Tag Archives: Science magazine

‘Superconductivity: The Musical!’ wins the 2018 Dance Your Ph.D. competition

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I can’t believe that October 24, 2011 was the last time the Dance Your Ph.D. competition was featured here. Time flies, eh? Here’s the 2018 contest winner’s submission, Superconductivity: The Musical!, (Note: This video is over 11 mins. long),

A February 17, 2019 CBC (Canadian Broadcasting Corporation) news item introduces the video’s writer, producer,s musician, and scientist,

Swing dancing. Songwriting. And theoretical condensed matter physics.

It’s a unique person who can master all three, but a University of Alberta PhD student has done all that and taken it one step further by making a rollicking music video about his academic pursuits — and winning an international competition for his efforts.

Pramodh Senarath Yapa is the winner of the 2018 Dance Your PhD contest, which challenges scientists around the world to explain their research through a jargon-free medium: dance.

The prize is $1,000 and “immortal geek fame.”

Yapa’s video features his friends twirling, swinging and touch-stepping their way through an explanation of his graduate research, called “Non-Local Electrodynamics of Superconducting Wires: Implications for Flux Noise and Inductance.”

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Jennifer Ouelette’s February 17, 2019 posting for the ars Technica blog offers more detail (Note: A link has been removed),

Yapa’s research deals with how matter behaves when it’s cooled to very low temperatures, when quantum effects kick in—such as certain metals becoming superconductive, or capable of conducting electricity with zero resistance. That’s useful for any number of practical applications. D-Wave Systems [a company located in metro Vancouver {Canada}], for example, is building quantum computers using loops of superconducting wire. For his thesis, “I had to use the theory of superconductivity to figure out how to build a better quantum computer,” said Yapa.

Condensed matter theory (the precise description of Yapa’s field of research) is a notoriously tricky subfield to make palatable for a non-expert audience. “There isn’t one unifying theory or a single tool that we use,” he said. “Condensed matter theorists study a million different things using a million different techniques.”

His conceptual breakthrough came about when he realized electrons were a bit like “unsociable people” who find joy when they pair up with other electrons. “You can imagine electrons as a free gas, which means they don’t interact with each other,” he said. “The theory of superconductivity says they actually form pairs when cooled below a certain temperature. That was the ‘Eureka!’ moment, when I realized I could totally use swing dancing.”

John Bohannon’s Feb. 15, 2019 article for Science (magazine) offers an update on Yapa’s research interests (it seems that Yapa was dancing his Masters degree) and more information about the contest itself ,

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“I remember hearing about Dance Your Ph.D. many years ago and being amazed at all the entries,” Yapa says. “This is definitely a longtime dream come true.” His research, meanwhile, has evolved from superconductivity—which he pursued at the University of Victoria in Canada, where he completed a master’s degree—to the physics of superfluids, the focus of his Ph.D. research at the University of Alberta.

This is the 11th year of Dance Your Ph.D. hosted by Science and AAAS. The contest challenges scientists around the world to explain their research through the most jargon-free medium available: interpretive dance.

“Most people would not normally think of interpretive dance as a tool for scientific communication,” says artist Alexa Meade, one of the judges of the contest. “However, the body can express conceptual thoughts through movement in ways that words and data tables cannot. The results are both artfully poetic and scientifically profound.”

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Getting back to the February 17, 2019 CBC news item,

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Yapa describes his video, filmed in Victoria where he earned his master’s degree, as a “three act, mini-musical.”

“I envisioned it as talking about the social lives of electrons,” he said. “The electrons starts out in a normal metal, at normal temperatures….We say these electrons are non-interacting. They don’t talk to each other. Electrons ignore each other and are very unsociable.”

The electrons — represented by dancers wearing saddle oxfords, poodle skirts, vests and suspenders — shuffle up the dance floor by themselves.

In the second act, the metal is cooled.

“The electrons become very unhappy about being alone. They want to find a partner, some companionship for the cold times,” he said

That’s when the electrons join up into something called Cooper pairs.

The dancers join together, moving to lyrics like, “If we peek/the Coopers are cheek-to-cheek.

