BEACON-sponsored “Business for Scientists” course at UI

With supplemental funding from NSF, BEACON is co-sponsoring a week-long “Business for Scientists” course offered at the University of Idaho, May 22-26. This course is designed to help junior faculty, postdocs, and scientific staff run their research program like a successful business (see the flyer for additional details). The course is free to attend, and there is travel and accommodation support available from BEACON. You must RSVP by emailing ibest@uidaho.edu by May 5. If you would like to apply for BEACON travel funds to this course, please contact Danielle Whittaker.

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Why We March

This post is written by NCA&T faculty Joe Graves

On the 13th of April, Nature, the publication of the British Association for Advancement of Science (and founded by Charles Darwin) endorsed the March for Science (https://www.marchforscience.com/ ). Nature is one of over 100 professional scientific organization that have endorsed the march, including the American Association for the Advancement of Science (AAAS), the Union of Concerned Scientists, the European Geosciences Union, American Chemical Society, and others. There are now over 500 satellite marches planned (including all the BEACON partner sites: Lansing, MI; Pullman WA and Moscow, ID; Seattle, WA; and Austin, TX). As a member of the coordinating committee for March for Science (Greensboro) I would like to extend to all BEACONites a personal invitation to join us on April 22nd, 2017 as we march to inform the public concerning the crucial importance of supporting both the scientific method of reasoning and enterprise for the health of our nation and world.

This march is about much more than recent cuts to science funding. Having said that, the projected cuts are stark. Last month, the American Institute of Biological Sciences (AIBS) released an analysis of the Trump administration’s FY 2018 budget’s impact on scientific research and education2. The Trump budget would increase military spending by 10% to approximately $639 billion dollars. To pay for this increase cuts are projected to occur for the Environmental Protection Agency (-30%), Department of Agriculture (-29%), Department of Energy offices of Science (-16%) and to the National Institutes of Health (-18%).   The National Oceanic and Atmospheric Administration grant programs would be cut by $250 million. These programs support coastal and marine research and education. The Sea Grant program, which provides research, education, and extension services, would be eliminated.

At a time when the world is in dire need of advances in scientific research such cuts could have disastrous consequences. Therefore it is imperative to march to demonstrate our passion for science and sound a call to support and safeguard the scientific community. The incredible and immediate outpouring of support for the marches has made clear that these concerns are also shared by the support of hundreds of thousands of people around the world.

It is also crucial to reject the mischaracterization of science as a partisan issue. Despite the popular conception that most scientists are political “liberals”, scientists have always displayed ideological views that cross the political spectrum. Let us not forget that Wernher Von Braun (who utilized Jewish slave labor to build his rockets) and Shiro Ichii (microbiologist head of Unit 761 that deployed anthrax and bubonic plague weapons on Chinese civilians) were scientists. In addition both of these men had their war crimes ignored because the technology they developed was desired by the United States after World War II had ended. Indeed, as I have mentioned in earlier posts, science as an enterprise and many scientists have often been ardent supporters of unjust and inhumane social policies. Indeed, despots of all varieties and flavors are more than happy to support scientific research and products that are consistent with their own political agenda. The US Supreme Court utilized the science of the racial polygenists (Louis Agassiz and Samuel Morton) to justify their decision that Dred Scott or any other Negro had “no rights that a white man was bound to respect” in 1857 (Graves 2005) and about 50 years later would deny that same racial science in not recognizing the right to citizenship of Bhagat Singh Thind under the Caucasian requirement (Bean and Lee 2009). Just as today there is no argument made by policy makers against the science involved in producing and deploying the “mother of all bombs”, GBU-43/B used in Afghanistan last week (http://www.cnn.com/2017/04/13/politics/afghanistan-isis-moab-bomb/ ), while at the same time they have no problem denying the physics and chemistry behind anthropogenic climate change.

What scientists agree on is the power of our method, dubbed “the scientific method” to provide the world utilitarian knowledge about nature. Evolutionary science is among those fields most fertile in that regard. As early as the 1940’s evolutionary biologists like Th. Dobzhansky warned the world concerning the danger resulting from the unchecked use of pesticides and antibiotics. At the time, these warnings were summarily ignored (e.g. Van den Bosch 1978), yet it is now recognized that we may be entering the “post-antibiotic” phase of human civilization (http://www.bbc.com/news/health-34857015). In a more strange case, scientists including evolutionary biologists utilized knowledge of past global level extinction events, warned the world concerning the fallacy of “limited nuclear war” (Ehrlich et al. 1983). These warnings have gone unheeded, as the United States still maintains a nuclear arsenal capable of killing the world’s population eight times over (although it can be argued that the movement to build more powerful non-nuclear engines of mass destruction is evidence that these warnings have been taken seriously).

The mistaken view that scientists are political liberals has given some of our current policymakers permission to reject overwhelming evidence, especially when it contradicts their specific political agenda or the profit motives of those who put them into office.  Nowhere is this more obvious than in the current attack on climate science. For example, Dr. Michael Mann warned congress of the dangers of this phenomenon over 14 years ago. Since that time he has been sued, forced to testify in front of congress, been investigated, and received death threats (Mann and Toles 2016).

So in reality, it is not that those in power do not accept science, it is that they “cherry pick” which science they will accept and support. The Republican Party has been historically anti-evolution mainly because much of its political base (evangelical Christians) is anti-evolution. It is now anti-climate science because much of its financial support comes from industries that want to continue developing and burning fossil fuels. Days after taking office, the Trump Administration initiated a poll asking American manufacturers how to best cut federal regulations to make it easier for companies to get their projects approved. There were 168 comments received and ½ were directed at the Environmental Protection Agency and 1/5 toward the Department of Labor. Some examples of these comments include:

BP wants to make it easier to drill for oil and gas in the Gulf of Mexico by reducing how often companies must renew their leases.

