Nuclear Proetry*

Remember this guy? The dude who’s reprogramming the Deinococcus genotype with a free-verse poem in nucleotides, which in turn code for a protein that decompiles into another poem that replies to the first?

He and I, we’ve been in touch. And among the latest tidbits I am authorized to reveal is the fact that he’s added a fluorescent marker to the sequence, so that microbes containing his art will glow red. And that said poems (which together form a rumination and a rejoinder on the futility of life, poet and germ in conversation) also make reference to something that is rosy of glow. I have seen these poems. I have seen the DNA and amino-acid sequences that code them. I have even seen something approaching the poem in its native form, which I am permitted to show you…

… and I am increasingly blown away by the amount of recursion and self-reference this dude can pack into a measly 192 codons. (Also, I am increasingly pissed-off by the fact that Christian Bök can do all this stuff armed with a PhD in bloody English— whereas I, with all my degrees in biology, couldn’t get a single readable genetic sequence out of two years of effort. If there is a moral here, I refuse to acknowledge it.)

I am further tickled to report that one of Christian’s favourite movies is John Carpenter’s The Thing, and that he is a fan of my own fanfician homage to that movie. (Which yes, as some of you have noticed, got a Black Quill Award (Editor’s Choice, Best Dark Scribble) over at Dark Scribe, as well as coming first in the Reader’s Choice poll over at Clarkesworld, and being a current finalist for a best-short-fiction BSFA Award. I was waiting to roll these announcements in with a couple of others, but Tor.com is running silent on one front and I bet none of you have heard of the Mir award on the other, so what the hell.)

And yes: Christian Bök’s monstrous microbial poem will be making an appearance in State of Grace. A shame my protagonist will have become too schizophrenic by then to properly appreciate it.


*Not a typo.

This entry was written by Peter Watts , posted on Sunday February 06 2011at 02:02 pm , filed under Dumbspeech, ink on art . Bookmark the permalink . Post a comment below or leave a trackback: Trackback URL.

44 Responses to “Nuclear Proetry*”

  1. Everything Christian does is interesting. Check out his “Motorized Razors,” if you haven’t already:

    http://www.youtube.com/watch?v=jrNpI0r7fa8

  2. I wonder – if genescans are ever going to be ubiquitous, will the people begin to put messages into their introns – the same way they tattoo their bodies now? “Born to repliCCAATTe”? You could carry a whole book inside you… or a porn picture in some post-.jpg format. Fun!

  3. Well, awesome.

    Though bacteria that give people rash that types out poems on their inflamed skin would have been even more nifty.

  4. peter darbyshire: You have just made my day. Especially joyful is this poem, or whatever the hell it is: http://www.youtube.com/watch?v=1uVugkG7CBc&feature=related

    Sure enough, it does sound like flying fish. Also, the Swedish Chef from the Muppet Show.

    And this:
    http://www.youtube.com/watch?v=1Zl1LLY7DBs&feature=related
    Of which John Lennon would thoroughly approve. “We eat cruel and unusual peppermint, for he is a jolly good fellow with so many candy knives.”

    From time to time, I love this Crawl.

  5. “Though bacteria that give people rash that types out poems on their inflamed skin would have been even more nifty.”

    ones that give you an evolving tattoo

  6. @Sheila

    One that responds to pressure, so that term “selective pressure” becomes utterly literal in regards to this particular strain 😀

  7. Hey, Peter—thanks for the continued interest in the project. I have just found out this week that one of my assistants has mislabelled the data sets used to generate the image of Protein 13 (so the illustration on your site is not a precisely accurate depiction of the molecule…). I am in the process of correcting my models for the protein, and I can certainly send you the updated imagery, if you like, in the interest of maintaining scientific truth…. ;+)

    Cheers, my friend,
    Christian
    :+)

  8. On the subject of rashes, are we ever going to find out what manner of biological corruption was eating Peter’s legs a couple weeks back? I feel a little blue-balled over that whole tease.

  9. @Hljóðlegur: They should have let Christian sing the national anthem at the Super Bowl.

  10. @Scott: I do not yet know what those lesions were. All I know is that the drugs ran out, and now they are back.

    As to Jayne’s suggestions on the subject of alphanumeric rashes, mine would qualify. As long as the poetry in question only contained the letter “o”.

