BEACON Researchers at Work: Evolution of plasmid host range

This week’s BEACON Researchers at Work blog post is by University of Idaho postdoc Wesley Loftie-Eaton.

WesleyI stumbled into the world of plasmids at my alma mater, the University of Stellenbosch in South Africa. My advisor, Prof. D. E. Rawlings, asked me to determine the biological implications of a very specific mutation within the origin of replication of two isogenic plasmids (Loftie-Eaton and Rawlings, 2009; Loftie-Eaton and Rawlings 2010). What started as a very simple and specific question quickly enthralled me with its true complexity. During that time I learned that you can’t understand plasmids, or anything in biology for that matter, without the context of evolution; and what better place to study plasmid evolution than at the University of Idaho alongside Dr. Eva M. Top and under the umbrellas of IBEST and BEACON.

Plasmid

Plasmids are genetic elements that replicate separately from the bacterial chromosome. Many can transfer horizontally between diverse bacteria, often resulting in the spread of antibiotic resistance (red insert on plasmid) to pathogens (red bacterium).

In case you’re not a plasmid geek like me, plasmids are generally circular (linear forms also exist) DNA entities that replicate autonomously in bacteria. The smallest plasmids are but a few hundred base pairs while the largest are over a million base pairs long (Kado et al., 1998). Based on sequence information, about half of plasmids are either self-transferable by means of conjugation or can be transferred (mobilized) by conjugative plasmids, while the remainder appear to be non-transferable (Smillie et al., 2010). Many plasmids are cryptic or do not encode any non-essential genes while others may carry genes that provide benefit to the bacterial host, allowing it to occupy and proliferate in an otherwise hostile niche (Kado et al., 1998). Depending on whether a plasmid provides its host with benefit or cost, they can be likened to symbionts or parasites, respectively, and like symbionts and parasites, they have a host range that is either narrow or broad.

Projects I am currently working on are focused on a) elucidating the molecular mechanisms that evolve to permit plasmids to shift, contract or expand their host range and b) to understand how broad host range plasmids proliferate and spread in complex microbial communities. The latter will not be discussed here. Besides the fundamental nature of these questions, they are relevant to human health due to the rampant plasmid-mediated spread of antibiotic resistance amongst pathogens.

When a plasmid conjugates to a naïve host it may not necessarily persist unless there is selection for its maintenance in that host. Failure to persist could be due to inefficient replication, poor partitioning or segregational loss of the plasmid during cell division, or plasmid-containing cells can simply be outcompeted by plasmid-free cells if the plasmid imposes a cost on the host. We know, however, that plasmid and host can rapidly adapt to each other while under strong selection for plasmid maintenance, after which the plasmid can continue to persist for prolonged periods even when the strong selection is removed (Bouma and Lenski, 1988; Dahlberg and Chao, 2003; Sota et al., 2010). Panels A and B in the figure below demonstrate exactly this; an initially unstable plasmid-host relationship evolved a more stable phenotype in less than 200 generations and after ~600 generations the plasmid was highly stable in that host1. Not clear from this figure (due to me not showing the full assay data) was that in the absence of antibiotic selection the ancestral plasmid tended towards extinction, however, a persistent relationship in which the plasmid was maintained in ~10% of the population due to horizontal transfer evolved within the first 100 generations (panel C, below)! Together with collaborators Sam Hunter and Haruo Suzuki I am currently working on elucidating the genetic changes behind this increase in persistence and collaborator Jose Ponciano is working on means to quantify how easy or difficult it is to switch between trajectories of persistence and extinction.

Figure 2

While under antibiotic selection for plasmid maintenance, plasmid stability evolved rapidly and resulted in a persistent state wherein the plasmid was maintained even when the antibiotic selection was removed. (A) Plasmid stability measured over 10 days in the absence of antibiotic for evolving cultures sampled every 100 generations [G] over the course of the evolution experiment. (B) Summary of the endpoint [day 10] data for each stability assay for three replicate lineages. (C) A prediction of whether the plasmid will persist or go to extinction in the absence of antibiotic selection for its maintenance.

