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?

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.

November 14, 2015

The Pace of Paper Construction

I recently found this graph amngst my files, having done this about a year ago to gauge the revisions of two papers [1, 2] published by myself and co-authors in 2014. The plotted function represents the number of words at a certain timepoint (draft completed every month). The plateaus represent a lack of development during that period.

[1] RED: Alicea, B.   Animal-oriented Virtual Environments: illusion, dilation, and discovery. F1000 Research, 3:202. doi: 10.12688/f1000research.3557.1 (2014).​

[2] BLUE: Alicea, B. and Gordon, R.   Toy Models for Macroevolutionary Patterns and Trends. Biosystems, 122, 25-37 (2014). Special Issue: Patterns of Evolution.

November 2, 2015

George Boole: 11001000

Today's Google Doodle is a real Boole Doodle, centuries of two. Said three times fast, of course. Here are blogposts by Stephen Wolfram and Mike James at I Programmer with more on its broader significance. The why of the blogpost title can be found here.

October 22, 2015

Arriving at October 21, 2015...... and beyond

Last year I marked the date, and this year it became a "thing" (at east on the internet). So here are a few links to celebrate the famous date from the "Back to the Future" trilogy.

Billings, L.   Time Travel Simulation Resolves "Grandfather Paradox". Scientific American, September 2 (2015).

"What 'Back to the Future, Part II' Got Wrong (and right)", from the University of Illinois, Urbana-Champaign.

A welcome to the future, from Doc Brown himself:

COURTESY: Universal Studios.

And now..... a bit farther into the future...... The Economics of Star Trek, which is a really active area of internet scholarship:

Transcript of the recent New York ComicCon panel on Trekonomics.

Podcast on the "Economics of Star Trek", courtesy of FW: Thinking.

A few other takes on the Star Trek economy from Noahpinion, Joseph Dickerson, and Slate.

In the future, Spock is on the money. COURTESY: Rick Webb, The Economics of Star Trek: the proto-post scarcity economy.

September 29, 2015

Reconsidering the Model as a Unit of Regulation: cybernetics and the adaptive outcome

Here is a preview of an essay Robert Stone and I have been working on as part of the Orthogonal Research initiative during the course of the last year. The formal title is: "The Foundations of Control and Cognition: The Every Good Regulator Theorem". This essay takes a classical tool from the cybernetics literature and applies it to game theoretic and other problems of our interest.

Robert Stone, cybernetics enthusiast

Robert Stone and myself, bringing cybernetics back to the "soft" but immensely-complex (social, brain, and biological) sciences. The full version (with notes, definitions, and additional references) can be found here.

A seemingly simple discrete system with feedback (which makes it not so simple during future iterations). COURTESY: intgr, Wikimedia commons.

I. Introduction
            In the history of scientific discovery, there have been examples of certain persons or facets of their work being considered ‘out of step’ with the dominant scientific or philosophical trends of the time. As such, they risk falling down a deep well in our cultural landscape, with their work’s efficacy lost to subsequent generations. If their work has merit, it may be considered ahead of its’ time by future generations. The timing of a given theory or great idea is largely determined by cultural and cognitive biases that favor the dominant paradigm [1]. In other cases, ideas at the paradigmatic vanguard end up resurrected in a more pragmatic way. The acceptance of such ideas occurs either gradually or in one fell swoop at a later point in time. Let us keep this in mind as we discuss Ronald C. Conant and W. Ross Ashby’s seminal work “Every Good Regulator Theorem” [2] (EGRT):

“[The EGRT is]….a theorem is presented which shows, under very broad conditions, that any regulator that is maximally both successful and simple must be isomorphic with the system being regulated…….Making a model is thus necessary.” [2]

The EGRT characterizes regulation with respect to cybernated control systems. In the case of Ashby and Conant [3], the EGRT developed within the context of several intersecting traditional fields. These include algorithmics, information theory, systems theory, and behavioral science. In such a context, models are exceedingly important. Given the reliance of the EGRT concept on inference and propositional thinking, there is an essential reliance on models. In fact, the EGRT exists at such a high level of abstraction that even with a high degree of specification may not be directly applicable in the real world [4]. However, there are certain advantages of cybernetic modeling that make their cross-contextual application useful.

