Fall 2017 elementary school science nights

We are excited to share some pictures from three local elementary school science nights that we had the pleasure of attending this semester. We ran booths at Marble, Whitehills, and Glencairn elementary schools here in Lansing introducing kids to evolution using a couple of highly interactive activities. Thanks everyone for volunteering and thank you Matthew Moreno for taking photos!

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Two BEACONites receive awards from Web of Science for their publication records

We are very excited to congratulate two amazing researchers, Amir Gandomi and Kalyanmoy Deb for their recent awards from Clarivate Analytics, formerly the Intellectual Property and Science business of Thomson Reuters, and owner of Web of Science.

Amir Gandomi was named a 2017 Clarivate Analytics Highly Cited Researcher based on his publication record, publishing Highly Cited Papers defined as those that rank in the top 1% by citations for field and publication year in the Web of Science. This list of researchers represent some of the world’s most influential minds as determined by a citation analysis of Web of Science data.

Kalyanmoy Deb was awarded the Lifetime Achievement Award for his highly cited research contributions in a wonderful event organized by Clarivate Analytics attended by a large audience in New Delhi including other awardees, scientific advisers to Government of India, and many dignitaries from Indian universities and industries.

One of his papers published in 2002 passed 10,000 citations by Web of Science and is ranked 174 out of 45,602,967 journal and conference articles recorded by Web of Science from 1900 to 2017. Kalyanmoy is the first recipient of this award. Besides this award, the Citation Awards 2017 event also gave away Research Excellence Awards to individual researchers and institutions in India for their impacting contributions.

The award citation stated “Professor Deb is recognized for research on multi-objective optimization using evolutionary algorithms, which are capable of solving complex problems across a range of fields involving trade-offs between conflicting preferences. A 2002 paper, with more than 10,000 citations, ranks among the 200 most-cited papers recorded in the Web of Science, 1900-2017, and is by far the most influential paper ever produced by an Indian scientist, as reflected by citations.”

See photos below of Kalyanmoy receiving his award.

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The phage from the local lagoon

This post is by MSU postdoc Sarah Doore

Earlier this year, I wrote a blog post about doing some hunting with a graduate class here at Michigan State University. I’m not talking about hunting in the traditional sense though, since what we sought were bacteriophages—or viruses that infect bacteria—in the local environment. We were specifically interested in bacteriophages that infect enteric bacteria, like Escherichia coli, Salmonella enterica, and Shigella flexneri.

We asked the students to come up with a location and methods they wanted to use to check for bacteriophages (“phages” for short), then did some hands-on isolation using non-pathogenic strains of bacteria in our lab. We got to look at some new phages and the students’ creativity helped us find at samples we never would’ve imagined testing before. The project was fun for the students and fun for us!

By spring, we’d already planned to repeat the activity in the same grad course and were trying to bring phage isolation to undergraduate biology labs at MSU. So, when a Nebraska high school teacher heard about the project and seemed interested in doing something similar for his science class, we brought him to our lab over the summer and showed him the ropes.

Fig 1. Jason fishing for some phage in Nebraska.

After taking him through the isolation procedure, we made a plan for how he could have his students isolate their own phages back in his classroom. We also sent Jason, one of the lab’s graduate students, to Nebraska to do a trial run and see what the classroom still needed. You can see Jason collecting a Nebraska water sample for this in Figure 1. Come fall, we sent a box full of supplies to the high school and anxiously waited for the phage hunting module to begin. We were SO curious to see where students would decide to look—and, even better, what types of phages they’d find.

On collection day, each of the 50 students got their own sterile tube and went to a place they thought would most likely have phage, or at least somewhere they thought might have interesting results. They labeled the tube with their sampling location, then brought it back to the classroom to test it for phage.

A few common themes emerged among the sample locations the students picked: pond and river water were popular choices, as were the school’s baseball and football fields. There were also some more creative ideas, like the two students who sampled their dogs’ water bowls and the one who scooped a deer’s footprint in the woods. One of my personal favorites was “pond by frog,” which is just specific enough to make you wonder: what frog? What was the frog up to? Could this frog be an unknown reservoir for enteric phages? (Spoiler: it wasn’t, and I’m oddly disappointed by this result.)

Back in the classroom, the students tested their samples to see if they had found any phage. Out of the 50 samples, 16 of these had phages in them. Most phages—11 out of 16—came from ponds. The rest of the phages came from the baseball field (3), football field (1), and grass outside the classroom (1). The students sent their samples to our lab at MSU so we could also take a closer look at these new phages.

