Brian Connelly: BEACON Articles tagged 'BEACON' on Brian Connelly en-us Mon, 28 Nov 2016 15:10:40 -0800 Mon, 28 Nov 2016 15:10:40 -0800 Jekyll v3.3.1 Data Visualization Presentation Online Brian Connelly Wed, 21 Aug 2013 10:58:00 -0700 visualizationplottingpresentationslidesBEACON I’ve posted the slides from the presentation on data visualization that I gave with Jared Moore and Luis Zaman at the 2013 BEACON Congress. Check them out on figshare and feel free to share. Even though we were only able to scratch the surface, we had some great discussions about how to create and share visualizations and how important it is to make your data “easily consumable” by your audience.

I’ve posted the slides from the presentation on data visualization that I gave with Jared Moore and Luis Zaman at the 2013 BEACON Congress. Check them out on figshare and feel free to share. Even though we were only able to scratch the surface, we had some great discussions about how to create and share visualizations and how important it is to make your data “easily consumable” by your audience.

For modern scientific data, a picture can be worth billions of words. In this session, we'll discuss some of the tools and techniques used to produce informative and effective visualizations. This includes tools for producing videos, which can be tremendously insightful for visualizing data over time and space. Finally, we'll discuss some of the technologies that allow data producers and consumers to manipulate and interact with data sets in ways that allow data to be viewed from new and different perspectives.

When Cooperating Means Just Saying No Brian Connelly Thu, 20 Jun 2013 14:24:00 -0700 BEACONcooperationquorum sensingevolutionPseudomonas aeruginosa This post originally appeared on the BEACON Blog on May 13, 2013.

Evolutionary biologists often talk like economists, particularly when the topic is cooperation. Instead of dollars, euros, or pounds, the universal currency in evolution is fitness. A species that cooperates cannot survive when competing against a non-cooperative opponent unless the fitness benefits provided by cooperation, such as those resulting from greater access to resources, outweigh the costs. To make matters more complicated, cooperative benefits often take the form of “public goods,” which benefit all nearby individuals, whether cooperator or not. This sets the stage for the emergence of “cheaters”, which exploit the cooperation of others without contributing themselves. Despite cooperation seeming at odds with the notion of “survival of the fittest”, we now have a good understanding of how cooperation can persist in the face of cheaters based on the tremendous work of Fischer, Haldane, Hamilton, Price, and those who have since followed. When the costs and benefits are favorable, and when close relatives are more likely to receive those benefits, cooperation can survive and even thrive.

Lab group
Just another day in the lab. Making plates with Belen Mesele (L) and Helen Abera (R), two of the people working on the project with me. Our wild-type cooperator strains produce beautiful blue-green colonies due to the production of pyocyanin, another behavior regulated by quorum sensing.

Environments are always changing, and since the environment plays a dominant role in determining the fitness costs and benefits associated with all traits, natural selection may quickly change between favoring cooperation and not. When the balance shifts so that cooperation becomes more costly than beneficial, cooperators risk being driven to extinction by cheaters or other non-cooperators that do not pay those costs. So how can cooperators survive these tough times? The answer is frustratingly simple—by not cooperating. The challenge, though, is in determining when to cooperate and when to be more self-centered. We humans and other primates are—perhaps very arguably—good at estimating whether or not cooperation will benefit ourselves and those with whom we are similar, either genetically or in our beliefs. We are able to do this by integrating a great deal of information about our world and the people in it. But we are not alone in this.

Surprisingly, it turns out that even relatively “simple” bacteria are extremely effective at determining whether or not to cooperate based on the state of their environment and the composition of their population. One of the ways that these bacteria accomplish this is through quorum sensing. With quorum sensing, individuals communicate with each other by releasing and detecting small molecules, which are used as signals. When an individual detects low levels of the signal, it can use this information to assume either that there are too few other cooperators nearby to produce sufficient benefits by cooperating, or that the public good will be flushed out of the environment before it can be used. However, when that individual detects high levels of the signal, it is likely that there are many relatives nearby that would benefit from cooperation. By communicating this way using signals specific to their own species, bacteria use quorum sensing to rapidly adjust their behaviors to maximize their fitness as the environment changes.