In the final act, Yapa gets his dancers to demonstrate what happens when the Cooper pairs meet the impurities of the materials they’re moving in. All of a sudden, a group of black-leather-clad thugs move onto the dance floor.

“The Cooper pairs come dancing near these impurities and they’re like these crotchety old people yelling and shaking their fists at these young dancers,” Yapa explained.

Yapa’s entry to the annual contest swept past 49 other contestants to earn him the win. The competition is sponsored by Science magazine and the American Association for the Advancement of Science.

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Congratulations to Pramodh Senarath Yapa.

Science (magazine) investigates Sci-Hub (a pirate site for scientific papers)

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Sci-Hub, a pirate website for scientific papers, and its progenitor, Alexandra Elbakyan, have generated a couple of articles and an editorial in Science magazine’s latest issue (April 28, 2016?). An April 29, 2016 article by Bob Yirka for phys.org describes one of the articles (Note: Links have been removed),

A correspondent for the Science family of journals has published an investigative piece in Science on Sci-Hub, a website that illegally publishes scholarly literature, i.e. research papers. In his article, John Bohannon describes how he made contact with Alexandra Elbakyan, the founder of what is now the world’s largest site for pirated scholarly articles, data she gave him, and commentary on what was revealed. Bohannon has also published another piece focused exclusively on Elbakyan, describing her as a frustrated science student. Marcia McNutt, Editor-in-Chief of the Science Family also weighs in on her “love-hate” relationship with Sci-Hub, and explains in detail why she believes the site is likely to cause problems for scholarly publishing heading into the future.

An April 28, 2016 American Association for the Advancement of Science (AAAS) news release provides some detail about the number of downloads from the Sci-Hub site,

In this investigative news piece from Science, contributing correspondent John Bohannon dives into data from Sci-Hub, the world’s largest pirate website for scholarly literature. For the first time, basic questions about Sci-Hub’s millions of users can be answered: Where are they and what are they reading? Bohannon’s statistical analysis is based on server log data supplied by Alexandra Elbakyan herself, the neuroscientist who created Sci-Hub in 2011. After establishing contact with her through an encrypted chat system, Bohannon and Elbakyan worked together to create a data set for public release: 28 million Sci-Hub download requests going back to 1 September 2015, including the digital object identifier (DOI) for every paper and the clustered locations of users based on their Internet Protocol address. In his story, Bohannon reveals that Sci-Hub usage is highest in China with 4.4 million download requests over the 6-month period, followed by India and Iran. But Sci-Hub users are not limited to the developing world, he reports; the U.S. is the fifth largest downloader and some of the most intense Sci-Hub activity seems to be happening on US and European university campuses, supporting the claim that many users could be accessing the papers through their libraries, but turn to Sci-Hub for convenience.

Bohanon’s piece appears to be open access. Here’s a link and a citation,

Who’s downloading pirated papers? Everyone by John Bohannon. Science (2016). DOI: 10.1126/science.aaf5664 Published April 28, 2016.

Comments

The analysis of the data is fascinating but I’m not sure why this is being billed as an ‘investigative’ piece. Generally speaking I would expect an investigative piece to unearth new information which has likely been hidden. At the very least, I would expect some juicy inside information (i.e., gossip).

Bohannon certainly had no difficulty getting information (from the April 28, 2016 Science article),

For someone denounced as a criminal by powerful corporations and scholarly societies, Elbakyan was surprisingly forthcoming and transparent. After establishing contact through an encrypted chat system, she worked with me over the course of several weeks to create a data set for public release: every download event over the 6-month period starting 1 September 2015, including the digital object identifier (DOI) for every paper. To protect the privacy of Sci-Hub users, we agreed that she would first aggregate users’ geographic locations to the nearest city using data from Google Maps; no identifying internet protocol (IP) addresses were given to me. (The data set and details on how it was analyzed are freely accessible)

Why would it be surprising that someone who has made a point of freeing scientific research and making it accessible also makes the data from her Sci-Hub site freely available? The action certainly seems consistent with her raison d’être.

