The Xenotext Experiment
A few of you may remember a throwaway bit of ecogothic ambience near the start of State of Grace:
“…pure tissue was so hard to come by these days. There was always something that didn’t belong. Viral DNA, engineered for the greater good but too indiscriminate to stay on target. Special marker genes, designed to make animals glow in the dark when exposed to some toxin the EPA had lost interest in twenty years before. Even DNA computers, custom-built for a specific task and then tramped carelessly into wild genotypes like muddy footprints on a pristine floor. Not to mention the fact that half the technical data on the planet was being stored genetically these days, and that stuff was always getting loose. Try sequencing a lung fluke and it was even money whether the base-pairs you read would code for protein or the technical specs on the Denver sewer system.”
The Orator at the End of Time. (Photo credit Michael Daly)
I think I originally came across that idea in an old episode of Star Trek Next Gen (“The Drumhead”, for the hardcores among you; a Klingon spy was caught encoding Federation secrets into blood proteins). Recent developments in DNA computing only reinforced the bug in my mind. But it turns out another Canadian — a poet named Christian Bök — is ten steps ahead of me. He’s using genetic engineering to produce living recursive metapoetry.
I first learned about Bök via a review of his book Eunoia: a freakish little masterpiece that tells its story in chapters that each use only a single vowel. (“Hassan can, at a handclap, call a vassal at hand and ask that all staff plan a bacchanal — a gala ball that has what pagan charm small galas lack. Hassan claps, and (ta-dah) an Arab lass at a swank spa can draw a man’s bath and wash a man’s back, as Arab lads fawn and hang…” You get the idea. The man is either a genius or the patron saint of OCD.)
I never read the book. I never forgot the concept. And then, a few months back, I was having dinner with a dude who started out as a high-schooling relative of an old grad-school buddy of mine, and who has somehow turned into a PhD candidate while I myself haven’t aged at all. Turns out he actually knows this Bök fellow personally, and he brought me up to speed on the man’s latest project.
The Xenotext Experiment. A collaboration with Stuart Kauffman at the University of Calgary’s Institute of Biocomplexity and Informatics. Bök is writing a 50-word English poem (probably about “the relationship between language and genetics”, he says), translating it into DNA, and inserting it into the genome of Conan the Bacterium — also known as Deinococcus radiodurans, the toughest microbial motherfucker on the planet, a microbe who laughs at hard vacuum and radiation hot enough to cook you to a cinder. Genes are the most stable storage medium that 4.7 billion years of evolution have been able to come up with (they beat the pants off DVDs), and Deinococcus carries some of the most stable genes. Bök is shooting for a poem that’ll still be around and iterating when the sun blows up. And it doesn’t stop there; not satisfied with simply inserting fifty words of nonfunctional junk into Conan’s DNA, he’s going to design the poem itself to code for the production of a protein which will itself decompile into a whole other poem.
Talk about bringing literature to life.
I really, really hope Bök publishes before State of Grace comes out. Because his poem just has to make a cameo appearance in the Oregon desert, and I’d hate to have to make up the words myself. I’d probably end up just stealing something from Aqualung.
Thanks to Sean Braune for bringing me up to speed on all this.
As a bioinformatician working in the field of molecular evolution I’m going to go out on a limb here and say that this bit of inserted DNA isn’t likely to remain intact very long for a few good reasons. One is that since it does code for a protein, but one that may fold into who knows what final three-dimensional shape, that codon will have a large impact on the cellular biology of the bacterium. Most misfolded proteins are aggregative which is bad news. If it is, you are likely to see negative selection on the gene.
Secondly bacteria tend to be rather streamlined genetically due to energy constraints. It is why they tend not to have junk DNA like pseudogenes, it is a waste of energy to copy that DNA every time you replicate, spending the energy to actually transcribe the gene and translate the protein is an even bigger energy sink. So again, we are likely to see negative selection on the gene.
And finally, in the absence of negative selection ( or positive selection which is hugely unlikely) the gene will merely evolve at a neutral rate, rapidly becoming a meaningless pseudogene. Which will likely be lost entirely.
Better to have done this in a single celled eukaryote, they have the energy budget to spare, which is why they can accumulate lots of junk in their genomes.
Stanislaw Lem’s Imaginary Magnitude, a book of reviews of nonexistent books, includes an account of bacteria taught (by ruthless culling) to reproduce in Morse code patterns that spell out poetry.
Another great post, and yet another book I have to check out. Watts, you make me feel like a child when you get all science-y. Your shit goes way beyond anything I’m used to. I’m both energized and humbled at the depth of things I simply had no idea about.
As I brief aside, I eagerly check my RSS feed each day in the hope that there will be some new word about State of Grace, or any other project you have in store. Could you reveal a snippet or two in some near-future post? My child-like mind will thank you for it.
