[-empyre-] Duration: Thanks to Week 3 Guests and Heading into Week 4

Sat Dec 1 09:20:47 AEDT 2018

Thank you for the introduction Tim, and thank you Josh for sharing our
conversation with the group.

One of my favourite landmarks is The Sagan Planet Walk. Stone markers for
the sun and each of the 8 (9!) planets mark a route from the Ithaca Commons
to the Science Center. The markers span less than a mile, proportionally
representing 3.67 billion miles of our cosmos, with a final plaque inviting
the walker to visit the final piece in this astronautical microcosm: The
Alpha Centauri Obelisk, our closest star system, standing 4,740 miles from
our starting location at the Imiloa Astronomy Center of Hawai‘i. Both the
walk itself and the reveal of the emptiness beyond Pluto speak to me of
scientific knowledge as lived experience.

I am a computer scientist by training, turned geneticist in my pursuit of
counterintuitive problems to engage. The gigantic impact of minute
variations in the sequence that defines us is such a problem. Genetic
testing has become affordable to the casual consumer granting us
information on our differences compared to a "reference" human. The subject
of genetic variation is slowly creeping into our living rooms, newspapers,
and most recently for me - Hulu advertisements. We are now able to exchange
seemingly exact information about our ancestry and discuss with our doctors
whether a test showing Alzheimers Disease biding its time is to be trusted.
These Promethean technologies define our genetic information in terms of
rates, differences, and consequence: a warped misquotation of the
underlying stillness of the human archive. Our tests are themselves
designed to only focus on variation - 23andme's SNP Array technology gives
us information about the state of our sequence at key well-studied
locations, sampling only 1 base of DNA in a span of hundreds of thousands.
Our consumption of DNA inevitably mirrors this assay. It is targeted,
quick, and ultimately reductive.

The ATGC exhibit on Cornell's McGraw Tower gives the viewer the opportunity
to live DNA variation as an experience, rather than a statistic. Slowly,
the piece supplies human genetics a unit at a time. While ultimately built
to make variation visible, it is the steady stream of intact genetic
sequence between the 24 individuals-as-lights that allows us to walk the
unisonal distance between the short harmonies that are genetic mutations.
When we first lit the tower, we counted the flashes with baited breath. I
had programmed the exhibit to begin 20 steps behind the first variation so
we could see one at the very beginning. I had examined the genetic region
to verify that we would have variations during the exhibit. I calculated
the rate at which we could expect variations, the number of variations per
hour, the number of people-as-lights that would be split between variant
and reference, ran the code at 100x the speed before and after the exhibit
to convince myself that the exhibit indeed exhibited change. Yet, when the
tower was lit,  no matter how long I stared from afar, I never saw my
second variation.

On Fri, Nov 30, 2018 at 7:50 AM Josh Strable <jjs369 at cornell.edu> wrote:

