Brian Connelly: seeds Articles tagged 'seeds' on Brian Connelly en-us http://bconnelly.net Mon, 28 Nov 2016 15:10:40 -0800 Mon, 28 Nov 2016 15:10:40 -0800 Jekyll v3.3.1 SEEDS Paper Published at EvoSoft Workshop Brian Connelly Tue, 31 Jul 2012 22:26:00 -0700 http://bconnelly.net/2012/07/seeds-paper-published-at-evosoft-workshop/ http://bconnelly.net/2012/07/seeds-paper-published-at-evosoft-workshop/ papersresearchsoftwareartifical lifeseedsgeccoevolution I recently went to Philadelphia for GECCO 2012, where I presented my paper The SEEDS Platform for Evolutionary and Ecological Simulations at the EvoSoft workshop. It was great to talk with people about modern Evolutionary Computation Software Systems, especially the DEAP team, who share a lot of my ideas.

]]>
I recently went to Philadelphia for GECCO 2012, where I presented my paper The SEEDS Platform for Evolutionary and Ecological Simulations at the EvoSoft workshop. It was great to talk with people about modern Evolutionary Computation Software Systems, especially the DEAP team, who share a lot of my ideas.

]]>
The Role of Environment in the Evolution of Cooperation Brian Connelly Mon, 25 Apr 2011 07:00:00 -0700 http://bconnelly.net/2011/04/the-role-of-environment-in-the-evolution-of-cooperation/ http://bconnelly.net/2011/04/the-role-of-environment-in-the-evolution-of-cooperation/ 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.

Simulation
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 https://www.youtube.com/embed/r80RMW4F4FM

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](http://adamwbrown.net/), for his [Biolume](http://adamwbrown.net/projects-2/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.  

]]>
http://bconnelly.net/2011/04/the-role-of-environment-in-the-evolution-of-cooperation/#comments