Friday, May 6, 2011
Sunday, May 1, 2011
Update: 5/1
The revised methods are in the dropbox, and I'm working to correct them (along with the intro) based on the suggested edits. Sara has made the slides for these portions and I believe they'll be posted to dropbox soon (Alex please check). Nick's data analysis is up, and we're waiting to get some feedback on what still needs to be analyzed or written up. Great job, guys!
Sunday, April 24, 2011
Update 4/24
Sara, Nick, and I met with Ian over the stats, and we're chugging through. I brought the methods section to writing group for discussion, and the revised copies are still trickling back in. We're getting there! Yay!
Thursday, April 21, 2011
And the hits just keep on coming...
Hey again,
As you have no doubt heard by now, I've got the complete data set. It is a glorious 250,000 lines of data (plus, I've tested it in R and it works beautifully!).
Still working on how exactly to do the stats, but now that the data are in a useful format, this part should be fairly straightforward (hopefully). Also, I've been getting help from both Ian and Eli so this thing is as good as done!
-Nick
As you have no doubt heard by now, I've got the complete data set. It is a glorious 250,000 lines of data (plus, I've tested it in R and it works beautifully!).
Still working on how exactly to do the stats, but now that the data are in a useful format, this part should be fairly straightforward (hopefully). Also, I've been getting help from both Ian and Eli so this thing is as good as done!
-Nick
Monday, April 18, 2011
Stats coming along
Hey everyone,
I just had a fruitful meeting with Eli Swanson (another grad student from the Holekamp lab) concerning our statistics and how to work with the tremendous amount of data in R.
At this point, it looks like the multiple regression with ANOVAs is our best bet. This will essentially tell us how each response variable is affecting things like percent signaling, fitness, etc...
The good news is that this should be far less complicated than I was initially thinking it would be (or at least now I just understand it better). I'm going to start writing my R scripts now that I understand what needs to be done (as soon I'm done for the day here in the lab).
I'll continue to keep you all updated on this process as things happen.
-Nick
I just had a fruitful meeting with Eli Swanson (another grad student from the Holekamp lab) concerning our statistics and how to work with the tremendous amount of data in R.
At this point, it looks like the multiple regression with ANOVAs is our best bet. This will essentially tell us how each response variable is affecting things like percent signaling, fitness, etc...
The good news is that this should be far less complicated than I was initially thinking it would be (or at least now I just understand it better). I'm going to start writing my R scripts now that I understand what needs to be done (as soon I'm done for the day here in the lab).
I'll continue to keep you all updated on this process as things happen.
-Nick
Saturday, April 16, 2011
Otherness and Fury: The Avida LAN party progress report
So, we've spent the last several hours running scripts on the hpcc gateway. We decided to go with plan B (running two runs: one with signaling and one without). We've got a good portion of our data and most of the runs are completed (or in process). Also, Alex is working on scripting something to make the tremendous volume of data more usable.
As far as the writing is concerned, we have completed a draft of the methods section, the title and abstract, and the acknowledgements all in the requirements for PLoS
We have made some progress on the statistics portion of the project as well.
Also, toad-panther and eel-worm.
Gnome-fria
Sara ended the evening with a Pfennig-fox, culminating in a bloody lip.
As far as the writing is concerned, we have completed a draft of the methods section, the title and abstract, and the acknowledgements all in the requirements for PLoS
We have made some progress on the statistics portion of the project as well.
Also, toad-panther and eel-worm.
Gnome-fria
Sara ended the evening with a Pfennig-fox, culminating in a bloody lip.
Friday, April 15, 2011
Update: 4/15
I met with Phil today to go over the methods from his point of view. His main suggestions were to target PLoS papers on artificial life, and he sent me one nice example paper to use as a reference.
I also met with Louise today to go over the methods draft. She suggested adding in a figure of how signaling works and details on some of the defaults. She also suggested that the introduction should set up the methods, so Sara and I may be working closer tomorrow.
Overall, Louise is "extremely excited" to see the results, and I think Phil is, too, so let's hope we get some!
I also met with Louise today to go over the methods draft. She suggested adding in a figure of how signaling works and details on some of the defaults. She also suggested that the introduction should set up the methods, so Sara and I may be working closer tomorrow.
Overall, Louise is "extremely excited" to see the results, and I think Phil is, too, so let's hope we get some!
Thursday, April 14, 2011
Update: 4/14
With the issues on Teragrid, we're pursuing the HPCC. Those accounts have been set up for all members of our projects, and at least one of us falls into the priority BEACON group. Alex is working on getting the HPCC together for us to all use.
