BEACON Researchers at Work: Evolution with video games

This week’s BEACON Researchers at Work blog post is by MSU graduate student Leigh Sheneman.

LeighMost all of us remember sitting around thinking up wild possibilities of what our future would hold. For me, this daydreaming took place in the early 80s in the middle of nowhere Texas. Since there was little to do, I spent a lot of time playing computer games. Thus, my top “this could never happen, but it would be cool…” statements of my childhood were: a) to have my name associated with a computer game and b) to always be able to ask why without getting in trouble. Now these both seem simple (at the time these were BIG, I promise), so simple that I actually do them on a daily basis.

How, you ask, do I get to program a video game while doing research? The answer is EvoSphere, a digital evolution package that is built using the same technology used to create your favorite video game. The scientific goal of the project is to co-evolve the bodies and brains of digital organisms in a 3D digital world, and to explore what is similar or different among different evolving systems in a common environment.

However, since EvoSphere is developed using a gaming engine, people outside the evolution and/or programing fields can boot up their favorite gaming device and watch evolution in action! Our youth are engrossed in the world of video games. With EvoSphere we are able to bridge a world that people already know with scientific ideas to inspire more interest in STEM research.

While all this exciting outreach is taking place, the researcher in me can use the very same system to dig into the all-important question of “Why?” On that note, EvoSphere’s code base is extremely modular, meaning you can easily develop a new environment for your test organisms to explore. Further, the organisms are modular too. As researchers this gives us the ability to give multiple brain types to the same body form, or vise versa. This is demonstrated nicely in a video we submitted for the Virtual Creatures Competition at GECCO 2014.

As the video demonstrates, we currently have three working brain types: Markov (coded by Dr. Arend Hintze), NEAT (Dr. Joel Lehman) and a genetic programming (Dr. Stephan M. Winkler). Dr. Hintze and David Phillips worked together on the three body structures available. Any brain will work with any morphology. I joined the group, led by Dr. Rob Pennock, in May and have added the sensing abilities that make the food eating experiment in the video possible.

I could expand on EvoSphere’s ability to evolve 100s of organisms at a time or the different ways we visualize changes over time, but the amazing advances in digital evolution the program brings are much more exciting. By linking the brain and morphology we are able to monitor how evolution changes both body and behavior over time. Additionally, the linkage between brain and body adds tons of complexity, for free! Which is huge, as a lack of complexity is a limiting factor in current research.

The group continues to refine the platform with more brain and body types. We hope to soon have an Avidian brain available through the efforts of Mike Wiesenauer. We are also committed to enhancing the ability to analyze the behaviors of organism in real-time. Our hope is to offer a platform that other labs can perform research in without a steep learning curve. As the community grows so will the number of brain and morphology types as well as possible environments. The plug and play nature of EvoSphere makes it easy to share experimental components with each other.

Our goals are scientific, but this work connects to my daydreams of youth. As the child who frequently got lost in video game titles such as Doom and Heretic, I also see how growing the EvoSphere community may one day allow gamers to experience a new level of play. For those who play as awful as I do, the creatures we encounter could evolve themselves to an easier level of play. The same exact opponents could evolve more difficult behaviors for those gamers who master objectives more efficiently. As you can see, to adapt enemies to the match the abilities of the player will bring the gaming industry to a whole new level. Once this circle is complete, my “this could never happen, but it would be cool…” statements will have been met beyond my wildest imagination!

For more information about Leigh’s work, you can contact her at leighs at egr dot msu dot edu.

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BEACON Researchers at Work: Transforming Science Education

This week’s BEACON Researchers at Work blog post is by MSU graduate student Wendy Johnson.

Wendy JohnsonI remember seeing the initial press releases about the launch of the BEACON Center at Michigan State. At the time I was teaching high school biology just down the road and finishing up a master’s degree in the (former) Division of Science and Math Education at MSU. My experiences as a teacher and in my master’s work had fueled my passion for improving public understanding of science and convinced me that reform in science education was absolutely necessary. I was pretty sure that I would soon leave the classroom and pursue doctoral study, but at the time I wasn’t sure whether that should be in evolutionary biology, education, or philosophy of science. I was equally interested in all three areas and each seemed integral to my goals.