We’re still in the process of characterizing all of them, but so far it looks like some have interesting morphologies (see Figure 2 for an example of what I’d call an interesting plaque morphology). One also has a unique host range that we haven’t seen yet. This phage infects Salmonella enterica, Escherichia coli, and Citrobacter freundii: three types of enteric bacteria that belong to the same family but are otherwise significantly different. This particular phage came from pond water near a cattail. So…maybe cattails make better homes for phages than frogs do?

Fig 2. On an agar plate like this, phages kill their host and leave a clear spot where bacteria would have grown (“the circle of death”), known as a plaque. This one has fuzzy edges and a little belly button in the middle.

Although we’ve only been doing this kind of isolation for about a year, we’ve already discovered a total of 36 new phages, some of which are pretty rare and/or have really unique qualities (like the broad host range mentioned above). We plan to keep challenging students to sample their environment as long as we have the resources to keep up with them.

Although bacteriophages have been studied for over a century, and we’ve known for awhile that they’re abundant, we don’t know as much about the diversity or identity of the phages that are out there in the environment. Hopefully now we’re starting to answer that question too, and in the process we’re beginning to appreciate our own local composition of microbes.

If you’re interested in doing some of your own citizen science, we’ve got some resources for you! Maybe you’re a teacher who wants to try this in your classroom, or you know of someone who might be interested.

The protocols can all be found on the Parent lab’s website here (under “Video Protocols”). There’s a written version for the entire process of phage isolation, with videos for certain steps that are easier to understand and do yourself after seeing someone else do them. You can also follow us and/or ask us questions on Twitter @phage4lyfe.

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In search of evolutionary hotspots

This post is by MSU grad student Emily Dolson

Imagine that an alien species arrives on earth. It happens to be able to live and reproduce in any part of the world, and, over successive generations, it begins to adapt to its new environment. Among other things, it adapts to eat new kinds of food. Where in the world would you expect the first alien capable of eating papayas to be born?

Most people would probably say South or Central America, since papayas live there. When asked why they said that, there are two potential explanations they might give:

  1. The ability to eat papayas is more beneficial in regions where papayas actually grow.
  2. Regions where papayas grow are also populated by similar plants, like guavas.

The first of these explanations is based on either a misunderstanding of the question or a misunderstanding of evolution (but don’t worry, it’s a common one!). We didn’t ask where aliens that eat papayas are most likely to survive long term; we asked where the very first alien that could eat a papaya would be born. Recall how natural selection works: mutations occur randomly, some happen to be useful, and organisms that have mutations that happen to be useful usually go on to be successful. The first alien to be born with the ability to eat papayas has presumably had some sort of mutation that (in the context of the rest of its genome) gave it this ability. That ability hasn’t yet had a chance to prove to be useful or not. This alien may never even encounter a papaya in its life, in which case having the ability to eat them will have no effect. The presence or absence of papayas can have no influence on the birth of the first alien that can even interact with them.

The second explanation, however, is plausible. South and Central America are home to other tropical fruits, such as guavas. Tropical fruits have similar physical and chemical properties. If an alien can eat a guava, it probably only needs a few subtle mutational tweaks to be able to eat a papaya (assuming that papaya-eating even requires further adaptation). Once a subset of the aliens in the tropics gain the ability to eat some sort of fruit, their progeny will likely go on to be very successful in the regions where these fruit grow. These aliens will be well-positioned, in both physical and mutational space, to begin eating other fruits, such as papayas.

While aliens are unlikely to invade earth and eat our tropical fruits, the phenomenon of a population encountering a set of entirely new challenges as it moves into a new geographic region (or as the geographic region in which it currently lives changes) is common. And it’s common for these new challenges to be related to each other. It’s no accident that plants with similar fruit live in the same region; plants in the same region experience the same selective pressures and may also have a shared evolutionary history. These factors generalize across a wide variety of scenarios. Thus, if some of the challenges of thriving in a new area are easier to solve than others, the easy ones can serve as “evolutionary building blocks” for the harder ones. The presence of such building blocks, i.e. simple adaptations that provide a good starting point for more complex adaptations, has been shown in previous work to be important to the evolution of complex traits (Lenski et al., 2003).

