Genomics Salon at Praxis 2018

Last month, several Genomics Salon organizers attended the University of Washington Praxis conference, an annual meeting hosted by the English department. The theme of this year’s event was “communicating across disciplines”, which seemed like a great opportunity for us to expand our horizons and learn how other fields approach discussion on complex topics. We registered to present a poster on our progress in building the Genomics Salon and each attended several presentations on topics that seemed relevant to the Salon or to our personal work at UW. Below are some reflections on the event.

Katherine Xue

Preparing for Praxis gave me the opportunity to think back to previous salon discussions and how they’ve changed over time. At the first-ever salon discussion on public understanding of science in June 2016, co-leader Molly Gasperini and I each gave five-minute “position statements” and then opened the floor to general discussion. Since then, salon leaders have explored many ways to incorporate case studies, graphs, figures, statistics, video clips, writing activities, and more as objects of discussion. Over time, it’s also become more common for us to break into small discussion groups so that more people have opportunities to speak. It was eye-opening for me to look through our handout archive and identify these diverse strategies for cultivating an open, inclusive discussion, and I’ll definitely be returning to these strategies in the future!

Eliah Overby

Designing our poster for Praxis gave me a chance to reflect on the success the Genomics Salon has achieved since it was founded 1.5 years ago. What stood out to me was the strong, consistent participation we’ve seen from departments beyond Genome Sciences and the variety of different departments we’ve been able to attract. We’ve seen participation from 40 departments, including STEM fields like Public Health Genetics, Biostatistics, and Astrobiology, and other fields of study, such as Philosophy, Law, and Communications.  Their participation has brought a different perspective to many of our salons and makes me optimistic that we are succeeding in our goal to create a cross-disciplinary, diverse space for intellectual discussion.

Hannah Gelman

Attending the Praxis conference was an opportunity to participate in the broader conversation taking place on campus about how to construct courses, assignments, and discussions consistent with the values of diversity, accessibility, and openness espoused so frequently across campus. As we think about the role of science in society, and how to use science in service of society, the presentations at Praxis brought home to me the importance and difficulty of developing authentic, two-way collaborations between scientists and the communities they seek to serve.

I attended a session called “Case studies of Oceanic Praxis”, led by a curator at the Burke Museum and 3 student assistants of Pacific Islander heritage who have worked together to research and build collective knowledge around the artifacts in the Burke’s Oceanic and Asian Cultures collection. The involvement of students and their communities in the Burke’s research efforts is truly collaborative – not only focusing on new insights into the meaning behind the objects in the Burke’s collection, but also on creating opportunities for communities to drive research directions and applications to be responsive to community needs.

I think it is so hard for scientists to develop meaningful collaborations like this one. In the biomedical sciences, we so often fall into a mindset where we are developing or providing something for the benefit of community partners, and the contributions of the community are often limited to supporting roles (i.e. providing data, guidance, outreach). As we host more discussions on science communication, or on the interaction of the scientific community with marginalized groups, I hope that we can think more expansively about the character of those collaborations, and how deeper collaborations could benefit both scientists and the communities they work with.

Bryce Taylor

The thing that stuck out to me most at Praxis was the range of teaching practices being used by educators in the English Department to develop unique, impactful courses. Through my sessions I heard great anecdotes about stretch courses (one primary assignment over multiple quarters), service learning (assignments outside the classroom to encourage practice of a topic), and ways to get students to teach themselves in class.

It seems like many of the instructors who presented viewed their classes as little experiments into pedagogy. At the time I was totally drawn in by the specific stories these researchers shared, but since then I can’t stop thinking about the mentality in general. In the Biology world, there are a generally a few “right” ways to teach a course. When I’ve taught undergrads I’ve invariably followed one of these templates that match courses I took in college. Going forward, I’d like to incorporate some ideas I got from Praxis into courses I teach and spend more time checking out what professors in other departments are up to in the classroom.


Our Praxis poster! Pictured left to right: Bryce Taylor, Jolie Carlisle, Eliah Overby, Hannah Gelman.