Bohannon steers away from making any serious criticisms of the current publishing régimes although he does mention a few bones of contention while laying them to rest, more or less. This is no great surprise since he’s writing for one of the ‘big three’, a journal that could be described as having a vested interest in maintaining the status quo. (For those who are unaware, there are three journal considered the most prestigious or high impact for scientific studies: Nature, Cell, and Science.)

Characterizing Elbakyan as a ‘frustrated’ student in an April 28, 2016 profile by John Bohannon (The frustrated science student behind Sci-Hub) seems a bit dismissive. Sci-Hub may have been borne of frustration but it is an extraordinary accomplishment.

The piece has resulted in at least one very irate librarian, John Dupuis, from an April 29, 2016 posting on his Confessions of a Science Librarian blog,

Overall, the articles are pretty good descriptions of the Sci-Hub phenomenon and relatively even-handed [emphasis mine], especially coming from one of the big society publishers like AAAS.

There was one bit in the main article, Who’s downloading pirated papers? Everyone, that really stuck in my craw. Basically, Sci-Hub — and all that article piracy — is librarians’ fault.

And for all the researchers at Western universities who use Sci-Hub instead, the anonymous publisher lays the blame on librarians for not making their online systems easier to use and educating their researchers. “I don’t think the issue is access—it’s the perception that access is difficult,” he says.

Fortunately it was countered, in the true “give both sides of the story” style of mainstream journalism, by another quote, this time from a librarian.

“I don’t agree,” says Ivy Anderson, the director of collections for the California Digital Library in Oakland, which provides journal access to the 240,000 researchers of the University of California system. The authentication systems that university researchers must use to read subscription journals from off campus, and even sometimes on campus with personal computers, “are there to enforce publisher restrictions,” she says.

But of course, I couldn’t let it go. Anderson’s response is perfectly fine but somehow there just wasn’t enough rage and exasperation in it. So I stewed about it over night and tweeted up a tweetstorm of rage this morning, with the idea that if the rant was well-received I would capture the text as part of a blog post.

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As you may have guessed by my previous comments, I didn’t find the article quite as even-handed as Dupuis did. As for the offence to librarians, I did notice but it seems in line with the rest of the piece which dismisses, downplays, and offloads a few serious criticisms while ignoring how significant issues (problematic peer review process,  charging exorbitant rates for access to publicly funded research, failure to adequately tag published papers that are under review after serious concerns are raised, failure to respond in a timely fashion when serious concerns are raised about a published paper, positive publication bias, …) have spawned the open access movement and also Sci-Hub. When you consider that governments rely on bibliometric data such as number of papers published and number of papers published in high impact journals (such as one of the ‘big three’), it’s clear there’s a great deal at stake.

Other Sci-Hub pieces here

My last piece about Sci-Hub was a February 25, 2016 posting titled,’ Using copyright to shut down easy access to scientific research‘ featuring some of the discussion around Elsevier and its legal suite against Sci-Hub.

Picture still not worth 1000 words but here are the 2011 International Science and Engineering Visualization Challenge winners

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About this time last year I wrote an impassioned piece on the importance of words (Feb. 22, 2011* posting) while making note of the 2010 International Science and Engineering Visualization Challenge winners. For the record, I haven’t changed my mind about the importance of either words or visuals; I still don’t believe that there’s a one size fits all approach to communicating about anything let alone science. (I have had more than one convo with graphic designers who bring up that ‘picture worth …’ as they explain why my words on the page are in a four-point font [I exaggerate but only mildly], so this protest was based on previous bad experiences rather than any hostility towards the Challenge.)

Science magazine (published by the American Association for the Advancement of Science [AAAS]) announced the winners for the 2011 International Science and Engineering Visualization Challenge today. Tomorrow, Science will feature the winning entries in its Feb. 3,  2012 issue. From the Feb. 2, 2012 news release on EurekAlert,

The international competition, currently in its ninth year, honors recipients who use visual media to promote understanding of scientific research. The criteria for judging the 212 entries, from 33 countries, included visual impact, effective communication, freshness and originality.

