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July 31, 2016

“That which I cannot build, I cannot understand”, Callie Clayton, BFA TX ’17

by Callie Clayton

In my last blog post I proposed that the “involvement of art, interactive-critical thinking and processing seem[s] a key interpretive element for larger topics of access, understanding and analyzing the purpose and effect of genetic engineering experiments.

After two additional weeks of reflection, observation and visual protocol interpretation drafts, I don’t believe that the “involvement of artinteractive-critical thinking and processing just seems a key interpretive element-

I avidly believe it is.

Up until two weeks ago, high school students that are taking part in the Genspace iGEM team had been coming to the lab to do serial dilution tests (test the survivability of e.coli after different time increments of dehydration followed by resuspension and plating onto agar- essentially, rehydrating e.coli samples to see how well they grow after different amounts of time being dehydrated as a basis of comparison to be executed with tardigrades-testing this water dwelling, eight legged micro animal’s ability to survive under dehydration conditions due to certain genes. Identifying and isolating these genes for potential use in the production of vaccines- allowing vaccines to retain effectiveness in the presence of heat when traveling to high temperature countries lacking access to certain vaccines is an ultimate goal of this project). They have also been isolating tardigrades (essentially extracting them from the water and moss they live in) and considering utilization of the CRISPR technique with the tardigrades. Twice a week and beginning two weeks ago, everyday, the high school students come to work on this project during which I participate and observe. Participate to understand protocol processesteaching methods + mediums for teaching, how students are learning and perhaps integrate another viewpoint- ex: commenting on changes in transparency of agar interacting with bacterial colony growth which results in light (when the petri dish is held up to be seen more clearly) highlighting certain “focal” points of this circular, 9 ” radial composition.

Common responses to these comments I make include but are not limited to: smiles of acknowledgement for the comment (I find these a bit funny and endearing), comments like “oh yeah! cool!” and “huhs” followed by what I have hoped to be looks of pondering, pondering alternate methods of viewing physical aspects of results/protocol steps.

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I muse about ideas and reactions to my visual interpretations within the lab context of collecting quantitative data for a “what does this mean and how will it have subsequent effects in the minute steps that add up to addressing a broader exploration/topic” versus a “what is this now and how can it be understood outside its current context” mindset.

How can alternate forms of interpretation such as poetry, process and visual similarities with patterns in literature, bee flight paths, people’s tracked habits, etc. patterns allow one step in an experiment, one petri dish, be appreciated and understood outside of the exclusively quantitative? However, that being said, one could argue the opposite- that all patterns are only able to become recognized as patterns due to their calculable, repetitive nature which allows us to quantify the image, action, anything; thus patterns fundamentally are the summarization of quantification? and can identified repetition ever be completely fixed? A habit, predicted flight behavior of bees, predicted and actual growth rate (number of colonies predicted for growth) and cell behavior with the uptake of certain plasmids, etc. exist as predictable as a pattern due to quantification but within a statistical range. I’ve come to better understand and believe in the idea of maximum 99.99% accuracy. Results and protocols in the lab are treated meticulously and done in repetition in order to set up conditions for accuracy however innumerable factors such as the nature of the human hand confirming human error, changes in environmental factors and the constant changing responses of living organisms means that prediction maintains variability, quantification exists within a range of error thus meaning pattern (summarized quantification) must be expressed through a range in order to be represented/explored/interpreted “accurately.” How do we interpret range in this context? I think of it as integrated multiplicity of interpretations. Multiple translations outside of numbers and observational text capitalizing on the 0.01% bias. So let me rephrase: How can considerations of quantification (pattern) be expanded to regularly necessitate interpretations besides numbers and observational text? In order to be “regular and intelligible form or sequence” as described by one definition in Oxford Dictionary, a pattern must undergo multiple forms of translation to be understood. Translation, interpretation and the infinite concept of languages, my friends.