[…] This post was mentioned on Twitter by torforgeauthors and Ian 'Cat' Vincent, Waldheri. Waldheri said: The Xenotext Experiment /by @peter_watts http://bit.ly/fo7gsh […]
See, on the one hand, I’m interested in poetry and how people can innovate in it. On the other hand, there’s points where I don’t see more than a gimmick, even when what the poet in question is trying tickles my formalist fancy.
heh heh Conan the Bacterium….. for some reason that made my day.
That said, whether it is good poetry or not, it is an amusing idea. Although I’d never do such a thing. I’d hesitate to say that even my favorite poets deserved immortality encoded in a living organism. So I’m glad he didn’t use a single celled eukaryote.
That said, I look forward to seeing the idea show up in the novel.
And better Auden than specs on the Denver sewer system.
Oh man. I love your blog entries about cool science stuff. My imagination went into immediate interstellar overdrive…
Funny, the whole Xenotext Experiment sounds just like something Greg Egan might have imagined. Oh, and Conan The Bacterium made my day too, but for some reason I found The Orator at the End of Time even funnier…
The full text of Eunoia, published by Coach House Press, can be found at:
http://archives.chbooks.com/online_books/eunoia/text.html?q=archives/online_books/eunoia/text.html
“…he’s going to design the poem itself to code for the production of a protein which will itself decompile into a whole other poem.”
Fuck Yeah!
Heh, i love the way this blog posting seems to have a fire in its eyes. There is one other (semi-)technical blog i follow that have a similar energy, and it talks about energetic chemical cocktails the writer is likely to refuse working with (they have a bad habit of either make big booms or turn just about anything into toxic fog, or both if your really lucky).
Its the kind of writing that makes me really wish i didn’t drop out of the educational system (mostly because i could not stomach the “social” elements of said system).
Hey, Peter:
Thanks for the posting about the project–I appreciate your enthusiasm for the concept. After nearly ten years of work, I have managed this summer to figure out the two poems (the one that I encode as a gene and the one that the cell creates in response)–and I have already modelled a tentative, enciphered sequence of amino acids that, according to the supercomputers, can actually fold into a viable protein likely to survive in the bacterium. I am currently finalizing the genetic sequence for this cipher, and I expect to synthesize the gene early in the new year, performing a test run on E. coli, just to be sure that the protein expresses properly, before transfecting everything as an episome into D. Radiodurans. I am hoping to have an organism within a year, and a book outlining all of this poetic material within two years–probably sooner….
Drop me a line: cbok@ucalgary.ca –and I can provide you with my phone number. I would be delighted to chat about “State of Grace”–the posted excerpt is great, and I would love to hear about the novel….
Cheers,
Christian Bök
Kac has also used a genetic process of encipherment in his artwork called Genesis – a project intended to show that “biological processes are now writerly.”5 Kac encodes a short verse from the Bible into a strand of DNA, which he then inserts into a microbe, exposing the germ to doses of mutagenic radiation. Kac suggests that, by “editing” such a text through mutation, we can foster an unguided, aleatory message in a more innovative form, rather than accept the dominant, biblical passage in its last inherited form.
…smells like …
XD
You know what would be uber cool and Douglas Adams like? If all life on this planet were wiped out by a mutated Conan the Bacterium because someone inserted a self-decompiling poem into it and set it free. POETRY, YOU HAVE KILLED US ALL.
HAHAHAHAHHAAAA. *whew* Adams would plotz, were he not dead and all. Talk about a last great act of performance art!
Holy cats, that’s amazing. I’m going to look into this further.
Also, thank you for another post to add to my folder of “Things to read when I feel like suck-starting a shotgun.” “..the toughest microbial motherfucker on the planet..” made my day.
I had to do it. I blame Windows NT.
http://drwho.virtadpt.net/archive/2010/11/30/conan-the-bacterium
(If it sucks, I’ll take it down and apologize publically. I don’t want to be a dick.)
HArharar!
Doctor – I laughed! Who knew bacteria had Austrian accents?
Of course, I am not a good barometer of what is socially acceptable, am I?
I had to share this with all. The most spectacular photo of a squid I’ve seen yet:
http://www.flickr.com/photos/kozyndan/5218491696/in/photostream/
Enjoy.
@the Doctor: It does not suck. It is awesome. Except the photo credit should go to Allan Weiss.
@ken: That’s pretty awesome too.
@Hljóðlegur: If it can live in a reactor core, it can have whatever accent it wants.
@Peter Watts: Yay! Glad you like it. Photo credit updated.
Woop woop! Peter has gigs:
Peter Watts writing Crysis 2 novelization:
http://www.mycrysis.com/news/crysis_2/crysis-2-novel-announced
Peter, what happened to Richard Morgan, wasn’t he supposed to do all that stuff for Crysis 2? Interesting!
