This music will be forever or dna programming

You can write about different things, even more - on different things. So programming as such is also not limited to certain frameworks, familiar to all stereotypes associated with computers. Earlier, Habré already published articles about the so-called literary programming and why it might be even better than classical programming . Unfortunately, it also explained why it is not so widespread - try to fit a good writer and programmer in one person. But if you take a poet ...







But I'm getting ahead of myself, this story began a little earlier, in 1966, when a man was born on August 10, who at birth received a very interesting name - Christian Book , which says at least that his parents were pretty eccentric people. The child subsequently matured and changed him to a more euphonic one, becoming the name Christian Bök. At the same time, it is important to note that he is not a Scandinavian - it is rather a tribute to the culture of the northern peoples, which is hinted at by the notorious "ö".



Despite the fact that the parents called their son so extravagantly, they still took good care of his education. Boeck earned his BA and MA from Carleton University and his PhD in English from York University in Toronto, where he first became interested in the avant-garde poetics of Canadian writers such as bpNichol, Steve McCaffery, and Darren Wershler-Henry. Perhaps his university years can be called the starting point of a very long route in the path of poetry. His passion for language was not in vain and made him think about eternity and literature as a way to leave his mark on this world.



He began, in principle, in a relatively standard way, with the release of poetry collections, in which he only revised some terms. For example, he decided to "confiscate" the term "crystallography" from geologists, and screw it into literature, since in his opinion it is best suited for writers, because "crystal" is also pure, and "grapho" means to write. His collection "Crystallography" was nominated for the prestigious Gerald Lampert Memorial Prize, which spurred him to continue his literary experiments. The next was the book Eunoia (Coach House Books, 2001), which had a very interesting structure - a lipogram, where each chapter had only one vowel. This collection won the Griffin Poetry Award in 2002.



The judges appreciated this pun especially when you consider that the title of this book contained five vowels and at the same time was the shortest word in the English language with such properties. According to the commission, Christian's approach made it possible to properly reveal the theme of the work and convey its meaning to the readers much better. As for me, this is an attempt to surpass previous and even current competitors, at the expense of their own style, and since the award was given, it can be considered successful. So far, everything has been within a fairly familiar framework for human understanding, and if everything had remained so, then this text itself did not exist.





In addition to his literary talents, Christian Boeck also began a teaching career at the University of Calgary, which means he gained access to laboratories, which was largely useful to him. Somewhere there, he noticed one interesting bacterium Escherichia coli, better known as E. coli. As you know, it is quite widespread and often lives in the intestines of warm-blooded animals, it is mostly harmless, with the exception of one strain. Christian did not care about danger, he decided to tackle this bacterium because of its prevalence and uniqueness, since, in his opinion, poetry should live forever.





E. coli was also chosen for reasons that it is much easier to work with it, which is proved by numerous experiments carried out earlier. Moreover, it was with her that biotechnology began. More precisely, it began with E. coli and one gourmet store in Honolulu, which no longer exists. It’s not a matter of the chef’s dirty hands; two rather significant scientists crossed there - Stanley Cohen, one of the founders of modern biotechnology and biochemist Herbert Boyer from the University of California at San Francisco. They came to Honolulu to take part in a meeting on DNA ring plasmids in bacteria.





Cohen suggested that it is possible to edit Escherichia coli by introducing plasmid DNA into it, which could allow researchers to multiply and clone plasmids in the bacteria themselves and would help in further research. Herbert Boyer specialized in working with enzymes, in particular, he presented the ECoRI enzyme, which is capable of cleaving a double-stranded DNA molecule and obtaining single-stranded identical ends.



Both saw the potential for bringing these two discoveries together in what would become genetic engineering. First, EcoRI should be used to cut both the plasmid DNA and its selected portion. Then, when the identical DNA terminals are open, the selected DNA fragment is attached to the plasmid DNA and cloned together into E. coli.