Ashby's graphical formulation of the EGRT Theorem with original notation. COURTESY: [2].

II. Background
Let us return to the notion of modeling as phenomenology. Systems engage in modeling not simply to purposely regulate their environments, but rather to reactively respond to input stimuli in a way that maintains higher-level states [5]. This ability to model becomes part of their structure at the most basic of levels, though it would be fair to say most modeling (in the way we will use the word) is the result of cognitive processes. The constructivist might argue that such metacognitive dynamics [6] would influence one’s proposed scientific model. Like Shakespeare’s Hamlet, however, the question of whether or not to model (or be) is one of survival, whether that survival be genetic or memetic. Rather than reviewing the proof step-by-step, let’s discuss its potential significance in a variety of use-cases. In the process, we will be transcending the traditional boundaries of autonomic, ‘choice’, or even cognitive.

          Simply put, the Every Good Regulator Theorem says that regulators operate on approximations (e.g. models) of the thing they are regulating. This requires a mapping of the natural world to the model. While one might consider the activities of encoding and translation to be inherently cognitive, genomic systems also perform biological control functions in the absence of cognition [7, 8]. In the biological control example, what matters is not intent, but accuracy. Rather than an actively goal-oriented criterion, what we observe here is passively goal-oriented system output. Accuracy of the approximated model influences the quality of regulation. Thus, there need not be agency on the part of any single system component. Indeed, to survive as a unit in an interrelated system, a regulating machine must construct an interactive model that includes inputs, outputs, and feedback.

Let us consider a couple cases of regulatory dynamics, which may be valuable in understanding the importance of this theorem. We can then move on to what could this mean for both further theoretical development and practical application. A good place to begin in cognitive science is game theory [9]. One of the most simple, effective, and most explanatory strategies in the Prisoners’ Dilemma game is the tit-for-tat strategy [10]. In this 2-player, 2x2 game, the tit-for-tat strategy is simple: ‘Do unto others as they have done unto you’ after an initial good faith move of cooperation. The strategy is simply to copy your opponent's behavior. If the opposing agent cooperates, so does the tit-for-tat strategizing agent; if they defect, the tit-for-tat strategist follows suit. The intended outcome of the strategy is to move the exchange towards an equilibrium (though this is not the only possible outcome, nor is the strategy perfect).

Of specific interest here is that the mechanics of the strategy requires a model to be held in memory by the agent employing tit-for tat (a 1-bit cooperate/defect model), regardless of the strategy employed by the other agent (whether that be a more sophisticated maximizing strategy, or random selections). While an economist might view this as free-riding behavior by one of the two agents, the selection of tit-for-tat by both players can produce a cooperative equilibrium, such as in the evolution of reciprocal altruism in biological systems. The EGRT suggests that the greater the memory for an agent, and the longer it has the opportunity to observe and integrate the moves of its opponent, the greater its’ potential for effective regulation.

Over time, this can lead to greater accuracy for the agent’s cognitive model and a more stable equilibrium game outcome. Further, this equilibrium state can be long-lasting, given extended memory capacity for more detailed models, and may evolve towards ‘a conspiracy of doves’, within a game of homo lupus homini. An agent with a greater memory capacity can also employ more elaborate (or deeper) strategies over time. This development of deeper strategies may also feedback into modifying its model of the external world [11]. Overall, the capability to regulate behavior of other players depends on the inferential and predictive capacities of each player’s model: in a highly complex competitive game environment, a good regulator has a superior model, or it will find itself regulated by a competing agent in the game, especially as the behaviors get more complex.

“The theorem has the interesting corollary that the living brain, so far as it is to be successful and efficient as a regulator for survival, must proceed, in learning, by the formation of a model (or models) of its environment.” [2]

An example of a basic 2x2 payoff matrix characterizing the Prisoner's Dilemma. COURTESY: "Extortion in Prisoner's Dilemma", Blank on the Map blog, September 19 (2012).