A trade association representing the pavement industry wants to preclude the U.S. Geological Survey from conducting what the group says is “advocacy research” into the environmental impact of coal tar. The Pavement Coatings Technology Council says this research could limit what it uses to seal parking lots and driveways.

Source: https://www.washingtonpost.com/politics/epa-emerges-as-major-target-after-trump-solicits-policy-advice-from-industry/2017/04/16/87a8a55a-205d-11e7-ad74-3a742a6e93a7_story.html?utm_term=.6f6e0eee7198&wpisrc=al_alert-COMBO-politics%252Bnation&wpmk=1

Clearly in the case of both of these comments, scientific principles and scientists working for these corporations are involved in both drilling for oil and gas, and developing the sealing technologies mentioned.

Thus I do not see the rejection of science as the most critical and urgent matter to be addressed by this march. More it is scientists themselves recognizing that science and its applications have always been political. In this light, it is time for people who support scientific research and evidence-based policies for the public good to take a stand and be counted. Many who take the podium this week will be not be willing to make the distinctions I have discussed above. They will be parroting time worn platitudes and trying to find the lowest common denominator concerning how and why science should be supported. On the contrary, I will be speaking to the need for scientists to rise up against those who are applying our craft to support the corporate greed that is driving the wanton destruction of our environment and against those who are applying our craft to maintain social injustice. I will call scientists to imagine a different way of working for humanity.

Indeed, for this to happen we as scientists will have to look inwards. We will have to ask questions about why we do what we do, and how the science enterprise is in the main still a Eurocentric, male-dominated, heterosexist project. If we can manage this conversation productively we will move towards the day when our community will be more representative of all socially-defined races and ethnicities, religions, gender identities, sexual orientations, abilities, socioeconomic backgrounds, political perspectives, and nationalities. And with this diversity, we will be more capable of implementing scientific research that actually does better the lives of all those who now depend on us more than ever before.

References

Bean, F.dD. and Lee, J. Plus ḉa Change. . .? Multiraciality and the Dynamics of Race Relations in the United States, Journal of Social Issues 65(1):205—209, 2009.

Ehrlich, P.R., Harte, J., Harwell, M.A., Raven, P.H., et al., Long-term biological consequences of nuclear war, Science 222: 1293—3000, 1983.

Graves, J.L., The Emperor’s New Clothes: Biological Theories of Race at the Millennium, (New Brunswick, NJ: Rutgers U. Press), 2005.

Mann, M. and Toles, T., The Madhouse Effect: How Climate Change Denial is Threatening Our Planet, Destroying Our Politics, and Driving Us Crazy (New York: Columbia University Press), 2016.

Van den Bosch, R., The Pesticide Conspiracy, (Berkeley, CA: U. California Press), 1978.

 

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Teeny tiny creepy crawlies: the phage in your backyard

This post is written by MSU postdoc Sarah Doore

When I was little, my dad would often take me around the backyard to hunt for bugs. Spiders—which are not bugs, but little me didn’t care about taxonomy at the time—were my favorite. Upon discovery, I could have spent hours watching arthropods just do their arthropod things. Each hunt was its own exciting adventure. What would I find today? Where would the best spiders be? The best caterpillars? Should I check plants or should I try looking under rocks?

Dr. Doore in the field gathering samples, ca. 1989

Four year-old me didn’t know she was laying the foundation for a future in science, but my bug-hunting days would end up shaping my interests in both expected and unexpected ways. In undergrad, I thought I was going to be an entomology major and study bugs—or rather, insects, as I eventually learned the distinction between the types of arthropods—forever. Well, instead of entomology, I ultimately got a PhD in microbiology. My dissertation research was on bacteriophages, or phage, which are viruses that infect bacteria. These weren’t the bugs my younger self had in mind, but phage tail fibers sort of look like spider legs, so…close enough?

I recently joined Kristin Parent’s lab at MSU as a BEACON postdoc. We’re both phage enthusiasts, and one day we were lamenting the dearth of phages that infect Shigella flexneri, the bacterial species our lab works with. We decided to remedy this. Could we find more Shigella phages by hunting for them in the environment?

“Phage hunting” has recently gained a significant following, with multiple universities contributing to phage discovery projects. The biggest of these is the Science Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Science (SEA-PHAGES) program, which is an alliance of over a hundred universities. Each university has a two-semester phage hunting program, where undergraduate students isolate and characterize bacteriophages they find in the environment. While Michigan State University is not (yet?) a member of this alliance, we wanted to give phage hunting a try. Besides, with an estimated 1031 phage particles in the world, we’re only beginning to scratch the surface of bacteriophage diversity. The more phage we find, the merrier!

Bacteriophage infecting a bacterium: our lab’s interpretation with Giant Microbes (left); under an electron microscope (right). Scale bar is 50nm.

Every fall, Dr. Parent teaches a section in the graduate course Integrative Microbial Biology (MMG801) here at MSU. While SEA-PHAGES focuses on undergraduate courses, we wanted to start on a very small scale to test our methods and gauge students’ responses before scaling up. The SEA-PHAGES program also spans two semesters, whereas our section would last just a few weeks. We asked groups of 2-3 students each to dig into the literature, develop hypotheses about where they were most likely to find phage, and come up with some possible methods to isolate them. They would be screening their samples on three types of Enterobacteria: Salmonella enterica, Escherichia coli, and Shigella flexneri.

A lot of those bacteria are found in the gut (hence the entero in Enterobacteria), which means they can also be found in poop. Because of this, most groups went for locations that were…less than sanitary. One group grabbed river sediment near a wastewater treatment plant, two groups took water from the Red Cedar River where it flows through campus, a couple groups went to locations where they thought they would find livestock or waterfowl manure, one group scraped some biofilm off a water buoy in the river, and one group decided to swab an apple from the student union.

