Update: 2/26

I met with Brian Connelly today after the BEACON seminar and his project suggestions echo Phil's. He did say signaling will be rather complicated, but we're aware of that, and Luis has some ideas related to that; perhaps we should meet with him.

I have passed on the config file info, and hopefully we can get something started before spring break. We REALLY need to get things going, but do be aware that the runs will take a bit. If you're waiting to write or look into perhaps how to run the stats, it might be good to formulate a plan now and/or begin writing so you don't have too much right before the deadline.

Alex, Phil, and I will be meeting Fridays 12:30-1:30pm, pending final confirmation.

Productive Meeting with Phil!

Alex and I met with Phil yesterday, and wow, was it productive. As the next steps, Alex is going to look at how sexual organisms are coded in Avida, and I am going to rifle through the config files and determine what parameters we need to change. We plan now to meet at least biweekly with Phil.

For your (especially Alex's) reference, scripts for parsing through data and other Avida-related things are in Titus' github materials from his CSE891 Course last fall. You can also look at the Avida Digital Life Platform site. Among many things, there you'll find a special section devoted to the birth/death of individuals that is of interest.

Regular Group Meeting

All,
After Alex and I meet with Phil, we should probably get together, review the experimental design, and decide how to move forward as a group. It looks like Mon. 2pm or Tues. 12pm are our best bets moving forward. If it's ok with you all, I'd like for us to set a regular group meeting next class.

To avoid a week of time lost, during the remainder of next week we should somehow try to solidify experiment plans, either via edits in googledocs or the blog. Communicate issues you have with the design and Alex and I will work to address them. Hopefully once we design the final experiment, it will be easier for you, Nick, to start working with Ian on what kind of stats we'll need to do, and for you, Sara, to talk to Charles/Louise about Avida and signaling papers. I don't want to saddle anyone with too much work as the deadlines approach.

Availability

I've posted the availability schedule as availability.pdf on googledocs. I'm not a fan of the format, and we have 5/6 responders, so look for an improved, inclusive version soon. I just wanted to be sure we're all on the same page for now.

Update: 2/18

All,

Experimental Design:
-Meeting: Alex and I are meeting with Phil on Tuesday from 4-5, location TBD.

-Proposed experiment: I am going to be overhauling the proposal, so please poke holes in and suggest alternatives to the current proposal. I am going to try to improve and rewrite the proposed experimental design in greater detail this weekend, so if you see a new version, I'd appreciate comments on that as well. I know there are things about this experiment that are not great; I am confident, however, that we can 'optimize' (haha) this design together.

Writing and Research:
New googledocs posts: I've added a few more articles. Of particular interest is Hohenlohe and Arnold, 2010 (suggested by Louise). Start there as you branch out.

File Sharing

All,
I've made and sent out an invitation for a collection on google docs. If you didn't get an invitation, please let me know. Right now, all that is there are papers for our general (and Sara's direct) use. Please put anything to be shared directly in this collection so everyone has access to resources.

People Posts and Availability

Glad to see you all have posted a bit about yourselves (I put mine as a comment to the first post, so hopefully you can see it).

Please remember to respond to the doodle on availability. Check your email for this link (it's editable, so I don't want to post here). I will make the results available to all once everyone's responded.

Thanks!

Nick's Research Interests

My name is Nick Testa and I am a first year Zoology/EEBB Ph.D. student in Alex Shingleton's lab. I am primarily interested in evolutionary developmental biology (evo-devo) and the interactions of genetics and developmental processes on evolution (although my interests are generally much broader). Currently, I am working on a project to elucidate the developmental mechanisms behind sexual size dimorphism (SSD). It is currently unknown which mechanisms interact (and how) to create the size difference seen between the sexes in Drosophila (I know this sounds vague, but if you are interested, just ask me about it and I can elaborate). Also, I am working on a couple of other projects involving coordinated organ growth. The idea is basically that each organ coordinates its growth with the rest during development (i.e. if you damage one organ, the rest slow their growth to allow it to catch up, keeping all organs the same size).

Introduction: Alex Peer

I'm a first-year CSE student in Dr. Chai's lab -- masters at the moment, but planning to go PhD. My interests are pretty broad, often too broad; right now I'm trying to focus on natural language processing, particularly as it represents / overlaps cognitive processes and internal representations of information, which is roughly AI -- but there again, too broad. Basically, my research group is making robots talk about cups.

I've spent a few years out of academia doing contract work, mostly web stuff, and I suspect I'm still thinking more like an engineer than a scientist. This class might help me figure out where to draw the line between those, and when to blur it; also how people think about stats in an experimental setting, and when evolutionary techniques are suited to solving a problem.

Update: 2/9

Now that we have Louise Mead and Phil McKinley on board, here is the tentative division of labor:

-Alex and Emily (with Phil and Louise): Experimental Design and Avida Coding; Methods, details in Discussion of paper
-Nick (with Phil, if necessary): Running and Analyzing the Data; Results and Discussion overview
-Sara (with Louise): Writing the introduction/lit review, conclusions, editing the paper for flow and PLOS format, and editing the presentation slides

-All: Pitching in when necessary; Final edits of paper (particularly discussion)

Please remember to post or comment to the blog. Also, let's discuss file sharing (on dropbox) and create a doodle poll for availability at the next meeting.

Sara's Research Interests

I am a first-year Zoology/EEBB Ph.D. student in Dr. Tom Getty’s lab. I am interested in how individuals maximize their inclusive fitness by balancing cooperation and competition when interacting with their kin. Maximizing inclusive fitness requires individuals to avoid directly competing with kin as much as possible, but this becomes more difficult in systems where interacting with kin cannot be avoided. Frog and toad tadpoles are one such case, as many species form aggregations, often comprised of siblings, before they are capable of leaving ponds. When resources are limited, larger tadpoles of many species have been seen to inhibit the growth of smaller individuals through the use of chemical signals; there is some evidence, however, of smaller tadpoles performing better when grouped with siblings rather than non-kin, even under poorer conditions, suggesting that siblings respond to one another’s signals in a way that maximizes inclusive and individual fitness for everyone. I plan to use two species that differ in kin-aggregating tendencies to test the hypothesis that kin-aggregating species will respond to sibling signals by limiting growth rate when a sibling’s marginal fitness benefits are greater, whereas species that do not exhibit kin preferences will show no change in competitive behavior regardless of the situation.

Signaling Loss group

Nick Testa
Emily Weigel
Sara Garnett
Alex Peer