If spatial layout does indeed impact the ease of adaptation, it would be useful to understand, both for evolutionary biology and evolutionary computation. As species shift their ranges in response to climate change, they will traverse regions where different traits are advantageous. Predicting how the positioning of these regions impacts evolution will help us predict whether the species will be able to survive. Evolutionary computation often takes advantage of evolutionary building blocks by rewarding solutions to different problems over time, but this is an imprecise art. If we could understand how to reward them differently across space to promote evolution of an overall solution, we could more easily generalize evolutionary computation to more problems.

Of course, it’s also entirely possible that these spatial effects are too small to care about. Recently, I’ve been trying to figure out whether or not that’s the case (Dolson and Ofria, 2017). Since this would be an incredibly labor intensive question to address in the lab or field, I’m using the Avida Digital Evolution platform to perform preliminary experiments on the computer. Once we know more, I’d be very interested in collaborating with wet lab biologists to see if our digital results are consistent with results from DNA-based systems.

Fig 1. Evolutionary hotspots across all eight environments. Background colors indicate which set of resources are present in each location. Polygons show the location of hotspots for the evolution of the ability to use each resource (legend indicates which resource corresponds to which line-type).

In Avida, I created eight different environments with different patterns of resources across space. I then let 100 different populations of digital organisms evolve independently in each environment. Within each of these runs, I found the location of the first organism with the ability to use each resource in each run. From these data, for each resource and each environment, I determined which regions appeared more often then we would expect to see by chance. These regions are “evolutionary hotspots.” Sure enough, each environment (except the control, which had all resources everywhere) had at least some hotspots (see Figure 1). In some environments, most of the hotspots overlap. In others, they are largely in different regions of the environment.

Fig 2. The sequences of environments experienced by the ancestors of the first organism to be able to use the XOR resource in one of the environments. Each color represents a different environment, and the length indicates long the lineage stayed in that environment for. Notice that many bars appear to end in a somewhat similar sequence of environments.

I’m now working on trying to predict why hotspots are where they are. Surprisingly, a number of seemingly obvious explanations (e.g. the number of resources present, the presence or absence of specific resources, and local diversity) do not appear to explain the pattern. Currently, it appears that the sequence of environments that a lineage experiences over evolutionary time may be a key variable (see Figure 2). I’m looking forward to understanding more soon!

References:

Lenski, R. E., Ofria, C., Pennock, R. T., & Adami, C. (2003). The evolutionary origin of complex features. Nature, 423(6936), 139-144.

Dolson, E. and Ofria, C. (2017).  Spatial resource heterogeneity creates local hotspots of evolutionary potential. In Proceedings of the 14th European Conference on Artificial Life. Vol. 14. pp. 122 – 129. MIT Press.

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Uncovering the function of host-associated microbial communities

This post is by MSU grad student Connie Rojas

Microbes colonize every surface of their hosts. Once established, they do not live in isolated patches, but instead form highly regulated, structurally and functionally organized communities, termed ‘microbiota’. Due to the interplay of the host’s immune system with its microbiota, many members are commensals or mutualists, performing functions critical for host health and physiology. In the human mouth, resident microbiota secrete antimicrobials and enzymes that contribute to oral health. In the mammalian gastrointestinal tract, microbiota synthesize vitamins, and supply the host with energy released from the fermentation of indigestible carbohydrates. In the human vagina, members of the microbiota produce lactic acid, which maintains a low pH environment thought to protect against infection. However, despite the explosion in microbiome research, we know very little about the additional functions microbes are performing within their hosts. We also do not know whether or how they have affected the behavior and evolution of their hosts.

The host generally maintains a stable microbiota. Stability ensures that beneficial symbionts and their associated functions persist over time. Host regulatory mechanisms like physical barriers, mucosal antibodies, and immune systems work to promote the growth of certain microbes, exclude others, and keep the microbiota in check. Furthermore, because some microbes are functionally redundant and can substitute for one another, community function can be retained despite shifts in composition. In fact, alterations to the function of these naturally occurring communities have been implicated in diseases like inflammatory bowel syndrome, type 2 diabetes, bacterial vaginosis, and colorectal cancer. Nevertheless, it is unknown the extent to which fluctuations in host and microbial environments, and resultant variation in the microbiota, can be afforded before these changes become detrimental. Years of research show that microbiota are often host species- and niche-specific, and across hosts, the microbiota varies with a myriad of factors like diet, age, antibiotic use, habitat, season, and environmental stressors. However, it is very likely that numerous other factors are driving variation in microbiota composition and function among hosts, and determining how this variation affects host phenotype is a key line of inquiry.