I took Sara's introduction to writing group. The main comments/criticisms were to focus the intro more and to include detailed paragraphs on the hypotheses and rationale for the project. Sara is revising this soon based on the comments.
Nick, Sara, and I met today to figure out how we want to graphically represent the data. we have a decent idea, so Nick is working on coding this and the associated stats.
Nick, Alex, Sara, and I are meeting at Nick's place Saturday to try to scrounge up some data and have a general working party on this project. With the numerous setbacks and challenges we've already had (and surmounted), all I can say is wish us luck!
I took Sara's introduction to writing group. The main comments/criticisms were to focus the intro more and to include detailed paragraphs on the hypotheses and rationale for the project. Sara is revising this soon based on the comments.
Nick, Sara, and I met today to figure out how we want to graphically represent the data. we have a decent idea, so Nick is working on coding this and the associated stats.
Nick, Alex, Sara, and I are meeting at Nick's place Saturday to try to scrounge up some data and have a general working party on this project. With the numerous setbacks and challenges we've already had (and surmounted), all I can say is wish us luck!
Sunday, April 10, 2011
Update 4/10
Hey All,
As an update, Phil was out of town Friday, so Alex and I did not meet with him, however, I am working on the methods (based on the methods of published Avida papers) and Alex has gotten the genomes written and everything seems to be coming together.
Keep up the good work, guys!
As an update, Phil was out of town Friday, so Alex and I did not meet with him, however, I am working on the methods (based on the methods of published Avida papers) and Alex has gotten the genomes written and everything seems to be coming together.
Keep up the good work, guys!
Sunday, April 3, 2011
Update
Hey Everyone, I've got a few updates to share will you all:
As far as TeraGrid goes, I'm on! I had a little bit of trouble connecting at first, but Dirk Colbry (the TeraGrid campus champion) was able to help me connect via ssh. Unfortunately, I'm having issues getting Alex's version of Avida onto TeraGrid (security issues with the scp command in ssh) so I will have that figured out by Monday or Tuesday.
I haven't been able to get Alex's Avida running on my computer anyways (I was testing it in the meantime and "Permission Denied" for some reason). This I will also try to have fixed by early this week.
Lastly, I've spoken with Ian about the statistics and he says we just have to wait until he goes over linear modeling and such during lecture. So unfortunately, there is no working too far ahead on the stats end (for now).
Once this is all figured out, I should be good to go. I'll continue to keep everyone updated on my progress/issues!
As far as TeraGrid goes, I'm on! I had a little bit of trouble connecting at first, but Dirk Colbry (the TeraGrid campus champion) was able to help me connect via ssh. Unfortunately, I'm having issues getting Alex's version of Avida onto TeraGrid (security issues with the scp command in ssh) so I will have that figured out by Monday or Tuesday.
I haven't been able to get Alex's Avida running on my computer anyways (I was testing it in the meantime and "Permission Denied" for some reason). This I will also try to have fixed by early this week.
Lastly, I've spoken with Ian about the statistics and he says we just have to wait until he goes over linear modeling and such during lecture. So unfortunately, there is no working too far ahead on the stats end (for now).
Once this is all figured out, I should be good to go. I'll continue to keep everyone updated on my progress/issues!
Friday, April 1, 2011
Signaling implementation in Avida
The code is, for the most part, done. Here's how we've implemented things:
The short version:
Organisms can both signal and receive signals. Signals are sent to everybody around them, and the best mate is chosen from all the received signals.
When organisms divide, their reproductive materials are preserved on a shelf labeled by the cell the organism was in; when another organism wants to mate with that organism, it retrieves a copy of most recent reproductive materials stored in that cell's shelf.
Initially, we require that signals be received to mate; later, we turn it off, and anyone who doesn't receive a signal (either doesn't try or didn't get a signal) just chooses a random shelf.
The long version:
We added two new instructions -- mate-signal and mate-receive. Organisms can do either or both, as often as they want.
When mate-signal is executed, a message (piggybacking off of the existing messaging code) is broadcast to all organisms within a certain radius of the sender. Only a certain number (default 8) of signals are 'remembered', the oldest signal is forgotten first. The message contains the cell ID of the signaler.