Josie Chandler recently wrote about her fascinating work that addressed how bacteria use quorum sensing to control the production of antibiotics. While she investigated this process as a means of competing with other species, it can also be viewed as a form of cooperation among members of the same species. By using antibiotics to kill off competitors, sometimes self-sacrificially, more resources become available to those that remain. And because species often have resistance to the antibiotics that they produce, those that remain after an antibiotic attack are likely to be close relatives.

The production of antibiotics is just one example of a behavior controlled by quorum sensing. Since its discovery in the early 1970s, quorum sensing has been observed across a wide variety of species. Among the behaviors regulated by quorum sensing, those related to cooperation and other social interactions are perhaps the most prevalent. Because of this, quorum sensing is believed to play a key role in allowing cooperation to persist in ever-changing environments.

Plated differences in colony morphologies
Colonies formed by two of our strains. Through the production of elastase, our cooperators are able to break down the proteins present in this milk agar plate, forming large, clear halos. Our non-cooperator strain does not produce elastase, so it is unable to break down the milk proteins, and a much smaller halo is produced.

Although the connection between quorum sensing and cooperation is now well known, little is understood about how these behaviors became interlinked. To begin addressing this, I am currently working in Ben Kerr’s Lab on a number of projects that investigate the co-evolution of cooperation and quorum sensing. To gain a broader picture of this process, we’re pairing microbial experiments with computational and mathematical models.  The cooperative behavior we’re focusing on in our study system, Pseudomonas aeruginosa, is the production of the digestive enzyme elastase. When secreted into the environment as a public good, elastase breaks down large proteins into smaller, usable sources of nutrients available to all cells in the surrounding area. In environments where these large and otherwise inaccessible proteins are the main nutrient source, this behavior is extremely beneficial. (Here is a short video demonstrating growth of our bacteria.)

Pseudomonas faces
In these environments, where the proteins are a limited source of resource, cooperators do better due to the benefits provided by elastase. We can measure the amount of cooperation occurring within populations by examining the size of the clearing that occurs when extracting and plating the elastase that is produced. Note: faces add no scientific value.

By exposing our populations to different environments over many generations, we are directly observing how communication and cooperation co-evolve. Through these experiments, we are investigating how quorum sensing enables cooperation to be maintained, the types of environments in which this occurs, and the different ways in which this regulation can occur. We hope that through this work, we can gain a greater understanding of the complex social processes that occur in natural ecosystems and in some of the infections that create tremendous health challenges.

The Role of Environment in the Evolution of Cooperation Brian Connelly Mon, 25 Apr 2011 07:00:00 -0700 avidaBEACONbiolumecooperationseedsevolutionVibrio choleraeresearch This post originally appeared on the BEACON Blog on April 25, 2011.

Cooperation is something that most people take for granted. It’s woven into just about every part of our lives. Our societies have even developed a wide variety of measures to make sure we’re cooperating, such as punishing those that don’t. This level of cooperation isn’t reserved to humans. Cooperation plays a vital role in nearly all forms of life, from our primate cousins to ants and termites, and all the way down to simple microorganisms such as bacteria. There’s even an astounding amount of cooperation going on within our bodies. Amazingly, of the ten trillion or so cells in the human body, over 90% of those are bacterial cells made up of thousands of different species.

Brian at the Trier Amphitheater
Brian at the Trier Amphitheater

While it’s easy to find examples of cooperation in nature, understanding how cooperation got its roots, how it evolved, and how it is maintained are very tricky questions, especially when viewing evolution as “survival of the fittest”.  If the goal is to outcompete everyone, why would one want to pay some costs to help others?  This is a question evolutionary biologists have been asking since Darwin, who wrote “If it could be proved that any part of the structure of any one species had been formed for the exclusive good of another species, it would annihilate my theory, for such could not have been produced through natural selection”.

Over the years, a lot has been learned about cooperation.  Most of this knowledge has come from studying cooperation using mathematical and computational models or by studying organisms in lab environments.  The problem with these methods, though, is that they only examine cooperation in contexts that don’t necessarily match real world situations.

My research focuses on understanding the different ways in which the environment can affect the evolution of cooperation.  Peter and Rosemary Grant summed this up nicely when they wrote, mimicking a famous quote by Theodosius Dobzhansky, “Nothing in evolutionary biology makes sense except in the light of ecology.”

