Evolutionary AI site with expert podcasts and a COVID-19 intervention demo

The Evolutionary AI research group at Sentient has moved to Cognizant Technology Solutions. The group includes several current and past BEACONites, including Risto Miikkulainen, Elliot Meyerson, Jason Liang, and Santiago Gonzalez, and past interns Aditya Rawal and Khaled Talukder.  The group has a new website, https://evolution.ml/; the earlier content (announced previously in this blog) is there, including video interviews with 17 academic and industry leaders  on “The Future of AI”, as well as the “Evolution is the New Deep Learning” microsite.

Following the idea of expert interviews, the site showcases five new podcasts in the Pulse of AI series (https://evolution.ml/podcasts). In these podcasts, Jason Stoughton discusses topics such as biological vs. computational evolution, trustworthy AI, AutoML, demystifying AI, and open-endedness with Stephanie Forrest, Joydeep Ghosh, Babak Hodjat, Quoc Le, Risto Miikkulainen, Jordan Pollack, and Ken Stanley.

There is also a new site on decision making (https://evolution.ml/esp), featuring research on “Evolutionary Surrogate-assisted Prescription.” The goal is to extend AI from predicting what will happen to prescribing what we should do about it. The idea is to first train a predictor neural network through supervised learning, and then use it as a surrogate to evolve a prescriptor neural network to make good decisions. The site features papers, visualizations, and demos on various game domains (including FlappyBird!) showing how this approach can be sample-efficient, reliable, and safe in sequential decision tasks.

A major new part of the site focuses on COVID-19 (https://evolution.ml/esp/npi): It demonstrates how the same technology can be used to model the potential effects of non-pharmaceutical intervention (NPI) strategies to contain and mitigate the pandemic. The predictor is trained with historical data on the number of cases and the NPIs over time in various countries, i.e. restrictions on schools and workplaces, public events and gatherings, and transportation. A Pareto front of prescriptors is then evolved to discover the best tradeoffs between minimizing cases and restrictions. To illustrate this principle, the site includes an interactive demo: you can explore how, given your preferred tradeoff, the pandemic could be contained and mitigated in different countries.

We invite you to explore the “evolution.ml” site—and perhaps also bring your own expertise in AI to help deal with COVID-19!

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Engaging Galápagos Students and Educators in Evolutionary Activities

This blog post is by Madison Bovee, Alexa Warwick, John G. Phillips, Brant G. Miller, and Christine Parent.

Evolutionary research is conducted across the globe, yet no location may be as emblematic as the Galápagos Islands (Figure 1). Made famous by Charles Darwin’s visit in 1835, long term research on the islands continues to advance the field of evolution. Even though international scientists frequently conduct research in locations like the Galápagos, all too often they collect data and leave without significant engagement with local communities and stakeholders. Given that evolution is a critical yet challenging topic to learn, efforts to engage these communities could help highlight the importance of the ecosystem they live in for evolutionary advances.

Figure 1. A map of the Galápagos Islands denoting the geological age of each island and sampling locations used by the Parent Lab in their evolutionary research on snails. Figure courtesy of Phillips et al. 2020. ES = Española, FA = Fernandina, FL = Floreana, PA = Pinta, RA = Rábida, SC = Santa Cruz, SA = Santiago SL = San Cristóbal. Isabela samples are partitioned by volcano: AL = Alcedo, DA = Darwin, CA = Cerro Azul, SN = Sierra Negra, WF = Wolf.

In Ecuador specifically, previous work has shown only 50% of the population are accepting of evolution, placing them 14th out of the 19 Latin American countries surveyed, and lower than most European countries (Pew Research Center 2014, Miller et al. 2006). Thus, it seems the evolutionary lessons from iconic organisms like the finches and tortoises have had a much greater impact outside of Ecuador than within its borders. Dr. Christine Parent’s lab at the University of Idaho (UI) has a history of public engagement in the Galápagos Islands using her research on snails (Parent and Crespi 2006, 2009; Parent et al. 2008, Kraemer et al. 2019, Phillips et al. 2020). Last year we began collaborating with one of the local Galápagos schools: Tomas de Berlanga School in Bellavista (island of Santa Cruz), thanks to funding from BEACON (DBI-0939454) and the National Science Foundation (#1751157 to Dr. Parent).

The team consisted of Dr. Parent, Dr. John Phillips (Parent Lab postdoc), Dr. Brant G. Miller (UI education faculty), Madison Bovee (UI pre-service elementary teacher), and Dr. Alexa Warwick (MSU faculty). We had the opportunity to work with students aged 9–11 years old. Our goal was to expose them to the fundamental importance of evolution in biology and in their everyday lives. We used inquiry-based learning strategies to enhance their understanding of basic evolutionary and ecological principles by using the ecosystems in their own backyard. We had three full days to help students become more familiar with evolutionary research within the Galápagos Islands.

Day one consisted of evaluating the students’ familiarity with the theory of evolution and practicing data collection and inference. The students were split into three smaller groups each led by one of our team members and assisted by a local teacher. First, we discussed how to make thoughtful observations and then asked them to observe their surroundings on a diversity walk that was literally in a park near their school. Students recorded their observations in their journals by completing the following prompts: “I notice”,  “I wonder”, and “It reminds me of”.  This activity allowed the students to start thinking like a scientist. Next they worked in pairs to analyze authentic science data as part of a Data Nugget, followed by group discussion about what they learned.

