallography came Eunoia, and a mainstream success rarely seen in the poetry world. Named for the shortest word in English to contain all five vowels, Eunoia comprises five chapters, each containing only one vowel. The work took seven years to complete. On release in 2001, it became the first book of poetry to appear on the Canadian Globe and Mail best sellers list, and was awarded the Griffin Poetry Prize the following year. It also saw international success, breaching the UK charts upon its release. Any poetry book reaching such heights would have been special; such an experimental work doing so was unprecedented. "It made my reputation as a poet," Bök admits.

    "Writing is inhibiting. Sighing, I sit, scribbling in ink this pidgin script. I sing with nihilistic witticism, disciplining signs with trifling gimmicks — impish hijinks which highlight stick sigils. Isn't it glib? Isn't it chic? I fit childish insights within rigid limits, writing schtick which might instill priggish misgivings in critics blind with hindsight. I dismiss nitpicking criticism which flirts with philistinism. I bitch; I kibitz - griping whilst criticizing dimwits, sniping whilst indicting nitwits, dismissing simplistic thinking, in which philippic wit is still illicit."
    An excerpt from 'Eunoia.'

    "These two books are, I guess, interested in 'beautiful thinking,' in the form of perfection, in careful thought. Structurally rigorous in its presentation, and beautifully rendered in its speech, cadences and musicality." Bök speaks like this; every phrase has a rhythm, each sentence is a potential stanza. He has an air of supreme confidence, a swagger that could easily be mistaken for arrogance. And conviction is important when you're trying to create undying poetry.

    The Xenotext

    The Xenotext is an extreme endeavor. It seems so simple at first, but each element relies on another, opening a rabbit hole of complexity. It starts with a couplet, two lines of poetry entwined and meant to be read in tandem, written by Bök:

    "Any style of life
    is prim

    The faery is rosy
    of glow"

    In a literary sense, the lines talk, each reflecting the other in structure, letter length and content. Tonally, the first is "masculine" and assertive, while the second is "feminine" and ephemeral. Bök calls them Orpheus and Eurydice, from the famous Greek tragedy of the man who traveled to the underworld in an attempt to bring his lover back to the land of the living.

    Structurally, the letters in the first poem correspond to those in the second -- it's a monoalphabetic substitution cipher. That means "L" is encoded as "R," "I" is encoded as "O," and so on. Such ciphers are common, but it's extremely difficult to create one that allows for functional words on both sides, let alone attractive or meaningful poetry.

    Going deeper down the rabbit hole, the poetry corresponds to genetics, with each of the cipher's letter pairings representing a DNA codon and an amino acid. DNA is represented in science by four letters, the programming units of life: G, A, T and C. A codon is a three-letter string combining any of those letters. For example, in the cipher, "N" equals "H" and a codon (i.e. ATG), while "H" equals "N" and an amino acid. (There are 21 amino acids, which can combine to make every type of protein there is.)

    With the first poem enciphered in Gs, As, Ts and Cs, it's then inserted into the genome of bacteria that can outlive humans. But this isn't just a random message like "It's a Small World." Instead, it sets in motion two things: The bacteria glow red, and they produce protein.

    And when deciphered, the protein's amino acid string reads as the second line of the poem. Oh, and the reason for it glowing red? It's a "self-reflective fulfillment," a reference to the poem it's writing, and its faery's "rosy glow."

    Christian Bök speaking at The Power Plant in Toronto, Canada.

    At this juncture it's worth taking a moment to consider Bök's background. He has a doctorate in English language and is an associate professor at the University of Calgary's creative writing faculty. While certainly an accomplished academic, one thing he cannot be described as is a biochemist.

    Bök has a doctorate in English Literature, not Biochemistry

    Bök has taught himself everything he needs to know in order to succeed. That includes studying genetics to create the cipher, studying proteomics in order to engineer the protein, and learning computer programming languages in order to run virtual models of his experiments before paying a lab to do them for him.

    Despite completing this considerable feat, Bök is fairly blasé about his achievement. "That's always been my joke: If it's written in English I should be able to figure out how to understand it. It's just words. Concepts that I can understand," he explained. "If I don't understand the meaning of the word, I look up the meaning of the word. If I don't understand the meaning of the words in the definition I look them up. It's honestly, it's just an exercise in immersion. A way of learning a new set of skills."

    The bacteria

    After spending years learning enough to write Orpheus and Eurydice, Bök turned his attention to the prevalent bacteria Escherichia coli (E. coli) as a host for his initial experiments. Best known as the bringer of serious food poisoning, E. coli is cheap and simple to grow in labs, making it a perfect test subject. Actually turning theoretical ideas into physical proof required yet more learning, and more patience. It wasn't until 2011, almost a decade after the journey began, that the breakthrough happened.

    "The Xenotext works!", an excited Bök announced to Poetry Foundation readers. "Yesterday, I received confirmation from the laboratory at the University of Calgary that my poetic cipher, gene X-P13, has in fact caused E. coli to fluoresce red in our test-runs. ... My poem does, in fact, cause the bacterium to write, in response, its own poem." It had taken Bök around a year to write the gene, and it had worked. But this was just an experiment. A precursor to the real test: Deinococcus radiodurans.

    The lifeform to be entrusted with Bök's prose is Deinococcus radiodurans, an extremophilic bacterium. It was first described in the '50s, when it survived what was then thought to be a life-obliterating dose of radiation. Although that's its most famous quality -- its species name is Latin for "radiation surviving"; its genus translates as "terrible berry" -- D. radiodurans has many skills. It's fine taking an acid bath, for one. It's also adept at dealing with dehydration, extreme cold, and it can survive in a vacuum. In ideal conditions, it's biologically immortal.