I study the gut microbiome of spotted hyenas! Photo Credit: Lily Johnson-Ulrich

My research seeks to understand the stability, composition, and function of the microbiota at various body-sites and elucidate the socio-ecological traits of hosts influencing its structure. While most microbiome research is conducted in humans and mice, typically within the context of host health and disease; I study these questions in wild spotted-hyenas (Crocuta crocuta). Due to their complex social behavior, hyenas are an excellent model system to explore how microbiota both influence host behavior and respond to host ecology.

Spotted-hyenas are large, social carnivores inhabiting much of Sub-Saharan Africa. They live in large groups, called ‘clans’, which are structured by linear dominance hierarchies, where an individual’s position determines its priority of access to resources. Their societies are also characterized by female dominance, male-biased dispersal, and a high degree of fission-fusion dynamics, such that individuals move freely among subgroups several times per day. Hyenas are reared in communal dens for the first 9mo of life, are weaned at 12-18mo old, and reach reproductive maturity at 24mo, although most females do not bear young until they are at least 36mo. In my current research, I am investigating how host factors like social dominance rank, group membership, and patterns of association affect hyena microbiota structure and function. Do individuals of varying social ranks differ in the stability and functional potential of their microbial communities? Are certain microbial genetic pathways lacking in one group vs. another? How similar are the communities, in terms of composition and function, of hyenas that associate very closely? Once again, can this variation have implications for host phenotype?

About to collect body-swabs and other biological samples from a hyena, after darting

We use next-generation sequencing technologies, mainly 16Sr RNA sequencing to profile the taxonomic composition of the microbiota, and metagenomic sequencing to characterize its function. From shotgun metagenomic data, it is also possible to infer microbial community dynamics. Populations of microbes, like members of any ecological community, cooperate and compete with each other, break-down and synthesize metabolites, and adapt rapidly to ever-changing environmental conditions. A recently developed mathematical framework by Sung and colleagues (2017) reconstructs community metabolic networks from metagenomic and available metabolic data. In these networks, the nodes represent major taxa, and the edges, which are color-coded, represent interactions (gray: cooperative; red: competitive; see Figure below). Metabolites that are imported and degraded by a species are shown in purple, and those that are synthesized and exported are in blue. I hope to use this framework to identify, for example, the molecules that are important for hyena gut community function, and evaluate whether the microbial community is dominated by competitive or cooperative interactions. Changes in community function and dynamics in response to extreme fluctuations in prey abundance (e.g. arrival of migratory wildebeest) will also be assessed this way.

The human gut microbiota metabolic community-level network constructed by Sung and colleagues (2017). Also, Connie’s dream figure.

Despite the interesting questions being asked, and the multitude of research on diverse host-microbiome systems being conducted, we still have a long way to go as a field. The things we do not know are too many to list. But I hope that revival of innovative culture-based techniques, advances in single-cell genomics, and development of more encompassing bioinformatics tools can help address the many existing gaps in our knowledge.

Reference

Sung et al. (2017). Global metabolic interaction network of the human gut microbiota for context-specific community-scale analysis. Nature Communications 8: 1-12.

 

 

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Judi Brown Clarke receives Sequoyah Fellowship medal

We are proud to announce that BEACON’s Director of Diversity, Judi Brown Clarke recently received a Sequoyah Fellowship medal making her a lifetime member of the American Indian Science & Engineering Society (AISES). The Fellowship is named in honor of Sequoyah, the great Cherokee Indian who perfected the Cherokee alphabet and syllabary in 1821, resulting in the Cherokee Nation becoming literate in less than one year. In this spirit, AISES Sequoyah Fellows are recognized for their commitment to the mission of “excellence in STEM” and to the entire American Indian community. They bring honor to AISES by engaging in leadership, mentorship, and other acts of service that support the students and professionals in the AISES family.

Judi Brown Clarke receiving a Sequoyah Fellow Medal at the 2017 AISES National Confernce in Denver, CO.

In addition, BEACON co-sponsored an Alaska Native (Haida) pre-college student who presented her summer research project about “Divergent Evolution of Shipworms and Clams,” and an undergraduate summer intern who presented her research “Curriculum Development Coupling Traditional Ecological Knowledge with STEM.”

Left to Right: intern Sarah Peele, Sonia Ibarra, Joseph Hilliare, Nevaeh Peele, Wendy F. Smythe, and Lauren Smythe.

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Beneficial bacteria in Oz

This post is by MSU grad student Colleen Friel

Pea fields (with yellow-flowered canola growing in the background) near Esperance, WA.