The BEACON Center announcement caught my attention because of the multidisciplinary approach and goals for advancing science, technology, education, and public understanding of evolution. I thought it sounded like a great place for someone like me, but I had no idea how. In the spring of 2011 a fellow teacher convinced me to apply to a Research Experience for Teachers program through MSU’s College of Engineering, although I thought there was no way I would actually be able to participate while working on my master’s thesis on evolution education. When I met with the program director, Andrew Kim, he told me that I might be interested in working on a project involving digital evolution. I had no idea what that meant, but the integration of biology with computer science and engineering seemed very interesting and exciting, and of course, I ended up working with BEACON members. That summer I absorbed all that I could by hanging around multiple group’s lab meetings (thank you!) and going to seminars. I used what I learned to translate BEACON’s mission for Bio/Computational Evolution in Action into engaging learning experiences for my high school biology students. In addition to developing a bacterial selection experiment, I worked with Rob Pennock, Louise Mead, and Jim Smith to develop curriculum using Avida-ED digital evolution software. The learning gains (and excitement!) that my students demonstrated were very encouraging, and the next summer I was back for more – this time working with Phil McKinley, Brian Connelly, and Eric Bruger using computational and biological models to study evolutionary questions about quorum sensing.

Explaining evolved robot behavior at the USA Science and Engineering Festival in Washington, DC in May 2014.

Explaining evolved robot behavior at the USA Science and Engineering Festival in Washington, DC in May 2014.

These experiences encouraged me to begin doctoral study. I decided that in collaboration with the BEACON Center I could be as interdisciplinary as I wanted, no matter what type of doctoral program I chose. In 2013 I started a science education program in the College of Education and joined the Ecology, Evolutionary Biology, and Behavior Program. Through these programs and BEACON I am able to simultaneously pursue all of my interests and integrate them with the aim of transforming science education and increasing public understanding of science.

I currently work with Rob Pennock on two BEACON affiliated projects: Avida-ED curriculum development and the Scientific Virtues Project. Though they seem quite different, I see a very important connection (aside from the fact that both are really fascinating). In the Scientific Virtues Project I interview scientists about the values (curiosity, objectivity, humility to evidence, etc.) that they bring to their work. Understanding these values is important from the perspective of philosophy and sociology of science, but it is also vital for transforming science education to better reflect the goals and practices of scientists.

Avida-ED is a perfect example of a teaching tool that engages students in the practices of science as called for by recent reform efforts such as Vision and Change in Undergraduate Biology and the Next Generation Science Standards for K-12 education. Not only can students develop and test their own hypotheses about evolutionary processes in Avida-ED, but they can actually watch processes such as random mutation, genetic drift, and selection acting on digital organisms in real time. Previous work in my own classroom as well as a larger national study conducted by Amy Lark demonstrated that the use of Avida-ED significantly improves students’ understanding of basic evolutionary processes. Currently the Avida-ED team is comparing student learning in undergraduate courses that use Avida-ED versus those that do not. Preliminary analysis has documented higher learning gains for students that use Avida-ED. Working with the program seems to be especially helpful for students in overcoming the common misconception that evolution is intentional or directed as well as helping them to appreciate the importance of random mutation in basic evolutionary processes. 

In addition to my BEACON work, I also teach courses for preservice teachers and work on the Carbon TIME curriculum and research project with Andy Anderson in the Department of Teacher Education. My work on Avida-ED and the Scientific Virtues Project both informs and is enhanced by my work in teacher education. For example, I am currently analyzing videos of teachers implementing the Carbon TIME curriculum to determine whether teachers’ orientation towards curiosity influences their students’ learning. This question was inspired by interviews with scientists who continually emphasize the important role of curiosity in guiding their work. It seems quite logical that science teaching that fosters curiosity would improve student learning, and my preliminary analysis are suggesting that it is indeed an important factor.

My own natural curiosity has fueled my interest in evolution, but it is also a natural fit with my goals of improving science education and public understanding of science. The study of evolution is a perfect example of the scientific process at its best as well as an ideal context for highlighting the relationships among science, technology, and society. I am thrilled to be a part of BEACON’s mission of “illuminating and harnessing the power of evolution in action to advance science and technology and benefit society.”

For more information about Wendy’s work, you can contact her at john3062 at msu dot edu.