Upon retrieving their chosen material, the groups then processed their samples in our lab. The students put some of their sample on agar plates or in liquid cultures of bacteria. The next day we checked the plates for the formation of plaques, which are small clearings where phage have killed all the bacterial cells in the region. We also checked the liquid cultures to see which ones had cleared: another indication of bacterial death.

Out of seven groups, the four that sampled in or around the river were all successful. Between those groups, the class isolated a total of 18 distinct phages! Much to our lab’s joy, most of those bacteriophages infect Shigella flexneri. Surprisingly few infected S. enterica or E. coli, which was the complete opposite of what we expected. Most previously-described enteric phages infect Salmonella or E. coli, which is why we were hoping to find some Shigella phages in the first place. Maybe Shigella phages just aren’t that popular or were assumed to be uncommon in the environment, so people haven’t been looking. (For more on the topic of fortuitous-but-unexpected results, I recommend reading Frederick Grinnell’s chapter on “Luck in Science” from The Scientific Attitude. The section on “controlled sloppiness” was particularly relevant to me.)

An agar plate with bacteria (white/opaque portion) and plaques (small dark circles). This is phage Jawnski from the University of Pittsburgh. Sarah often sees plaques like this when she closes her eyes after a long day in the lab.

We kept the students updated with our findings while we characterized their phages. We sent them pictures of their phage under the electron microscope. We tested the phages’ host ranges and sequenced their genomes, which we’re still in the process of analyzing. We see some unique properties of these Shigella phages, and we hope to submit a paper on our findings this summer. At the end of the semester, students’ reviews were very positive: “very interesting lecture and cool project!” and “I REALLY loved the fact that the homework assignment was hands-on field and benchwork.” There was only one criticism: they wish it had lasted longer!

Now we’re working to get similar modules into undergraduate courses here at MSU and in other schools. Phage hunting can be fun for everyone, and hopefully the thrill of discovery can get more students interested in science. So although this isn’t the kind of hunting my younger self ever would have thought about, I think she’s okay with it. The experience of getting your hands dirty, wondering whether to check under rocks (or buoys!), thinking about what you might find where…these are all the ingredients of science. As long as there are new phages to be uncovered and new questions to be asked and answered, the hunt will continue.

References and resources:

Hendrix R.W. et al. (1999) Evolutionary relationships among diverse bacteriophages and prophages: all the world’s a phage. Proc. Nat. Acad. Sci. USA 96:2192-2197.

Grinell, Frederick. The Scientific Attitude. New York: Guilford Publ. 1992. Print.

Science Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Science: https://seaphages.org/

 

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Join the conversation: links between communication and cooperation in bacteria

This post is written by UI postdoc Eric Bruger (twitter: @elbruger13)

Eric’s first (and less antagonistic) conversation with the stubborn tot mentioned herein.

We are used to thinking of ourselves as helpful beings, and humans are comparatively more cooperative in relation to many other species. The ability to cooperate is a major reason humans have been able to colonize much of the globe and form the complex societies we live in today. But the occurrence of cooperative behavior is far from a foregone conclusion: evolutionary theory tells us as much [1], and anyone who has tried to get a two-year-old child out the door can probably relate to the following recent exchange with my daughter:

“Ella, can you get your shoes on?”
“No.”
“We have to go to the store.”
“No store.”
“We need to get in the car so we can go to the store.”
“No car.”
“Don’t you want to go outside?”
“No go outside.”
“Please, Ella…”
(wanders off and starts playing with stuffed Cookie Monster instead)

As with winning that negotiation with a stubborn child (when that is even possible), the incentives to cooperate must be correctly aligned, whether that be directed more by benefits for cooperating or costs for opting to not cooperate. What may not be as apparent is that there are countless examples of cooperative interactions within and between other species in nature. This even extends to microscopic organisms that we generally consider to be non-cognitive (although see [2 & 3] for further discussion). Well known among microbiologists, but interesting nonetheless, you do not need to have a brain to cooperate with others!

Bioluminescence provides one of nature’s more amazing (biological) light shows, here available in liquid flask or solid petri plate formats!

During my doctoral research in the Waters Lab at Michigan State University, a central question that interested me was how cooperation among bacteria might be preserved and how it was impacted by their ability to communicate. My favorite system to examine these questions was the bacterium Vibrio harveyi, a well-studied organism known for its ability to carry out a form of communication termed “quorum sensing” (QS) and also the ability to produce light, or bioluminesce. V. harveyi cells produce the enzyme luciferase, which catalyzes a reaction between its substrate and oxygen, and emits a resulting bluish hue of light. The light emitted by one cell alone is not visible to the naked eye, but it is visible when cells are present in dense clusters or in cultures where billions of cells are present, forming a detectable phenotype. The light response is regulated by QS and is only fully activated after levels of bacterially-produced chemical signals exceed a critical concentration – this is affected by prevailing environmental conditions and often driven by local cell densities.

Because QS controls the expression of a large number of V. harveyi‘s genes, and up-regulates many more than it down-regulates, activating QS is a cost burden on participating bacterial cells. So what’s the upside of having QS, and why wouldn’t these bacteria just evolve to save on this cost by not not quorum sensing? This phenomena of defectors has actually been observed in many experimental, clinical, and natural samples, lending support to the idea that defecting is increasing the fitness of these cells. However, defecting can come at other costs. The inability to sense and respond to signal levels could have negative effects when there are important correlated traits like resistance to toxic chemicals, in varying environments, in conditions where interactions between members of the same type – cooperator or defector – more often than with other types, or in the case that QS-regulated traits provide large fitness benefits.

One of the benefits QS provides for V. harveyi is the ability to grow and produce higher yields on complex protein substrates like casein compared to non-QS defectors.

