Dance your Ph.D.

Have you ever been asked to explain your Ph.D., or for that matter, any complex project, to someone who won’t even understand the words in the title?

Imagine you’re Maureen McKeague, working on “Selection of a DNA aptamer for homocysteine using systematic evolution of ligands by exponential enrichment.” How would you summarize that in a way that conveyed the general sense of the work without trivializing it, or alternatively, putting your listener to sleep?

One answer is to create a dance video. This year’s “Dance Your Ph.D.” contest run by Science, received 45 submissions from around the world. I was impressed with all four of the finalists, but voted for McKeague’s because it seemed to most naturally fit the choreography to the logic of the research and I liked the dance itself.

Selection of a DNA aptamer for homocysteine using SELEX from Maureen McKeague on Vimeo.

You can enter your own vote on the Science site.

Now I’m trying to imagine how to choreograph my own dissertation, The Logical Structure Underlying Temporal References in Natural Language.

The four P’s of pragmatism

In a 2006 book, Healing Psychiatry: Bridging the Science/Humanism Divide, David H. Brendel notes that psychiatry “is torn by opposing sensibilities. Is it primarily a science of brain functioning or primarily an art of understanding the human mind in its social and cultural context?” He sees the divide between science and humanism as a sickness of psychiatry, one that makes it difficult to heal the emotional conflicts and wounds of patients.

To address the divide, he turns to the pragmatism of Charles Sanders Peirce, William James, and John Dewey. He presents pragmatism in a simple formula (the four P’s) that could apply to most other domains (e.g., Shields, 2008):

  1. the practical dimensions of all scientific inquiry;
  2. the pluralistic nature of the phenomena studied by science and the tools that are used to study those phenomena;
  3. the participatory role of many individuals with different perspectives in the necessarily interpersonal process of scientific inquiry;
  4. and the provisional and flexible character of scientific explanation. (Brendel, 2006, p. 29)

Any such formula has its limitations, but this one seems remarkably effective at capturing salient aspects of pragmatism. The first p, practical, emphasizes pragmatism’s insistence on considering the consequences of any concept, to steer away from abstractions and idealizations that have no conceivable effects in our ordinary experience. The second p, pluralistic, reflects the fact that pragmatism is not so much one method or theory, but rather, an approach that considers any tools that may increase understanding, thereby achieving better practical consequences. It also reflects the assumption that interesting phenomena are unlikely to be captured within a simple category or single way of viewing. The third p, participatory, follows from the second in that multiple perspectives, Peirce’s community of inquiry, are needed to accommodate a pluralistic understanding. And the fourth p, provisional (cf. fallibilism), acknowledges that in a complex and ever-changing world, any understanding is subject to change as we learn more or as events occur.


  • Brendel, David H. (2006). Healing psychiatry: Bridging the science/humanism divide. Cambridge, Ma: MIT Press.
  • Shields, Patricia M. (2008, March/April). Rediscovering the taproot: Is classical pragmatism the route to renew public administration? Public Administration Review, 68, (2), 205-221. Washington, DC. (PAR Interview)

Perseid meteor shower

Don’t miss the annual Perseid meteor shower, which should be especially good this year:

Sky watchers could catch a dazzling treat Thursday night and early Friday morning, with the peak of the annual Perseid meteor shower… The Perseid shower occurs each year when the Earth passes through a wide stream of debris shed by the comet Swift-Tuttle, which orbits the sun once every 130 years or so and last passed through the inner solar system in 1992…Views of the shower are expected to be particularly good this year, since the moon will set early in the evening.

via Short Sharp Science: Moonless sky sets stage for dazzling meteor show.

Tracking the Oil Spill

The New York Times has some interesting interactive graphics and multimedia on the oil spill in the Gulf, e.g., Map and Estimates of Oil Spilled in the Gulf of Mexico. Be sure to use the “Play” button to see how the spill has developed between April 22 and today.

The story of how this has happened and the ongoing saga have much more impact than figures about “millions of gallons,” especially when estimates vary widely and change frequently. But it’s clearly working its way up the list of the world’s largest oil spills.

As the world continues to demand more oil, producers enter even more treacherous situations. Even if we had good oversight, instead of the cozy relationships we now see between regulators and industry, we’re likely to see more such disasters.

Impossible motion: magnet slopes

A gravity-defying illusion has won the 2010 Best Illusion of the Year Contest, held yesterday in Naples, Florida.

Koukichi Sugihara, from the Meiji Institute for Advanced Study of Mathematical Sciences, Japan, developed the illusion, which you can see in the video below. Wooden balls appear to roll up the channels, as if they are pulled by a magnet. We’re fooled by assuming that each supporting column is vertical, and that the longest column in the center is the tallest.

This is is similar to the Adelbert Ames’s illusions, such as the Ames room or Ames window, all of which demonstrate that perception is an interaction of the perceiver with the environment.

The Best Visual illusion of the Year Contest is a celebration of the ingenuity and creativity of the world’s premier visual illusion research community. Contestants from all around the world submitted novel visual illusions (unpublished, or published no earlier than 2009), and an international panel of judges rated them and narrowed them to the TOP TEN. At the Contest Gala in the Naples Philharmonic Center for the Arts, the top ten illusionists presented their creations and the attendees of the event voted to pick the TOP THREE WINNERS! via Results of the 2010 Contest now announced!