They first discussed collaboration at a grocery store near Waikiki Beach. Their conversation over a late supper led to a scientific achievement that subsequently shook the world of science. Over the course of a year, they cloned DNA molecules obtained by splicing DNA fragments from two different plasmids, thus creating recombinant DNA. The foundations of biotechnology were laid.



Boyer and Cohen took different paths, both concerned about the safety of recombinant DNA technology (leading to the 1975 Asilomar conference where scientists, ethicists and journalists speculated about the implications of genetic engineering). While Cohen remained in academia and defended recombinant DNA technology in congressional hearings, Boyer saw the potential for profit. In 1976 in South San Francisco, Boyer and venture capitalist Robert Swenson founded Genentech, the world's first biotech company.



Genentech pioneers at the California Institute of Technology were the first to synthesize DNA in the laboratory. They wanted to use E. coli as a factory to synthesize mammalian proteins. The proof of principle was demonstrated earlier by Cohen and his colleagues at Stanford when they used bacteria to make a functioning mouse cell protein. Scientists at Genentech eventually succeeded in producing a human hormone called somatostatin in bacteria - and thus ushered in the era of commercial biotechnology. The production of insulin and growth hormone began shortly thereafter.



The essence of the first experiment



Since for biotechnologists, E. coli was a familiar thing and was often used in various kinds of research, the choice of our poet becomes quite clear. It remains to find what exactly he was inspired by, why he even decided to contact biotechnology. Moreover, one should take into account another interesting fact - his previous work, "Eunoia", became an absolute bestseller, and he could rest on his laurels, since for poetry, especially Canadian, such an achievement is very impressive.



But no. Interested in an experiment by Park Chung-Wong and his team of scientists at the Pacific Northwest National Laboratory in Richland, Washington, who were able to encrypt the lyrics of Walt Disney's song "It's A Small World" in bacteria, and then reconstruct the message after several generations of playback, Böck decided try something similar with an original work, namely a poem. But just writing a verse into the gene was not enough for the Canadian. He decided to do something differently.  





“What I was hoping to do,” says Boeck, “was to push these projects a little bit, trying to get the body to actually read the message and do something in response ... I designed the poem in such a way that when it is implanted into that body, the body can actually read sequence of genes and interpret it as a set of instructions for building a protein. "




At the same time, Beck suggested, the body should be able to decipher the second poem encrypted inside the first.



"In essence, I have to write one poem so that it can be translated by the body into another poem."




The main impact driving this grand experiment came from some unusually commonplace place: the puzzle pages of a daily newspaper. Boeck wondered, looking at cryptograms, in which a person analyzes the order and frequency of letters in order to decipher a distinguishable sentence, why puzzle creators never thought of making the original, coded message distinguishable by itself.



Why not create a puzzle that can code one grammatically correct sentence inside another? So that the charade is in itself and can change over time. This is how Xenotext was born.



Like the poem encoded in the bacteria itself, the Xenotext is in two parts. The first volume, published this fall in Coach House Books, is described by the poet as "a kind of movie trailer" for what appears in the second volume, which will detail the results of the ongoing experiment. "The real xenotext poems, the data, all this crazy sci-fi stuff - all this will appear in the second book."



In the spirit of the thinkers of the past, Boeck conceived an exercise that explores the aesthetic potential of genetics in the modern environment, in order to make literal the famous aphorism of William S. Burroughs, who declared: "The word is now a virus." In this experiment, he proposed to consider some of the sociological implications of biotechnology, creating "Xenotext" - a beautiful, anomalous poem where "foreign words" could exist, like a harmless parasite, inside the cell of another life form.



Another scientist, Stuart Kaufman, agreed to provide Boeck with his laboratory in his spare time so that he could compose a sample of his "living poetry." Kaufman is a renowned theorist who argued that the complex but ordered structure of every living system arises spontaneously from the fundamental principles of self-organization, no less important than the laws of selective evolution. He was first educated in the humanities (with the intention of becoming a poet) and then pursued a career in the study of genetics. Thus, the paths of the two people crossed, and they decided to work together to immortalize their names.