Student observation in her notebook about the finch (‘el pinzon’) and wondering how it can sit on a cactus without hurting itself.

A pair of students working on a Data Nugget.

As the students were now prepared to think more abstractly, day two focused on evolutionary learning and preparation to have the students create their own inquiry projects. To start the day we had two scientists present, Dr. Christine Parent and Dr. Satoshi Chiba (Tohoku University), who have been conducting snail research on the Galápagos and other oceanic islands. These presentations showed the students exciting examples of evolutionary research and highlighted the value and unique opportunities that come from research in the Galápagos Islands. Students then explored evolutionary ideas through the bird beak activity, inspired by beak evolution of finches in the Galápagos. Students used different tools to represent a bird’s beak and considered the relationship between the beak and a bird’s ability to find food and survive in a given environment. Finally, we ended the day with each of the three groups of students coming up with 50 questions about snails. We then discussed what makes a question testable and whether we could answer the question within our time frame and other restrictions (only collecting snail shells rather than live snails). Once the question was selected students discussed their methodology and materials to prepare for day three.

Dr. Parent presenting to all the students.

Exploring evolution with the bird beak activity.

Day three solely consisted of the students investigating their inquiry-based question about snails, by collecting and analyzing data to make claims answering their selected question. The three groups and all chose similar, but unique questions that they felt were testable and interesting. We had the opportunity to conduct this exercise on a local coffee plantation to collect our data by looking for snail shells. Each group then prepared and presented their results.

Looking for snail shells for their inquiry projects.

Holding snail shells found on the diversity walk.

A group of students presenting their project results.

The students grew within these three days tremendously and so did the team. We had to overcome barriers that we didn’t expect, such as the language barrier (it was a bilingual school but the younger students were not as comfortable with English), lack of knowledge of the students’ background in science, and how active and energetic the students were. However, we adapted to these changes within the first day and we used these barriers to our advantage. For example, we were able to enhance their background in evolution on the first day which led to our other two days running smoother since we knew what knowledge they were relying on. We also created lessons that were culturally relevant and used hands-on activity which helped the students relate to our lessons.

Our efforts were successful as evaluated by the students’ pre- and post-assessments. Overall, 88% of the 42 students who completed the post-assessment agreed or strongly agreed that they liked science and 56% wanted to be a scientist. About half of the students (52%) agreed or strongly agreed that different organisms can have the same common ancestor and just under half (45%) said they could explain how natural selection worked. Thus, we think their knowledge about evolution grew and their curiosity sparked. In addition, they learned more about the importance of the Galapagos in conducting scientific research, and 71% responded to the post-assessment question “Why do you think the Galápagos attracts so many scientists?” with mention of the unique plants and animals found there. For example, one student wrote “Hay especies endemicas, cual significa, que están ubicadas en un solo lugar en el mundo, en este caso Galápagos” (There are endemic species, which means that they are located in only one place in the world, in this case Galápagos).  We also taught them how to do inquiry-based research and helped these students to “think like a scientist”. When they were asked what the most interesting thing they learned, 76% mentioned the snails, suggesting their experience investigating their own snail questions was impactful. For example, one student wrote “De trabajar en grupo y sobre los caracoles” (working in groups and about the snails). This inquiry experience is a tool they will be able to use the rest of their lives and now they also have the information to use this tool right in their backyard.

Finally, we greatly appreciate the assistance from the local teachers with classroom management and translating instructions during the three days of working with the students, as well the school administrators with logistics and planning, especially Michelle Rothenbach and Justin Scoggin. We look forward to continuing to collaborate with teachers and students from the Tomas de Berlanga School on evolutionary education in the future.

An overview of NSF-REU funded undergraduate research conducted in conjunction with our BEACON outreach can also be found here: https://www.uidaho.edu/sci/biology/news/features/2019/galapagos


Kraemer, A. C., Philip, C. W., Rankin, A. M., & Parent, C. E. (2019). Trade-offs direct the evolution of coloration in Galápagos land snails. Proceedings of the Royal Society of London. Series B. Biological Sciences, 286(1894), 1–9. doi: 10.1098/rspb.2018.2278

Miller, J. D., Scott, E. C., & Okamoto, S. (2006). Public Acceptance of Evolution. Science, 313(5788), 765–766. doi: 10.1126/science.1126746

Parent, C. E., & Crespi, B. J. (2009). Ecological opportunity in adaptive radiation of Galápagos endemic land snails. American Naturalist, 174(6), 898–905. doi: 10.1086/646604

Parent, C. E., & Crespi, B. J. (2006). Sequential Colonization and Diversification of Galápagos Endemic Land Snail Genus Bulimulus (Gastropoda, Stylommatophora). Evolution, 60(11), 2311. doi: 10.1554/06-366.1

Pew Research Center. 2014. Religion in Latin America: Widespread change in a historically catholic region.

Phillips, J. G., Linscott, T. M., Rankin, A. M., Kraemer, A. C., Shoobs, N. F., & Parent, C. E. (2020). Archipelago-wide patterns of colonization and speciation among an endemic radiation of Galápagos land snails. Journal of Heredity, esz068, 92–102. doi: 10.1093/jhered/esz068.