In another experiment (different plasmid and host)2 we found that a transposon encoded on a plasmid native to that host ‘jumped’ to the introduced plasmid, which was being maintained under antibiotic selection. The result was increased stability of the introduced plasmid, even in the absence of antibiotic selection, and loss of the native plasmid. Encoded on the transposon are a toxin-antitoxin (TA) system and a resolvase, both of which we have now shown to promote plasmid stability (Loftie-Eaton et al., in prep.). Even more significant, however, was that the evolved plasmid that acquired the transposon was completely stable in other beta- and gamma-proteobacteria in which its ancestor was unstable. Thus, acquisition of a transposon encoding stability functions resulted in an apparent expansion of the plasmid’s host range and more broadly, we demonstrated the interplay and fate of genes that could arguably be labeled as “selfish”.

In yet another system one of the outcomes was a deletion mutation within the plasmid’s origin of replication. Though much work remains to be done, this mutation has me extremely excited. The type and location of the mutation is the same as the mutation I set out to understand during my PhD. The exciting part is that the plasmids I studied then belong to a different family and evolved in the environment, whereas here the mutations occurred during experimental evolution in the lab. Preliminary results showed that this deletion abolished the plasmid’s ability to replicate in a previously permissive host, which already is novel information, however, if my hypothesis based on my previous research withhold scrutiny, then these results will demonstrate that what we observe during experimental evolution in the lab also occurs in nature, and vice versa. Validation!

Though far from complete, what we’ve learned thus far is that plasmid host-range can evolve quite rapidly, that such rapid changes tend to occur through mutations that result in gain or loss of function and that there are multiple molecular solutions that can lead to stable plasmid-host relationships. From the perspective of a plasmid geek this is fascinating, but from a medical perspective it’s concerning; once a multidrug resistance plasmid has established in a population it intends to stay, even if the antibiotics that initially selected for its maintenance are removed from the system! However, by accumulating more data of this kind we hope to define general patterns in the evolution of plasmid host range that can aid in the development of novel drugs to inhibit the spread and establishment of multidrug resistance plasmids.

Acknowledgements: 

1The experimental work was done by undergraduate Kelsie Bashford.

2Much of the experimental work was done by undergraduates Ryan Simmons and Stephen Burley as well as our lab manager Linda Rogers.

References

Loftie-Eaton, W., and D. E. Rawlings. 2009. Comparative biology of two natural variants of the IncQ-2 family plasmids, pRAS3.1 and pRAS3.2. J Bacteriol 191:6436-6446.

Loftie-Eaton, W., and D. E. Rawlings. 2010. Evolutionary competitiveness of two natural variants of the IncQ-like plasmids, pRAS3.1 and pRAS3.2. J Bacteriol 192:6182-6190.

Kado, C. I. 1998. Origin and evolution of plasmids. Antonie Van Leeuwenhoek 73:117-126.

Smillie, C., M. P. Garcillan-Barcia, M. V. Francia, E. P. Rocha, and F. de la Cruz. 2010. Mobility of plasmids. Microbiol Mol Biol Rev 74:434-452.

Stewart, F. M., and B. R. Levin. 1977. The population biology of bacterial plasmids: a priori conditions for the existence of conjugationally transmitted factors. Genetics 87:209-228.

Ponciano, J. M., L. De Gelder, E. M. Top, and P. Joyce. 2007. The population biology of bacterial plasmids: a hidden Markov model approach. Genetics 176:957-968.

Bergstrom, C. T., M. Lipsitch, and B. R. Levin. 2000. Natural selection, infectious transfer and the existence conditions for bacterial plasmids. Genetics 155:1505-1519.

Bouma, J. E., and R. E. Lenski. 1988. Evolution of a bacteria/plasmid association. Nature 335:351-352.

Sota, M., H. Yano, H. M, Julie, G. W. Daughdrill, Z. Abdo, L. J. Forney, and E. M. Top. 2010. Shifts in the host range of a promiscuous plasmid through parallel evolution of its replication initiation protein. ISME J 4:1568-1580.

Dahlberg, C., and L. Chao. 2003. Amelioration of the cost of conjugative plasmid carriage in Eschericha coli K12. Genetics 165:1641-1649.

Loftie-Eaton, W., Burleigh, S., Simmons, R., Rogers, L., Hunter, S., Settles, M., Ponciano, J.M. and Eva Top. Transposition of a toxin-antitoxin system and plasmid-host coevolution increase plasmid persistence and host range. In preparation.

For more information about Wesley’s work, you can contact him at wesleyl at uidaho dot edu.

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Why lactation rooms matter

This post is by UW graduate student Carrie Glenney, and is cross-posted from the UW biology graduate student blog Science Positive.

A lack of access to lactation rooms might be a widespread issue for women in academia. As demonstrated in the Biology Department at University of Washington, it can also be a relatively simple problem to solve. Ensuring lactation room access for all women in academia would send a very important message: we support you.