  11. @Scott well at least you’re not feeling necrotic fasciitis balled about the whole thing, lol.

  12. @peter darbyshire: By the gods, it would have improved the very fabric of reality. Truly.

  13. @Peter

    Maybe it’s fanmail? A sigh of appreciation, like “Oooooooooooooooooooh!”

    Look for the H-shaped lesion. And the exclamation mark.

    On a more serious note, wish you a speedy recovery. Hope your insurance is good enough to motivate healthcare system into actually identifying the bug responsible.

  14. I was going to suggest an allergic reaction to bug bites, but toxic fanmail that breaks out on your leg is much more sci fi.

    On the topic of Bok and his poetry scheme, I must quote someone I know whose reaction to the idea was, “reads more like a cat coughing up a hairball than high art.” Clearly a fan of Aria of the Three Horned Enemy?

  15. “All I know is that the drugs ran out, and now they are back.”

    Maybe they’ve colonized something in your environment and you got reinfected?

  16. checking in with some enthusiastic applause for all things mr BOK
    watch the videos y’all

  17. In a book club discussion of Blindsight, I enjoyed this comment:

    Watts could probably take on Ellison in a grimmer-than-thou slapfight

    Slapfight!

    Entire discussion is here:

    http://absolutewrite.com/forums/showthread.php?p=5805054

  18. @Peter re: lesions etc. Remarks are on facebook about your unintended foray into Horror Writer Fame. Kudos on that.

    A friend of mine has a kid who has had repeated MRSA infections. The kid has a strong immune system and hasn’t yet succumbed to necrotizing fascitis or any such thing.

    Yet getting rid of MRSA/NF (“NF”==”necrotizing fascitis”) is a real bitch. The travails of these folks reminds me that one of the reasons that austerity of decor and avoidance of ostentation is bedbugs. Simply stated, the more bare you can keep your digs, the less hiding places for bedbugs and nasty microbes. Why be sparse of furniture and dust all of the time, when we all love to “get more stuff” and eliminating allergens from our environment leads to a degraded or over-sensitized histamine response system? Simple: the less places for bedbugs to hide the easier to get them out, and the less places or particles for bacteria to colonize, the easier to deny them a place from which to re-infect.

    Someone mentioned that if you’ve got MRSA on your skin, it’s probably in your nose as well. From there it can easily re-infect the skin. So anything you do to get rid of the bedbugs will work best if you do a total purge of both self and environment. Steam the bedding as you gobble azithromycin and don’t forget to toss out all of the houseplants and burn your computer data and OS state image to DVDs, and prepare to buy a new laptop if the old one gets fx0r3d when you soak it down with antiseptics. Or just take every last thing you absolutely must have to a storehouse in Outer WhereAmI and fumigate your old digs and slap a Quarantined Forever sign on the door there.

    Seriously, Bruce Sterling covered this a bit obliquely in his “Holy Fire”, a story about folks who survived the inevitable day when the sort of organism that thrives in commercial bathroom cleaning products become the dominant organisms in the human-occupied environment. Eventually all that can be done is to abandon and torch the human-occupied environment as an endless source of re-infection. Treat the human and the increasingly-resistant organism retrenches to the local surround, and then re-infects the human. Ping-ponging like a case of chlamydia between a prostitute and her pimp. All that can be done is to OD on antibiotics and never stay in one place long enough to establish an environment that can re-infect you. Live in the wild and let the natural world be your best defense.

    Remember, I Am Not A Doctor but some things are better drenched with thiomerosal (merthiolate) than neosporin. Lots of things can evolve quickly to evade antibiotics. Not so many can evolve to thrive on an alcohol solution of mercury and iodine.

    Looking forward to you getting better and defeating Ellison in that slapfight, which we’d all probably pay good money to see.

  19. I see US Border Agents are still keeping us very safe:

    Canadian sues claiming abuse at U.S. border
    ———————————————————————————————-
    Loretta Van Beek of Stratford, Ontario, who said she travels to the U.S. regularly to vacation in Georgia, said agents sent her to secondary inspection because she failed to declare raspberries.

    She said agents questioned her during a two-hour session, then ordered her to strip. She said one agent aggressively groped her breasts and genital area for an extended period of time while the other watched. Then they photographed and fingerprinted her and sent her back to Canada, the suit said…
    http://www.freep.com/article/20110210/NEWS05/102100560/1007/news05/Canadian-sues-claiming-abuse-U-S-border

  20. ^
    |

    We like to call that “The Beaudry”. That’ll teach you Canadians to come down here, flaunting your clean cities and universal health care.