Technology and SciFi societies

Hello all! I’m Bryce Taylor, a postdoc in Genome Sciences. On October 5th, Jolie Carlisle, a graduate student in Genome Sciences, and I led a Salon on Science Fiction at the Simpson Center. It was our second time leading a discussion on the topic, and this time our focus was on utopian and dystopian views of how emerging technologies may impact future societies. We were excited to tackle this topic as we’re huge fans of the genre, and appreciate how science fiction pieces can act as thought experiments for ways human nature will direct use of new tools.

Group discussion on portrayals of SciFi societies

We first discussed the connection between science and society, and whether technology can change human nature. The room generally felt that while technology can impact the human experience by giving us access to new opportunities, it does not change human nature. One participant brought up the example of literature from past eras that show living conditions that are totally foreign to us, and yet are navigated by people with very familiar emotional responses to relatable events. SciFi provides a similar lens where we can imagine how a future version of ourselves with the same basic motivations would act in response to some technology.

Part of this time was spent on equity in disseminating the benefits of technological progress. My favorite moment of the session came in a comment about the song “The Space Program” by A Tribe Called Quest, which uses travel to a colony on Mars as a metaphor for how minorities in the US are frequently not given immediate access to the benefits of technological advancement. It’s a piece I had not thought of specifically as science fiction, but it fit the discussion well and is a nice summary of a critical concern among Salon participants that day. As a music fan, I sense that more and more artists are bringing in elements of science fiction to their work, which I imagine is inspired by the increasing role of scifi in pop culture generally, perhaps combined with more than a little David Bowie nostalgia. For further reference, check out St. Vincent (e.g. Digital Witness; about screen addiction), Public Service Broadcasting (e.g. Gagarin; a tribute to the first cosmonaut), and ANOHNI (e.g. Watch Me; a song about Stockholm syndrome in a surveillance state) for catchy examples (warning: some of the examples include explicit language).

Small group discussions on technological themes

We next broke into smaller groups to discuss two general themes of technological application: surveillance and genetic engineering. The surveillance discussion focused on the novels 1984 and Brave New World, which are explorations of a fascist and communist dystopian future, respectively. This discussion quickly moved towards how modern media dissemination through targeted outlets creates a series of thought silos where ideas and interpretation spread rapidly within but not between ideological clusters. Attendees also noted how contemporary surveillance, such as through Facebook or smartphones, is tolerated or maybe even welcomed in exchange for the convenience it brings, e.g., more accurate anticipation of user wants and needs. This discussion felt urgent, as the topic is rapidly changing our current experience.

The genetic engineering discussion focused on how this technology will impact diversity. I came into the discussion expecting to talk about genetic diversity– depending on approaches taken, using genetic engineering to “correct” disease alleles may also remove genetic variants associated with particular ethnic backgrounds that may in turn impact phenotypic diversity. The group, however, was more focused on diversity of experiences. One member brought up the deaf community as an example. Some members of this community are concerned about cochlear implants, which are given at birth and remove an infants’ agency in deciding their life experience. Genetic engineering could conceivably extend this by removing traits from all future generations. This point really stuck with me after the Salon and will surely prompt a long reading list on the topic.

Related topics in the news

Since our Salon took place, I’ve come across two interesting news stories that related to our discussion group topics. The first is a product made by Google called “Clips“. It’s an internet-connected camera that continuously watches for movement and uses an algorithm to “decide” when to capture photos or video for future consumption by the user. It’s billed as a hands-free solution for parents or pet owners who want to capture fun, spontaneous moments. It was quickly called out as a potential surveillance threat. Google clearly considered this in their design by making the camera “audio free”, which tech enthusiasts speculated was a way to prevent attempts by law enforcement to acquire recordings from a crime suspect’s house.

There has additionally been an announcement of the first known human to attempt gene editing with CRISPR on themselves. This individual claims they can make targeted edits in their arm to promote muscle growth. Based on my limited understanding of their approach, I see it as highly unlikely to yield impressive biceps. However, this same person is selling a home CRISPR kit that will likely receive a boost in exposure from the coverage his antics have received. DIY genetic engineering is currently a regulatory grey area that desperately needs more attention going forward. The announcement is additionally a potential point at which we could plant a flag to demarcate the “human genetic engineering era”, if such a future comes to be.