During breaks in setting up experiments- waiting for new agar plates to cool and set, solutions to dehydrate, etc. I’ve asked a number of high school students about how they understand and interpret content taught in the lab- tardigrade anatomy, CRISPR basics, 3A Assembly protocols, etc and what “type” of learners they perceive themselves to be. One student noted the importance of color in cognitively differentiating content within written and drawn information. “Writing becomes a blob of lines and color that mixes together” in an undefined way in that student’s opinion. Intentional color and alternating use of visual and written content she agreed may help her better interpret what is being taught. Upon my suggestion of “icon” visuals to piece together protocols with, in conversation with a small group of students, one student acknowledged that while icons could potentially simplify protocol building and interpretation, icons = another language such as hieroglyphics which adds an additional step of time and translation. Additionally, protocols are different lab to lab (similar to cooking- similar or same end result, minute differences in protocol peppered throughout) – meaning standardization is difficult. Work initiated and being done by the Synthetic Biology Open Language, a project and initiative funded by the NSF, federal agencies and other sponsors, started a readable visual simplification of genetic parts, devices and systems. While the symbols facilitate interpretation of certain genetic parts well, they don’t address the next step of ‘protocol’ and piecing a protocol together. (below from http://sbolstandard.org/visual/)

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I had a great talk with one of the cofounders of the lab around the evolution of interpretation and languages in synthetic biology. Essentially it’s all about the development of “languages” he said (as I have come to understand myself as well). In order to expand rate and quantity of not only synthetic biology lab work, but also any lab or “hand-crafted” work as he said, languages for facilitating this work must be expanded upon. With hand manipulation of a majority of elements in an experiment comes human error, problematic experiments, confusion on what went wrong and decreased rate of results. In order to increase accuracy and efficiency, attempts through standardization have resulted in the recent development of many programmed operating languages developing to be read and carried out by a computer. The day when a protocol can be electronically sent from one computer to another to then be carried out by that computer seems to be approaching. This development of automation points to potential increases in productivity, thus allowing not only for expansion of biotech companies and more engagement in the DIYBio realm due to decreased necessary time investment, but at a fundamental scale- this allows people to spend more time ideating, conceptualizing than carrying out repetitive protocol steps in the lab. I find these developments of programmed languages for synthetic biology exciting however potentially limiting? Will understanding of actions being carried out from a protocol by the computer and the meaning / effect of those actions be hindered by the ease of technology’s commanding role? And how does this type of development affect the public without extensive understanding of science least synthetic biology, their process of learning in the DIYBio, Synthetic Biology communities? Could these communities become perhaps commercialized in unwise ways because the language containing the knowledge about what’s happening to those cells is encrypted in a code that makes executing protocols concerningly easy (touch of a button). With generally ok national public engagement / understanding in the sciences, does this engage or disengage people? I feel the simultaneous development of visual languages is imperative to address educational aspects of the Synthetic Biology community- facilitating understanding while efficiency is increased.

While at Genspace, I’ve come to recognize difficulties it and other community bio-labs face as nonprofits- similar to familiar challenges for all nonprofits. A wonderful yet potentially difficult aspect of a space in which everyone interested in taking a class and becoming involved in the community is welcome, is that unsurprisingly multitudes of collaborations, projects and ideas come out of this space each year. However, as is such with “personal projects,”and funding challenges at times, the completion and documentation of ideas/projects sometimes lacks. A really exciting project started by Genspace’s 2014 iGEM team is Open Lab Blueprint, a site for aiding the creation of community bio-labs, including a proposal for a lab protocol platform. While started, it was never completed due momentum slowing after the competition deadline. I’m excited to be talking with a designer next week about the platform called “Bioglyphics” and plans for its future development.

This week’s title “That which I cannot build, I cannot understand” was heard in the lab and is a take off of Nobel Prize winning physicist Richard Feynman’s quote: “What I cannot create, I cannot understand.”More insight on this quote to come in the next post.

DNA Isolation Draft

Plans for upcoming week:

Continue protocol drawings and equipment use standards to make a booklet for beginners in community biolab classes such as the beginner biotech class at Genspace.

Write interpretations of lab protocols- free verse poetry.

Consider questions, prompts, topics to be considered as alternate methods of interpretation and integrate them in booklet.

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