February 12, 2016

Darwin Day, Past and Present

For this year's Darwin Day (his 207th posthumous birthday), we take a tour of Darwin Day features from both the past and present.

Panel discussion at the Darwin Centennial Celebration, University of Chicago circa 1959.

First stop: last year's Synthetic Daisies post for Darwin Day, featuring portraits of Charles Darwin throughout the course of his lifetime.

Second stop: 2009, and Nature's special issue for Darwin's 200th birthday, which includes many nice multimedia features.

Third stop: Google's Doodle from February 12, 2009 and  a Doodle-like short movie from 2014. Link to the Doodle design and animated movie can be found below. The movie is quite elaborate, as each letter making up "Google" are treated as terminal taxa in a prototypical tree of life.

Darwin Day Google Doodle from 2014. COURTESY: Vimeo and Devone Paul

Final stop: The Selfish Gene. This year's Darwin Day roughly coincides with the 40th anniversary of "The Selfish Gene" by Richard Dawkins. This work established the gene as the fundamental unit of natural selection, and provided a strong defense of Darwinian ideas. Enjoy these readings by John Brockman ("About Richard Dawkins") and Matt Ridley ("In Retrospect: The Selfish Gene").

Happy Darwin Day!

January 31, 2016

Annual Research Symposium, coming soon to the Beckman Institute

The 6th Annual Society for Postdoctoral Scholars (SOPS) Postdoctoral Research Symposium is coming soon to the Beckman Institute at UIUC! In 6 short days, my colleagues and I will be hosting 18 talks and 24 poster presentations in a day-long event. While the formal registration period is closed, we encourage people to stop by and attend the lectures and poster session.

The event will take place at the Beckman Institute on the UIUC campus. Founded around 25 years ago through a financial gift from Arnold Beckman (of Beckman Instruments fame), the Institute is a catalyst for interdisciplinary research [1]. Our Symposium does certainly seem to be the pinnacle of multidisciplinarity this year, as our talks and posters will cover a wide range of topical areas and academic fields.

Breakdown of presenting talks and posters by topical category.


[1] for more on the benefits of interdisciplinary research, please see: Ledford, H.   How to solve the world's biggest problems. Nature News, September 16 (2015).

December 26, 2015

Newtonmas meets Festivus

A series of Easter eggs for your holiday season! Since December 23rd is Festivus and December 25th is Isaac Newton's birthday (Newtonmas), it makes sense to combine the two into a discussion about the physics of pole balancing.

Inverted pendulum in dynamic equilibrium? Festivus pole. Next up, the airing of grievances!

Newtonmas poster (with fractals). The physics of planetary precession is why we celebrate today! COURTESY: Felix Andrews.

The pole balancing problem, also called the inverted pendulum, is a classic model system in the application of reinforcement learning (a form of supervised learning). The problem requires the supervisor to keep a pole banaced while the base moves back and forth along a one-dimensional plane. This should keep eveyone at the Festivus party busy until the airing of grievances! 

An example of balancing an inverted pendulum (e.g. pole) on a cart. COURTESY: MIT Signals and Systems course, Lecture 26.

Many applications of the inverted pendulum involve balancing the inverted pendulum on a cart [1]. The application of reinforcement learning is often (but not necessarily) used to drive the controller, or where to move the cart in response to inertial forces generated by the free-swinging pole. Using the cart as the base of support, motion of the pole is translated along a single degree of freedom. You may recall the last Synthetic Daisies post in which we discussed holonomic motion. The dynamic equilibrium exhibited by the inverted pendulum is a linear version of those physics.

A demonstration of the first-order Lagrangian used in pendulum mechanics can be found in this video, COURTESY: PhysicsHelps YouTube channel.

The description of this sometimes chaotic [2] motion can be described using Lagrangian mechanics, which is a more refined form of Newton's equation of motion [3]. Yet the policy required to maintain balance of the pole can be rather simple, largely involving first-order, closed-loop feedback and and an iterative function. Hence, Newtonmas is really a celebration of the physical processes that govern our holiday adventures. Happy Newtonmas to all, and to all a good (well-controlled) system!

[1] there are many demonstrations of this (class projects, hobbyists) on YouTube. This is also a classic benchmark for control systems design.

[2] the identification of chaos in an inverted pendulum (particularly when we move to the double pendulum case) stems from the Lagrangian representation. For more, please see the following references: 

a) Kim, S-Y. and Hu, B.   Bifurcations and transitions to chaos in an inverted pendulum. Physical Review E, 58(3), 3028-3035 (1998).

b) Duchesne, B., Fischer, C.W., Gray C.G., Jeffrey, K.R.   Chaos in the motion of an inverted pendulum: an undergraduate laboratory experiment. American Journal of Physics, 59(11), 987-992 (1991).

[3] some practical pointers to the difference between Newtonian and Lagrangian physics can be found on the Physics StackExchange here and here,

December 14, 2015

Klinotactic Thoughts and Holonomic Fun

What a week for models of movement! The first item is the most recent OpenWorm Journal Club (hosted on Google Hangouts and YouTube) called "Closing the Loop from Brain Cells to Behavior". This session explored the implications of two papers by Eduardo Izquirdo and Randall Beer [1] on C. elegans  Neuromechanics.

This work focuses on the existence of klinotaxis in C. elegans movement generation. Klinotaxis occur as small but important neural circuit generates movement signals in response to the environment. Specifically, sinusoidal movement of the head occurs as a function of central pattern generation in the brain and behavioral response to the environment.

The second item involves the BB8 droid from the upcoming Star Wars movie. As the first spherical rolling droid of the Star Wars metaverse, BB8 is also a very real mechanical prototype called the Sphero. And now you can build your own [2]! By capitalizing on a principle called holonomic motion, the body moves independently of the head, which balances on the rolling body. The following article (How does BB8 Work?) discusses the innovation and the details behind the patent registered by Disney Labs.

[1] Izquierdo, E.J. and Beer, R.D. (2015).  An integrated neuromechanical model of steering in C. elegans. Proceedings of ECAL, 199-206. MIT Press  AND  Izquierdo, E.J., Williams, P. and Beer, R.D. (2015).  Information flow through the C. elegans klinotaxis circuit. PLoS One, 10(10), e0140397.

[2] For more information, please see: Berkey, R.   Make your own Star Wars VII BB8 Droid. Nerdist blog, June 7 (2015)  AND  How does BB8 Work? http://www.howbb8works.com/

November 17, 2015

Lecture on Open Science, November 18!

I am presenting a lecture to the Webmasters Workshop series at UIUC tomorrow, November 18th. The title is "The Role of Web 2.0 Tools and Digital Practice in Doing Open Science". Physical location will be in the GSLIS Building, room 126 (501 E. Daniel). Virtual location (slideshow) is here. Virtual co-location (archived video) can be found here.

Please come if you are able! Here are some screenshots and takeaways from the presentation.