The traits turned on by QS includes the production of extracellular proteases at high cell densities. These enzymes are cooperative public goods, as the benefits generated by them can be shared amongst the entire surrounding community. Growth on complex growth substrates like casein, which requires breakdown for cells to fully access, is aided by the production of these proteases. Some of our work [4] examined competitive outcomes between cooperator and defector strains in casein media. The results provided a demonstration that, while unregulated cooperation was susceptible to exploitation by defectors, QS-regulation provided a degree of protection against this and allowed cooperators to persist in the presence of defectors. This was true even in large well-mixed populations, where theory predicts they should be most susceptible to such exploits.

To test whether or not QS could stabilize cooperative behaviors over longer timescales, we conducted a 2,000 generation experimental evolution with replicate populations of Vibrio harveyi. Replicate populations of either the wild type (WT) strain that possesses a functional QS system and cooperates depending on signal levels, or a mutant strain that unconditionally cooperates regardless of external inputs like cell density, were passaged in a casein media. We found that non-QS defectors evolved from both strain backgrounds, but the resulting dynamics of the defectors were very different depending on the strain from which they evolve. From the unconditional cooperator strain, defectors rapidly evolved and uniformly swept those populations. These defectors exhibit a nonluminescent phenotype resulting from no QS activation of luciferase production. Alternatively, in nearly all WT populations, bioluminescent clones persisted at significant levels for the entirety of the experiment. Ongoing sequencing work is pursuing the molecular bases of these changes to determine whether parallel or diverse evolutionary paths are followed in our experimental populations.

Together, the competition and experimental evolution results we have observed show that bacterial chemical communication, in the form of QS, allows V. harveyi to maintain greater levels of cooperation within mixed populations and may be required to allow cooperation to persist [5]. QS appears to be playing a critical role that may be shifting the balance of costs and benefits in cooperation’s favor. So keep up the conversation, and good things might just happen – just don’t count on that two-year-old to agree with you!

References

  1. West, S. A., Griffin, A. S., Gardner, A., & Diggle, S. P. (2006). Social evolution theory for microorganisms. Nature Reviews Microbiology, 4(8), 597-607.
  2. Lyon, P. (2015). The cognitive cell: bacterial behavior reconsidered. Frontiers in microbiology, 6, 264.
  3. Shapiro, J. A. (2007). Bacteria are small but not stupid: cognition, natural genetic engineering and socio-bacteriology. Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences, 38(4), 807-819.
  4. Bruger, E. L., & Waters, C. M. (2016). Bacterial quorum sensing stabilizes cooperation by optimizing growth strategies. Applied and Environmental Microbiology, 82(22), 6498-6506.
  5. Czárán, T., & Hoekstra, R. F. (2009). Microbial communication, cooperation and cheating: quorum sensing drives the evolution of cooperation in bacteria.PloS One, 4(8), e6655.
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Reporting back! Highlights from the Public Engagement Workshop

This post is by UT Austin postdoc Tessa Solomon-Lane. Tessa is working with Hans Hofmann (UT Austin), Travis Hagey (MSU), and Alexa Warwick (MSU) on public engagement at BEACON.

The majority of scientists engage with public audiences about STEM topics, through classroom visits, leading lab tours, giving interviews, writing blogs, hosting podcasts, and more. There are ways to increase the efficacy of engagement using data from the learning and communication sciences. However, these best practices are rarely taught in graduate training programs. This curriculum gap has consequences not only for public engagement, but also for professional development. Public engagement builds skills that are fundamental to professional success, including enhanced communication, teaching, and leadership skills and enriched understanding of one’s own research and field.

We held our first full-day Public Engagement Workshop in February 2017 at the University of Texas at Austin, which aimed to recruit, motivate, and train graduate students and postdocs, and to pair them with engagement opportunities. Resources from the workshop can be found on our UT Austin Libraries Guide.  

Here are some of the highlights from the workshop:

Dr. Anthony Dudo gives an overview of the primary areas of research on science communication. Photo by Rayna Harris.

Evidence-based practices. Research on how scientists engage with the public about STEM topics can be used to develop evidence-based best practices for public engagement. As organizers who have been involved in public engagement for many years, it was surprising to us to learn about this rich literature. To provide this background and perspective for workshop participants, we welcomed Dr. Anthony Dudo, Assistant Professor in the Department of Advertising and Public Relations at UT Austin, to lead the morning session. He provided an overview of the research, context for the current state of public engagement in STEM, and discussed his own work on the science of science communication.

A slide from Dr. Anthony Dudo’s presentation describing the failure of the Deficit Model. Alas, people are not sponges and do not absorb and retain all of the information provided to them, about science or any other topic.

Two main messages from Dr. Dudo’s presentations continued to be discussed throughout the day. They were also especially relevant to our mission of broadening participation and the scope of public engagement. First, when engaging with the public, many scientists still operate within the Deficit Model, in which interactions between STEM professionals and the public eliminate the public’s scientific knowledge deficits. However, simply providing information—no matter how eloquently communicated—does not eliminate knowledge deficits or lead the public to adopt the perspectives of STEM experts. If the goal of engagement is not to educate, what is the purpose? Dr. Dudo’s second main take-away was the importance of identifying your ultimate reasons for engaging with the public. Why is it important to know the scientific information that you’re sharing? Ultimate goals could include promoting careers and diversity in science, advocating for a particular position on policy, supporting increases for scientific funding, and more. Identifying these ultimate goals is critical to developing and evaluating successful engagement. This session was the highlight for many participants!

Workshop participants discussing their engagement materials in small groups.

