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
beth-morton.jpg
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.

Recap: citizen science

See this week’s handout here.

This week’s genomics salon, led by Orlando de Lange (blog, other blog, and  twitter), focused on citizen science. We opened with two main questions: what is citizen science, and why do citizen science? Orlando gave us a few working definitions to get started: citizen science is science that includes amateurs, and it encompasses public participation projects, community labs, and crowdfunding. From the professional scientists’ points of view, citizen science may help in data collection and analysis, fundraising, and education.

The “science” in citizen science
Early on, someone raised the issue of agency, or intentionality, a theme that stayed with us through the rest of the discussion. Many citizen science projects like Galaxy Zoo or SETI@home rely on very intentional public gathering or analysis of data. Others like Foldit or eBird incorporate a game-like, competitive aspect, and still others like TestMyBrain bring in citizen scientists themselves as subjects of research. In projects like Games With Purpose, games that serve primarily as entertainment can also be scientifically useful. These projects contrast dramatically with models in the social sciences – for instance, of community-driven forestry, in which a nonspecialist community is actively involved in ecological management. So how important is it that citizen scientists be actively and consciously engaged in research, and how much do current citizen-science projects fulfill these goals?

Testimonials
We got to hear from two actual practitioners of citizen science. Brian Koepnick, a graduate student in the Baker lab, talked about his experiences with Foldit, in which amateurs try to solve protein structures in a gamified environment. He told us about how Foldit players, who typically don’t have biochemistry backgrounds, could often come up with unusual and creative solutions to problems in protein design. Returning to the theme of individuality, we discussed how Foldit players are involved in hypothesis generation (that is, proposing different protein structures), requiring a degree of creativity not always seen in public participation projects.
Max Showalter, a graduate student in oceanology, told us about HiveBio, a local community biology lab. He gave the example of Citizen Salmon, a project in which amateur biologists test samples of salmon from local grocery stores and fish markets to find out where the fish originated. He also commented that community labs can be very different depending on their communities. Some are run mainly by professional scientists who enjoy working on projects in their spare time, and others may feature closer collaborations between scientists and artists. HiveBio runs mainly through classes and a membership model, providing basic equipment and training for community members of all ages to get involved with scientific projects. We discussed how the HiveBio model compares to outreach, and the degree to which community labs tend to play roles in research and education.

Citizen science and the future
We ended by discussing how citizen science might change traditional science. In fields like bioinformatics, competitions along the Kaggle model (for instance, those sponsored by the local nonprofit Sage Bionetworks) have already brought biological problems like cancer prediction to the attention of larger communities of programmers and data scientists. Several people raised concerns, however, about the lack of accountability or oversight on public projects, as well as the importance of expertise in interpreting complex biological datasets. In more equipment-intensive experimental biology fields, there was less optimism about whether citizen science would become a major player; it seems significant that most well-known citizen-science projects are in natural history and astronomy. As a final note, we returned to the term “citizen science” and the distinction it implies between scientist and citizen. There’s more work to be done, it seems, for the democratizing goals of citizen science to be fully realized.

Further resources
I wrote a long article on citizen science in my previous life as a science journalist, so at risk of shameless self-citation, that pretty well sums up most information I have on the subject – see here. That article ran with a(n arbitrary and incomplete) list of citizen scientist projects sampled from various fields – see here. For those in the Seattle area, the local HiveBio community lab is always looking for volunteers – email info@hivebio.edu to get involved.

Citizen Science Discussion with Dr. Orlando de Lange this Thursday!

Thursday, September 15, 4:30pm (Foege S-110)

Citizen Science

Orlando de Lange (Electrical Engineering)

For the past century, scientific research has primarily been conducted by highly trained individuals working in accredited institutions, but the internet and other technological changes have made it easier for non-specialists to be involved. This session will explore multiple models of public involvement in the daily practice of scientific research, ranging from citizen science to crowdfunding to DIYbio. What are the goals of citizen science, and how well do existing projects fulfill them? What new models remain to be explored?