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> ----------empyre- soft-skinned space----------------------
>
> Thank you for the invitation and opportunity to contribute to -empyre-
> soft-skinned space, and Tim, for the generous introductions.
>
> We were motivated by the theme for the 2018 Cornell Council for the Arts
> Biennial — *Duration: Passage, Persistence, Survival* — to explore
> inarguably one of the most durable storage mediums on Earth:
> deoxyribonucleic acid, or DNA, the molecule that organizes and manages the
> blueprints of life, for life.
>
> DNA is comprised of 4 nucleotides (adenine [A], thymine [T], guanine [G]
> and cytosine [C]) that form polymer chains.  Individual, polymerized chains
> are able to form bonds with itself or with other complementary chains,
> i.e., to self-assemble molecularly, ultimately to form the double helical
> structure realized in the early 1950s  by R. Franklin, F. Crick and J.
> Watson.  This self-assembling, or hybridization, pairs A with T and G with
> C, forming the “inner rungs” of the double helix.  These expansive chains
> of DNA, constructed of this simple 4 letter alphabet, are arranged in
> vastly varied configurations — governed by a base-4 quaternary code,
> combinatorial uniqueness in DNA scales by 4^n, where *n* is the number of
> bases within each sequence.  For example, a sequence of 10 nucleotides
> would have 4^10 or greater than 1 million combinations of A/T/G/C.  The
> nuclear genome of a single human cell houses ~6.4 billion nucleotides
> divvied up among 23 pairs of linear DNA molecules called chromosomes.  The
> human body has ~10 trillion cells; within each cell resides nearly 1.8
> meters of DNA, which means each human has about 16 billion kilometers of
> DNA stored in them.  Furthermore, DNA is far from static (though it is
> negatively charged), as nucleotides in a genome are continually being
> inserted, deleted, rearranged and modified, which over evolutionary time
> allows *Persistence* and *Survival* via mutation.  To say the least, DNA
> is an inexhaustible, evolvable medium.
>
> As a medium of archive, DNA retains information about the genome for
> thousands to millions of years.  Ancient DNA recovered from ancient
> specimens offers sufficient preservation to be read in bacterial hosts, a
> true and elegant testament to its *Duration:*.  With current sequencing
> technologies and their reduced costs, the ability to interpret nearly any
> genome, modern or ancient, has become commonplace.  By interpreting the
> genome, by essentially digging through genetic archives, we gain knowledge
> about the deep past, migration, adaptation, ecosystems, disease, and we are
> provided templates for strategizing cures and adaptabilities to a changing
> climate.
>
> For the Biennial, our genome-inspired light installation, *ATGC*,
> depicted a nucleotide-by-nucleotide “walk” through genomic sequence of 24
> globally representative human populations.  Each nucleotide was represented
> by a different color of LED light (A, red; T, green; G, white; C, blue),
> and each LED light represented a different genome.  The lights blinked in
> syncopation until genomic variation in an individual genomic variant was
> encountered.  Nucleotide variation in a population resulted in a brief
> pause in syncopated sequence of blinking lights.  We had no control over
> when or if variation was detected in the genome; we simply wrote a code to
> decipher these genomes.  It was clear, however, by observing the
> installation, human populations are extremely similar at the genomic level,
> despite how appearance, expression, etc across individuals, cultures,
> populations may differ.  Might we then think of the genome as *Cagean*,
> in which heredity content is indeterminate and contingent upon chance?
>
> Josh Strable, Kate Greder, Yasir Ahmed-Braimah & Juan Felipe Beltrán
>
> On Tue, Nov 27, 2018 at 1:42 PM Timothy Conway Murray <tcm1 at cornell.edu>
> wrote:
> ----------empyre- soft-skinned space----------------------
>
> Josh Strable (US)
> Josh Strable is an NSF-NPGI Postdoctoral Fellow in the Plant Biology
> Section of the School of Integrative Plant Science at Cornell University.
> His research identifies and characterizes genes and genetic networks that
> underlie leaf and floral development in the grasses, as well as
> understanding the genetic basis of how environmental stress influences
> plant growth and development.  Josh earned his Ph.D. in Plant Biology from
> Iowa State University and holds a M.S. and B.S. in Biology from the
> University of Iowa.
>
> Kate Greder (US)
> Kate Greder is a PhD student in the Department of Fiber Science and
> Apparel Design, at Cornell University.  Her research focuses on
> spatialization in the fashion system and the subsequent
> onto-epistemological questions that emerge within design theory.  Prior to
> Cornell, she worked in art conservation at Iowa State University and she
> holds a Bachelor of Arts degree in Philosophy from the University of
> California at Santa Cruz.
>
>
> Yasir Ahmed-Braimah (US)
> Yasir Ahmed-Braimah is a postdoctoral research fellow in the Department of
> Molecular Biology and Genetics at Cornell. His research utilizes various
> approaches to understand classical evolutionary genetics problems, such as
> adaptation and speciation. Yasir earned his PhD in Biology from the
> University of Rochester, and holds an M.S. and B.S. in Biology from the
> University of Iowa.
>
>
> Juan Felipe Beltrán (US/Colombia)
> Juan Felipe Beltrán is a Colombian Ph.D. Student in Computational Biology
> at Cornell. Before coming to Cornell, Juan Felipe worked on Human-Computer
> Interaction and Musical Rhythm Analysis at NYU in Abu Dhabi, where he
> completed his Bachelor's in Computer Science. His research at Cornell
> focuses on the application of machine learning and similarity analysis to
> study genetic disease and the human microbiome.
>
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> http://empyre.library.cornell.edu
>
> _______________________________________________
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