Although women make up more than 50% of science PhDs earned, they are more likely than men to leave the academic sciences at every stage on the way to obtaining a tenured position at a college or university. A study by Marc Goulden, Karie Frasch, and Mary Ann Mason suggests that becoming a mom may be one major determinant of this trend: married mothers with young children are less likely than both single and married women without young children, and 35% less likely than married fathers, to achieve tenure at a college or university.

Leaky pipeline

PhD students and post-docs specifically may face obstacles that make having a child feel antithetical to continuing in academia: a lack of paid and limited unpaid parental leave, limited affordable childcare, or lack of advisor or departmental support. Although many of these issues affect fathers as well as mothers, surveys with University of California post-doctoral scholars at both the beginning and end of their programs showed that of those who had children during their post-doc, women were twice as likely as men to change their career goal away from “professor with a research emphasis”.

Effect of Children on career 

Why does having a baby seem to hinder a woman’s academic career but not a man’s? What unique obstacles do female PhD students and post-docs with children face on the pathway to a career in academia?

I had my son during the third year of my PhD and I anticipated and experienced some of the issues addressed above. But the complete lack of one resource in particular surprised me the most. In many cases, this resource is actually a legal right. It’s relatively straightforward to provide. And I think mandating its presence in every department would go a long way towards making mothers in academia feel more accepted and supported.

Lactation rooms.

Returning to work after having or adopting a baby can be HARD, no matter where you work, and no matter how much you might love your job. You might be operating on a handful of hours of sleep a night. Your body might be still healing from childbirth. You might feel a mix of emotions about returning to work and physically being apart from your baby. You might not feel physically or emotionally ready to come back to work but at the same time feel that you don’t have a choice. And for those mothers who are able and chose to breastfeed, there’s the where, when, and how to navigate around pumping.

Logistically, continuing to breastfeed even when you’re not physically around your baby can be tricky. For those who aren’t familiar, here are some of the logistics. A woman’s body produces only the amount of milk it thinks the baby needs. The body forecasts how much milk it thinks it should make based on how much was used in the past. If less is used, less is made in the future. In order to convince your body to continue making the same amount of milk even when your baby isn’t around, you need to remove milk at least as frequently as your baby would (in the range of every 2 to 4 hours) and sometimes more often (because pumps don’t remove milk as efficiently as a baby). Pumping frequently and for enough time is important for maintaining milk production, but it’s also essential to prevent a very painful infection called mastitis. Once the milk is pumped, most moms store it in the fridge or freezer and it’s given to their baby through a bottle when the mom isn’t around to breastfeed. Removing the milk requires a pump (most women use electric pumps), plastic pieces that need to be washed after each use, cold storage, and a stress-free environment. 

The last requirement may surprise you. Milk flow actually requires the release of the hormone oxytocin (the “love” hormone), a process usually stimulated by baby. In the absence of baby, women use other methods to encourage milk flow (like looking at a photo of her baby), but stress, fatigue, or even being cold can make this very difficult. Therefore, a private, clean, comfortable space with a locking door is essential. Ideally, there is also a sink for washing parts, a fridge for milk storage, and desk space so work can continue if desired. Most PhD students and post-docs share an office with others so they cannot or understandably might not want to pump in their office. Often women are relegated to bathrooms to pump, but any place where you would not want to eat lunch is also not a place where a mom will want to pump milk for her baby. Pumping can take 10-30 minutes a session and has to happen every 2-4 hours, so location convenience is also an important factor for accessibility. 

Source: milkitkit.com

Source: milkitkit.com

When Hannah Kinmonth-Schultz (also a PhD student and mom) and I decided to ask the Biology Department for a lactation room, we first conducted a departmental survey to determine the need. We found that the need was far greater than we’d anticipated: 7 of the 86 total female respondents (8%) said they anticipated a need for a lactation room within the next 12 months or have a current need. 81% of respondents who already have children said they would have benefited from a departmental lactation room.  Convenience was an important factor: only 1 mom reported using the campus lactation facility located about a five minute walk away. Other moms used the bathroom (and one mom reported throwing all her milk away for sanitation purposes) or borrowed other people’s offices if they didn’t have their own. One mom commented, “I can’t tell you how many uncomfortable places I have pumped!”