The other finalists are all worth watching, too.

Open world learning

People often talk of the Internet as a venue for open learning. But this openness often means simply that students can explore a vast array of resources, perhaps coming across sources that neither they nor their teacher expected.

It’s useful to think about the various ways that new information and communication technologies (ICTs) create additional possibilities for open learning, including both its benefits and costs. Several years ago, Umesh Thakkar, Eric Jakobsson, and I along with others developed such an analysis for the case of Biology Workbench (see Molecular Science Student workbench and Swami). The general idea is that Biology Workbench could facilitate open world learning.

Biology Workbench is a suite of computational tools and data sources, which is used by scientists across a wide range of disciplines to explore and analyze protein and nucleic acid sequence databases. There is a wide variety of analysis and modeling tools, within a point and click interface that ensures file format compatibility.

Thus, Biology Workbench is not an alternative tool for teaching biological concepts, although students who work within it can expand their understanding of biology significantly. Rather, it is an exemplar of a venue for learning, one in which students explore genetics, protein structure and function, physics, chemistry, and other domains of inquiry, invoking processes of pattern-matching, probabilistic reasoning, and both inductive and deductive analysis. Its potential significance for learning relates to three major ways in which it is an open system.

Open Data and Problems

The Workbench architecture provides the potential for using information technology to provide an open world of learning and exploration. Previous approaches to using computers in education have focused on the creation of closed worlds in which students could navigate and explore. Many of these computational environments are excellent and useful, but they are limited. Students are not encouraged to investigate the unknown. In general, students cannot investigate phenomena that the creators of the environment themselves do not know.

The open environment of the Biology Workbench is fundamentally different. By providing access to essentially all that is known about biomolecular sequences and structures, together with powerful analysis and visualization tools, the Workbench makes it possible for students to learn more than what their mentors and teachers know, and even to generate new basic knowledge. The key idea here is not only that there is a large amount of material, but that the data are constantly changing as a result of scientific work. This is true of course for the Web in general, but appears more striking in the case of rapidly changing molecular data (see point #2 below).

This aspect of the Workbench was exemplified by one instructor who was using the Workbench in a university class. She commented that once the students went beyond working through specified exercises, they were essentially doing original biological research, doing analyses that perhaps had not been done before, and she was hard pressed to know how to grade their work.

Open Computational Environment

In addition to providing a window to the entire world of molecular biology, the Biology Workbench is open in a second sense. It is continually growing, adding new features that extend its capabilities and domain of applicability. New domains of applicability include the ability to reconstruct metabolic pathways by utilizing data from newly developed microarrays (gene chips and metabolic flux chips) and the ability to do molecular simulations. The Workbench continues to grow as the whole field of computational molecular biology grows, because it is more than a computer program. It is a computational environment that integrates tools for exploring and learning about all aspects of molecular biology. This dynamic growth is both a plus and a challenge for teachers or curriculum designers who might reasonably seek consistency in their curricula.

Open Community

The Biology Workbench exists within a community of investigators working across a variety of areas within molecular biology. These investigators are not only users, but creators of the system, as they add their research results to the available corpus of articles or their findings result in additions or other modifications of the databases. This community is a powerful resource for education, but it does not exist to meet educational needs per se.

Students who attempt to learn through the Workbench are able to enter into that community of investigators. In so doing, they have stepped outside of the protected world of the classroom. Their learning becomes much less structured, even potentially hazardous without the assurance of carefully vetted curricula, but it can also be far more engaging and applicable to learning beyond the classroom.

Search engines’ dirty secret

I just saw a reference to a New Scientist article, Search engines’ dirty secret – 31 March 2010 about the energy use of search engines, such as Google. The author, James Clarage, who is a physicist at the University of St Thomas in Houston, does some rough calculations to show alarmingly high energy costs:

Google serves up approximately 10 million search results per hour, so one search has the same energy cost as turning on a 100-watt light bulb for an hour…We’ve all heard the future of information architecture is cloud computing. It just might be a cloud of carbon dioxide.

Tim Rustige had the same reaction I did: Yes, web searches use energy, but it can’t be that much. In New Scientist 3rd April 2010 ‘Search’s dirty secret’ he runs through some more detailed calculations to show that the energy use by Google is much less, perhaps 1% of what Clarage estimates.

Neither author takes into account the energy us of the home computer or smart phone that access Google. That’s likely to be many times the cost of what Google does. When that’s factored in, along with the costs of manufacturing, servicing, shipping, and disposing computers, it’s clear that Clarage’s basic point is still valid. There is a serious environmental impact of search engines and computers, and much needs to be done to improve their efficiency.

Happy Pi day!

Happy Pi day!  It’s March 14, or 3/14, the first three digits in the decimal expansion of Pi.

This only works for those of us living in Belize, Micronesia, Palau, Philippines, the US, and sometimes, Canada. The 95% of the world that more logically puts the day first thinks of today as 14/3. They’ll have to wait until July 22, but will have the consolation of knowing that 22/7 is a better approximation of Pi than 3.14.