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How Claire from the BA test kitchen made me rethink our scientific role models

This blog post is by MSU faculty member Arend Hintze.

I love making stuff, let it be wood crafting or building cosplay Halloween costumes for my kids. However, I also like to do things the right way.  Consequently, I have to learn new skills all the time. To that end, I watch a lot making of videos and tutorials.  Over time I realized that I spend a lot of time watching experts on YouTube doing things.  At first, I thought I am just a sucker for infotainment, but then I took a closer look at my YouTube-history. I found confirmation for the infotainment preference. I watch a lot of Physics Girl, Computerphile, Numberphile, the Backyardscientist, Captain Disillusion, Today I Found Out, Scott Manley, the Slowmo-Guys, SciManDan, and Veritassium. These all fall into the category of science or technology dissemination. But I also saw that I follow Claire from the Bon Appétit test kitchen, Adam from Tested, Peter Brown, Odin Makes. All YouTuber’s who are experts in what they do, but instead of disseminating scientific content or technological advancements, they usually build or create things.

Claire Saffitz from Bon Appétit’s BA Test Kitchen

Here comes the strange observation. Me being a scientist, I feel much more connected with the makers. I have a much deeper emotional connection with Claire and Adam than with Bill Nye or Neil deGrasse Tyson. But why is that?

Most science YouTubers talk about scientific facts, and how they can be understood. They debunk false claims and fake news. Or they show advancements, and how sophisticated detectors allow us to understand the very stuff reality is made from. While I love all of that, I don’t feel myself doing science properly represented. Yes, accomplishments are great, but 99.9% of the time, I don’t feel like I accomplished something.  Scientific discoveries are rare, most experiments fail, and results keep contradict each other until much later when suddenly everything makes sense. No, I don’t have imposter syndrome, that is an entirely different thing.  Almost by definition, we scientists work on the edge of the known. If we didn’t try to push this boundary, we wouldn’t do our job right. If our experiments worked out every single time, we could have known the answer beforehand. It is “being wrong” that is informative. It is “not knowing” what drives the quest for knowledge, and it is a long, cumbersome, and often frustrating path.

However, the typical US education is not preparing students for such challenges. STEM education makes science “fun,” everything has an answer, and tests only require you to regurgitate these answers. Our kids experience immediate rewards not only in their learning environments but also in how they play. Digital games are optimized for instant rewards, which is what makes them so addictive.  Critical thinking is nice, but you also need to come up with new and creative ways to solve problems.

We need to show our students and children that failures are an integral part of learning.  We need to show them how to deal with setbacks. I think students learn the most from watching others fail and deal with failure than just being baffled by other’s accomplishments. One allows you to empathize, and the other makes you depressed.

Adam Savage from Tested and MythBusters

This is the reason why I watch MythBusters with my kids, where “failure is always an option.”

This is the reason why I try to get my kids with questions as quickly as possible to a point where they don’t know anymore. I want them to be comfortable with not knowing. I need them to enjoy this state, as it is the motor for curiosity and creative exploration. I stereotypically respond to the “I don’t know” answer with “take a guess!”

This is also the reason why I emotionally bond with Adam and Claire. Both explore, both fail often, and both do “not know” in front of the camera. The only difference between Adam and Claire is in their ability to cope. Adam has more than ten years of experience from MythBusters in not getting the expected results. That is probably the reason why he can enjoy what he does so much more.  He lets you feel how little he is bothered by failure. Similarly, Claire shows how frustrated she is when something doesn’t go according to plan. She also lets us experience how she deals with that frustration: A sigh, a comment, and then she goes on. No regrets! Now she knows more, and now she can try something new, which ultimately leads to the answer.

I don’t want the other science YouTubers and science advocates to change what they do, please keep up the great work. I enjoy every bit of what you are doing. The reason why I think Adam and Claire are also such great science role models is their ability to struggle publicly. They show how failing is an integral part of finding the solution, and their ability to cope with that frustration is exemplary.

Thank you for that, and I promise I keep failing, thank you for leading by example.

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Goodman Extends BEACON’s Collaborations in China

This post is by BEACON’s Executive Director Erik Goodman.

On Oct. 19, 2019, I left East Lansing for China, with stops in Shantou, Guangzhou and Shanghai. I received a warm and wonderful reception everywhere I went, in spite of tariffs, trade wars, and all the political difficulties that fill the news.

My first stop was in Shantou, on the southern coast of China, a few hours from Guangzhou, Shenzhen and HongKong. At Shantou University, I was warmly welcomed by Prof. Zhun Fan (on left with his wife, her parents, and son, and yes, the ChaoShan-style food was yummy! Zhun is a former doctoral advisee of mine, and he now leads the Laboratory for Robotics and Intelligent Manufacturing, and also the Provincial Key Laboratory for Digital Signal and Information Processing (DSIP). BEACON is a co-founder of a joint center, the Center for Evolutionary Intelligence and Robotics, established between Prof. Fan’s laboratory and BEACON, with additional partners at Guangdong University of Technology and Nanjing University of Aeronautics and Astronautics. During four days in Shantou, I gave three lectures and heard reports from students and faculty about their research progress. Discussions led to many new ideas to explore. I met with Shantou University Provost Wang to review our past collaboration and investigate the possibility of broadening it next year to include more participation in the application of evolutionary computation to civil engineering. Prof. Wang is an expert in structural health monitoring and energy capture to power sensors, areas in which MSU CEE also has expertise. During the visit, the provincial government announced continuing support for the DSIP Key Laboratory, and also 1M RMB (about US$140,000) in support of the activities of the joint center with BEACON. The joint center received an excellent rating from the government on its operations to date. Included in that are Goodman’s annual visits and the visit of Chaoda Peng, a graduate student at Guangdong University of Technology, to BEACON for two years, working with Goodman. Peng is advised by Prof. Hailin Liu, who has also been a long-term visitor to BEACON.