III. Further Considerations
Let us now consider a more complicated scenario where we might be able to uncover the universal components of the EGRT phenomenology. The context will be two people on a blind date (this can actually be a complicated scenario). If one has been in one of these (terrifying) contexts, then one can already see where we are going. The cognitive agents are continually competing to increase the efficacy of their models of the other agent, while also attempting to constrain the modeling of the other agent towards a compact image they prefer. Although rarely implemented successfully, winning strategies include accurately modeling the other actor and influencing the state of their mental model. This can include both elaborate, multi-step strategies, and simpler strategies, the complexity of which is does not indicate their effectiveness. If the goal is a continuation of relations, the acquisition and intentional obfuscation of information occurs at appropriate times and in appropriate ways. Furthermore, this information has contextual value. As in most scenarios involving imperfect or asymmetrical information [12], your model must be superior to become the leader of the interaction [13], and thus control of regulation.

Does regulation even require what we would call cognition? This of course depends on our definition of cognition and regulation. However, let us consider that a bacterium does not have a “cognitive” or mental model of its environment, yet appears to have little trouble getting around and controlling some aspects of its landscape. The similarities between chemotactic sensation and mental models built upon multisensory stimuli serve as evidence for the universal character of the EGRT. In fact, Heylighen [14] has proposed that cybernetic regulation is a highly-generalized form of cognition. Yet do thermostats or other mechanical systems possess anything approaching what we consider cognition? While none of these has the cognitive capacity of a brain, they do have information processing capabilities from their physical or electronic structure, memory states, and crude models of how things ‘should’ be, towards which they regulate conditions. Non-cognitive systems possessing these characteristics are obviously still capable of rudimentary communication, control, decision making, and regulation, at least abstractly. We should also expect some degree of continuity that crosses the boundary of the cognitive and non-cognitive, since cognitive systems evolved from less intentional ones with more rudimentary forms of behavioral control.

“...success in regulation implies that a sufficiently similar model must have been built, whether it was done explicitly, or simply developed as the regulator was improved.” [2]

IV. Conclusion
Earlier, we had touched upon the history of scientific discovery, and contextual model building. A scientific theory is simply a model, and its value lies in its efficacy and repeatability (thus its’ trustworthiness and ability to aid in regulation). Theoretical models have tended, historically, to shift from informal, conceptual models towards formal mathematical ones (consider Comte’s Philosophy of Science). As a given model acquires more data, and as those data create ever-more accurate model revisions with higher fidelity. The overall capacity to aid regulation increases via feedback. Thus, the model’s value to humans increases. However, as noted by the example of ahead of their time thinking, scientific thought does not exist in a vacuum, and the landscape conditions need to be aligned so that the model can prove fruitful. Consider how we are witnessing an explosion in robust formal mathematical and/or computer models either aiding or besting human cognitive efforts [15, 16]. Informational revisions of the model often occur faster than the landscape conditions change, so adaptive cross-contextual models may prove more successful in dynamic situations, such as ones which are developed by human thought and human cultural systems.

            This ability to cross the boundary between cognitive and non-cognitive with models may challenge either our informal, colloquial conception of cognition or the universality criterion of the formal EGRT. As both features of cognition and more universal mechanisms, information processing, memory, communication, and selection can occur without any kind of cognitive superstructure. Perhaps the context of what we call “cognition” is too limiting. What about human cognition then is truly universal, and what is unique to a certain set mechanisms and representational models? For example, are models of so-called cellular decision-making [17] an unduly anthropomorphic representation of cellular differentiation and metabolism, or is it drawing upon a common set of universal properties that can only be abstracted from the system by an appropriate model?

Rather than trying to solve this philosophical puzzle now, let us take leave to consider that a deep truth like the one perhaps contained within the formalism of the EGRT should make us question scientific knowledge in a manner akin to reconsidering our firmly-held beliefs. It should make us reconsider how well we understand the relationship between nature and our own conceptual models. In that, it kindles the same spark from which all great scientific theories alight: It leads us to more questions, new ways of thinking about things, and guides us towards more accurate, repeatable, and otherwise ‘good’ models.