Resources for engaging public audiences. When the activation energy required to do something new appears high, it is often easier not to participate. During the workshop, we wanted to demonstrate that preparing for public engagement can be time efficient by having participants begin developing their engagement materials during the workshop itself. We used a simple format and scientific materials in which the participant has already invested time. For example, when sharing research with the public, the core scientific storyline can be distilled from scientific manuscripts, talks, posters, and grants. Once developed, the same engagement materials (e.g., presentation or activity / game) can then be adapted for use with audiences of different ages and backgrounds. I have used variations of ‘Build-a-Brain’ with both preschoolers and college students and can attest that everyone enjoys building brains with Play-Doh! We also discussed strategies for assessing audiences and strategies for adapting engagement materials. A number of participants asked questions and offered suggestions for engaging with reluctant audiences. This topic may be especially relevant for those advocating for a specific policy position, such as teaching evolution in Texas schools.

Lunch panel with graduate student and postdoc organizers of public engagement programs. Amanda Perofsky (They Blinded Me with Science), Travis Hagey (BEACON science education postdoc), Becca Tarvin and Katie Lyons (Austin Science Advocates), Mariska Brady (Science Under the Stars), and Mariana Rodriguez (Crockett High School Internship Program) (left to right).

Showcasing public engagement programs. To achieve our goal of broadening participation and the scope of public engagement, it is critical to connect participants with opportunities to engage. Research has shown that this concrete end goal is important to successful training, and scientists who have engaged with the public are more likely to engage again. We assembled a panel of organizers from public engagement programs (primarily at UT Austin) to discuss a wide variety of opportunities to engage. The panel featured Mary Miller, director of UTeach; Becca Tarvin and Katie Lyons, co-founders (along with Lauren Castro) of Austin Science Advocates; Mariana Rodriguez, co-organizer of the Crocket High School Internship Program; Mariska Brady, former organizer of Science Under the Stars; and Amanda Perofsky, co-host of They Blinded Me with Science. Check out the BEACON Science Communication Resources for more information on how to get involved at your Institution!

We surveyed participants before and after the workshop on measures of internal and external efficacy, which can predict future public engagement behavior. Zero indicates no change. Positive score indicates perceived improvement post-workshop.

Impact of our Public Engagement Workshop. We surveyed participants before and after the workshop to quantify workshop efficacy, identify changes in participant perceptions about public engagement, and improve future workshops. Overall, our feedback was overwhelmingly positive! The majority of participants agreed or strongly agreed (89%) that the goals of the workshop were met and that the information presented was relevant (100%). All participants reported that they were likely or very likely to use their new information to improve their public engagement (100%), and almost everyone was likely or very likely to engage more often (83%). We also asked questions related to internal and external efficacy, which are good predictors of engaging with the public in the future. We asked participants 1) if they were a skilled communicator, 2) if scientists can effect change, and 3) if colleagues were supportive of their public engagement efforts. Although we are limited by a small sample size, more participants rated their communication skills as higher after the workshop and fewer rated their skills as lower (Figure 1), suggesting the workshop had a positive impact on this metric. No change in efficacy or colleague support was detected. We have also begun integrating feedback to improve future workshops. For example, more participants were neutral towards the lunch panel, independent work time, and audience appropriateness sessions than the others; therefore, we will focus on feedback to improve these sessions. We will also be sure to provide background and original research in future workshops because nearly all participants rated Dr. Dudo’s session as useful or very useful (94%). Finally, participants suggested a number of topics for future workshops that we hope to incorporate, including engagement with policy and policy makers.

We want to thank our participants from four different BEACON Institutions who attended in person and via video conferencing! Stay tuned for more updates and future events.

 

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Avida-ED Summer Workshop

This summer we will be holding two workshops on the use of Avida-ED; one at the University of Washington from June 21-23, and one at Michigan State University from July 27-29.  Avida-ED is a free, web-based program designed to teach both principles of evolution and the nature of science. Workshop participants, in teams of two, will learn how to use this program, and incorporate it into courses that they teach.  We have extended the application deadline; applications will be accepted on a rolling basis through April 10.  Please visit https://avida-ed.beacon-center.org/active-lens-train-the-trainers-2017-edition/ to apply.  If you have any questions, feel free to contact me at mwiser@msu.edu

 

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Food for thought: research-based courses replace regurgitation with digestion!

This post is by UW research scientist Katie Dickinson

Katie Dickinson

This blog is based on a true story…

After work the other day, I walked with a friend to a nearby café for dinner. After ordering, we each pulled out our laptops to get a little work done while we waited for our sandwiches. I pulled up my BEACON blog draft, eager to share some of the changes UW Biology is making to its introductory courses. The empty table next me was soon occupied by two students, who started quizzing each other as they prepared for a final exam.

I attempted to tune out the music and chatter as I edited the blog post, but bits and pieces of conversation from the nearby table made me take notice. “What about Lamarck? Was he the giraffe guy?”, one student asked the other. “Do you think we need to know about him?” My ears perked up when I next heard the name ‘Linnaeus’ and, “Google that acronym for the taxonomy….Isn’t it something about King Philip and spaghetti?” “Is that important, do you think?” “Define evolution,” one student prompted the other. I twitched in my seat as the students struggled. My friend turned to me and whispered with a mischievous grin, “This is killing you, isn’t it?”

It was killing me! I am honored and excited to be part of a team of PIs, graduate students, and researchers who are seeking to transform the first two quarters of the undergraduate Biology experience at the University of Washington. With support from BEACON and an HHMI-funded grant awarded to Dr. Scott Freeman, we are creating a course-based undergraduate research experience (CURE) — a series of lab modules that provide introductory biology students with the opportunity to perform authentic research. Goals of our new curriculum include improving undergraduate students’ understanding of key evolutionary concepts and their ability to design experiments, while also increasing their emotional engagement with their learning, academic performance, confidence, resiliency, and professional identity.