Increasing agricultural sustainability is an important research focus in the face of climate change, rapid population increase, and growing food insecurity. Synthetic nitrogen fertilizers have fueled a huge boom in agricultural productivity in recent decades, but they come with serious environmental consequences. Fertilizer manufacturing requires large fossil fuel inputs, and fertilizer runoff poses environmental and public health threats such as eutrophication of waterways and marine ecosystems, destruction of coral reefs, and algal blooms. For example, runoff from farms along the Mississippi River has led to a dead zone in the Gulf of Mexico that is 8,776 square miles, or roughly the size of the state of New Jersey.

One alternative source of nitrogen comes from the interactions between a subset of plants called legumes and specialized soil bacteria known as rhizobia. This interaction begins when plants growing in low nitrogen environments release a chemical signal from their roots. If this signal is detected by a compatible rhizobium, the rhizobium releases its own signaling molecules that initiate morphological changes in the plant root. Root hairs curl to encompass the rhizobium, and the plant houses the rhizobium in special organs called nodules. Inside the nodules, rhizobia convert atmospheric nitrogen (N2) to ammonia (NH3), which plants are able to use. In exchange, the plant supplies its rhizobia with sugars from carbon fixed during photosynthesis.

There is a wide range of outcomes in this interaction. Due to incompatibilities in signaling and other molecular events required for successful colonization, not all rhizobia can form nodules on all legumes. In addition, some rhizobia-legume combinations can form nodules but fail to fix nitrogen after nodulation. Evolutionary theory predicts that there is strong pressure on the rhizobia to cheat in a “tragedy of the commons” situation: since a single plant usually is colonized by a number of different rhizobial strains in the wild, each strain faces pressure to dedicate resources to its own reproduction rather than to nitrogen fixation for the plant. This trend is predicted to lead to a total breakdown of the mutualism, where all rhizobia fix little to no nitrogen for their plant hosts. However, this is not the case, suggesting that plants are able to control their rhizobial partners in some way and prevent this “cheating.” This might arise in the form of plants being able reward more effective rhizobia, punish less effective rhizobia, or select for more effective rhizobia during colonization.

The ability to select for more effective rhizobial strains is very important for the application of biological nitrogen fixation in agriculture. When rhizobia are used in agriculture, seeds are usually inoculated with a single rhizobial strain that has been shown to fix large amounts of nitrogen in combination with a given crop plant. However, this inoculant strain is frequently outcompeted by native rhizobia that are able to form nodules on the crop plant but fix little to no nitrogen for their host. Some legumes have demonstrated the ability to pick out the strains of rhizobia that effectively fix nitrogen for them, while excluding ineffective strains. However, not all legumes are very good at this, and we do not know what mechanism plants use for this purpose.

Making friends with the locals.

I spent the summer of 2016 at the Centre for Rhizobium Studies (CRS) at Murdoch University in Perth, Western Australia (WA) to study how plants select for effective rhizobia. Clovers are commonly used as forage crops in WA agriculture, since they are able to tolerate the challenges facing growers in WA, including low rainfall and acidic and sandy soils. The Mediterranean clover Trifolium purpureum and the South African clover Trifolium polymorphum are two such species. Both species have an effective native rhizobial partner that nodulates and effectively fixes nitrogen. If you inoculate one plant with the other’s effective rhizobia, the rhizobia will form nodules but will not fix nitrogen. If the plants are inoculated with a mixture of the two strains, the plant will pick out its effective strain and only form nodules with that strain, even if it is outnumbered 100:1.

To explore how the plants are doing this, we made bacterial mutants in which the gene for one of the proteins necessary for nitrogen fixation was deleted. We then inoculated these mutants onto the plants to see whether they were able to detect the ability to fix nitrogen, or if they used another marker to determine if a strain was an effective partner. We are also testing how the rhizobia strains react to the signals sent out by the plant and how well they are able to grow on the root systems of the different plant species. This will tell us if the the nodulation patterns we see are being determined by competition between the rhizobia rather than selection by the plant.. Understanding how plants select effective rhizobia can help make commercial rhizobial inoculants more efficient.

Planting Lebeckia in a field of nonwetting soil.