The next stop was Guangdong University of Technology, in Guangzhou, a 3-hour train ride from Shantou (a “slow” train—only 120mph). I was hosted by Prof. Hailin Liu and gave a presentation on recent work I am involved in at BEACON, and met with students and faculty involved in evolutionary computation. In the evening, they took me on a river tour of downtown Guangzhou, and the picture shows how much more light show there is in Guangzhou than in Times Square, New York! Coordinated moving images on a series of a dozen or more buildings! Absolutely spectacular!

Goodman with Prof. Lihong Xu, BEACON Advisory Professor, at Tongji University, with advertisement of Goodman’s lecture.

I then returned to Shanghai and met for two days with the greenhouse control team at Tongji University, in a collaboration extending more than ten years, resulting in dozens of joint papers and in control systems being tested in commercial-sized greenhouses. Yuanping Su and Chunteng Bao are BEACON visitors working with me this year, and I was delighted to participate in the doctoral defense of Leilei Cao, who was another two-year visitor in BEACON. His work was nominated for an outstanding dissertation award. I lectured at Tongji University to about two hundred graduate students about our recent work on evolutionary deep learning and about my solid fuel rocket optimization work using a heterogeneous parallel genetic algorithm. I also gave a similar talk at East China Normal University the next day, for about 50 graduate students.

Then it was off to India for a month of collaboration on a short course, industry workshop, and book, with BEACON’s Prof. Kalyanmoy Deb and two distinguished Indian scholars. But that’s for another blog!

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Using lessons from Facebook and fence-building to understand the evolution of deadly bacteria

This blog post is by University of Idaho graduate student Clinton Elg.

Evolution of a Deadly Bacteria

Vibrio cholerae is bacteria that resides in water and causes deadly cholera disease. While areas of the world with functional sewage and potable water are largely unaffected, there is still no definitive cure for the disease. It remains rampant in less developed regions and often acts as a deadly second act after natural disaster and wars destroy infrastructure.

Bacteria are constantly evolving, and this includes illness-causing bacteria like V. cholera. Evolution leads to new major outbreaks called pandemics, with each new pandemic strain of bacteria acting like an updated software version which outcompetes and outperforms older versions. V. cholerae is now in its seventh pandemic, and the latest strain namedEl Tor V. cholerae” contains two unique pieces of DNA not found in earlier pandemics. Scientists have named these unique pieces of DNA Vibrio Seventh Pandemic Island (VSP) I & II. The VSP’s contains around 33 genes, with each gene a DNA “blueprint” that the bacteria will convert into a protein “machine”. What kind of machinery do these VSP genes encode for? How does this new cellular machinery help El Tor V. cholerae outcompete older pandemics of the disease?

Breakthrough at Michigan State University and Tufts University

In 2018, a remarkable discovery was made by PhD Candidate Geoffrey Severin and Miriam Ramliden, in the Chris Waters lab at Michigan State University (MSU) and the Wai-Leung Ng lab at Tufts University, respectively. It had been known that a VSP gene named dncV was important for El Tor V. cholerae to cause disease, but the reason remained elusive. The team discovered that increasing the number of “blueprint” copies of dncV within El Tor V. cholerae produced smaller populations of bacteria when grown on solid surfaces. These bacteria populations are called “colonies”, and scientists call colonies that shrink “small colony variants”. They later discovered that dncV encodes a molecular “switch” that activates the cell shrinking machinery of another VSP gene called capV. In the larger picture, this small colony variation may help explain why this is the leading strain sickening people around the world and is an early clue to unraveling the novel functions of the VSP’s in El Tor V. cholerae.


Figure 1. Representative images of a typical El Tor Vibrio cholerae colony (left) and a small colony variant of El Tor V. cholerae engineered to express excess dncV (right).

Figure 2. Dr. Chris Waters (L) and Geoffery Severin (R) from Michigan State University.


Building a Fence (Around Gene Networks)

Despite this scientific home run, much work remains. Imagine a human analogy: the tools required to create a fence include a hammer, nails, wood, level, chalk string, shovel, and concrete. From looking at these tools piled on the ground, one might reasonably predict that somebody is planning to build a fence.  In the VSP’s of El Tor V. cholera, we have a pile of 33 new and strange tools and we only know what 2 of them do!  Now imagine the tools for fence building were jumbled in a pile of other random tools. Without knowing what the tools are, or what tasks they might accomplish, how would you pick out the seven tools and their association with fence building? In a biological sense, we have 31 unknown genes in the VSP’s of El Tor V. cholera that group into an unknown number of “gene networks”. Each gene network is a group of genes that work together to accomplish a specific cellular task.