“Now that we know that any regulator (if it conforms to the qualifications given) must model what it regulates, we can proceed to measure how efficiently the brain carries out this process. There can no longer be question about whether the brain models its environment: it must.” [2]

[1] Kuhn, T.   Structure of Scientific Revolutions. University of Chicago Press (1962). 

[2] Conant, R.C. and Ashby, W.R.   Every good regulator of a system must be a model of that system. International Journal of Systems Science, 1(2), 89–97 (1970).

[3] Ashby, W.R.   Introduction to Cybernetics. Chapman and Hall (1962).

[4] Fishwick, P.   The Role of Process Abstraction in Simulation. IEEE Transactions on Systems, Man, and Cybernetics, 18(1), 18-39 (1988).

[5] Brooks, R.   Intelligence Without Representation. Artificial Intelligence, 47, 139-159 (1991).

[6] Kornell, N. Metacognition in Humans and Animals. Current Directions in Psychological Science, 18(1), 11-15 (2009).

[7] Ertel, A. and Tozeren, A.   Human and mouse switch-like genes share common transcriptional regulatory mechanisms for bimodality. BMC Genomics, 23(9), 628 (2008).

[8] Gormley, M. and Tozeren, A.   Expression profiles of switch-like genes accurately classify tissue and infectious disease phenotypes in model-based classification. BMC Bioinformatics, 9, 486 (2008).

[9] Gintis, H.   Game Theory Evolving. Princeton University Press (2000).

[10] Imhof, L.A., Fudenberg, D., and Nowak, M.A.   Tit-for-tat or Win-stay, Lose-shift? Journal of Theoretical Biology, 247(3), 574–580 (2007).

[11] Liberatore, P. and Schaerf, M.   Belief Revision and Update: Complexity of Model Checking. Journal of Computer and System Sciences, 62(1), 43–72 (2001).

[12] Rasmussen, E.   Games and Information: an introduction to game theory. Blackwell Publishing (2006).

[13] Simaan, M. and Cruz, J.B.   On the Stackleberg Strategy in Nonzero-Sum Games. Journal of Optimization Theory and Applications, 11(5), 533-555 (1973).

[14] Heylighen, F.   Principles of Systems and Cybernetics: an evolutionary perspective. CiteSeerX, doi: (1992).

[15] LeCun, Y., Bengio, Y., and Hinton, G. Deep Learning. Nature, 521, 436-444 (2015).

[16] Ferrucci, D., Brown, E., Chu-Carroll, J., Fan, J., Gondek, D., Kalyanpur, A.A., Lally, A., Murdock, J.W., Nyberg, E., Prager, J., Schlaefer, N., and Welty, C.   Building Watson: an overview of the DeepQA project. AI Magazine, Fall (2010).

[17] Kobayashi, T.J., Kamimura, A.   Theoretical aspects of cellular decision-making and information-processing. Advances in Experimental Medicine and Biology, 736, 275-291 (2012).

UPDATE (9/30): During the editorial process, Rob and I had a discussion about using the word "alight" (in the final paragraph). I was not sure about the correct word usage, but Rob assured me that it was being used correctly in this context. But to back this up even further (and to gratuitously insert an informatics Easter Egg), here is the Google Ngram history of "alight" usage since 1800. 

September 14, 2015

Hodgepodge Blogpost, September 2015

Welcome to the blogging hodgepodge for this month. I wanted to clear up by reading queue, and present some of these ideas and articles in an entertaining way. The topics include: modeling, significant results, and hidden variables (but perhaps not discussed in a conventional manner). As a bonus, we get career advice for scientific researchers and relevant discussion.

Mutant phenptypes from the Fukushima area of Japan. COURTESY: National Geographic.