While I was in Australia, I traveled throughout much of WA, going 500+ km north of Perth to West Binnu, WA and going 700+ km southeast to Esperance, WA. During these expeditions, I assisted with field work for ongoing projects at the CRS. These projects ranged from assessing the negative effects of various pesticide treatments on rhizobial colonization in pea crops to planting field trials of the newly domesticated crop Lebeckia, which can grow in very sandy and unique nonwetting soils that plague parts of WA. It was an amazing experience to be able to interact with growers across such a large part of the country and learn how different agriculture is in Australia compared to the US. The landscape, flora, and fauna were shockingly different, and it was shocking to be able to drive for hours without seeing much evidence of humans. It was fascinating to learn how agriculture has adapted to the heat, low rainfall, and challenging soils present in WA. I look forward to using the knowledge, techniques, and relationships I developed in Australia to inform my work and increase our understanding of legume-rhizobia interactions.

 

 

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Frame your science to make it accessible, including for your representative

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.

BEACON Congress resources (2017)

As a scientist communicating with the public, what if you want to go beyond sharing your science with an interested audience and advocate for Science? What if the audience doesn’t listen or believe you?

Tessa Solomon-Lane speaking at our BEACON Congress sandbox

At the 2017 Congress, we were excited to lead two public engagement sandboxes on topics specifically requested by BEACONites grappling with making their communication goals a reality: framing and public policy. Most scientists already engage with public audiences about STEM topics, from causal conversations to lab tours, blog posts, Twitter, and public talks. These interactions are fun, energizing, and rewarding. They can also be challenging. While many scientists engage because they want to share their science with interested audiences, situations arise when a scientist may want to change someone’s mind. Maybe there’s a vocal creationist in the audience. Scientists themselves may also seek out ‘controversial’ topics (e.g., vaccinations), audiences they disagree with, or complicated issues that do not have a one valid solution (e.g., climate change).

How does a scientist communicate effectively to these different publics? Our first sandbox focused on framing, a way of presenting information that appeals to and resonates with the audience, while ethically maintaining the integrity and accuracy of the science. This is one of the most important parts of effective communication, to the public or other scientists. The second sandbox focused on bridging the gap between STEM and public policy. There is a rapidly growing interest among STEM professionals to engage with public policy and policy makers. Our original data also show that BEACONites are interested in policy engagement; however, rates of engagement are relatively low.

How important is it that scientists engage with policy makers?

Here are some of the highlights from the sandboxes:

Build a Frame: Matching the scientific context to the audience

Frames are “interpretive storylines that set a specific train of thought in motion, communicating why an issue might be a problem, who or what might be responsible for it, and what should be done about it” (Nisbet, 2010).

To effectively frame a message, it is critical to identify your specific goals. What do you want your message to accomplish? Who is your audience, and what do they care about? Keep in mind that facts alone are not convincing! Researchers have debunked the Deficit Model, which imagines that if experts communicate information ‘correctly,’ then the public will automatically accept that information and take on those expert perspectives. It can be easy to forget that this approach does not work because it’s exciting to share data. Decisions about what content to communicate and how to frame it also brings up interesting ethical considerations. In building a storyline, think about what gets left out, what to simplify, and whether the resulting message remains accurate.

Delivery also matters. Humans are highly social animals, and relationships are important. Speak with respect. Be enthusiastic (if appropriate for the topic). Listen early and often. Meet people where they are and be able to go off script and have a conversation. Resist the temptation to view ‘quality of life’ frames as ‘dumbing down.’ Be humble about the skills we develop as scientists and take for granted. We recognize that science generates questions, but the public often wants answers. (Are eggs good for you, or not?!) Separating information from misinformation, or good science from bad science, is not a trivial task. Finally, not everyone wants to engage. Or your effort may not be worth it. Respectfully taking ‘no’ for answer can build trust and credibility, so not engaging can be a beneficial decision.

Bridging the gap between STEM and public policy 

Framing scientific messages for elected officials was the most requested topic at our UT Austin Public Engagement Workshop. There are many strategies for engaging with public policy and policy makers. Dr. Judi Brown Clarke, BEACON Diversity Director and former Lansing City Council president, running in the general election for Lansing mayor, provided insight on these questions, engagement strategies, and more.

Dr. Judi Brown Clarke speaking at our policy sandbox

To get started, know who represents you, from local to the federal government. These elected officials—or in reality, their staff—are who you will be engaging with. Know your audience and build a relationship with the staffers. Politicians hear from all kinds of lobby groups, and they should hear from scientists, too! You could advocate for the institution of science, basic research funding, and/or share the importance of your work. It is also critical to be solution-oriented. Scientists may make decisions based on data, but political decision-making is driven by money and special interest groups. The budget is a zero sum game. Why should money go towards your cause, not someone else’s? Representatives also don’t have the background or the time to be an expert in everything, so it’s important to be specific. For example, rather than expressing disapproval about draft legislation, hoping someone will learn from your teachable moment, provide specific changes to the text and explain your reasoning.