need for lactation room

Beyond the need for a space to meet the physical needs of pumping moms, providing an accessible lactation room for every mom in academia sends an important message: we support you and your family. Many women in academia who want to have children are hearing a different message: this is not the time or place for a baby. In addition to the implicit message sent by the lack of resources and support from the institution itself, many women may be discouraged outright by mentors, advisors, or even peers. I have had personal experiences with this* and I’m sure others have as well.  Academia is an environment where there’s often little distinction between “work” and “life”, let alone a balance, and it’s easy to feel like family planning should take the back burner or you’ll risk harming your career. So returning to work to find that the most basic of necessities, like a place to pump, aren’t available to you can make you feel like your choice to have a child is not supported. In addition, some advisors may not understand the importance of providing the time and physical space for pumping (although my advisor was wonderfully accommodating); or a female graduate student might feel understandably reticent about broaching the topic of breastfeeding with a male advisor. In the comment section of our departmental survey, one mom addressed the emotional toll of having no place to pump by saying “having a lactation room in the biology department while I was nursing would have gone a long way towards helping me feel accepted. I felt extreme guilt and very alone. As a result I think that my research progress suffered much more than it would have if impacted just by my new time constraints.” Another said “stopping pumping because of lack of convenient facilities was especially hard for me and not ideal for baby.” Even though breastfeeding is hard, many moms want to keep at it because it can have such wonderful benefits: money savings from not needing to buy formula (~$100/month), nutritional and immunity benefits for baby, and the baby-mother bonding that breastfeeding facilitates. Yet ¼ of the respondents in our survey said they quit breastfeeding earlier than they wanted to because they had nowhere to pump.

This is just a snapshot demonstrating the need for a lactation facility in one department at one university, but it wouldn’t be a stretch to imagine that other departments have a similar scenario- and they may not even know it.

As Stanford University stated in 2006 “… a woman’s prime childbearing years are the same years she is likely to be in graduate school, doing postdoctoral training, and establishing herself in a career.” If we want to support women in academia, one of the most important things we can do is acknowledge that some will want to start their families during this timeand to support them when they do. I’m proud to be of a department that is taking steps in this direction by establishing a lactation room** (it should be available soon). Even when space is limited or money is tight, a little creativity can help convert a space to be used for this purpose. For example, our department is currently converting the departmental break room in the Kincaid building into a shared space that can function as a private lactation room during non-meal hours.

Of course, we need a multi-pronged approach to support women in academia and to support both women AND men who want to start families while in academia. Ensuring access to lactation rooms is only one step… but a meaningful one.

Other than the departmental survey we conducted last year, I don’t know of any studies that have been done to look at whether there is a widespread lack of access to lactation rooms in universities and colleges. In hopes of getting the dialogue about this issue rolling: if you are (or know of) someone*** at a university or college who needs a lactation room and doesn’t have access to one, or has a story about starting a lactation room at another department or institution, or just wants to lend your support, please visit our facebook group Lactademia.

* I would like to extend a thank you to my own advisor (Ben Kerr) and the Kerr lab. They have given me nothing but support, including moving offices around so I would have a place to pump. Thank you!

** Special thanks to all who helped make the UW Biology Department lactation room a reality:Hannah Kinmonth-Schultz, Diversity committee members Horacio de la Iglesia, Andrea Prado, Rose Ann Cattolico, Greg Wilson, Linda Martin-Morris, Sarah Eddy, Julian Avila, and Camilla Crifo; Executive committee members Toby Bradshaw, Michele Conrad, Carl Bergstrom, David Perkel, and Jennifer Ruesink; Graduate Program Director Marissa Heringer.

*** The issue of access to lactation rooms also affects lab technicians, faculty, and many others in the academic world. This article focuses primarily on post-docs and graduate students because those are the individuals I’ve interacted with the most about this issue and the levels of academia with which I am most familiar. But the ultimate goal is “access for all.”

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BEACON Researchers at Work: The Evolution of Gene Distribution in Bacteria

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

NateWardOne of the strengths of BEACON is its focus on interdisciplinary research. Through gathering together scientists and educators from different backgrounds, BEACON can address problems that people from one field alone cannot solve. One example of this is Avida, which combines insights from computer science and biology to simulate evolution. Avida is an example of what can be achieved when computer scientists and biologists collaborate together; problems that seem difficult in one discipline are much easier to solve when approached with insight from another discipline.