    Those could have been weaponized raspberries, and you can smuggle those things anywhere. I, for one, applaud their thoroughness. The days when we could afford to not sexually assault people over an errant bushel of delicious fruit are over.

  21. Raspberries are an agricultural product, can harbor invasive pests, and as such, are a big no-no when crossing borders. Not harmless in that respect.

    I don’t think that means they get to grab your boobs, though.

  22. You could be smuggling raspberries in them though, right?

    I admit, my own first hand knowledge of the female breast is rather limited, but it seems plausible, with their marsupial like breast-pouches.

  23. It seems impossible for some members of the border patrol to be civilized. A simple “Excuse me, Madam. You are not allowed to take fruits over the border. They may spread dangerous plant diseases” would have done the job, too.
    Some days ago I read about the FBI hunting Amish countrymen illegally selling unpasteurized milk: http://www.boingboing.net/2011/02/03/the-amish-raw-milk-b.html
    And I really should go to the next tourist fair with this and other examples and ask if it is really advisable to visit the USA …

  24. @ScottC: Har har, “first hand knowledge.”

    Do not attempt to smuggle raspberries with your boobs. Too much sway. They would crush the raspberries, causing you to look like you are sweating blood.

  25. Well, clearly, there is some sort of misconduct here above and beyond the garden variety overzealousness of the border patrol.

    If the woman is to be believed (which is a dubious proposition, if you ask me…we all know those uppity Canadians love to cross our border and commit felony sass against our jackbooted patriots), and even assuming failure to declare raspberries is grounds for a full body search, I’m pretty certain they’re supposed to have a female officer on hand to conduct those for women who request them. Having a male officer conduct any kind of search on her while another one leers in the background, doesn’t seem above board even if the search was valid, and conducted without lewdness.

    (Apologies to Christian Bok for the hijack)

  26. Drat. In a triumphant declaration of my capacity for reading comprehension, I somehow missed where it said, in the first sentence, that both of the officers were females.

    That will be enough out of me then.

  27. Well I would hope that they’ve take samples of the horror blotch on your leg, and identify it soon. Maybe you should do a donations run for money for more drugs. I lived with a girl who got bit by a brown widow (they managed to catch it, got the university to identify it), and the wound, on her arm, necrotized. She was sick for a couple days (brown widow bites don’t usually kill, if you’re young and healthy.) and covered her arm whenever she could, and it stayed black blue and brown for three or four months.
    I assume she took antibiotics for the necrotized flesh. Oddly, she did not gain a fear of spiders as a result. But then, she was a courier. Kind of a dying species here in Vancouver (or as some people call it, ‘wankcouver.”).

  28. Eh. ‘Taken.” Hates me them typos.

  29. In re Christian Bok, it occurs to me that It’s a bluff.

    No one is going to pay good money for lab time to have Bok’s poem enshrined in DNA. I think the art project was the proposition that it be done, and the public reaction to that proposal, not the actual bacterium with the poem.

    Conceptual art.

  30. On the topic of Bok and his poetry scheme, I must quote someone I know whose reaction to the idea was, “reads more like a cat coughing up a hairball than high art.”

    Speaking as someone intimately-acquainted with hairball-urfing cats, as someone with three degrees and a couple of post-docs in biology, as someone with first-hand experience with the difficulties of even basic genetic sequencing, much less synthesizing a functional gene which encodes two distinct levels of semantic content exploring a philosophical theme — I can say with a fair degree of confidence that this “person you know” is a fucking idiot.

  31. I don’t know. I think the big loser in all of this is the consumer. In these uncertain economic times, we are already faced with shrinking value in our product sizes, as common product containers are stealthily replaced with smaller volumes, while the prices remain the same or creep up. I was dismayed to find that my cans of tuna are no longer the same size, and I can’t quite get two whole sandwiches out of one can anymore.

    Now, even our poets are scaling back on their phonetics. I remember a time when we could get a full range of vowels in our poetry, not just one.

    Furthermore, the scourge of e-books was bad enough, taking the simple joy of owning, reading, and interacting with a book, and reducing it to having to read on a small, battery powered screen. Now we are being forced to read our poetry on (literally), a microscopic level.

