BioInformaticsHack

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Part of the remote Chaos Experience - rC3 we will host a Workshop with Adam Zaretsky.

Read more and interact about rC3 and the Hackteria Global Network assembly here in the forum.

RandoGeneCode Workshop

VASTAL - The Vivoarts School for Transgenic Aesthetics Ltd. presents: a poetics based Tutorial for BLAST, a cornerstone bioinformatics tool at NCBI. BLAST is the Basic Local Alignment Search tool using poetry, drawing and homologies to interpret genetic code.

Description

This is a lab about Rolling Dice, Understanding Bioinformatics Databases, Poetry, DNA Code, Drawing, Anatomical Research, Chance and Genetic Mutation. Using a foldable or randoAccees 'DNA Icosahedron' we will make a Random DNA sequence and translate it into: a poem, a drawing of the poem, a documentation chance DNA sequence in a bioinformatics database, a drawing of the actual living being that has our DNA poem in it's genome, and a drawing of the parts of that being that contain our poem. You will understand Online DNA Databases like no one else after you take this lab. No previous biology knowledge is required. Just bring your ability to draw, play in platforms and write poetry!

But what if we are not all cloistered into Gaussian distributed hyperMicro ‘individuated’ target groups with Click Bait sexual partnerz, Click Bait Politicz and Click Bait Cradle to Grave Economies? What if the cistopia, dystopia of systopia already came with the brains and sinews of poetic misinterpretation? Then the libidinal economy of complete, Non-anonymous, privacy-less Kafkaesque pornography as the spread eagle interface of big data, is not eclipsing free will through Cancel Culture and platform-government-corporate surveillance. No, it is the return of the repressed software engineer’s psyches that has colluded around the dank memic fire of privatization.

Activities

More about drawing of images from the BLAST Results:

Do some research on one of the coded NCBI BLAST organisms and the links in the BLAST results.

Look for:

A – The organism that the BLAST gene is in (latin name, common name, unusual anatomy, interesting facts, financial worth, living conditions, behavior, food, reproductive style, etc.) Do some media grabbing of the organism i.e. screen grabs or image downloads of the organisms.

B – The part of the organism that the gene from our sequence effects, i.e. what this gene does where in the body and life of the Organism. Do some media grabbing of the anatomy affected by the gene, i.e. screen grabs or image downloads of the gene or anatomical effects of the gene on the body of the organism. Metabolic cartoons are accepted.

C – Optional: do some media grabbing of the actual scientists listed and the places they work, i.e. screen grabs of pages from their website, emails, image downloads of their labs, their faces, the research, the data, even text files from their published papers or websites.

D – Feel free to incorporate web research media grab assets into your drawings through collage. This can be done by printing web grabs or images and gluing them into your sketch books or actually sketching versions of them.

E - If this is confusing, remember that this is a Literature Review and Anthropology of Science Genre Science Fiction Research Project. The Bioinformatics and Cultural Research into poetic homologues is actually a Speculative Design Fiction Semiotics Survey treating Science as a Genre in the Anthropology of Literature. I hope that clears up any confusion.

DNA Dobbelsteen (pdf) https://waag.org/sites/waag/files/Publicaties/DNA_dice.pdf

Stages:

Words translated to DNA using Icosahedron Choose any of the triplets for each amino acid as they are redundant WE chose one triplet of the redundant triplets for each amino acid, i.e.

V for Valine can be GTT or GTC or GTA or GTG so you pick one.

sketch your poem

find your poem in the genome of an organism through BLAT, BLAST or FASTA (online bioinformatics search engine, the google of genomes) Draw your organism, the organ(s) affected, shape of the genetic byproduct and/or the scientist involved in the research. Compare your poem to a program that already exists in sequence data from biodiverse life. Understand the difference between synthetic biology, standard code subroutines and embedding programs in gene drives as having a rather different relation to data processing: involving meat bodies as metabolizing, somewhat cognizant and irritated by being the factory.

List your word or short haiku

the sequence in DNA that corresponds to your word A - Create a short haiku or poem

Start by assembling a Three to Five Word Nonsense Poem (with related sequence)

Choose 3-5 words already translated on our shared google doc to make an absurd poem.

For instance:

Macaroni Advertise Psychedelic Requirements


Write this into your lab notes.


B - Translate Poem to DNA Code

Write the words and the translation to sequence data that your poem forms by picking 4 to 7 words from the google doc:

For instance:


Macaroni Advertise Psychedelic Requirements


is


ATG GCC TGT GCA CGC CAA AAT ATT

GCT GAC GTA GAA AGG ACT ATT TCT GAG

CCA AGT TAT TGT CAT GAA CAG GAG TTA ATT TGT

CGT GAG CAA GTA ATT CGC GAA ATG GAG AAT ACC TCA


Write this into your lab notes.