Like Avida, the work I am doing right now is interdisciplinary. I am currently a PhD student in the computer science department with a background in computer engineering, however, one of my PhD advisors, Dr. Julius Jackson, is a professor in the Department of Microbiology and Molecular Genetics at Michigan State University. The work I am trying to do right now is to create software that will simulate the evolution of bacteria starting roughly four billion years ago. The major goal of our software is to discover how evolution shapes the distribution and organization of genes on the bacterial chromosome. Because of this, we named our software: Gene Distribution Lab.

Evolution selects for the organisms with the fittest characteristics for their given environmental niche to survive. Likewise, evolution selects for the chromosomes that have the best organization of genes. One feature of chromosomal organization that evolution appears to select for is genes that are functionally related to be next to each other spatially on the chromosome. The observation that bacteria often have functionally related genes close to each other on the chromosome is called the gene clustering phenomenon.

Although there are many different models that scientists have proposed to explain the gene clustering phenomenon, we are starting our investigation by looking at one model specifically. The lab I work for has proposed a model called the Limited Protein Mobility Model. This model states that when genes of related function are close together, the proteins they code for will also be close together, furthermore when these proteins are close together they can process the reaction they both interact in better than if they are far apart.

Although my background prepared me to write the code for Gene Distribution Lab, grasping the underlying biology was a challenging but necessary step at the start of this project. With my background in engineering and computer science I often find it easier to grasp problems of biology through thinking about these problems in terms I am familiar with. So to really understand the Limited Protein Mobility Model, I wanted to put it in context of an engineering problem.

Metabolic pathways in bacteria function a lot like assembly lines. First of all, precursors in the cell are initially processed by the pathway; this can be thought of as the “raw material” that is modified by the assembly line. At each step in the assembly line, a worker will perform some operation on the unfinished product, such as soldering on wires, reshaping the material, adding on paint, or something of that nature. Only after the last step will the final product be useful for what it is intended for.

Likewise, in each step in a metabolic pathway, a protein will modify the unfinished product, that is, the intermediate, such that the intermediate is closer to its form as the desired end product. Proteins will operate on the intermediates, which is analogous to how workers in a factory operate on the unfinished product to bring it closer to completion.

One big difference between a metabolic pathway and an assembly line is that pathways operate in a different way due to the scale difference and the fluid medium that they are in. Intermediates and proteins are suspended in the cytoplasm of the cell, and move around randomly due to the laws of chemical diffusion. So imagine, instead of a belt carrying everything around the assembly line, all the workers and the unfinished products were drifting around randomly in a pool of thick gel. It would be very hard to complete the final product this way. Each worker could only modify the unfinished product if the right pieces drifted over to them, and even then they couldn’t send the product directly over to the next worker in line. The problem would be exacerbated if the workers were all very far apart, because it would take longer to initially start creating end products and many pieces of the unfinished product (the intermediates), would simply drift away out of reach of any worker. We propose a similar process promotes the gene clustering phenomenon. Genes that produce proteins in the same pathway will tend to cluster together on the chromosome because it is easier to make end products when proteins are close together.

Gene Distribution Lab tests this prediction by simulating the evolution of early bacteria. These bacteria start off with a very small chromosome and a number of genes they are required to have to code for proteins in a pathway. The chromosomes then undergo segment duplication, segment deletion, and point mutations which have the potential to disable genes they have. An organism dies if it loses the last copy of a gene necessary for survival. So far we have verified that organisms in Gene Distribution Lab are able to accumulate and dissipate clusters in their chromosome, and soon we will be able to show the effects of the Limited Protein Mobility Model on the selection pressure to maintain clusters.

For more information about Nate’s work, you can contact him at wardnath at msu dot edu.

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BEACON Researchers at Work: Going with the Flow

This week’s BEACON Researchers at Work blog post is by University of Texas postdoc Alex Jordan (www.alexjordan.org).

Alex JordanThe Rift Lakes in Africa, one of which has been famously dubbed “Darwin’s Dreampond,” are perhaps the best places on earth to visualize the process of evolution. The multitudinous species, with their dazzling array of colors, shapes, and life-histories give a first-hand insight into the incredible power of natural and sexual selection to generate natural splendor. Seconds after diving into the water, you will have seen ten or more species, from maternal crevice nesters to biparental mouthbrooders, from ambush predators that mimic a rotting corpse to streamlined laterally compressed assassins, and from bright metallic blue and yellow fusiforms to deep red and black algae-grazers. All these species come from a handful of known founder taxa, with well characterized evolutionary histories. There is no place like this on earth, and it’s where I do my research whenever I am able, and whenever I’m not, I content myself with bringing them into the lab and watching them there.