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BEACON Researchers at Work: Black in Science

This week’s BEACON Researchers at Work blog post is by Bradley Watson. Bradley spent two summers working as an undergraduate researcher at Kellogg Biological Station with BEACON faculty Kay Gross, and is now a master’s student at University of Nebraska Omaha. The original post appears on his blog here

I was writing this in a different mindset and with a different goal until Ferguson, MO happened. That ongoing tragedy popularized by racial tensions but equally influenced by economic inequality made me want to finish this little essay. I had forgotten how sheltered I was by my environment but I still think my experiences are relevant and representative of the struggles of other blacks who are infiltrating fields that were/are dominated by white people.

Bradley Watson and posterI was in a lab meeting this summer and offered to drive some samples of the prairie plants we study back to Omaha with me if we needed more time to process them. Our PI said that she could get the biomass processed here in Michigan and joked that I would be a huge target for the cops driving through Chicago in a car full of dried plants. All six of us at the lab meeting (me being the only black person) laughed our heads off. We extended the hypothetical situation into stories about me trying to explain that the dried grass in the black plastic bags was for an experiment leading the police to call our PI to ask if this story was true. Someone even said the word marijuana… IN A LAB MEETING! At the end of it all I was taken aback. My boss, a 60 something year old white Christian lady from the heartland of America had put herself in my shoes and recognized that things were a little different for me.

She used the phrase, “a black man.” Many people shy away from blatant acknowledgement of racial differences but she didn’t and I respect her for it. I have been one of a few blacks and often the only black person in my classes for a long time. I left the Bahamas where I was in the racial majority for school in Canada where I was often mistaken for being Nigerian or Jamaican but not really discriminated against because that country is so diverse. After a year there I moved to a school in Charleston, South Carolina. I knew racism was historically a part of southern culture but I always thought that being international, well spoken, and well-mannered (by my nature and to the point of being timid sometimes) meant that I wouldn’t be a victim of this racism… wrong! I remember the first girl to cross the street as I approached. It was on a well-lit side walk at around 10 pm. I was shocked when I realized that she was just avoiding walking past me but I rationalized it; she could just be avoiding the threat of a male instead of the threat of a black. Then there was a night when I was escorting a white female friend home from a party and stopped two fratastic guys from harassing her. They left her alone and laughed at me… slapping me on my ass as I walked by. I chalked that one up to their inebriation and the idiocy encouraged in some fraternities. One thing I could never justify was why blacks made up 10% of the population in the US but my school had nearly 100% black janitorial staff and more than 95% white professors. I remember just one black Biology professor and I’m only calling him black because it takes just a little yellowing of the skin or crimping of the hair to be perceived as such! The final wake up call for me was in a plant taxonomy class surrounded by white peers whom I got along extremely well with. I forgot how we got to this point in the conversation but the professor, another older white lady, looked at me and said something like “Do you know how long they tried to keep your people out of this school?” (The best use of “your people” I have ever heard, btw.) It was a shock for me; she recognized this bias and felt strongly about it while I was trying to ignore it. But what choice do I have? Am I supposed to think about my race all the time?

I think the answer to that is no, but I have to be aware of it. I just started a teaching assistantship and had some trouble with my paperwork… I admit that I was being a little slack but I had just gotten into town and was balancing departmental and international student paperwork and orientations simultaneously. I can’t help but imagine that my superiors consider the fact that I’m the only black TA when I screw up. So as a black man I feel pressure to avoid making mistakes at all costs whether it’s having too many friends riding in my car at one time or playing my music too loud in the lab. I just don’t feel like I’ll get as many second chances as others. Ironically, one of my good friends told me he thought people would take it easy on me since I’m a Black Bahamian. I don’t know which of the two adjectives would encourage this lax attitude the most in his mind.