Beyond phone calls and emails, there are excellent opportunities to engage locally and build community relationships. Know your representatives’ positions on issues relevant to STEM fields, and support local candidates. You can offer to serve as a science ‘translator’ for local staffers who can make science accessible and correct misconceptions. You can also invite your representatives for a lab tour. It may surprise you who accepts the invitation! Finally, there are fellowships that place scientists in Congressional offices.

Of the 435 members in the House of Representatives, there is 1 chemist, 1 microbiologist, 1 physicist, and 7 engineers. However, more and more STEM professionals are getting involved in politics. Some are even running for office themselves! If you’re interested, check out 314Action, an organization started by chemist and breast cancer researcher Shaughnessy Naughton, to help scientists run for office.

Learn more from our framing and policy resources here. Resources include calls to action and approaches to engagement; how to’s and recommendations; science communication online toolkits, training, and resources; and STEM & public policy training and resources. We will also be running a day long workshop similar to our sandboxes at UT Austin in the spring of 2018.

Special thanks to our invited speakers Dr. Judi Brown Clarke, Dr. Rob Pennock, and Kim Ward and Jessi Adler, from the Michigan State Communications & Brand Strategy, who contributed to these sandboxes.

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Smells like Mean Sprit

This post is written by BEACON’s own managing director Danielle Whittaker about her work that has been accepted pending minor revisions in a special issue of Journal of Comparative Physiology A. 

Dueling Juncos ~ Junco picture from Cortes Island Canada. Photo courtesy of Island Light Photography

Fighting is risky – at best, it uses up energy and time, and at worst, it results in injury and death. But the potential rewards can be major, like food, territory, maybe even a chance to mate with another female. How does an animal decide when to take that risk, and when to skip it? The answer may be found in their opponent’s smell.

Fighting ability and aggressive behavior are often linked to testosterone. In most animal species, males usually have higher levels of testosterone than females, though there is variation in both sexes. Testosterone alone doesn’t explain variation in behavior and other linked traits, however. Hormones like testosterone function as signaling molecules that tell receiving tissues to turn certain functions on or off, like building muscle or changing levels of stress hormones. Androgen receptors in the tissues receive that message, and the strength of the tissue’s response to the message depends on how many receptors it has. For example, Dr. Kim Rosvall and colleagues at Indiana University found that the density of androgen receptors in the brains of dark-eyed juncos, a common songbird, was related to aggressive behavior in response to an intruder.

Is there any way that birds can get information about their potential rivals’ hormones and hormone receptors, in order to predict their behavior and decide whether or not to attack? A likely mechanism is odor. For nearly a decade, I’ve been studying how dark-eyed juncos and other birds use odor from preen oil, secreted from the uropygial gland and spread on the feathers during preening, to assess and choose mates (see past blog posts here and here). I teamed up with Kim Rosvall to study the links between odor, aggression, testosterone, and uropygial gland androgen receptors of these same birds.

Danielle Whittaker picking up chicks. (Note: these are not juncos.)

At Mountain Lake Biological Station in Virginia, we located breeding juncos on their territories. Each subject was either a female incubating eggs, or a male mated to a female who was incubating. Incubation is a time when the birds are likely to aggressively defend their territories, to ensure they are able to care for the nestlings when they hatch. We presented each bird with a junco in a cage (we call this a “simulated territorial intrusion”). The bird typically responds with aggressive behavior, like swooping over or dive-bombing the cage (“flyovers”) or, if it’s a male, singing at the intruder. Spending time close to the cage is also considered aggressive. We measured all of these behaviors and then captured the bird to take samples. We measured the testosterone levels in their blood, the volatile compounds in their preen oil, and the levels of gene expression of androgen receptors in their uropygial glands.

The odor of a bird predicted how aggressively that bird would behave towards an intruder. These odors are complex, with 15 or more individual components, like a perfume. Different components correlated with different aggressive behaviors, such that different aspects of an individual’s odor related to how many songs they sang towards the intruder (in males), how much time they spent near the intruder’s cage (in females), and how many times they swooped over the cage (in both sexes). This level of detail suggests that an astute rival could detect not only how aggressive their opponent may be, but also what type of response they would be likely to face.