Recap: dual-use research of concern

Influenza H5N1

Our discussion started by focusing on research studies on a strain of avian influenza (H5N1) that is highly pathogenic in humans, but apparently lacks the ability to efficiently transmit between humans. A concern is that increased human-to-human transmissibility could evolve in a natural setting, potentially resulting in a global pandemic. To investigate this concern, researchers evolved a new version of this strain in the lab that has acquired the ability to readily transmit between ferrets, a model organism for this type of work. In our discussion, the overall tone towards these studies was one of concern, with some people questioning whether they should have been done at all. Because there are devastating consequences to this strain being accidentally or intentionally released from a research lab (potentially seeding a global pandemic), the benefits of the research should outweigh the risks. But can we accurately evaluate the risks, given that the potential for human error or malfeasance is difficult to predict and the potential consequences so large? And aside from release from labs where this research is approved, what about the risk of other scientists or non-scientists synthesizing the genome of the strain themselves? The potential benefits were also called into question. Though the scientists who conducted the studies claim their findings will help inform surveillance efforts, many countries of interest apparently do not have good enough surveillance infrastructure to make this effective. And although these studies identified one way transmission could evolve in ferrets in the lab, there was doubt whether it would be likely to evolve the same way in humans in a natural setting.

Synthesizing a morphine precursor in yeast

We also discussed a recent study where the authors engineered a strain of yeast capable of synthesizing a precursor to morphine (http://science.sciencemag.org/content/349/6252/1095). Further development of this system could dramatically cuts down on the time and cost of production of the morphine precursor, making painkillers more available worldwide, but some have raised the concern it could be used in an unregulated way to produce illegal drugs (https://www.theguardian.com/science/2015/aug/13/yeast-cells-genetically-modified-to-create-morphine-like-painkiller).

What are actual examples where dual-use research has gone wrong?

The group brought up a few examples, including the 1977 influenza epidemic, the origin of which is unclear, but is thought to have arisen either from a misguided vaccine trail or a lab accident (http://mbio.asm.org/content/6/4/e01013-15.full). Another example was an outbreak of foot and mouth disease in England that may have resulted from accidental release from the lab (https://en.wikipedia.org/wiki/Foot-and-mouth_disease#United_Kingdom_2007)

Botulinum toxin

Our discussion also focused on the publication of a newly discovered botulinum toxin without a known antidote at the time of publication. We were surprised at the apparent lack of concern of government regulatory agencies about the potential for this toxin to be used in a harmful way. The lab that discovered the new toxin was more concerned and were reluctant to share the bacteria expressing this toxin with other labs, which ultimately identified an effective antidote. This topic lead us to the question…

Who should decide whether dual-use research should be conducted?

We agreed that we need to make this decision as a society, and that regulations should probably be enforced at multiple levels (e.g., awarding grants, publication of articles) since no level is perfect. Certain areas of dual-use research (e.g., fracking) are probably easier to control by standard governance than others (e.g., influenza transmissibility, geoengineering), the latter of which could have immediate irreversible impacts.

Genomics Salon Summary – 07/14 & 08/04

Thursday, July 14, 4:30pm (Foege S-110)
Jolie Carlisle (Genome Sciences) and Hugh Haddox (MCB)
Medicine is suffering from a “one-size-treat-all” treatment strategy. A desire for better treatment options has generated initiatives to develop medicines for demographic groups based on characteristics like race, sex, and age. This session will examine the pros and cons of such approaches and how culture has influenced the design of clinical trials. It will also examine the potential to use genetic information from individual patients to design personalized medical treatments: where has this approach been successful and what obstacles stand in its way?
Thursday, August 4, 4:30pm (Foege S-110)
Bioscience as change agent: rhetorics of restraint and inevitability in response to advances in genetic technologies
Leah Ceccarelli (Communication)
Last year, a group of scientists and bioethicists published an editorial in Science calling for a moratorium on the use of CRISPR-Cas9 for germline genome modification, drawing comparisons to the 1975 Asilomar letter calling for voluntary deferral of certain kinds of recombinant DNA research. This session will compare the rhetoric of these two influential statements. How does the language and framing of these two letters portray bioscience and its capacity for change? What do they suggest about our collective ability to shape the course of technological change?

Public Understanding of Science

Thank you so much for bringing your thoughts, experiences, and energy to the discussion today and for making our first salon session such a success. You can use this website to access discussion handouts and stay up to date with salon events.
We welcome any feedback on today’s discussion and suggestions for topics for future sessions! We are interested in exploring different discussion formats and topics and would love to know what you think. Just shoot me an email (ksxue@uw.edu) or leave a comment in our anonymous feedback box:  http://freesuggestionbox.com/pub/qeqaffq
We’re also looking for volunteers to lead discussions later in the summer, so also let one of us know if that’s a prospect that interests you. Don’t feel like you need to have a topic already in mind! The other organizers and I are happy to work with you to prepare for and structure a discussion on a topic that interests you.
As a final follow-up to today’s discussion, here’s are some media guides for scientists, developed based on surveys of science journalists:
Thanks again, and hope to see you on July 14 to discuss medicine and identity!
Your friendly salon organizers,
Katherine, Jolie, and Hugh
Here is the link for the 06/23/16 handout.