Translate Poem to a Drawing

Draw your poem from the sequence as as a symbolic or descriptive drawing, i.e. illustrate your poem. i.e. draw a picture of: Macaroni Advertise Psychedelic Requirements (Your word choices here!) Yes, I am asking you to illustrate your poem as a creative drawing.


Draw this into your lab notes.


F===ind your Poem sequenced in an Online Bioinformatic Database===

After our introduction to BLAST, https://blast.ncbi.nlm.nih.gov/Blast.cgi , find a homology related to your poem inside the genome of any organism. A homology is a similar sequence to the one you enter.

Reminder:

BLAT works best for beginners: Click Genome Search All and Click All Results (no minimum matches) type in your squence without spaces ATGC only and if you are feeling lucky, press the Im Feeling Lucky Button.

https://genome.ucsc.edu/cgi-bin/hgBlat


BLAST = Basic Local Alignment Search Tool

BLAST finds regions of similarity between biological sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance.


Draw a version of the BLAT and or FASTA results including sketches of BLAST, Blat or FASTA Platform Interface.

Do you think it is strange that any poem you translate into DNA is already in the sequenced genome of a living organism? What does this mean in terms of evolution, literature or statistics?

Draw this into your lab notes.


Draw your Organism

Draw the Organism(s) where you found your poetic biological sequence region. You may not know the organism but you can do some Online Image Research on the organism(s) found from the homology search. I am asking for you to literally draw the results of a google image search or other online .jpg, .gif or .png that you find related to your organism.


Draw this into your lab notes.

Draw magnification of Anatomy Showing where the Gene Action is happening

Draw your Organism’s anatomical place where the gene has an effect on the body of the organism. Make Online Image Research on this place in the organism that the gene effects. Draw this place (i.e. liver of rat or nuclear membrane of mutant yeast). You may also duplicate any metabolic cartoon or even an obscure, unrelated image that pops up during your search. This is where your poem homology lives in the body of the organism.

Draw this into your lab notes

Research and Document Scientists and their contact information

Pretend you are a Detective. Write Names of Scientists and Institutions involved in Research on this gene. Start with Authors listed on publications related to the research on the sequence poem you derived randomly. From the Author’s names, you can find their institutions, email, phone number and any other information on scientific personalities/architecture/research related to the research. Some of these can include drawings of their online photos and even drawings of their labs or the buildings they work in.

More about drawing of images from the BLAT Results:

Do some research on one of the coded FASTA BLAT organisms and the links in the results. Don’t be afraid to screen grab link results and then click further in and/or use new vocabulary that you learn from your random walk through Bioinformatics Database culture.

More details are better:

A – The organism that the BLAT/FASTA gene is in (latin name, common name, unusual anatomy, interesting facts, financial worth, living conditions, behavior, food, reproductive style, etc.) Do some media grabbing of the organism i.e. screen grabs or image downloads of the organisms.

B – The part of the organism that the gene from our sequence effects, i.e. what this gene does where in the body and life of the Organism. Do some media grabbing of the anatomy affected by the gene, i.e. screen grabs or image downloads of the gene or anatomical effects of the gene on the body of the organism. Metabolic cartoons are accepted.

C – Optional: do some media grabbing of the actual scientists listed and the places they work, i.e. screen grabs of pages from their website, emails, image downloads of their labs, their faces, the research, the data, even text files from their published papers or websites.

D – Feel free to incorporate web research media grab assets into your drawings through collage. This can be done by printing web grabs or images and gluing them into your sketch books. Actually, sketching versions of them might be faster.

E - If this is confusing, remember that this is a Literature Review and Anthropology of Science Genre Science Fiction Research Project. The Bioinformatics and Cultural Research into poetic homologues is actually a Speculative Design Fiction Semiotics Survey treating Science as a Genre in the Anthropology of Literature. I hope that clears up any confusion.

Related info

About Adam Zaretzky

Adam headshot.jpg

Adam Zaretsky is a WetLab art practitioner mixing ecology, biotechnology, non-human relations, body performance and gastronomy. His art practice focuses on an array of legal, ethical, social and libidinal implications of biotechnological materials and methods with a focus on transgenic humans. Zaretsky is a former researcher at the MIT department of biology and he also runs a public life arts school: VASTAL (The Vivoarts School for Transgenic Aesthetics Ltd.)