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.

[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.

June 17, 2015

Breaking the Threshold of 150,000 Reads

Great news! According to Blogger analytics, Synthetic Daisies blog has just surpassed 150,000 reads! This calls for a milestone post -- as a cake with candles would be logistically and conceptually difficult. In addition, Synthetic Daisies now has 300+ posts in the archives.

Most recent logo design, trite subtitle.

When I started Synthetic Daisies, it was loosely modeled on a style typical of the science blogosphere in 2008 (with a bit more casual approach). I was also (and have been since the late-90s) inspired by what Wired's approach to web content. This landscape has changed quite a bit, and so has Synthetic Daisies. Having my own blog has allowed me to address my own set of interests in my own style. I've also been presented with unique opportunities for scholarship which are not typically "blog-like", but interesting nonetheless.

Allowing myself to be myself since December 2008.

Finally, aside from the ten pages hosted here, the nine most read posts (circa June 2015, courtesy Blogger Analytics) are as follows:
Post Name







Theoretical Essay



Theoretical Essay