LTER Tour Summer 2013This brings us to the issue of affirmative action. I was in my senior year of undergrad applying for a travel grant so we could show off the work our lab group had done that year. This time the professor I’m talking about was one of the sweetest ladies you’ll meet; she happened to be middle-aged and, surprise, white. She asked about my parent’s education and incomes and I had to admit that they both had master’s degrees and made OK money even though that wouldn’t help my chances of getting funded. In the end I didn’t get that funding so she took the time to call in and find out why. It turned out that I should have mentioned more of my research experiences than I had in my essay. Later I met a black professor and told him about this experience and he told me that there was other funding for black students that would have gotten me to that conference. This past summer I told a black administrator at one of my favorite schools that I couldn’t find funding there so I went to another institution. He also let me know that he knew where to find funding for me, a fellow black. Some people think these pockets of funding for minorities are unfair but I disagree. When the number of minorities in scientific leadership roles reflects the percentage of minorities in the general population I will concede that affirmative action is unnecessary.  I have been blessed with mentors and professors who invested in me regardless of (or possibly because of) my race but when I meet black professors there is something else there. The three ladies I mentioned earlier were the kind of allies M. L. K. was looking for when he wrote his letter from that jail in Birmingham but meeting black professors is like meeting Dr. King himself for me. Being in the presence of a successful black academic, or even their work for that matter, makes me feel like I now have to succeed because it really is possible since others have done it before me. I’m almost certain that female students experience the same emotions when they meet strong women in leadership roles.

So, yeah… black in science… black in this world. I just want to be treated like everyone else but I am no longer naive enough to expect that. This human experience is crazy, and what’s even crazier is that we can alter other’s experiences by sharing our own ;)

 For more information about Bradley’s work, check out his website.

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BEACON Researchers at Work: Mating behavior in treefrogs

This week’s BEACON Researchers at Work blog post is by NC A&T undergraduate Darian Mollock, who worked as an Undergraduate Research Apprentice (URA) at MSU’s Kellogg Biological Station in summer 2014.

getty labMy name is Darian Mollock, I am a junior double major in Lab Animal Science and Animal Science at North Carolina Agricultural and Technical State University. This summer I worked with Michael Kuczynski as an Undergraduate Research Apprentice at the Kellogg Biological Station studying sexual selection and communication in gray treefrogs. The project I worked on was investigating how male calling behavior may change based on an individual’s physical condition and age, and also how female mating preferences and choosiness are influenced by these factors. 

I arrived at the biological station shortly after the beginning of the gray treefrog breeding season. During this time of year, male frogs gather in large choruses where they call to attract females who then choose mates based on certain properties of the calls (length, rate, etc.). Part of our research involved examining female preferences and choosiness in mate selection. In order to assess female mating behavior we had to capture sexually receptive females in the field so we could bring them back to lab for behavioral testing. To ensure that females were sexually responsive we could only collect mated pairs that were already in amplexus (the mating position). Prior to coming to KBS I had never done late night field work in ponds before, so I was excited for my first night to begin. Strapping on my chest waders and head lamp, I headed into the pond to search for the mated pairs. After getting over the initial fear of being in a pond at night not knowing what was lurking in the abyss (I had heard stories of large snapping turtles…), I went in. It was a thrill collecting the gray treefrogs in their natural habitat, and the noise from all of the calling males was deafening. My first night we collected fifty mated pairs – one hundred frogs in total.

photo 3 (1)After we collect the mated pairs we bring the frogs back to the lab and store them in Tupperware containers until the females can be tested. To examine female mate choice we used a series of playback tests that we ran in a small sound chamber. The chamber consisted of a flat tabletop surrounded by sound-dampening blankets with a speaker placed at both ends of the chamber. We would place females in the center of this chamber and observe their response to different frog calls that we could broadcast from the speakers. Specifically, we broadcast attractive (long duration) calls and unattractive (short duration) calls from opposing sides of the chamber. Across multiple trials we would lower the playback volume of the attractive call relative to the unattractive call. A lower playback level would simulate the attractive male calling from farther away making it a more costly choice for the females. We examined whether females would switch their preference and move towards the unattractive call when the attractive call was played at lower volume. We then investigated whether a female’s age, size, or physical condition influenced whether she would switch her preference.

Now that the mating season has come to an end we are in the process of analyzing the data we have collected throughout the summer. With our data we will determine whether larger, better condition females are willing to travel greater perceived distances to reach a more attractive mate than smaller, poor condition females.

The overall ten week internship has been remarkable; I have grasped a vast amount of knowledge about field research hands-on. When you are around someone that is passionate about their research you cannot help but get inspired. I am glad I was able to assist as an undergraduate in Michael’s research project. I have picked up valuable skills during my internship that I will carry with me in my future endeavors.

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BEACON Researchers at Work: Directed and Real Evolution

This week’s BEACON Researchers at Work blog post is by University of Texas at Austin faculty Andy Ellington.