    When are consumers going to rise up against Big Poetry, and say we’re not going to take it anymore? I’m tired of being pushed around.

  32. Peter: I can say with a fair degree of confidence that this “person you know” is a fucking idiot.

    Nonsense! Oh, for sure, this “person I know” is not an idiot. He’s just as smart and degreed as you, I believe, if in another field.

    Comparing the entire concept to hairballs is a nod to the onomatopoeia of Bok’s work, since I think I linked my message to him about it to either Aria or Razors. Specifically, our poet makes sounds that mimic other things – motorized razors = machine-like noises. And they’re harsh guttural sounds, with lots of repetition, like, oh, a cat coughing up a hairball.

    So the comment has several levels: not just that Mr. Bok is making “hairball” sounds but that the whole process has a hairball-like feature? His plan is to induce a bacterium to take up something as part of its natural processes, and then cough remnants of that foreign matter back out again. Sounds like ….hairballs!

    Make no mistake, I enjoyed the heck out of his readings. That’s why “someone I know” had a chance to comment – I got all excited about it and sent the link to about seven other poor souls. I don’t think my clever friend was as enamored, but I still think his comment was cute.

    I also ran my idea that the actual art was purely conceptual, not intended to actually be done, but to get the idea out there, across a English grad student e-friend of mine who claims to have known Bok, and he said, “No way.” He claims that if Christian said he was gonna do it, he intended to.

    Dang, Peter. If I have understood Mr. Bok and his philosophy, poetry had gotten too dour, kept all the joy for the writer, leaving the reader with less pleasant emotions. He’s putting the funny in the poems on purpose, to hear him tell it. I’d love to hear him do a poem called Cats, because it would have some artful hairball ack-acks, and they’d fill the listener with glee. Okay, this listener.

    @ScottC: hee hee!

  33. H, I am willing to believe that people would spend time and money on biological art. See http://www.sciencegallery.com/visceral

  34. S, Don’t know if you can see this?

    It mentions that a third party who was a student of Bok’s agrees it is not just performance art, that Bok intends to actually have the DNA insertion done.

  35. S, Don’t know if you can see this?

    Your comment or a link? I see new comments when they’re posted because I subscribed to the discussion.


    It mentions that a third party who was a student of Bok’s agrees it is not just performance art, that Bok intends to actually have the DNA insertion done.

    but not sure what you are referring to here. did you mean to include a url?

  36. Off topic of the proetry, but feel people might want to know. For those of you who don’t keep up with facebook, Peter just posted

    In hospital. Morphine. No wifi. Flesh-eating disease. Most of inside of right calf gone down to muscle. No reliable internet access for a week at least. Sorry.

    Hopefully someone will keep us updated as to whether he needs any fund raising etc if the expenses go high.

  37. Here to say the same as Sheila did up above.

    Everyone, please wish Peter well. :(

  38. *look of horror*

    Thanks for the update. No Facebook at work here.

    Get well, Watts. We will keep a good thought.

  39. Holy shit. You’re racking up quite the resume of bizarre unfortunate circumstances. =(

    Best wishes, man.

  40. Dammit. With anyone else, all the “flesh eating bacteria” jokes would have been just that–jokes. I can’t believe your luck as of later, Peter.

    Please get better soon, Peter.

  41. Hey, this rude violation of D. radiodurans is more common-place than I thought? Here’s an article from 2003 in which the lyrics to “It’s a Small World After All” were inserted into one:

    http://www.newscientist.com/article/dn3243-data-stored-in-multiplying-bacteria.html

    Good to know those vital data are being stored for future generations.

  42. Also!

    If a genetically modified D radiodurans gets loose and kills off humanity, I would very much prefer Poetry, rather than Disney, wielded the axe. To have died of “It’s a Small World After All” would be a terrible epitaph for our race.

  43. That 2003 news article is citation 1 in The Xenotext Experiment:


    P Wong et al., “Organic Data Memory Using the DNA Approach” (Jan 2003) 46 Communications of the ACM 95-98.

  44. Oddly enough, I was skimming through a review of dna computing research today and finally decided to wipe it from my kindle since there was no way I’d get through that whole review absorbing it in any great depth.

    oh hai people I am working late