Geoff and Chris decided that they needed a way to predict the number of gene networks and the genes that constitute each network. They reached out to Dr. Eva Top at University of Idaho and began a collaboration with her PhD student Clint Elg from the Bioinformatics and Computation Biology (BCB) program.

Figure 3. Dr. Eva Top (L) and Clint Elg (R) at the University of Idaho.

Using The Math Behind Facebook to Predict Gene Networks

To provide predictions of the gene networks in the VSP islands of El Tor V. cholera, Clint turned to what may seem an unlikely place: Facebook. Have you ever been on Facebook and seen a new friend recommended to you? Underlying this are complex mathematical models that predict social circles like your family or your co-workers. The predictions are made by seeing how mutually related (or “correlated”) you are to another user profile: the more you post or respond to another person, the higher your mathematical correlation.

In a similar fashion, we can use the thousands of bacterial DNA genomes available on the internet to see how often certain genes correlate with each other. Instead of predicting their social networks, we are predicting their gene networks! For example, consider the two genes found by Geoff, Wai-Leung, and Chris that provide small colony morphology, vc0178 and vc0179. These genes do nothing individually, but when found together they allow a change in bacteria size. Since evolution selects for DNA that provides some sort of advantage, we should expect these two genes to co-reside in bacterial genomes at a much higher rate than two randomly chosen genes.

The result is an alpha version of software, correlogy, built with the help of mathematician Ben Riddenhour from the Institute for Modeling Collaboration and Innovation (IMCI). Correlogy predicted vc0178 and vc0179 to be highly correlated by using data from thousands of bacterial genomes, matching what Geoff and Chris had biologically demonstrated in the lab! More importantly, the software has predicted gene networks for the remaining 31 VSP genes of unknown function and interactions. These predictions give protein specialists like Geoff and Chris a place to start investigating the VSP genes which fuel the modern Seventh Cholera Pandemic.

Figure 4. VSP gene networks as predicted by correlogy. Gene vc0179 encodes protein DncV, and gene vc0178 encodes protein CapV. These two genes work together as a gene network to allow the small colony morphology found in the modern El Tor Pandemic strain.

BEACON and Collaborative Science

Our research into the deadly disease of cholera is making important discoveries. We would like to express gratitude to the tax-payer funded National Science Foundation (NSF) and particularly the BEACON program. The NSF BEACON program enabled important insight into the evolution of a lethal bacteria by encouraging and funding a meaningful collaboration between biologists, protein specialists, computer scientists, and mathematicians.

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An Instinct for Truth: a new book by BEACON co-founder Robert T. Pennock

Book cover for An Instinct for TruthRobert T. Pennock, a BEACON co-founder and co-PI, has just published a new book. An Instinct for Truth: Curiosity and the Moral Character of Science is an exploration of the scientific mindset—such character virtues as curiosity, veracity, attentiveness, and humility to evidence—and its importance for science, democracy, and human flourishing.

The title comes from a quote from Charles Darwin, who wrote in a letter to a scientist colleague that “I believe there exists, & I feel within me, an instinct for truth, or knowledge or discovery, of something of the same nature as the instinct of virtue…”

Some of the research for the book was supported by BEACON. An Instinct for Truth provides the philosophical basis for the Scientific Virtues Toolbox responsible conduct of research (RCR) workshops that Pennock and colleagues developed for BEACON. They are now running virtue-based RCR workshops for various departments across campus and plan to expand nationally.

Pennock is also applying this scientific virtue-based approach to try to improve STEM education, arguing for the importance of teaching the values that comprise the scientific mindset. Software like Avida-ED and Salmon Run help teach evolution but they also are evolutionary playgrounds where students can exercise their scientific curiosity.

Robert T. Pennock is a Distinguished Professor at Lyman Briggs College at Michigan State University, with appointments in the departments of Philosophy and Computer Science & Engineering. In addition to BEACON, Pennock is affiliated with MSU”s Ecology, Evolutionary Biology, and Behavior (EEBB) program and Socially Engaged Philosophy of Science (SEPOS).

The book is published by MIT Press. Below is the book overview from the publisher’s website:

Exemplary scientists have a characteristic way of viewing the world and their work: their mindset and methods all aim at discovering truths about nature. In An Instinct for Truth, Robert Pennock explores this scientific mindset and argues that what Charles Darwin called “an instinct for truth, knowledge, and discovery” has a tacit moral structure—that it is important not only for scientific excellence and integrity but also for democracy and human flourishing. In an era of “post-truth,” the scientific drive to discover empirical truths has a special value.

Taking a virtue-theoretic perspective, Pennock explores curiosity, veracity, skepticism, humility to evidence, and other scientific virtues and vices. He explains that curiosity is the most distinctive element of the scientific character, by which other norms are shaped; discusses the passionate nature of scientific attentiveness; and calls for science education not only to teach scientific findings and methods but also to nurture the scientific mindset and its core values.

Drawing on historical sources as well as a sociological study of more than a thousand scientists, Pennock’s philosophical account is grounded in values that scientists themselves recognize they should aspire to. Pennock argues that epistemic and ethical values are normatively interconnected, and that for science and society to flourish, we need not just a philosophy of science, but a philosophy of the scientist.