    These are hardy bacteria, for sure. But D. radiodurans' most spectacular facet is its unique (in current scientific knowledge) ability to repair huge portions of its own DNA. Because its chromosome is repeated many times over, it's able to recognize if a segment is destroyed, and repair it. Think of its genome like a RAID drive configuration in a server or a computer: a loop of redundancies that's always watching for errors.

    D. radiodurans could still be around after we're gone, waiting for the sun to explode and consume the world

    Because of its qualities, D. radiodurans is the subject of much research -- it's been touted as potentially invaluable for the fight against cancer, the search for immortality and even as a possible link to life on Mars. Regardless of our own abilities to bend it to our will, there is every chance that D. radiodurans will be around after we're gone, sitting there, waiting for the sun to explode and consume the world. For Bök, it was the perfect host for his latest opus. One that will protect his poetry from the jaws of eternity with every picogram of its being.

    The trouble with D. radiodurans

    D. radiodurans' ability to look after itself has proved a problem. After reworking the code for the new bacterium, Bök has run two experiments, both of which have failed. "From a scientific standard, my scientific collaborators believe I've succeeded," he elaborated. But, despite his nascent expertise in the subject, Bök is not a scientist, he's a poet. And his poem is being destroyed.

    There are three things that Bök needs to achieve for his The Xenotext to be a success. First, he has to prove the gene sequence has been integrated into D. radiodurans' genome. Second, D. radiodurans has to, in response, build the protein and glow red. Finally, he has to read the protein's genome and decipher it as the Eurydice poem. The first two have been checked off -- the final has not. "Every time we look for the protein we only detect part of it," Bök lamented. "[D. radiodurans is] destroying the protein too quickly for us to be able to read the entire poem."

    Why this is happening is a mystery -- if Bök had the answer, he would have devised a solution by now. That's not to say a solution can't be found. The protein destruction was "a chronic problem" in his early E. coli experiments, but he managed to solve it. When it came to reworking the experiment for D. radiodurans, he "simply transplanted that construct into the new organism," but that didn't work as planned. He is now dedicated to revising the process so that Eurydice will be readable.

    Even if Bök "succeeds," he may not have actually created an undying poem. When questioned, Bök acknowledges the hyperbole: "Short of designing something that benefits the organism or enhances its survivability, there's probably no way to really guarantee that the poem persists." So, as stable an organism as we think this is, evolution must still play a factor in some way, even if D. radiodurans is capable of repairing its own DNA and preserving it against mutational drift.

    Book 1

    After the successful E. coli experiments, Bök began work on his first book since Eunoia. Published in October, The Xenotext: Book 1 is at once a collection of apocalyptic poetry and a scientific primer in genetic and proteomic engineering.

    "The work I've written is tantamount to a poet trying to render the song, the poem, the lyrical effort as immortal. To render a poem deathless, capable of surviving in the face of its own extinction." A complex and self-referential work, it examines the threat of human extinction juxtaposed against art's ability to transcend generations.

    It's not coincidence that The Xenotext itself is named for Orpheus and Eurydice, the former so bold that he rode into Hades to rescue his lover, only to turn around and see her disappear. They're doomed to spend eternity in each other's hearts, but not arms, just as the bacterium and its protein will spend a lifetime calling one another's names. "[Book 1] addresses the degree to which we are good stewards of the planet, the degree to which we can ethically preserve our culture heritage against planetary disaster. The degree to which we've done a good job of being custodians of life on the Earth."

    The dark themes it deals with could so easily make it inaccessible, but the beauty and precision of the prose is the perfect counterweight. That Bök has also weaved the basic principles of the experiment, and a primer in the sciences, is truly impressive. "The first book is me clearing my throat. It's kind of a movie trailer for the second book," he mused. In fact, the entire book is itself a metaphor, an Orphic volume about poetry, the poet, sciences and the experiment. Next will be the Eurydicean book, which will dive into the poetry's response through a sci-fi horror exploration of the bacteria themselves.

    Book 2

    It's when talking of Book 2 that Bök's confidence in his own abilities begins to waver. He managed to obtain funding for his project, proving that despite his nonscientific background he had the knowledge to see his proposal through. The problem is that funding is finite. "I've got just enough money to try again maybe once or twice more," Bök said. Unfortunately, the lab team he was working with has moved onto new projects, so he'll have to rebuild that from scratch.

    Before he can hope to find a solution, though, Bök needs a hypothesis for why it's not working. "I still think I can figure it out," he asserted. "If I do so, then I'll undoubtedly publish the book to much fanfare." With well over a decade of work on The Xenotext behind him, it's clear that Bök never stopped learning. He's likely studying the obscurities of proteomics as you read this, searching for his answer.

    But what if the answer never arrives? "I'm worried that I'll end up having to sigh in failure and say, 'Well, here's the outcome of the project as it stands to far,'" he said. "That would be, I think, the worst outcome for me. That I have to present the testament to its failure."

    'The Xenotext: Book 1' is available from Coach House Books in paperback, e-book, or PDF.

    Image credits: Dr. Michael Daly (Deinococcus radiodurans, modified); International Festival of Authors (Bök portrait); Coach House Books ('The Xenotext' graphic, modified).

    Aaron writes about design, technology, video games, and whatever 'culture' is supposed to be. After cutting his teeth at The Verge, he joined Engadget as a Senior Editor in 2014. In his spare time he enjoys scouring the world for beautiful furniture, taking long walks on the beach, training orphaned dolphins, and making up facts about himself.

    Ethics: Aaron's partner is an employee of Ysbryd Games. As such he has no input into articles about Ysbryd or its games. His partner has also had fiction published by Abaddon Books, which is in the same group of companies as the game developer Rebellion. As the two companies remain distinct, this does not compromise his ability to cover video games created by Rebellion.
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