My name is Alex Jordan, and I’m a fish nerd. From early on in life I’ve kept fish, and worked through keeping and breeding most of the major groups, finally arriving at the cichlids. I got my first job in an aquarium store just after school, and only stopped working in them once I finished my PhD. These days, I’m the Integrative Biology Postdoctoral Fellow at the University of Texas at Austin, but I still spend most of my time looking into fish tanks. I am interested in how animals perceive and respond to changing social conditions, and how changes in individual behavior affect broader social networks. I seek to understand the cognitive, behavioral, and genetic basis for socially mediated plasticity in behavior. In essence, I want to know how who we are with affects what we do, and how what we do affects who we are with.

CichlidsAlthough they may seem simple, these are fundamental questions about evolutionary processes that can influence the strength and direction of selection, the preferences of and strategies employed by animals, and ultimately the course of evolution. To really understand the interaction between social and individual behavior though, we need to understand what exactly passes between individuals living in social groups that might influence behavior of other group members. At the most basic level, we must first characterize how information flows among individuals within these groups to understand how they might influence each other. From there we can build up into more complex questions about what kinds of cues are given out by individuals, how these cues are perceived by others, what meaning they may come to have, and how they eventuate in different behaviors. In my BEACON funded research, I seek to answer these fundamental questions about information flow in biological networks using the African Rift Lake cichlid Astatotilapia burtoni.

Observing fish behaviorMost animals are social at some point in their lives, but often these social connections are difficult to characterize because groups are fission-fusion, that is to say they continually break apart and reform, or the interactions among animals are difficult to assess or measure. The cichlid A. burtoni is different in that it forms stable social groups with easily definable social roles. In each group there will typically be one or two dominant males that are brightly colored and highly aggressive, subordinate males who lack color and behave submissively, and females who shoal with other females and are generally not aggressive. The interactions among groups members are stable over time and easily observable by eye – aggression takes the form of fast chases and bites, courtship involves a very clear transverse body quivering display, and submissive fish may expose their flanks or swim away. Using these behaviors, I create networks of different types and ask how the flow of information moves along edges within these networks.

Experimental testing arena. TOP photo shows initial training, BOTTOM photo shows social learning.

Experimental testing arena. TOP photo shows initial training, BOTTOM photo shows social learning.

To do so, I train fish to associate a certain colored LED light with a food reward by hijacking commercial automatic feeders with an arduino microcontroller that controls both the light cue and the food reward. The tanks are all filmed from above with remote triggered HD webcams for later automated tracking. The fish are left almost entirely to themselves in this process, the experimental design means that we need to enter the room barely more than once a week. The arrays of tanks, with cameras, automatic feeders, microcontrollers, and LEDs remind me strongly of the scene of human battery cells from The Matrix. The major difference is that I want my fish to lead full happy lives and have plenty of room to swim, although arguably that was true for the humans in those cells, if only in their minds. Anyway, I digress… Once individual fish have learnt the cue, I place them into groups of uninformed individuals and ask how their position in the social hierarchy and their network metrics influence the degree of social learning by the naïve group members. With this design, I can also manipulate characteristics of the group to determine how group structure and network shape affects the acquisition of information. Taking these empirical results, I collaborate with the Adami lab to create visual models to assess how changing group characteristics affect attention and visual cues passing among group members, and how the network structure itself changes as learning is achieved. Once we understand the fundamental rules of information flow in these social systems, we can build these into designs that ask more complex questions.

Alex and sunsetThis will happen when I return to the lakes, where I have a system already set up to manipulate the social networks of groups in massive communities of thousands of fish living in shells on the lake floor. Using the basic rules of information flow I am discovering with my current project, I want to understand how males assess the costs and benefits of increasing the expression of their own sexual traits under the current social conditions. My previous work has examined similar questions but has only been able to look at changes in social conditions and associated changes in individual behavior (or vice-versa), I have not yet been able to look under the hood to understand exactly what type of information is being exchanged among social group members and how individuals perceive it. My BEACON projects will allow me to head back to Darwin’s Dreampond with a new toolkit to understand the interaction between the social environment and the evolution of behavior. Because changing social conditions can rapidly alter both the strength and direction of selection acting on traits, diving back into Lake Tanganyika with a new understanding of social information transfer really will allow me to see evolution in action.

For more information about Alex’s work, you can contact him at lyndonjordan at utexas dot edu.

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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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