In a new paper stemming from a complexity class taught by Sara Walker and Hyunju Kim, we find evidence that biological networks are critically poised between order and chaos. To quantify this effect, we measure the average sensitivity of 66 gene regulatory networks from a wide variety of living systems and find that the values cluster near the critical value of one. This suggests an adaptive advantage to balancing order and chaos: Living systems must be ordered enough to preserve information and maintain regularity but not so rigid that they cannot change and evolve. The fact that this applies across a wide swath of biological processes gives further credence to the idea that there are mathematical frameworks capable of capturing features general to all life.
Biological networks are close to critical sensitivity. (A) 66 published Boolean network models of genetic regulation (red) have sensitivity near the critical value of 1. The schematic depicts the sensitivity measure, equal to the average number of nodes whose states are changed at timestep t + 1 (green) when one node’s state is changed at timestep t (light blue). Also shown are sensitivities of random ensembles preserving various aspects of the original networks. Preserving only the number of edges and mean activity bias (gray) produces much more chaotic networks. Preserving the causal structure and activity bias of each node in the network (tan) produces sensitivity generally nearer to 1, and further restricting to have the same number of canalizing functions (yellow) is closer still. This indicates that the specific structure and types of Boolean functions beyond average connectivity are important to criticality. (B) Naive random Boolean network theory does not correctly predict average sensitivity for most biological network models. Plotting average sensitivities for each network and its random ensembles separately reveals that most networks have sensitivity that is significantly different from that predicted by various random ensembles. The mean and standard deviation for each ensemble is shown for 100 samples from each ensemble.
Last weekend, the Beyond Center hosted an outreach booth at Phoenix Comic Fest, talking to attendees about the fundamental work the Beyond center does in fields as disparate as cancer research, the nature of time, and the origin of life. We shared information on past speakers, future events, and research paper topics--exciting kids and adults alike in our research, and informing members of the public about our free and accessible lecture series.
In addition, Tessa Fisher was a panelist on three panels during Phoenix Comic Fest. The first, Captain Kirk: Planting Seeds Across the Galaxy, was a comedic examination of the romantic adventures of Star Trek's most famous captain in the context of what we actually know about interspecies mating and hybridization here on Earth. The second, Exobiology: Ice Fishing on Europa, featured her work on developing network theory-derived biosignatures for exoplanets. Lastly, Rampages Against Bad Science had Tessa and several other scientist opine on what they considered to be the worst science they'd seen in science fiction recently (in Tessa's case, the fact that in Alien: Covenant, despite being lured to an uncharted planet where it was obvious a terrible ecological catastrophe had happened recently, no one thought to wear environmental suits or protection). This is her third year participating in science panels at Phoenix Comic Fest.
Catch Sara Walker filming a master class for the World Science University at the World Science Festival in June!
Immerse yourself in an intense and intimate day with some of the foremost experts in astrobiology, theoretical physics, and astrophysics. This event offers science enthusiasts a curated curriculum that goes beyond a popular-level presentation.
We are providing a limited number of exclusive, complimentary seats to the taping of master classes that will subsequently be presented on the World Science U digital platform.
More details about this event are available on the WSF website.
For Sara's list of event see here.
Don't miss the upcoming episode of NOVA Wonders, titled "Are We Alone" featuring our very own Paul Davies.
The episode will air on Arizona PBS tomorrow (May 9, 2018) at 8:00 p.m. and is sure to be a fascinating show. Following the release, you can watch the episode online at anytime via http://www.pbs.org/show/nova/.
We are pleased to announce that Inform, a cross-platform C library for information-theoretic analysis of dynamical systems, is now in print (doi: 10.3389/frobt.2018.00060). Inform uses high-level wrappers, including Python and R, to expedite the application of information theory to dynamical systems without sacrificing performance.
Inform easily converts time series observations into distributions and has a huge repertoire of information measures that can be applied to these distributions, including Shannon Entropy, Mutual Information, Transfer Entropy, and Active Information - to name just a few. Application of Inform is extremely simple. For example, using PyInform, we can compute the Active Information of a dynamical series in a single line of code:
To download inform and see the full list of Inform functions visit the documentation at https://elife-asu.github.io/Inform/.
Sara Imari Walker