“I propose to encode a short verse into a DNA sequence in order to implant it into a bacterium, after which I plan to document the course of this experiment for publication. I also plan to make corresponding works of art for the subsequent exhibition, ”Boeck shared his plans.




The result was the following.



The fluorescent protein conveyed one message:

the faery is rosyof glowin fatewe rely ...



And the complementary codons guiding its construction are the second, with a different meaning:

any style of lifeis primoh staymy lyre ...



«, , — « », . « », — . — , . «, », — , — . ».




The poem is short (so that the encoded genetic text can easily fit into the genome without affecting the function of the organism itself). The work ultimately deals with the relationship between language and genetics, doing it self-reflectively and introspectively. This conveys the beauty of both the poetic text and its biotic form.



However, E. coli did not particularly satisfy the requirements for the immortality of the work, which the poet so wanted to achieve for his works. Moreover, the previously mentioned Pak Chung-Wong turned out to be much more insane. For his experiments, he used a very interesting bacterium - Deinococcus radiodurans.



Deinococcus radiodurans





Deinococcus radiodurans is an extremophilic bacterium, one of the most radiation-resistant organisms. It can survive cold, dehydration, vacuum and acidity, which is why it is known as polyestremophile and is listed in the Guinness Book of World Records as the most resistant bacterium in the world.



A specific expansion of some protein families was observed in the analysis of several bacterial genomes. In many cases, there seems to be some connection between the protein families and the habitat of bacteria. D. radiodurans has a number of families that are significantly expanded in relation to other bacteria.



D. radiodurans can withstand a dose of up to 10,000 grays, despite the fact that a person is only able to withstand 5 grays.



 Presumably, high resistance to the action of ionizing radiation arose as a consequence of the emergence of resistance to drying, since the mechanisms of DNA damage, and, consequently, resistance to radiation and drying are similar, besides, D. radiodurans synthesizes the so-called. LEA proteins that prevent protein aggregation during drying.



The choice becomes generally clear - this bacterium is almost impossible to kill, it can survive in a nuclear reactor, it perfectly tolerates heat, drought, cold and radiation. Therefore, if something is written inside a given bacterium, then it is quite possible that it will persist for millions of years or even outlive humanity. Moreover, it will multiply on an incredible scale.



The value of the experiment



The Xenotext experiment seeks to “infect” the language of genetics with the poetic vectors of its own discourse, doing this in order to expand poetry itself beyond the formal boundaries of the book. Boeck foresaw that as poetry adapts to the millennial state of such innovative technology, a poem may soon resemble a strange genre of science fiction, and a poet may become a kind of technician working in a linguistic laboratory. The poet hopes that the project will really spark controversy about the future of science and poetics.



“We foresee that if science can improve the process of implanting lengthy textual information into the embryo, then we can not only provide a secure method of transmitting secret documents, but also watermark cells to track the movement of microbial diseases or plant products. We believe that with such rapid technological development, the books of the future may no longer take the form of codes, scrolls or tablets, but instead they can be integrated into the very lives of their readers. "


The project highlights the extent to which modern social environments now take for granted that the discursive structures of epidemiology (as seen, for example, in terms such as viral marketing or viral computing) can be applied to conveying ideas throughout our culture.



If the poet plays the role of "host" for the "germ" of the word, then he may have to invent a more innovative vocabulary to describe this "epidemic" called language. Such a poem could demonstrate that with the help of nanoscopic biological emissaries, we could begin to transmit messages across interstellar distances or even more epochal intervals, so that, unlike any other cultural artifact created so far (with the possible exception of probes- pioneers or Voyagers), such a poem, stored in the genome of a bacterium, could presumably outlive Earth civilization itself, preserved as a secret message in a bottle accidentally thrown into a giant ocean, thereby perpetuating us.







UPD: corrected the title of the article so as not to mislead the followers of the genetic programming method.



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