January 25, 2010

Roosting on Structures

Last week I observed some birds above the University power plant smoke stack. I ended up making a video of their flight pattern. My interest in this stems from the widespread use of bird flocks as a model for understanding collective flocking (an instance of emergent behavior), in addition to some work I have done on modeling roosting behaviors among birds [1]. They were orbiting the power plant in a toroidal pattern, stretching out their orbit in slightly different directions on every cycle.

Image of birds circling the MSC smokestack, Michigan State University.

On one day, I saw them make a few cycles in one direction, then make a loop to the outside of the orbit in order to change direction. On another day, then decided to roost after making their series of orbits.

[1] this is available as a paper and talk presented at Understanding Complex Systems, 2006 (Champaign-Urbana, IL).

UPDATE (12/10/2013): the paper has been accepted and is now available on the bioRxiv.

Alicea, B.   Filling up the tree: considering the self-organization of avian roosting behavior. bioRxiv, doi:10.1101/000349.

January 10, 2010

Dynamics Days Wednesday, Thursday overview

Sorry for the late post, but I haven't been able to get around to this posting until today. The half for Dynamics Days was almost as good as the first half. The first talk of Wednesday was by Steve Strogatz, who introduced us to a phenomenon called chimera spiral waves. The interesting thing about these waves is that they are spiral-like with discrete color-bands in the outer part of the spiral, but are disordered and pixellated in the inner part of the spiral. There is an arXIv paper on the topic if you are interested in learning more.

Other topics covered were computational neuroscience, chaos in boolean networks, and complex networks. There was a presentation on so-called "neural avalanches" , where discharges of electrical activity in the brain exhibit power-law behavior in time. Some of the complex networks speakers focused on an idea called "community structure", where the goal is to find the structure within and between groups in a network. A related topic of interest was the finding the "giant component" in networks first proposed by Erdos and Renyi.

Overall, excellent conference. The next Dyanmics Days (2011) is supposed to be at Duke University and should be quite interesting.

January 8, 2010


Hod Lipson's group at Cornell has recently released a new data mining tool based on last year's paper "Distilling Free-Form Natural Laws from Experimental Data". The package is called Eureqa, and can be downloaded from here. More later.....

January 5, 2010

Dynamics Days, Day 2 afternoon

My afternoon was taken up by poster preparations, although I did get to attend the second set of talks. Of these, two students of Adilson Motter delivered very interesting presentations.

One of these was on metabolic networks, and how the concept of synthetic lethality can be used to understand adaptive responses to physiological challenges. In this case, a challenge such as heat shock induced the mass upregulation of genes in a generalized response. However, this response is sub-optimal in the sense that it inhibits growth. The speaker (Sean Cornelius) was able to do simulations that "shut off" this stress response and subsequently maintained growth. Whether or not the same result would be seen in a natural systems is an open question.

The sub-optimality question is one I have raised in an arXiv paper with regard to human performance. That is, challenges such as exercise or high stress environments might trigger responses that immediately lead to sub-optimal physiological indicators, but in the long run produce highly optimized performance indicators. This question has also been raised more generally about fitness landscapes in the evolutionary biology literature.

My poster seemed to go over well, and will be on display until tomorrow evening. Until then......

Dynamics Days, Day 2 Morning

Day 2 of Dynamics Days is halfway over. A couple of interesting (and biologially relevant) talks in the morning sessions:

Jonathan Widom (Northwestern) delivered what ws probably the best talk of the morning on nucleosomes positioning. Apparently, nucleosomes use their own code(embedded in the genome) to find stretches of double helix to bind to. Even better, it seems as though transcription factors and nucleosomes compete for stratches of DNA to bind, with the former binding evolutionarily-conserved promoters and the latter having a preference for promoters tht no longer have a function.

Chris Fall (UIC) deviered a really interesting talk on mitochondrial modulation of Calcium channels, a function normally ascribed to endoplasmic reticulum. The mitochondria is becoming incresingly acknowledged as a complex system, and Chris' talk took that trend a couple of additional steps forward.

Both the Widom and Fall talks hinted that the mechanisms behind their respective topics were cell-type specific. Being a cellular reprogrammer, this piqued my curiosity somewhat. Perhaps these are things to look at in cells that have been reprogrammed to pluripotency.

Two other talks of note dealt with the collective behavior of cell populations. Actually, the last talk of yesterday (by Raymond Goldstein from Cambridge) also dealt with this topic. Harry Swinney told us about growth inhibition in bacteria, and Wolfgang Losert had some intriguing things to say about cell motility (in particular some video of would healing and migration in skin cells).

January 4, 2010

Dynamics Days, Day 1 Morning

The first few talks of Dynamics Days were quite good. My favorite was from Fred MacIntosh (who I spoke with last night at the reception) on cytoskeletal networks. He's working on active cytoskeleton networks which are made to be firm and moved around in the cell by actin/myosin motors. He mentioned an application of this to the production of motion in biomimetic devices, which is something that got me really excited (and started the wheels in my head turning). More later.....

January 3, 2010

Dynamics Days, Day 0

I just arrived in Evanston, IL (home of Northwestern University) to attend Dynamics Days 2010. It's being held at the Hilton Garden Inn, and sponsored by NICO. So far, it promises to be an excellent assortment of talks and posters. More as the conference progresses.

January 1, 2010

breve - Artificial Life software

Here's a link to a software package I've been working with recently:


breve allows you to evolve animal bodies in simulated environments. The bodies are created out of polygons, and fitness is calculated by the animal's ability to move. More later.....