Interactive metaphors

At the September 14th Salon, attendees delved into the topic of Metaphor in Science, guided by co-moderators Leah Ceccarelli, a Professor in Communication, and myself, a PhD student in Public Health Genetics. As the first Genomics Salon held in the Simpson Center for the Humanities, it was a successful gathering of varied disciplinary backgrounds and experiences — a metaphorical bringing together of upper, lower, and outside campus.

As a rhetorical scholar, Leah studies public discourse about science, which keeps bringing her back to metaphor. She gave Salon attendees a taste of her 2013 book “On the Frontier of Science: An American Rhetoric of Exploration and Exploitation,” which examines the promises and pitfalls of the frontier metaphor of science. For example, sequencing the human genome in the 1990’s and early 2000’s was cast as a “mapping” expedition, akin to fulfilling the manifest destiny of the American frontier. This metaphor portrayed the Human Genome Project as individualistic, male, and competitive, which ironically was in stark contrast to the actuality of the massive international collaboration required to complete it.

My foray into studying metaphor was more recent, in the form of my Master’s thesis in Public Health Genetics in 2013-4. Intrigued by the dominant metaphors about the genome such as “blueprint,” “map,” and “recipe,” I wondered if increasing access to personal genetic information (e.g., via consumer genomic testing or clinical sequencing) would lead to new metaphorical framings.


Metaphor of “the genome is a map.” Credit: The Economist

Many people think of metaphors as conscious – even artistic – linguistic choices that people make. This isn’t necessarily wrong, and indeed reflects the conception of metaphor traced back to Aristotle, who wrote that in the rhetorical arts, “the greatest thing by far is to have a command of metaphor.” The modern, cognitive perspective on metaphor, however, recognizes it as intrinsic to not only how we speak, but how we think, feel, and act. What this means in practice for metaphor scholars is that metaphors are not handed to you on a plate. Rather, you have to study texts, identify fragments of metaphorical language, and from there work backwards to construct or articulate the underlying metaphorical concept.

Metaphors interact: vehicle and tenor

Leah demonstrated this practice to Salon attendees with a classic example from metaphor scholars Lakoff and Johnson, the metaphor “argument is war.” We rarely say that exact phrase out loud, but rather draw upon it when we say things like “taking sides,” “hold your ground,” or “defend a position” in an argument. Each part of the metaphor, “argument” and “war,” have commonplaces, or things you link with them.  The associated commonplaces are those that arise when you put the two ideas together. The metaphorical vehicle, “war,” highlights some aspects of its subject or tenor, “argument” (e.g., hostility and rivalry)  while simultaneously deflecting others (e.g., reason and deliberation). It’s the interaction of these two parts of the metaphor, the tenor and vehicle, that do the metaphorical heavy-lifting. However, as is clear from this example, the interaction of vehicle with tenor and the subsequent enhancement or erosion of aspects of the tenor can be problematic.

Metaphors interact: metaphor and audience

Another layer of interaction that occurs with metaphor is that of metaphor and audience. Specially, people bring their unique background knowledge and assumptions to a metaphor, which will inevitably shape how they view or interpret it. For example, at the Salon we had attendees work through example metaphors from my thesis project, as an exercise in identifying and articulating metaphorical concepts as “X is Y.” The text came from interviews and focus groups conducted in a research study trying to understand people’s willingness to participate in genomic research and their interest in receiving information back about their genomes. (Note these were spontaneous uses of metaphorical language.) One participant said that she would be interested to receive information back about her genome: “…it would be nice to know, I guess I’m thinking of credit score like, here’s your credit score and here’s how you can improve it.”

Salon attendees had strong and conflicting reactions to this metaphor. Some participants thought it was a dangerous oversimplification of genetic information, that it could be boiled down to one number of overall risk. Others thought it was useful in that it points out the evolving nature of genetic information – that the meaning might be unknown today but  later clarified or updated through further research. Others viewed the metaphor positively because it suggests that, like credit scores, genetic information can seem mysterious and impenetrable, something people would need a lot of guidance to unpack. The conversation around this metaphor made one thing clear: the associated commonplaces of “Genetic information is a credit score” manifested differently for different people, perhaps based on their preexisting ideas about genetics and/or credit scores.