Ellington PortraitEvolution in Action. That’s the BEACON motto. It always struck me as a bit wishful. Because evolution is mostly glacial. Sure, it can bury you over time. But it’s like that scene in “A Fish Called Wanda” where Ken is running over Otto with a steamroller. You really have to be stuck to see it.

Anyway, my lab works on directed evolution. Which is the much faster, more engineered younger brother of natural selection. We can make molecules and pathways and organisms jump on our own timescale, which is typically shorter than the timescale of the typical graduate student thesis, although some of those can be glacial, too. We introduce many mutations at the outset or else carry out procedures that are inherently hypermutagenic, direct populations through bottlenecks with great speed, and amplify the survivors with efficiency. This works whether we’re talking about molecules in vitro or viruses or microbes that have decent replication cycles. It does not work if we’re talking about rabbits. We’ll have to work on that.

But this brings up the interesting and useful point I was not making. BEACON is as much about education as it is about science. And the general populace can think about something like a rabbit evolving much more easily than they can something like beta-lactamase (although the evolution of drug resistance is one of those canards that the Creationists generally steer clear of, for good reason). And since we can’t run fast cycles of rabbit evolution, turning fluffy bunnies into the sort of killer rabbits that stymied John Cleese in a different Python movie (Holy Grail with its Holy Hand Grenade of Antioch), it is not as easy to viscerally demonstrate evolution that resonates.

But of course we would all argue that it’s the same thing: generating and culling alleles is evolution. This is the fundamental definition. Diversity. Selection. Replication. At any timescale, in any system. I sometimes have trouble making this point when talking with colleagues about origins, because many biologists are closet Vitalists who sadly want to separate discussions of origins from discussions of evolution. Nonetheless, the fundamentals are sound, just like with the economy.

Now, how do we better represent these fundamentals to the public? My goal in BEACON has in part been to show Evolution in Action by developing kits that show ribozyme evoluton in real-time. Ribozyme populations placed into a very good environment of enzymes and substrates can lead to their own reproduction and winnow to those variants that are the most active, with a parallel fluorescence readout.

I’d now like to better encourage the spread of directed evolution throughout the BEACON community. I think we can begin to discuss how to encourage experiments that demonstrate evolution and that lead to products that are of commercial interest and value. And that these will feedback and reinforce our mission statement.

Since many BEACON-ites are interested in computer evolution, this will require a fundamental restructuring of how we meld computer and biological processes. We could have a wonderfully fun discussion of whether electrons replicate or not, and if they don’t whether or not computer algorithms are in fact evolving. But it would be a somewhat fruitless discussion, because in reality all we’re doing is moving the goalposts: just as I claim my enzyme bath allows ribozymes to replicate, computer scientists can claim that their cozy electronic interiors allow programs to replicate. Of course, there’s also the modeling of evolution that is not evolution itself.

Both types of research may find their way into biology. Have we ever really thought about how to make automatons and viruses more alike? If I wanted to make a virus that had at its core rule sets that were not unlike the rule sets in an algorithm, could I do that? That would be super hard and interesting. In contrast, can computer scientists make automatons that have at their core rule sets that resemble those of viruses. This, this is a much more worthy goal.

Modeling is a more obvious crossover, especially with Avida and all. Still, the use of Avida to retrodict and the use of Avida to predict could be refined. In particular, can viruses or other synthetic systems be set up to run down the same pathways that Avida has already plumbed, and will they get th same answers? This is particularly important because the time is coming, and coming quickly, when we will use computation to plumb fitness landscapes in advance of evolution. Tools already exist to begin to predict host:pathogen interactions, and the further ability to predict evolutionary dynamics of the random “viral chatter” that goes on between human populations and the many things assaulting human populations is of particularly import, given the recent news of how Koyaanisqatsi seems to be at our doorstep, at least for viruses.

I am reminded by a venerable senior colleague that the last reference is only for the olds, like me. For those of you of a certain age, you may remember the iconic crying Indian, saddened over the destruction of our environment, that would show up on public service announcements. Around that time, there was also a movie, Koyaanisqatsi, nominally translated from Hopi as “World Out of Balance,” that was anextended word picture that showed how we were moving away from nature. Yeah, we were all hippies back then. Anyway, when Ebola shows up on your doorstep and says ‘hi,’ it seems to me that the world is out of balance, and that it’s time to do something more than cry about it.

For more information about Andy’s work, you can contact him at ellingtonlab at gmail dot com.

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