As a gift for today, New Scientist offers five tasty facts about the famous ratio “We did consider giving you 3.14 facts but alas we had five…”

Climate change’s OJ Simpson moment

Bill McKibben has just written an excellent article: Climate Change’s OJ Simpson Moment | Mother Jones. Although one can read it as yet another argument pro or con on climate change, it’s even more a sophisticated analysis of how the discourse has developed over the last 20 years, in the process giving a surprisingly sympathetic account of climate change deniers.

He starts by discussing the positive reaction to his first book, The End of Nature, which was one of the first books for a general audience on climate change:

And here’s what’s odd. In 1989, I could fit just about every scientific study on climate change on top of my desk. The science was still thin. If my reporting made me think it was nonetheless convincing, many scientists were not yet prepared to agree.

Now, you could fill the Superdome with climate-change research data…Every major scientific body in the world has produced reports confirming the peril. All 15 of the warmest years on record have come in the two decades that have passed since 1989. In the meantime, the Earth’s major natural systems have all shown undeniable signs of rapid flux: melting Arctic and glacial ice, rapidly acidifying seawater, and so on.

Somehow, though, the onslaught against the science of climate change has never been stronger, and its effects, at least in the US, never more obvious: fewer Americans believe humans are warming the planet.

But McKibben doesn’t just rail agains the deniers of global warming, or pull out reams of reports, data, and arguments. Instead, he  talks about how we all respond to disturbing news and to mountains of evidence we don’t have the capacity to sort through. I felt as if he were speaking to all of us across a wide range of complex topics in the modern era–health, economics, education.

He goes on then to show how evidence alone is not the issue; in fact, its effect can be contrary to what you might think at first:

the immense pile of evidence now proving the science of global warming beyond any reasonable doubt is in some ways a great boon for those who would like, for a variety of reasons, to deny that the biggest problem we’ve ever faced is actually a problem at all.

The “OJ Simpson moment” relates to the problem that the defense faced in the OJ Simpson murder trial, in which “it was pretty clear their guy was guilty. Nicole Brown’s blood was all over his socks, and that was just the beginning.” How could they cast doubt, when there appeared to be no remotely reasonable doubt? McKibben shows how, ironically, one resource they had was the immense body of evidence against their client.

He also shows how ordinary language is shaped and changed. One reason the deniers of global warming are winning the debate is that they’re able to connect with our fear of change, of having to do something. As McKibben says:

The great irony is that the climate skeptics have prospered by insisting that their opponents are radicals. In fact, those who work to prevent global warming are deeply conservative, insistent that we should leave the world in something like the shape we found it. We want our kids to know the world we knew. Here’s the definition of radical: doubling the carbon content of the atmosphere because you’re not completely convinced it will be a disaster.

Fort Worth Museum of Science and History

As a reward for hours spent with packing, house repairs, and financial stuff, my mother and I went to the Fort Worth Museum of Science and History yesterday.

We had a good lunch at the Stars Cafe and a fascinating, though all too brief, visit to the exhibits, including interesting talks staff about the Museum’s history. In addition to being our reward, the visit was a commemoration. it was nearly 60 years ago, on George Washington’s birthday, that my parents and I moved to Fort Worth from Houston. On his birthday this year, my mother will be packing her belongings to move to Austin.

Not long after we arrived, she enrolled me in The Frisky and Blossom Club, the first class of the Museum School. So, a return to the Museum marked both her time in Fort Worth and the evolution of the Museum itself, from being a children’s museum in a house to the recently renovated, massive complex of today.

The current Museum is grand and spacious, with atriums and courtyards. But the prior Fort Worth Children’s Museum was a wonderful place in a different way, with a sense of mysteries tucked away in crowded rooms and clubs devoted to astronomy and insects. But it was my first encounter with the Museum at its Summit house location that hooked me on museums:

The museum’s history actually began in 1939 when the local council of Administrative Women in Education began a study of children’s museums, with the idea of starting one in Fort Worth. Two years later the charter was filed, but it would be almost four years before the museum would find a physical home. With the help of the city’s school board, the museum opened in early 1945 in two rooms in De Zavala Elementary School.

In 1947 the museum moved into the large R.E. Harding House at 1306 Summit, where it kept growing in size and popularity. Three years later two significant entities appeared: The Ladies Auxiliary of the Fort Worth Children’s Museum (now the Museum Guild), and “The Frisky and Blossom Club,” the forerunner of Museum School®. Soon it became apparent that a much larger facility was needed to serve the growing needs of the community. Ground was broken for a new facility in 1952. On January 25, 1954, the museum open the building at 1501 Montgomery Street. The following year the Charlie Mary Noble Planetarium, the first public planetarium in the region, opened.

In 1968 the name was changed to the Fort Worth Museum of Science and History so that adults even without children could enjoy the Museum. It worked! Today more than half the Museum’s visitors are adults. Much of that is due to the addition of the Omni Theater in 1983. The Omni was the first IMAX® dome theater in the Southwest and continues to be one of the most successful in the world.