Metaphors in practice

Once you start looking for metaphorical language, you see and hear it everywhere. What is not always so obvious, however, is the underlying metaphorical concept, or the “X is Y” statement. I’m interested to hear how you hear and see metaphorical language in your daily work or research. Please drop me a line here and tell me your metaphors! Myself and co-Salon organizer Jolie Carlisle may follow-up with you for a subsequent article that dives deeper into the metaphors we work with and experience on a daily basis.


Science, art, and proofs without words

One of my favorite examples of science and art is easy to mistake for a piece of floor tile:


Credit: Wikimedia Commons, CC-BY

But I don’t just like it for decoration. The regular pattern of colored squares is meant to represent a mathematical relationship. Specifically, it shows the odd numbers theorem, which states that the sum of consecutive odd numbers, starting from 1, is a perfect square.

To see it, start from the black square on the bottom left, and move up and out. Count how many small squares make up the larger squares made by adding each new row. Like this:


On the left, the innermost square has just 1 square.

1 = 1*1

Adding the next ring, of 3 white squares, gives us a larger square with area 4.

1 + 3 = 4 = 2*2

The next ring of black squares adds 5 to this total.

1 + 3 + 5 = 9 = 3*3

And so on. Each ring of black or white squares is an odd number. Adding them all up, starting from 1, gives you a square. There you have it: the odd numbers theorem.

This picture is an example of what’s called a proof without words. The idea is that a single, well-designed image can demonstrate a mathematical truth. It’s like the logical equivalent of a picture being worth a thousand words.

I find it beautiful and compelling that images can say so much about something like math. Of course, math and beauty have been interlinked since the Greeks. Simple mathematical relationships can be found (though sometimes spuriously) in the contours of pasta and the spirals of seashells. The idea of a proof without words points to something important: mathematicians and scientists are intensely visual. Our work is imbued with a sense of aesthetics. A good proof or experiment is not just rigorous, it is elegant, and beautiful.

This thinking was part of the motivation behind the discussion that fellow grad student Sam Entwisle and I led on August 31, on the relationship between science and art. Science and art are often thought of as being diametrically opposed. Some people even relegate them to opposite hemispheres of the brain–logical operations on the left, creative thinking on the right. But science and art have historically informed and inspired each other. We wanted to explore this relationship in the past and present.

We hoped to invite artists to our discussion and to look at actual pieces of art. We were lucky to have local artists and illustrators Tami Tolpa, Kate Thompson, and Susan Zoccola to help us prepare for and guide the discussion. Together, we curated a collection of images showing some of the many ways that science and art can interact.

Our full collection and the descriptions are online, but here are some highlights. I hope these images leave you feeling like I did–curious, thoughtful, and inspired.

Some images like Audubon’s illustrations or images from the Hubble Space Telescope draw directly from nature.

Illustrations can pave the ways for new ways of seeing. Andreas Vesalius’s detailed, realistic drawings in De humani corporis fabrica libri septem revolutionized the study of anatomy.


Credit: Andreas Vesalius, De humani corporis fabrica libri septem, via Wikimedia Commons

Illustrations and infographics today play a similar role in science education and communicaton. Here’s one early infographic by Edward Minard that summarizes the troop losses of Napoleon’s campaign of 1812 (it’s been lauded by modern information scientists as well).


Credit: Edward Minard, via Wikimedia Commons


Similarly, comics combine narratives and images to explore scientific concepts in creative and engaging ways.


Credit: Maki Naro, The Antibody

Under the mantle of BioArt, some artists are using biological materials directly within their works. Some of these materials may be familiar to scientists. Scientists since Alexander Fleming have used microbes to “paint” images in petri dishes, and the American Society for Microbiology even holds an annual Agar Art contest to showcase these microbial masterpieces.


Credit: Jasmine Temple, Sunset at the End

But some BioArt uses biological materials to raise questions about the role of biotechnology in society. In Paul Vanouse’s work The America Project, visitors to an installation donate their spit, and the artist pools the spit, extracts DNA, and amplifies certain regions using PCR to form familiar images of power, like a crown or a flag.


Credit: Paul Vanouse, The America Project

These pieces of art can have powerful effects. Here’s one image that, in my group at least, provoked perhaps the most visceral reactions (and subsequent discussion).