Flawed Models Cannot Be Made Idealistic

"Essentially, all models are wrong, but some are useful" -- George Box. What makes for a bad model? Poor assumptions, oversimplication/vagueness, or underfitting with respect to available data? These articles address some of these issues, with particular relevance to societal consequences.

Kirchner, L.   When Big Data Becomes Bad. ProPublica, September 2 (2015).

O'Neil, C.   Big Data, Disparate Impact, and the Neoliberal Mindset. Mathbabe blog, September 7 (2015).

Schuster, P.   Models: From Exploration to Prediction -- Bad Reputation of Modeling in Some Disciplines Results from Nebulous Goals. Complexity, doi:10.1002/cplx.21729 (2015).

Rickert, J.   How do you know if your model is going to work? Part 2: Intraining set measures. R-bloggers, September 8 (2015).

Once upon a time, this was a viable model of how nature worked. COURTESY: Geocentric Model, Redorbit.

The Real World is Complex, Idealized Methods Notwithstanding

The debate over replicability in Psychology (and by extension sciences that are not particle physics) rages on. This month, a shot was fired from the "Psychology is not very replicable" camp. The Open Science Collaboration published a paper in Science showing that many replications of experiments fail to reproduce the same levels of statistical significance and power as the original studies.

Critics have blamed this lack of replicability on a number of culprits, including shortcomings of the NHST approach itself. Two potential culprits I have pointed to previously include complexity and cultural context, the latter which we will return to in a bit.

What explains these replicated results? . COURTESY: Figure 1, Science, 349, doi:10.1126/science.aac4716 (2015) AND Loria, TechInsider.

Open Science Collaboration.   Estimating the reproducibility of psychological science. Science, doi:10.1126/science.aac4716 (2015).

Loria, K.   Everything that's wrong with psychology studies in 2 simple charts. TechInsider, August 28 (2015).

Barrett, L.F.   Psychology is not in Crisis. NYTimes Opinion, September 1 (2015).

The Unreasonable Effectiveness of Cultural Context*

* a play on: Wigner, E.   The Unreasonable Effectiveness of Mathematics in the Natural Sciences.

Vanderbilt, T.   Why Futurism Has a Cultural Blindspot. We predicted cell phones, but not women in the workplace. blog, September 10 (2015).

* the latest critique of futurism, this time from a sociological perspective.

Yau, N.   Bourdieu’s Food Space chart, from fast food to French Laundry. Flowing Data blog, June
21 (2012).

* our contemporary Economic World, according to Pierre Bourdieu (as told by Leigh Wells).

Career Advice (Not Avarice):

Hossenfelder, S.   How to publish your first scientific paper. Backreaction blog, September 11 (2015).

* this blog post not only provides advice on how to get started as a published researcher, but also gives advice on how to formulate research ideas and structure manuscripts that will garner the interest of editors and reviewers.

Curry, S.   Peer review, preprints and the speed of science. Guardian, September 7 (2015).

* yet another article in favor of the open-science movement, in this case advocating for mechanisms (e.g. preprint servers, open peer review) that have the potential to speed up and otherwise improve the research enterprise.

McDonnell, J.J.   Creating a Research Brand. Science, 349, 758 (2015).

This author uses a marketing metaphor to help imporive the efficiency of a researcher's efforts. The advice bolis down to the following:

* promote results, publications, and lectures all around a central theme.

* find the right breadth of research. This should be greater than a hyper-specialized topic, but narrow enough to constitute a unique niche.

August 26, 2015

Scientific Bytes and Pieces, August 2015

Welcome to this month's version of Scientific Bytes and Pieces. The first feature is a sad note: complexity theorist John Holland has passed away at the age of 86. The father of genetic algorithms and a pioneer in the field of complex adaptive systems, Holland's contributions will live on. Here are two obituaries: one from the New York Times and another from the Washington Post (written by Holand's colleague Scott Page).

R,I,P. John Holland. COURTESY: Plexus Institute.

The SAVE/Point collaboration and Stefano Meschiari have developed an interactive game called Super Planet Crash. This "hours-of-fun"-type game simulates the gravitational dynamics of solar systems. Build your own solar system today! The virtual world physics come courtesy of algorithms designed to detect exoplanets.