“In An Instinct for Truth, a wide-ranging volume on philosophical, historical, religious and sociological aspects of the scientific vocation, Robert T. Pennock shows that not only is curiosity a powerful motivator in the drive for reliable knowledge, it also, if guided by a virtuous scientist, leads to socially beneficial outcomes. Any practicing scientist or student of science can benefit from Pennock’s observations about why we do science, or more, how to do science right.” — Rush D. Holt, CEO and Executive Publisher, American Association for the Advancement of Science

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BEACON alum Wendy Smythe receives AISES Professional of the Year award

Dr. Wendy Smythe, former BEACON Postdoctoral Research Fellow (2016-2018) received the American Indian Science and Engineering Society (AISES) Professional of the Year Award. 

Wendy Smythe, now a tenure track assistant professor at the University of Minnesota Duluth (UMD), received the AISES award based on her overall leadership and technical achievements.

She is Alaska Native Haida from Hydaburg, Alaska. Her Haida name is K’ah Skaahluwaa (laughing lady), from the Xáadas (Haida) clan of Sdast’ aas (Fish egg house). She works with Indigenous communities to couple STEM discipline with Traditional Ecological Knowledge (TEK) in K-12 education. Through her work, she seeks to increase the number of Indigenous people represented in STEM disciplines, increase diversity and innovation, and teach the next generation of Indigenous leaders.

Wendy has a dual Ph.D. in both environmental science and engineering and estuary and ocean systems from Oregon Health and Science University. Two years ago, she founded the Geoscience Foundation Education program in her tribal community of Hydaburg, Alaska, in collaboration with the tribe (Hydaburg Cooperative Association) and the Hydaburg School District.

In the fall of 2019, she joined UMD’s American Indian Studies Department, as a tenure track assistant professor, as the first scientist to join the department leading the new Masters of Tribal Resource and Environmental Stewardship program. She recently completed a technology and policy fellowship with the National Science Foundation’s AAAS Program.


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The evolution of academic posters: from Poster 1.0 to Better Poster 2.0 to Hybrid Poster 1.5

By: Natalie Vande Pol (PhD Candidate, Michigan State University)

This week marks the start of my 6th year as a PhD student in the Microbiology and Molecular Genetics program at Michigan State University. I have been extremely fortunate to attend a professional conference in my research field every summer since I began my graduate program. At 4 of those 5 conferences, I have presented a poster describing my research. (Figure 1) And until this year, there was a standard procedure for writing and designing a scientific poster. This year, that all changed…

Figure 1: MC11 poster session, July 2018 (Lodge, D.J., Cantrell, S.A., Luangsa-ard, J. et al. IMA Fungus (2018) 9: 52. https://doi.org/10.1007/BF03449438)

It all started with a video produced by Mike Morrison (@mikemorrison), an Industrial/Organizational Psychology PhD student at Michigan State University. In the video, Mr Morrison makes the argument that the standard poster format used by most academics is overly technical and usually obscures the main finding(s) of the science being presented (Figures 2 & 3). Also, the time required to parse the information on a poster means that most people attending a poster session are only able to really engage with 3-6 posters in an hour, severely limiting the dissemination of potentially useful knowledge through the scientific community. Mr. Morrison proposes an alternative poster design, which he calls “Poster 2.0” (Figure 4, Video). The biggest changes to the poster layout are 1) a large, central, simple takeaway message that summarizes the point of the poster in accessible language; 2) a “standalone” bar on the left with a very basic introduction, methods, and discussion; and 3) an “ammo” bar on the right with anything that the presenter might want to have handy when talking about their poster. The standalone bar is meant for someone to read about your research in more detail without needing to engage with the presenter. In addition, Mr. Morrison suggests including a QR code, which he suggests pointing to the paper associated with the poster subject so that readers can access the additional detail they might want.

Figure 2: “Poster 1.0” by Mr. Mike Morrison

Figure 3: My “Poster 1.0” at IMC11, July 2018.

Figure 4: “Poster 2.0” by Mike Morrison

“How to create a better research poster in less time (including templates)” by Mike Morrison

The big advantage to the Poster 2.0 format is that the takeaway message is highly accessible, meaning that it is a short, prominently displayed message in plain language and large font that can be read and understood in the time it takes to walk past the poster. It is also supposed to be very easy and fast to write the poster since the language is simple and the “ammo bar” is unformatted. The disadvantages of this format is that the very low detail of the introduction, methods, and intermediate results make it somewhat difficult for a reader to learn more about the project when the presenter is absent. Since most posters are hung and available all day in advance of the actual poster session, this can be disadvantageous. Now, some would say that this simply means that during the poster session, the reader will come and discuss the poster with the presenter, or read the paper using the QR code (if there is a paper and if the reader has a QR scanner on their phone). However, I have also overheard some more “old-fashioned” academics who regard this lack of instantaneously available detail and new format as “gimmicky” and faintly unacceptable/unprofessional.