Here’s a brief description of the some of the winning entries,

Solve the Protein Puzzle: A multiplayer online computer game puzzle, called “Foldit,” that allows users to bend and fold amino acids into realistic proteins and solve the problem of protein folding was developed by Seth Cooper of the University of Washington, Seattle and his team.

“We strove to make the visualizations in folding both fun to look at and informative about where there are problems with the protein that players might be able to fix,” said Cooper, a first-place winner in the Interactive Games category. “We tried to make the visualizations clear and approachable, so the game can be played by people who don’t have a scientific background.”

View a Cell in 3D: The movie “Rapid Visual Inventory & Comparison of Complex 3D Structures” depicts a novel three-dimensional model view of a whole cell in minute detail and helps biologists better understand complex visual data for a general audience. The video was selected as the first-place Video category winner by the judges as well as the People’s Choice.

“Morphing the cell from the complicated native model to the simplified version and back gets general audiences excited about the subject matter and reminds even expert audiences of the complex interplay of randomness and specific interaction that enables life to exist,” said winning animator Graham T. Johnson of the Scripps Research Institute in San Diego, California, and now at the University of California San Francisco.

See the Beauty of a Mouse’s Eye: The first-place photograph, “Metabolomic Eye,” is a metabolic snapshot of the diversity of cells in a mouse eye retina, derived from a technique called computational molecular phenotyping (CMP), explained neuroscientist Bryan William Jones of the University of Utah’s Moran Eye Center in Salt Lake City. The image shows a unique view of normal tissue functioning and reveals complex metabolic signals while preserving the anatomical context of a tissue, added Jones.

Build a Human Body: “Build-a-Body is a great way to virtually learn about human anatomy,” said game designer Jeremy Friedberg of Spongelab Interactive about his educational science game, which won an Honorable Mention, that allows users to use drag and drop tools to learn about organs of the human body. “Our free, open platform fosters a global science community by stitching together educational content, teaching tools and powerful data surrounding class and student performance.”

Since I try to focus on nanotechnology for this blog, here’s a carbon nanotube image that won an honourable mention in this year’s competition in the illustration category,

Variable-diameter carbon nanotubes This 3-D illustration shows the production of variable-diameter carbon nanotubes. University of Nebraska-Lincoln electrical engineering professor, Dr. Yongfeng Lu, discovered laser-based production techniques that can precisely control the length, diameter and properties of carbon nanotubes. Using these highly electrically and thermally conductive nanotubes, Lu’s team developed methods to improve transistors and sensors that may one day speed up computers and other electrical devices, while minimizing energy consumption and heat generation. They also discovered how to control a carbon nanotube’s diameter from one end to the other, which alters its characteristics. Lu envisions variable-diameter nanotubes customized for specific uses. This 3-D illustration was developed to help Dr. Lu’s team to visualize these nano-scale discoveries for diverse audiences. [Image courtesy of Joel Brehm, University of Nebraska-Lincoln Office of Research and Economic Development

To me, they look like bowling pins made of pine cones.

*’Feb. 22, 2012 posting’ corrected to ‘Feb. 22, 2011 posting’ on  July 16, 2021.

Open Source Physics wins SPORE

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A SPORE, Science Prize for Online Resources in Education from the American Association for the Advancement of Science (AAAS), was awarded to the Open Source Physics (OSP) website founded by  Wolfgang Christian and colleagues, Francisco Esquembre and Lyle Barbato.

Here’s an excerpt from the essay the three scientists wrote for Science magazine (published by AAAS) about their website,

Scientists routinely use computer modeling and computation in innovative research, including predicting the nature of He4 at extremely low temperatures and the impact of human activity on climate. Why does computer-based modeling remain absent from many educational programs?

The Open Source Physics (OSP) project, www.compadre.org/osp/, seeks to enhance computational physics education by providing a central Web site containing computer modeling tools, simulations, curricular resources such as lesson plans, and a computational physics textbook that explains the pedagogic simulations’ algorithms. Our resources are based on small single-concept simulations packaged with source codes that can be examined, modified, recompiled, and freely redistributed to teach fundamental computational skills. Students at all levels will benefit from these interactive simulations by learning to question and assess the simulation’s assumptions and output.