Credit: Patricia Piccinini, The Naturalist

I’ll end with one of my favorites, an anatomical cross-section “quilled” (rolled together) using Japanese mulberry paper and the gilded edges of old books.


Credit: Lisa Nilsson, Angelico



Recap: Lightning Talks at SoundBio

IMG_20170804_190530Last Friday, five of our salon contributors gave public talks at the SoundBio lab, a nonprofit DIY biology lab in Seattle. These talks were the result of the Talk Stream from this Spring’s Salon SciComm workshop series. Our group worked together to draft and practice a series of presentations for a general audience. Each talk was 5-10 minutes with minimal slides, and were based on topics we each thought would be novel and exciting to science-interested people.

Bryce Taylor, Postdoctoral Fellow

Bryce Taylor

My talk focused on ways model organism research can tell us about ourselves. I focused on how efforts to understand the function of genes in yeast and other model organisms gave us a head start in interpreting the human genome. I then honed in on an example where different versions of human genes were engineered into yeast. This allowed scientists to determine whether certain individuals carried versions with a reduced function that could predispose them to diseases like cancer.

Hannah Gelman, Postdoctoral Fellow

Hannah Gelman

My talk (entitled Driven by Data: A scientist reads the news) was about how anyone can use scientific reasoning to evaluate claims about science made in the popular media. I started by describing the 2011 neutrino speed controversy, in which physicists who observed neutrinos moving faster than the speed of light enlisted the help of the scientific community, including their competitors, to evaluate the accuracy of their findings. In the end, the physics-defying measurement was due to a small error which was found in the collaborative investigation. The reasoning process that the scientists went through when deciding whether to accept the neutrino measurement can be applied by anyone, to any scientific claim (and can be adapted to evaluate lots of other kinds of claims).

1) Is the claim consistent with our expectations? If not, why?
2) What did the study do? Are there any problems with this?
3) Does the study support the claim? If so, are we ready to change our expectations?
With audience participation, we examined a health claim popularized by the New York Times: the “Scientific 7 Minute Workout”. By examining the article text and a few additional publicly accessible resources we were able to conclude that while the study referenced by the New York Times might have been sound, the claims made by the paper were not supported by the study or by other information provided.  We ended by discussing the responsibilities of scientists, journalists, and readers in ensuring that information is conveyed accurately.

Sarah Nelson, Research Scientist

Sarah Nelson
My talk took a critical look at the growing world of the “quantified self:” the way people are increasingly accessing and using personal data to influence their thoughts and actions. I began with an introspective personal anecdote about how I’ve started tracking my daily bike commutes with a smartphone app. Despite years of intrinsically enjoying this part of my routine, I am now drawn to checking my “stats.” I then introduced consumer genomic testing as another type of quantified self activity. I described how customers can access reams of “raw” or uninterpreted genetic data through these tests, which can then be taken to various third-party interpretation tools online. I showed why these interpretations should be taken with a huge grain of salt, despite how fun and interesting they may be. Quantified self technologies will likely continue to grow in the future, so I encouraged the audience to take note of when and why they are engaging in such practices and to ask what other knowledge they might be leaving out.
Seungsoo Kim, PhD Candidate
Seungsoo Kim
My talk explained what a genome is, how it works, and why we should care. We can understand the genome at multiple levels, from being the basis of heredity and why you look like your parents, to being present in each of your many different cells and telling those cells how to do their many different “jobs,” and even to how the physical genome is packaged in three-dimensional space. I used the analogy of a cookbook, where you get some recipes from your mother and others from your father. The recipes in a cookbook represent genes, which are not used by all cells – each cell type has a favorite subset, which it “bookmarks” using epigenetic modifications. Finally, I described a few ways in which the genome’s functions can go wrong in disease, which is one reason we should continue to research how the genome works.


Elizabeth Morton, Postdoctoral Fellow
My talk was on the development and use of green fluorescent protein (GFP) as an imaging technology.  I described how this protein was isolated from a jellyfish native to the Pacific Northwest and explained how GFP finally allowed us to track molecules in living cells, an advancement that eventually led to a Nobel Prize.  I explained a little about the scientists that were involved in the discovery of GFP and their various contributions.  I wrapped up with showing the array of different colors of fluorescent proteins available now, with some brief examples of particularly medically-relevant applications of GFP today.