When mate-receive is executed, a message is selected from among all those received. Currently it's selected at random, I'm going to change that to by merit this weekend. The message -- the cell ID of the signaler -- is stored as mateID in the receiver's phenotype. During this procedure, all received signals are 'forgotten' (mostly for coding convenience, as the only code I dug deep enough to find for that datatype was a pop). With pure random selection this forgetfulness seemed like it might become an interesting analogue for attention, but if we switch to choosing by merit it shouldn't make any difference. I'm still a little worried that choosing by merit may have unintended consequences, I haven't fully thought out where that pressure will be applied.
If the organism has received no signals, mateID is instead set to -2 to indicate a failed receive. (I need to change this slightly, as it will currently overwrite any previous successful receives!)
When an organism divides via divide-sex, it goes into the birth chamber and checks in with our new (and awkwardly named) cBirthMateSelectHandler_GameteStorage. This mate selection class first stores the offspring created by the divide -- the gamete, more or less -- in an array indexed by the parent's cell ID. Gametes are stored until overwritten by another entry for that cell ID.
If the organism has received a signal, it checks to see if a gamete is available for the cell ID stored in its mateID: if yes, it's used to generate offspring; if not, mating fails. (Note that here, organisms that have signaled but not yet divided will not have stored their gametes; in this case, very early in the sim the spot will be empty, and for the rest of the sim will contain the gamete of a dead organism. This should be rare enough to not cause problems.)
If the organism has not received a signal, we check the new SIGNAL_RECV_NECESSARY_TO_MATE configuration parameter. If it's true, mating fails. If it's false, this organism chooses a random cell ID; if a gamete is stored for this cell ID, it's used to generate offspring; if not, mating fails (and this case should be pretty rare).
And that's it. Now (well, after I make the above mentioned small changes) we have to get it running on something, make sure we can get the data we need out of Avida without further modification (we may need to set signaling to a task, for example), and then see if Avida can find any holes in our model that need to be patched up.
The short version:
Organisms can both signal and receive signals. Signals are sent to everybody around them, and the best mate is chosen from all the received signals.
When organisms divide, their reproductive materials are preserved on a shelf labeled by the cell the organism was in; when another organism wants to mate with that organism, it retrieves a copy of most recent reproductive materials stored in that cell's shelf.
Initially, we require that signals be received to mate; later, we turn it off, and anyone who doesn't receive a signal (either doesn't try or didn't get a signal) just chooses a random shelf.
The long version:
We added two new instructions -- mate-signal and mate-receive. Organisms can do either or both, as often as they want.
When mate-signal is executed, a message (piggybacking off of the existing messaging code) is broadcast to all organisms within a certain radius of the sender. Only a certain number (default 8) of signals are 'remembered', the oldest signal is forgotten first. The message contains the cell ID of the signaler.
When mate-receive is executed, a message is selected from among all those received. Currently it's selected at random, I'm going to change that to by merit this weekend. The message -- the cell ID of the signaler -- is stored as mateID in the receiver's phenotype. During this procedure, all received signals are 'forgotten' (mostly for coding convenience, as the only code I dug deep enough to find for that datatype was a pop). With pure random selection this forgetfulness seemed like it might become an interesting analogue for attention, but if we switch to choosing by merit it shouldn't make any difference. I'm still a little worried that choosing by merit may have unintended consequences, I haven't fully thought out where that pressure will be applied.
If the organism has received no signals, mateID is instead set to -2 to indicate a failed receive. (I need to change this slightly, as it will currently overwrite any previous successful receives!)
When an organism divides via divide-sex, it goes into the birth chamber and checks in with our new (and awkwardly named) cBirthMateSelectHandler_GameteStorage. This mate selection class first stores the offspring created by the divide -- the gamete, more or less -- in an array indexed by the parent's cell ID. Gametes are stored until overwritten by another entry for that cell ID.
If the organism has received a signal, it checks to see if a gamete is available for the cell ID stored in its mateID: if yes, it's used to generate offspring; if not, mating fails. (Note that here, organisms that have signaled but not yet divided will not have stored their gametes; in this case, very early in the sim the spot will be empty, and for the rest of the sim will contain the gamete of a dead organism. This should be rare enough to not cause problems.)
If the organism has not received a signal, we check the new SIGNAL_RECV_NECESSARY_TO_MATE configuration parameter. If it's true, mating fails. If it's false, this organism chooses a random cell ID; if a gamete is stored for this cell ID, it's used to generate offspring; if not, mating fails (and this case should be pretty rare).
And that's it. Now (well, after I make the above mentioned small changes) we have to get it running on something, make sure we can get the data we need out of Avida without further modification (we may need to set signaling to a task, for example), and then see if Avida can find any holes in our model that need to be patched up.