Being a rebellious, tech-loving millennial, I decided to give the Poster 2.0 format a shot when writing a poster for a conference earlier this month. The first thing I learned was that it’s actually really hard to distil the main takeaway message, especially from my preliminary and incomplete results, which is what most posters describe. Moreover, it’s also really hard to distill an introduction, methods, results, and discussion into less than a quarter of the poster space. Ultimately, writing this poster was no faster than any of the other 4 posters I’ve written. In the end, I decided to create a hybrid version, which I jokingly called “Poster 1.5.” Poster 1.5 maintains the large, simple, prominent takeaway message and slightly abbreviated text, but has significantly more text than 2.0 and lacks the ammo bar. Finally, since I was presenting preliminary data, I had no paper to which to direct a QR code, so I eliminated that element as well. I will point out, the QR code doesn’t need to point to a paper, it could point to any form of supplementary multimedia (videos, audio, etc.), the presenter’s website, and so much more.

It turns out, I’m not the only one to have the idea for a hybrid. There is an active academic Twitter community around Poster 2.0, with followers posting pictures of their implementations and adaptations. Dr. Andrew R. Smith (@AndrewRSmith), an Associate Professor of Psychology at Appalachian State University posted a template for his own rendition of a Poster 1.5 (Figure 5).

Figure 5: “Poster 1.5” by Dr. Andrew R. Smith

When I presented my Poster 1.5, I had the most “traffic” at my poster than ever, especially from a more generalized audience. In the past, most of the people who have visited my posters were specialists who picked out keywords from my poster title and were working with the same organism. With the main takeaway of the poster front and center, I also met people who were interested in my methods and intermediate findings and the applications/implications for broader research. Discussion was more animated and since my entire poster was already written in plainer language, it was a lot easier for me to develop a generalized “schpiel” on the spot, rather than sifting through all the details and trying to create a schpiel adapted for each listener. It was much easier to add detail than to subtract it.

In conclusion, I think that the conversation and experimentation that Mr. Morrison instigated has been invaluable to academia. The same-old Poster 1.0 format has been so standard that nobody (except Mr. Morrison) even questioned whether there might be a better way to do things. Just having challenged the status-quo has radically shaken up poster design and new adaptations are being explored all the time. I’m very excited to see how poster design continues to evolve and expect we will see the rise of many new poster “species” tailored to the needs of different fields and content types.

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BEACON Team wins Best Paper Award in Evolutionary Machine Learning Track at GECCO 2019

Zhichao Lu and colleagues accepting the Best Paper Award at GECCO 2019

Congratulations to BEACONites Zhichao Lu, Ian Whalen, Vishnu Boddeti, Yashesh Dhebar, Kalyanmoy Deb, Erik Goodman, and Wolfgang Banzhaf! Their paper “NSGA-Net: Neural Architecture Search using Multi-Objective Genetic Algorithm” won the Best Paper Award in the Evolutionary Machine Learning track at GECCO 2019 in Prague.

There were in total 64 papers submitted to the Evolutionary Machine Learning (EML) track, only 16 of which were accepted as full papers. Two papers were nominated for Best Paper Award. Zhichao Lu and colleagues won the award based on the on-site voting from the conference attendees.

Here is the abstract of the paper, which can be accessed from arXiv: https://arxiv.org/abs/1810.03522

This paper introduces NSGA-Net – an evolutionary approach for neural architecture search (NAS). NSGA-Net is designed with three goals in mind: (1) a procedure considering multiple and conflicting objectives, (2) an efficient procedure balancing exploration and exploitation of the space of potential neural network architectures, and (3) a procedure finding a diverse set of trade-off network architectures achieved in a single run. NSGA-Net is a population-based search algorithm that explores a space of potential neural network architectures in three steps, namely, a population initialization step that is based on prior-knowledge from hand-crafted architectures, an exploration step comprising crossover and mutation of architectures, and finally an exploitation step that utilizes the hidden useful knowledge stored in the entire history of evaluated neural architectures in the form of a Bayesian Network. Experimental results suggest that combining the dual objectives of minimizing an error metric and computational complexity, as measured by FLOPs, allows NSGA-Net to find competitive neural architectures. Moreover, NSGA-Net achieves a comparable error rate on the CIFAR-10 dataset when compared to other state-of-the-art NAS methods while using orders of magnitude less computational resources. These results are encouraging and show the promise to further use of EC methods in various deep-learning paradigms.

The source code for the paper can be accessed from GitHub: https://github.com/ianwhale/nsga-net

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Genome Hackers – a near-peer, interdisciplinary summer program for high school girls

By: Cindy Yeh, Graduate Student, (Dunham Lab, Genome Sciences), University of Washington

Only 26% of the computing professional workforce is made of women, less than 10% of whom are women of color (ncwit.org). This is in contrast to the gender distribution in the life sciences, which is much closer to 50%. As technology continues to play an increasingly important role in our lives, addressing this gender disparity by giving young women access and exposure to computational thinking early is imperative.

I was introduced to programming as a high schooler, but never really learned how to code until I started my PhD program at the University of Washington in the Genome Sciences Department. Programming felt more intuitive when I was trying to implement a biological concept, such as finding the longest matching pattern in a DNA sequence using a suffix array or extracting information from FASTA files. Learning computer science can be intimidating, but I figured if this method allowed me to better understand its logic, it could be a great way to introduce young women to coding and make technical fields more accessible. Indeed, many research studies have found that integrated approaches are much more effective than traditional, non-interdisciplinary curricula. Furthermore, developing integrated lessons require many hours of professional development for which many teachers may not have time (Lin et al., 2018; Struyf et al. 2019; Salami et al., 2015; Stohlmann et al., 2012; Thibaut et al., 2018).