In the café, as I listened to the students next to me, they seemed committed, bright and knowledgeable; yet it sounded like they were memorizing and regurgitating material rather than learning. Although information was being exchanged between the students, connections seemed to be lacking. Did these students understand why the things they were learning and doing mattered? Or were they packing their brains full, only to dump the information after the exam?

I thought about the pilot class I assisted with this winter quarter. The students ran an experiment based on experimental evolution of the bacterium Escherichia coli. Students explored the evolution of antibiotic resistance by exposing E.coli to various antibiotics and selecting resistant mutants. These mutants, along with a sensitive ancestor, were transferred daily in drug-free media for several weeks (Fig 1). During weeks the bacteria were being transferred, students learned and practiced R-based statistical analysis and data visualization — skills that they would use to interpret their experimental results. After ~3 weeks of transferring bacteria (over 150 generations of growth!), the students compared competitive fitnesses and the minimum inhibitory concentrations (MICs) of ancestor strains to their descendant strains (i.e., pairs of strains from the beginning and end of transfers). Students presented their results at a poster session, where they discussed various topics such as the cost of antibiotic resistance and the nature of compensation.

Figure 1: Lab overview for the first course in the UW Introductory Biology CURE. In the broadest terms, the lab involves (1) selection for drug resistant mutants, (2) propagation of these mutants and a drug-sensitive control strain for several generations in the absence of drugs, (3) assessment of competitive fitness and the level of drug resistance of all ancestors and descendants from the evolution experiment, (4) visualization and analysis of the data using R and (5) presentation of the research experience as a poster (Parts 4 and 5 not shown).

As a follow-up to the winter quarter course, which highlighted evolutionary phenomena from a population level, we are offering a pilot course this spring, to integrate concepts from the cellular and molecular levels. In this second course of the Intro Bio CURE series, students will analyze the products of their own evolution experiments from the prior quarter. Students will sequence the relevant gene(s) of their sensitive and resistant bacterial isolates, look for mutations, and explore how those mutations change protein structure and cellular processes. In this way, the students will gain an understanding of the genetic and phenotypic features of drug resistance. They will present their findings in a poster session at the end of the class, encouraging synthesis of the material.

Our goal is to enable students to trace genotype to phenotype at the cellular level, and connect evolution to molecular biology by linking phenotype to fitness. We also want to engage undergraduates in work that represents cutting edge science, potentially has applications for public health, and helps build their confidence and skills for high achievement in these and future science courses. We hope that the hands-on discovery aspects of the course will help students make connections and improve their understanding of evolution as a unifying theory that underlies all the life sciences.

Figure 2: Instructor, Dr. Joya Mukerji, setting up lab for class. Dr. Mukerji is in charge of developing Course-Based Undergraduate Research Experiences for biology students at the University of Washington.

My reflection on the pilot class was interrupted by the arrival of food. Despite my munching, I could still hear the students at the adjacent table. In addition to the biology final, one of the students had a statistics final coming up. She was complaining about not understanding the purpose of statistics and was glad to be getting the class over with. She was stressed because she had been struggling to find time to study while also commuting and holding down a full-time job. Hearing her concerns brought me back to another important goal we are aiming for in our course design: to improve the retention of undergraduates interested in STEM majors, with a particular emphasis on underrepresented minority students, women in male-dominated fields, and students from economically- and educationally disadvantaged backgrounds. The goal of infusing research into the introductory biology series is not “to weed out” students, but rather to ensure that all students taking intro bio are able to experience the excitement of doing authentic research. Often, apprenticeship-style research positions are scarce and are offered as unpaid internships, due to financial constraints. Factors like these make it particularly challenging for students from less-privileged backgrounds to gain laboratory experience.

We hope that providing all UW students with a credit-bearing research experience early during their academic careers will lessen barriers to students’ entering STEM fields. In addition, students’ increased understanding of the real-world relevance of evolutionary concepts and the sense of project ownership cultivated via participating in the CURE may help reduce achievement gaps and enhance retention in the process. Partnering our BEACON grant with the HHMI-funded CURE experience has provided a unique opportunity for students to learn useful lab skills, better understand the scientific process, and explore experimental evolution in the context of a medically-relevant subject.

As I finished my dinner, the students at the next table were trying to understand why bacteria have both “donuts and spaghetti” (plasmids and the chromosome). I decided maybe it was time for me to introduce myself….

Thanks to the amazing team of researchers who are making the UW Introductory Biology CURE come alive: Joya Mukerji, Scott Freeman, Ben Kerr, Peter Conlin, Kelly Hennessey, and Hannah Jordt. In addition, thanks to Luis Zaman and Chase O’Neil who have helped with the lab troubleshooting.

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Undergraduate Diversity at Evolution 2017 Conference Travel Award

Please remind any undergraduate students to apply for our conference travel award that fully funds them to attend the annual Evolution meetings this June 23-27 in Portland, OR! The application deadline is March 31, 2017. Check out the details below and on our website. We are also looking for mentors (grad students, postdocs, faculty) for the program.

CONFERENCE TRAVEL AWARD
For the 14th year we will fund a cohort of domestic and international undergraduates to (1) present a poster at the meetings, (2) receive mentoring from graduate students, postdocs and faculty, and (3) participate in a career-oriented ‘Undergraduate Futures in Evolutionary Biology’ panel and discussion. The program is sponsored by SSE/BEACON and covers the costs of travel, registration, food and accommodation at the meetings. The application deadline is Friday, March 31st, and decisions will be announced by Friday, April 7th.

Applications are welcomed from all undergraduates, and the admissions goal is to create a diverse pool of students. An overview of the program and the online application can be found at: http://beacon-center.org/ude/. Applications consist of a short statement of interest, a letter of recommendation, and the title and abstract of the poster to be presented.