Friday, March 25, 2011
Update 3/25
Good job this week with presentation stuff (Great slides, Sara!). Alex is chugging along with the code (thanks!), and I hope that we're all starting to outline (mentally? on paper?) how we're going to support him. Nick, as things calm down in lab, please meet with Ian about the stats; he seemed to indicate our stats are going to be complex.
Saturday, March 19, 2011
Update 3/19: A few additional notes
In the meeting with Phil, it was suggested that we email Chris Chandler to see if some of the issues he's solved will be useful to us. I just emailed Chris, so we're waiting on a response now.
Also, Phil suggested sending him notes and code the night before meetings on issues we're having so he can think about it overnight. Let's try to do that in the future. He also suggested that we should use something similar to his send/retrieve code for broadcasting and look at the devo lab wiki and the Avida documentation (online and within copy) more as we run into problems.
Also, Phil suggested sending him notes and code the night before meetings on issues we're having so he can think about it overnight. Let's try to do that in the future. He also suggested that we should use something similar to his send/retrieve code for broadcasting and look at the devo lab wiki and the Avida documentation (online and within copy) more as we run into problems.
Update 3/19
Alex and I had a productive meeting with Phil, we've relaxed some assumptions, and hopefully we will have some running code soon. Additionally, Sara has made some wonderful slides, so everyone please look at them in prep for Tuesday.
Thursday, March 17, 2011
TerraGrid
Hey everyone,
I just got an email that our TerraGrid account has been added! I will email you all with login info once it is made available.
I just got an email that our TerraGrid account has been added! I will email you all with login info once it is made available.
Wednesday, March 16, 2011
3/16 Update -- Presentation Slides
I've sent around a draft of our update presentation for next Tuesday. If there's anything that isn't clear about our experimental design and plans, please let me know so that I can make changes.
Tuesday, March 15, 2011
Update 3/14
Today was productive! Alex and Nick discussed the code and runs, and Emily and Sara discussed the experimental design with Ian.
Updates to the experimental design:
1. Threshold loss: "Loss" is now defined as the point when 95% of the population no longer has the signaling genes. This is to combat a small number of signalers hanging out but the population as a whole losing the signal much earlier.
2. Runs will be at least 2500 and intended to measure the effect of linkage and population size on signal loss. Check my math.
genotype (2; linked or unlinked) X percentage of guaranteed success of signal (5; 100%, 75, 50, 25, 0%) X population size (5; 200%, 100, 50, 25, 10%) X runs (50) =2500
Updates to the experimental design:
1. Threshold loss: "Loss" is now defined as the point when 95% of the population no longer has the signaling genes. This is to combat a small number of signalers hanging out but the population as a whole losing the signal much earlier.
2. Runs will be at least 2500 and intended to measure the effect of linkage and population size on signal loss. Check my math.
genotype (2; linked or unlinked) X percentage of guaranteed success of signal (5; 100%, 75, 50, 25, 0%) X population size (5; 200%, 100, 50, 25, 10%) X runs (50) =2500
Thursday, March 3, 2011
Update 3/3
Alex has gotten Avida to compile and will be working on getting things going. Unfortunately, Phil had to cancel this week, but we're still shooting for after the break to begin runs. Also, Sara is working with the updated proposal to begin writing the introduction.
Chugging along... but everyone still enjoy your breaks!
Chugging along... but everyone still enjoy your breaks!
Tuesday, March 1, 2011
Update: 3/1
Alex and I have now scheduled things with Phil, and Alex is working to get Avida going to better understand how to modify the existing code. We'll discuss this Friday with Phil, but I just wanted to keep you guys posted. Also, I've been updating the proposal as we go, so hopefully we'll be able to used this as a skeleton for out paper.
Sara, can you find the PLOS guidelines? If we've got to write to those, it would be good if we know what they are.
Sara, can you find the PLOS guidelines? If we've got to write to those, it would be good if we know what they are.
Friday, February 25, 2011
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.
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.
Wednesday, February 23, 2011
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.
Sunday, February 20, 2011
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.
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.
Friday, February 18, 2011
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.
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.
Tuesday, February 15, 2011
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.
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.
Sunday, February 13, 2011
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!
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!
Thursday, February 10, 2011
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).
Wednesday, February 9, 2011
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.
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.
-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.
Tuesday, February 8, 2011
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.
Thursday, February 3, 2011
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