Screenshot of Super Planet Crash. WARNING: it is not as easy as it looks.

Next up is a recent article from FiveThirtyEight Blog called "Science Isn't Broken". Despite the sizable body of blog posts and articles lamenting the "brokenness" of the modern scientific enterprise, it turns out that such fears are misplaced. As it turns out, science is a hard enterprise, and prone to error, unexpectedness, and revision. Since I believe that couching these realities as symptoms of dysfunction does the scientific community more harm than good, this discussion is a welcome contribution to our understanding of how science is done.

Interestingly, whenever the topic of "broken science" comes up, cognitive biases are almost never mentioned. Yet cognitive biases play an integral role in decision-making and interpretation. Even algorithms have been shown to exhibit significant social biasJim Davies offers us an article via called "Why You’re Biased About Being Biased" in which he reviews the state of cognitive bias research. An accessible tour of the field as well as food for thought (and reevaluation of those thoughts).

Another reason why science is hard rather than broken is the existance of chaotic behavior. Strange and unpredictable phenomena such as transient chaos challenge the expectations and arguments of the "science is broken" crowd. Some people, such as Tamas Tel, find joy in these types of phenomena. See the recent Chaos article "The Joy of Transient Chaos" for this perspective. While not particularly accessible to a popular science audience, the article should give you a glimpse into an alternate perspective.

An artistic take on a series of hyperlinked documents. COURTESY:

Despite the hard nature of the scientific enterprise, every once in a while breakthroughs are made. This year is a milstone for several of these. The word "hypertext" is 50 years old, and the Einstein's publication on General Relativity is 100 years old. On a related note, Einstein's "Annus Mirabilis" was 110 years ago this year. So much for broken science.

Following-up on a previous Synthetic Daisies post about Theory Hackathons, here is an article that makes the case for hackers to support the cause of scientific data analysis. While the focus is on taming the glut of Neuroscience data, the same principle would apply to all large-scale data. Can hackers help to make sense of data and can they help us bridge the gulf between data and theory? Perhaps we will discuss this in a future post.

July 30, 2015

Theory Hackathons

The theoretical physicist/surfer Garrett Lisi has a long-range vision called the scientific hostel. A scientific hostel is a facility (in a desirable location such as Maui) where scientists can visit and do science/interact for short periods of time.

I have pursued another type of collective scientific endeavor called the theory hackathon [1]. The initial version of this idea occurred in November 2014 when Dr. Richard Gordon (part of the DevoWorm project) visited Champaign-Urbana for a few days of collaboration and discussion. The proceedings here hosted by Orthogonal Research.

In their original form, hackathons are multi-day events that bring programmers together from far-flung physical locations. The "hacking" involves solving problems in a collaborative atmosphere, with the extended period of collaboration allowing for participants to benefit from "extended cognitive flow" [2]. A theory hackathon is quite similar, except that instead of programmers solving programming puzzles, theorists work to solve scientific puzzles.

Some images of the hackathon proceedings (lecture component taken at the Champaign (IL) Public Library).

The basic outline of a theory hackathon (held over several days) involves three interrelated activities: exploration of ideas, organizational sessions, and a formal talk. The session held between Richard and I was primarily to flesh out some pre-existing ideas, but this could be done on a larger scale and with a more formalized schedule.

Traditional Hackathon, with programming and programmers.

Beginnings of a theory hackathon?

As mentioned previously, our hackathon session was pretty informal. A more formal framework might include several activities:

* one-on-one or small group brainstorming sessions. This can be done using a electronic whiteboard or Python notebook to keep track of the cumulative efforts. The idea is to collectively explore a problem and develop as much of a solution as you can in a few hours.

* discussions and follow-ups on previous and outstanding projects. This is largely organizational, but including the housekeeping function as a part of the theory hackathon can drive forward those old ideas in new ideas. It's the "fresh eyes for an old problem" principle at work.