For inquires, please contact one of the organizers:
Alexa Warwick – awarwick@msu.edu
Richard Kliman – rmkliman@cedarcrest.edu
Scott Edwards – sedwards@fas.harvard.edu.

MENTORS NEEDED
We are also looking for graduate students, postdocs and faculty members who would like to serve as mentors to undergraduate awardees during Evolution 2017 (June 23-27 in Portland, OR). Mentors meet with pairs of students and attend talks with them, introduce them to colleagues, network and generally make the meeting a welcoming place for them. Although costs are not covered for mentors it is an unusually rewarding experience. Mentors must be able to attend the introductions meet up on Friday, June 23, around 6:30PM. Contact Dr. Richard Kliman (rmkliman@cedarcrest.edu) if you are interested in serving as a mentor. You can also indicate your interest in mentoring via the conference registration form.

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The Diversity of Ways that BEACONites Engage the Public

This post is by UT Austin postdoc Tessa Solomon-Lane. Tessa is working with Hans Hofmann (UT Austin), Travis Hagey (MSU), and Alexa Warwick (MSU) on public engagement at BEACON.

Public engagement is central to BEACON’s mission. The Center supports these efforts through Education & Diversity budget requests; dedicated postdoctoral positions for public engagement, science education, and diversity; support for engagement events and the development of educational materials; and more. It should, therefore, come as no surprise that BEACONites engage with the public about STEM topics in many different ways. How many? We’re glad you asked! In November 2016, we sent a survey out to the entire BEACON community to find out.

Ninety-three BEACONites responded from seven different Universities: Michigan State (54%), The University of Texas at Austin (20.4%), University of Idaho (10.8%), University of Washington (8.6%), North Carolina A&T State University (3.2%), Yale (1.1%), and University of California, Irvine (1.1%). Most were biologists (71%), computer scientists (16.1%), and neuroscientists (6.5%). Participants represented a range of career stages (Fig 1a), from undergraduates to faculty and staff, and experience levels (Fig 1b), from no experience to more than 50 public engagement events, thus far!

Using a list of public engagement activities generated at our BEACON Congress Sandboxes in 2016, we asked participants about the many ways they have engaged with the public, from hosting a podcast to judging a science festival to writing a popular science book. We then categorized the 31 engagement activities, a priori, as face-to-face engagement with K12 students and/or adults; public interviews on a variety of platforms (e.g., newspaper, television, podcast); producing media of various kinds (e.g., blog, online video, book); facilitating engagement for others (e.g., as an organizer of a public engagement program or BEACON public engagement, science education, or diversity postdoc); facilitating research experiences (e.g., mentoring an undergraduate or high school research assistant), or engaging with public policy and policy makers (e.g., serving as an elected official, registering an opinion in state or local government). Participants could also indicate that they had not yet engaged with the public.

There were marked differences in the ways that BEACONites engage with the public (Fig 2). More than 80% of participants had engaged with the public face-to-face or by facilitating research experiences for others. These data are informative because it allows us to identify engagement activities that scientists are attracted to and/or that are more accessible. For example, the most popular face-to-face activities were K12 classroom visits (51%), organizing or presenting at a science festival or expo (44%), and organizing or giving a lab or core facility tour (43%). With this information, BEACON and public engagement organizers can ensure that appropriate training and popular engagement opportunities are available.

We also identified public groups that are not being reached. For example, engagement with policy and policy makers was strikingly underrepresented. Less than 20% of participants had served in elected office, communicated with policy makers about STEM topics, or communicated with local school boards, parent teacher associations, or home school communities. This finding is especially significant in the current political climate. Influential voices in both government and media are amplifying false scientific claims made by vocal public groups (e.g., anti-vaxxers, anti-GMOers, climate change deniers, and creationists), which can sway policy decisions and impact lives and livelihoods. BEACON does not currently have any public engagement training or programs that focus on policy, but plans are in the works to address this important type of engagement. In the meantime, check out resources from the AAAS Center for Public Engagement with Science & Technology, the Engaging Scientists & Engineers in Policy (ESEP) Coalition, and 314 Action.

Most survey participants indicated that they had engaged the public through multiple activities, for example, visiting a K12 classroom and hosting radio show. Therefore, we were also interested in whether there were patterns to the different kinds of activities in which individuals participated. Hierarchical cluster analysis suggests that the suites of activities individuals participated in may cluster in meaningful ways (Fig 3), indicating that those activities may share particular qualities. To begin making sense of these shared qualities, we labeled each activity based on 1) our a priori categories (Fig 2), 2) if it necessarily involves K12 students, and 3) if it requires in-person interactions. Individuals may have fundamental preferences for the type of audience they engage with (children vs. adults) and the format of the activity (e.g., in person vs. online).

Several interesting patterns stand out. First, the three major clusters (Fig 3, A, B, C) are made up of distinct mixes of categories. Cluster C contains the majority of the face-to-face, interview, and facilitating research activities. In comparison, cluster A is primarily policy engagement and producing media. Cluster B is a mix. Second, category, audience, and format interact. For example, cluster C contains the majority of face-to-face, in-person, and K12 engagement activities. Cluster A contains no engagement activities that necessarily involve K12 students, and cluster B only contains one. Third, specific activities appear to be distinct from others in their a priori category. In cluster A, adapting materials for individuals with disabilities and engaging the community about health are clearly distinct from the other facilitating engagement and face-to-face activities, respectively. Similarly, giving interviews for television or film did not cluster with giving interviews for written works, podcasts, radio, or online video. As we continue to analyze these data, other factors may become important, as well, such as the level of investment required.

Although we are working with a limited sample size, we aim to use this kind of data to inform our public engagement efforts and spending. On a personal level, we could also use these data to make personalized recommendations for future public engagement based on an individual’s previous activities. For example, someone may be interested in branching out to a new, but similar, form of engagement. Or based on my own engagement experience, which includes the activities in clusters B and C, but only one in cluster A, I could expand to a new activity but a familiar format.