In 2017, as first year graduate students, my colleague, Andria Ellis, and I received a small grant from the National Center for Women in Information Technologies (NCWIT) to run a one-week, half-day summer camp for high school girls called Genome Hackers. We wanted our program not to have our participants walk away as experts in computer science or genomics, but to introduce them to concepts that they otherwise would never have the opportunity to learn prior to college. The idea was that if they were challenged by these topics in the future, they would seem less abstract or intimidating. We also wanted to teach real-world applications of computer science and how it specifically is used in genomics. With a team of graduate student instructors, our participants learned how to perform PCR to isolate and amplify a particular gene and subsequently Sanger sequence the PCR product to retrieve raw sequences. Simultaneously, we taught them the basics in programming through Python. By the end of the camp, the participants had written transcription and translation scripts, where they can directly take their Sanger sequencing results and determine the amino acid sequences of their gene. Furthermore, they shared their sequencing results with other students and generated a phylogenetic tree to investigate the relatedness of the same gene from various species. They also used their final amino acid sequence to generate a predicted protein structure compared across species as well.

Figure 1: 2017 participants learning how to pipette

Genome Hackers culminates in a poster session where the students share with scientists in the department (and with their family and friends!) their many accomplishments over the course of the week. This really helps tie the week together, and participants walk away with something concrete that they can show off. Furthermore, our camp is affordable ($50/week with scholarship available); this is in contrast to many other biotechnology camps where fees can be a deciding factor for many applicants, usually costing, at the minimum, $300, per week (these can sometimes cost upwards of $500 per participant!).

Figure 2: Participants working hard on their transcription and translation scripts

After receiving overwhelmingly positive feedback from graduate students, faculty, teachers, and parents, we will be running Genome Hackers in 2019 for its third year in a row. We are also running iterations of this camp through two other campuses (SoundBio Labs and University of Chicago). Here we will determine what aspects of our current curriculum are easy to implement and what areas need improvement. Our final goal is to package our program into something any high school biology teacher or graduate student can pick up and implement on their own without my or Andria’s presence.

Figure 3: 2017 participants presenting their findings to those teachers, parents, and scientists at University of Washington

Figure 4: 2018 participants presenting their findings to those teachers, parents, and scientists at University of Washington

Several of our former participants have now also participated in Girls Who Code at Fred Hutch or gone on to pursue technical degrees. One former participant has even returned to Genome Hackers as a near-peer mentor and may lead her own session this year. I never would have guessed that this was something I would accomplish (or even want to accomplish) as a graduate student. While I did put a lot of energy towards outreach and service as an undergraduate, being able to take what I have learned in the lab as a graduate student and materialize it into teaching high school students has been one of the most rewarding activities I’ve ever pursued in and outside of my scientific career. Andria and I are also both very lucky that our PIs (Cole Trapnell and Maitreya Dunham, respectively) appreciate outreach activities and continue to encourage us to pursue them.

Figure 5: Group photo from 2018. Cindy and Andria and are the ends of the front row.

We are always searching for new ideas or collaborators who may be interested in running their own version of Genome Hackers. We have a website (genomehackers.org) and an e-mail (genomehackersuw@nullgmail.com) and are very interested in hearing your comments.

Figure 6: Students’ confidence and interest levels before and after Genome Hackers

Participant Testimonials:

“I have been taught coding before, but I feel like […this program] introduced a new coding language very well.”


“I liked how I got to see how programming aided genome scientists.”


“My favorite part was getting to learn a new coding language, and combining two of my passions.”


“I wasn’t very interested in coding, but after actually doing some coding I now really like it and I might look into doing coding for a career with biology.”


“I will remember creating my first science poster. It felt amazing learning how to reach a conclusion and finally getting to have something to show for it.”


“I was really proud of myself for figuring out how to code a DNA strand into RNA.”




Lin, Y.-T., Wang, M.-T., Wu, C.-C., 2018. Design and Implementation of Interdisciplinary STEM Instruction: Teaching Programming by Computational Physics. The Asia-Pacific Education Researcher 28, 77–91. doi:10.1007/s40299-018-0415-0

Salami, M.K.A., Makela, C.J., Miranda, M.A.D., 2015. Assessing changes in teachers’ attitudes toward interdisciplinary STEM teaching. International Journal of Technology and Design Education 27, 63–88. doi:10.1007/s10798-015-9341-0

Stohlmann, M., Moore, T., Roehrig, G., 2012. Considerations for Teaching Integrated STEM Education. Journal of Pre-College Engineering Education Research 2, 28–34. doi:10.5703/1288284314653

Struyf, A., Loof, H.D., Pauw, J.B.-D., Petegem, P.V., 2019. Students’ engagement in different STEM learning environments: integrated STEM education as promising practice? International Journal of Science Education 41, 1387–1407. doi:10.1080/09500693.2019.1607983

Thibaut, L., Knipprath, H., Dehaene, W., Depaepe, F., 2018. The influence of teachers’ attitudes and school context on instructional practices in integrated STEM education. Teaching and Teacher Education 71, 190–205. doi:10.1016/j.tate.2017.12.014

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