The benefits of understanding how cooperation is maintained are huge.  For billions of years, life existed only as single-celled organisms.  At some point, cells began cooperating with each other, and our first multicellular ancestors emerged.  Cooperation among bacteria also plays a large role in diseases like cholera, which killed over 100,000 people in 2010.  A substantial factor in the spread of cholera is quorum sensing, a cooperative process that bacteria use to coordinate behaviors.  By understanding how cooperation works in infections like Cholera, treatments can potentially be designed to disrupt cooperation, and perhaps lessen the strength of the infection or limit its spread.  Further, by understanding how the environment affects this behavior, researchers will have a better idea of how their results in laboratory environments will translate to natural environments like the body.

In simulations of cooperative behaviors, cooperators exist in patches which are constantly invaded by cheaters, or those that take advantage of the cooperation without themselves contributing.

My background is in computer science, so to start understanding how the environment can affect cooperation, I’ve used computational models of cooperation in Avida and SEEDS an open source package I’ve co-developed. My initial models looked at the role that environmental disturbance plays in cooperation and demonstrated that cooperation increases as environmental conditions worsen.

Some of my other work examined the effect that the amount of resource present in the environment has on cooperation.  We found that the more resource an individual had, the more likely they were to cooperate, since the costs relative to their wealth decreased.  This only occurred after a certain point, though.  Below this point, it the benefits provided by cooperation just didn’t outweigh the costs, so no cooperation occurred.

Another study looked at how the number of social interactions one has affects a population’s ability to maintain cooperation and diversity.  Here we found that as the number of interactions go up, at one point populations quickly lose the ability to maintain diversity.  Although these results were targeted at a small system, I still wonder if they could tell us anything about the direction our increasingly-connected society is heading.

View this video at

One of the really outstanding aspects of both BEACON and MSU is the opportunity for collaboration.  I’m extremely fortunate to have an advisor, Dr. Philip McKinley who personifies this spirit of collaboration.  One such collaboration that he initiated was a meeting with Dr. Chris Waters, a fairly new faculty member in the Department of Microbiology and Molecular Genetics. This was at a point where I’d finished some of my initial computational work on cooperation and had become familiar with how cooperative behaviors were being studied using microorganisms.  Meeting with Chris was really exciting for me, since I’d known about some of his earlier work with quorum sensing in bacteria.

Plates of Vibrio cholerae used to measure cooperation in different environments
Plates of Vibrio cholerae used to measure cooperation in different resource environments

What I didn’t expect to happen was that Chris offered me the opportunity to start asking the same kinds of questions about how environment affects cooperation in his lab – using real bacteria!  Now, I’ve always been the kind of person who gets excited about learning and trying new things, so I was thrilled.  Still, my microbiology background was nonexistent, and pretty much the only thing I remembered about biology (which I hadn’t taken since my freshman year of high school) was how to draw the stages of mitosis. Fortunately, Chris was really helpful at getting me started, and with the help of other people in the lab, I was able to perform some initial experiments. I’m now at a point where I’m performing some pretty complex (although maybe just to me) experiments that I designed based on what I’d learned.  I’ve seen first hand that what I do in the wet lab improves and inspires my computational work, and that the computational work can also improve and inspire the wet lab work.  I’m hoping that this sets the pace for the rest of my career.  I don’t know if I’ll ever not feel at least a little like an outsider in a microbiology lab, but I know I want to continue approaching problems from multiple perspectives.  Great collaborations really make that possible. There’s an enormous amount of exciting research going on within BEACON, but I’m equally excited about the possibilities for outreach and education.  Because evolution usually takes place on very long time scales, it can be extremely hard to demonstrate processes such as selection in a way that’s seen and understood within a few minutes.  When this is accomplished, though, evolution moves away from being just a vague concept to people and becomes a whole lot more approachable.  Sometimes, this means stripping away the notions of what life is based on our limited set of examples on earth and looking to alternate worlds.

Biolume project. Rendering by Adam Brown.
Biolume project. Rendering by Adam Brown.
One unique opportunity that being a part of this community has afforded me is a collaboration with BEACON’s artist in residence, [Adam Brown](, for his [Biolume]( project.  In this project, glowing, sensing, noisy, and evolving robotic units will be attached to the walls and interact with each other and with people who walk by.  Once I found out that Adam was planning to create large populations of these Biolumes, I was immediately excited by the possibility of evolving behaviors on these robots in a way that visitors could observe and, most importantly, affect!  I can’t think of a better way for people to learn about topics like natural selection than to participate in the process of selection, and define which behaviors are beneficial in the environment and which ones should quickly lead to extinction.