* semi-public lectures. Part of developing theory is working at organizing concepts, references, and data in a lecture format. This part ofo the theory hackathon might involve developing a lecture either ad-hoc or in advance, and then deconstructing the contents in a group setting.

Theory hackathons can be organized around a specific topic (e.g. developmental biology), or the mechanics of theory-building itself [3]. Either way, they can lead to fruitful collaborations and long-lasting ideas. If not, there will still be fledgling ideas to follow up on. While theory hackathons will undoubetedly produce many loose ends, subsequent collaborative meetings and hackathons can help advance this work further.

UPDATE (5/21/2018): If you want to develop your own Hackathon, please check out the badge series on Hackathons, hosted by the OpenWorm Foundation (on Badgelist). Begin with planning your agenda (Hackathon I), then move on to putting your plan into action (Hackathon II, Hackathon III).

[1] h/t Stephen Larson, for coining this phrase during one of our meetings.

[2] For more, please see: Csikszentmihalyi, M.   The Systems Model of Creativity: The Collected Works of Mihaly Csikszentmihalyi. Dordrecht, Springer (2014). 

[3] For one example of theory-building as a formal activity, please see: Weick, K.E.   Theory Construction as Disciplined Imagination. Academy of Management Review, 14(4), 516-531 (1989).

July 26, 2015

Having a Positive Celestial Body Image is Important

Lots of planetary science news in the last few weeks. Between the arrival of the New Horizons probe at the Pluto mini-system and the discovery of the Kepler-452b exoplanet, lots of great pictures to behold. And as is often the case, space science leads to greater knowledge about our own planet, but more about that at the end of the post.

As the New Horizons probe approached Pluto, we began to gain an appreciation for this far-flung corner of the solar system. This includes the planet itself, which may exhibit Nitrogen cycling between its atmosphere and surface glaciers.

The anticipation builds as one zooms in. COURTESY: Discovery News.

Not only do we have an up-close accounting of Pluto's surface, we also gained knowledge about Pluto's environs, which consists of a number of celestial bodies. The two main bodies are Pluto and its main moon Charon. Notably, Pluto and Charon orbit a common center-of-gravity, which is a bit different from the relationship between Earth and the Moon.

Map of the Pluto mini-system (top) and the tidal locking between Pluto and Charon (bottom). TOP: IAU. BOTTOM: Stephanie Hoover, Wikimedia Commons.

While the discovery of exoplanets is no longer news, ones that resemble Earth still cause people to stand up and take notice. The latest exoplanet discovery is called Kepler-452b, which is within the circumstellar habitable zone of Kepler-186

Diagram and artist's renditions of Kepler-452b, the latest and greatest earth-like exoplanet. COURTESY:

Finally, I would be remiss if I did not mention the possibility of an intense El Nino this coming year and the associated climatological modeling

Comparing powerful El Nino events: 1997-1998 and (coming soon?) 2015-2016. COURTESY: NOAA.

June 30, 2015

Posters at the International C. elegans Meeting

UCLA and Los Angeles. COURTESY: UCLA Department of Physiology.

I just returned from the International C. elegans Meeting in Los Angeles (being hosted on the UCLA campus). There are posters, talks, workshops, and much fun to be had. I will give a more detailed discussion of some of the sessions in a future post.

Some people (not me) took turns wearing the "worm suit".

There were several days of talks and posters, plus the famous C. elegans art and variety shows. Talks ranged from Physiology to Evolution and Development. The worm art show is somewhat unique to the conference, The OpenWorm group was able to meet up and discuss research strategies. 

There was also a worm art show. Here are some of the entries. 

Aside form partaking in the intellectual and social festivities, I also presented two posters on Saturday night. One was in the area of experimental evolution, and the other on the DevoWorm project.

Sample of the Experimental Evolution poster. Full poster can be viewed/downloaded here.

Sample of the DevoWorm poster. Full poster can be viewed/downloaded here.

My week was not all worm biology. I also sampled some botany, courtesy of the Mildred Mathias Botanical Garden, UCLA.