Students who learn physics concepts via static pictures may be led to construct incomplete or incorrect mental models that hamper their understanding of physical concepts.

The website is useful for university students although there are plans to make resources suitable for K-12 students, from the Nov. 24, 2011 news item on physorg.com,

Christian is currently working toward involving K-12 students, such as his wife’s middle-school students, who as seventh graders are learning about concepts such as temperature. Christian was able to adapt a college-level molecular dynamics simulation for them to explore changes in the phases of matter.

“The students could heat and cool the system, and then we could ask them questions like, ‘At what temperature does it melt?'” Christian says. “They got visual feedback from the simulation and had to make decisions about the basic concepts.”

The SPORE award is part of an ongoing initiative by Science magazine to recognize outstanding online science education efforts. From the Nov. 24, 2011 news item on physorg.com,

Science magazine developed the Science Prize for Online Resources in Education (SPORE) to promote the best online materials in science education. The acronym SPORE suggests a reproductive element adapted to develop, often in adverse conditions, into something new. Similarly, these winning projects can be seen as the seeds of progress in science education, despite considerable challenges to educational innovation. Each month, Science publishes an article by a recipient of the award, which explains the winning project. The article about Open Source Physics (OSP) will be published on November 25.

“We’re trying to advance science education,” says Bruce Alberts, editor-in-chief of Science. “This competition provides much-needed recognition to innovators in the field whose efforts promise significant benefits for students and for science literacy in general. The publication in Science of an article on each Web site will help guide educators around the globe to valuable free resources that might otherwise be missed.”

I have featured two previous SPORE winners, in the Universe Awareness posting and in the Ask a Biologist posting.

Highlighting the 2011 Dance Your Ph.D. contest

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Science magazine (published by the American Association for the Advancement of Science [AAAS]) has been holding a Dance Your PhD contest since 2008* (as best I can determine from a Sept. 17, 2010 posting by Katherine for SciFri). In any case, this year they received a record number of entries (from an Oct. 14, 2011 posting by John Bohannon on Science Now),

Have you ever wondered what nanotube chemistry might look like as a dance? Or fruit fly sex? Or protein x-ray crystallography? Look no further. As part of the 2011 Dance Your Ph.D. contest, scientists who study those phenomena and more have converted their research into dance videos for your enjoyment and edification. And today the 16 finalists of this annual contest are revealed below.

A record 55 dances were created for this year’s contest, submitted by scientists around the globe, from the United States and Canada to Europe, India, and Australia. As the contest rules state, each dance must be based on the scientist’s own Ph.D. research thesis, and that scientist must participate in the dance. For many of the graduate students who danced, the research they depicted is still ongoing. For some of the older contestants, the project is a distant, perhaps harrowing memory from their early days in science. The dances are divided into four categories based on subject: physics, chemistry, biology, and social science. (The criteria for those categories are explained here.)

One of this year’s finalists is from the DeRosa lab at Carleton University in Ottawa, Canada. Titled, “DNA Aptamers as a Tool for Studying Mental Health Disease.” Erin McConnell and her troop are featured in the video below, *ETA February 27, 2024: The video is no longer here, please follow the link to Vimeo: DNA Aptamers as a Tool for Studying Mental Health Disease from Erin McConnell on Vimeo.*

I haven’t had time to review the other finalists but given this one, I can hardly wait.

The DeRosa lab also had a finalist in last year’s Dance Your PhD contest. It’s not the only reason I contacted the lab’s leader, Maria DeRosa but it did add a piquant flavour to my interview with her, which I will be posting tomorrow (Oct. 25, 2011).

*ETA Oct 24, 2011 1500 hours: There is an Oct. 18, 2011 article by Bob Weber for the Globe and Mail newspaper about the Canadian finalists in the 2011 Dance Your PhD contest. The contest was informally created in 2007 according to its originator John Bohannon.