Gas chromatography-mass spectrometry chromatogram of junco preen oil, showing volatile compound peaks. By Helena Soini, modified from Whittaker et al 2013

Next we looked at whether this relationship was due to testosterone and androgen receptors affecting that odor. We found that in males only, both circulating testosterone and uropygial gland androgen receptors interacted to predict that male’s odor. This relationship was not found in females, which suggests that maybe a different hormone is responsible for communicating a female’s likelihood of attack.

This study shows us that individual odor in birds contains a wealth of information for potential rivals as well as potential mates. The links between hormones, behavior, and smell suggests that this signal is “honest” and can’t be bluffed. For many years, people believed that birds had little to no sense of smell (and some still do), but more and more studies are debunking this idea. Similarly, humans are believed to have a poor sense of smell compared to other mammals… but I often wonder just how much of our judgments of each other, and the decisions we make as a result, are based on smell, without us even knowing it.

 

 

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UCI Summer Undergraduate Research Fellowship Program

This post is written by UC Irvine grad student Aide Macias Munoz

Adiya Moore, Aide Macias-Muñoz and Aline Rangel Olguin during a coffee break at the Ward Watt Festschrift

My advisor Adriana Briscoe is a Faculty Affiliate of BEACON, and I have been fortunate to be a member of this supportive community since starting my PhD in 2012. I appreciate that BEACON has many projects aimed at increasing diversity in science, some of which highlight the importance of mentoring at all educational levels. This summer our department of Ecology and Evolutionary Biology at the University of California, Irvine partnered with UCI Graduate Division to host North Carolina A&T students through the Summer Undergraduate Research Fellowship program. Graduate students from our department were assigned a mentee interested in working in our labs. Mentors were required to participate in a teaching seminar for an academic quarter aimed at learning techniques for effective mentoring. During this seminar, we discussed the importance of communication, differences between a mentor and advisor, and we designed a research project that complemented the students’ busy schedules. Aside from the research projects that we planned for our mentees, they were required to participate in classes such as writing courses, GRE prep classes, and presentation workshops.

Before her UCI visit, my mentee Adiya Moore and I communicated through email about her potential project in the lab. I shared with her NSF proposals that I had written for the particular project that she would assist with and two review articles relating to the project. She arrived to our lab ready to work. Upon arrival, we met to discuss the aims of the project, to plan a schedule, and to answer any questions that she might have. Her project was to investigate gene duplication, gene expression and cis-regulation of vision-related genes in Heliconius melpomene butterflies. Due to time constraints, she had to focus her analyses on a small subset of genes. During the first week, she learned how to use NCBI BLAST and MEGA to make gene trees and look for gene duplications. Next, I gave her gene expression data which she plotted and analyzed for our genes of interest. The rest of her time was spent identifying the location of these genes in a reference genome and looking for areas of open chromatin near these genes. Aside from learning bioinformatics tools, we worked in the lab to do DNA extractions and PCRs.

Adiya Moore standing by her poster at UCI summer research symposium.

In order to complete the project, I had already done some of the data processing and had output files ready for Adiya to work with. It was an interesting experience for me to examine ways in which someone else might learn best. Adiya was a quick learner, and I realized that an effective way was for me to show her how to do something and explain the rationale, then she did it with my supervision, and then she did it on her own. We met weekly to discuss progress and set goals and I checked in daily in case she had any questions. Since the summer program also required students to write a mock NSF proposal and scientific article, I shared my proposals with her to use as examples and I proofread her essays. Students also had to do a presentation at the end of the summer, so Adiya presented a talk to our lab during 3 separate lab meetings. I received good feedback from Adiya about the mentoring style that I employed over the summer. While she worked a lot on her own, I had beforehand talked with her about the project and taught her how to do what needed to be done, and I was always available if she had questions.

Our summer together ended with a lab trip to Colorado for a conference. The conference (Ward Watt Festschrift) took place at the Rocky Mountain Biological Laboratory, a site full of biodiversity and interesting research projects. Adiya, Aline –a visiting undergraduate student from UNAM, and I presented posters and discussed our research and career goals with faculty in attendance. Many professors were impressed by Adiya’s work and tried to convince her to continue in academia. Upon our return from the conference, Adiya did both a talk and a poster in a UCI symposium for summer research students. While her goal is to attend dental school, Adiya put in a huge effort to learn about our lab and to complete the project. It was an extremely rewarding experience to work in the lab with such a driven and self-motivated undergraduate.

Arches National Park- We saw this on our drive to Colorado.

Rocky Mountain Biological Laboratory

Aline Rangel Olguin, Aide Macias-Muñoz, and Adiya Moore exploring Emerald Lake during a conference break.

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