Also this:
ABOUT THE AUTHOR:
Peter Watts has spent much of his adult life deciding whether to be a writer or a scientist, settling somewhere in between both. His original novels, Starfish, Maelstrom, and Behemoth are all universally acknowledged as some of the best hard sci-fi of the last 20 years. [b]His most recent novel, Blindsight, was published by Tor in 2006 and was met by both critical and commercial success.[/b] He currently lives in Toronto, Ontario, Canada.
It true? If so, congrats!
Mirik, cool! thanks for pointing that out. also in their article,
You may also leave questions for the author Peter Watts in the comments section, we’ll take a selection of the best questions and present them to him. An article with all of his answers will be published in the near future.
I only have boring logistical type of questions, so I’m not leaving any comments there, or here for that matter.
Hey ken, that photos and the other sea creature photos in your stream are really great. and in one of them you link to a photo of a hatchling critter which is really awesome.
Did any of you ever read a short story where there is an atheist (?) geneticist (?) daughter of an Islamic man and he (or someone?) in the story decides to honor his religion by having their holy text encoded in to their genes, and then someone realizes that makes them an easy target for biological warfare, so his daughter works on a technique to help them (don’t want spoilers too much)
Sorry I can’t remember many details. It was interesting enough for part of it to stick in my head though.
Sheila, I is drawing a blank on that short story, even though it sounds familiar. I want to say Arthur C Clarke, but I don’t know why.
Sheila – the story you’re thinking of is Written in Blood, by Chris Lawson.
As for the Xenotext project, if the poem mutates into other forms, will there be natural selection of the bacteria based on artistic merit? will it mutate into a dirty limerick?
Michael_gr, thank you kindly. I found him online and wish his short story collection of the same name was within my grasp. I bet I found the short story in some best-of if not asimovs. I can probably scrounge it up again.
It would appear that NASA have found something that could give ol’ conan a run for its money.
http://www.slashgear.com/nasa-find-new-lifeform-arsenic-microbe-widens-likelihood-of-extraterrestrial-life-02117300/
a microbe that can live in a arsenic lake, yeiks…
Sheila – the story you’re thinking of is Written in Blood, by Chris Lawson.
Of course someone here knew!
@The Doctor: If it can live in a reactor core, it can have whatever accent it wants.
Agree. And eventually, it will become the Governor of a state of Bacteria by its own hand.
Okay, okay, sorry – I surfed out on a wave of pop culture references, but wiped out near the shore. No more Schwarzennegger jokes.
Hmmm. Very interesting, but I have a question, I do.
It’s simple enough to -say- you’re coding a gene that writes a poem, and then in is transcribed into another poem, but doesn’t that mean you’ll essentially have to encrypt the letters in your poem into some combination of T’s, G’s, C’s and A’s?
Then, for someone to read this poem, they will need to be able to decrypt your code, which will be contained in an (essentially) arbitrary number of bases between the regions marking the beginning and end of the gene, the transcription activity switches, etc. That seems like it would require some fairly difficult decryption work to translate back into English, if you didn’t have the key. He’s using codons, but there’s no way for the decrypter to know that this is the case…
Matt,
I got curious about what you asked, and thought maybe I could come up with a translation of your paragraph with some simple substitution by codons as a trivial example. But since I don’t know much biology, I am not sure what you mean about ‘arbitrary number of bases between the regions’. Do you mean that there will be arbitrary noise of varying lengths interspersed throughout a sentence?
Anyway, because I was curious about that, I looked at the citations in the xenotext article. First is to a paper in 2003 in the Communications of the ACM which is kick ass because I have a subscription to that and can see it online for instant gratification. So then, I can follow papers that cite it. And how fucking cool is this? I found one that goes in to depth about using templates to code information and is available online for anyone.
I figure it will answer you questions way better than doing some silly demo of translating your paragraph by someone (me) who doesn’t know biology.
it lets you address a shit-ton of memory space.
DNA Sequence Design Using Templates
http://www.springerlink.com/content/02x18g5811l27h21/
I think that link might be broken. Here is the sample paper directly
http://www.ohmsha.co.jp/ngc/vol-20-3-5.pdf
i just wanted to know…..
when the Blindsight’s prequel “state of grace” will be finally released for sale????
please.
I cannot say. The manuscript is due at the publisher for mid-April, though. You’ll probably want to tack a year onto that.
a year!
Do you have more short stories in the works between now and then?
(It crosses the line of politeness the amount of curiosity I have for when you will publish new material (or anyone I like to read, for that matter)… so I think turn about is fair play and you should sometimes ask your readers when we have new features coming out. to keep us polite.)
Ps. to my above comment re “shit-town of memory”. take that with a very small grain of salt. and I was amused today to see an email from amazon s3 telling me that they were increasing the maximum supported object size from 5 gigabytes to 5 terabytes. I read the email pretty early this morning, and it feels like something I remember hazily from dreamland.