Long-term, our goal is to fundamentally change how and why scientists learn to communicate with diverse and influential audiences. Effective STEM public engagement may be central to ensuring the future of scientific research in these uncertain times.

If you haven’t had a chance yet to participate in our short survey (< 4 min), you can tell us about the ways you engage by clicking here!

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EiA 2.0: Designing an Effective Exhibit on Evolution

This post is written by MSU Museum Education Assistant Nick VanAcker

Ever since its creation in 2010, the BEACON Evolution in Action Gallery at the Michigan State University Museum has been a fantastic resource for our visitors to learn about evolution research. Julie Fick, co-education manager at the MSU Museum, wrote a great post about the initial creation of this exhibit, which you can read here. I won’t repeat everything she wrote, but as a little background:

The EiA gallery serves three main purposes:

  • To inform audiences about BEACON’s mission and presence as a world-class NSF center at MSU
  • To increase public understanding of evolution
  • To showcase current evolution research being conducted here at MSU

The initial exhibit featured panels about the BEACON Center, Dr. Kay Holekamp’s research on hyenas, and Dr. Richard Lenski’s research on E. coli. It was a really fantastic exhibit about evolution research and its applications. However, after conducting some audience evaluation, one flaw in the exhibit was discovered. Despite the fact that the gallery is called “Evolution in Action”, nowhere in the gallery – or in the whole museum, for that matter – actually explained how evolution works.

Figure 2

And that’s where I came in! My name is Nick VanAcker, and I joined the staff of the museum in December 2015 as an undergraduate zoology and museum studies student to assist in revamping the exhibit.

We wanted to achieve three main goals:

  • Develop a central “EvoHub” in the exhibit space which would effectively teach the four main tenants of evolution: Variation, Inheritance, Selection and Time.
  • Create an interactive touch screen station at the entrance to the science floor, to introduce visitors to concepts like common ancestry and evolutionary trees
  • Replace the “Hyenas Rule” portion of the exhibit with Drs. Ashlee and Matt Rowe’s work on venom evolution in grasshopper mice and bark scorpions

The EvoHub

Stage 1 of the process was creating the EvoHub. We wanted the EvoHub to act as a central anchor for the gallery. Guests could visit the hub, learn what makes evolution occur, and apply that knowledge to other areas of the gallery.

Some rough text for the exhibit panels had already been written when I came on, and it separated evolution into four sections using the acronym “VIST” – Variation, Inheritance, Selection, and Time. Each of these sections also had an interactive element to go along with them – some sort of game or activity to reinforce the concepts of each section.

Even though we thought the text was reasonably clear and easy to understand, and that the interactives would be engaging and educational, that doesn’t mean that visitors would think the same.

So, we asked them!

In March 2016, we turned the EiA Gallery into a laboratory, and created a mock-up of the future EvoHub. This included panels printed on large sheets of paper and attached to the walls with binder clips, interactives made out of cardboard, foam and tape…anything that would get the general gist of the exhibit across to visitors.

Figure 3

The point of the mock-up wasn’t to test design or style; it was purely about information. Was the content we had written being read and absorbed by visitors? Were the interactives effective and fun teaching tools? What bits of the exhibit did visitors really like?

We conducted a lot of surveys, and found out that, for the most part, the content was really effective! We needed to tweak some of the language on the panels to make it clearer, but overall, visitors were leaving the gallery with a better understanding of evolution than when they entered.

Figure 4A lot of the interactives worked out well, too – like flip panels showing our evolutionary ancestors, and a magnet board highlighting variation through facial features. But others presented problems. For example, we initially had a “tasting station”, where visitors could lick a paper strip coated in a bitter compound to show variation (only some of the population is able to taste it). But that proved disappointing – if you have the necessary genes to taste the compound, you were stuck with an extremely bitter taste in your mouth. If you don’t have the genes…you’re just eating paper!

Figure 5

Based on our results, we made some edits. A few interactives (like the tasting station) were cut, and others (like an activity already in the gallery using Legos as pieces of genetic code) were updated. Eventually, after working with a graphic designer, exhibit fabricator, and many members of the staff providing input…we had our finished EvoHub!

Figure 6

Figure 7

Figure 8

Figure 9

Even at this stage, the EvoHub isn’t quite complete – we’re still working to fabricate several of the interactives, and those will be installed in the gallery soon.

The Tree of Life

Figure 10

Stage 2 of the process was simpler: creating an interactive touch screen station at the entrance to the science floor, to introduce visitors to concepts like common ancestry and evolutionary trees. We reviewed a few different software options for this touch screen, and ultimately went with Harvard’s DeepTree (or, as we’re branding it, The Tree of Life).

To be frank, DeepTree is exciting. It’s designed specifically for museums, and shows the history and relationships of all life on earth, past and present. Using the touchscreen, visitors are able to fly through the tree, map evolutionary relationships, and even experiment with evolution using FloTree, an embedded program that allows visitors to become environmental barriers, causing evolution to occur.

Having DeepTree installed at the entrance to the science floor really frames our science exhibits in a new way. It creates connections across exhibits, and really visualizes that every biological process is, in the end, a product of evolution.

Venom Evolution

Figure 11

Finally, stage 3 of the process…is still occurring! If you’ve been to the museum recently, you’ll know that we’ve de-installed the “Hyenas Rule” portion of the EiA gallery, and we plan to install the Rowe exhibit on venom evolution in grasshopper mice and bark scorpions soon!

It’s going to feature a lot of great graphics, videos, venomous specimens, and most importantly: awesome information about the evolution research happening right here at MSU! But, if you just can’t wait, you can read about some of the research the Rowe lab is doing here and here.

Figure 12

 

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